Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 171 of 198
Found at i:53729449 original size:23 final size:23
Alignment explanation
Indices: 53729423--53729498 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
53729413 AGTGTTATTG
53729423 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACGT
53729446 ATCAGTGGTAGCTTCGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACGT
*
53729469 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACGT
53729492 ATCAGTG
1 ATCAGTG
53729499 TGGCACTTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACGT
Found at i:53732379 original size:9 final size:9
Alignment explanation
Indices: 53732365--53732395 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
53732355 GTTAAACGAA
53732365 TCGAGTTAT
1 TCGAGTTAT
*
53732374 TCGAGTTAA
1 TCGAGTTAT
53732383 TCGAGTTAT
1 TCGAGTTAT
53732392 TCGA
1 TCGA
53732396 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:53732466 original size:9 final size:9
Alignment explanation
Indices: 53732449--53732485 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
53732439 TGAGTTTTCG
53732449 AATTCGAAT
1 AATTCGAAT
*
53732458 AACTCGAAT
1 AATTCGAAT
53732467 AATTCGAAT
1 AATTCGAAT
53732476 AATTCGAAT
1 AATTCGAAT
53732485 A
1 A
53732486 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:53738041 original size:13 final size:14
Alignment explanation
Indices: 53738023--53738064 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
53738013 TCTCAATTTT
53738023 ATTTTAATAAT-TA
1 ATTTTAATAATATA
*
53738036 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
53738051 ATTTTAAATAATAT
1 ATTTT-AATAATAT
53738065 TCTCCATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
15 9 0.38
16 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:53738054 original size:15 final size:17
Alignment explanation
Indices: 53738027--53738063 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
53738017 AATTTTATTT
53738027 TAATAATTAATTTTAAA
1 TAATAATTAATTTTAAA
53738044 -AATAA-TAATTTTAAA
1 TAATAATTAATTTTAAA
53738059 TAATA
1 TAATA
53738064 TTCTCCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATAATTAATTTTAAA
Found at i:53740042 original size:114 final size:114
Alignment explanation
Indices: 53739842--53740062 Score: 352
Period size: 114 Copynumber: 1.9 Consensus size: 114
53739832 AAAATAAATG
* * * *
53739842 AAGGTGATTTGACCGTAGTTGCTTCGGCAACGAATGTACCACCTTTTAACTTGGACCCAACGATC
1 AAGGTGATTTGACCGTAGTTACTTCGGCAACAAATGTACCACCTTGTAACTCGGACCCAACGATC
53739907 AGGTTGGGTAACAAGGTGTTACAATATTAATATTTATTGAATCGGTAAC
66 AGGTTGGGTAACAAGGTGTTACAATATTAATATTTATTGAATCGGTAAC
* * * * * *
53739956 AAGGTTATTTGTCTGTAGTTACTTCGGCAACAAATGTGCTACCTTGTAACTCGGACCCAGCGATC
1 AAGGTGATTTGACCGTAGTTACTTCGGCAACAAATGTACCACCTTGTAACTCGGACCCAACGATC
53740021 AGGTTGGGTAACAAGGTGTTACAATATTAATATTTATTGAAT
66 AGGTTGGGTAACAAGGTGTTACAATATTAATATTTATTGAAT
53740063 GGTTCAAATT
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (114 bp):
AAGGTGATTTGACCGTAGTTACTTCGGCAACAAATGTACCACCTTGTAACTCGGACCCAACGATC
AGGTTGGGTAACAAGGTGTTACAATATTAATATTTATTGAATCGGTAAC
Found at i:53740614 original size:31 final size:29
Alignment explanation
Indices: 53740544--53740617 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
53740534 GGCTCAGGTT
* *
53740544 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
53740573 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
53740604 ACATTTTAGTCACT
1 ACATTTTAGTCACT
53740618 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:53741236 original size:31 final size:29
Alignment explanation
Indices: 53741172--53741240 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
53741162 ACGATAATGT
* *
53741172 AAGTGACTAAAACGTAACATTTCAAACAT
1 AAGTGACTAAAACGTAACATGTCAAACAA
* *
53741201 AAGTGACTAAAATGTAACCTGAGTCAAACAA
1 AAGTGACTAAAACGTAACAT--GTCAAACAA
53741232 AAGTGACTA
1 AAGTGACTA
53741241 TTTTGGTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACATGTCAAACAA
Found at i:53741343 original size:38 final size:38
Alignment explanation
Indices: 53741257--53741343 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 38
53741247 TAGTTTACCC
* * *
53741257 TATAATTTATTACTTAATTTTAATTATTAATCAGTTAA
1 TATAATTTATTAATTAAATTTAAATATTAATCAGTTAA
*
53741295 TGTAGA-TTATTAATTAAATTTAAATATTATGATCA-TTAA
1 TATA-ATTTATTAATTAAATTTAAATATTA--ATCAGTTAA
53741334 -ATAATTTATT
1 TATAATTTATT
53741344 CTTACCTTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
37 1 0.03
38 30 0.75
39 5 0.12
40 4 0.10
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (38 bp):
TATAATTTATTAATTAAATTTAAATATTAATCAGTTAA
Found at i:53751431 original size:16 final size:16
Alignment explanation
Indices: 53751412--53751446 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
53751402 GTTGTATGTC
53751412 TCTATCTTT-GTAGATA
1 TCTAT-TTTAGTAGATA
53751428 TCTATTTTAGTAGATA
1 TCTATTTTAGTAGATA
53751444 TCT
1 TCT
53751447 TTGTAGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.51
Consensus pattern (16 bp):
TCTATTTTAGTAGATA
Found at i:53751454 original size:12 final size:12
Alignment explanation
Indices: 53751414--53751458 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 12
53751404 TGTATGTCTC
53751414 TATCTTTGTAGA
1 TATCTTTGTAGA
53751426 TATCTATTTTAGTAGA
1 TATC---TTT-GTAGA
53751442 TATCTTTGTAGA
1 TATCTTTGTAGA
53751454 TATCT
1 TATCT
53751459 GACAAACTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 14 0.48
13 3 0.10
15 3 0.10
16 9 0.31
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (12 bp):
TATCTTTGTAGA
Found at i:53754530 original size:2 final size:2
Alignment explanation
Indices: 53754523--53754555 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
53754513 AGCTTAAGCA
53754523 AT AT AT 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 AT AT AT A
53754556 ACCCTTATTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53755725 original size:41 final size:40
Alignment explanation
Indices: 53755638--53755731 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 40
53755628 TACGAAACGT
* * * *
53755638 TTCTAGTTGGAAGCGTTTTCAATTGATTTGCAGAAAAGCG
1 TTCTAGCTAGAAGCGTTTTCAAATGATTTGCAGAAAAGCC
53755678 TGTCTAGCTAGAAGCGTTTTCAACAT-ATTTGCAGGAAAA-CAC
1 T-TCTAGCTAGAAGCGTTTTCAA-ATGATTTGCA-GAAAAGC-C
53755720 TTCTAGCTAGAA
1 TTCTAGCTAGAA
53755732 ACACTTTCTG
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
40 1 0.02
41 38 0.83
42 7 0.15
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (40 bp):
TTCTAGCTAGAAGCGTTTTCAAATGATTTGCAGAAAAGCC
Found at i:53755905 original size:23 final size:22
Alignment explanation
Indices: 53755845--53755907 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
53755835 GGGTTTTGTA
53755845 ATTTTTTTATA-TTTTTTAAAT
1 ATTTTTTTATATTTTTTTAAAT
* *
53755866 -TTAAATTTTATGGTTTTTTTAAAT
1 ATT--TTTTTAT-ATTTTTTTAAAT
*
53755890 ATTTTTTTATAATTTTTT
1 ATTTTTTTATATTTTTTT
53755908 GAGATGTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 9
0.70 0.11 0.20
Matches are distributed among these distances:
20 2 0.06
22 12 0.38
23 6 0.19
24 10 0.31
25 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (22 bp):
ATTTTTTTATATTTTTTTAAAT
Found at i:53759455 original size:56 final size:57
Alignment explanation
Indices: 53759350--53759573 Score: 292
Period size: 57 Copynumber: 4.0 Consensus size: 57
53759340 TATTGTTACT
* * * *
53759350 ATTTGCATGCTGTCATAAATTGAATTAAAGTTGTTGTTTGAGTGTTTCAAATTGAGC
1 ATTTTCATGCTGTCTTAAATTGAATTAAAGTTGCTGTTTTAGTGTTTCAAATTGAGC
* * * * *
53759407 ATTTTCATACTATCTTAAATTGAA-TCAAGATGCTGTTTTAGTGATTCAAATTGAGC
1 ATTTTCATGCTGTCTTAAATTGAATTAAAGTTGCTGTTTTAGTGTTTCAAATTGAGC
* * *
53759463 ATTTTCATGCTGTCATAAATTGAATTAAAGTTGGTGTTTTAGTGTATCAAATTGAGC
1 ATTTTCATGCTGTCTTAAATTGAATTAAAGTTGCTGTTTTAGTGTTTCAAATTGAGC
* * *
53759520 ATTTTCATGCTGTCTTAAATTAAATT-AAGTTGCT-ATTTAATGTTTCAAATTGAG
1 ATTTTCATGCTGTCTTAAATTGAATTAAAGTTGCTGTTTTAGTGTTTCAAATTGAG
53759574 TATTATTATG
Statistics
Matches: 143, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
55 17 0.12
56 55 0.38
57 71 0.50
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (57 bp):
ATTTTCATGCTGTCTTAAATTGAATTAAAGTTGCTGTTTTAGTGTTTCAAATTGAGC
Found at i:53759526 original size:57 final size:57
Alignment explanation
Indices: 53759350--53759603 Score: 277
Period size: 57 Copynumber: 4.5 Consensus size: 57
53759340 TATTGTTACT
* * * *
53759350 ATTTGCATGCTGTCATAAATTGAATTAAAGTTGTTGTTTGAGTGTTTCAAATTGAGC
1 ATTTTCATGCTGTCATAAATTGAATTAAAGTTGCTGTTTTAGTGTATCAAATTGAGC
* * * * *
53759407 ATTTTCATACTATCTTAAATTGAA-TCAAGATGCTGTTTTAGTG-ATTCAAATTGAGC
1 ATTTTCATGCTGTCATAAATTGAATTAAAGTTGCTGTTTTAGTGTA-TCAAATTGAGC
*
53759463 ATTTTCATGCTGTCATAAATTGAATTAAAGTTGGTGTTTTAGTGTATCAAATTGAGC
1 ATTTTCATGCTGTCATAAATTGAATTAAAGTTGCTGTTTTAGTGTATCAAATTGAGC
* * * * * *
53759520 ATTTTCATGCTGTCTTAAATTAAATT-AAGTTGCT-ATTTAATGTTTCAAATTGAGT
1 ATTTTCATGCTGTCATAAATTGAATTAAAGTTGCTGTTTTAGTGTATCAAATTGAGC
* *
53759575 ATTATT-ATGTTGTCCA-AAATTAAATTAAA
1 ATT-TTCATGCTGT-CATAAATTGAATTAAA
53759604 ATGTTGCTTC
Statistics
Matches: 167, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
55 36 0.22
56 59 0.35
57 71 0.43
58 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (57 bp):
ATTTTCATGCTGTCATAAATTGAATTAAAGTTGCTGTTTTAGTGTATCAAATTGAGC
Found at i:53759903 original size:32 final size:33
Alignment explanation
Indices: 53759839--53759906 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
53759829 TCACATTTTT
53759839 AACATAATCCAACTCAACTATGTTTTTTTCTAA
1 AACATAATCCAACTCAACTATGTTTTTTTCTAA
53759872 AACATAATCCAACTCAACTATG-TTTTTTCTAA
1 AACATAATCCAACTCAACTATGTTTTTTTCTAA
53759904 AAC
1 AAC
53759907 TCAACATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 13 0.37
33 22 0.63
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.37
Consensus pattern (33 bp):
AACATAATCCAACTCAACTATGTTTTTTTCTAA
Found at i:53762395 original size:25 final size:27
Alignment explanation
Indices: 53762367--53762421 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 27
53762357 CATTTCAATT
53762367 ATGTGTTAAT-TTC-AAGACTTATGTA
1 ATGTGTTAATATTCAAAGACTTATGTA
*
53762392 A--TGTTAGTGATTCAAAGACTTATGTA
1 ATGTGTTAAT-ATTCAAAGACTTATGTA
53762418 ATGT
1 ATGT
53762422 TTTTAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
23 6 0.25
25 4 0.17
26 13 0.54
28 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (27 bp):
ATGTGTTAATATTCAAAGACTTATGTA
Found at i:53762462 original size:9 final size:9
Alignment explanation
Indices: 53762450--53762499 Score: 82
Period size: 9 Copynumber: 5.6 Consensus size: 9
53762440 TCAATTTGGG
53762450 TAATTCGGT
1 TAATTCGGT
*
53762459 TAATTCGGG
1 TAATTCGGT
53762468 TAATTCGGT
1 TAATTCGGT
*
53762477 TAATGCGGT
1 TAATTCGGT
53762486 TAATTCGGT
1 TAATTCGGT
53762495 TAATT
1 TAATT
53762500 TTTAACCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (9 bp):
TAATTCGGT
Found at i:53762468 original size:18 final size:18
Alignment explanation
Indices: 53762442--53762499 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
53762432 GTAGTGATTC
*
53762442 AATTTGGGTAATTCGGTT
1 AATTCGGGTAATTCGGTT
53762460 AATTCGGGTAATTCGGTT
1 AATTCGGGTAATTCGGTT
* *
53762478 AATGCGGTTAATTCGGTT
1 AATTCGGGTAATTCGGTT
