Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 151 of 226
Found at i:49478898 original size:23 final size:22
Alignment explanation
Indices: 49478853--49478898 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
49478843 TCACGCCAGT
* *
49478853 TGCTCCCGCACGTCGCGCTTAC
1 TGCTCCCGCACGTCGCACGTAC
49478875 TGCTCCGCGCACGTCGCACGTAC
1 TGCTCC-CGCACGTCGCACGTAC
49478898 T
1 T
49478899 CAACAGCCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.11, C:0.43, G:0.24, T:0.22
Consensus pattern (22 bp):
TGCTCCCGCACGTCGCACGTAC
Found at i:49479845 original size:3 final size:3
Alignment explanation
Indices: 49479837--49479866 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
49479827 TTTATCTTAC
*
49479837 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49479867 CTACTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:49481511 original size:22 final size:24
Alignment explanation
Indices: 49481484--49481547 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 24
49481474 TTATTTAAAA
49481484 TAAATAAATTAATATTATTAAA-G
1 TAAATAAATTAATATTATTAAATG
*
49481507 -AAATAAATTAA-AGTACTTAAATG
1 TAAATAAATTAATATTA-TTAAATG
*
49481530 TTAATAAA-TAATATTATT
1 TAAATAAATTAATATTATT
49481548 GAAAATGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
21 3 0.09
22 16 0.47
23 6 0.18
24 9 0.26
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (24 bp):
TAAATAAATTAATATTATTAAATG
Found at i:49483520 original size:30 final size:30
Alignment explanation
Indices: 49483458--49483520 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
49483448 AGCCCTATAT
* * *
49483458 AGTTCCAAGCCTGTTGAAGACAGTAAGCAA
1 AGTTACAAGCCTGTTGAAGACAGCAAGAAA
*
49483488 AGTTACAAGCCTGTTGAAGACGGCAAGAAA
1 AGTTACAAGCCTGTTGAAGACAGCAAGAAA
49483518 AGT
1 AGT
49483521 GCGAGCCTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (30 bp):
AGTTACAAGCCTGTTGAAGACAGCAAGAAA
Found at i:49483537 original size:16 final size:16
Alignment explanation
Indices: 49483516--49483546 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49483506 GACGGCAAGA
49483516 AAAGTGCGAGCCTGTC
1 AAAGTGCGAGCCTGTC
*
49483532 AAAGTGTGAGCCTGT
1 AAAGTGCGAGCCTGT
49483547 TGAATTGCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (16 bp):
AAAGTGCGAGCCTGTC
Found at i:49487776 original size:22 final size:21
Alignment explanation
Indices: 49487727--49487777 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
49487717 TATATCTTTA
49487727 GAATTTTTAAAGGATTAAATC
1 GAATTTTTAAAGGATTAAATC
49487748 GAATTTTTAAAGGATTAAATC
1 GAATTTTTAAAGGATTAAATC
49487769 GAATTTTTA
1 GAATTTTTA
49487778 TAATTTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (21 bp):
GAATTTTTAAAGGATTAAATC
Found at i:49488700 original size:18 final size:19
Alignment explanation
Indices: 49488670--49488706 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
49488660 CATGAGCACA
49488670 TGTATCATAACA-TTCATT
1 TGTATCATAACATTTCATT
49488688 TGTATACAT-ACATTTCATT
1 TGTAT-CATAACATTTCATT
49488707 CAATGTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (19 bp):
TGTATCATAACATTTCATT
Found at i:49490633 original size:29 final size:28
Alignment explanation
Indices: 49490586--49490646 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
49490576 ATGGCCAACC
* *
49490586 ATGTTGATATTATGTTTTTGTTAAAGTGT
1 ATGTTGATATGATGATTTTGTT-AAGTGT
* *
49490615 ATGTTGTTATGATGATTTTGTTGAGTGT
1 ATGTTGATATGATGATTTTGTTAAGTGT
49490643 ATGT
1 ATGT
49490647 AGCTTGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (28 bp):
ATGTTGATATGATGATTTTGTTAAGTGT
Found at i:49494866 original size:18 final size:19
Alignment explanation
Indices: 49494836--49494872 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
49494826 CATGAGCATA
49494836 TGTATCATAACA-TTCATT
1 TGTATCATAACATTTCATT
49494854 TGTATACAT-ACATTTCATT
1 TGTAT-CATAACATTTCATT
49494873 CAATGTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (19 bp):
TGTATCATAACATTTCATT
Found at i:49496799 original size:29 final size:28
Alignment explanation
Indices: 49496752--49496812 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
49496742 ATGGCCAACC
* *
49496752 ATGTTGATATTATGTTTTTGTTAAAGTGT
1 ATGTTGATATGATGATTTTGTT-AAGTGT
* *
49496781 ATGTTGTTATGATGATTTTGTTGAGTGT
1 ATGTTGATATGATGATTTTGTTAAGTGT
49496809 ATGT
1 ATGT
49496813 AGCTTGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (28 bp):
ATGTTGATATGATGATTTTGTTAAGTGT
Found at i:49500111 original size:22 final size:21
Alignment explanation
Indices: 49500083--49500127 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
49500073 ATCTTTAGAA
*
49500083 TTTTTAAGGGATTAAATCGAAT
1 TTTTTAAAGGA-TAAATCGAAT
49500105 TTTTTAAAGGATAAATCGAAT
1 TTTTTAAAGGATAAATCGAAT
49500126 TT
1 TT
49500128 GGATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (21 bp):
TTTTTAAAGGATAAATCGAAT
Found at i:49501056 original size:18 final size:19
Alignment explanation
Indices: 49501026--49501062 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
49501016 CATGAGCATA
49501026 TGTATCATAACA-TTCATT
1 TGTATCATAACATTTCATT
49501044 TGTATACAT-ACATTTCATT
1 TGTAT-CATAACATTTCATT
49501063 CAATGTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (19 bp):
TGTATCATAACATTTCATT
Found at i:49518735 original size:18 final size:19
Alignment explanation
Indices: 49518705--49518741 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
49518695 CATGAGCATA
49518705 TGTATCATAACA-TTCATT
1 TGTATCATAACATTTCATT
49518723 TGTATACAT-ACATTTCATT
1 TGTAT-CATAACATTTCATT
49518742 CAATGTCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.46
Consensus pattern (19 bp):
TGTATCATAACATTTCATT
Found at i:49525929 original size:22 final size:23
Alignment explanation
Indices: 49525902--49525965 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 23
49525892 TTATTTAAAA
49525902 TAAATAAATTAATATTATTAAA-G
1 TAAATAAA-TAATATTATTAAATG
*
49525925 -AAATAAACTAA-AGTACTTAAATG
1 TAAATAAA-TAATATTA-TTAAATG
*
49525948 TTAATAAATAATATTATT
1 TAAATAAATAATATTATT
49525966 GAAAATGGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
21 3 0.09
22 15 0.45
23 6 0.18
24 9 0.27
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.38
Consensus pattern (23 bp):
TAAATAAATAATATTATTAAATG
Found at i:49532060 original size:22 final size:22
Alignment explanation
Indices: 49532032--49532079 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
49532022 ATGTAAGATA
49532032 AATTTGAAATGATTTTACTTTT
1 AATTTGAAATGATTTTACTTTT
49532054 AATTTGAAATGATTTTACTTTT
1 AATTTGAAATGATTTTACTTTT
49532076 AATT
1 AATT
49532080 AACATTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.54
Consensus pattern (22 bp):
AATTTGAAATGATTTTACTTTT
Found at i:49539384 original size:19 final size:18
Alignment explanation
Indices: 49539360--49539557 Score: 66
Period size: 19 Copynumber: 10.4 Consensus size: 18
49539350 TATTTTCTCA
49539360 TAAAAATCATAAAAATTAT
1 TAAAAAT-ATAAAAATTAT
*
49539379 TAAAAAATAAAAAATATTAT
1 T-AAAAATATAAAA-ATTAT
* * *
49539399 TGAAAGTATTAAAA-T-T
1 TAAAAATATAAAAATTAT
49539415 TAAAAATACT-AAAATTGAT
1 TAAAAATA-TAAAAATT-AT
**
49539434 ATAAACTTATAAAAATTAT
1 -TAAAAATATAAAAATTAT
* *
49539453 AATAAAATA-ATAAAATTAA
1 TA-AAAATATA-AAAATTAT
* *
49539472 TAAAATTAATAAACCA-TATT
1 TAAAAAT-ATAAA-AATTA-T
*
49539492 TAAAAATCTTAAAAACTTAT
1 TAAAAAT-ATAAAAA-TTAT
* * *
49539512 CAAAATCATAAAAAAATCA-
1 TAAAA--ATATAAAAATTAT
49539531 TAAAAACTTATAAAAATTAT
1 TAAAAA--TATAAAAATTAT
*
49539551 AAAAAAT
1 TAAAAAT
49539558 TTACTTGAAA
Statistics
Matches: 129, Mismatches: 29, Indels: 43
0.64 0.14 0.21
Matches are distributed among these distances:
16 11 0.09
17 4 0.03
18 8 0.06
19 49 0.38
20 48 0.37
21 7 0.05
22 2 0.02
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (18 bp):
TAAAAATATAAAAATTAT
Found at i:49539527 original size:30 final size:30
Alignment explanation
Indices: 49539493--49539556 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
49539483 AACCATATTT
* *
49539493 AAAAATCTTAAAAACTTATCAAAATCATAA
1 AAAAATCATAAAAACTTATAAAAATCATAA
*
49539523 AAAAATCATAAAAACTTATAAAAATTATAA
1 AAAAATCATAAAAACTTATAAAAATCATAA
49539553 AAAA
1 AAAA
49539557 TTTACTTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (30 bp):
AAAAATCATAAAAACTTATAAAAATCATAA
Found at i:49539546 original size:11 final size:9
Alignment explanation
Indices: 49539359--49539555 Score: 84
Period size: 9 Copynumber: 20.8 Consensus size: 9
49539349 ATATTTTCTC
*
49539359 ATAAAAATC
1 ATAAAAATT
49539368 ATAAAAATT
1 ATAAAAATT
*
49539377 ATTAAAAAAT
1 A-TAAAAATT
*
49539387 AAAAAATATT
1 ATAAAA-ATT
** *
49539397 ATTGAAAGT
1 ATAAAAATT
*
49539406 ATTAAAATT
1 ATAAAAATT
49539415 -TAAAAA-T
1 ATAAAAATT
49539422 ACT-AAAATT
1 A-TAAAAATT
*
49539431 GATATAAACTT
1 -ATA-AAAATT
49539442 ATAAAAATT
1 ATAAAAATT
*
49539451 ATAATAAAAT
1 ATAA-AAATT
49539461 A-ATAAAATT
1 ATA-AAAATT
49539470 A-ATAAAATT
1 ATA-AAAATT
49539479 AATAAACCATATT
1 -ATAAA--A-ATT
49539492 -TAAAAATCT
1 ATAAAAAT-T
49539501 -TAAAAACTT
1 ATAAAAA-TT
*
49539510 ATCAAAATCAT
1 ATAAAAAT--T
* *
49539521 AAAAAAATC
1 ATAAAAATT
49539530 ATAAAAACTT
1 ATAAAAA-TT
49539540 ATAAAAATT
1 ATAAAAATT
49539549 ATAAAAA
1 ATAAAAA
49539556 ATTTACTTGA
Statistics
Matches: 146, Mismatches: 21, Indels: 42
0.70 0.10 0.20
Matches are distributed among these distances:
7 1 0.01
8 11 0.08
9 73 0.50
10 40 0.27
11 17 0.12
12 1 0.01
13 3 0.02
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (9 bp):
ATAAAAATT
Found at i:49542229 original size:28 final size:28
Alignment explanation
Indices: 49542178--49542235 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
49542168 ATATAGGTAG
* *
49542178 AATATATATATATATATGCAATAGGAAA
1 AATATATATATACATATACAATAGGAAA
*
49542206 AATATATATATACATAGTAC-ATAGTAAA
1 AATATATATATACATA-TACAATAGGAAA
49542234 AA
1 AA
49542236 GAAATTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.31
Consensus pattern (28 bp):
AATATATATATACATATACAATAGGAAA
Found at i:49543138 original size:7 final size:7
Alignment explanation
Indices: 49543126--49543153 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
49543116 CCAGTTCAAG
49543126 TTTTTAT
1 TTTTTAT
49543133 TTTTTAT
1 TTTTTAT
49543140 TTTTTAT
1 TTTTTAT
