Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 8 of 106
Found at i:3782468 original size:51 final size:51
Alignment explanation
Indices: 3782391--3782571 Score: 132
Period size: 51 Copynumber: 3.7 Consensus size: 51
3782381 TTAATCATAA
3782391 TAATA-TTAAATTATAAATAAAATATTAATAATTAAATTA-TACTAAAATAT
1 TAATATTTAAATTATAAATAAAATATTAATAATTAAATTATTA-TAAAATAT
* * * * * *
3782441 TAATATTTAAATTATAAA-ATTATTATTATTATTTTAATTATTTATAAATTAT
1 TAATATTTAAATTATAAATA-AAATATTAATAATTAAATTA-TTATAAAATAT
* * * *
3782493 TAATATTTTAATT-T--ATTATATATT--T--TTAATTTATTATAAAATAT
1 TAATATTTAAATTATAAATAAAATATTAATAATTAAATTATTATAAAATAT
** *
3782537 TAATATTTAAACAATAAAATAAAA-ATAAATAATTA
1 TAATATTTAAATTAT-AAATAAAATATTAATAATTA
3782572 TATATAATAA
Statistics
Matches: 98, Mismatches: 20, Indels: 25
0.69 0.14 0.17
Matches are distributed among these distances:
44 20 0.20
45 7 0.07
47 3 0.03
48 4 0.04
49 6 0.06
50 6 0.06
51 31 0.32
52 19 0.19
53 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (51 bp):
TAATATTTAAATTATAAATAAAATATTAATAATTAAATTATTATAAAATAT
Found at i:3782474 original size:26 final size:28
Alignment explanation
Indices: 3782438--3782538 Score: 77
Period size: 26 Copynumber: 3.7 Consensus size: 28
3782428 TATACTAAAA
*
3782438 TATTAATATTTAAATTA-TA-AAATTAT
1 TATTATTATTTAAATTATTATAAATTAT
*
3782464 TATTATTATTTTAATTATTTATAAATTAT
1 TATTATTATTTAAATTA-TTATAAATTAT
* * * *
3782493 TAATA-T-TTTAATTTATTATATATTTT
1 TATTATTATTTAAATTATTATAAATTAT
* *
3782519 TAAT-TTATTATAAAATATTA
1 TATTATTATT-TAAATTATTA
3782539 ATATTTAAAC
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
26 29 0.48
27 9 0.15
28 11 0.18
29 11 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TATTATTATTTAAATTATTATAAATTAT
Found at i:3782488 original size:30 final size:28
Alignment explanation
Indices: 3782452--3782514 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
3782442 AATATTTAAA
3782452 TTATAAAATTATTATTATTATTTTAA-TTAT
1 TTATAAAATTATTA--A-TATTTTAATTTAT
3782482 TTAT-AAATTATTAATATTTTAATTTAT
1 TTATAAAATTATTAATATTTTAATTTAT
3782509 TATATA
1 T-TATA
3782515 TTTTTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
26 8 0.27
27 6 0.20
28 3 0.10
29 9 0.30
30 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TTATAAAATTATTAATATTTTAATTTAT
Found at i:3782529 original size:18 final size:18
Alignment explanation
Indices: 3782479--3782530 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
3782469 TTATTTTAAT
* *
3782479 TATTTATAAATTATTA-A
1 TATTTTTAATTTATTATA
3782496 TA-TTTTAATTTATTATA
1 TATTTTTAATTTATTATA
3782513 TATTTTTAATTTATTATA
1 TATTTTTAATTTATTATA
3782531 AAATATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 11 0.35
17 5 0.16
18 15 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTTTAATTTATTATA
Found at i:3782530 original size:44 final size:42
Alignment explanation
Indices: 3782463--3782544 Score: 121
Period size: 44 Copynumber: 1.9 Consensus size: 42
3782453 TATAAAATTA
*
3782463 TTATTATTATTTTAATTATTTATAAATTATTAATATTTTAAT
1 TTATTATTATTTTAATTATTTATAAAATATTAATATTTTAAT
3782505 TTATTATATATTTTTAATT-TATTATAAAATATTAATATTT
1 TTATTAT-TA-TTTTAATTAT-TTATAAAATATTAATATTT
3782545 AAACAATAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
42 7 0.19
43 3 0.08
44 26 0.72
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (42 bp):
TTATTATTATTTTAATTATTTATAAAATATTAATATTTTAAT
Found at i:3782539 original size:18 final size:18
Alignment explanation
Indices: 3782500--3782540 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3782490 TATTAATATT
* * *
3782500 TTAATTTATTATATATTT
1 TTAATTTATTATAAAATA
3782518 TTAATTTATTATAAAATA
1 TTAATTTATTATAAAATA
3782536 TTAAT
1 TTAAT
3782541 ATTTAAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATTTATTATAAAATA
Found at i:3788827 original size:16 final size:16
Alignment explanation
Indices: 3788802--3788835 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3788792 TAATATTTGA
*
3788802 TTATATATAAAATATT
1 TTATAAATAAAATATT
*
3788818 TTATAAATAAAATCTT
1 TTATAAATAAAATATT
3788834 TT
1 TT
3788836 GCAACTTTAT
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:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATAAATAAAATATT
Found at i:3804985 original size:14 final size:15
Alignment explanation
Indices: 3804968--3804996 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3804958 ATTAATTTTG
3804968 ATTAATTA-TAATTA
1 ATTAATTATTAATTA
3804982 ATTAATTATTAATTA
1 ATTAATTATTAATTA
3804997 TAAAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTAATTATTAATTA
Found at i:3805091 original size:13 final size:13
Alignment explanation
Indices: 3805073--3805097 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3805063 TTATTTTAAT
3805073 TTTTAAAAAATTA
1 TTTTAAAAAATTA
3805086 TTTTAAAAAATT
1 TTTTAAAAAATT
3805098 TTAAAATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTTAAAAAATTA
Found at i:3806693 original size:27 final size:27
Alignment explanation
Indices: 3806641--3806693 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3806631 AGTATTGATA
** *
3806641 TTAAAATAATAATAATTTTTTTTAAGT
1 TTAAAATAATAATAATTTCATGTAAGT
*
3806668 TTAAAATAATAATCATTTCATGTAAG
1 TTAAAATAATAATAATTTCATGTAAG
3806694 GATGTCAGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (27 bp):
TTAAAATAATAATAATTTCATGTAAGT
Found at i:3811387 original size:30 final size:31
Alignment explanation
Indices: 3811314--3811387 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
3811304 ATTTTAAAAA
* *
3811314 TTTTA-TTTTTTA--TTACATTTAATCAAAT
1 TTTTATTTTTTTATTTTAAATTAAATCAAAT
* *
3811342 CTTTATATTTTTATTTTAAATTAAAT-AAAT
1 TTTTATTTTTTTATTTTAAATTAAATCAAAT
3811372 TTTTATTTTTTTATTT
1 TTTTATTTTTTTATTT
3811388 GGAACTCTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
28 4 0.11
29 6 0.16
30 18 0.49
31 9 0.24
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (31 bp):
TTTTATTTTTTTATTTTAAATTAAATCAAAT
Found at i:3817497 original size:23 final size:22
Alignment explanation
Indices: 3817471--3817514 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3817461 ATAGTAACAA
*
3817471 TTTTT-AAAATATCACGTAATTT
1 TTTTTAAAAAAATCA-GTAATTT
3817493 TTTTTAAAAAAATCAGTAATTT
1 TTTTTAAAAAAATCAGTAATTT
3817515 ACATTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (22 bp):
TTTTTAAAAAAATCAGTAATTT
Found at i:3819147 original size:33 final size:27
Alignment explanation
Indices: 3819088--3819144 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
3819078 GTATTTAAAA
3819088 AGATAGTTTCATAAATGAAAAAGAATG
1 AGATAGTTTCATAAATGAAAAAGAATG
3819115 AGATAGTTTCATAAATGAAAAAGAATG
1 AGATAGTTTCATAAATGAAAAAGAATG
3819142 AGA
1 AGA
3819145 ATGGGACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.25
Consensus pattern (27 bp):
AGATAGTTTCATAAATGAAAAAGAATG
Found at i:3819446 original size:16 final size:17
Alignment explanation
Indices: 3819425--3819468 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3819415 ACATGACATT
3819425 AAACAAATAA-AA-AATA
1 AAACAAATAATAATAA-A
3819441 AAACAAATAATAATAAA
1 AAACAAATAATAATAAA
*
3819458 AAACAACTAAT
1 AAACAAATAAT
3819469 TTAAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 10 0.40
17 13 0.52
18 2 0.08
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (17 bp):
AAACAAATAATAATAAA
Found at i:3819455 original size:15 final size:16
Alignment explanation
Indices: 3819425--3819463 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3819415 ACATGACATT
3819425 AAACAAATAAAAAATA
1 AAACAAATAAAAAATA
3819441 AAACAAATAATAATAA-A
1 AAACAAATAA-AA-AATA
3819458 AAACAA
1 AAACAA
3819464 CTAATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
17 9 0.43
18 2 0.10
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (16 bp):