53762496 AATT
1 AATT
53762500 TTTAACCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (18 bp):
AATTCGGGTAATTCGGTT
Found at i:53763915 original size:42 final size:42
Alignment explanation
Indices: 53763833--53763938 Score: 149
Period size: 43 Copynumber: 2.5 Consensus size: 42
53763823 GGGTATATCT
* *
53763833 AACAACCGAAGTTTATCTTCTCATTTTTTAAATTCTTTTTTC
1 AACAACCCAAGATTATCTTCTCATTTTTTAAATTCTTTTTTC
* * *
53763875 AATAACCCAATATTATCTTCTCCTCTTTTTAAATTCTTTTTTC
1 AACAACCCAAGATTATCTTCTCAT-TTTTTAAATTCTTTTTTC
*
53763918 AACAACCCAAGATTATTTTCT
1 AACAACCCAAGATTATCTTCT
53763939 TTTAAAATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 19 0.35
43 36 0.65
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.47
Consensus pattern (42 bp):
AACAACCCAAGATTATCTTCTCATTTTTTAAATTCTTTTTTC
Found at i:53770337 original size:41 final size:40
Alignment explanation
Indices: 53770280--53770489 Score: 197
Period size: 41 Copynumber: 5.1 Consensus size: 40
53770270 TTCAGCAGCA
* *
53770280 TTTTTATCTAAGCGCCGCTAATGCTCGGATCTTTAGCGGTG
1 TTTTTATCTAAGCGCCGCTAATGCTCGG-CCTTTAGCGGCG
* *
53770321 TTTTTATCTGAGCGCCGCTAACT-CTCTGGCCTTTGGCGGCG
1 TTTTTATCTAAGCGCCGCTAA-TGCTC-GGCCTTTAGCGGCG
* **
53770362 TTTTTATCTAAGCACCGCTAATGCTCAGATCTTTAGCGGCG
1 TTTTTATCTAAGCGCCGCTAATGCTC-GGCCTTTAGCGGCG
* * * * *
53770403 TTTTTATTTGAGCGCCACTAATTCTATGGCCTTTAGCGGCG
1 TTTTTATCTAAGCGCCGCTAATGCT-CGGCCTTTAGCGGCG
* * * ***
53770444 TTTGTGTCTAAGCGCCGCTAATGTATTTACCTTTAGCGGCG
1 TTTTTATCTAAGCGCCGCTAATG-CTCGGCCTTTAGCGGCG
53770485 TTTTT
1 TTTTT
53770490 GCCGAAACGC
Statistics
Matches: 136, Mismatches: 28, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
40 1 0.01
41 131 0.96
42 4 0.03
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (40 bp):
TTTTTATCTAAGCGCCGCTAATGCTCGGCCTTTAGCGGCG
Found at i:53770406 original size:82 final size:82
Alignment explanation
Indices: 53770280--53770466 Score: 284
Period size: 82 Copynumber: 2.3 Consensus size: 82
53770270 TTCAGCAGCA
* * *
53770280 TTTTTATCTAAGCGCCGCTAATGCTCGGATCTTTAGCGGTGTTTTTATCTGAGCGCCGCTAACTC
1 TTTTTATCTAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTATCTGAGCGCCACTAACTC
* *
53770345 TCTGGCCTTTGGCGGCG
66 TATGGCCTTTAGCGGCG
* * *
53770362 TTTTTATCTAAGCACCGCTAATGCTCAGATCTTTAGCGGCGTTTTTATTTGAGCGCCACTAATTC
1 TTTTTATCTAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTATCTGAGCGCCACTAACTC
53770427 TATGGCCTTTAGCGGCG
66 TATGGCCTTTAGCGGCG
* *
53770444 TTTGTGTCTAAGCGCCGCTAATG
1 TTTTTATCTAAGCGCCGCTAATG
53770467 TATTTACCTT
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 94 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.36
Consensus pattern (82 bp):
TTTTTATCTAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTATCTGAGCGCCACTAACTC
TATGGCCTTTAGCGGCG
Found at i:53770478 original size:82 final size:82
Alignment explanation
Indices: 53770284--53770489 Score: 254
Period size: 82 Copynumber: 2.5 Consensus size: 82
53770274 GCAGCATTTT
* * * * * *
53770284 TATCTAAGCGCCGCTAATGCTCGGATCTTTAGCGGTGTTTTTATCTGAGCGCCGCTAACTCTCTG
1 TATCTAAGCACCGCTAATGCTCAGACCTTTAGCGGCGTTTTTATCTGAGCGCCACTAACTCTATG
* *
53770349 GCCTTTGGCGGCGTTTT
66 GCCTTTAGCGGCGTTTG
* * *
53770366 TATCTAAGCACCGCTAATGCTCAGATCTTTAGCGGCGTTTTTATTTGAGCGCCACTAATTCTATG
1 TATCTAAGCACCGCTAATGCTCAGACCTTTAGCGGCGTTTTTATCTGAGCGCCACTAACTCTATG
53770431 GCCTTTAGCGGCGTTTG
66 GCCTTTAGCGGCGTTTG
* * *
53770448 TGTCTAAGCGCCGCTAATG-T-ATTTACCTTTAGCGGCGTTTTT
1 TATCTAAGCACCGCTAATGCTCA--GACCTTTAGCGGCGTTTTT
53770490 GCCGAAACGC
Statistics
Matches: 109, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
80 1 0.01
81 1 0.01
82 107 0.98
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (82 bp):
TATCTAAGCACCGCTAATGCTCAGACCTTTAGCGGCGTTTTTATCTGAGCGCCACTAACTCTATG
GCCTTTAGCGGCGTTTG
Found at i:53771044 original size:15 final size:15
Alignment explanation
Indices: 53771023--53771060 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
53771013 TTTAAGGTTA
53771023 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
53771038 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
53771053 ATTTAGGG
1 ATTTAGGG
53771061 TTTCAACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:53771063 original size:14 final size:14
Alignment explanation
Indices: 53770996--53771063 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
53770986 TACGGGGTAT
*
53770996 AGATTTAAGGTTTG
1 AGATTTAGGGTTTG
* *
53771010 GGATTTAAGG-TT-
1 AGATTTAGGGTTTG
*
53771022 A-ATTTAGGGGTTAG
1 AGATTTA-GGGTTTG
*
53771036 AGGTTTAGGGGTTTG
1 AGATTTA-GGGTTTG
53771051 AGATTTAGGGTTT
1 AGATTTAGGGTTT
53771064 CAACGGTCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 5 0.12
12 2 0.05
13 3 0.07
14 16 0.37
15 17 0.40
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (14 bp):
AGATTTAGGGTTTG
Found at i:53771732 original size:2 final size:2
Alignment explanation
Indices: 53771725--53771749 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53771715 ATTATAATTA
53771725 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
53771750 ATAGGTGCGT
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:53780178 original size:43 final size:43
Alignment explanation
Indices: 53780119--53780500 Score: 150
Period size: 43 Copynumber: 8.9 Consensus size: 43
53780109 GGCGTTTTTT
* * ** *
53780119 AAAAAGCGCCGCTAAAGGCCCTGTCCTTTAGCGGCGTTTGTAA
1 AAAAAGCACCGCTAAAGACAATGACCTTTAGCGGCGTTTGTAA
* * *
53780162 AAAAAGCACCGTTAAAGACAATGACTTTTAGCGGCGTTTGTGA
1 AAAAAGCACCGCTAAAGACAATGACCTTTAGCGGCGTTTGTAA
* * * ** * **
53780205 AAAAAGCGCCACTAAAG-CTCATGGTCTTTAGCGGCGTTTATGG
1 AAAAAGCACCGCTAAAGAC-AATGACCTTTAGCGGCGTTTGTAA
* * * *** * **
53780248 GAAAAGCGCCGCTAAAG-CTCATGGTTTTTAGCGGCGTTTATGG
1 AAAAAGCACCGCTAAAGAC-AATGACCTTTAGCGGCGTTTGTAA
* * * ** * **
53780291 GAAAAGCGCCACTAAAGATC-ATGGTCTTTAGCAGCGTTTGTGG
1 AAAAAGCACCGCTAAAGA-CAATGACCTTTAGCGGCGTTTGTAA
* * ** *
53780334 AAAAAGCGCCGCTAAAGGAC-ATGATCTTTAGCGGCGATTCCTAC
1 AAAAAGCACCGCTAAA-GACAATGACCTTTAGCGGCG-TTTGTAA
** * * * * * *
53780378 ACCAA-CGCCGCTAAAGACCATTATCTTTAGCGGCGCTTG-GA
1 AAAAAGCACCGCTAAAGACAATGACCTTTAGCGGCGTTTGTAA
* * * ** *
53780419 GAAAATCGCCGCTAAAGGAC-ATGGTCTTTAGCGGCGTTTGTAG
1 AAAAAGCACCGCTAAA-GACAATGACCTTTAGCGGCGTTTGTAA
* * *
53780462 AAAAAGCGCCGCTAAAGGAC-ATGATCTTTAGCGGTGTTT
1 AAAAAGCACCGCTAAA-GACAATGACCTTTAGCGGCGTTT
53780501 TTTTCATAAA
Statistics
Matches: 278, Mismatches: 52, Indels: 18
0.80 0.15 0.05
Matches are distributed among these distances:
41 2 0.01
42 32 0.12
43 235 0.85
44 8 0.03
45 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (43 bp):
AAAAAGCACCGCTAAAGACAATGACCTTTAGCGGCGTTTGTAA
Found at i:53780234 original size:86 final size:84
Alignment explanation
Indices: 53780119--53780500 Score: 294
Period size: 86 Copynumber: 4.5 Consensus size: 84
53780109 GGCGTTTTTT
* * ** * *
53780119 AAAAAGCGCCGCTAAAGGC-CCT-GTCCTTTAGCGGCGTTTGTAAAAAAAGCACCGTTAAAGACA
1 AAAAAGCGCCACTAAA-GCTCATGGT-CTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGAC-
*
53780182 ATGACTTTTAGCGGCGTTTGTGA
63 ATGA-TTTTAGCGGCGTTTATGA
* * *
53780205 AAAAAGCGCCACTAAAGCTCATGGTCTTTAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGCTCAT
1 AAAAAGCGCCACTAAAGCTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAG-ACAT
* *
53780270 GGTTTTTAGCGGCGTTTATGG
65 -GATTTTAGCGGCGTTTATGA
* * *
53780291 GAAAAGCGCCACTAAAGATCATGGTCTTTAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGGACAT
1 AAAAAGCGCCACTAAAGCTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAA-GACAT
**
53780356 GATCTTTAGCGGCGATTCCT-A
65 GAT-TTTAGCGGCG-TTTATGA
** * ** * *
53780377 CACCAA-CGCCGCTAAAGAC-CATTATCTTTAGCGGCG-CT-TGGAGAAAATCGCCGCTAAAGGA
1 -AAAAAGCGCCACTAAAG-CTCATGGTCTTTAGCGGCGTTTGTGGA-AAAAGCGCCGCTAAA-GA
* *
53780438 CATGGTCTTTAGCGGCGTTTGT-A
62 CATGAT-TTTAGCGGCGTTTATGA
* ** * *
53780461 GAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGTGTTT
1 -AAAAAGCGCCACTAAAGCTCATGGTCTTTAGCGGCGTTT
53780501 TTTTCATAAA
Statistics
Matches: 241, Mismatches: 42, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
84 11 0.05
85 64 0.27
86 156 0.65
87 10 0.04
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (84 bp):
AAAAAGCGCCACTAAAGCTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACATG
ATTTTAGCGGCGTTTATGA
Found at i:53780350 original size:129 final size:127
Alignment explanation
Indices: 53780188--53780500 Score: 364
Period size: 129 Copynumber: 2.4 Consensus size: 127
53780178 GACAATGACT
* * ** * **
53780188 TTTAGCGGCGTTTGTGAAAAAAGCGCCACTAAAGCTCATGGTCTTTAGCGGCGTTTATGGGA-AA
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTTAT-ACACAA
* * *
53780252 AGCGCCGCTAAAG-CTCATGGTTTTTAGCGGCGTTTATGG-GAAAAGCGCCACTAAA-GATCATG
65 A-CGCCGCTAAAGAC-CATGATCTTTAGCGGCG-CT-TGGAGAAAAGCGCCACTAAAGGA-CATG
53780314 GTC
125 GTC
* ** *
53780317 TTTAGCAGCGTTTGTGGAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGATTCCTACACCA
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCG-TTTATACACAA
* * *
53780382 ACGCCGCTAAAGACCATTATCTTTAGCGGCGCTTGGAGAAAATCGCCGCTAAAGGACATGGTC
65 ACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTGGAGAAAAGCGCCACTAAAGGACATGGTC
* *
53780445 TTTAGCGGCGTTTGTAGAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGTGTTT
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTT
53780501 TTTTCATAAA
Statistics
Matches: 158, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
127 5 0.03
128 72 0.46
129 75 0.47
130 6 0.04
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (127 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTTATACACAAA
CGCCGCTAAAGACCATGATCTTTAGCGGCGCTTGGAGAAAAGCGCCACTAAAGGACATGGTC
Found at i:53782570 original size:40 final size:39
Alignment explanation
Indices: 53782496--53782584 Score: 99
Period size: 40 Copynumber: 2.3 Consensus size: 39
53782486 AAAAAACTAG
* ** **
53782496 TATTATTATTATAGTTAGTTATTATTTTTCGTAAAACCC
1 TATTATTATTATAGTTAGCTATTATTTTGAGTAAAAAAC
*
53782535 TAATTATTATTGTTAGTTA-CTATTATTTTGAGTAAAAAAC
1 T-ATTATTATT-ATAGTTAGCTATTATTTTGAGTAAAAAAC
53782575 TATTATTATT
1 TATTATTATT
53782585 TTTATTGTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
39 10 0.24
40 26 0.62
41 6 0.14
ACGTcount: A:0.34, C:0.07, G:0.08, T:0.52
Consensus pattern (39 bp):
TATTATTATTATAGTTAGCTATTATTTTGAGTAAAAAAC
Found at i:53787970 original size:20 final size:21
Alignment explanation
Indices: 53787944--53787985 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
53787934 CATTATGTTA
*
53787944 TTTTTTTATTAATTTAGTGTG
1 TTTTTTAATTAATTTAGTGTG
53787965 TTTTTTAAATTAATTTAGTGT
1 TTTTTT-AATTAATTTAGTGT
53787986 AAAAAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (21 bp):
TTTTTTAATTAATTTAGTGTG
Found at i:53788093 original size:163 final size:164
Alignment explanation
Indices: 53787856--53788756 Score: 629
Period size: 163 Copynumber: 5.5 Consensus size: 164
53787846 GGCCATTTCT
* * * *
53787856 TCGTATTTTTTTCTCGGTATTTTATTACTT-TAAAAAATATCA-TAATTTCTAATTTTATAATTT
1 TCGTATTTTTTTCTCGGAATTTTATTACTTCCAAAAAAAATCATTATTTTCTAATTTTATAATTT
* *
53787919 TACATTATTTCAGTGCATTATGTTATTTTTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGT
66 TATATTATTTCAGTACATTATGTTATTTTTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGT
*
53787984 GTAAAAAAAACTCAACCCTTATTCCTGCCCTTTGC
131 GTAAAAAAAACTCAACCTTTATT-CTGCCCTTTGC
*
53788019 TCGTATTATTTTTC-C-GAATTTTATTACTTCCAAAAAAAAT-ATTATTTTCGT-ATTTTATTAT
1 TCGTATT-TTTTTCTCGGAATTTTATTACTTCCAAAAAAAATCATTATTTTC-TAATTTTATAAT
* * * * * *
53788080 TTTATATTATTTCAGTACATTTTGCTAGAAATATTTGTATTAA-TTA-TTTCTAAATTTTTAAA-
64 TTTATATTATTTCAGTACATTATG-T---TATTTTTTTATTAATTTAGTGTGT---TTTTTAAAT
** **** * * *
53788142 -AA---AGT-TAGTAAGCGTTC-ACTCTTTACTTCGGCCATTTGT
122 TAATTTAGTGTAAAAAAAACTCAAC-CTTTA-TTCTGCCCTTTGC
* * *
53788181 TCGTATTTTTTTCTCGGCATTTTATTACTT-TAAAAAAATATCATAATTTT-TAATTTTATAATT
1 TCGTATTTTTTTCTCGGAATTTTATTACTTCCAAAAAAA-ATCATTATTTTCTAATTTTATAATT
** *
53788244 TTATATTATTTCAGCGCATTATGTTATTTCTTTATTAATTTAGTGTG-TTTTTAAATTAATTTAG
65 TTATATTATTTCAGTACATTATGTTATTTTTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAG
*
53788308 TGTAAAAAAAAACCTAAACC-TTATTCCTGCCCTTTGC
130 TGT-AAAAAAAA-CTCAACCTTTATT-CTGCCCTTTGC
* * * * *
53788345 TCGTATTATTTTC-CCGAATTTGATTACTTCCAAAAAAATAT-ATTATTTTCGT-ATTATATTAT
1 TCGTATTTTTTTCTCGGAATTTTATTACTTCCAAAAAAA-ATCATTATTTTC-TAATTTTATAAT
* * * * ** ** *
53788407 TTTATATTATTTTAGTACATTCTGTTTAAAAATTTTCTATTAATTTTTTCCGAATTTTTAAA--A
64 TTTATATTATTTCAGTACATTATG-TT---ATTTTTTTATTAATTTAGTGTG-TTTTTTAAATTA
** **** * * *
53788470 A---AGT-TAGTAAGTGTTC-ACTCTTTACTTCGGCCATTTGT
124 ATTTAGTGTAAAAAAAACTCAAC-CTTTA-TTCTGCCCTTTGC
* ** * *
53788508 TCGTATTTTTTTCTCGGCATTTTATTACTTTTAAAAAATATCA-TAATTTCTAATTTTATAATTT
1 TCGTATTTTTTTCTCGGAATTTTATTACTTCCAAAAAAAATCATTATTTTCTAATTTTATAATTT
* * *** *
53788572 TACATTATTTCAGTGCATTATGTT-TGAAATTTATTAATTTAATGTGTTTTTTAAATTAATTTAG
66 TATATTATTTCAGTACATTATGTTAT-TTTTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAG
*
53788636 TGT--AAAAAA---AACCTTTATTTCTGCACTTTGC
130 TGTAAAAAAAACTCAACCTTTA-TTCTGCCCTTTGC
* * * *
53788667 TCGTATTATTTTC-CCGAATTTTATTACTTCCAATAAAACTAT-ATTATTTTCGT-ATTTTATTA
1 TCGTATTTTTTTCTCGGAATTTTATTACTTCCAA-AAAA-AATCATTATTTTC-TAATTTTATAA
*
53788729 TTTTATATTATTTCAGTACATTTTGTTA
63 TTTTATATTATTTCAGTACATTATGTTA
53788757 GAAATATTTG
Statistics
Matches: 562, Mismatches: 118, Indels: 118
0.70 0.15 0.15
Matches are distributed among these distances:
157 8 0.01
158 24 0.04
159 55 0.10
160 48 0.09
161 13 0.02
162 59 0.10
163 190 0.34
164 103 0.18
165 11 0.02
166 7 0.01
167 11 0.02
168 25 0.04
170 8 0.01
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (164 bp):
TCGTATTTTTTTCTCGGAATTTTATTACTTCCAAAAAAAATCATTATTTTCTAATTTTATAATTT
TATATTATTTCAGTACATTATGTTATTTTTTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGT
GTAAAAAAAACTCAACCTTTATTCTGCCCTTTGC
Found at i:53788546 original size:327 final size:324
Alignment explanation
Indices: 53787833--53788913 Score: 1693
Period size: 327 Copynumber: 3.3 Consensus size: 324
53787823 GTTACTAAAA
* *
53787833 CACTCTTTACTTCGGCCATTTCTTCGTATTTTTTTCTCGGTATTTTATTACTTTAAAAAATATCA
1 CACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATTACTTTAAAAAATATCA
*
53787898 TAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATTTTTTTATTAATTTAGTG
66 TAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATTTATTTATTAATTTAGTG
53787963 TGTTTTTTAAATTAATTTAGTGTAAAAAAAA-CTCAACCCTTATTCCTGCCCTTTGCTCGTATTA
131 TGTTTTTTAAATTAATTTAGTGTAAAAAAAACCT-AA-CCTTATTCCTGCCCTTTGCTCGTATTA
*
53788027 TTTTTCCGAATTTTATTACTTCCAAAAAAA-ATATTATTTTCGTATTTTATTATTTTATATTATT
194 TTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATTTTATTATTTTATATTATT
* *
53788091 TCAGTACATTTTGCTAGAAATATTTGTATTAATTATTTCTAAATTTTTAAAAAAGTTAGTAAGCG
259 TCAGTACATTTTGTTAGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAAGTTAGTAAG-G
53788156 TT
323 TT
53788158 CACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATTACTTTAAAAAAATATC
1 CACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATTACTTT-AAAAAATATC
* * * *
53788223 ATAATTTTTAATTTTATAATTTTATATTATTTCAGCGCATTATGTTATTTCTTTATTAATTTAGT
65 ATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATTTATTTATTAATTTAGT
53788288 GTG-TTTTTAAATTAATTTAGTGTAAAAAAAAACCTAAACCTTATTCCTGCCCTTTGCTCGTATT
130 GTGTTTTTTAAATTAATTTAGTGT-AAAAAAAACCT-AACCTTATTCCTGCCCTTTGCTCGTATT
* *
53788352 ATTTTCCCGAATTTGATTACTTCCAAAAAAATATATTATTTTCGTATTATATTATTTTATATTAT
193 ATTTTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATTTTATTATTTTATATTAT
* * * * * *
53788417 TTTAGTACATTCTGTTTAAAAAT-TTTCTATTAATTTTTTCCGAATTTTTAAAAAAGTTAGTAAG
258 TTCAGTACATTTTG-TTAGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAAGTTAGTAAG
53788481 TGTT
322 -GTT
53788485 CACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATTACTTTTAAAAAATATC
1 CACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATTAC-TTTAAAAAATATC
** *
53788550 ATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTT-TGAAATTTATTAATTTAA
65 ATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTAT-TTATTTATTAATTTAG
* *
53788614 TGTGTTTTTTAAATTAATTTAGTGTAAAAAAAACCT----TTATTTCTGCACTTTGCTCGTATTA
129 TGTGTTTTTTAAATTAATTTAGTGTAAAAAAAACCTAACCTTATTCCTGCCCTTTGCTCGTATTA
*
53788675 TTTTCCCGAATTTTATTACTTCCAATAAAACTATATTATTTTCGTATTTTATTATTTTATATTAT
194 TTTTCCCGAATTTTATTACTTCCAA-AAAAATATATTATTTTCGTATTTTATTATTTTATATTAT
53788740 TTCAGTACATTTTGTTAGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAAGTTAGTAA--
258 TTCAGTACATTTTGTTAGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAAGTTAGTAAGG
**
53788803 AA
323 TT
* * *
53788805 CATTC-TTACTTCGGCCATTTGTTCGT-TTTTTTTCCTCCGCATTTTATTACTTTAAAAGATATC
1 CACTCTTTACTTCGGCCATTTGTTCGTATTTTTTT-CTCGGCATTTTATTACTTTAAAAAATATC
*
53788868 ATAATTTCTAATTTTATAATTTTACATTATTTCAATGCATTATGTT
65 ATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTT
53788914 TGAAATTTAT
Statistics
Matches: 702, Mismatches: 43, Indels: 29
0.91 0.06 0.04
Matches are distributed among these distances:
318 64 0.09
319 36 0.05
320 4 0.01
322 54 0.08
323 86 0.12
325 72 0.10
326 138 0.20
327 219 0.31
328 29 0.04
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (324 bp):
CACTCTTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGGCATTTTATTACTTTAAAAAATATCA
TAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTATTTATTTATTAATTTAGTG
TGTTTTTTAAATTAATTTAGTGTAAAAAAAACCTAACCTTATTCCTGCCCTTTGCTCGTATTATT
TTCCCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTC
AGTACATTTTGTTAGAAATATTTGTATTAATTATTTCTGAATTTTTAAAAAAGTTAGTAAGGTT
Found at i:53790407 original size:33 final size:32
Alignment explanation
Indices: 53790370--53790436 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 32
53790360 TATTTAGGGG
* *
53790370 TTAGGGATTTAGGGTCTGGTTAGGGTTTAAGGA
1 TTAGGGATTCAGGGTCGGGTTAGGGTTT-AGGA
53790403 TTAGGGATTCAGGGTCGGGTTAGGGTTTAGGA
1 TTAGGGATTCAGGGTCGGGTTAGGGTTTAGGA
53790435 TT
1 TT
53790437 TAGATTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.19, C:0.04, G:0.40, T:0.36
Consensus pattern (32 bp):
TTAGGGATTCAGGGTCGGGTTAGGGTTTAGGA
Found at i:53791307 original size:41 final size:41
Alignment explanation
Indices: 53791248--53791325 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
53791238 TAGTTTGATA
53791248 AATTTTATGTGTAATGTTTAATTTTTCGTTACTGTCTGTGT
1 AATTTTATGTGTAATGTTTAATTTTTCGTTACTGTCTGTGT
**
53791289 AATTTTATGTGTGGTGTTTAATTTTTCGTTACTGTCT
1 AATTTTATGTGTAATGTTTAATTTTTCGTTACTGTCT
53791326 CTGTTTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.18, C:0.08, G:0.18, T:0.56
Consensus pattern (41 bp):
AATTTTATGTGTAATGTTTAATTTTTCGTTACTGTCTGTGT
Found at i:53791751 original size:43 final size:43
Alignment explanation
Indices: 53791644--53791913 Score: 344
Period size: 43 Copynumber: 6.3 Consensus size: 43
53791634 AGGTTATATT
* * * * *
53791644 TTTAGCGGTGTTTTTGCGAGAAGCGCCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
** * *
53791686 TTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAGGTCATGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
53791729 TATAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * **
53791772 TATAGCGGCGTTTGCGGGAAAAGCGCCGCTAAAGGTCATGACC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
53791815 TTTAACGGAGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
53791858 TTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
53791901 TTTATCGGCGTTT
1 TTTAGCGGCGTTT
53791914 TTTCTGGCGC
Statistics
Matches: 199, Mismatches: 28, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
42 31 0.16
43 168 0.84
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:53792081 original size:31 final size:31
Alignment explanation
Indices: 53792043--53792101 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
53792033 TTTTCTTTCC
* *
53792043 CTCTTCTCC-TTCTTTTTTTTTCTCTTCTCTT
1 CTCTTCTCCTTTCCTTTTCTTTC-CTTCTCTT
53792074 CTCTTCTCCTTTCCTTTTCTTTCCTTCT
1 CTCTTCTCCTTTCCTTTTCTTTCCTTCT
53792102 TTTTCTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (31 bp):
CTCTTCTCCTTTCCTTTTCTTTCCTTCTCTT
Found at i:53792088 original size:5 final size:5
Alignment explanation
Indices: 53792080--53792192 Score: 69
Period size: 5 Copynumber: 23.4 Consensus size: 5
53792070 TCTTCTCTTC
* * *
53792080 TCCTT TCCTT TTCTT TCC-T TCTTT TTCTT T-CTT T--TT TCTTCTT CTCCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TC--CTT -TCCTT
* * * *
53792129 TCCTT TTCTT TCC-T TCTTT TCCTT T-CTT TCCTC TCCTT TCCTT TTCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
* *
53792177 TCTTT TTCTT T-CTT TC
1 TCCTT TCCTT TCCTT TC
53792193 TTCTTCTTTC
Statistics
Matches: 83, Mismatches: 16, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
3 3 0.04
4 18 0.22
5 55 0.66
6 3 0.04
7 2 0.02
8 2 0.02
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (5 bp):
TCCTT
Found at i:53792095 original size:10 final size:10
Alignment explanation
Indices: 53792082--53792188 Score: 85
Period size: 10 Copynumber: 10.5 Consensus size: 10
53792072 TTCTCTTCTC
53792082 CTTTCCTTTT
1 CTTTCCTTTT
53792092 CTTTCCTTCTT
1 CTTTCCTT-TT
*
53792103 -TTTCTTTCTT
1 CTTTCCTT-TT
* *
53792113 TTTTCTTCTTCTC
1 CTTTC--CTT-TT
53792126 CTTTCCTTTT
1 CTTTCCTTTT
*
53792136 CTTTCCTTCT
1 CTTTCCTTTT
53792146 -TTTCC-TTT
1 CTTTCCTTTT
* *
53792154 CTTTCCTCTC
1 CTTTCCTTTT
53792164 CTTTCCTTTT
1 CTTTCCTTTT
*
53792174 CTTTCTTTTT
1 CTTTCCTTTT
53792184 CTTTC
1 CTTTC
53792189 TTTCTTCTTC
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
8 2 0.03
9 10 0.13
10 50 0.63
11 9 0.11
13 8 0.10
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
CTTTCCTTTT
Found at i:53792125 original size:44 final size:43
Alignment explanation
Indices: 53792044--53792194 Score: 179
Period size: 44 Copynumber: 3.5 Consensus size: 43
53792034 TTTCTTTCCC
*
53792044 TCTTCTCCTTCTTTTTTTTTCTCTTCTCTTCTCTTCTCCTTTCCTTT
1 TCTT-TCCTTCTTTTTCTTTCT-TT-T-TTCTCTTCTCCTTTCCTTT
53792091 TCTTTCCTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTT
1 TCTTTCCTTCTTTTTCTTTCTTTTTTC-TCTTCTCCTTTCCTTT
*
53792135 TCTTTCCTTCTTTTCCTTTC---TTTC-C-TCTCCTTTCCTTT
1 TCTTTCCTTCTTTTTCTTTCTTTTTTCTCTTCTCCTTTCCTTT
*
53792173 TCTTT-CTTTTTCTTTCTTTCTT
1 TCTTTCCTTCTT-TTTCTTTCTT
53792195 CTTCTTTCCC
Statistics
Matches: 96, Mismatches: 4, Indels: 15
0.83 0.03 0.13
Matches are distributed among these distances:
37 5 0.05
38 25 0.26
39 1 0.01
41 4 0.04