49543147 TTTTTAT
1 TTTTTAT
49543154 AATTGTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTAT
Found at i:49543224 original size:19 final size:17
Alignment explanation
Indices: 49543202--49543323 Score: 79
Period size: 18 Copynumber: 6.8 Consensus size: 17
49543192 TTATTATGAT
49543202 TTTTTATAAGTTTTTAAGA
1 TTTTTATAA-TTTTT-AGA
*
49543221 TTTTTATACATATTTA-A
1 TTTTTATA-ATTTTTAGA
*
49543238 TTCTTCATAATTTATTAGA
1 TT-TTTATAATTT-TTAGA
*
49543257 TTTTTATAAGTTTATATAAA
1 TTTTTATAA-TTT-T-TAGA
*
49543277 TTTTAAT-ATTTTTA-A
1 TTTTTATAATTTTTAGA
* *
49543292 GTTTTAATAATTTTTATA
1 -TTTTTATAATTTTTAGA
49543310 TTTTTATGAATTTT
1 TTTTTAT-AATTTT
49543324 AAATTATTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 21
0.75 0.06 0.18
Matches are distributed among these distances:
15 1 0.01
16 9 0.10
17 20 0.23
18 25 0.29
19 21 0.24
20 10 0.12
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (17 bp):
TTTTTATAATTTTTAGA
Found at i:49543301 original size:26 final size:25
Alignment explanation
Indices: 49543258--49543315 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 25
49543248 TTTATTAGAT
49543258 TTTTATAAGTTTATATAAATTTTAATA
1 TTTT-TAAGTTTATAT-AATTTTAATA
*
49543285 TTTTTAAGTTT-TAATAATTTTTATA
1 TTTTTAAGTTTAT-ATAATTTTAATA
49543310 TTTTTA
1 TTTTTA
49543316 TGAATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 16 0.55
26 9 0.31
27 4 0.14
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (25 bp):
TTTTTAAGTTTATATAATTTTAATA
Found at i:49543328 original size:25 final size:23
Alignment explanation
Indices: 49543273--49543328 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
49543263 TAAGTTTATA
*
49543273 TAAATTTTAATATTTTTAAGTTT
1 TAAATTTTAATATTTTTAAATTT
*
49543296 TAATAATTTTTATATTTTTATGAATTT
1 T-A-AATTTTAATATTTTTA--AATTT
49543323 TAAATT
1 TAAATT
49543329 ATTTTTATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
23 1 0.04
24 1 0.04
25 19 0.70
26 1 0.04
27 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
TAAATTTTAATATTTTTAAATTT
Found at i:49544432 original size:41 final size:39
Alignment explanation
Indices: 49544387--49544518 Score: 122
Period size: 40 Copynumber: 3.3 Consensus size: 39
49544377 AGCGGCATTT
* *
49544387 TTAGCGGCGTTTGGACAAAAAACGCCACTAAAAATCGAGCA
1 TTAGCGGCGTTT-AACAAAAAACGCCGCTAAAAAT-GAGCA
* * ** *
49544428 TTAGCGGCGCTTTTA-TAAAAACGCCGCTAAAGGTAGAGAA
1 TTAGCGGCG-TTTAACAAAAAACGCCGCTAAAAAT-GAGCA
* * * *
49544468 TTAGAGGCGCTTAACAGAAAACGCCGCTAAAAATTAGCA
1 TTAGCGGCGTTTAACAAAAAACGCCGCTAAAAATGAGCA
49544507 TTAGCGGCGTTT
1 TTAGCGGCGTTT
49544519 TCTGAAAATC
Statistics
Matches: 71, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
39 16 0.23
40 42 0.59
41 10 0.14
42 3 0.04
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (39 bp):
TTAGCGGCGTTTAACAAAAAACGCCGCTAAAAATGAGCA
Found at i:49544532 original size:39 final size:41
Alignment explanation
Indices: 49544404--49544538 Score: 127
Period size: 40 Copynumber: 3.4 Consensus size: 41
49544394 CGTTTGGACA
* * *
49544404 AAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTTAT-
1 AAAAACGCCGCTAAAAATAGAGCATTAGCGGCGCTTTTCTG
** * * ** *
49544444 AAAAACGCCGCTAAAGGTAGAGAATTAGAGGCGCTTAACAG
1 AAAAACGCCGCTAAAAATAGAGCATTAGCGGCGCTTTTCTG
*
49544485 -AAAACGCCGCTAAAAAT-TAGCATTAGCGGCG-TTTTCTG
1 AAAAACGCCGCTAAAAATAGAGCATTAGCGGCGCTTTTCTG
*
49544523 AAAATCGCCGC-AAAAA
1 AAAAACGCCGCTAAAAA
49544539 GCCTAAGCCA
Statistics
Matches: 74, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
38 9 0.12
39 20 0.27
40 45 0.61
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
AAAAACGCCGCTAAAAATAGAGCATTAGCGGCGCTTTTCTG
Found at i:49544640 original size:41 final size:41
Alignment explanation
Indices: 49544580--49544733 Score: 184
Period size: 41 Copynumber: 3.8 Consensus size: 41
49544570 TTTGGGGCCC
*
49544580 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTATCCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTATCCT
* * **
49544621 TTAGCGACGTTTTTGAAGAAGCGCCGGTAATGCTCTGGCCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTATCCT
* * * ** *
49544662 TTAGCGGCATTTTTTAATAAGCGCCGCTAATGCTAAGAT-TT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCT-CTATCCT
*
49544703 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAAT
49544734 ATATTTTTAT
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTATCCT
Found at i:49544717 original size:82 final size:82
Alignment explanation
Indices: 49544575--49544733 Score: 221
Period size: 82 Copynumber: 1.9 Consensus size: 82
49544565 GAGTTTTTGG
* ** *
49544575 GGCCCTTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTATCCTTTAGCGACGTTTTTGAAGA
1 GGCCCTTAGCGGCATTTTTTAAGAAGCGCCGCTAATGCTAGATCCTTTAGCGACGTTTTTGAAAA
*
49544640 AGCGCCGGTAATGCTCT
66 AGCGCCGCTAATGCTCT
* * * *
49544657 GGCCTTTAGCGGCATTTTTTAATAAGCGCCGCTAATGCTAAGAT-TTTTAGCGGCGTTTTTGAAA
1 GGCCCTTAGCGGCATTTTTTAAGAAGCGCCGCTAATGCT-AGATCCTTTAGCGACGTTTTTGAAA
49544721 AAGCGCCGCTAAT
65 AAGCGCCGCTAAT
49544734 ATATTTTTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
82 65 0.97
83 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (82 bp):
GGCCCTTAGCGGCATTTTTTAAGAAGCGCCGCTAATGCTAGATCCTTTAGCGACGTTTTTGAAAA
AGCGCCGCTAATGCTCT
Found at i:49545040 original size:15 final size:16
Alignment explanation
Indices: 49545020--49545053 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
49545010 CAAATATGGT
49545020 GTTTATGGATTT-AGG
1 GTTTATGGATTTAAGG
49545035 GTTTATGGATTTAAGG
1 GTTTATGGATTTAAGG
49545051 GTT
1 GTT
49545054 AGAGGTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (16 bp):
GTTTATGGATTTAAGG
Found at i:49545152 original size:7 final size:7
Alignment explanation
Indices: 49545140--49545221 Score: 55
Period size: 7 Copynumber: 11.9 Consensus size: 7
49545130 CTAGATTGGG
49545140 TTAGGGT
1 TTAGGGT
*
49545147 TTAGGGA
1 TTAGGGT
49545154 TTAGGGAT
1 TTAGGG-T
49545162 TTAGGG-
1 TTAGGGT
*
49545168 -TCGGG-
1 TTAGGGT
*
49545173 TTAGGAT
1 TTAGGGT
*
49545180 TTAAGGT
1 TTAGGGT
*
49545187 TTAGGGG
1 TTAGGGT
49545194 TTAGGG-
1 TTAGGGT
*
49545200 CTAGAGGT
1 TTAG-GGT
49545208 TTAGGGGT
1 TTA-GGGT
49545216 TTAGGG
1 TTAGGG
49545222 GTTAAGAGCT
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
5 4 0.07
6 6 0.10
7 33 0.57
8 14 0.24
9 1 0.02
ACGTcount: A:0.20, C:0.02, G:0.44, T:0.34
Consensus pattern (7 bp):
TTAGGGT
Found at i:49545917 original size:19 final size:18
Alignment explanation
Indices: 49545893--49545931 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
49545883 AATTATAAGA
49545893 AAAAATAAAATACAAAAAT
1 AAAAATAAAATA-AAAAAT
**
49545912 AAAAATGGAATAAAAAAT
1 AAAAATAAAATAAAAAAT
49545930 AA
1 AA
49545932 TTCTTTATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAATAAAATAAAAAAT
Found at i:49549808 original size:5 final size:5
Alignment explanation
Indices: 49549800--49549847 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
49549790 CGAACAAATA
* *
49549800 ATTCG ATTCG ATTCG ATTCG ATTTCT ATCTC- ACTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG A-TTCG AT-TCG ATTCG ATTCG ATTCG AT
49549848 AAAATTTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.05
5 29 0.78
6 6 0.16
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42
Consensus pattern (5 bp):
ATTCG
Found at i:49550559 original size:9 final size:9
Alignment explanation
Indices: 49550545--49550664 Score: 112
Period size: 9 Copynumber: 14.2 Consensus size: 9
49550535 CAAAATCAAA
49550545 AACTTACAT
1 AACTTACAT
49550554 AACTTACAT
1 AACTTACAT
*
49550563 AA--GACAT
1 AACTTACAT
*
49550570 AAATTACAT
1 AACTTACAT
*
49550579 AACCTAC-T
1 AACTTACAT
* *
49550587 TA-GTACAT
1 AACTTACAT
49550595 AACTTACAT
1 AACTTACAT
*
49550604 AACTTAGAT
1 AACTTACAT
49550613 AA--TACAT
1 AACTTACAT
49550620 AACTTACAT
1 AACTTACAT
* *
49550629 AATTTACTT
1 AACTTACAT
49550638 AA--TACAT
1 AACTTACAT
49550645 AACTTACAT
1 AACTTACAT
49550654 AACTTACAT
1 AACTTACAT
49550663 AA
1 AA
49550665 ATATCCCTTA
Statistics
Matches: 90, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
7 21 0.23
8 4 0.04
9 65 0.72
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.33
Consensus pattern (9 bp):
AACTTACAT
Found at i:49550576 original size:25 final size:25
Alignment explanation
Indices: 49550545--49550664 Score: 152
Period size: 25 Copynumber: 4.8 Consensus size: 25
49550535 CAAAATCAAA
49550545 AACTTACATAACTTACATAAGACAT
1 AACTTACATAACTTACATAAGACAT
* * *
49550570 AAATTACATAACCTAC-TTAGTACAT
1 AACTTACATAACTTACATAAG-ACAT
* *
49550595 AACTTACATAACTTAGATAATACAT
1 AACTTACATAACTTACATAAGACAT
* * *
49550620 AACTTACATAATTTACTTAATACAT
1 AACTTACATAACTTACATAAGACAT
49550645 AACTTACATAACTTACATAA
1 AACTTACATAACTTACATAA
49550665 ATATCCCTTA
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
24 3 0.04
25 75 0.94
26 2 0.03
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.33
Consensus pattern (25 bp):
AACTTACATAACTTACATAAGACAT
Found at i:49550580 original size:50 final size:50
Alignment explanation
Indices: 49550518--49550664 Score: 163
Period size: 50 Copynumber: 2.9 Consensus size: 50
49550508 ATCAAATTAA
* ** *
49550518 ATAAGTTACATAATACACAAAAT-CAAAAACTTACATAACTTACATAAGAC
1 ATAAATTACATAATACACTTAATAC-ATAACTTACATAACTTACATAAGAC
* * * *
49550568 ATAAATTACATAA-CCTACTTAGTACATAACTTACATAACTTAGATAATAC
1 ATAAATTACATAATAC-ACTTAATACATAACTTACATAACTTACATAAGAC
* **
49550618 ATAACTTACATAATTTACTTAATACATAACTTACATAACTTACATAA
1 ATAAATTACATAATACACTTAATACATAACTTACATAACTTACATAA
49550665 ATATCCCTTA
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.01
50 79 0.98
51 1 0.01
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.31
Consensus pattern (50 bp):
ATAAATTACATAATACACTTAATACATAACTTACATAACTTACATAAGAC
Found at i:49550620 original size:16 final size:16
Alignment explanation
Indices: 49550549--49550664 Score: 78
Period size: 16 Copynumber: 7.0 Consensus size: 16
49550539 ATCAAAAACT
49550549 TACATAACTTACATAA
1 TACATAACTTACATAA
* *
49550565 GACATAAATTACATAA
1 TACATAACTTACATAA
* *
49550581 CCTAC-TTA-GTACATAA
1 --TACATAACTTACATAA
*
49550597 CTTACATAACTTAGATAA
1 --TACATAACTTACATAA
49550615 TACATAACTTACATAA
1 TACATAACTTACATAA
*
49550631 TTTACTTAA--TACATAA
1 --TACATAACTTACATAA