AAACAAATAAAAAATA
Found at i:3819657 original size:8 final size:8
Alignment explanation
Indices: 3819608--3819658 Score: 52
Period size: 8 Copynumber: 6.2 Consensus size: 8
3819598 GCTTATGAAA
3819608 AATATAAT
1 AATATAAT
3819616 AATAATAAT
1 AAT-ATAAT
3819625 ATATATAA-
1 A-ATATAAT
3819633 ATATATAA-
1 A-ATATAAT
*
3819641 AATAAAAT
1 AATATAAT
3819649 AATATAAT
1 AATATAAT
3819657 AA
1 AA
3819659 AAAAAATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
7 5 0.13
8 21 0.55
9 10 0.26
10 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AATATAAT
Found at i:3819657 original size:22 final size:22
Alignment explanation
Indices: 3819606--3819669 Score: 53
Period size: 25 Copynumber: 2.8 Consensus size: 22
3819596 TTGCTTATGA
3819606 AAAAT-ATAATAATAATAATATAT
1 AAAATAATAA-AATAA-AATATAT
3819629 ATAAATATATAAAATAAAATAATAT
1 A-AAATA-ATAAAATAAAAT-ATAT
3819654 AATAA-AA-AAAATAAAA
1 AA-AATAATAAAATAAAA
3819670 AAATTTTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
22 9 0.25
23 2 0.06
24 9 0.25
25 12 0.33
26 4 0.11
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATAATAAAATAAAATATAT
Found at i:3819798 original size:15 final size:15
Alignment explanation
Indices: 3819758--3819852 Score: 65
Period size: 15 Copynumber: 6.5 Consensus size: 15
3819748 AAAAAATNTG
*
3819758 TAATAAT-AAGAA-A
1 TAATAATAAAAAATA
* *
3819771 TAAGAATAGAAAATA
1 TAATAATAAAAAATA
*
3819786 TGATAATAAAAAATA
1 TAATAATAAAAAATA
3819801 TAATAA-AATAAAA-A
1 TAATAATAA-AAAATA
* **
3819815 TAATAATTAATTA-A
1 TAATAATAAAAAATA
3819829 TAATAACTAAAAAATA
1 TAATAA-TAAAAAATA
3819845 TAGATAAT
1 TA-ATAAT
3819853 TGCATTAGCA
Statistics
Matches: 62, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
13 6 0.10
14 21 0.34
15 27 0.44
16 4 0.06
17 4 0.06
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.27
Consensus pattern (15 bp):
TAATAATAAAAAATA
Found at i:3819805 original size:12 final size:13
Alignment explanation
Indices: 3819758--3819844 Score: 59
Period size: 14 Copynumber: 6.2 Consensus size: 13
3819748 AAAAAATNTG
*
3819758 TAATAATAAGAAA
1 TAATAATAAAAAA
*
3819771 TAAGAATAGAAAATA
1 TAATAATA-AAAA-A
*
3819786 TGATAATAAAAAA
1 TAATAATAAAAAA
3819799 T-ATAATAAAATAA
1 TAATAATAAAA-AA
*
3819812 AAATAATAATTAATTAA
1 TAATAATAA--AA--AA
3819829 TAATAACTAAAAAA
1 TAATAA-TAAAAAA
3819843 TA
1 TA
3819845 TAGATAATTG
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
12 9 0.15
13 11 0.18
14 18 0.30
15 7 0.12
16 4 0.07
17 8 0.13
18 3 0.05
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (13 bp):
TAATAATAAAAAA
Found at i:3819820 original size:17 final size:17
Alignment explanation
Indices: 3819794--3819844 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
3819784 TATGATAATA
3819794 AAAAAT-ATAATAAAAT
1 AAAAATAATAATAAAAT
* *
3819810 AAAAATAATAATTAATT
1 AAAAATAATAATAAAAT
*
3819827 AATAATAACTAA-AAAAT
1 AAAAATAA-TAATAAAAT
3819844 A
1 A
3819845 TAGATAATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 6 0.21
17 19 0.68
18 3 0.11
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATAATAATAAAAT
Found at i:3835486 original size:21 final size:21
Alignment explanation
Indices: 3835462--3835529 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
3835452 TCAAGAAGAG
3835462 GATGATGGTGATGATTACGAT
1 GATGATGGTGATGATTACGAT
** * *
3835483 GATGATTATGATGAGTATGAT
1 GATGATGGTGATGATTACGAT
**
3835504 GATGATGG-GTATGATTTGGAT
1 GATGATGGTG-ATGATTACGAT
3835525 GATGA
1 GATGA
3835530 GTTGGTGCCG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 1 0.03
21 36 0.97
ACGTcount: A:0.29, C:0.01, G:0.34, T:0.35
Consensus pattern (21 bp):
GATGATGGTGATGATTACGAT
Found at i:3835502 original size:15 final size:15
Alignment explanation
Indices: 3835484--3835519 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3835474 GATTACGATG
3835484 ATGATTATGATGAGT
1 ATGATTATGATGAGT
* *
3835499 ATGATGATGATGGGT
1 ATGATTATGATGAGT
3835514 ATGATT
1 ATGATT
3835520 TGGATGATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.39
Consensus pattern (15 bp):
ATGATTATGATGAGT
Found at i:3841576 original size:23 final size:24
Alignment explanation
Indices: 3841550--3841594 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
3841540 TTTTTTTCGA
*
3841550 TATGACATGTAAC-TTTTTTTAAC
1 TATGACATGTAACATGTTTTTAAC
*
3841573 TATGGCATGTAACATGTTTTTA
1 TATGACATGTAACATGTTTTTA
3841595 TATATGATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (24 bp):
TATGACATGTAACATGTTTTTAAC
Found at i:3841600 original size:24 final size:22
Alignment explanation
Indices: 3841549--3841601 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
3841539 ATTTTTTTCG
*
3841549 ATATGACATGTAACTTTTTTTA
1 ATATGACATGTAACTGTTTTTA
*
3841571 ACTATGGCATGTAACATGTTTTTA
1 A-TATGACATGTAAC-TGTTTTTA
3841595 TATATGA
1 -ATATGA
3841602 TGTGTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 1 0.04
23 12 0.48
24 11 0.44
25 1 0.04
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.45
Consensus pattern (22 bp):
ATATGACATGTAACTGTTTTTA
Found at i:3842197 original size:29 final size:29
Alignment explanation
Indices: 3842155--3842218 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
3842145 ATGTGATCAT
3842155 GTCATCGTGTCATATCAGCATACTATATC
1 GTCATCGTGTCATATCAGCATACTATATC
*
3842184 GTCATCGTGTCATATCAGCATACTATGTC
1 GTCATCGTGTCATATCAGCATACTATATC
*
3842213 ATCATC
1 GTCATC
3842219 TATTATAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (29 bp):
GTCATCGTGTCATATCAGCATACTATATC
Found at i:3842480 original size:4 final size:4
Alignment explanation
Indices: 3842471--3842495 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3842461 TTTAAATTGC
3842471 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
3842496 AGGATTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:3860843 original size:2 final size:2
Alignment explanation
Indices: 3860836--3860861 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3860826 ATGTGTTTGG
3860836 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
3860862 AACCTGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:3867148 original size:15 final size:16
Alignment explanation
Indices: 3867118--3867148 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3867108 CGAAGCATAA
3867118 AGAGAAAATAACAAAG
1 AGAGAAAATAACAAAG
3867134 AGAGAAAAT-ACAAAG
1 AGAGAAAATAACAAAG
3867149 CGACGATCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.68, C:0.06, G:0.19, T:0.06
Consensus pattern (16 bp):
AGAGAAAATAACAAAG
Found at i:3870459 original size:2 final size:2
Alignment explanation
Indices: 3870452--3870489 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3870442 TCTTGCATTA
3870452 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3870490 TTGGATGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3870636 original size:27 final size:28
Alignment explanation
Indices: 3870606--3870659 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
3870596 ATTCATAAAT
3870606 TATTTAAAGAAA-TTTATATTTATATTA
1 TATTTAAAGAAATTTTATATTTATATTA
** *
3870633 TATTTAATTAAATTTTATATTTTTATT
1 TATTTAAAGAAATTTTATATTTATATT
3870660 TTAAGTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
TATTTAAAGAAATTTTATATTTATATTA
Found at i:3870681 original size:28 final size:29
Alignment explanation
Indices: 3870618--3870681 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
3870608 TTTAAAGAAA
* * *
3870618 TTTATATTTATATTATATTTAATTAAATT
1 TTTATTTTTATATTATAGTTAAATAAATT
* *
3870647 TTATATTTTTATTTTA-AGTTAAATAAGTT
1 TT-TATTTTTATATTATAGTTAAATAAATT
3870676 TTTATT
1 TTTATT
3870682 ACCAAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 4 0.14
29 14 0.48
30 11 0.38
