Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 182 of 210
Found at i:60460943 original size:22 final size:23
Alignment explanation
Indices: 60460915--60460958 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
60460905 CTCAACACCA
60460915 AAATTGAGAGGAAATTT-AGAGG
1 AAATTGAGAGGAAATTTGAGAGG
60460937 AAATTGAGAGGAAATTTGAGAG
1 AAATTGAGAGGAAATTTGAGAG
60460959 AGGATTAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (23 bp):
AAATTGAGAGGAAATTTGAGAGG
Found at i:60462988 original size:14 final size:15
Alignment explanation
Indices: 60462965--60463001 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
60462955 ATTTCAGTAG
60462965 AAATGA-TTTCTAGA
1 AAATGATTTTCTAGA
60462979 AAAT-ATTTTCTAGA
1 AAATGATTTTCTAGA
60462993 AAATGATTT
1 AAATGATTT
60463002 ACTTTCTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 16 0.76
15 4 0.19
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (15 bp):
AAATGATTTTCTAGA
Found at i:60470415 original size:29 final size:29
Alignment explanation
Indices: 60470373--60470431 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
60470363 ATTGTTGCAA
60470373 TGGAAATTGTCTGCAGTTTTCAATGAAAC
1 TGGAAATTGTCTGCAGTTTTCAATGAAAC
*
60470402 TGGAAATTGTCTGCTGTTTTCAATGAAAC
1 TGGAAATTGTCTGCAGTTTTCAATGAAAC
60470431 T
1 T
60470432 TTTAAAATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (29 bp):
TGGAAATTGTCTGCAGTTTTCAATGAAAC
Found at i:60474664 original size:18 final size:17
Alignment explanation
Indices: 60474636--60474670 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
60474626 ATTATTAATA
*
60474636 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
60474653 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
60474671 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:60474670 original size:16 final size:16
Alignment explanation
Indices: 60474632--60474681 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
60474622 ATTGATTATT
60474632 AATA-ATTTT-ATTAA
1 AATATATTTTAATTAA
60474646 ATTATATATTTTAATTAA
1 A--ATATATTTTAATTAA
*
60474664 AATATA-TTTAATAAA
1 AATATATTTTAATTAA
60474679 AAT
1 AAT
60474682 TATGTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 1 0.03
15 11 0.35
16 8 0.26
17 5 0.16
18 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATATTTTAATTAA
Found at i:60474890 original size:44 final size:45
Alignment explanation
Indices: 60474827--60474923 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 45
60474817 CTATTACACC
*
60474827 TCCATTCCATTCAACCAAACACA-AGA-ATACTATTACGCATCTAT
1 TCCATTACATTCAACCAAACA-ATAGATATACTATTACGCATCTAT
* * * *
60474871 TCCATTACATTCAACCAAACAATTGATTTGCTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGATATACTATTACGCATCTAT
60474916 TCCATTAC
1 TCCATTAC
60474924 GCCTCTATTC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.48
45 23 0.50
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGATATACTATTACGCATCTAT
Found at i:60474924 original size:16 final size:16
Alignment explanation
Indices: 60474903--60474951 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
60474893 TTGATTTGCT
60474903 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
60474919 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
60474935 ATTAAGCCTCTATTCC
1 ATTACGCCTCTATTCC
60474951 A
1 A
60474952 ATACAGCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.22, C:0.35, G:0.06, T:0.37
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:60475384 original size:24 final size:23
Alignment explanation