43 3 0.03
44 36 0.38
45 2 0.02
46 16 0.17
47 4 0.04
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (43 bp):
TCTTTCCTTCTTTTTCTTTCTTTTTTCTCTTCTCCTTTCCTTT
Found at i:53792131 original size:34 final size:35
Alignment explanation
Indices: 53792092--53792203 Score: 131
Period size: 34 Copynumber: 3.2 Consensus size: 35
53792082 CTTTCCTTTT
53792092 CTTTCCTTCTT-TTTCTTTCTTTTTTC-TTCTTCTC
1 CTTTCCTT-TTCTTTCTTTCTTTTTTCTTTCTTCTC
* *
53792126 CTTTCCTTTTCTTTCCTTCTTTTCCTTTCTTTCCTCTC
1 CTTTCCTTTTCTTTCTTTC-TTT--TTTCTTTCTTCTC
* *
53792164 CTTTCCTTTTCTTTCTTT-TTCTTTCTTTCTTCTT
1 CTTTCCTTTTCTTTCTTTCTTTTTTCTTTCTTCTC
53792198 CTTTCC
1 CTTTCC
53792204 CTCTCCTTCT
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
33 2 0.03
34 32 0.48
35 3 0.04
36 2 0.03
37 4 0.06
38 24 0.36
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (35 bp):
CTTTCCTTTTCTTTCTTTCTTTTTTCTTTCTTCTC
Found at i:53792189 original size:10 final size:10
Alignment explanation
Indices: 53792052--53792201 Score: 76
Period size: 10 Copynumber: 15.0 Consensus size: 10
53792042 CCTCTTCTCC
*
53792052 TTCTTTTTTT
1 TTCTTTCTTT
53792062 TTCTCTTCTCTT
1 TTCT-TTCT-TT
* *
53792074 CTCTTCTCCTT
1 TTCTT-TCTTT
* *
53792085 TCCTTT-TCT
1 TTCTTTCTTT
*
53792094 TTCCTTCTTT
1 TTCTTTCTTT
53792104 TTCTTTCTTT
1 TTCTTTCTTT
*
53792114 TT-TCTTCTTC
1 TTCT-TTCTTT
* *
53792124 TCCTTTCCTT
1 TTCTTTCTTT
*
53792134 TTCTTTCCTT
1 TTCTTTCTTT
* *
53792144 CT-TTTC-CT
1 TTCTTTCTTT
* *
53792152 TTCTTTCCTC
1 TTCTTTCTTT
* *
53792162 TCCTTTCCTT
1 TTCTTTCTTT
53792172 TTCTTTCTTT
1 TTCTTTCTTT
53792182 TTCTTTCTTT
1 TTCTTTCTTT
53792192 CTTC-TTCTTT
1 -TTCTTTCTTT
53792202 CCCTCTCCTT
Statistics
Matches: 106, Mismatches: 25, Indels: 18
0.71 0.17 0.12
Matches are distributed among these distances:
8 2 0.02
9 14 0.13
10 70 0.66
11 13 0.12
12 7 0.07
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:53792200 original size:44 final size:41
Alignment explanation
Indices: 53792052--53792211 Score: 148
Period size: 44 Copynumber: 3.8 Consensus size: 41
53792042 CCTCTTCTCC
* *
53792052 TTCTT-TTTTTTTCTCTTCTCTTCTCTTCTCCTTTCCTTTTCT
1 TTCTTCTTTTTTT-TCTTTTCTT-TCCTCTCCTTTCCTTTTCT
* *
53792094 TTCCTTCTTTTTCTTTCTTTTTTCTTCTTCTCCTTTCCTTTTCT
1 TT-CTTCTTTTT-TTTCTTTTCT-TTCCTCTCCTTTCCTTTTCT
* *
53792138 TTC--C-TTCTTTTCCTTTCTTTCCTCTCCTTTCCTTTTCT
1 TTCTTCTTTTTTTTCTTTTCTTTCCTCTCCTTTCCTTTTCT
*
53792176 TTCTTTTTCTTTCTTTCTTCTTCTTTCCCTCTCCTT
1 TTCTTCTT-TTT-TTTCTT-TTCTTT-CCTCTCCTT
53792212 CTCTTCCCCC
Statistics
Matches: 98, Mismatches: 9, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
38 22 0.22
39 8 0.08
40 3 0.03
41 2 0.02
42 4 0.04
43 9 0.09
44 38 0.39
45 12 0.12
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (41 bp):
TTCTTCTTTTTTTTCTTTTCTTTCCTCTCCTTTCCTTTTCT
Found at i:53792291 original size:27 final size:27
Alignment explanation
Indices: 53792260--53792318 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
53792250 ATGGGCAGTA
53792260 CCGCCCATGGGAATGGCACCATCGGTG
1 CCGCCCATGGGAATGGCACCATCGGTG
* *
53792287 CCGCCCATGGGAATGGCACCTTTGGTG
1 CCGCCCATGGGAATGGCACCATCGGTG
53792314 CCGCC
1 CCGCC
53792319 ATCAGTGGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.15, C:0.36, G:0.32, T:0.17
Consensus pattern (27 bp):
CCGCCCATGGGAATGGCACCATCGGTG
Found at i:53800334 original size:2 final size:2
Alignment explanation
Indices: 53800314--53800365 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
53800304 TAATATCATC
* *
53800314 TA TA TA TC TA TC TA T- 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
53800355 TA TA TA TA TA T
1 TA TA TA TA TA T
53800366 CAATTACACT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53801782 original size:63 final size:63
Alignment explanation
Indices: 53801704--53801833 Score: 260
Period size: 63 Copynumber: 2.1 Consensus size: 63
53801694 AAAATTATTT
53801704 TTATTAATATTTGTATGTAAATTATTAAATTAATTTGTTATATTAAAATATAAGCCCCGCACA
1 TTATTAATATTTGTATGTAAATTATTAAATTAATTTGTTATATTAAAATATAAGCCCCGCACA
53801767 TTATTAATATTTGTATGTAAATTATTAAATTAATTTGTTATATTAAAATATAAGCCCCGCACA
1 TTATTAATATTTGTATGTAAATTATTAAATTAATTTGTTATATTAAAATATAAGCCCCGCACA
53801830 TTAT
1 TTAT
53801834 ATTGAAACGA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (63 bp):
TTATTAATATTTGTATGTAAATTATTAAATTAATTTGTTATATTAAAATATAAGCCCCGCACA
Found at i:53802656 original size:6 final size:6
Alignment explanation
Indices: 53802647--53802674 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53802637 TTCAATATTG
53802647 GAAAAA GAAAAA GAAAAA GAAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAA
53802675 CTGAGTGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:53807465 original size:20 final size:19
Alignment explanation
Indices: 53807432--53807476 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
53807422 TTAAGTTTTT
53807432 AAAATTTTTGAAAAAGAATA
1 AAAATTTTTGAAAAA-AATA
*
53807452 AAAATATTTT-AAAAAATTA
1 AAAAT-TTTTGAAAAAAATA
53807471 AAAATT
1 AAAATT
53807477 AAAATTTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.04
19 8 0.35
20 10 0.43
21 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
AAAATTTTTGAAAAAAATA
Found at i:53808338 original size:2 final size:2
Alignment explanation
Indices: 53808331--53808377 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
53808321 ATGAAATTTC
53808331 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
53808373 TA TA T
1 TA TA T
53808378 CTGCTTCCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53808508 original size:6 final size:6
Alignment explanation
Indices: 53808497--53808522 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
53808487 TATATCATGT
53808497 TGATTA TGATTA TGATTA TGATTA TG
1 TGATTA TGATTA TGATTA TGATTA TG
53808523 GATAAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (6 bp):
TGATTA
Found at i:53809836 original size:11 final size:12
Alignment explanation
Indices: 53809810--53809863 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 12
53809800 AACTAATCCT
53809810 CTCTCAAATTTC
1 CTCTCAAATTTC
*
53809822 CTCTC-AATTTG
1 CTCTCAAATTTC
*
53809833 CTCTTAAATTTC
1 CTCTCAAATTTC
*
53809845 TTC-CAAATTT-
1 CTCTCAAATTTC
53809855 CTCTCAAAT
1 CTCTCAAAT
53809864 CCATATTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
10 2 0.06
11 20 0.59
12 12 0.35
ACGTcount: A:0.26, C:0.28, G:0.02, T:0.44
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:53809836 original size:23 final size:22
Alignment explanation
Indices: 53809809--53809863 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
53809799 AAACTAATCC
53809809 TCTCTCAAATTTCCTCTC-AATT
1 TCTCTCAAATTTCCTC-CAAATT
* *
53809831 TGCTCTTAAATTTCTTCCAAATT
1 T-CTCTCAAATTTCCTCCAAATT
53809854 TCTCTCAAAT
1 TCTCTCAAAT
53809864 CCATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.45
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCCAAATT
Found at i:53809904 original size:51 final size:51
Alignment explanation
Indices: 53809823--53809922 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
53809813 TCAAATTTCC
* *
53809823 TCTCAATTTGCTCTTAAATTTCTTCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTACTCTTAAATTTCCTCCAAATTTCTCTCAAATCCATATTTAA
* * * *
53809874 TCTCAATTTACTC-TCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTACTCTTAAATTTCCTC-CAAATTTCTCTCAAATCCATATTT
53809923 TTAAATAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 9 0.21
51 33 0.79
ACGTcount: A:0.27, C:0.25, G:0.01, T:0.47
Consensus pattern (51 bp):
TCTCAATTTACTCTTAAATTTCCTCCAAATTTCTCTCAAATCCATATTTAA
Found at i:53811081 original size:7 final size:7
Alignment explanation
Indices: 53811069--53811094 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53811059 TAGTCGATTG
53811069 GTATTTA
1 GTATTTA
53811076 GTATTTA
1 GTATTTA
53811083 GTATTTA
1 GTATTTA
53811090 GTATT
1 GTATT
53811095 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:53811770 original size:18 final size:18
Alignment explanation
Indices: 53811743--53811782 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
53811733 CAGGTGCGTT
* *
53811743 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTGTATGTA
*
53811761 TCCTAACCCTTGTATGTT
1 TCCTAACCCTTGTATGTA
53811779 TCCT
1 TCCT
53811783 TTTTCGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.30, G:0.10, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTGTATGTA
Found at i:53812729 original size:13 final size:13
Alignment explanation
Indices: 53812711--53812762 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
53812701 AGTTTAGCAA
53812711 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
53812724 TGCTTTTAAAAAG
1 TGCTTTTGAAAAG
*
53812737 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
53812750 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
53812763 CTTGGTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 2 0.06
13 27 0.84
14 3 0.09
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:53812986 original size:24 final size:24
Alignment explanation
Indices: 53812952--53812997 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
53812942 TATATGAAAT
* *
53812952 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
53812976 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
53812998 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:53828305 original size:21 final size:20
Alignment explanation
Indices: 53828257--53828305 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
53828247 TTAGTTTTAA
*
53828257 ATGTTTTAGCCTTTAAAACC
1 ATGTTTTAGCCATTAAAACC
* *
53828277 AAGTTTTTAGCCATTAAATCGC
1 ATG-TTTTAGCCATTAAAAC-C
53828299 ATGTTTT
1 ATGTTTT
53828306 GAATAAAAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.09
21 18 0.78
22 3 0.13
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (20 bp):
ATGTTTTAGCCATTAAAACC
Found at i:53829473 original size:23 final size:23
Alignment explanation
Indices: 53829447--53829492 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
53829437 TGTTTCATAG
53829447 CTCAAGTGTCAAATTATCTTAAA
1 CTCAAGTGTCAAATTATCTTAAA
53829470 CTCAAGTGTCAAATTATCTTAAA
1 CTCAAGTGTCAAATTATCTTAAA
53829493 GTGTATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (23 bp):
CTCAAGTGTCAAATTATCTTAAA
Found at i:53847444 original size:12 final size:14
Alignment explanation
Indices: 53847405--53847440 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
53847395 GACTCTATTT
53847405 TAATTATATTAAGA
1 TAATTATATTAAGA
53847419 TAATTAATATTAAGA
1 TAATT-ATATTAAGA
53847434 TAATTAT
1 TAATTAT
53847441 TAAGGATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (14 bp):
TAATTATATTAAGA
Found at i:53851740 original size:43 final size:43
Alignment explanation
Indices: 53851686--53851932 Score: 271
Period size: 43 Copynumber: 5.7 Consensus size: 43
53851676 TTCTAAAAAT
* * *
53851686 GCCGTTAAAGGTCATGGTCTTTAGCAGCGCTTACCACACAAAC
1 GCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAACAAAC
*
53851729 GCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCACACAAAC
1 GCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAACAAAC
* * *
53851772 ACCGCTAAAGGTCATGGTCTTTAGCGGAGCTTACAAAACAAAC
1 GCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAACAAAC
* * * *
53851815 TCCGCTGAAGGTCATGGACTTTAGCGGCGCTTACCAAACAAAT
1 GCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAACAAAC
* * ** * **
53851858 GCCGCTAAA-GACAACGACCTTTAGCGGCGCTTCCCTTACAAAC
1 GCCGCTAAAGGTC-ATGGTCTTTAGCGGCGCTTACCAAACAAAC
*** * *
53851901 GCCGCTAAATACCCTGATCTTTAGCGGCGCTT
1 GCCGCTAAAGGTCATGGTCTTTAGCGGCGCTT
53851933 CTCTATAAAA
Statistics
Matches: 175, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
42 2 0.01
43 172 0.98
44 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (43 bp):
GCCGCTAAAGGTCATGGTCTTTAGCGGCGCTTACCAAACAAAC
Found at i:53851923 original size:129 final size:129
Alignment explanation
Indices: 53851693--53851932 Score: 302
Period size: 129 Copynumber: 1.9 Consensus size: 129
53851683 AATGCCGTTA
* * * * **
53851693 AAGGTCATGGTCTTTAGCAGCGCTTACCACACAAACGCCGCTAAAGGTCATGGTCTTTAGCGGCG
1 AAGGTCATGGACTTTAGCAGCGCTTACCAAACAAACGCCGCTAAAGGACACGACCTTTAGCGGCG
** *
53851758 CTTACCACACAAACACCGCTAAAGGTCATGGTCTTTAGCGGAGCTTACAAAACAAACTCCGCTG
66 CTTACCACACAAACACCGCTAAAGACCATGATCTTTAGCGGAGCTTACAAAACAAACTCCGCTG
* *
53851822 AAGGTCATGGACTTTAGCGGCGCTTACCAAACAAATGCCGCTAAA-GACAACGACCTTTAGCGGC
1 AAGGTCATGGACTTTAGCAGCGCTTACCAAACAAACGCCGCTAAAGGAC-ACGACCTTTAGCGGC
* ** * * * *
53851886 GCTTCCCTTACAAACGCCGCTAAATACCCTGATCTTTAGCGGCGCTT
65 GCTTACCACACAAACACCGCTAAAGACCATGATCTTTAGCGGAGCTT
53851933 CTCTATAAAA
Statistics
Matches: 92, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
128 2 0.02
129 90 0.98
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (129 bp):
AAGGTCATGGACTTTAGCAGCGCTTACCAAACAAACGCCGCTAAAGGACACGACCTTTAGCGGCG
CTTACCACACAAACACCGCTAAAGACCATGATCTTTAGCGGAGCTTACAAAACAAACTCCGCTG
Found at i:53851949 original size:129 final size:127
Alignment explanation
Indices: 53851675--53851953 Score: 292
Period size: 129 Copynumber: 2.2 Consensus size: 127
53851665 GCGGCGTTTA
* * *
53851675 TTTCTAAAAATGCCGTTAAAGGTCATGGTCTTTAGCAGCGCTTACCACACAAACGCCGCTAAAGG
1 TTTCTAAAAATGCCGCTAAAGGTCATGGACTTTAGCAGCGCTTACCAAACAAACGCCGCTAAAGG
* * ** ** *
53851740 TCATGGTCTTTAGCGGCGCTTACCACACAAACACCGCTAAAGGTCATGGTCTTTAGCGGAGC
66 ACACGACCTTTAGCGGCGCTTACCACACAAACACCGCTAAAGACCATGATCTTTAGCGGAGC
* * * * *
53851802 TTACAAAACAAACT-CCGCTGAAGGTCATGGACTTTAGCGGCGCTTACCAAACAAATGCCGCTAA
1 TTTC-TAA-AAA-TGCCGCTAAAGGTCATGGACTTTAGCAGCGCTTACCAAACAAACGCCGCTAA
* ** * * * *
53851866 A-GACAACGACCTTTAGCGGCGCTTCCCTTACAAACGCCGCTAAATACCCTGATCTTTAGCGGCG
63 AGGAC-ACGACCTTTAGCGGCGCTTACCACACAAACACCGCTAAAGACCATGATCTTTAGCGGAG
53851930 C
127 C
53851931 TTCTCTATAAAATGCCGCTAAAG
1 TT-TCTA-AAAATGCCGCTAAAG
53851954 ACCCTGATCT
Statistics
Matches: 120, Mismatches: 25, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
127 3 0.03
128 5 0.04
129 109 0.91
130 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (127 bp):
TTTCTAAAAATGCCGCTAAAGGTCATGGACTTTAGCAGCGCTTACCAAACAAACGCCGCTAAAGG
ACACGACCTTTAGCGGCGCTTACCACACAAACACCGCTAAAGACCATGATCTTTAGCGGAGC
Found at i:53852044 original size:43 final size:43
Alignment explanation
Indices: 53851698--53852058 Score: 229
Period size: 43 Copynumber: 8.4 Consensus size: 43
53851688 CGTTAAAGGT
* * * **
53851698 CATGGTCTTTAGCAGCGCTTAC-CACACAAACGCCGCTAAAGGT
1 CATGATCTTTAGCGGCGCTTTCAC-CACAAACGCCGCTAAAGAC
* * * **
53851741 CATGGTCTTTAGCGGCGCTTAC-CACACAAACACCGCTAAAGGT
1 CATGATCTTTAGCGGCGCTTTCAC-CACAAACGCCGCTAAAGAC
* * * ** * * **
53851784 CATGGTCTTTAGCGGAGCTTACAAAACAAACTCCGCTGAAGGT
1 CATGATCTTTAGCGGCGCTTTCACCACAAACGCCGCTAAAGAC
*
53851827 CATGGA-CTTTAGCGGCGC-TT-ACCAAACAAATGCCGCTAAAGAC
1 CAT-GATCTTTAGCGGCGCTTTCACC--ACAAACGCCGCTAAAGAC
* * * *
53851870 AACGACCTTTAGCGGCGC-TTC-CCTTACAAACGCCGCTAAATAC
1 CATGATCTTTAGCGGCGCTTTCACC--ACAAACGCCGCTAAAGAC
* * *
53851913 CCTGATCTTTAGCGGCGCTTCTCTA-TA-AAATGCCGCTAAAGAC
1 CATGATCTTTAGCGGCGCTT-TC-ACCACAAACGCCGCTAAAGAC
* * * * *
53851956 CCTGATCTTTAGCGGTGTTTTTCTCCA-AAACGCCGCTAAATAC
1 CATGATCTTTAGCGGCG-CTTTCACCACAAACGCCGCTAAAGAC
* *
53851999 CATGATCTTTAGCGGTGCTTTCACCACAAACGCCGCTATAGAC
1 CATGATCTTTAGCGGCGCTTTCACCACAAACGCCGCTAAAGAC
* * *
53852042 CATTACCTTTAGTGGCG
1 CATGATCTTTAGCGGCG
53852059 TTTTTTTAAA
Statistics
Matches: 260, Mismatches: 45, Indels: 26
0.79 0.14 0.08
Matches are distributed among these distances:
41 1 0.00
42 10 0.04
43 242 0.93
44 5 0.02
45 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (43 bp):
CATGATCTTTAGCGGCGCTTTCACCACAAACGCCGCTAAAGAC
Found at i:53852558 original size:66 final size:66
Alignment explanation
Indices: 53852392--53852559 Score: 207
Period size: 66 Copynumber: 2.5 Consensus size: 66
53852382 CTCACTACAG
* * *
53852392 CCTCTGCTTCTCTC-ACTGTCGCATCTGCTTTAAGCTGCTGCTGGAGTTCTTCATGCTTTCGTTG
1 CCTCAGCTTCTCTCGA-TGTTGCATCTGCTTTAAGTTGCTGCTGGAGTTCTTCATGCTTTCGTTG
53852456 AA
65 AA
* * * *
53852458 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTG-TAGCTGGAGTTCTTCATATCTTT-TTT
1 CCTCAGCTTCTCTCGATGTTGCATCTGCTTTAAGTTGCT-GCTGGAGTTCTTCAT-GCTTTCGTT
53852521 GAA
64 GAA
* *
53852524 CCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTT
1 CCTCAGCTTCTCTCGATGTTGCATCTGCTTTAAGTT
53852560 TTGTAATTTG
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
65 1 0.01
66 83 0.94
67 4 0.05
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGATGTTGCATCTGCTTTAAGTTGCTGCTGGAGTTCTTCATGCTTTCGTTGA
A
Found at i:53856720 original size:23 final size:22
Alignment explanation
Indices: 53856681--53856741 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
53856671 ACATTATTTA
53856681 TATATTTTT--AATTTAATCTC
1 TATATTTTTAAAATTTAATCTC
*
53856701 TTTATTTTTAAAAATTTAATCTC
1 TATATTTTT-AAAATTTAATCTC
*
53856724 TATATTTTTCAAATTTAA
1 TATATTTTTAAAATTTAA
53856742 AAATTTAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.23
22 8 0.23
23 19 0.54
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATTTTTAAAATTTAATCTC
Found at i:53857083 original size:22 final size:23
Alignment explanation
Indices: 53857035--53857077 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
53857025 TCCTATACAC
* *
53857035 AATTTATATTATTTTTAATAAAA
1 AATTCATATTATTTTCAATAAAA
53857058 AATTCATATTA-TTTCAATAA
1 AATTCATATTATTTTCAATAA
53857078 TTAATTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTCATATTATTTTCAATAAAA
Found at i:53861965 original size:41 final size:41
Alignment explanation
Indices: 53861772--53861942 Score: 297
Period size: 41 Copynumber: 4.2 Consensus size: 41
53861762 AGCACTTCAT
* * * * *
53861772 CTGCTAGGTTTAAAGTCTAATTCAGTTCACTGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
53861813 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
53861854 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
53861895 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
1 CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
53861936 CTGCTAG
1 CTGCTAG
53861943 ACATATAGTC
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 125 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.30
Consensus pattern (41 bp):
CTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGC
Found at i:53861965 original size:82 final size:82
Alignment explanation
Indices: 53861795--53861970 Score: 289
Period size: 82 Copynumber: 2.1 Consensus size: 82
53861785 AGTCTAATTC
53861795 AGTTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
1 AGTTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
* * * *
53861860 GGCTTATAGCCTGATTC
66 GACATATAGCCTGAATA
*
53861877 AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
1 AGTTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
*
53861942 GACATATAGTCTGAATA
66 GACATATAGCCTGAATA
*
53861959 ATTTCACTGGCA
1 AGTTCACTGGCA
53861971 ATAAATCCGA
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 86 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (82 bp):
AGTTCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
GACATATAGCCTGAATA
Found at i:53863554 original size:23 final size:23
Alignment explanation
Indices: 53863527--53863572 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
53863517 TAATTTGTTA
53863527 TATTAA-ACATATATTAACCTTAT
1 TATTAATAC-TATATTAACCTTAT
53863550 TATTAATTTACTATATTAACCTT
1 TATTAA--TACTATATTAACCTT
53863573 TACTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATACTATATTAACCTTAT
Found at i:53871286 original size:23 final size:23
Alignment explanation
Indices: 53871259--53871304 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
53871249 TAATTTGTTA
53871259 TATTAA-ACATATATTAACCTTAT
1 TATTAATAC-TATATTAACCTTAT
53871282 TATTAATTTACTATATTAACCTT
1 TATTAA--TACTATATTAACCTT
53871305 TACTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
25 12 0.60
26 2 0.10
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (23 bp):
TATTAATACTATATTAACCTTAT
Found at i:53874401 original size:20 final size:20
Alignment explanation
Indices: 53874377--53874451 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
53874367 GAAAATAAGA
* *
53874377 GCACCGAAGTGCGAATAGGG
1 GCACCGAAGTGCAAACAGGG
* * * *
53874397 ACACCAAAGTGTATACAGGG
1 GCACCGAAGTGCAAACAGGG
53874417 GCACCGAAGTGCAAACAGGG
1 GCACCGAAGTGCAAACAGGG
53874437 GCACCGAAGTGCAAA
1 GCACCGAAGTGCAAA
53874452 ATCCCGTACA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.23, G:0.32, T:0.09
Consensus pattern (20 bp):
GCACCGAAGTGCAAACAGGG
Found at i:53875826 original size:11 final size:11
Alignment explanation
Indices: 53875806--53875839 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
53875796 TTAAAATTTC
*
53875806 TTAATGAAACT
1 TTAATAAAACT
*
53875817 TTAATAAAACC
1 TTAATAAAACT
53875828 TTAATAAAACT
1 TTAATAAAACT
53875839 T
1 T
53875840 CGTAAGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (11 bp):
TTAATAAAACT
Found at i:53879204 original size:105 final size:105
Alignment explanation
Indices: 53878987--53879212 Score: 244
Period size: 105 Copynumber: 2.2 Consensus size: 105
53878977 CACACACCCA
* * * * *
53878987 TGTCCTTGCCCATGTGGCTCACATATCCTAGGCACATGCCCATGTCCTCTACCTGTGTGGTTCTA
1 TGTCCTTGCCCATGTGACTCACATAGCCTAGGCACACGCCCATGTCCTCTACCTGTATGGTCCTA
* * * * *
53879052 AAGCATAAGTAGTGAGTTACACGGCCTAGGCACATGTCTG
66 AAGCACAAATAGAGAGTTACACGGCCTAGGCAAACGTCTG
* * * *
53879092 TGTCCTTGCCCGTGTGACTCACATGGCCTGGGCACACGCCCATGTCC-CTGGCC-GTATGGTCCT
1 TGTCCTTGCCCATGTGACTCACATAGCCTAGGCACACGCCCATGTCCTCT-ACCTGTATGGTCCT
* *
53879155 AAATCACAAATAGAGAGTTACACGG-CTTGGACAAACG-CTGG
65 AAAGCACAAATAGAGAGTTACACGGCCTAGG-CAAACGTCT-G
53879196 TGTGCCTTGCCCATGTG
1 TGT-CCTTGCCCATGTG
53879213 GCTCCAAATC
Statistics
Matches: 100, Mismatches: 17, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
103 6 0.06
104 39 0.39
105 55 0.55
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.26
Consensus pattern (105 bp):
TGTCCTTGCCCATGTGACTCACATAGCCTAGGCACACGCCCATGTCCTCTACCTGTATGGTCCTA
AAGCACAAATAGAGAGTTACACGGCCTAGGCAAACGTCTG
Found at i:53881930 original size:90 final size:88
Alignment explanation
Indices: 53881596--53882056 Score: 536
Period size: 90 Copynumber: 5.2 Consensus size: 88
53881586 AACAAAATAA
* * * *
53881596 ATTTATAGATACAAGAAAATACGAAAATTCTAGAAAACTAATATACGAAAATATAAAATTTGACC
1 ATTTACAGATACAA-AAAATACGAACATTCTAGAAAACTGATATACGAAAATATAAAATTCGACC
* *
53881661 AACATATAATACAGGCTAAAATTG