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (29 bp):
TTTATTTTTATATTATAGTTAAATAAATT
Found at i:3870919 original size:31 final size:31
Alignment explanation
Indices: 3870859--3870937 Score: 76
Period size: 31 Copynumber: 2.6 Consensus size: 31
3870849 AATAATTAAT
* *
3870859 TATA-AAAATTTATTTAATTTAAAATAAAAA
1 TATATAAATTTTATTAAATTTAAAATAAAAA
*
3870889 TATATAAATTTTATTAAATATTATAA-AAAAA
1 TATATAAATTTTATTAAAT-TTAAAATAAAAA
3870920 TA-ATTAAAATTTT-TTAAA
1 TATA-T-AAATTTTATTAAA
3870938 AAACTATACT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
30 5 0.12
31 25 0.60
32 12 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
TATATAAATTTTATTAAATTTAAAATAAAAA
Found at i:3883701 original size:1 final size:1
Alignment explanation
Indices: 3883695--3883723 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
3883685 AGTAGGACCA
3883695 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
3883724 TCTTCCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:3886541 original size:24 final size:23
Alignment explanation
Indices: 3886514--3886564 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
3886504 TAATGAACAA
3886514 ATTTAAAAAAATTTTAAAATATTT
1 ATTTAAAAAAATTTT-AAATATTT
* * *
3886538 ATTTAGAAAGATTTTAAATTTTT
1 ATTTAAAAAAATTTTAAATATTT
3886561 ATTT
1 ATTT
3886565 TGATATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
ATTTAAAAAAATTTTAAATATTT
Found at i:3901165 original size:12 final size:12
Alignment explanation
Indices: 3901148--3901188 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
3901138 TTCAAGCTGG
3901148 AAAAAATTCAAA
1 AAAAAATTCAAA
3901160 AAAAAATTCAAA
1 AAAAAATTCAAA
*
3901172 AAAAAACT-AAA
1 AAAAAATTCAAA
3901183 AAAAAA
1 AAAAAA
3901189 GAACTTAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAAATTCAAA
Found at i:3901961 original size:14 final size:14
Alignment explanation
Indices: 3901942--3901970 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3901932 CAAAAATTAT
3901942 AACTTATAAAAAAA
1 AACTTATAAAAAAA
3901956 AACTTATAAAAAAA
1 AACTTATAAAAAAA
3901970 A
1 A
3901971 TTATCAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AACTTATAAAAAAA
Found at i:3903017 original size:21 final size:21
Alignment explanation
Indices: 3902969--3903126 Score: 79
Period size: 21 Copynumber: 7.3 Consensus size: 21
3902959 TAGTAAATTA
3902969 AATTTTAAAATTTAATGAATC
1 AATTTTAAAATTTAATGAATC
* * *
3902990 AACTTTAAGATTTGATGAA-C
1 AATTTTAAAATTTAATGAATC
* *
3903010 AGATTTTATAATATT-GTGAATCC
1 A-ATTTTAAAAT-TTAATGAAT-C
* ** * *
3903033 ATTTTATAAAAGTTGGATGGATT
1 AATTT-TAAAA-TTTAATGAATC
* * * * *
3903056 GATATTGAGAATTTTATGAATT
1 AAT-TTTAAAATTTAATGAATC
*
3903078 AATTTTAAAGTTTAATGAA-C
1 AATTTTAAAATTTAATGAATC
3903098 AAATTTTAAAATTTAATGAATC
1 -AATTTTAAAATTTAATGAATC
*
3903120 AGTTTTA
1 AATTTTA
3903127 GGATTTTATG
Statistics
Matches: 99, Mismatches: 28, Indels: 20
0.67 0.19 0.14
Matches are distributed among these distances:
20 2 0.02
21 63 0.64
22 16 0.16
23 11 0.11
24 7 0.07
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.42
Consensus pattern (21 bp):
AATTTTAAAATTTAATGAATC
Found at i:3904503 original size:29 final size:29
Alignment explanation
Indices: 3904436--3904505 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
3904426 TAAGAGAAAT
* **
3904436 TATACATGAACAAATACAAAAGAAAAAGT
1 TATATATGAACAAATACAAAAGAAAAAAA
*
3904465 TGTATATGAACAAATACAAGAA-AAAAAAA
1 TATATATGAACAAATACAA-AAGAAAAAAA
*
3904494 TATATGTGAACA
1 TATATATGAACA
3904506 GGTACTCAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 32 0.94
30 2 0.06
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (29 bp):
TATATATGAACAAATACAAAAGAAAAAAA
Found at i:3905268 original size:17 final size:18
Alignment explanation
Indices: 3905235--3905270 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 18
3905225 TTTCATTTTA
3905235 TTTTGTTCTTATCTTCTC
1 TTTTGTTCTTATCTTCTC
3905253 TTTT-TTCTT-TCTT-TC
1 TTTTGTTCTTATCTTCTC
3905268 TTT
1 TTT
3905271 CTTTGCATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.28
16 4 0.22
17 5 0.28
18 4 0.22
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTTGTTCTTATCTTCTC
Found at i:3911804 original size:2 final size:2
Alignment explanation
Indices: 3911799--3911830 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3911789 GGAGAGACAC
3911799 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3911831 GAGGTATAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3918169 original size:16 final size:17
Alignment explanation
Indices: 3918139--3918170 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3918129 AATTTTTAAA
3918139 ATATATTTTTAATTATC
1 ATATATTTTTAATTATC
3918156 ATATATTTTT-ATTAT
1 ATATATTTTTAATTAT
3918171 GATTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATATTTTTAATTATC
Found at i:3938935 original size:18 final size:18
Alignment explanation
Indices: 3938912--3938946 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3938902 GATAGCCATC
3938912 GATGGCGACGATGACAAT
1 GATGGCGACGATGACAAT
3938930 GATGGCGACGATGACAA
1 GATGGCGACGATGACAA
3938947 AAGGGAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.17, G:0.34, T:0.14
Consensus pattern (18 bp):
GATGGCGACGATGACAAT
Found at i:3940030 original size:16 final size:17
Alignment explanation
Indices: 3939996--3940034 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
3939986 TTTCTCATTT
*
3939996 CTATTTATATTATTTAA
1 CTATTTATATTAGTTAA
3940013 CTATTTATA-TAGTTAA
1 CTATTTATATTAGTTAA
3940029 CTATTT
1 CTATTT
3940035 TGCAAAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (17 bp):
CTATTTATATTAGTTAA
Found at i:3940101 original size:14 final size:13
Alignment explanation
Indices: 3940062--3940109 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
3940052 GATATTTAAC
3940062 TATTTATATTTTA
1 TATTTATATTTTA
*
3940075 TACATTATAATTTTA
1 TA-TTTAT-ATTTTA
3940090 TATTTAATATTTTA
1 TATTT-ATATTTTA
*
3940104 AATTTA
1 TATTTA
3940110 AATAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 3 0.10
14 16 0.55
15 10 0.34
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTATATTTTA
Found at i:3945440 original size:29 final size:29
Alignment explanation
Indices: 3945389--3945466 Score: 115
Period size: 29 Copynumber: 2.7 Consensus size: 29
3945379 GTAGGGATCC
3945389 AATTATAAA-TTTTTAAAAAAT-AAAAAA
1 AATTATAAATTTTTTAAAAAATAAAAAAA
*
3945416 AATTATAAATTTTTTTCAAAAATAAAAAAA
1 AATTATAAA-TTTTTTAAAAAATAAAAAAA
*
3945446 AATTATAAAATTTTTAAAAAA
1 AATTATAAATTTTTTAAAAAA
3945467 ATTAACCCCC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
27 9 0.20
29 21 0.47
30 15 0.33
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (29 bp):
AATTATAAATTTTTTAAAAAATAAAAAAA
Found at i:3946091 original size:14 final size:13
Alignment explanation
Indices: 3946068--3946130 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 13
3946058 TATTTCTATT
*
3946068 TAAATTTAAAATA
1 TAAATATAAAATA
3946081 CTAAATATAAAACTA
1 -TAAATATAAAA-TA
*
3946096 TAATGTATAAAATA
1 TAA-ATATAAAATA
*
3946110 TAAATAGTTAAATA
1 TAAATA-TAAAATA
3946124 T-AATATA
1 TAAATATA
3946131 TCTAACTAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
12 1 0.02
13 6 0.15
14 25 0.61
15 9 0.22
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (13 bp):
TAAATATAAAATA
Found at i:3946495 original size:2 final size:2
Alignment explanation
Indices: 3946488--3946535 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
3946478 NNNNNNNNNN
3946488 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3946530 A- AT AT A
1 AT AT AT A
3946536 AAAATTTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3946957 original size:18 final size:18
Alignment explanation