49550647 CTTACATAACTTACATAA
1 --TACATAACTTACATAA
49550665 ATATCCCTTA
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
16 54 0.68
17 4 0.05
18 21 0.27
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.33
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:49550628 original size:34 final size:33
Alignment explanation
Indices: 49550549--49550664 Score: 89
Period size: 34 Copynumber: 3.5 Consensus size: 33
49550539 ATCAAAAACT
*
49550549 TACATAACTTACATAA--GACATAAATTACATAACC
1 TACATAACTTACATAACTTACAT-AA-TACATAA-C
* * *
49550583 TAC-TTA-GTACATAACTTACATAACTTAGATAA-
1 TACATAACTTACATAACTTACATAA--TACATAAC
* *
49550615 TACATAACTTACATAATTTACTTAATACATAAC
1 TACATAACTTACATAACTTACATAATACATAAC
49550648 TTACATAACTTACATAA
1 -TACATAACTTACATAA
49550665 ATATCCCTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
32 16 0.24
33 6 0.09
34 44 0.67
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.33
Consensus pattern (33 bp):
TACATAACTTACATAACTTACATAATACATAAC
Found at i:49554428 original size:14 final size:14
Alignment explanation
Indices: 49554409--49554436 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49554399 GAGATGACAT
49554409 TGACGACAGAACAC
1 TGACGACAGAACAC
49554423 TGACGACAGAACAC
1 TGACGACAGAACAC
49554437 AAACTTTGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.21, T:0.07
Consensus pattern (14 bp):
TGACGACAGAACAC
Found at i:49556312 original size:65 final size:66
Alignment explanation
Indices: 49556232--49556376 Score: 188
Period size: 65 Copynumber: 2.2 Consensus size: 66
49556222 GGCAACATCG
*
49556232 AGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAACTGAAAGCAGATGCAGCA
1 AGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAGC-AGCAACTGAAAACAGATGCAGCA
*
49556295 G-C
64 GTA
* * * *
49556297 AGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTTAAAACAGATGCGGCAGT
1 AGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTGAAAACAGATGCAGCAGT
49556362 A
66 A
*
49556363 AGAGAAGCGGAGGT
1 AGAGAAGCTGAGGT
49556377 GGCAACTAGA
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 1 0.01
65 52 0.74
66 17 0.24
ACGTcount: A:0.41, C:0.17, G:0.28, T:0.14
Consensus pattern (66 bp):
AGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTGAAAACAGATGCAGCAGT
A
Found at i:49556408 original size:21 final size:21
Alignment explanation
Indices: 49556384--49556445 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
49556374 GGTGGCAACT
*
49556384 AGAGAAGTACAGGCTGCAGCA
1 AGAGAAGTAGAGGCTGCAGCA
* ** *
49556405 AGAGAAGCAGAGGCTAAAGCG
1 AGAGAAGTAGAGGCTGCAGCA
*
49556426 AGGGAAGTAGAGGCTGCAGC
1 AGAGAAGTAGAGGCTGCAGC
49556446 GAGGGAAGCA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.37, C:0.16, G:0.39, T:0.08
Consensus pattern (21 bp):
AGAGAAGTAGAGGCTGCAGCA
Found at i:49556446 original size:21 final size:21
Alignment explanation
Indices: 49556394--49556458 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
49556384 AGAGAAGTAC
* *
49556394 AGGCTGCAGCAAGAGAAGCAG
1 AGGCTGCAGCGAGGGAAGCAG
** *
49556415 AGGCTAAAGCGAGGGAAGTAG
1 AGGCTGCAGCGAGGGAAGCAG
49556436 AGGCTGCAGCGAGGGAAGCAG
1 AGGCTGCAGCGAGGGAAGCAG
49556457 AG
1 AG
49556459 TAGCGTCAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.35, C:0.15, G:0.43, T:0.06
Consensus pattern (21 bp):
AGGCTGCAGCGAGGGAAGCAG
Found at i:49556850 original size:43 final size:43
Alignment explanation
Indices: 49556803--49557064 Score: 292
Period size: 43 Copynumber: 6.0 Consensus size: 43
49556793 AGGTGTTGGC
*
49556803 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGT
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * ** * *
49556846 CTTTAGCGGCGTTTGTGGAAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGTGGCGTTTTTGG-TCAAAGCGCCGCTAAAGATCAGGGT
* ** * *
49556890 CTTTAGTGGCATTTTTGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
* *
49556933 CTTTAGTGGCGTTTTGTGGTCGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGTGGCGTTTT-TGGTCAAAGCGCCGCTAAAGATCAGGGT
* * ** * *
49556977 CTATT-GCGGCGTTTTAGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CT-TTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
* *
49557020 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
49557063 CT
1 CT
49557065 ATTCCGGCGT
Statistics
Matches: 176, Mismatches: 39, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
42 2 0.01
43 104 0.59
44 68 0.39
45 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (43 bp):
CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATCAGGGT
Found at i:49556906 original size:87 final size:86
Alignment explanation
Indices: 49556762--49557064 Score: 331
Period size: 87 Copynumber: 3.5 Consensus size: 86
49556752 ATCTGCCAAA
* ** * *** * **
49556762 TTTAGTGGCGTTTTTTTAAAAA-CGCCACTAAAGGTGTTGGCCTTTAGTGGCGTTTTTGGTCAAA
1 TTTAGTGGCGTTTGTGGAAAAAGCGCCACTAAAGATCAGGGTCTTTAGTGGCGTTTTTGGGGAAA
* *
49556826 GCGCCGCTAAAGATAAGGGTC
66 GCGCCGCTAAAGATTAGGTTC
* * *
49556847 TTTAGCGGCGTTTGTGGAAAAAAGCGCCACTAAAGATCATGGTCTTTAGTGGCATTTTTGGGGAA
1 TTTAGTGGCGTTTGTGG-AAAAAGCGCCACTAAAGATCAGGGTCTTTAGTGGCGTTTTTGGGGAA
49556912 AGCGCCGCTAAAGATTAGGTTC
65 AGCGCCGCTAAAGATTAGGTTC
*** * * * *
49556934 TTTAGTGGCGTTTTGTGGTCGAAGCGCCGCTATAGATCAGGGTCTATT-GCGGCGTTTTAGGGGA
1 TTTAGTGGCG-TTTGTGGAAAAAGCGCCACTAAAGATCAGGGTCT-TTAGTGGCGTTTTTGGGGA
49556998 AAGCGCCGCTAAAGATTAGGTTC
64 AAGCGCCGCTAAAGATTAGGTTC
** * *
49557021 TTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGTCT
1 TTTAGTGGCGTTTGTGGAAAAAGCGCCACTAAAGATCAGGGTCT
49557065 ATTCCGGCGT
Statistics
Matches: 190, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
85 13 0.07
86 38 0.20
87 130 0.68
88 9 0.05
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (86 bp):
TTTAGTGGCGTTTGTGGAAAAAGCGCCACTAAAGATCAGGGTCTTTAGTGGCGTTTTTGGGGAAA
GCGCCGCTAAAGATTAGGTTC
Found at i:49557074 original size:43 final size:43
Alignment explanation
Indices: 49556803--49557222 Score: 276
Period size: 43 Copynumber: 9.7 Consensus size: 43
49556793 AGGTGTTGGC
* * *
49556803 CTTTAGTGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * *
49556846 CTTTAGCGGCGTTTGTGGAAAAAAGCGCCACTAAAGATCATGGT
1 CTTTAGCGGCGTTTGTGG-TCAAAGCGCCGCTAAAGATCAGGGT
* * * ** * *
49556890 CTTTAGTGGCATTTTTGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * *
49556933 CTTTAGTGGCGTTTTGTGGTCGAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCG-TTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
** * *
49556977 CTATT-GCGGCGTTT-TAGGGGAAAGCGCCGCTAAAGATTAGGTT
1 CT-TTAGCGGCGTTTGT-GGTCAAAGCGCCGCTAAAGATCAGGGT
* *
49557020 CTTTAGTGGCGTTTGTGGTCAAAGCGCCGCTATAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* * *** * * * ** *
49557063 CTATT-CCGGCGTTTGAGAAAAAAACGCCGCTAAAAACCCTGAT
1 CT-TTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* ** * * *
49557106 CTATAGCGGCGCCTCTAG-CACAAACGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCGTTTGTGGTCA-AAGCGCCGCTAAAGATCAGGGT
* **** * ***
49557149 CTTTAGCGGCGCTTCAACT-AAAGCGCCGCTAAAGGTCTTAGT
1 CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
* *
49557191 CTTCAGCGGCGTTTGTGCT-AGAAGCGCCGCTA
1 CTTTAGCGGCGTTTGTGGTCA-AAGCGCCGCTA
49557223 TAGACCAACA
Statistics
Matches: 288, Mismatches: 78, Indels: 22
0.74 0.20 0.06
Matches are distributed among these distances:
42 37 0.13
43 179 0.62
44 70 0.24
45 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGTCAAAGCGCCGCTAAAGATCAGGGT
Found at i:49557336 original size:22 final size:22
Alignment explanation
Indices: 49557308--49557350 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
49557298 TTGCGGAGCT
*
49557308 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
49557330 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
49557351 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:49561672 original size:16 final size:17
Alignment explanation
Indices: 49561651--49561682 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
49561641 CGTTCTATAC
49561651 TAAAACAAAT-TACCGG
1 TAAAACAAATATACCGG
49561667 TAAAACAAATATACCG
1 TAAAACAAATATACCG
49561683 TTGAAGGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.19, G:0.09, T:0.19
Consensus pattern (17 bp):
TAAAACAAATATACCGG
Found at i:49561941 original size:21 final size:21
Alignment explanation
Indices: 49561915--49561956 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
49561905 ACCGGAGGAA
49561915 AGGAAAGA-AGAGAGGGCGAAG
1 AGGAAAGAGAGA-AGGGCGAAG
*
49561936 AGGAAAGAGAGAATGGCGAAG
1 AGGAAAGAGAGAAGGGCGAAG
49561957 GTGAGGAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.48, C:0.05, G:0.45, T:0.02
Consensus pattern (21 bp):
AGGAAAGAGAGAAGGGCGAAG
Found at i:49567209 original size:41 final size:41
Alignment explanation
Indices: 49567119--49567210 Score: 107
Period size: 41 Copynumber: 2.2 Consensus size: 41
49567109 ACGGCCTACC
* *
49567119 ACACGGTCTACCACATAGGCTACCACATGTTCGTGTGACCA
1 ACACGGTCTACCACATAGGCTACCACATGCTCGTGTAACCA
* *
49567160 ACACGGTCTACCACAT-GGCTTACCATATGGCT-GTGTAACCG
1 ACACGGTCTACCACATAGGC-TACCACAT-GCTCGTGTAACCA
*
49567201 ACATGGTCTA
1 ACACGGTCTA
49567211 TAACACAACC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
40 3 0.07
41 39 0.89
42 2 0.05
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (41 bp):
ACACGGTCTACCACATAGGCTACCACATGCTCGTGTAACCA
Found at i:49567955 original size:37 final size:38
Alignment explanation
Indices: 49567889--49567960 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
49567879 TCAGCCCAAA
*
49567889 GTTCATAGAAAACAACAGAAAGAAGGAAGATTGTGAAG
1 GTTCATAGAAAACAACAGAAAGAAGGAAGAATGTGAAG
*
49567927 GTTCATAGGAAACAA-AGAAAGATA-GAAGAATGTG
1 GTTCATAGAAAACAACAGAAAGA-AGGAAGAATGTG
49567961 GAAAAAGAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 16 0.52
38 15 0.48
ACGTcount: A:0.50, C:0.07, G:0.26, T:0.17
Consensus pattern (38 bp):
GTTCATAGAAAACAACAGAAAGAAGGAAGAATGTGAAG
Found at i:49579721 original size:41 final size:41
Alignment explanation
Indices: 49579676--49579920 Score: 186
Period size: 41 Copynumber: 6.0 Consensus size: 41
49579666 TTGCCATACG
* * *
49579676 GCCTACCACACGGTTATGTGACCCACACGATCTACCACATA
1 GCCTACCACACGGTCATGTGACCCACACGGTCTGCCACATA
* * * * * *