Indices: 60475351--60475402 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
60475341 TCAAATACTA
* *
60475351 AAATTTATCCTTGAATTTTATTT
1 AAATTTATCCCTAAATTTTATTT
60475374 ACAATTTATCCCTAAATTTTATTT
1 A-AATTTATCCCTAAATTTTATTT
60475398 AAATT
1 AAATT
60475403 ACGACTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.52
Consensus pattern (23 bp):
AAATTTATCCCTAAATTTTATTT
Found at i:60475470 original size:11 final size:12
Alignment explanation
Indices: 60475456--60475487 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
60475446 TTTTTATATA
60475456 TTATTTAT-TAT
1 TTATTTATCTAT
60475467 TTATTTATCTAT
1 TTATTTATCTAT
60475479 TTA-TTATCT
1 TTATTTATCT
60475488 CTTACCCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTTATCTAT
Found at i:60475563 original size:3 final size:3
Alignment explanation
Indices: 60475555--60475598 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
60475545 TTGTTGCTCG
* *
60475555 TAT TAT TAT TAT TAT TAT TAT TATT TAT TTT TAC TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T
60475599 TAATTAGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:60481466 original size:12 final size:12
Alignment explanation
Indices: 60481449--60481491 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
60481439 GAGATTAGAC
60481449 TTGCAAGATCAG
1 TTGCAAGATCAG
**
60481461 TTGCAAGCGCAG
1 TTGCAAGATCAG
* *
60481473 CTGCAGGATCAG
1 TTGCAAGATCAG
60481485 TTGCAAG
1 TTGCAAG
60481492 CGCAGCTGCA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (12 bp):
TTGCAAGATCAG
Found at i:60481482 original size:24 final size:24
Alignment explanation
Indices: 60481450--60481503 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
60481440 AGATTAGACT
*
60481450 TGCAAGATCAGTTGCAAGCGCAGC
1 TGCAGGATCAGTTGCAAGCGCAGC
60481474 TGCAGGATCAGTTGCAAGCGCAGC
1 TGCAGGATCAGTTGCAAGCGCAGC
60481498 TGCAGG
1 TGCAGG
60481504 TATAATTAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.26, C:0.24, G:0.33, T:0.17
Consensus pattern (24 bp):
TGCAGGATCAGTTGCAAGCGCAGC
Found at i:60489559 original size:44 final size:44
Alignment explanation
Indices: 60489328--60489777 Score: 274
Period size: 44 Copynumber: 9.9 Consensus size: 44
60489318 TCACCATAGC
* * *
60489328 AAATCTTATCTCCCTGAAGTTGCAATAGAGCAGATTGAAGTTACCATGGT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG----CA--AT
* * * * * * * *
60489378 GAATCTTATCTCCCTAAAGTTGCAATGGAACATATTAAAGCTAC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAAT
* * * * * * * *
60489422 AAATCTTATCTTCCTGAAATTGTAGTGAAGAAAATTAAAGCTAT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAAT
* ** * * * * * *
60489466 AAATTTTATCTCTTTAAAGATGTATTGGAGTGAGA-TGAAACAAT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGCAAT
* * *
60489510 GAATCTTATCTCCATGAAGTTGCAGTGGACCAGATTGAAGCAAT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAAT
* * * * *
60489554 AAATCTTATCTTCCTGAAGTTACAGTGGAGCAGGTTGAAACTAT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAAT
* * * * * *
60489598 AAATCTTATTTCCCCGAAATTGAAGTGGAACAGATTAAAGCTACAAATT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG---C-AA-T
* ** * *
60489647 ACAAATCTTATCTCTCTGAAGTTTTAGTGGAGCAGATTGAAGCTAC
1 --AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAAT
* * * *
60489693 AAATCTTATCTCCCTGACGTTACAGTGGAGCAGATTGAAACTACT
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC-AAT
* *
60489738 -AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGATTGAAGC
1 AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC
60489778 GACAATTCAT