65 AACAAATAATACAGACTAAAATTG
* * * *
53881685 ATTTACAGATACAAAAAATACAAATATTTTAGAAAATTGATATACGAAAATATAAAATTCGACCA
1 ATTTACAGATACAAAAAATACGAACATTCTAGAAAACTGATATACGAAAATATAAAATTCGACCA
* *
53881750 ACAAATAATA-GGGCTAAAATTG
66 ACAAATAATACAGACTAAAATTG
* *
53881772 ATTTACAGATACAAAAAATATGATCATTCTAGAAAACTGATATACGAAAATATAAAATTCGACCA
1 ATTTACAGATACAAAAAATACGAACATTCTAGAAAACTGATATACGAAAATATAAAATTCGACCA
53881837 ACAAATAATACAGACTAAAATAT-
66 ACAAATAATACAGACTAAAAT-TG
* * * * *
53881860 TTTTACAAAT-CTAAAATTATTACGAACATTCTAGAAAACTAATATACAAAAATATAAAATTCGA
1 ATTTACAGATAC-AAAA--AATACGAACATTCTAGAAAACTGATATACGAAAATATAAAATTCGA
*
53881924 CAAACAAATAATAC-GAACTAAAATAT-
63 CCAACAAATAATACAG-ACTAAAAT-TG
* ** * * * * * * *
53881950 TTTTATTGATCCAAAAATAATTCTATCATTTTACAAAACTGATATATGAAAATATAAAATTCGAC
1 ATTTACAGATAC-AAAA-AATACGAACATTCTAGAAAACTGATATACGAAAATATAAAATTCGAC
53882015 CAACAAATAATACAGACTAAAATTG
64 CAACAAATAATACAGACTAAAATTG
53882040 ATTTACAGATACAAAAA
1 ATTTACAGATACAAAAA
53882057 TAATAAGAAA
Statistics
Matches: 320, Mismatches: 43, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
87 81 0.25
88 75 0.23
89 20 0.06
90 138 0.43
91 6 0.02
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.27
Consensus pattern (88 bp):
ATTTACAGATACAAAAAATACGAACATTCTAGAAAACTGATATACGAAAATATAAAATTCGACCA
ACAAATAATACAGACTAAAATTG
Found at i:53882026 original size:180 final size:175
Alignment explanation
Indices: 53881596--53882056 Score: 534
Period size: 175 Copynumber: 2.6 Consensus size: 175
53881586 AACAAAATAA
* * ** * * *
53881596 ATTTATAGATACAAGAAAATACGAAAATTCTAGAAAACTAATATACGAAAATATAAAATTTGACC
1 ATTTACAGATACAA-AAAATATGATCATTCTACAAAACTGATATACGAAAATATAAAATTCGACC
* * * * * * *
53881661 AACATATAATACAGGCTAAAATTGATTTACAGATACAAAAAATACAAATATTTTAGAAAATTGAT
65 AACAAATAATACAGACTAAAATTGATTTACAAATACAAAAAATACAAACATTCTAGAAAACTAAT
* * **
53881726 ATACGAAAATATAAAATTCGACCAACAAATAATAGGGCTAAAATTG
130 ATACAAAAATATAAAATTCGACAAACAAATAATAGAACTAAAATTG
*
53881772 ATTTACAGATACAAAAAATATGATCATTCTAGAAAACTGATATACGAAAATATAAAATTCGACCA
1 ATTTACAGATACAAAAAATATGATCATTCTACAAAACTGATATACGAAAATATAAAATTCGACCA
* * *
53881837 ACAAATAATACAGACTAAAATAT-TTTTACAAAT-CTAAAATTATTACGAACATTCTAGAAAACT
66 ACAAATAATACAGACTAAAAT-TGATTTACAAATAC-AAAA--AATACAAACATTCTAGAAAACT
53881900 AATATACAAAAATATAAAATTCGACAAACAAATAATACGAACTAAAATAT-
127 AATATACAAAAATATAAAATTCGACAAACAAATAATA-GAACTAAAAT-TG
* ** * * * *
53881950 TTTTATTGAT-CCAAAAATAATTCTATCATTTTACAAAACTGATATATGAAAATATAAAATTCGA
1 ATTTACAGATACAAAAAAT-A-T-GATCATTCTACAAAACTGATATACGAAAATATAAAATTCGA
*
53882014 CCAACAAATAATACAGACTAAAATTGATTTACAGATACAAAAA
63 CCAACAAATAATACAGACTAAAATTGATTTACAAATACAAAAA
53882057 TAATAAGAAA
Statistics
Matches: 244, Mismatches: 30, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
174 1 0.00
175 77 0.32
176 14 0.06
177 58 0.24
178 17 0.07
179 3 0.01
180 73 0.30
181 1 0.00
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.27
Consensus pattern (175 bp):
ATTTACAGATACAAAAAATATGATCATTCTACAAAACTGATATACGAAAATATAAAATTCGACCA
ACAAATAATACAGACTAAAATTGATTTACAAATACAAAAAATACAAACATTCTAGAAAACTAATA
TACAAAAATATAAAATTCGACAAACAAATAATAGAACTAAAATTG
Found at i:53882530 original size:57 final size:58
Alignment explanation
Indices: 53882469--53882593 Score: 139
Period size: 58 Copynumber: 2.2 Consensus size: 58
53882459 GGGATGCTGA
** * *
53882469 CCATCAGTGTCCCAGTGCCCAAA-AATATATTTTTT-AATTCTGGTACAAGGGTG-TCGG
1 CCATCAGTGTCCCAGCACCAAAAGAAT-TATTTTTTAAATTCTGGTACAAGGGTGCT-AG
* * * *
53882526 CCATCTGTGTCCTAGCACCAAAAGAATTATTTTTTAAATTTTGGTATAAGGGTGCTAG
1 CCATCAGTGTCCCAGCACCAAAAGAATTATTTTTTAAATTCTGGTACAAGGGTGCTAG
53882584 CCATCAGTGT
1 CCATCAGTGT
53882594 GTTAGCACCC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
57 26 0.46
58 29 0.52
59 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (58 bp):
CCATCAGTGTCCCAGCACCAAAAGAATTATTTTTTAAATTCTGGTACAAGGGTGCTAG
Found at i:53884872 original size:2 final size:2
Alignment explanation
Indices: 53884865--53884892 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53884855 AACCTATCTC
53884865 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
53884893 GTGAAGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53890275 original size:27 final size:26
Alignment explanation
Indices: 53890235--53890291 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
53890225 CACAAAGAAA
*
53890235 AGTTCAGTGCCTGGAGAAAAGCTTGG
1 AGTTCAGTGCCTGGACAAAAGCTTGG
* * *
53890261 AGTTCTAGTTCCTGGACTAAAGCTTGT
1 AGTTC-AGTGCCTGGACAAAAGCTTGG
53890288 AGTT
1 AGTT
53890292 GTGCTGATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (26 bp):
AGTTCAGTGCCTGGACAAAAGCTTGG
Found at i:53896040 original size:17 final size:18
Alignment explanation
Indices: 53896008--53896052 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
53895998 TTAAGAATTT
53896008 AAAAATTAAATAAATTAAC
1 AAAAA-TAAATAAATTAAC
*
53896027 AAAAATAAAT-AATTAAG
1 AAAAATAAATAAATTAAC
*
53896044 ATAAATAAA
1 AAAAATAAA
53896053 AGAGAACAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 14 0.58
18 5 0.21
19 5 0.21
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
AAAAATAAATAAATTAAC
Found at i:53896096 original size:12 final size:12
Alignment explanation
Indices: 53896079--53896103 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53896069 AAGATTAGAC
53896079 AATAAAGAAGAT
1 AATAAAGAAGAT
53896091 AATAAAGAAGAT
1 AATAAAGAAGAT
53896103 A
1 A
53896104 GATGGAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AATAAAGAAGAT
Found at i:53902776 original size:31 final size:31
Alignment explanation
Indices: 53902736--53902795 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
53902726 TTGGTGATTT
* *
53902736 AAATGAAAACTTTC-TACTAATTTAGTGACCA
1 AAATAAAAACTTACTTA-TAATTTAGTGACCA
*
53902767 AAATAAAAACTTACTTATAGTTTAGTGAC
1 AAATAAAAACTTACTTATAATTTAGTGAC
53902796 TAATAATGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (31 bp):
AAATAAAAACTTACTTATAATTTAGTGACCA
Found at i:53904231 original size:43 final size:42
Alignment explanation
Indices: 53904130--53904475 Score: 377
Period size: 43 Copynumber: 8.1 Consensus size: 42
53904120 TTATTTTTAT
* * * ***** *
53904130 AAACGCCACTAAAGGTCATGTTCTTCAGCGGCGCTACAAAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTCCAC
* * *
53904172 AAACGCCGCTAAAGGTCAGGGTCTTTAGCGGCGCTTTTCCTAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTCC-AC
* * *
53904215 AAACACCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTTTCCAC
* * *
53904258 AAACACCGCTGAAGATCATGTTCCTTAGCGGCGCTTGTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-TTCCAC
* *
53904301 AAACGCCGCTAAAGATCATGTTCCTTAGCGGCGATTTTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCG-CTTTTCCAC
*
53904344 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAT
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTTTCCAC
*
53904387 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCTTCCGC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-TTCCAC
* * * * * *
53904430 AAATGCCACTAAAGGTCATGTTATTTTAGCGGCGTTTTTACAC
1 AAACGCCGCTAAAGATCATGTT-CTTTAGCGGCGCTTTTCCAC
53904473 AAA
1 AAA
53904476 TGCCTCTATT
Statistics
Matches: 264, Mismatches: 33, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
42 35 0.13
43 210 0.80
44 19 0.07
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTCCAC
Found at i:53904479 original size:43 final size:43
Alignment explanation
Indices: 53904172--53904475 Score: 396
Period size: 43 Copynumber: 7.1 Consensus size: 43
53904162 GCTACAAAAA
* * *
53904172 AAACGCCGCTAAAGGTCAGGGTCTTTAGCGGCGC-TTTTCCTAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCC-AC
* * *
53904215 AAACACCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTTCAAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
* * * *
53904258 AAACACCGCTGAAGATCATGTTCCTTAGCGGCGCTTGTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
* *
53904301 AAACGCCGCTAAAGATCATGTTCCTTAGCGGCGATTTTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
*
53904344 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAT
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
* *
53904387 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTCTTCCGC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
* * * * *
53904430 AAATGCCACTAAAGGTCATGTTATTTTAGCGGCG-TTTTTACAC
1 AAACGCCGCTAAAGATCATGTT-CTTTAGCGGCGCTTTTTCCAC
53904473 AAA
1 AAA
53904476 TGCCTCTATT
Statistics
Matches: 233, Mismatches: 26, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
43 218 0.94
44 15 0.06
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
Found at i:53904932 original size:87 final size:87
Alignment explanation
Indices: 53904836--53905006 Score: 270
Period size: 87 Copynumber: 2.0 Consensus size: 87
53904826 CTCTGCTCTT
* *
53904836 CTTCCCTCGCTGCAGCGTCTGCTTCTCTCGATGCCGCATCTACTTTAAGTTGTAGCTGGAGTTCT
1 CTTCCCTCGCTGCAGCCTCTGCTTCCCTCGATGCCGCATCTACTTTAAGTTGTAGCTGGAGTTCT
*
53904901 TCATATTTCTTTTGAACCTTTG
66 TCATATTTCCTTTGAACCTTTG
* * * * *
53904923 CTTCTCTCGCTGTAGCCTCTGCTTCCCTCGCTGCCGCCTCTGCTTTAAGTTGTAGCTGGAGTTCT
1 CTTCCCTCGCTGCAGCCTCTGCTTCCCTCGATGCCGCATCTACTTTAAGTTGTAGCTGGAGTTCT
53904988 TCATATTTCCTTTGAACCT
66 TCATATTTCCTTTGAACCT
53905007 CAACTGTGGT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 76 1.00
ACGTcount: A:0.12, C:0.30, G:0.18, T:0.40
Consensus pattern (87 bp):
CTTCCCTCGCTGCAGCCTCTGCTTCCCTCGATGCCGCATCTACTTTAAGTTGTAGCTGGAGTTCT
TCATATTTCCTTTGAACCTTTG
Found at i:53904945 original size:21 final size:21
Alignment explanation
Indices: 53904921--53904967 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
53904911 TTTGAACCTT
* *
53904921 TGCTTCTCTCGCTGTAGCCTC
1 TGCTTCCCTCGCTGCAGCCTC
*
53904942 TGCTTCCCTCGCTGCCGCCTC
1 TGCTTCCCTCGCTGCAGCCTC
53904963 TGCTT
1 TGCTT
53904968 TAAGTTGTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.43, G:0.19, T:0.36
Consensus pattern (21 bp):
TGCTTCCCTCGCTGCAGCCTC
Found at i:53908814 original size:22 final size:22
Alignment explanation
Indices: 53908788--53908833 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
53908778 AAACTCTATT
53908788 CCTTAGACCC-TAAACCGTAAAC
1 CCTTA-ACCCTTAAACCGTAAAC
*
53908810 CCTTAACCCTTAAACCTTAAAC
1 CCTTAACCCTTAAACCGTAAAC
53908832 CC
1 CC
53908834 ACGAACCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.35, C:0.39, G:0.04, T:0.22
Consensus pattern (22 bp):
CCTTAACCCTTAAACCGTAAAC
Found at i:53908845 original size:22 final size:21
Alignment explanation
Indices: 53908794--53908846 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
53908784 TATTCCTTAG
**
53908794 ACCCTAAACCGTAAACCCTTA
1 ACCCTAAACCGTAAACCCCGA
*
53908815 ACCCTTAAACCTTAAACCCACGA
1 ACCC-TAAACCGTAAACCC-CGA
53908838 ACCCTAAAC
1 ACCCTAAAC
53908847 AATAATGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 18 0.67
23 5 0.19
ACGTcount: A:0.40, C:0.40, G:0.04, T:0.17
Consensus pattern (21 bp):
ACCCTAAACCGTAAACCCCGA
Found at i:53909096 original size:21 final size:22
Alignment explanation
Indices: 53909054--53909098 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
53909044 ATTAACTGTA
* **
53909054 AACCCTCAAACCCTTAGCCCTT
1 AACCCTCAAACACTTAAACCTT
53909076 AACCCT-AAACACTTAAACCTT