Indices: 3946936--3946986 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
3946926 ACATAAATTT
3946936 TAAAAAATTTTTTTTAAA
1 TAAAAAATTTTTTTTAAA
*
3946954 TAAAGTAATTTTTTTTAAA
1 TAAA-AAATTTTTTTTAAA
* *
3946973 GAATAAATTTTTTT
1 TAAAAAATTTTTTT
3946987 ATTAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (18 bp):
TAAAAAATTTTTTTTAAA
Found at i:3947676 original size:18 final size:18
Alignment explanation
Indices: 3947655--3947692 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3947645 TTTTAAAAAG
3947655 TTTTAAAATTTTATAATT
1 TTTTAAAATTTTATAATT
* *
3947673 TTTTATAATTTTATAGTT
1 TTTTAAAATTTTATAATT
3947691 TT
1 TT
3947693 ATCTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTAAAATTTTATAATT
Found at i:3948160 original size:22 final size:22
Alignment explanation
Indices: 3948120--3948161 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3948110 GCTATGCTCT
**
3948120 GATTTCTCTTTCCCGCATTTCA
1 GATTTCTCTTTCCAACATTTCA
*
3948142 GATTTCTCTTTCTAACATTT
1 GATTTCTCTTTCCAACATTT
3948162 TCAAGACACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.17, C:0.26, G:0.07, T:0.50
Consensus pattern (22 bp):
GATTTCTCTTTCCAACATTTCA
Found at i:3948558 original size:28 final size:28
Alignment explanation
Indices: 3948515--3948586 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
3948505 TAGTTTGTAA
* *
3948515 GTAACAACAACA-TTTT-AAGTATTAAAGT
1 GTAACAACAATATTTTTGAA-TATGAAA-T
*
3948543 GTAACAA-AATATTTTTGAATATGACAT
1 GTAACAACAATATTTTTGAATATGAAAT
3948570 GTAACAACAATATTTTT
1 GTAACAACAATATTTTT
3948587 TTAACATGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 11 0.29
28 25 0.66
29 2 0.05
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (28 bp):
GTAACAACAATATTTTTGAATATGAAAT
Found at i:3948601 original size:29 final size:29
Alignment explanation
Indices: 3948541--3948617 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
3948531 AAGTATTAAA
* *
3948541 GTGTAACAA-AATA-TTTTTGAATATGAC
1 GTGTAACAACAATATTTTTTTAACATGAC
* *
3948568 ATGTAACAACAATATTTTTTTAACATGGC
1 GTGTAACAACAATATTTTTTTAACATGAC
*
3948597 GTGTAACAACAGTATTTTTTT
1 GTGTAACAACAATATTTTTTT
3948618 TTTCAATATG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 8 0.19
28 4 0.10
29 30 0.71
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (29 bp):
GTGTAACAACAATATTTTTTTAACATGAC
Found at i:3948724 original size:45 final size:45
Alignment explanation
Indices: 3948631--3948727 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 45
3948621 CAATATGGTA
* *
3948631 TGTAACAACCTAACTATAACGTGTCACATGTTTTTGCATATGATG
1 TGTAACAACCTAACCATAACGTGTCACATATTTTTGCATATGATG
* *
3948676 TGTAACAACCTAACCATGAGGTGTCACATATTTTTGTACATA-GA-G
1 TGTAACAACCTAACCATAACGTGTCACATATTTTTG--CATATGATG
3948721 TGTAACA
1 TGTAACA
3948728 TGTTTTTGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
45 40 0.87
46 2 0.04
47 4 0.09
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (45 bp):
TGTAACAACCTAACCATAACGTGTCACATATTTTTGCATATGATG
Found at i:3948778 original size:68 final size:68
Alignment explanation
Indices: 3948678--3948805 Score: 195
Period size: 68 Copynumber: 1.9 Consensus size: 68
3948668 ATATGATGTG
* *
3948678 TAACAACCTAACCATGAGGTGTCACATATTTTTGTACATAG-AGTGTAACATGTTTTTGTACATG
1 TAACAACCTAACCATGACGTGTAACATATTTTTGTACATAGCA-TGTAACATGTTTTTGTACATG
3948742 GCGA
65 GCGA
* * *
3948746 TAACAACCTAAGCATGTCGTGTAACATGTTTTTGTACATAGCATGTAACATGTTTTTGTA
1 TAACAACCTAACCATGACGTGTAACATATTTTTGTACATAGCATGTAACATGTTTTTGTA
3948806 TATAATGTGT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 53 0.98
69 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (68 bp):
TAACAACCTAACCATGACGTGTAACATATTTTTGTACATAGCATGTAACATGTTTTTGTACATGG
CGA
Found at i:3948797 original size:24 final size:24
Alignment explanation
Indices: 3948765--3948843 Score: 95
Period size: 24 Copynumber: 3.3 Consensus size: 24
3948755 AAGCATGTCG
*
3948765 TGTAACATGTTTTTGTACATAGCA
1 TGTAACATGTTTTTGTACATAACA
* **
3948789 TGTAACATGTTTTTGTATATAATG
1 TGTAACATGTTTTTGTACATAACA
* * *
3948813 TGTAATATGTTTTTGTACATGACG
1 TGTAACATGTTTTTGTACATAACA
3948837 TGTAACA
1 TGTAACA
3948844 ACCTAACCAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (24 bp):
TGTAACATGTTTTTGTACATAACA
Found at i:3948873 original size:93 final size:92
Alignment explanation
Indices: 3948701--3948874 Score: 260
Period size: 92 Copynumber: 1.9 Consensus size: 92
3948691 ATGAGGTGTC
* * *
3948701 ACATATTTTTGTACATAGAGTGTAACATGTTTTTGTACATGGCGATAACAACCTAAGCATGTCGT
1 ACATATTTTTGTACATAGAGTGTAACATGTTTTTGTACATGACGATAACAACCTAACCATGACGT
3948766 GTAACATGTTTTTGTACATAGCATGTA
66 GTAACATGTTTTTGTACATAGCATGTA
* * * *
3948793 ACATGTTTTTGTATATA-ATGTGTAATATGTTTTTGTACATGACGTGTAACAACCTAACCATGAC
1 ACATATTTTTGTACATAGA-GTGTAACATGTTTTTGTACATGACG-ATAACAACCTAACCATGAC
3948857 GTGTAACATGTTTTTGTA
64 GTGTAACATGTTTTTGTA
3948875 TATGGTGTGT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
91 1 0.01
92 38 0.52
93 34 0.47
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (92 bp):
ACATATTTTTGTACATAGAGTGTAACATGTTTTTGTACATGACGATAACAACCTAACCATGACGT
GTAACATGTTTTTGTACATAGCATGTA
Found at i:3969905 original size:2 final size:2
Alignment explanation
Indices: 3969893--3969925 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3969883 AACTTAGTAC
*
3969893 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3969926 GACATATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 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):
TA
Found at i:3982578 original size:15 final size:15
Alignment explanation
Indices: 3982548--3982576 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3982538 TTTTTACTTT
3982548 TAAAAAATAAATAAA
1 TAAAAAATAAATAAA
3982563 TAAAAAA-AAATAAA
1 TAAAAAATAAATAAA
3982577 ATCAAACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAAAATAAATAAA
Found at i:3991622 original size:25 final size:24
Alignment explanation
Indices: 3991576--3991622 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
3991566 TATGTTGAAA
* *
3991576 AAAATTTAAAATTTTTATAAATGT
1 AAAATTTAAAATTTTAAAAAATGT
3991600 AAAATTATAAAATTTTAAAAAAT
1 AAAATT-TAAAATTTTAAAAAAT
3991623 AAGAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
AAAATTTAAAATTTTAAAAAATGT
Found at i:3992622 original size:16 final size:16
Alignment explanation
Indices: 3992601--3992631 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3992591 TTTTATTTTA
3992601 AATTAATTATAATTAT
1 AATTAATTATAATTAT
*
3992617 AATTAATTATTATTA
1 AATTAATTATAATTA
3992632 ATTAAAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTAATTATAATTAT
Found at i:3993575 original size:18 final size:21
Alignment explanation
Indices: 3993531--3993575 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
3993521 AATTTTAAGT
*
3993531 AATATTTAAAAAGATATTTGA
1 AATATTCAAAAAGATATTTGA
*
3993552 ATTATTCAAAAA-AT-TTT-A
1 AATATTCAAAAAGATATTTGA
3993570 AATATT
1 AATATT
3993576 TTTTTATTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.29
19 3 0.14
20 2 0.10
21 10 0.48
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (21 bp):
AATATTCAAAAAGATATTTGA
Found at i:4043758 original size:28 final size:29
Alignment explanation
Indices: 4043715--4043774 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
4043705 ATTTTTGGTC
*
4043715 TTGGTATATAACATCTGCTGCTGAAG-TT
1 TTGGTATATAACATCTGCTGATGAAGCTT
* * *
4043743 TTGGTATGTAATATCTGGTGATGAAGCTT
1 TTGGTATATAACATCTGCTGATGAAGCTT
4043772 TTG
1 TTG
4043775 CCTTAGCACG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (29 bp):
TTGGTATATAACATCTGCTGATGAAGCTT
Found at i:4047445 original size:2 final size:2
Alignment explanation
Indices: 4047438--4047482 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