49579717 GCCTACCACATGTTCGTGTGACACACACGGTCTGCTAAAT-
1 GCCTACCACACGGTCATGTGACCCACACGGTCTGCCACATA
* * * * * * * * *
49579757 GTCTTACTATATGGTCCTGTGACCGATACGGTCTACCACACA
1 G-CCTACCACACGGTCATGTGACCCACACGGTCTGCCACATA
* * * * * * *
49579799 ACCTACCACACGGTCGTGTGACCCACATGATCTGTCGCATG
1 GCCTACCACACGGTCATGTGACCCACACGGTCTGCCACATA
* *
49579840 GCCTACCACACGGTCATGTGACCCACACGGTCTGTCACATG
1 GCCTACCACACGGTCATGTGACCCACACGGTCTGCCACATA
* * * * *
49579881 GCCTACCACATGATCGTGTAACCCACATGGTCTGCCACAT
1 GCCTACCACACGGTCATGTGACCCACACGGTCTGCCACAT
49579921 GACTAGTTAC
Statistics
Matches: 155, Mismatches: 47, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
40 1 0.01
41 154 0.99
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.23
Consensus pattern (41 bp):
GCCTACCACACGGTCATGTGACCCACACGGTCTGCCACATA
Found at i:49579860 original size:82 final size:82
Alignment explanation
Indices: 49579675--49579915 Score: 250
Period size: 82 Copynumber: 2.9 Consensus size: 82
49579665 TTTGCCATAC
* * * *
49579675 GGCCTACCACACGGTTATGTGACCCACACGATCTACCACATAGCCTACCACATGTTCGTGTGACA
1 GGCCTACCACACGGTCATGTGACCCACACGGTCTACCACATAGCCTACCACATGATCGTGTGACC
*
49579740 CACACGGTCTGCTAAAT
66 CACATGGTCTGCTAAAT
* * * * * * * * * * * *
49579757 GTCTTACTATATGGTCCTGTGACCGATACGGTCTACCACACAACCTACCACACGGTCGTGTGACC
1 GGCCTACCACACGGTCATGTGACCCACACGGTCTACCACATAGCCTACCACATGATCGTGTGACC
* **
49579822 CACATGATCTG-TCGCAT
66 CACATGGTCTGCT-AAAT
** * *
49579839 GGCCTACCACACGGTCATGTGACCCACACGGTCTGTCACATGGCCTACCACATGATCGTGTAACC
1 GGCCTACCACACGGTCATGTGACCCACACGGTCTACCACATAGCCTACCACATGATCGTGTGACC
49579904 CACATGGTCTGC
66 CACATGGTCTGC
49579916 CACATGACTA
Statistics
Matches: 121, Mismatches: 36, Indels: 3
0.76 0.22 0.02
Matches are distributed among these distances:
81 1 0.01
82 120 0.99
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (82 bp):
GGCCTACCACACGGTCATGTGACCCACACGGTCTACCACATAGCCTACCACATGATCGTGTGACC
CACATGGTCTGCTAAAT
Found at i:49579913 original size:123 final size:123
Alignment explanation
Indices: 49579677--49579919 Score: 263
Period size: 123 Copynumber: 2.0 Consensus size: 123
49579667 TGCCATACGG
* * * *
49579677 CCTACCACACGGTTATGTGACCCACACGATCTACCACATAGCCTACCACATGTTCGTGTGACACA
1 CCTACCACACGGTCATGTGACCCACACGATCTACCACATAGCCTACCACACGGTCATGTGACACA
* * * * * * * *
49579742 CACGGTCTGCTAAATGTCTTACTATATGGTCCTGTGACCGATACGGTCTACCACACAA
66 CACGGTCTGCTAAATGGCCTACCACATGATCCTGTAACCCACACGGTCTACCACACAA
* * ** * * *
49579800 CCTACCACACGGTCGTGTGACCCACATGATCTGTCGCATGGCCTACCACACGGTCATGTGACCCA
1 CCTACCACACGGTCATGTGACCCACACGATCTACCACATAGCCTACCACACGGTCATGTGACACA
* * * *
49579865 CACGGTCTG-TCACATGGCCTACCACATGATCGTGTAACCCACATGGTCTGCCACA
66 CACGGTCTGCT-AAATGGCCTACCACATGATCCTGTAACCCACACGGTCTACCACA
49579920 TGACTAGTTA
Statistics
Matches: 96, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
122 1 0.01
123 95 0.99
ACGTcount: A:0.25, C:0.34, G:0.19, T:0.23
Consensus pattern (123 bp):
CCTACCACACGGTCATGTGACCCACACGATCTACCACATAGCCTACCACACGGTCATGTGACACA
CACGGTCTGCTAAATGGCCTACCACATGATCCTGTAACCCACACGGTCTACCACACAA
Found at i:49579933 original size:82 final size:81
Alignment explanation
Indices: 49579678--49579942 Score: 242
Period size: 82 Copynumber: 3.2 Consensus size: 81
49579668 GCCATACGGC
* * * * *
49579678 CTACCACACGGTTATGTGACCCACACGATCTACCACATAGCCTACCACATGTTCGTGTGACACAC
1 CTACTACACGGTCATGTGACCCACACGGTCTACCACATAGCCTACCACATGATCGTGTGACCCAC
* * * *
49579743 ACGGTCTGCTAAATGT
66 ATGGTCTGCCACATGA
* * * * * * * * *
49579759 CTTACTATATGGTCCTGTGACCGATACGGTCTACCACACAACCTACCACACGGTCGTGTGACCCA
1 C-TACTACACGGTCATGTGACCCACACGGTCTACCACATAGCCTACCACATGATCGTGTGACCCA
* * * *
49579824 CATGATCTGTCGCATGGC
65 CATGGTCTGCCACAT-GA
* ** * *
49579842 CTACCACACGGTCATGTGACCCACACGGTCTGTCACATGGCCTACCACATGATCGTGTAACCCAC
1 CTACTACACGGTCATGTGACCCACACGGTCTACCACATAGCCTACCACATGATCGTGTGACCCAC
49579907 ATGGTCTGCCACATGA
66 ATGGTCTGCCACATGA
* *
49579923 CTAGTTACACGATCATGTGA
1 CTA-CTACACGGTCATGTGA
49579943 TACAGTTTAC
Statistics
Matches: 140, Mismatches: 41, Indels: 5
0.75 0.22 0.03
Matches are distributed among these distances:
81 5 0.04
82 133 0.95
83 2 0.01
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.23
Consensus pattern (81 bp):
CTACTACACGGTCATGTGACCCACACGGTCTACCACATAGCCTACCACATGATCGTGTGACCCAC
ATGGTCTGCCACATGA
Found at i:49582456 original size:61 final size:58
Alignment explanation
Indices: 49582348--49582479 Score: 167
Period size: 61 Copynumber: 2.2 Consensus size: 58
49582338 ACCACAATAA
* *
49582348 TATTAAATTAATATAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
1 TATTAAATTAATAGAATACTTATCAAGAAAAATATTAAATTAAATTTAATATTAAATC
** * *
49582406 TATTAAATTAATAGAATTTTTATCTATAAGAAAAATATTAAATTTAATTTAATATTAAATT
1 TATTAAATTAATAGAATACTTATC---AAGAAAAATATTAAATTAAATTTAATATTAAATC
49582467 TATTTAAA-TAATA
1 TA-TTAAATTAATA
49582480 TTAAATTTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
58 21 0.33
61 38 0.59
62 5 0.08
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (58 bp):
TATTAAATTAATAGAATACTTATCAAGAAAAATATTAAATTAAATTTAATATTAAATC
Found at i:49582476 original size:17 final size:18
Alignment explanation
Indices: 49582438--49582476 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
49582428 TCTATAAGAA
49582438 AAATATTAAATTTAATTT
1 AAATATTAAATTTAATTT
49582456 -AATATTAAATTT-ATTT
1 AAATATTAAATTTAATTT
49582472 AAATA
1 AAATA
49582477 ATATTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATATTAAATTTAATTT
Found at i:49599628 original size:15 final size:15
Alignment explanation
Indices: 49599610--49599641 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
49599600 TTCTGCTCTA
49599610 TTCTATTTTGTTCTG
1 TTCTATTTTGTTCTG
*
49599625 TTCTATTTTGTTTTG
1 TTCTATTTTGTTCTG
49599640 TT
1 TT
49599642 TTGTTGAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.12, T:0.72
Consensus pattern (15 bp):
TTCTATTTTGTTCTG
Found at i:49599646 original size:20 final size:20
Alignment explanation
Indices: 49599592--49599646 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
49599582 CATACATTTG
*
49599592 CTATTTTGTTCTGCTCTATT
1 CTATTTTGTTCTGTTCTATT
49599612 CTATTTTGTTCTGTTCTATT
1 CTATTTTGTTCTGTTCTATT
* * *
49599632 TTGTTTTGTTTTGTT
1 CTATTTTGTTCTGTT
49599647 GAACTACCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.07, C:0.13, G:0.13, T:0.67
Consensus pattern (20 bp):
CTATTTTGTTCTGTTCTATT
Found at i:49599860 original size:15 final size:14
Alignment explanation
Indices: 49599827--49599882 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
49599817 ACCAAATTAA
*
49599827 CCCACTAGCCTAAAG
1 CCCAATAGCCT-AAG
49599842 -CCAATTAGCCTAAG
1 CCCAA-TAGCCTAAG
*
49599856 CCCAATA-CCTTAG
1 CCCAATAGCCTAAG
49599869 CCCAACTAGCCTAA
1 CCCAA-TAGCCTAA
49599883 ACCAGAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
13 10 0.29
14 10 0.29
15 14 0.41
ACGTcount: A:0.34, C:0.38, G:0.11, T:0.18
Consensus pattern (14 bp):
CCCAATAGCCTAAG
Found at i:49600967 original size:3 final size:3
Alignment explanation
Indices: 49600959--49601035 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
49600949 ACTGAACATT
*
49600959 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49601007 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
49601036 TCTGTACTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:49601209 original size:16 final size:15
Alignment explanation
Indices: 49601188--49601217 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
49601178 TGATGTGATA
49601188 TATTATTATTTTAAAT
1 TATTATT-TTTTAAAT
49601204 TATTATTTTTTAAA
1 TATTATTTTTTAAA
49601218 AATTTATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTATTTTTTAAAT
Found at i:49601433 original size:2 final size:2
Alignment explanation
Indices: 49601426--49601455 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
49601416 TATTTTGTAC
49601426 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49601456 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49601576 original size:2 final size:2
Alignment explanation
Indices: 49601569--49601599 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
49601559 TTATTTGTAC
49601569 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 A
49601600 ACCTATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49603645 original size:8 final size:8
Alignment explanation
Indices: 49603634--49603661 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
49603624 TAATAAAAAC
49603634 ATTTTTAT
1 ATTTTTAT
49603642 ATTTTTAT
1 ATTTTTAT
49603650 ATTTTTAT
1 ATTTTTAT
49603658 ATTT
1 ATTT
49603662 AATTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
ATTTTTAT
Found at i:49604031 original size:21 final size:20
Alignment explanation
Indices: 49604000--49604038 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
49603990 TTTTTAATAA
49604000 TTTTAAATTTTTAAAATTAT
1 TTTTAAATTTTTAAAATTAT
49604020 TTTTATAATTTTTAAAATT
1 TTTTA-AATTTTTAAAATT
49604039 TAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTAAATTTTTAAAATTAT
Found at i:49606938 original size:19 final size:20
Alignment explanation
Indices: 49606896--49606941 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
49606886 TATATCAATA
* *
49606896 TTTACCAAGATTTTTAAAGT
1 TTTACCAAAATTTTTAAAGG
49606916 TTTACCAAAATTTTT-AAGG
1 TTTACCAAAATTTTTAAAGG
49606935 TTTACCA
1 TTTACCA
49606942 CGATACCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (20 bp):
TTTACCAAAATTTTTAAAGG
Found at i:49606995 original size:19 final size:20
Alignment explanation
Indices: 49606953--49606995 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
49606943 GATACCTATG
*
49606953 GATTTATCAAAATTTTTAAA
1 GATTTATCAAAATTTATAAA
49606973 GATTTATCAAAATTTAT-AA
1 GATTTATCAAAATTTATAAA
49606992 GATT
1 GATT
49606996 ATACGATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (20 bp):
GATTTATCAAAATTTATAAA
Found at i:49607082 original size:20 final size:20
Alignment explanation
Indices: 49607059--49607106 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
49607049 CGTTACCAAA
49607059 ATTTCTAAG-G-TTATACTAAT
1 ATTTCTAAGTGTTTATA--AAT
*
49607079 ATTTTTAAGTGTTTATAAAT
1 ATTTCTAAGTGTTTATAAAT
49607099 ATTTCTAA
1 ATTTCTAA