1 AACCCTCAAACACTTAAACCTT
53909097 AA
1 AA
53909099 ATCCCAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.38, C:0.38, G:0.02, T:0.22
Consensus pattern (22 bp):
AACCCTCAAACACTTAAACCTT
Found at i:53909194 original size:14 final size:14
Alignment explanation
Indices: 53909174--53909206 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
53909164 TAGAACATAT
53909174 ATAAACCCTAAATC
1 ATAAACCCTAAATC
*
53909188 CTAAACCCTAAATC
1 ATAAACCCTAAATC
53909202 ATAAA
1 ATAAA
53909207 ACATATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAACCCTAAATC
Found at i:53909232 original size:39 final size:40
Alignment explanation
Indices: 53909146--53909233 Score: 117
Period size: 39 Copynumber: 2.2 Consensus size: 40
53909136 CTGGCCATAT
* * *
53909146 TCCTTAAACCCCGAATCATAGAACATATATAAACCCTAAA
1 TCCTTAAACCCCAAATCATAAAACATATATAAACCATAAA
* *
53909186 TCC-TAAACCCTAAATCATAAAACATATATAAACTATAAA
1 TCCTTAAACCCCAAATCATAAAACATATATAAACCATAAA
53909225 -CCTTAAACC
1 TCCTTAAACC
53909234 TCAACCCTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
38 2 0.05
39 37 0.88
40 3 0.07
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (40 bp):
TCCTTAAACCCCAAATCATAAAACATATATAAACCATAAA
Found at i:53909883 original size:208 final size:207
Alignment explanation
Indices: 53909623--53910280 Score: 996
Period size: 208 Copynumber: 3.2 Consensus size: 207
53909613 TTTTGGCAAT
* * * * * ** * * *
53909623 GCGCCACTAATGTCTCTAAATCTGAAAAAGAAAACACTATCGTTTGCCTAAAACTATTATCGATA
1 GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCGATA
*
53909688 ATGCTTGAATTTTACTGCGTTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAGAAAACGA
66 ATGCTTGAATTTTACCGCGTTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAGAAAACGA
** * *
53909753 CGGCGTATGCTTAAAACTTTTTGCGGCGCTT-TAGAGGAAGCGCTGCTAATGATTGACTTTAGCG
131 CGGCGTATGCTTAAAACTTTTTGCGGCGCTTCTCTA--AAGCGCCGCTAATGATTGACTTCAGCG
*
53909817 GCGATTTCTTCGAA
194 GCGATTTCTTTGAA
53909831 GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCGATA
1 GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCGATA
* * * *
53909896 ATGCTTGATTTTTGCCGCATTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAAAAAACGA
66 ATGCTTGAATTTTACCGCGTTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAGAAAACGA
*
53909961 CGGCGTATGCTTAAAACTTTTTGCGGCGCTTCCTCTAAAGCGCCGCTAATGATTGACTTCAGCAG
131 CGGCGTATGCTTAAAACTTTTTGCGGCGCTT-CTCTAAAGCGCCGCTAATGATTGACTTCAGCGG
53910026 CGATTTCTTTGAA
195 CGATTTCTTTGAA
*
53910039 GCGTCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCGATA
1 GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCGATA
* * * * *
53910104 ATGCTTGACTTTTACGGCGTTTTTTGCAAAGCGTCACTAATGTCCCTAAGCACAACAGAAAACGA
66 ATGCTTGAATTTTACCGCGTTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAGAAAACGA
*
53910169 CGGCGTATGCTTAAAACTTTTTGCGGCGCTTCCTCTAAAGCACCGCTAATGATTGACTTCAGCGG
131 CGGCGTATGCTTAAAACTTTTTGCGGCGCTT-CTCTAAAGCGCCGCTAATGATTGACTTCAGCGG
*
53910234 CGATTTCTTTGTA
195 CGATTTCTTTGAA
53910247 GCGCCACTATTG-GTTCTAAAACTCAACAAGAAAA
1 GCGCCACTATTGTG-TCTAAAACTCAACAAGAAAA
53910281 TGACGTCGTT
Statistics
Matches: 413, Mismatches: 34, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
207 1 0.00
208 410 0.99
210 2 0.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (207 bp):
GCGCCACTATTGTGTCTAAAACTCAACAAGAAAACGTTGTCATTTGCCTAAAACTATTACCGATA
ATGCTTGAATTTTACCGCGTTTTTCGCGAAGCGCCACTAATGTCCCTAAGCACAACAGAAAACGA
CGGCGTATGCTTAAAACTTTTTGCGGCGCTTCTCTAAAGCGCCGCTAATGATTGACTTCAGCGGC
GATTTCTTTGAA
Found at i:53912331 original size:8 final size:9
Alignment explanation
Indices: 53912259--53912350 Score: 96
Period size: 9 Copynumber: 10.2 Consensus size: 9
53912249 TTGGGTAATT
53912259 TTCGGGTAA
1 TTCGGGTAA
53912268 TTCGGGTAA
1 TTCGGGTAA
**
53912277 TTTATGGTAA
1 -TTCGGGTAA
*
53912287 TTCGGTTAA
1 TTCGGGTAA
* *
53912296 TTTGGTTAA
1 TTCGGGTAA
*
53912305 TTCGGTTAA
1 TTCGGGTAA
*
53912314 TTCGGTTAA
1 TTCGGGTAA
53912323 -TCGGGTAA
1 TTCGGGTAA
*
53912331 TTCTGGTAA
1 TTCGGGTAA
53912340 TTCGGGTAA
1 TTCGGGTAA
53912349 TT
1 TT
53912351 TTTAACCAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
8 7 0.10
9 57 0.80
10 7 0.10
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.42
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:53914494 original size:17 final size:16
Alignment explanation
Indices: 53914469--53914505 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
53914459 TAATAATCAA
53914469 TATTAGTCAAAAAATTT
1 TATTAGTC-AAAAATTT
*
53914486 TATTGGTCAAAAATTT
1 TATTAGTCAAAAATTT
53914502 TATT
1 TATT
53914506 TTTATTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (16 bp):
TATTAGTCAAAAATTT
Found at i:53920365 original size:42 final size:42
Alignment explanation
Indices: 53920310--53920409 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
53920300 CTATATGAAT
* *
53920310 GGCACTAAGTGTGCGGAATTAAAATGATGATGTTGAATAATA
1 GGCACTAAGTGTGCGAAATTAAAATGATGATGTTGAATAACA
*
53920352 GGCACTAAGTGTGCGAAATTAAAATGATGATGTTGAATAACG
1 GGCACTAAGTGTGCGAAATTAAAATGATGATGTTGAATAACA
53920394 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
53920410 TACCGAGAGC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.36, C:0.10, G:0.28, T:0.26
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAATTAAAATGATGATGTTGAATAACA
Found at i:53921311 original size:23 final size:24
Alignment explanation
Indices: 53921244--53921326 Score: 98
Period size: 23 Copynumber: 3.5 Consensus size: 24
53921234 CGATTCAAGT
* *
53921244 CCAATTTTGGTGTAAAAATGCTGC
1 CCAATTTTGGTGTATATATGCTGC
*
53921268 CCAA-TTTGGTGTCTATATGCTGC
1 CCAATTTTGGTGTATATATGCTGC
* *
53921291 CCAA-TTTGGTGTATATTTGCTGT
1 CCAATTTTGGTGTATATATGCTGC
*
53921314 CAAATTTTGGTGT
1 CCAATTTTGGTGT
53921327 TAAAAAAATG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 39 0.76
24 12 0.24
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (24 bp):
CCAATTTTGGTGTATATATGCTGC
Found at i:53929491 original size:17 final size:17
Alignment explanation
Indices: 53929458--53929745 Score: 130
Period size: 17 Copynumber: 16.5 Consensus size: 17
53929448 AAAACACAAA
53929458 AAAATTTTA-AAACACG
1 AAAATTTTAGAAACACG
* *
53929474 AGAATTTTAGAGACACG
1 AAAATTTTAGAAACACG
*
53929491 AAAATTCTTAAAAACACG
1 AAAATT-TTAGAAACACG
53929509 AAAATTTT-GAAAACACG
1 AAAATTTTAG-AAACACG
*
53929526 ACAATTTT-GAAACACG
1 AAAATTTTAGAAACACG
*
53929542 AGAAATTTTTTTGAAAACACG
1 A-AAA--TTTTAG-AAACACG
*** *
53929563 ---ATTTTTTTAACGCG
1 AAAATTTTAGAAACACG
53929577 AAAATTTGT-GAAACACG
1 AAAATTT-TAGAAACACG
* *
53929594 AGAATTGTT-GAAATCAAG
1 AAAATT-TTAGAAA-CACG
* *
53929612 AAAATTTTGGAAAACACA
1 AAAATTTTAG-AAACACG
* *
53929630 AAAATTTTTGAAATACG
1 AAAATTTTAGAAACACG
*
53929647 AAAGTTTTTAGAAAACACG
1 AAA-ATTTTAG-AAACACG
* *
53929666 AAAATTTTTTTG-ATCATCG
1 AAAA--TTTTAGAAACA-CG
* *
53929685 -GAATTTTTGAGAACACG
1 AAAATTTTAGA-AACACG
53929702 AAAA-TTTATGAAACACAG
1 AAAATTTTA-GAAACAC-G
**
53929720 AAGTTTTTAGAAAACACG
1 AAAATTTTAG-AAACACG
53929738 AAAATTTT
1 AAAATTTT
53929746 TTTGGCGACA
Statistics
Matches: 208, Mismatches: 36, Indels: 54
0.70 0.12 0.18
Matches are distributed among these distances:
14 5 0.02
15 5 0.02
16 22 0.11
17 70 0.34
18 65 0.31
19 28 0.13
20 6 0.03
21 7 0.03
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (17 bp):
AAAATTTTAGAAACACG
Found at i:53929506 original size:35 final size:33
Alignment explanation
Indices: 53929458--53929745 Score: 131
Period size: 35 Copynumber: 8.2 Consensus size: 33
53929448 AAAACACAAA
*
53929458 AAAATTTTAAAACACGAGAATTTT-AGAGACACG
1 AAAATTTTAAAACACGAGAATTTTGA-AAACACG
*
53929491 AAAATTCTTAAAAACACGAAAATTTTGAAAACACG
1 AAAATT-TT-AAAACACGAGAATTTTGAAAACACG
* *
53929526 ACAATTTTGAAACACGAGAAATTTTTTTGAAAACACG
1 AAAATTTTAAAACACGAG-AA---TTTTGAAAACACG
* ** * *
53929563 --ATTTTTTTAACGCGAAAATTTGTG-AAACACG
1 AAAATTTTAAAACACGAGAATTT-TGAAAACACG
* * * * *
53929594 AGAATTGTTGAAATCAAGAAAATTTTGGAAAACACA
1 AAAATT-TT-AAAACACGAGAATTTT-GAAAACACG
* *
53929630 AAAATTTTTGAAATACGA-AAGTTTTTAGAAAACACG
1 AAAA-TTTTAAAACACGAGAA--TTTT-GAAAACACG
** * *
53929666 AAAATTTTTTTGATCATCG-GAATTTTTGAGAACACG
1 AAAA--TTTTAAAACA-CGAGAA-TTTTGAAAACACG
*
53929702 AAAATTTATGAAACAC-AGAAGTTTTTAGAAAACACG
1 AAAATTT-TAAAACACGAGAA--TTTT-GAAAACACG
53929738 AAAATTTT
1 AAAATTTT
53929746 TTTGGCGACA
Statistics
Matches: 198, Mismatches: 33, Indels: 46
0.71 0.12 0.17
Matches are distributed among these distances:
31 10 0.05
32 2 0.01
33 17 0.09
34 20 0.10
35 63 0.32
36 55 0.28
37 27 0.14
38 4 0.02
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (33 bp):
AAAATTTTAAAACACGAGAATTTTGAAAACACG
Found at i:53929638 original size:68 final size:67
Alignment explanation
Indices: 53929507--53929638 Score: 144
Period size: 68 Copynumber: 1.9 Consensus size: 67
53929497 CTTAAAAACA
* * * **
53929507 CGAAAATTTTGAAAACACGACAATTTTGAAACACGAGAAATTTTTTTGAAAACACGATTTTTTTA
1 CGAAAATTTTGAAAACACGACAATTTTGAAACAC-AGAAATATTTTGGAAAACACAAAATTTTTA
53929572 ACG
65 ACG
*
53929575 CGAAAATTTGTG-AAACACGAGAATTGTTGAAATCA-AGAAA-ATTTTGGAAAACACAAAAATTT
1 CGAAAATTT-TGAAAACACGACAATT-TTGAAA-CACAGAAATATTTTGGAAAACAC-AAAATTT
53929637 TT
62 TT
53929639 GAAATACGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
67 12 0.22
68 32 0.59
69 8 0.15
70 2 0.04
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.30
Consensus pattern (67 bp):
CGAAAATTTTGAAAACACGACAATTTTGAAACACAGAAATATTTTGGAAAACACAAAATTTTTAA
CG
Found at i:53929655 original size:18 final size:19
Alignment explanation
Indices: 53929448--53929747 Score: 123
Period size: 18 Copynumber: 16.9 Consensus size: 19
53929438 ATTTTAAAAA
* **
53929448 AAAACACAAAAAAATTTT-
1 AAAACACGAAAATTTTTTG
* *
53929466 AAAACACGAGAA-TTTTAG
1 AAAACACGAAAATTTTTTG
* * *
53929484 -AGACACGAAAA-TTCTTA
1 AAAACACGAAAATTTTTTG
53929501 AAAACACGAAAA--TTTTG
1 AAAACACGAAAATTTTTTG
*
53929518 AAAACACGACAA--TTTTG
1 AAAACACGAAAATTTTTTG
53929535 -AAACACGAGAAATTTTTTTG
1 AAAACACGA-AAA-TTTTTTG
53929555 AAAACACG---ATTTTTT-
1 AAAACACGAAAATTTTTTG
* * *
53929570 -TAACGCGAAAA-TTTGTG
1 AAAACACGAAAATTTTTTG
* *
53929587 -AAACACGAGAA-TTGTTG
1 AAAACACGAAAATTTTTTG
* * *
53929604 AAATCAAGAAAA-TTTTGG
1 AAAACACGAAAATTTTTTG
*
53929622 AAAACAC-AAAAATTTTTG
1 AAAACACGAAAATTTTTTG
* * *
53929640 -AAATACGAAAGTTTTTAG
1 AAAACACGAAAATTTTTTG
53929658 AAAACACGAAAATTTTTTTG
1 AAAACACGAAAA-TTTTTTG
* *
53929678 --ATCATCG-GAA-TTTTTG
1 AAAACA-CGAAAATTTTTTG
* *
53929694 AGAACACGAAAA-TTTATG
1 AAAACACGAAAATTTTTTG
* *
53929712 -AAACAC-AGAAGTTTTTAG
1 AAAACACGA-AAATTTTTTG
53929730 AAAACACGAAAATTTTTT
1 AAAACACGAAAATTTTTT
53929748 TGGCGACATG
Statistics
Matches: 210, Mismatches: 48, Indels: 47
0.69 0.16 0.15
Matches are distributed among these distances:
14 5 0.02
16 25 0.12
17 68 0.32
18 69 0.33
19 24 0.11
20 12 0.06
21 7 0.03
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAACACGAAAATTTTTTG
Found at i:53929690 original size:72 final size:72
Alignment explanation
Indices: 53929614--53929749 Score: 211
Period size: 72 Copynumber: 1.9 Consensus size: 72
53929604 AAATCAAGAA
* *
53929614 AATTTTGGAAAACACAAAAATTTTTGAAATAC-GAAAGTTTTTAGAAAACACGAAAATTTTTTTG
1 AATTTTGGAAAACACAAAAATTTATGAAACACAG-AAGTTTTTAGAAAACACGAAAATTTTTTTG