Statistics
Matches: 303, Mismatches: 87, Indels: 26
0.73 0.21 0.06
Matches are distributed among these distances:
43 3 0.01
44 226 0.75
45 2 0.01
46 1 0.00
47 2 0.01
48 2 0.01
49 1 0.00
50 34 0.11
51 32 0.11
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (44 bp):
AAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAAT
Found at i:60489657 original size:51 final size:51
Alignment explanation
Indices: 60489598--60489696 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
60489588 TTGAAACTAT
*
60489598 AAATCTTATTTCCCCGAAATTGAAGTGGAACAGATTAAAGCTACAAATTAC
1 AAATCTTATCTCCCCGAAATTGAAGTGGAACAGATTAAAGCTACAAATTAC
* * * ** * *
60489649 AAATCTTATCTCTCTGAAGTTTTAGTGGAGCAGATTGAAGCTACAAAT
1 AAATCTTATCTCCCCGAAATTGAAGTGGAACAGATTAAAGCTACAAAT
60489697 CTTATCTCCC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (51 bp):
AAATCTTATCTCCCCGAAATTGAAGTGGAACAGATTAAAGCTACAAATTAC
Found at i:60489683 original size:139 final size:139
Alignment explanation
Indices: 60489511--60489782 Score: 370
Period size: 139 Copynumber: 2.0 Consensus size: 139
60489501 TGAAACAATG
* *
60489511 AATCTTATCTCCATGAAGTTGCAGTGGACCAGATTGAAGCAATAAATCTTATCTTCCTGAAGTTA
1 AATCTTATCTCCATGAAGTTGCAGTGGACCAGATTGAAGCAACAAATCTTATCTCCCTGAAGTTA
* *
60489576 CAGTGGAGCAGGTTGAAACTA-TAAATCTTATTTCCCCGAAATTGAAGTGGAA-CAGATTAAAGC
66 CAGTGGAGCAGATTGAAACTACT-AATCTTATCTCCCCGAAATTGAAGT-GAAGCAGATTAAAGC
*
60489639 TACAAATTACA
129 GACAAATTACA
** * * *
60489650 AATCTTATCTCTC-TGAAGTTTTAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGACGTT
1 AATCTTATCTC-CATGAAGTTGCAGTGGACCAGATTGAAGCAACAAATCTTATCTCCCTGAAGTT
* * * *
60489714 ACAGTGGAGCAGATTGAAACTACTAATCTTATCTCCCTGAAGTTGTAGTGAAGCAGATTGAAGCG
65 ACAGTGGAGCAGATTGAAACTACTAATCTTATCTCCCCGAAATTGAAGTGAAGCAGATTAAAGCG
60489779 ACAA
130 ACAA
60489783 TTCATATACC
Statistics
Matches: 116, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
138 3 0.03
139 111 0.96
140 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (139 bp):
AATCTTATCTCCATGAAGTTGCAGTGGACCAGATTGAAGCAACAAATCTTATCTCCCTGAAGTTA
CAGTGGAGCAGATTGAAACTACTAATCTTATCTCCCCGAAATTGAAGTGAAGCAGATTAAAGCGA
CAAATTACA
Found at i:60490296 original size:21 final size:21
Alignment explanation
Indices: 60490267--60490306 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
60490257 AGAAACAATG
**
60490267 ACAGAAGAAATGGAAGCAAAA
1 ACAGAAGAAACAGAAGCAAAA
*
60490288 ACAGTAGAAACAGAAGCAA
1 ACAGAAGAAACAGAAGCAA
60490307 GAGCAGCGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.12, G:0.23, T:0.05
Consensus pattern (21 bp):
ACAGAAGAAACAGAAGCAAAA
Found at i:60493369 original size:18 final size:19
Alignment explanation
Indices: 60493334--60493369 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
60493324 TCAAATCTCA
*
60493334 ATATCAATAATCCCTAAAT
1 ATATAAATAATCCCTAAAT
60493353 ATATAAATAAT-CCTAAA
1 ATATAAATAATCCCTAAA
60493370 AAGAACTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.31
Consensus pattern (19 bp):
ATATAAATAATCCCTAAAT
Found at i:60495119 original size:18 final size:19
Alignment explanation
Indices: 60495092--60495133 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
60495082 CTATGCCAAC
*
60495092 ATTTTTTTAT-ACAATTTA
1 ATTTTATTATCACAATTTA
*
60495110 ATTTTATTATCCACACTTTA
1 ATTTTATTAT-CACAATTTA
60495130 ATTT
1 ATTT
60495134 CTCCATCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
20 11 0.55
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTATTATCACAATTTA
Found at i:60499586 original size:45 final size:45