49607107 AGTTTTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 18 0.75
21 1 0.04
22 5 0.21
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.50
Consensus pattern (20 bp):
ATTTCTAAGTGTTTATAAAT
Found at i:49607113 original size:20 final size:21
Alignment explanation
Indices: 49607076--49607148 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 21
49607066 AGGTTATACT
*
49607076 AATATTT-TTAAGTGTTTATA-
1 AATATTTCTAAAGTGTTTA-AC
49607096 AATATTTCTAAAGT-TTTAAC
1 AATATTTCTAAAGTGTTTAAC
* * *
49607116 AATATTCCTAAAG-GTTCACC
1 AATATTTCTAAAGTGTTTAAC
*
49607136 ATTATTTCTAAAG
1 AATATTTCTAAAG
49607149 ATTTTCCTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 38 0.86
21 5 0.11
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (21 bp):
AATATTTCTAAAGTGTTTAAC
Found at i:49607385 original size:20 final size:20
Alignment explanation
Indices: 49607296--49607407 Score: 63
Period size: 20 Copynumber: 5.7 Consensus size: 20
49607286 GGATATTTAG
* *
49607296 CTTTAAAAATTTGGGTAAAT
1 CTTTAGAAATTTTGGTAAAT
* *
49607316 CCTTATG-CATTTTGGTATAA-
1 CTTTA-GAAATTTTGGTA-AAT
*
49607336 CCTTAGAAAATTTT-GTAAAT
1 CTTTAG-AAATTTTGGTAAAT
* *
49607356 -TCTCGTAAATTTTGGTAAAT
1 CTTTAG-AAATTTTGGTAAAT
* *
49607376 CTTTAGAAATATTGG-AAAA
1 CTTTAGAAATTTTGGTAAAT
*
49607395 CTTTGGAAATTTT
1 CTTTAGAAATTTT
49607408 AGCATGCCAA
Statistics
Matches: 70, Mismatches: 15, Indels: 15
0.70 0.15 0.15
Matches are distributed among these distances:
19 26 0.37
20 34 0.49
21 10 0.14
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (20 bp):
CTTTAGAAATTTTGGTAAAT
Found at i:49607403 original size:19 final size:20
Alignment explanation
Indices: 49607362--49607404 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
49607352 AAATTCTCGT
* *
49607362 AAATTTTGGTAAATCTTTAG
1 AAATATTGGTAAAACTTTAG
*
49607382 AAATATTGG-AAAACTTTGG
1 AAATATTGGTAAAACTTTAG
49607401 AAAT
1 AAAT
49607405 TTTAGCATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (20 bp):
AAATATTGGTAAAACTTTAG
Found at i:49607504 original size:20 final size:20
Alignment explanation
Indices: 49607435--49607577 Score: 92
Period size: 20 Copynumber: 7.0 Consensus size: 20
49607425 TGTCTCAATG
*
49607435 AAATCTTTAGAAATTTTGGT
1 AAATCCTTAGAAATTTTGGT
* * * **
49607455 AAAAACCCTTAGATATATTAAT
1 --AAATCCTTAGAAATTTTGGT
49607477 AAATCCTTAGAAATTTTGGT
1 AAATCCTTAGAAATTTTGGT
* * *
49607497 ATAA-CCTTAAAAATTCTAGT
1 A-AATCCTTAGAAATTTTGGT
* *
49607517 AAATCCTTACATATTTTGGT
1 AAATCCTTAGAAATTTTGGT
* *
49607537 ATAA-CCTTATAAATTTCGGT
1 A-AATCCTTAGAAATTTTGGT
* * *
49607557 AATTTCTTAAAAATTTTGGT
1 AAATCCTTAGAAATTTTGGT
49607577 A
1 A
49607578 TGCCAAAATA
Statistics
Matches: 92, Mismatches: 25, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
19 3 0.03
20 71 0.77
21 4 0.04
22 14 0.15
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (20 bp):
AAATCCTTAGAAATTTTGGT
Found at i:49607520 original size:40 final size:39
Alignment explanation
Indices: 49607435--49607578 Score: 135
Period size: 40 Copynumber: 3.6 Consensus size: 39
49607425 TGTCTCAATG
* * * * *
49607435 AAATCTTTAGAAATTTTGGTAAAAACCCTTAGATATATTAAT
1 AAATCCTTAGAAATTTTGGT-ATAA-CCTTAAAAAT-TTAGT
49607477 AAATCCTTAGAAATTTTGGTATAACCTTAAAAATTCTAGT
1 AAATCCTTAGAAATTTTGGTATAACCTTAAAAATT-TAGT
* * * *
49607517 AAATCCTTACATATTTTGGTATAACCTTATAAATTTCGGT
1 AAATCCTTAGAAATTTTGGTATAACCTTAAAAATTT-AGT
* * *
49607557 AATTTCTTAAAAATTTTGGTAT
1 AAATCCTTAGAAATTTTGGTAT
49607579 GCCAAAATAT
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 2 0.02
40 63 0.72
41 3 0.03
42 19 0.22
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (39 bp):
AAATCCTTAGAAATTTTGGTATAACCTTAAAAATTTAGT
Found at i:49607686 original size:20 final size:20
Alignment explanation
Indices: 49607642--49607692 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
49607632 TAGGTAAATT
* *
49607642 CTTAGAAATTTGGGTAAAGC
1 CTTAGAAATTTGGCTAAACC
* *
49607662 TTTAGAAATTTTGCTAAACC
1 CTTAGAAATTTGGCTAAACC
*
49607682 CTTAGATATTT
1 CTTAGAAATTT
49607693 CATTATAAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (20 bp):
CTTAGAAATTTGGCTAAACC
Found at i:49610311 original size:32 final size:32
Alignment explanation
Indices: 49610275--49610338 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
49610265 TTGGTAAATG
49610275 ATACCAGTGTTTGCTAATATGAAACTGATTAT
1 ATACCAGTGTTTGCTAATATGAAACTGATTAT
49610307 ATACCAGTGTTTGCTAATATGAAACTGATTAT
1 ATACCAGTGTTTGCTAATATGAAACTGATTAT
49610339 CTTCAGCTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (32 bp):
ATACCAGTGTTTGCTAATATGAAACTGATTAT
Found at i:49616292 original size:23 final size:23
Alignment explanation
Indices: 49616261--49616318 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
49616251 ATAACACTTC
*
49616261 AAAA-ATTTTATTTTCATTTATT
1 AAAATATTTTATTTGCATTTATT
*
49616283 AAAATATTTT-GTTGCATTTATT
1 AAAATATTTTATTTGCATTTATT
*
49616305 AAAACTATATTATT
1 AAAA-TATTTTATT
49616319 ACGTATGGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 18 0.62
23 10 0.34
24 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.53
Consensus pattern (23 bp):
AAAATATTTTATTTGCATTTATT
Found at i:49618702 original size:17 final size:18
Alignment explanation
Indices: 49618664--49618703 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
49618654 ACAATTCCTA
* *
49618664 AGAAGATGGGAAAGAATC
1 AGAAAATGGAAAAGAATC
49618682 AGAAAATGGAAAAGAAT-
1 AGAAAATGGAAAAGAATC
49618699 AGAAA
1 AGAAA
49618704 GGGCAGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.60, C:0.03, G:0.28, T:0.10
Consensus pattern (18 bp):
AGAAAATGGAAAAGAATC
Found at i:49621085 original size:20 final size:21
Alignment explanation
Indices: 49621062--49621103 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
49621052 TTTAATTTTT
*
49621062 AAAAAATTTTAAATAT-ATTA
1 AAAAAATGTTAAATATAATTA
*
49621082 AAAAAATGTTAAGTATAATTA
1 AAAAAATGTTAAATATAATTA
49621103 A
1 A
49621104 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAAAATGTTAAATATAATTA
Found at i:49621125 original size:27 final size:27
Alignment explanation
Indices: 49621095--49621178 Score: 116
Period size: 27 Copynumber: 3.0 Consensus size: 27
49621085 AAATGTTAAG
49621095 TATAATTAATTTTAAAATTTTAATATA
1 TATAATTAATTTTAAAATTTTAATATA
49621122 TATAATTAATTTTAAAATTTTAATATA
1 TATAATTAATTTTAAAATTTTAATATA
*
49621149 TAT-TTTAATATATTTAAAATTTTTAATATA
1 TATAATT-A-AT-TTTAAAA-TTTTAATATA
49621179 CTTAATATAT
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
26 2 0.04
27 31 0.60
28 2 0.04
29 7 0.13
30 10 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TATAATTAATTTTAAAATTTTAATATA
Found at i:49621157 original size:39 final size:39
Alignment explanation
Indices: 49621111--49621198 Score: 108
Period size: 39 Copynumber: 2.2 Consensus size: 39
49621101 TAATTTTAAA
*
49621111 ATTTTAATATATATAATTAA-TTTTAAAAT-TTTAATATAT
1 ATTTTAATATATATAA--AATTTTTAAAATACTTAATATAT
* *
49621150 ATTTTAATATATTTAAAATTTTTAATATACTTAATATAT
1 ATTTTAATATATATAAAATTTTTAAAATACTTAATATAT
49621189 ATTTTTAATA
1 A-TTTTAATA
49621199 GGTAAAGGCA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 2 0.05
38 8 0.19
39 25 0.58
40 8 0.19
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (39 bp):
ATTTTAATATATATAAAATTTTTAAAATACTTAATATAT
Found at i:49621188 original size:29 final size:28
Alignment explanation
Indices: 49621105--49621192 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 28
49621095 TATAATTAAT
49621105 TTTAAAA-TTTTAATATATATAAT-TA-A
1 TTTAAAATTTTTAATATAT-TAATATATA
**
49621131 TTTTAAAA-TTTTAATATATATTTTAATATA
1 -TTTAAAATTTTTAATATAT-TAAT-ATATA
49621161 TTTAAAATTTTTAATATACTTAATATATA
1 TTTAAAATTTTTAATATA-TTAATATATA
49621190 TTT
1 TTT
49621193 TTAATAGGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
27 21 0.40
29 17 0.33
30 13 0.25
31 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (28 bp):
TTTAAAATTTTTAATATATTAATATATA
Found at i:49621261 original size:19 final size:19
Alignment explanation
Indices: 49621239--49621280 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
49621229 TTTAAAATTT
49621239 TTAAA-AAACTTAAAAAAAA
1 TTAAATAAA-TTAAAAAAAA
* *
49621258 TTAAATATATTAAAAAATA
1 TTAAATAAATTAAAAAAAA
49621277 TTAA
1 TTAA
49621281 GTATAACCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TTAAATAAATTAAAAAAAA
Found at i:49621269 original size:9 final size:9
Alignment explanation
Indices: 49621257--49621390 Score: 55
Period size: 9 Copynumber: 16.3 Consensus size: 9
49621247 CTTAAAAAAA
49621257 ATTAAATAT
1 ATTAAATAT
*
49621266 ATTAAAAAAT
1 ATT-AAATAT
*
49621276 ATTAAGTAT
1 ATTAAATAT
***
49621285 AACCAAT-T
1 ATTAAATAT
49621293 -TTAAA-AT
1 ATTAAATAT
*
49621300 -TTTAATAT
1 ATTAAATAT
49621308 ATTAAA-AT
1 ATTAAATAT
* *
49621316 TTTTAATAT
1 ATTAAATAT
*
49621325 ATTCAATAT
1 ATTAAATAT
49621334 ATT---T-T
1 ATTAAATAT
49621339 -TTAAATAT
1 ATTAAATAT
49621347 ATTGAAAT-T
1 ATT-AAATAT
49621356 -TTAAATAT
1 ATTAAATAT
49621364 ATTAAAT-T
1 ATTAAATAT
49621372 -TT-AATAT
1 ATTAAATAT
*
49621379 ATTTAATAT
1 ATTAAATAT
49621388 ATT
1 ATT
49621391 TTTAATAGGT
Statistics
Matches: 93, Mismatches: 16, Indels: 32
0.66 0.11 0.23
Matches are distributed among these distances:
4 2 0.02
5 1 0.01
6 4 0.04
7 15 0.16
8 16 0.17
9 43 0.46
10 12 0.13
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (9 bp):
ATTAAATAT
Found at i:49621285 original size:19 final size:19
Alignment explanation
Indices: 49621248--49621285 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
49621238 TTTAAAAAAC
49621248 TTAAAAAAAATTAAATATA
1 TTAAAAAAAATTAAATATA
* *
49621267 TTAAAAAATATTAAGTATA
1 TTAAAAAAAATTAAATATA
49621286 ACCAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
TTAAAAAAAATTAAATATA
Found at i:49621321 original size:17 final size:17
Alignment explanation
Indices: 49621293--49621397 Score: 99
Period size: 17 Copynumber: 5.9 Consensus size: 17
49621283 ATAACCAATT
49621293 TTAAAA-TTTTAATATA
1 TTAAAATTTTTAATATA
49621309 TTAAAATTTTTAATATA
1 TTAAAATTTTTAATATA
49621326 TTCAATATATTTTTTAAATATA
1 TT-AA-A-A-TTTTT-AATATA
* *
49621348 TTGAAATTTTAAATATA
1 TTAAAATTTTTAATATA
49621365 TT-AAA-TTTTAATATA
1 TTAAAATTTTTAATATA
49621380 TTTAATATATTTTTAATA
1 -TTAA-A-ATTTTTAATA