4047428 TGTTTGTTAC
4047438 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4047480 AT A
1 AT A
4047483 CACATGTTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4070434 original size:15 final size:15
Alignment explanation
Indices: 4070414--4070443 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4070404 TTCAATTTAT
4070414 AATAATAAATAATTA
1 AATAATAAATAATTA
4070429 AATAATAAATAATTA
1 AATAATAAATAATTA
4070444 TTCTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAATAAATAATTA
Found at i:4071776 original size:13 final size:13
Alignment explanation
Indices: 4071758--4071796 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
4071748 ATGCAAAGTC
*
4071758 GAATGTTTCGATT
1 GAATGTTTTGATT
4071771 GAATGTTTTGATT
1 GAATGTTTTGATT
4071784 GAATGTTTTGATT
1 GAATGTTTTGATT
4071797 AAATAATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.23, T:0.51
Consensus pattern (13 bp):
GAATGTTTTGATT
Found at i:4092523 original size:15 final size:15
Alignment explanation
Indices: 4092498--4092531 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4092488 TATATATTTT
4092498 TATTTTAAATTAAATA
1 TATTTTAAATTAAA-A
4092514 TATTTT-AATTAAAA
1 TATTTTAAATTAAAA
4092528 TATT
1 TATT
4092532 ACTTGTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 7 0.39
16 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTTAAATTAAAA
Found at i:4093524 original size:35 final size:35
Alignment explanation
Indices: 4093478--4093575 Score: 196
Period size: 35 Copynumber: 2.8 Consensus size: 35
4093468 TTAAAAAATA
4093478 TTATTAAATTATAATAATGAGTAATTTTGTTTAAT
1 TTATTAAATTATAATAATGAGTAATTTTGTTTAAT
4093513 TTATTAAATTATAATAATGAGTAATTTTGTTTAAT
1 TTATTAAATTATAATAATGAGTAATTTTGTTTAAT
4093548 TTATTAAATTATAATAATGAGTAATTTT
1 TTATTAAATTATAATAATGAGTAATTTT
4093576 ATCATTTTAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (35 bp):
TTATTAAATTATAATAATGAGTAATTTTGTTTAAT
Found at i:4108539 original size:2 final size:2
Alignment explanation
Indices: 4108522--4108559 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
4108512 GAACCCTTTT
* *
4108522 TA TA TT TA TG 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
4108560 AAGATAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4115314 original size:29 final size:30
Alignment explanation
Indices: 4115269--4115325 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
4115259 ATATTTAATT
*
4115269 AAATTTTTATATTTTAATT-TTAAATTAAAC
1 AAATTTTTATATATTAATTATT-AATTAAAC
4115299 AAATTTTTATA-ATTAATTATTAATTAA
1 AAATTTTTATATATTAATTATTAATTAA
4115326 TATGATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (30 bp):
AAATTTTTATATATTAATTATTAATTAAAC
Found at i:4115560 original size:18 final size:17
Alignment explanation
Indices: 4115534--4115570 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
4115524 AATTTTAAAA
4115534 TTTTAAAAAAATATTATT
1 TTTTAAAAAAATA-TATT
*
4115552 TTTTTAAAAAATATATT
1 TTTTAAAAAAATATATT
4115569 TT
1 TT
4115571 AATGATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTAAAAAAATATATT
Found at i:4118337 original size:2 final size:2
Alignment explanation
Indices: 4118332--4118358 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4118322 AAATTTGACA
4118332 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4118359 CTATTCCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4119886 original size:27 final size:27
Alignment explanation
Indices: 4119851--4120068 Score: 140
Period size: 27 Copynumber: 8.0 Consensus size: 27
4119841 TATTCTAAGA
*
4119851 ATACGTTTACCCA-CTAGAGATGGATGG
1 ATACCTTTACCCATC-AGAGATGGATGG
* *
4119878 ATACTTTTACTCA-CTAGAGATGGATGG
1 ATACCTTTACCCATC-AGAGATGGATGG
* * *
4119905 ATACCTTTACTCATCAGAGGTGGATGA
1 ATACCTTTACCCATCAGAGATGGATGG
* *
4119932 ATACCTTTACCTATCAGA-AGTGAATGG
1 ATACCTTTACCCATCAGAGA-TGGATGG
* * **
4119959 CTACCTTTA-CCATCAGAGGTGGATAT
1 ATACCTTTACCCATCAGAGATGGATGG
* * *
4119985 ATACTTTTTACCCATCAGAGGTGGATAG
1 ATAC-CTTTACCCATCAGAGATGGATGG
* * * *
4120013 ATACCCTTTACTCACTAAAAG-TGAATGG
1 ATA-CCTTTACCCA-TCAGAGATGGATGG
* * * *
4120041 ATACTTTTACCCATAAGAGGTAGATGG
1 ATACCTTTACCCATCAGAGATGGATGG
4120068 A
1 A
4120069 AAGCGAAGCG
Statistics
Matches: 153, Mismatches: 30, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
26 19 0.12
27 94 0.61
28 35 0.23
29 5 0.03
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (27 bp):
ATACCTTTACCCATCAGAGATGGATGG
Found at i:4119929 original size:54 final size:53
Alignment explanation
Indices: 4119866--4120051 Score: 164
Period size: 54 Copynumber: 3.4 Consensus size: 53
4119856 TTTACCCACT
*
4119866 AGAGATGGATGGATACTTTTACTCA-CTAGAGATGGATGGATACCTTTACTCATC
1 AGAGGTGGATGGATACTTTTAC-CATC-AGAGATGGATGGATACCTTTACTCATC
* * * *
4119920 AGAGGTGGATGAATACCTTTACCTATCAGA-AGTGAATGGCTACCTTTAC-CATC
1 AGAGGTGGATGGATACTTTTACC-ATCAGAGA-TGGATGGATACCTTTACTCATC
** * *
4119973 AGAGGTGGATATATACTTTTTACCCATCAGAGGTGGATAGATACCCTTTACTCA-C
1 AGAGGTGGATGGATAC-TTTTA-CCATCAGAGATGGATGGATA-CCTTTACTCATC
* * *
4120028 TAAAAGTGAATGGATACTTTTACC
1 -AGAGGTGGATGGATACTTTTACC
4120052 CATAAGAGGT
Statistics
Matches: 106, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
53 20 0.19
54 57 0.54
55 16 0.15
56 13 0.12
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (53 bp):
AGAGGTGGATGGATACTTTTACCATCAGAGATGGATGGATACCTTTACTCATC
Found at i:4138504 original size:39 final size:39
Alignment explanation
Indices: 4138461--4138536 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
4138451 TATTTGAGTT
*
4138461 TTTAACTTATT-AGTTGATATATAATATTTTATCTAAACA
1 TTTAACTTATTGA-TTGATACATAATATTTTATCTAAACA
* * * *
4138500 TTTAATTTATTGATTGATGCATAATTTTTTATTTAAA
1 TTTAACTTATTGATTGATACATAATATTTTATCTAAA
4138537 AAATAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 30 0.97
40 1 0.03
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.53
Consensus pattern (39 bp):
TTTAACTTATTGATTGATACATAATATTTTATCTAAACA
Found at i:4139089 original size:30 final size:31
Alignment explanation
Indices: 4139048--4139106 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
4139038 CAAAAGTTTT
* *
4139048 AAAATTTTATAATTTTCT-TTTACTTTTTAA
1 AAAATTATATAATTTTATCTTTACTTTTTAA
4139078 AAAATTATATAATTTTATCTTTACTTTTT
1 AAAATTATATAATTTTATCTTTACTTTTT
4139107 CTTCAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (31 bp):
AAAATTATATAATTTTATCTTTACTTTTTAA
Found at i:4139122 original size:33 final size:30
Alignment explanation
Indices: 4139048--4139134 Score: 102
Period size: 33 Copynumber: 2.8 Consensus size: 30
4139038 CAAAAGTTTT
*
4139048 AAAATTTTATAATTTTCTTTTACTTTTTAA
1 AAAATTTTATAATTTTATTTTACTTTTTAA
* **
4139078 AAAATTATATAATTTTATCTTTACTTTTTCTTC
1 AAAATTTTATAATTTTAT-TTTAC-TTTT-TAA
4139111 AAAATTTTATAATTTTATTCTTAC
1 AAAATTTTATAATTTTATT-TTAC
4139135 AAATGTAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
30 16 0.33
31 5 0.10
32 5 0.10
33 22 0.46
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.57
Consensus pattern (30 bp):
AAAATTTTATAATTTTATTTTACTTTTTAA
Found at i:4141772 original size:30 final size:30
Alignment explanation
Indices: 4141733--4141791 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
4141723 GCAAACGTGG
4141733 AAAACTAATACTCATCAGATTTGTCTGTTA
1 AAAACTAATACTCATCAGATTTGTCTGTTA
* * *
4141763 AAAATTAATAGTCATCAGATTTGTTTGTT
1 AAAACTAATACTCATCAGATTTGTCTGTT
4141792 TGTGTGTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (30 bp):
AAAACTAATACTCATCAGATTTGTCTGTTA
Found at i:4149073 original size:14 final size:14
Alignment explanation
Indices: 4149054--4149083 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4149044 AACAAAATTT
4149054 AAAAAAAAAACTCA
1 AAAAAAAAAACTCA
4149068 AAAAAAAAAACTCA
1 AAAAAAAAAACTCA