53929678 ATCATCGG
65 ATCATCGG
* * *
53929686 AATTTTTGAGAACACGAAAATTTATGAAACACAGAAGTTTTTAGAAAACACGAAAATTTTTTTG
1 AATTTTGGAAAACACAAAAATTTATGAAACACAGAAGTTTTTAGAAAACACGAAAATTTTTTTG
53929750 GCGACATGGG
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 57 0.98
73 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (72 bp):
AATTTTGGAAAACACAAAAATTTATGAAACACAGAAGTTTTTAGAAAACACGAAAATTTTTTTGA
TCATCGG
Found at i:53929952 original size:20 final size:20
Alignment explanation
Indices: 53929927--53929965 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
53929917 CGTGATCTTA
53929927 TTAAAACACGAGAATTTTTT
1 TTAAAACACGAGAATTTTTT
*
53929947 TTAAAACACGAGGATTTTT
1 TTAAAACACGAGAATTTTT
53929966 GAATATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (20 bp):
TTAAAACACGAGAATTTTTT
Found at i:53930607 original size:12 final size:11
Alignment explanation
Indices: 53930578--53930628 Score: 58
Period size: 10 Copynumber: 5.1 Consensus size: 11
53930568 CCGACTGTGA
53930578 TATTTTT-TTC
1 TATTTTTCTTC
53930588 TATTTTTCTTC
1 TATTTTTCTTC
53930599 TA-TTTT-TTC
1 TATTTTTCTTC
53930608 T-TTTTTCTTC
1 TATTTTTCTTC
*
53930618 -CTTTTTCTTC
1 TATTTTTCTTC
53930628 T
1 T
53930629 TTCCTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 8 0.22
10 23 0.64
11 5 0.14
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (11 bp):
TATTTTTCTTC
Found at i:53930612 original size:19 final size:19
Alignment explanation
Indices: 53930580--53930630 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
53930570 GACTGTGATA
53930580 TTTTTTTCTATTTTTCTT-C
1 TTTTTTTCT-TTTTTCTTCC
53930599 TATTTTTTCTTTTTTCTTCC
1 T-TTTTTTCTTTTTTCTTCC
53930619 TTTTTCTTCTTT
1 TTTTT-TTCTTT
53930631 CCTTTTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTTTCTTTTTTCTTCC
Found at i:53930791 original size:21 final size:21
Alignment explanation
Indices: 53930729--53930791 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
53930719 GCCCCCCTTC
* *
53930729 TCTTCCTCTCTCTCTCTTTTCTT
1 TCTT-CTCT-TCTTTCTTTTTTT
* *
53930752 TCTTGTCTTTTTTCTTTTTTT
1 TCTTCTCTTCTTTCTTTTTTT
53930773 TCTTCTCTTCTTTCTTTTT
1 TCTTCTCTTCTTTCTTTTT
53930792 GGCTGCTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 27 0.79
22 3 0.09
23 4 0.12
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (21 bp):
TCTTCTCTTCTTTCTTTTTTT
Found at i:53931242 original size:30 final size:30
Alignment explanation
Indices: 53931202--53931288 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 30
53931192 ATATTGGGCC
*
53931202 AAATGTAATTTTTAAAAAGTTTAGGGGTT-
1 AAATGAAATTTTTAAAAAGTTTAGGGGTTG
* *
53931231 AAAGTGAAATTTTGAGAAAGTTTAGGGGTTG
1 AAA-TGAAATTTTTAAAAAGTTTAGGGGTTG
* * * *
53931262 GAATGTAATTTTTGAAAAGTTCAGGGG
1 AAATGAAATTTTTAAAAAGTTTAGGGG
53931289 CCAAAATGTA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 3 0.06
30 42 0.89
31 2 0.04
ACGTcount: A:0.36, C:0.01, G:0.28, T:0.36
Consensus pattern (30 bp):
AAATGAAATTTTTAAAAAGTTTAGGGGTTG
Found at i:53931297 original size:30 final size:30
Alignment explanation
Indices: 53931173--53931299 Score: 93
Period size: 30 Copynumber: 4.3 Consensus size: 30
53931163 ATTTGGGGTA
*
53931173 AAAATGTAATTTTAGGAAAA-TATT--GGGCC
1 AAAATGTAATTTT-TGAAAAGT-TTAGGGGCC
* **
53931202 -AAATGTAATTTTTAAAAAGTTTAGGGGTT
1 AAAATGTAATTTTTGAAAAGTTTAGGGGCC
* * **
53931231 AAAGTG-AAATTTTGAGAAAGTTTAGGGGTT
1 AAAATGTAATTTTTGA-AAAGTTTAGGGGCC
** *
53931261 GGAATGTAATTTTTGAAAAGTTCAGGGGCC
1 AAAATGTAATTTTTGAAAAGTTTAGGGGCC
53931291 AAAATGTAA
1 AAAATGTAA
53931300 ATTATGTTTT
Statistics
Matches: 76, Mismatches: 16, Indels: 11
0.74 0.16 0.11
Matches are distributed among these distances:
27 6 0.08
28 13 0.17
29 10 0.13
30 39 0.51
31 8 0.11
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (30 bp):
AAAATGTAATTTTTGAAAAGTTTAGGGGCC
Found at i:53932319 original size:16 final size:16
Alignment explanation
Indices: 53932298--53932330 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
53932288 AATGGAAAGG
53932298 TTGAAAAGGATAACAA
1 TTGAAAAGGATAACAA
*
53932314 TTGAAAAGGATATCAA
1 TTGAAAAGGATAACAA
53932330 T
1 T
53932331 GGAATGGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (16 bp):
TTGAAAAGGATAACAA
Found at i:53934448 original size:46 final size:45
Alignment explanation
Indices: 53934398--53934541 Score: 150
Period size: 46 Copynumber: 3.2 Consensus size: 45
53934388 TATTCTGCCA
**
53934398 GCCTTTATGACGCATTTTGTTAGCCTTTGTAGCGTAATCTGATTTG
1 GCCTTTATG-CGCATTTTGTTAGCCTTTGCGGCGTAATCTGATTTG
* * * * *
53934444 GCCTTTATGGCGTATTTTGCTAGCCTTTGCGGTGTATTCT-A-TTA
1 GCCTTTAT-GCGCATTTTGTTAGCCTTTGCGGCGTAATCTGATTTG
* * *
53934488 GCCTTTGTG-GCATATTTTTTAGCCTTTGCGGCGTAATTTGATTTG
1 GCCTTTATGCGCAT-TTTGTTAGCCTTTGCGGCGTAATCTGATTTG
53934533 GCCTTTATG
1 GCCTTTATG
53934542 GCGTATTCTA
Statistics
Matches: 78, Mismatches: 16, Indels: 9
0.76 0.16 0.09
Matches are distributed among these distances:
42 3 0.04
43 21 0.27
44 10 0.13
45 11 0.14
46 32 0.41
47 1 0.01
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (45 bp):
GCCTTTATGCGCATTTTGTTAGCCTTTGCGGCGTAATCTGATTTG
Found at i:53934480 original size:22 final size:22
Alignment explanation
Indices: 53934411--53934527 Score: 83
Period size: 22 Copynumber: 5.3 Consensus size: 22
53934401 TTTATGACGC
**
53934411 ATTTTGTTAGCCTTTGTAGCGT
1 ATTTTGTTAGCCTTTGCGGCGT
* * * **
53934433 AATCTGATTTGGCCTTTATGGCGT
1 ATTTTG--TTAGCCTTTGCGGCGT
* *
53934457 ATTTTGCTAGCCTTTGCGGTGT
1 ATTTTGTTAGCCTTTGCGGCGT
* * * *
53934479 ATTCTATTAGCCTTTGTGGCAT
1 ATTTTGTTAGCCTTTGCGGCGT
53934501 ATTTT-TTAGCCTTTGCGGCGT
1 ATTTTGTTAGCCTTTGCGGCGT
*
53934522 AATTTG
1 ATTTTG
53934528 ATTTGGCCTT
Statistics
Matches: 70, Mismatches: 22, Indels: 6
0.71 0.22 0.06
Matches are distributed among these distances:
21 18 0.26
22 35 0.50
24 17 0.24
ACGTcount: A:0.15, C:0.16, G:0.23, T:0.46
Consensus pattern (22 bp):
ATTTTGTTAGCCTTTGCGGCGT
Found at i:53934489 original size:68 final size:68
Alignment explanation
Indices: 53934342--53934495 Score: 191
Period size: 68 Copynumber: 2.3 Consensus size: 68
53934332 GTTTGTGGCA
* * * * *
53934342 CATTCTATTAACCTTTGTGGTGTAATCTGATTTGGCTTTTATGGCGTATTCTGCCAGCCTTTATG
1 CATTCTATTAGCCTTTGTAGCGTAATCTGATTTGGCCTTTATGGCGTATTCTGCCAGCCTTTACG
53934407 ACG
66 ACG
* * * * *
53934410 CATTTTGTTAGCCTTTGTAGCGTAATCTGATTTGGCCTTTATGGCGTATTTTGCTAGCCTTTGCG
1 CATTCTATTAGCCTTTGTAGCGTAATCTGATTTGGCCTTTATGGCGTATTCTGCCAGCCTTTACG
**
53934475 GTG
66 ACG
*
53934478 TATTCTATTAGCCTTTGT
1 CATTCTATTAGCCTTTGT
53934496 GGCATATTTT
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.16, C:0.18, G:0.21, T:0.45
Consensus pattern (68 bp):
CATTCTATTAGCCTTTGTAGCGTAATCTGATTTGGCCTTTATGGCGTATTCTGCCAGCCTTTACG
ACG
Found at i:53934539 original size:89 final size:90
Alignment explanation
Indices: 53934411--53934574 Score: 249
Period size: 89 Copynumber: 1.8 Consensus size: 90
53934401 TTTATGACGC
* * * *
53934411 ATTTTGTTAGCCTTTGTAGCGTAATCTGATTTGGCCTTTATGGCGTATTTTGCTAGCCTTTGCGG
1 ATTTTGTTAGCCTTTGCAGCGTAATCTGATTTGGCCTTTATGGCGTATTCTACTAACCTTTGCGG
*
53934476 TGTATTCTATTAGCCTTTGTGGCAT
66 TGTACTCTATTAGCCTTTGTGGCAT
* * *
53934501 ATTTT-TTAGCCTTTGCGGCGTAATTTGATTTGGCCTTTATGGCGTATTCTACTAACCTTTGTGG
1 ATTTTGTTAGCCTTTGCAGCGTAATCTGATTTGGCCTTTATGGCGTATTCTACTAACCTTTGCGG
53934565 TGTACTCTAT
66 TGTACTCTAT
53934575 GTATTGATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
89 61 0.92
90 5 0.08
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (90 bp):
ATTTTGTTAGCCTTTGCAGCGTAATCTGATTTGGCCTTTATGGCGTATTCTACTAACCTTTGCGG
TGTACTCTATTAGCCTTTGTGGCAT
Found at i:53940288 original size:22 final size:22
Alignment explanation
Indices: 53940263--53940311 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
53940253 ATAAGTTAGC
*
53940263 AACCTGGTGAACCTTACCATTA
1 AACCTGGTGAACCTTACAATTA
* *
53940285 AACCTGGTGGACCTTACAATTC
1 AACCTGGTGAACCTTACAATTA
53940307 AACCT
1 AACCT
53940312 AACGGGCCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.27
Consensus pattern (22 bp):
AACCTGGTGAACCTTACAATTA
Found at i:53942728 original size:25 final size:24
Alignment explanation
Indices: 53942690--53942759 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 24
53942680 ACAAACCGAC
53942690 CCACAACTCGTGTGAGCATTTACAG
1 CCACAACTC-TGTGAGCATTTACAG
* *
53942715 CCACAACTCATGTGATCATTTACCG
1 CCACAACTC-TGTGAGCATTTACAG
*
53942740 TCACAACTTCTGTGAGCATT
1 CCACAAC-TCTGTGAGCATT
53942760 GTTCTCGCGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 37 0.95
26 2 0.05
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (24 bp):
CCACAACTCTGTGAGCATTTACAG
Found at i:53945449 original size:52 final size:52
Alignment explanation
Indices: 53945367--53945472 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 52
53945357 GAGCCTATTT
* *
53945367 ATAGGCTAAATTTGTAGGTCAAATACTCTTAAAATAAGCCACACTAATCAGA
1 ATAGGCTAAATTCGTAGGTCAAATAATCTTAAAATAAGCCACACTAATCAGA
* *
53945419 ATAGGTTAAATTCGTAGGTCAAATAATCTTAAAATAATCCACACTAATCAGA
1 ATAGGCTAAATTCGTAGGTCAAATAATCTTAAAATAAGCCACACTAATCAGA
53945471 AT
1 AT
53945473 TTGATTGGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.28
Consensus pattern (52 bp):
ATAGGCTAAATTCGTAGGTCAAATAATCTTAAAATAAGCCACACTAATCAGA
Found at i:53946301 original size:30 final size:30
Alignment explanation
Indices: 53946265--53946333 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
53946255 CACGAGCATT
53946265 GTTTTGAGCATCCAAGAAATCGTCTTGCAA
1 GTTTTGAGCATCCAAGAAATCGTCTTGCAA
* *
53946295 GTTTTGAGCATCCAAGAAATCTTCTTGCAT
1 GTTTTGAGCATCCAAGAAATCGTCTTGCAA
53946325 GTTTTGAGC
1 GTTTTGAGC
53946334 GAAAGAAGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (30 bp):
GTTTTGAGCATCCAAGAAATCGTCTTGCAA
Found at i:53948420 original size:37 final size:37
Alignment explanation
Indices: 53948370--53948444 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
53948360 CAGATTCAAG
53948370 GGAGCCTTCAACCCTAGATGATTTTACTTAATTTTTA
1 GGAGCCTTCAACCCTAGATGATTTTACTTAATTTTTA
53948407 GGAGCCTTCAACCCTAGATGATTTTACTTAATTTTTA
1 GGAGCCTTCAACCCTAGATGATTTTACTTAATTTTTA
53948444 G
1 G
53948445 TTTTCTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (37 bp):
GGAGCCTTCAACCCTAGATGATTTTACTTAATTTTTA
Found at i:53949487 original size:27 final size:27
Alignment explanation
Indices: 53949436--53949487 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
53949426 ACATATCAAA
*
53949436 TTATAATATTTTTATTTTCATATTACT
1 TTATAATATTTTTATGTTCATATTACT
53949463 TTATAAT-TTATTTAATGTTCA-ATTA
1 TTATAATATT-TTT-ATGTTCATATTA
53949488 TTATAACCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 2 0.09
27 14 0.64
28 6 0.27
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.60
Consensus pattern (27 bp):
TTATAATATTTTTATGTTCATATTACT
Found at i:53950924 original size:27 final size:27
Alignment explanation
Indices: 53950886--53950941 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
53950876 AAGTCACTTG
53950886 ATGAGAAATGAGAAATTTGTGGGAGGT
1 ATGAGAAATGAGAAATTTGTGGGAGGT
53950913 ATGAGAAATGAGAAATTTGTGGGAGGT
1 ATGAGAAATGAGAAATTTGTGGGAGGT
53950940 AT
1 AT
53950942 TTATAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.36, T:0.27
Consensus pattern (27 bp):
ATGAGAAATGAGAAATTTGTGGGAGGT
Done.