49621398 GGTAAAAAGA
Statistics
Matches: 75, Mismatches: 3, Indels: 18
0.78 0.03 0.19
Matches are distributed among these distances:
15 9 0.12
16 11 0.15
17 21 0.28
18 7 0.09
19 3 0.04
20 10 0.13
21 6 0.08
22 8 0.11
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
TTAAAATTTTTAATATA
Found at i:49621391 original size:9 final size:9
Alignment explanation
Indices: 49621300--49621391 Score: 61
Period size: 9 Copynumber: 10.3 Consensus size: 9
49621290 ATTTTAAAAT
49621300 TTTAATATA
1 TTTAATATA
* *
49621309 -TTAAAATT
1 TTTAATATA
49621317 TTTAATATA
1 TTTAATATA
*
49621326 TTCAATATA
1 TTTAATATA
49621335 TTTTTTAAATATA
1 ---TTT-AATATA
*
49621348 TTGAA-AT-
1 TTTAATATA
49621355 TTTAA-ATA
1 TTTAATATA
49621363 TATTAA-AT-
1 T-TTAATATA
49621371 TTTAATATA
1 TTTAATATA
49621380 TTTAATATA
1 TTTAATATA
49621389 TTT
1 TTT
49621392 TTAATAGGTA
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
7 10 0.15
8 12 0.18
9 34 0.52
10 2 0.03
12 2 0.03
13 6 0.09
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (9 bp):
TTTAATATA
Found at i:49621469 original size:17 final size:17
Alignment explanation
Indices: 49621449--49621485 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
49621439 AAAAGTTTAA
49621449 AAAATGTTAAATATATT
1 AAAATGTTAAATATATT
* *
49621466 AAAATTTTAAATATGTT
1 AAAATGTTAAATATATT
49621483 AAA
1 AAA
49621486 GAAAATGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
AAAATGTTAAATATATT
Found at i:49621475 original size:36 final size:39
Alignment explanation
Indices: 49621421--49621494 Score: 109
Period size: 36 Copynumber: 2.0 Consensus size: 39
49621411 AATATTTTTC
*
49621421 AATATATTTAAAATTTTAAA-AAGTTTAA-AAAATGTTA
1 AATATATTTAAAATTTTAAATAAGTTAAAGAAAATGTTA
*
49621458 AATATA-TTAAAATTTTAAATATGTTAAAGAAAATGTT
1 AATATATTTAAAATTTTAAATAAGTTAAAGAAAATGTT
49621495 GAGTATAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 13 0.39
37 12 0.36
38 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.41
Consensus pattern (39 bp):
AATATATTTAAAATTTTAAATAAGTTAAAGAAAATGTTA
Found at i:49633164 original size:88 final size:88
Alignment explanation
Indices: 49633015--49633190 Score: 289
Period size: 88 Copynumber: 2.0 Consensus size: 88
49633005 GTAAGCGTCG
* * *
49633015 CAAAGAAACCAAAGCCCAACGACGCCGTCTTCTGAGCATTTGGGGATTTAGTGGCGTTTTCGGTG
1 CAAAGAAACCAAAGCCCAACGACGCCGTCTTCAGAGCATTTGGGGATTTAGTGGCATTTTCGGTA
49633080 AAGCGCCGCTAATGCTCAGGACT
66 AAGCGCCGCTAATGCTCAGGACT
** * *
49633103 CAAAGAAACTGAAGCCCGACGACGCCGTTTTCAGAGCATTTGGGGATTTAGTGGCATTTTCGGTA
1 CAAAGAAACCAAAGCCCAACGACGCCGTCTTCAGAGCATTTGGGGATTTAGTGGCATTTTCGGTA
49633168 AAGCGCCGCTAATGCTCAGGACT
66 AAGCGCCGCTAATGCTCAGGACT
49633191 TTAGCGGCGT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 81 1.00
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (88 bp):
CAAAGAAACCAAAGCCCAACGACGCCGTCTTCAGAGCATTTGGGGATTTAGTGGCATTTTCGGTA
AAGCGCCGCTAATGCTCAGGACT
Found at i:49633264 original size:202 final size:203
Alignment explanation
Indices: 49632906--49633302 Score: 625
Period size: 202 Copynumber: 2.0 Consensus size: 203
49632896 AGCGCCGCAA
* * *
49632906 AAACCGAAGCCCAACGATGCCGTTTTCTGAGCATTCGGGGATTTAGTGGCGTTTTCGGTAAAGCG
1 AAACCGAAGCCCAACGACGCCGTTTTCAGAGCATTCGGGGATTTAGTGGCATTTTCGGTAAAGCG
* * *
49632971 TCGCTAATGCTCAGGACTTTAGCTGCGTTTTTGAGTAAGCGTCGCAAAGAAACCAAAGCCCAACG
66 CCGCTAATGCTCAGGACTTTAGCGGCGTTTTTGAGTAAGCGCCGCAAAGAAACCAAAGCCCAACG
* * * * *
49633036 ACGCCGTCTTCTGAGCATTTGGGGATTTAGTGGCGTTTTC-GGTGAAGCGCCGCTAATGCTCAGG
131 ACACCGTCTTCTGAGCATTCGGGGATTTAGCGGCGTTTTCGGGGGAAGCGCCACTAATGCTCAGG
49633100 ACTCAAAG
196 ACTCAAAG
* * *
49633108 AAACTGAAGCCCGACGACGCCGTTTTCAGAGCATTTGGGGATTTAGTGGCATTTTCGGTAAAGCG
1 AAACCGAAGCCCAACGACGCCGTTTTCAGAGCATTCGGGGATTTAGTGGCATTTTCGGTAAAGCG
* *
49633173 CCGCTAATGCTCAGGACTTTAGCGGCGTTTTTGAGTAGGCGCCGCAAAGAAACCGAAGCCCAACG
66 CCGCTAATGCTCAGGACTTTAGCGGCGTTTTTGAGTAAGCGCCGCAAAGAAACCAAAGCCCAACG
* *
49633238 ACACCGTTTTCTGAGCATTCGGGGATTTAGCGGCTTTTTCGGGGGAAGCGCCACTAATGCTCAGG
131 ACACCGTCTTCTGAGCATTCGGGGATTTAGCGGCGTTTTCGGGGGAAGCGCCACTAATGCTCAGG
49633303 GCTTTAGCGG
Statistics
Matches: 176, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
202 154 0.88
203 22 0.12
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (203 bp):
AAACCGAAGCCCAACGACGCCGTTTTCAGAGCATTCGGGGATTTAGTGGCATTTTCGGTAAAGCG
CCGCTAATGCTCAGGACTTTAGCGGCGTTTTTGAGTAAGCGCCGCAAAGAAACCAAAGCCCAACG
ACACCGTCTTCTGAGCATTCGGGGATTTAGCGGCGTTTTCGGGGGAAGCGCCACTAATGCTCAGG
ACTCAAAG
Found at i:49633361 original size:116 final size:114
Alignment explanation
Indices: 49633103--49633393 Score: 384
Period size: 116 Copynumber: 2.5 Consensus size: 114
49633093 GCTCAGGACT
* * * * * * * * *
49633103 CAAAGAAACTGAAGCCCGACGACGCCGTTTTCAGAGCATTTGGGGATTTAGTGGCATTTTCGGTA
1 CAAAAAAACCGAAGCCCAACGACACCGTTTTCTGAGCATTCGGGGATTTAGCGGCTTTTTCGGGA
* * *
49633168 AAGCGCCGCTAATGCTCAGGACTTTAGCGGCGTTTTTGAGTAGGCGCCG
66 AAGCGCCACTAATGCTCAGGACTTTAGCGGCGTTTTTGAGAAAGCGCCG
*
49633217 CAAAGAAACCGAAGCCCAACGACACCGTTTTCTGAGCATTCGGGGATTTAGCGGCTTTTTCGGGG
1 CAAAAAAACCGAAGCCCAACGACACCGTTTTCTGAGCATTCGGGGATTTAGCGGCTTTTTC-GGG
* * *
49633282 GAAGCGCCACTAATGCTCAGGGCTTTAGCGGCGTTTTTTGTGAAAGCGCCG
65 AAAGCGCCACTAATGCTCAGGACTTTAGCGGCG-TTTTTGAGAAAGCGCCG
* **
49633333 CAAAAAAACCTAAGCCCAACGATTCCGTTTTCTGAGCATTCGGGGATTTAGCGGCGTTTTT
1 CAAAAAAACCGAAGCCCAACGACACCGTTTTCTGAGCATTCGGGGATTTAGCGGC-TTTTT
49633394 GATGAAGCGC
Statistics
Matches: 156, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
114 54 0.35
115 32 0.21
116 65 0.42
117 5 0.03
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (114 bp):
CAAAAAAACCGAAGCCCAACGACACCGTTTTCTGAGCATTCGGGGATTTAGCGGCTTTTTCGGGA
AAGCGCCACTAATGCTCAGGACTTTAGCGGCGTTTTTGAGAAAGCGCCG
Found at i:49634778 original size:147 final size:146
Alignment explanation
Indices: 49634558--49634955 Score: 351
Period size: 147 Copynumber: 2.7 Consensus size: 146
49634548 TTGTCTATGG
* * * * * ** *
49634558 TATTAGTGGCGTTT-TTCAGGAAACGCCACAAGCT-TGAGTTAACTGTTGGGGAAACGACTTCGT
1 TATTAGTGGCGTTTATTCA-AAAACGCCA-GAGATGTGAGCTAAGTGTTGATGAAACGACTGCGT
** * *
49634621 TTCAACTTATATTTAGTGGCGCTTTAATTAAAACACCGCAAAATTGTTTTAACA-TTTATAGAAA
64 TTTGACTTATAGTTAGTGGCGCTTTAATTAAAACACCGCAAAAATGTTTTAA-ATTTTATAGAAA
* * *
49634685 CGATGCCGTTTTG-TAAATGT
128 CAAGGCCGTTTTGCT--ATAT
* ** * * **
49634705 TATTCGTGGCGATTT-TTTGAAAACGCCATG-GATTTGAGGTAAGTGTTGATGATGCGACTGCGT
1 TATTAGTGGCG-TTTATTCAAAAACGCCA-GAGATGTGAGCTAAGTGTTGATGAAACGACTGCGT
* *** * * * *
49634768 TTTGATTTATAGTTAGTGGCGCTTCGCTTAGAACGCCGCAAAAATGTTTTAAATTTTATTGATAC
64 TTTGACTTATAGTTAGTGGCGCTTTAATTAAAACACCGCAAAAATGTTTTAAATTTTATAGAAAC
*
49634833 AAGGCCGTTTTGCTGTAT
129 AAGGCCGTTTTGCTATAT
* **
49634851 TATTAGTGGCGTTTATTCAAAAACGCCAGAGGTGTGAGCTATTTGTTGATGAAACGACTGCGTTT
1 TATTAGTGGCGTTTATTCAAAAACGCCAGAGATGTGAGCTAAGTGTTGATGAAACGACTGCGTTT
* *
49634916 TGACTTATAGTTAGTGGCGC-TTATTTATAAACACTGCAAA
66 TGACTTATAGTTAGTGGCGCTTTAATTA-AAACACCGCAAA
49634956 TGGTTAATTT
Statistics
Matches: 197, Mismatches: 47, Indels: 15
0.76 0.18 0.06
Matches are distributed among these distances:
145 8 0.04
146 82 0.42
147 101 0.51
148 6 0.03
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (146 bp):
TATTAGTGGCGTTTATTCAAAAACGCCAGAGATGTGAGCTAAGTGTTGATGAAACGACTGCGTTT
TGACTTATAGTTAGTGGCGCTTTAATTAAAACACCGCAAAAATGTTTTAAATTTTATAGAAACAA
GGCCGTTTTGCTATAT
Found at i:49634955 original size:146 final size:145
Alignment explanation
Indices: 49634608--49634955 Score: 344
Period size: 146 Copynumber: 2.4 Consensus size: 145
49634598 AACTGTTGGG
* ** * *
49634608 GAAACGACTTCGTTTCAACTTATATTTAGTGGCGCTTTAATTAAAACACCGCAAAATTGTTTTAA
1 GAAACGACTGCGTTTTGACTTATAGTTAGTGGCGC-TTAATTAAAACACCGCAAAAATGTTTTAA
* * * * **
49634673 CATTTATAGAAACGATGCCGTTTTGTAAATGTTATTCGTGGCGATTTTTTGAAAACGCCATGGAT
65 CATTTATAGAAACAAGGCCGTTTTGT-AATATTATTAGTGGCGATTTTTCAAAAACGCCATGGAT
* *
49634738 TTGAGGTAAGTGTTGAT
129 GTGAGCTAAGTGTTGAT
** * ** * *
49634755 GATGCGACTGCGTTTTGATTTATAGTTAGTGGCGCTTCGCTTAGAACGCCGCAAAAATGTTTTAA
1 GAAACGACTGCGTTTTGACTTATAGTTAGTGGCGCTT-AATTAAAACACCGCAAAAATGTTTTAA
* * *
49634820 -ATTTTATTGATACAAGGCCGTTTTGCT-GTATTATTAGTGGCG-TTTATTCAAAAACGCCA-GA
65 CA-TTTATAGAAACAAGGCCGTTTTG-TAATATTATTAGTGGCGATTT-TTCAAAAACGCCATG-
* **
49634881 GGTGTGAGCTATTTGTTGAT
126 GATGTGAGCTAAGTGTTGAT
* *
49634901 GAAACGACTGCGTTTTGACTTATAGTTAGTGGCGCTTATTTATAAACACTGCAAA
1 GAAACGACTGCGTTTTGACTTATAGTTAGTGGCGCTTAATTA-AAACACCGCAAA
49634956 TGGTTAATTT
Statistics
Matches: 161, Mismatches: 34, Indels: 13
0.77 0.16 0.06
Matches are distributed among these distances:
145 7 0.04
146 84 0.52
147 69 0.43
148 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (145 bp):
GAAACGACTGCGTTTTGACTTATAGTTAGTGGCGCTTAATTAAAACACCGCAAAAATGTTTTAAC
ATTTATAGAAACAAGGCCGTTTTGTAATATTATTAGTGGCGATTTTTCAAAAACGCCATGGATGT
GAGCTAAGTGTTGAT
Found at i:49636959 original size:13 final size:13
Alignment explanation
Indices: 49636943--49637107 Score: 120
Period size: 13 Copynumber: 12.5 Consensus size: 13
49636933 TTACTAAAAT
*
49636943 TTACTTTAATATA
1 TTACTTAAATATA
*
49636956 TTACTTGAATATA
1 TTACTTAAATATA
49636969 TTACTTAAATA-A
1 TTACTTAAATATA
* *
49636981 TTTACCTAAATACA
1 -TTACTTAAATATA
*
49636995 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
49637009 TTGGTTAAATTTA
1 TTACTTAAATATA
*
49637022 TTACTTAAATATG
1 TTACTTAAATATA
*
49637035 TTACTTAAATACA
1 TTACTTAAATATA
*
49637048 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
49637062 TTGTTTAAATTTA
1 TTACTTAAATATA
*
49637075 TTACTTAAATATG
1 TTACTTAAATATA
*
49637088 TTACTTAAATACA
1 TTACTTAAATATA
49637101 TTACTTA
1 TTACTTA
49637108 CTAAAATTTA
Statistics
Matches: 116, Mismatches: 28, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
12 7 0.06
13 92 0.79
14 11 0.09
15 6 0.05
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:49637024 original size:53 final size:53
Alignment explanation
Indices: 49636967--49637116 Score: 266
Period size: 53 Copynumber: 2.8 Consensus size: 53
49636957 TACTTGAATA
*
49636967 TATTACTTAAATAAT-TTACCTAAATACATTACTTACTAAAATTTGGTTAAATT
1 TATTACTTAAAT-ATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
*