4149082 AA
1 AA
4149084 GAATGAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.80, C:0.13, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAAAAAAAACTCA
Found at i:4152444 original size:2 final size:2
Alignment explanation
Indices: 4152437--4152470 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4152427 TAGTAGTAAG
4152437 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4152471 CCAAGTTGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4159448 original size:3 final size:3
Alignment explanation
Indices: 4159434--4159485 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
4159424 TGGGGATAGG
* * * * * *
4159434 GAA GAG GAA GAA GAA GAA GAT GAT GAT GAA GAG GAA GAT GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
4159482 GAA G
1 GAA G
4159486 TTGATGAAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.54, C:0.00, G:0.38, T:0.08
Consensus pattern (3 bp):
GAA
Found at i:4159464 original size:15 final size:15
Alignment explanation
Indices: 4159446--4159495 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
4159436 AGAGGAAGAA
*
4159446 GAAGAAGATGATGAT
1 GAAGAAGAAGATGAT
* *
4159461 GAAGAGGAAGATGAA
1 GAAGAAGAAGATGAT
*
4159476 GAAGAAGAAGTTGAT
1 GAAGAAGAAGATGAT
4159491 GAAGA
1 GAAGA
4159496 CAATGAAGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.50, C:0.00, G:0.36, T:0.14
Consensus pattern (15 bp):
GAAGAAGAAGATGAT
Found at i:4159466 original size:27 final size:28
Alignment explanation
Indices: 4159434--4159511 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 28
4159424 TGGGGATAGG
4159434 GAAGAGGAA-GAAGAAGAAGATGATGAT
1 GAAGAGGAATGAAGAAGAAGATGATGAT
* *
4159461 GAAGAGGAAGATGAAGAAGAAGAAGTTGAT
1 GAAGAGG-A-ATGAAGAAGAAGATGATGAT
*
4159491 GAAGA-CAATGAAGAAGAAGAT
1 GAAGAGGAATGAAGAAGAAGAT
4159512 AGCGATGAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
27 20 0.45
28 2 0.05
29 1 0.02
30 21 0.48
ACGTcount: A:0.53, C:0.01, G:0.35, T:0.12
Consensus pattern (28 bp):
GAAGAGGAATGAAGAAGAAGATGATGAT
Found at i:4159491 original size:18 final size:17
Alignment explanation
Indices: 4159440--4159495 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
4159430 TAGGGAAGAG
4159440 GAAGAAGAAGAAGATGAT
1 GAAGAAGAAGAAG-TGAT
* *
4159458 GATGAAGAGGAA--GAT
1 GAAGAAGAAGAAGTGAT
4159473 GAAGAAGAAGAAGTTGAT
1 GAAGAAGAAGAAG-TGAT
4159491 GAAGA
1 GAAGA
4159496 CAATGAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 13 0.42
18 18 0.58
ACGTcount: A:0.52, C:0.00, G:0.36, T:0.12
Consensus pattern (17 bp):
GAAGAAGAAGAAGTGAT
Found at i:4163493 original size:2 final size:2
Alignment explanation
Indices: 4163486--4163513 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4163476 TTTCAGATTC
4163486 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
4163514 TTCAATTTAT
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:4173951 original size:44 final size:44
Alignment explanation
Indices: 4173836--4174100 Score: 329
Period size: 44 Copynumber: 6.0 Consensus size: 44
4173826 ATGCAGTAGA
* * *
4173836 ATATATTTTATTATCTAGTTGAAT-TCAACTAGACTCATTTAGGA
1 ATATATTTTGTTATCTAGTTG-ATCTCAACTAGGCTCATTTAGGT
* *
4173880 ATATA-TTTGTTATTTAGTTGAACTCAACTAGGCTCATTTAGGT
1 ATATATTTTGTTATCTAGTTGATCTCAACTAGGCTCATTTAGGT
*
4173923 ATATATTTTGTTATCTAGTTGATTTCAACTAGGCAT-ATTTAGGT
1 ATATATTTTGTTATCTAGTTGATCTCAACTAGGC-TCATTTAGGT
* * *
4173967 ATATATTTTATAATCTTGTTGATCTCAACTAGGCTCATTTAGGT
1 ATATATTTTGTTATCTAGTTGATCTCAACTAGGCTCATTTAGGT
* *
4174011 ATATATTTTGTTATCTATAGTTGATCTCAACTAGACTCACTTAGGT
1 ATATATTTTGTTATC--TAGTTGATCTCAACTAGGCTCATTTAGGT
* * * * *
4174057 ATATATTTTGTTATCTAGTTAATCTTAATTAGACTCGTTTAGGT
1 ATATATTTTGTTATCTAGTTGATCTCAACTAGGCTCATTTAGGT
4174101 TCTATATATA
Statistics
Matches: 193, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.01
43 37 0.19
44 113 0.59
45 1 0.01
46 41 0.21
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.46
Consensus pattern (44 bp):
ATATATTTTGTTATCTAGTTGATCTCAACTAGGCTCATTTAGGT
Found at i:4174020 original size:88 final size:86
Alignment explanation
Indices: 4173836--4174065 Score: 320
Period size: 87 Copynumber: 2.6 Consensus size: 86
4173826 ATGCAGTAGA
* * *
4173836 ATATATTTTATTATCTAGTTGAATTCAACTAGACTCATTTAGGAATATATTTGTTATTTAGTTGA
1 ATATATTTTGTTATCTAGTTGATTTCAACTAGACTCATTTAGGTATATATTT-TTATTTAGTTGA
4173901 ACTCAACTAGGCTCATTTAGGT
65 ACTCAACTAGGCTCATTTAGGT
*
4173923 ATATATTTTGTTATCTAGTTGATTTCAACTAGGCAT-ATTTAGGTATATATTTTATAATCTT-GT
1 ATATATTTTGTTATCTAGTTGATTTCAACTAGAC-TCATTTAGGTATATATTTT-T-AT-TTAGT
*
4173986 TGATCTCAACTAGGCTCATTTAGGT
62 TGAACTCAACTAGGCTCATTTAGGT
* *
4174011 ATATATTTTGTTATCTATAGTTGATCTCAACTAGACTCACTTAGGTATATATTTT
1 ATATATTTTGTTATC--TAGTTGATTTCAACTAGACTCATTTAGGTATATATTTT
4174066 GTTATCTAGT
Statistics
Matches: 128, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
86 1 0.01
87 47 0.37
88 44 0.34
89 3 0.02
90 33 0.26
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (86 bp):
ATATATTTTGTTATCTAGTTGATTTCAACTAGACTCATTTAGGTATATATTTTTATTTAGTTGAA
CTCAACTAGGCTCATTTAGGT
Found at i:4174098 original size:90 final size:87
Alignment explanation
Indices: 4173836--4174100 Score: 329
Period size: 90 Copynumber: 3.0 Consensus size: 87
4173826 ATGCAGTAGA
* * *
4173836 ATATATTTTATTATCTAGTTGAATTCAACTAGACTCATTTAGGAATATA-TTTGTTATTTAGTTG
1 ATATATTTTGTTATCTAGTTG-ATTCAACTAGACTCATTTAGGTATATATTTTGTTATCTAGTT-
4173900 AA-CTCAACTAGGCTCATTTAGGT
64 AATCTCAACTAGGCTCATTTAGGT
* * * *
4173923 ATATATTTTGTTATCTAGTTGATTTCAACTAGGCAT-ATTTAGGTATATATTTTATAATCTTGTT
1 ATATATTTTGTTATCTAGTTGA-TTCAACTAGAC-TCATTTAGGTATATATTTTGTTATCTAGTT
*
4173987 GATCTCAACTAGGCTCATTTAGGT
64 AATCTCAACTAGGCTCATTTAGGT
*
4174011 ATATATTTTGTTATCTATAGTTGATCTCAACTAGACTCACTTAGGTATATATTTTGTTATCTAGT
1 ATATATTTTGTTATC--TAGTTGAT-TCAACTAGACTCATTTAGGTATATATTTTGTTATCTAGT
* * * *
4174076 TAATCTTAATTAGACTCGTTTAGGT
63 TAATCTCAACTAGGCTCATTTAGGT
4174101 TCTATATATA
Statistics
Matches: 152, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
86 1 0.01
87 43 0.28
88 47 0.31
89 2 0.01
90 59 0.39
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.46
Consensus pattern (87 bp):
ATATATTTTGTTATCTAGTTGATTCAACTAGACTCATTTAGGTATATATTTTGTTATCTAGTTAA
TCTCAACTAGGCTCATTTAGGT
Found at i:4174100 original size:134 final size:131
Alignment explanation
Indices: 4173836--4174079 Score: 364
Period size: 134 Copynumber: 1.8 Consensus size: 131
4173826 ATGCAGTAGA
*
4173836 ATATATTTTATTATCTAGTTGAATTCAACTAGACTCATTTAGGAATATATTTGTTATTTAGTTGA
1 ATATATTTTATAATCTAGTTGAATTCAACTAGACTCATTTAGGAATATATTTGTTATTTAGTTGA
* * * *
4173901 ACTCAACTAGGCTCATTTAGGTATATATTTTGTTATCTAGTTGATTTCAACTAGGCATATTTAGG
66 ACTCAACTAGACTCACTTAGGTATATATTTTGTTATCTAGTTAATTTCAACTAGACATATTTAGG
4173966 T
131 T
* * *
4173967 ATATATTTTATAATCTTGTTG-ATCTCAACTAGGCTCATTTAGGTATATATTTTGTTATCTATAG
1 ATATATTTTATAATCTAGTTGAAT-TCAACTAGACTCATTTAGGAATATA-TTTGTTAT-T-TAG
*
4174031 TTGATCTCAACTAGACTCACTTAGGTATATATTTTGTTATCTAGTTAAT
62 TTGAACTCAACTAGACTCACTTAGGTATATATTTTGTTATCTAGTTAAT
4174080 CTTAATTAGA
Statistics
Matches: 101, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
130 2 0.02
131 42 0.42
132 8 0.08
133 1 0.01
134 48 0.48
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (131 bp):
ATATATTTTATAATCTAGTTGAATTCAACTAGACTCATTTAGGAATATATTTGTTATTTAGTTGA
ACTCAACTAGACTCACTTAGGTATATATTTTGTTATCTAGTTAATTTCAACTAGACATATTTAGG
T
Found at i:4174652 original size:12 final size:13
Alignment explanation
Indices: 4174626--4174654 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
4174616 TTCACATATT
4174626 GTGACAAATACTA
1 GTGACAAATACTA
4174639 GTGACAAA-ACTA
1 GTGACAAATACTA
4174651 GTGA
1 GTGA
4174655 TAATATTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.21
Consensus pattern (13 bp):
GTGACAAATACTA
Found at i:4175871 original size:2 final size:2
Alignment explanation
Indices: 4175864--4175909 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4175854 TGATCAAGAA
4175864 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4175906 AT AT
1 AT AT
4175910 GTAATTNNNN
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4200163 original size:20 final size:21
Alignment explanation
Indices: 4200138--4200184 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
4200128 AATGATATGA
*
4200138 TAATATATTGAATTCACG-AT
1 TAATATATAGAATTCACGTAT
* *
4200158 TAATATGTAGAATTTACGTAT
1 TAATATATAGAATTCACGTAT
4200179 TAATAT
1 TAATAT
4200185 TACATCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (21 bp):
TAATATATAGAATTCACGTAT
Found at i:4203091 original size:20 final size:20
Alignment explanation
Indices: 4203066--4203103 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
4203056 GTTGGCCCCA
4203066 TTTGACTTATTGAAGTATAG
1 TTTGACTTATTGAAGTATAG
*
4203086 TTTGACTTATTGGAGTAT
1 TTTGACTTATTGAAGTAT
4203104 GATTTTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.47
Consensus pattern (20 bp):
TTTGACTTATTGAAGTATAG
Found at i:4219232 original size:17 final size:17
Alignment explanation
Indices: 4219210--4219249 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
4219200 TAATTATATT
*
4219210 AAAATATATAAAAATTA
1 AAAATATATAAAAATAA
*
4219227 AAAATATATAAAAGTAA
1 AAAATATATAAAAATAA
4219244 AAAATA
1 AAAATA
4219250 ATTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
AAAATATATAAAAATAA
Found at i:4219244 original size:16 final size:17
Alignment explanation
Indices: 4219210--4219246 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
4219200 TAATTATATT
*
4219210 AAAATATATAAAAATTA
1 AAAATATATAAAAAGTA
4219227 AAAATATAT-AAAAGTA
1 AAAATATATAAAAAGTA
4219243 AAAA
1 AAAA
4219247 ATAATTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAAATATATAAAAAGTA
Found at i:4224768 original size:2 final size:2
Alignment explanation
Indices: 4224761--4224804 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4224751 CGTTTAACCT
4224761 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
4224803 TA
1 TA
4224805 CACACACAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4235505 original size:15 final size:15
Alignment explanation
Indices: 4235466--4235505 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
4235456 TTTATAATGC
*
4235466 AATATGATTATAAAT
1 AATATGATTGTAAAT
* *
4235481 AATGTGATTGTAAGT
1 AATATGATTGTAAAT
4235496 AATATGATTG
1 AATATGATTG
4235506 CAAAGAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.40
Consensus pattern (15 bp):
AATATGATTGTAAAT
Found at i:4236255 original size:2 final size:2
Alignment explanation
Indices: 4236248--4236277 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4236238 AACCCTTATC
*
4236248 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4236278 AGGTATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4264933 original size:39 final size:39
Alignment explanation
Indices: 4264879--4264955 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
4264869 TGACCGAGTA
4264879 AGGGCTTCAGTCATTCCAAACCTAATTGGCTTGCATTTG
1 AGGGCTTCAGTCATTCCAAACCTAATTGGCTTGCATTTG
4264918 AGGGCTTCAGTCATTCCAAACCTAATTGGCTTGCATTT
1 AGGGCTTCAGTCATTCCAAACCTAATTGGCTTGCATTT
4264956 AAGCAGTTCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (39 bp):
AGGGCTTCAGTCATTCCAAACCTAATTGGCTTGCATTTG
Found at i:4266355 original size:22 final size:22
Alignment explanation
Indices: 4266325--4266400 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 22
4266315 ATCTCTTAAA
4266325 TATATTTTTAATATCATATTTTT
1 TATATTTTTAATAT-ATATTTTT
*
4266348 T-TATTTTTATTATAATATTATATAT
1 TATATTTTTAATAT-ATATT-T-T-T
4266373 TATATTTTTTAATATA-ATTTTT
1 TATA-TTTTTAATATATATTTTT
4266395 TATATT
1 TATATT
4266401 ATATATTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
21 2 0.04
22 21 0.47
23 3 0.07
24 2 0.04
25 5 0.11
26 3 0.07
27 9 0.20
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (22 bp):
TATATTTTTAATATATATTTTT
Found at i:4266388 original size:12 final size:14
Alignment explanation
Indices: 4266368--4266423 Score: 64
Period size: 13 Copynumber: 4.1 Consensus size: 14
4266358 TATAATATTA
4266368 TATATTATATTTTT
1 TATATTATATTTTT
4266382 TA-A-TATAATTTTT
1 TATATTAT-ATTTTT
*
4266395 TATATTATATATTT
1 TATATTATATTTTT
*
4266409 TATTTTA-ATTTTT
1 TATATTATATTTTT
4266422 TA
1 TA
4266424 CTTATATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
12 3 0.08
13 16 0.44
14 14 0.39
15 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATATTATATTTTT
Found at i:4266418 original size:27 final size:27
Alignment explanation
Indices: 4266352--4266507 Score: 104
Period size: 27 Copynumber: 5.7 Consensus size: 27
4266342 ATTTTTTTAT
* * * *
4266352 TTTTATTATAATATTATATATTATATT
1 TTTTATTTTAATTTTTTATATTATATA
* *
4266379 TTTTAATATAATTTTTTATATTATATA
1 TTTTATTTTAATTTTTTATATTATATA
*
4266406 TTTTATTTTAATTTTTTA-CTTATATTA
1 TTTTATTTTAATTTTTTATATTATA-TA
** * *
4266433 TATAAAATTTAATTTCTTATATT-T-TA
1 T-TTTATTTTAATTTTTTATATTATATA
* * *
4266459 GTTTAATTTTTAA-TTCTTGTATTATATA
1 -TTTTA-TTTTAATTTTTTATATTATATA
4266487 TTTTATTTTAATATATTTTAT
1 TTTTATTTTAAT-T-TTTTAT
4266508 TTTAATTATA
Statistics
Matches: 101, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
26 25 0.25
27 53 0.52
28 17 0.17
29 6 0.06
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (27 bp):
TTTTATTTTAATTTTTTATATTATATA
Found at i:4266436 original size:48 final size:48
Alignment explanation
Indices: 4266384--4266514 Score: 133
Period size: 48 Copynumber: 2.7 Consensus size: 48
4266374 ATATTTTTTA
4266384 ATATAATTTTTTATATTATATATTTTATTTTAATTTTT-TACTTATATT
1 ATATAATTTTTTAT-TTATATATTTTATTTTAATTTTTATACTTATATT
** * * * * *
4266432 ATATAAAATTTAATTTCTTATATTTTAGTTTAATTTTTAATTCTTGTATT
1 ATATAATTTTTTATTT-ATATATTTTATTTTAATTTTT-ATACTTATATT
*
4266482 ATAT-ATTTTATT-TTAATATATTTTATTTTAATT
1 ATATAATTTT-TTATTTATATATTTTATTTTAATT
4266515 ATAATATTAT
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
47 2 0.03
48 46 0.70
49 5 0.08
50 13 0.20
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (48 bp):
ATATAATTTTTTATTTATATATTTTATTTTAATTTTTATACTTATATT
Found at i:4266502 original size:15 final size:15
Alignment explanation
Indices: 4266482--4266513 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4266472 TTCTTGTATT
4266482 ATATATTTTATTTTA
1 ATATATTTTATTTTA
4266497 ATATATTTTATTTTA
1 ATATATTTTATTTTA
4266512 AT
1 AT
4266514 TATAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:4272360 original size:20 final size:21
Alignment explanation
Indices: 4272322--4272360 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
4272312 ATATTTAAAG
* *
4272322 AAATTGTTAAATTATTTTTAA
1 AAATTGTTAAATAAATTTTAA
4272343 AAATT-TTAAATAAATTTT
1 AAATTGTTAAATAAATTTT
4272361 CATTCTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
AAATTGTTAAATAAATTTTAA
Found at i:4272661 original size:29 final size:30
Alignment explanation
Indices: 4272616--4272672 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
4272606 TTTGATTAAA
4272616 AATAAAAAATATAAAAATTTAATTGAATGT
1 AATAAAAAATATAAAAATTTAATTGAATGT
* *
4272646 AATATAAAA-ATAAAAATTTATTTGAAT
1 AATAAAAAATATAAAAATTTAATTGAAT
4272673 TTTTTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (30 bp):
AATAAAAAATATAAAAATTTAATTGAATGT
Found at i:4273053 original size:2 final size:2
Alignment explanation
Indices: 4273046--4273072 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4273036 CCCTTGAGTG