49637020 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGTTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
49637073 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTT
49637117 AAGTATATAT
Statistics
Matches: 94, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
52 2 0.02
53 92 0.98
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.45
Consensus pattern (53 bp):
TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
Found at i:49637497 original size:9 final size:9
Alignment explanation
Indices: 49637483--49637840 Score: 290
Period size: 9 Copynumber: 41.3 Consensus size: 9
49637473 ATAAATAGCA
49637483 TACATAACT
1 TACATAACT
49637492 TACATAA--
1 TACATAACT
*
49637499 TACAAAACT
1 TACATAACT
49637508 TACATAACT
1 TACATAACT
* *
49637517 TAAATATCT
1 TACATAACT
*
49637526 TACACAACT
1 TACATAACT
*
49637535 TACATAACC
1 TACATAACT
49637544 TACATAA--
1 TACATAACT
49637551 TACATTTAACT
1 TACA--TAACT
49637562 TACATAACT
1 TACATAACT
49637571 TACATAACT
1 TACATAACT
49637580 TACATAA--
1 TACATAACT
*
49637587 TACAAAACT
1 TACATAACT
49637596 TACATAACT
1 TACATAACT
* *
49637605 TAAATATCT
1 TACATAACT
*
49637614 TACACAACT
1 TACATAACT
*
49637623 TACATAACC
1 TACATAACT
49637632 TACATAA--
1 TACATAACT
49637639 TACATTTAACT
1 TACA--TAACT
49637650 TACATAACT
1 TACATAACT
*
49637659 TACATAATACA
1 TACAT-A-ACT
49637670 TA-ATAACT
1 TACATAACT
49637678 TAC--AACT
1 TACATAACT
*
49637685 TACATAACA
1 TACATAACT
*
49637694 TACATTACT
1 TACATAACT
**
49637703 TTGATAACT
1 TACATAACT
49637712 TACATAACT
1 TACATAACT
49637721 TACATAA--
1 TACATAACT
*
49637728 TACACAACT
1 TACATAACT
*
49637737 TACATAGCT
1 TACATAACT
*
49637746 TACTTAA--
1 TACATAACT
49637753 TACATAACT
1 TACATAACT
49637762 TACATAA--
1 TACATAACT
*
49637769 TACACAACT
1 TACATAACT
*
49637778 TACATAGCT
1 TACATAACT
*
49637787 TACTTAA--
1 TACATAACT
49637794 TACATAACT
1 TACATAACT
49637803 TACATAA--
1 TACATAACT
**
49637810 TACATACAAG
1 TACATA-ACT
49637820 TACATAACT
1 TACATAACT
*
49637829 TACATAATT
1 TACATAACT
49637838 TAC
1 TAC
49637841 TTAATACATA
Statistics
Matches: 278, Mismatches: 43, Indels: 56
0.74 0.11 0.15
Matches are distributed among these distances:
7 57 0.21
8 5 0.02
9 195 0.70
10 9 0.03
11 12 0.04
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:49637535 original size:43 final size:43
Alignment explanation
Indices: 49637463--49637629 Score: 207
Period size: 43 Copynumber: 3.9 Consensus size: 43
49637453 ATAACATAAC
* * *
49637463 AACTTACATAA--TAAATAGCATACATAACTTACATAATACAA
1 AACTTACATAACTTAAATATCTTACACAACTTACATAATACAA
*
49637504 AACTTACATAACTTAAATATCTTACACAACTTACATAACCTACAT
1 AACTTACATAACTTAAATATCTTACACAACTTACATAA--TACAA
* * *
49637549 AA--TACATTTAACTTACATAACTTACATAACTTACATAATACAA
1 AACTTACA--TAACTTAAATATCTTACACAACTTACATAATACAA
49637592 AACTTACATAACTTAAATATCTTACACAACTTACATAA
1 AACTTACATAACTTAAATATCTTACACAACTTACATAA
49637630 CCTACATAAT
Statistics
Matches: 107, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
41 11 0.10
43 59 0.55
45 37 0.35
ACGTcount: A:0.49, C:0.20, G:0.01, T:0.31
Consensus pattern (43 bp):
AACTTACATAACTTAAATATCTTACACAACTTACATAATACAA
Found at i:49637575 original size:88 final size:87
Alignment explanation
Indices: 49637483--49637848 Score: 392
Period size: 88 Copynumber: 4.2 Consensus size: 87
49637473 ATAAATAGCA
49637483 TACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACATAACCTACA
1 TACATAA-TTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACATAACCTACA
*
49637548 TAATACATTTAACTTACATAACT
65 TAATACATTCAACTTACATAACT
49637571 TACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACATAACCTACA
1 TACATAA-TTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACATAACCTACA
*
49637636 TAATACATTTAACTTACATAACT
65 TAATACATTCAACTTACATAACT
* * * ** * *
49637659 TACATAA-TACATAATAACTTACAACTTACATAACATACAT-TACTTTGATAACTTACATAACTT
1 TACATAATTACATAAT-AC--AAAACTTACATAACTTAAATAT-CTTACACAACTTACATAACCT
*
49637722 ACATAATACA--CAACTTACATAGCT
62 ACATAATACATTCAACTTACATAACT
* * * * * ** *
49637746 TACTTAA-TACATAACTTACATAA--TACACAACTTACATAGCTTACTTAA--TACATAACTTAC
1 TACATAATTACATAA--TACAAAACTTACATAACTTAAATATCTTACACAACTTACATAACCTAC
* *
49637806 ATAATACATACAA-GTACATAACT
64 ATAATACATTCAACTTACATAACT
*
49637829 TACATAATTTACTTAATACA
1 TACATAA-TTACATAATACA
49637849 TAAATATATA
Statistics
Matches: 246, Mismatches: 21, Indels: 27
0.84 0.07 0.09
Matches are distributed among these distances:
82 20 0.08
83 18 0.07
84 21 0.09
85 6 0.02
86 11 0.04
87 27 0.11
88 98 0.40
89 45 0.18
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (87 bp):
TACATAATTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACATAACCTACAT
AATACATTCAACTTACATAACT
Found at i:49637603 original size:25 final size:25
Alignment explanation
Indices: 49637434--49637836 Score: 109
Period size: 25 Copynumber: 15.8 Consensus size: 25
49637424 CTTATATATA
* *
49637434 AACTTGCATAACTTACGTAATAACAT
1 AACTTACATAACTTACATAAT-ACAT
*
49637460 AACAACTTACATAA--TAAATAGCATACAT
1 ---AACTTACATAACTTACATA--ATACAT
*
49637488 AACTTACATAA--TACAAAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
* * *
49637513 AACTTAAATATCTTACACAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
*
49637540 AACCTACATAA--TACAT--T---T
1 AACTTACATAACTTACATAATACAT
49637558 AACTTACATAACTTACATAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
* *
49637585 AA--TACAAAACTTACATAACTTAAAT
1 AACTTACATAACTTACATAA--TACAT
* *
49637610 ATCTTACACAACTTACATAACCTACAT
1 AACTTACATAACTTACATAA--TACAT
49637637 AA--TACATTTAACTTACATAACTTACAT
1 AACTTACA--TAACTTACATAA--TACAT
* *
49637664 AATACATA-ATAACTTACA-ACTTACAT
1 -A-ACTTACATAACTTACATA-ATACAT
* * **
49637690 AACATACATTACTTTGATAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
*
49637717 AACTTACATAA--TACACAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
* *
49637742 AGCTTACTTAA--TACATAACTTACAT
1 AACTTACATAACTTACATAA--TACAT
* * *
49637767 AA--TACACAACTTACATAGCTTACTT
1 AACTTACATAACTTACATA--ATACAT
49637792 AA--TACATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAT
**
49637815 ACAAGTACATAACTTACATAAT
1 A-ACTTACATAACTTACATAAT
49637837 TTACTTAATA
Statistics
Matches: 296, Mismatches: 43, Indels: 73
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.04
20 5 0.02
21 1 0.00
23 11 0.04
24 7 0.02
25 127 0.43
26 23 0.08
27 81 0.27
28 14 0.05
29 13 0.04
30 1 0.00
31 2 0.01
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAT
Found at i:49640184 original size:21 final size:21
Alignment explanation
Indices: 49640159--49640206 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
49640149 CTACAACTTA
*
49640159 AAGCAGAGGC-GACAACGAGGG
1 AAGCAGAGGCTG-CAACGAGAG
*
49640180 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAACGAGAG
49640201 AAGCAG
1 AAGCAG
49640207 CGAGAGAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.38, C:0.19, G:0.42, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCTGCAACGAGAG
Found at i:49640208 original size:12 final size:12
Alignment explanation
Indices: 49640191--49640218 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
49640181 AGCAGAGGCT
49640191 GCAGCGAGAGAA
1 GCAGCGAGAGAA
49640203 GCAGCGAGAGAA
1 GCAGCGAGAGAA
49640215 GCAG
1 GCAG
49640219 AGGTTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.43, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:49640448 original size:31 final size:31
Alignment explanation
Indices: 49640412--49640506 Score: 77
Period size: 31 Copynumber: 3.1 Consensus size: 31
49640402 ATATATGTTG
* * *
49640412 ATTGAATCAAAATTAAAGTTTCGTGCATTTA
1 ATTGAATCAAAATTAAAGTTTCATACATATA
* * * * *
49640443 TTTGAACCACAATCAAAATTTCATACATATA
1 ATTGAATCAAAATTAAAGTTTCATACATATA
* * *
49640474 ATTGTATC-AAATTAAAG-TTCATATATACA
1 ATTGAATCAAAATTAAAGTTTCATACATATA
49640503 ATTG
1 ATTG
49640507 CACATTAAAT
Statistics
Matches: 48, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
29 14 0.29
30 6 0.12
31 28 0.58
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (31 bp):
ATTGAATCAAAATTAAAGTTTCATACATATA
Found at i:49641182 original size:21 final size:21
Alignment explanation
Indices: 49641156--49641211 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
49641146 AACAGTGGTG
* *
49641156 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTATA
* *
49641177 GCGGTGAGATTGGATATTATA
1 GCGGTGAGATTAGATACTATA
*
49641198 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
49641212 AACAATGGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.34, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTATA
Found at i:49649989 original size:57 final size:57
Alignment explanation
Indices: 49649813--49650058 Score: 306
Period size: 57 Copynumber: 4.4 Consensus size: 57
49649803 AATGCCTTAC
* * *
49649813 AACAATAGGGGAGGTATGCCA--GCC-AACAACATGGGGGGAGGAATGCCGCCTCCT
1 AACAATATGGGAGGAATGCCACCGCCTAACAACATGGGAGGAGGAATGCCGCCTCCT
* * *
49649867 AACAATATGGGAGGAATGCCGCCTCCTAACAATAT--G-GGAGGAATGCCGCCTCCT
1 AACAATATGGGAGGAATGCCACCGCCTAACAACATGGGAGGAGGAATGCCGCCTCCT
* **
49649921 AACAGTATGGGAGGAATGCCACCGCGGAACAACATGGGAGGAGGAATGCCGCCTCCT
1 AACAATATGGGAGGAATGCCACCGCCTAACAACATGGGAGGAGGAATGCCGCCTCCT
* * * *
49649978 AACAATATGGGAGGAATGCCGCCTCCTAACAACATGGGAGGAGGAATGCCGCCGCCG
1 AACAATATGGGAGGAATGCCACCGCCTAACAACATGGGAGGAGGAATGCCGCCTCCT
* * *
49650035 AACAACATGGGTGGGATGCCACCG
1 AACAATATGGGAGGAATGCCACCG
49650059 GGTCCACCGA
Statistics
Matches: 163, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
54 65 0.40
55 1 0.01
56 3 0.02
57 94 0.58
ACGTcount: A:0.30, C:0.25, G:0.31, T:0.14
Consensus pattern (57 bp):
AACAATATGGGAGGAATGCCACCGCCTAACAACATGGGAGGAGGAATGCCGCCTCCT
Found at i:49650053 original size:27 final size:27
Alignment explanation
Indices: 49649783--49650054 Score: 243
Period size: 27 Copynumber: 10.0 Consensus size: 27
49649773 TAGAAGTCCA
49649783 CCTCCTAACAACATGGGAGGAATG-C-
1 CCTCCTAACAACATGGGAGGAATGCCG
* * * * *
49649808 CTTAC-AACAATAGGGGAGGTATGCCAG
1 CCTCCTAACAACATGGGAGGAATGCC-G
49649835 ---CC-AACAACATGGGGGGAGGAATGCCG
1 CCTCCTAACAACAT---GGGAGGAATGCCG
*
49649861 CCTCCTAACAATATGGGAGGAATGCCG
1 CCTCCTAACAACATGGGAGGAATGCCG
*
49649888 CCTCCTAACAATATGGGAGGAATGCCG
1 CCTCCTAACAACATGGGAGGAATGCCG