4273046 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4273073 GAAGAAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4273083 original size:2 final size:2
Alignment explanation
Indices: 4273078--4273110 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
4273068 ATATAGAAGA
4273078 AG AG AG AG AG AG AG AG NAG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG
4273111 GAAGAACTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4273100 original size:15 final size:14
Alignment explanation
Indices: 4273078--4273110 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
4273068 ATATAGAAGA
4273078 AGAGAGAGAGAGAG
1 AGAGAGAGAGAGAG
4273092 AGNAGAGAGAGAGAG
1 AG-AGAGAGAGAGAG
4273107 AGAG
1 AGAG
4273111 GAAGAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.00
Consensus pattern (14 bp):
AGAGAGAGAGAGAG
Found at i:4273100 original size:17 final size:16
Alignment explanation
Indices: 4273078--4273110 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
4273068 ATATAGAAGA
4273078 AGAGAGAGAGAGAGAG
1 AGAGAGAGAGAGAGAG
4273094 NAGAGAGAGAGAGAGAG
1 -AGAGAGAGAGAGAGAG
4273111 GAAGAACTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.00
Consensus pattern (16 bp):
AGAGAGAGAGAGAGAG
Found at i:4280738 original size:15 final size:16
Alignment explanation
Indices: 4280713--4280752 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
4280703 TTCTTAATAT
4280713 ATATATATATATATTA
1 ATATATATATATATTA
4280729 ATAT-TATATATATTA
1 ATATATATATATATTA
*
4280744 ACATATATA
1 ATATATATA
4280753 AAAAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATATATATATATTA
Found at i:4294792 original size:11 final size:11
Alignment explanation
Indices: 4294778--4294844 Score: 62
Period size: 11 Copynumber: 5.5 Consensus size: 11
4294768 ATTTTAATTT
4294778 TTAATAAAATA
1 TTAATAAAATA
4294789 TTAATATTAAATTA
1 TTAATA--AAA-TA
*
4294803 TAAATAAAATA
1 TTAATAAAATA
4294814 TTAATATTAAATTA
1 TTAATA--AAA-TA
*
4294828 TAAATAAAATA
1 TTAATAAAATA
4294839 TTAATA
1 TTAATA
4294845 TTTAAATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
11 20 0.43
12 6 0.13
13 6 0.13
14 14 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAATAAAATA
Found at i:4294808 original size:25 final size:25
Alignment explanation
Indices: 4294780--4294854 Score: 141
Period size: 25 Copynumber: 3.0 Consensus size: 25
4294770 TTTAATTTTT
4294780 AATAAAATATTAATATTAAATTATA
1 AATAAAATATTAATATTAAATTATA
4294805 AATAAAATATTAATATTAAATTATA
1 AATAAAATATTAATATTAAATTATA
4294830 AATAAAATATTAATATTTAAATTAT
1 AATAAAATATTAATA-TTAAATTAT
4294855 CAATTATTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 40 0.82
26 9 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATAAAATATTAATATTAAATTATA
Found at i:4294877 original size:27 final size:27
Alignment explanation
Indices: 4294841--4294972 Score: 69
Period size: 27 Copynumber: 5.0 Consensus size: 27
4294831 ATAAAATATT
*
4294841 AATATTTAAATTATCAATTATTAATAA
1 AATAATTAAATTATCAATTATTAATAA
*
4294868 AATAATTAAAAATAT-AA-TA--AACTAA
1 AATAATT-AAATTATCAATTATTAA-TAA
* * * ** *
4294893 TATCATTTAAATTAT--ATAAACAATATT
1 AAT-AATTAAATTATCAATTATTAATA-A
* *
4294920 AATAATTAAATCATCAATTATTAATAT
1 AATAATTAAATTATCAATTATTAATAA
** *
4294947 TTTAAATAAATTATCAATTATTAATA
1 AATAATTAAATTATCAATTATTAATA
4294973 TTAAAAAAAT
Statistics
Matches: 79, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
24 3 0.04
25 12 0.15
26 16 0.20
27 35 0.44
28 13 0.16
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (27 bp):
AATAATTAAATTATCAATTATTAATAA
Found at i:4295139 original size:18 final size:20
Alignment explanation
Indices: 4295111--4295168 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
4295101 AAAATTAATC
*
4295111 ATAATAATATTTATA-TTAA
1 ATAATAATATTAATATTTAA
4295130 ATAA-AATATTAATATTTAA
1 ATAATAATATTAATATTTAA
*
4295149 ATTATTAATAATTAATATTT
1 A-TAATAAT-ATTAATATTT
4295169 TAATTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 9 0.27
19 9 0.27
20 2 0.06
21 3 0.09
22 10 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAATAATATTAATATTTAA
Found at i:4295154 original size:15 final size:15
Alignment explanation
Indices: 4295131--4295198 Score: 57
Period size: 15 Copynumber: 4.3 Consensus size: 15
4295121 TTATATTAAA
*
4295131 TAAAATATTAATATT
1 TAAATTATTAATATT
*
4295146 TAAATTATTAATAAT
1 TAAATTATTAATATT
4295161 TAATATT-TTAATTAAATT
1 TAA-ATTATTAA-T--ATT
*
4295179 CTAGATTATTAATATT
1 -TAAATTATTAATATT
4295195 TAAA
1 TAAA
4295199 AATCTAATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
15 23 0.55
16 7 0.17
18 6 0.14
19 6 0.14
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (15 bp):
TAAATTATTAATATT
Found at i:4297276 original size:24 final size:24
Alignment explanation
Indices: 4297241--4297360 Score: 97
Period size: 24 Copynumber: 5.1 Consensus size: 24
4297231 AACCATGGCT
4297241 TGTCACAGATTTTTGTATATGACG
1 TGTCACAGATTTTTGTATATGACG
* * *
4297265 TGTCACATATTTTTGTACATGATG
1 TGTCACAGATTTTTGTATATGACG
* * *
4297289 TGTTACACG----TT-AATCATGACT
1 TGTCACA-GATTTTTGTAT-ATGACG
* * *
4297310 TGTCACAGGTTTTTGTACATAACG
1 TGTCACAGATTTTTGTATATGACG
*
4297334 TGTTACAGATTTTTGTATATGACG
1 TGTCACAGATTTTTGTATATGACG
4297358 TGT
1 TGT
4297361 AACACGCTAA
Statistics
Matches: 71, Mismatches: 18, Indels: 14
0.69 0.17 0.14
Matches are distributed among these distances:
20 2 0.03
21 12 0.17
24 56 0.79
25 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (24 bp):
TGTCACAGATTTTTGTATATGACG
Found at i:4297298 original size:69 final size:69
Alignment explanation
Indices: 4297206--4297401 Score: 248
Period size: 69 Copynumber: 2.8 Consensus size: 69
4297196 TTTCATAGGC
* * * * *
4297206 TTTTGTACATGACGTATCACACGTTAACCATGGCTTGTCACAGATTTTTGTATATGACGTGTCAC
1 TTTTGTACATGACGTGTAACACGTTAATCATGACTTGTCACAGGTTTTTGTATATGACGTGTCAC
*
4297271 ATAT
66 AGAT
* * * * *
4297275 TTTTGTACATGATGTGTTACACGTTAATCATGACTTGTCACAGGTTTTTGTACATAACGTGTTAC
1 TTTTGTACATGACGTGTAACACGTTAATCATGACTTGTCACAGGTTTTTGTATATGACGTGTCAC
4297340 AGAT
66 AGAT
* * * * *
4297344 TTTTGTATATGACGTGTAACACGCTAATCATAACTTGTCATAGGTTTTTATATATGAC
1 TTTTGTACATGACGTGTAACACGTTAATCATGACTTGTCACAGGTTTTTGTATATGAC
4297402 ATTTAACATC
Statistics
Matches: 108, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 108 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (69 bp):
TTTTGTACATGACGTGTAACACGTTAATCATGACTTGTCACAGGTTTTTGTATATGACGTGTCAC
AGAT
Found at i:4298365 original size:4 final size:4
Alignment explanation
Indices: 4298356--4298386 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
4298346 GGGTTTCTTT
4298356 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
4298387 ATAGGTTCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:4303501 original size:19 final size:19
Alignment explanation
Indices: 4303488--4303533 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
4303478 AATATATAAT
4303488 ATAAAAAATTATATTAAAA
1 ATAAAAAATTATATTAAAA
* * *
4303507 ATAAAAAATAAGATT-ATA
1 ATAAAAAATTATATTAAAA
4303525 ATAAAAAAT
1 ATAAAAAAT
4303534 AAAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
ATAAAAAATTATATTAAAA
Found at i:4303522 original size:24 final size:25
Alignment explanation
Indices: 4303468--4303561 Score: 82
Period size: 27 Copynumber: 3.6 Consensus size: 25
4303458 TAATTTTATA
* * *
4303468 ATTAAATTAAAATATATAATATAAAAA
1 ATTATATTAAAA-ATA-AAAATAAAAG
*
4303495 ATTATATTAAAAATAAAAA-ATAAG
1 ATTATATTAAAAATAAAAATAAAAG
* *
4303519 ATTATAATAAAAAATAAAAATAAAAT
1 ATTAT-ATTAAAAATAAAAATAAAAG
4303545 ATATGATATTAAAAATA
1 AT-T-ATATTAAAAATA
4303562 TGTTTAAGAG
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
24 8 0.15
25 16 0.29
26 8 0.15
27 21 0.38
28 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
ATTATATTAAAAATAAAAATAAAAG
Done.