** *
49649915 CCTCCTAACAGTATGGGAGGAATGCCA
1 CCTCCTAACAACATGGGAGGAATGCCG
* **
49649942 CCGCGGAACAACATGGGAGGAGGAATGCCG
1 CCTCCTAACAACAT--G-GGAGGAATGCCG
*
49649972 CCTCCTAACAATATGGGAGGAATGCCG
1 CCTCCTAACAACATGGGAGGAATGCCG
49649999 CCTCCTAACAACATGGGAGGAGGAATGCCG
1 CCTCCTAACAACAT--G-GGAGGAATGCCG
* * * *
49650029 CCGCCGAACAACATGGGTGGGATGCC
1 CCTCCTAACAACATGGGAGGAATGCC
49650055 ACCGGGTCCA
Statistics
Matches: 204, Mismatches: 27, Indels: 30
0.78 0.10 0.11
Matches are distributed among these distances:
24 22 0.11
25 4 0.02
26 1 0.00
27 119 0.58
28 2 0.01
29 4 0.02
30 52 0.25
ACGTcount: A:0.30, C:0.25, G:0.30, T:0.15
Consensus pattern (27 bp):
CCTCCTAACAACATGGGAGGAATGCCG
Found at i:49650054 original size:84 final size:83
Alignment explanation
Indices: 49649837--49650054 Score: 296
Period size: 84 Copynumber: 2.6 Consensus size: 83
49649827 TATGCCAGCC
* * * *
49649837 AACAACATGGGGGGAGGAATGCCGCCTCCTAACAATATGGGAGGAATGCCGCCTCCTAACAATAT
1 AACAACAT-GGGGGAGGAATGCCGCCGCCGAACAACATGGGAGGGATGCCGCCTCCTAACAATAT
49649902 GGGAGGAATGCCGCCTCCT
65 GGGAGGAATGCCGCCTCCT
** * *
49649921 AACAGTAT--GGGAGGAATGCCACCGCGGAACAACATGGGAGGAGGAATGCCGCCTCCTAACAAT
1 AACAACATGGGGGAGGAATGCCGCCGCCGAACAACATGGGA-G-GG-ATGCCGCCTCCTAACAAT
49649984 ATGGGAGGAATGCCGCCTCCT
63 ATGGGAGGAATGCCGCCTCCT
*
49650005 AACAACATGGGAGGAGGAATGCCGCCGCCGAACAACATGGGTGGGATGCC
1 AACAACATGGG-GGAGGAATGCCGCCGCCGAACAACATGGGAGGGATGCC
49650055 ACCGGGTCCA
Statistics
Matches: 115, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
81 26 0.23
82 1 0.01
83 1 0.01
84 56 0.49
85 2 0.02
86 2 0.02
87 27 0.23
ACGTcount: A:0.29, C:0.25, G:0.31, T:0.14
Consensus pattern (83 bp):
AACAACATGGGGGAGGAATGCCGCCGCCGAACAACATGGGAGGGATGCCGCCTCCTAACAATATG
GGAGGAATGCCGCCTCCT
Found at i:49650803 original size:21 final size:19
Alignment explanation
Indices: 49650770--49650810 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
49650760 ACGTTTGGTT
*
49650770 AATTATGTTTATTTTCTTTA
1 AATTAAGTTTATTTT-TTTA
49650790 AATTAAGTGTTATTTTTTTA
1 AATTAAGT-TTATTTTTTTA
49650810 A
1 A
49650811 TTTCATGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.61
Consensus pattern (19 bp):
AATTAAGTTTATTTTTTTA
Found at i:49650823 original size:21 final size:19
Alignment explanation
Indices: 49650768--49650836 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 19
49650758 TTACGTTTGG
49650768 TTAA-TTATGTTTATTTTCT
1 TTAATTTATGTTTATTTT-T
* *
49650787 TTAAATTAAGTGTTATTTTT
1 TTAATTTATGT-TTATTTTT
*
49650807 TTAATTTCATGTATTATTTAT
1 TTAATTT-ATGT-TTATTTTT
49650828 TTAATTTAT
1 TTAATTTAT
49650837 TATTTTTTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
19 4 0.10
20 14 0.33
21 24 0.57
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.64
Consensus pattern (19 bp):
TTAATTTATGTTTATTTTT
Found at i:49651563 original size:22 final size:22
Alignment explanation
Indices: 49651538--49651585 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
49651528 TCAATTCCTT
*
49651538 TCAATTTTCTTCCAAAATTCTC
1 TCAATTTCCTTCCAAAATTCTC
49651560 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCCAAAATTCTC
49651582 TCAA
1 TCAA
49651586 ATCCATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (22 bp):
TCAATTTCCTTCCAAAATTCTC
Found at i:49655423 original size:126 final size:125
Alignment explanation
Indices: 49655102--49655453 Score: 537
Period size: 126 Copynumber: 2.8 Consensus size: 125
49655092 TCCAAACATG
** * *
49655102 CTACTGTAGCAAAAATGCGTCCACAATGGCGTGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACAAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
49655167 TAGAAGCGATTTTATATTATTTGCTCAGAAACGTC-AAAAAAAATTATTTCTCACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTCACATGAC
* *
49655226 CTACTGTAGCAAAAGCGCGTCCACAAGGCCGCAATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACAAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
49655291 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTC-CGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTC-TCACATGAC
* * * *
49655352 CTACTGTAGCAAAAGCGCGTTCACGAGGGCGCGTTTTTACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACAAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
** *
49655417 TAGAAGCGATTTTATACTATTTTATAAGAAACGTCAA
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
49655454 CTCGAAATTA
Statistics
Matches: 208, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
124 93 0.45
125 6 0.03
126 107 0.51
127 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACAAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTCACATGAC
Found at i:49656404 original size:16 final size:16
Alignment explanation
Indices: 49656383--49656413 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49656373 TGATTTAATT
*
49656383 TATTTTTATTTTGTTC
1 TATTTTTAATTTGTTC
49656399 TATTTTTAATTTGTT
1 TATTTTTAATTTGTT
49656414 ATCGGATTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.03, G:0.06, T:0.74
Consensus pattern (16 bp):
TATTTTTAATTTGTTC
Found at i:49656650 original size:8 final size:9
Alignment explanation
Indices: 49656628--49656653 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
49656618 TTAATTTATA
49656628 TAAAAATTT
1 TAAAAATTT
49656637 TAAAAATTT
1 TAAAAATTT
49656646 TAAAAATT
1 TAAAAATT
49656654 CCAAAATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAAAAATTT
Found at i:49657950 original size:24 final size:24
Alignment explanation
Indices: 49657921--49657977 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
49657911 AACATTTTTT
*
49657921 TATTATTATCGTCAGTGTTATTA-
1 TATTATTATCATCAGTGTTATTAC
* * *
49657944 TACTTATTCTCATTATTGTTATTAC
1 TA-TTATTATCATCAGTGTTATTAC
49657969 TATTATTAT
1 TATTATTAT
49657978 ATTTAGTGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 2 0.07
24 23 0.85
25 2 0.07
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.56
Consensus pattern (24 bp):
TATTATTATCATCAGTGTTATTAC
Found at i:49659234 original size:23 final size:23
Alignment explanation
Indices: 49659208--49659323 Score: 178
Period size: 23 Copynumber: 5.0 Consensus size: 23
49659198 GCAACACTAC
* *
49659208 TATGTAGTCGAAGCTACCACTGT
1 TATGTAGCCGAAGCTACCACTGA
*
49659231 TATGTAGCTGAAGCTACCACTGA
1 TATGTAGCCGAAGCTACCACTGA
* *
49659254 AATGTAGCCGAAGCTACCACTGT
1 TATGTAGCCGAAGCTACCACTGA
49659277 TATGTAGCCGAAGCTACCACTGA
1 TATGTAGCCGAAGCTACCACTGA
*
49659300 AATGTAGCCGAAGCTACCACTGA
1 TATGTAGCCGAAGCTACCACTGA
49659323 T
1 T
49659324 CAATAACACT
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
TATGTAGCCGAAGCTACCACTGA
Found at i:49659276 original size:46 final size:46
Alignment explanation
Indices: 49659209--49659321 Score: 208
Period size: 46 Copynumber: 2.5 Consensus size: 46
49659199 CAACACTACT
* *
49659209 ATGTAGTCGAAGCTACCACTGTTATGTAGCTGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTGAA
49659255 ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTGAA
49659301 ATGTAGCCGAAGCTACCACTG
1 ATGTAGCCGAAGCTACCACTG
49659322 ATCAATAACA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (46 bp):
ATGTAGCCGAAGCTACCACTGTTATGTAGCCGAAGCTACCACTGAA
Found at i:49659575 original size:18 final size:17
Alignment explanation
Indices: 49659550--49659587 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
49659540 TTTTCCTTCT
49659550 ACATTC-AATATTAATTC
1 ACATTCAAATA-TAATTC
49659567 ACATATCAAATATAATTC
1 ACAT-TCAAATATAATTC
49659585 ACA
1 ACA
49659588 ATTTATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 11 0.58
19 4 0.21
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (17 bp):
ACATTCAAATATAATTC
Found at i:49660818 original size:22 final size:23
Alignment explanation
Indices: 49660788--49660847 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
49660778 TTTATTTGTA
*
49660788 TTAATAATTTATTATATTATT-ATT
1 TTAA-AATTTATTATA-CATTAATT
*
49660812 TT-AAATTTATCATACATTAATT
1 TTAAAATTTATTATACATTAATT
*
49660834 TTAAAATTCATTAT
1 TTAAAATTTATTAT
49660848 GTAGTGCCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 3 0.10
22 15 0.50
23 10 0.33
24 2 0.07
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAAAATTTATTATACATTAATT
Found at i:49664346 original size:15 final size:16
Alignment explanation
Indices: 49664320--49664358 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
49664310 CGCCAATAAA
49664320 TATTTT-ATAATAATT
1 TATTTTAATAATAATT
*
49664335 T-TTTTAATAATATTT
1 TATTTTAATAATAATT
49664350 TATTTTAAT
1 TATTTTAAT
49664359 TTTTTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 4 0.19
15 10 0.48
16 7 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTTAATAATAATT
Found at i:49664532 original size:16 final size:16
Alignment explanation
Indices: 49664513--49664551 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
49664503 AAAATCAAAT
*
49664513 AAAATTATATTATATA
1 AAAATTACATTATATA
*
49664529 AAAAATACATTATATA
1 AAAATTACATTATATA
49664545 AAAATTA
1 AAAATTA
49664552 AATGAGTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATTACATTATATA
Found at i:49665027 original size:20 final size:21
Alignment explanation
Indices: 49665002--49665044 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
49664992 TTAAATTTCG
*
49665002 AATATAATATT-AAGTCTTAC
1 AATATAATATTGAAGTCATAC
49665022 AATATAATATTGAAGTCATAC
1 AATATAATATTGAAGTCATAC
49665043 AA
1 AA
49665045 ATTTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (21 bp):
AATATAATATTGAAGTCATAC
Found at i:49667772 original size:16 final size:16
Alignment explanation
Indices: 49667751--49667784 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
49667741 TGTTTATTTT
*
49667751 TTAATTTTATGTATTA
1 TTAATTTAATGTATTA
*
49667767 TTAATTTAATTTATTA
1 TTAATTTAATGTATTA
49667783 TT
1 TT
49667785 TTTTACATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTAATTTAATGTATTA
Found at i:49673567 original size:24 final size:24
Alignment explanation
Indices: 49673535--49673581 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
49673525 AATATTATAA
49673535 TTTTTTTATTTACCAAAAAATATT
1 TTTTTTTATTTACCAAAAAATATT
49673559 TTTTTTTATTTACCAAAAAATAT
1 TTTTTTTATTTACCAAAAAATAT
49673582 AAAAAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTTTTATTTACCAAAAAATATT
Done.