Alignment explanation
Indices: 60499533--60499645 Score: 147
Period size: 45 Copynumber: 2.5 Consensus size: 45
60499523 ATTTGCTTTA
* *
60499533 TTTTGTTGTGTACCCATAGCCATAGGC-GAATTCCATGTGCAGTGT
1 TTTTGTTGTGTATCCATAGCCATAGGCAG-ATTCCATCTGCAGTGT
* * *
60499578 TTTTGTTGTGTATCTACAGCCATAGGCAGATTCCATCTGCGGTGT
1 TTTTGTTGTGTATCCATAGCCATAGGCAGATTCCATCTGCAGTGT
* *
60499623 TTTTATTGTGTGTCCATAGCCAT
1 TTTTGTTGTGTATCCATAGCCAT
60499646 TGACAGTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
45 57 0.98
46 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (45 bp):
TTTTGTTGTGTATCCATAGCCATAGGCAGATTCCATCTGCAGTGT
Found at i:60501977 original size:21 final size:23
Alignment explanation
Indices: 60501952--60502002 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 23
60501942 AAATATTTTC
* *
60501952 ATATTAATATTTCAA-TA-ACAT
1 ATATTAATATTACAATTATAAAT
60501973 ATATT--TATTACAATTATAAAT
1 ATATTAATATTACAATTATAAAT
60501994 ATATTAATA
1 ATATTAATA
60502003 ATAAATGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 7 0.29
20 2 0.08
21 13 0.54
23 2 0.08
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTAATATTACAATTATAAAT
Found at i:60509633 original size:24 final size:25
Alignment explanation
Indices: 60509536--60509633 Score: 76
Period size: 25 Copynumber: 4.0 Consensus size: 25
60509526 GTCATTAGGG
* *
60509536 TTACCGAT-TTCAGCTCTTATGAGC
1 TTACCGTTATTCAGCTCGTATGAGC
* * * * *
60509560 ATATCGATACTCAGCTTGTATGAGC
1 TTACCGTTATTCAGCTCGTATGAGC
* * *
60509585 TTACTGTTATTCAGCTCGGAGGAGC
1 TTACCGTTATTCAGCTCGTATGAGC
60509610 TTACCGTT-TATC-GCTCGTATGAGC
1 TTACCGTTAT-TCAGCTCGTATGAGC
60509634 ATACATGTAC
Statistics
Matches: 56, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
24 17 0.30
25 39 0.70
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (25 bp):
TTACCGTTATTCAGCTCGTATGAGC
Found at i:60522875 original size:3 final size:3
Alignment explanation
Indices: 60522867--60522909 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
60522857 ATATGAAGCT
60522867 TTC TTC TTC TTC TT- TTCC TTC TTC TTC TTC TTC -TC ATTC TTC T
1 TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC -TTC TTC T
60522910 AATCTAGGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 4 0.11
3 28 0.78
4 4 0.11
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:60522890 original size:18 final size:18
Alignment explanation
Indices: 60522867--60522909 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
60522857 ATATGAAGCT
* *
60522867 TTCTTCTTCTTCTTTTCC
1 TTCTTCTTCTTCTTCTCA
60522885 TTCTTCTTCTTCTTCTCA
1 TTCTTCTTCTTCTTCTCA
60522903 TTCTTCT
1 TTCTTCT
60522910 AATCTAGGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (18 bp):
TTCTTCTTCTTCTTCTCA
Found at i:60522962 original size:27 final size:27
Alignment explanation
Indices: 60522925--60522989 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
60522915 AGGGATTTTG
60522925 AAAAATTAAAAGGAAAATTAATTAATA
1 AAAAATTAAAAGGAAAATTAATTAATA
*
60522952 AAAAATTAAAAGGAAAATTAATTAATT
1 AAAAATTAAAAGGAAAATTAATTAATA
*
60522979 AAAAGTTAAAA
1 AAAAATTAAAA
60522990 TGATAGGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (27 bp):
AAAAATTAAAAGGAAAATTAATTAATA
Found at i:60523862 original size:37 final size:37
Alignment explanation
Indices: 60523812--60523887 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
60523802 TTTTTTTGTA
*
60523812 AATGATCTGATTTTGTTTGGCCAAGCAGAAGAGGATC
1 AATGATCTGATTTTGTTTGGCCAAGCAAAAGAGGATC
60523849 AATGATCTGATTTTGTTTGGCCAAGCAAAAGAGGATC
1 AATGATCTGATTTTGTTTGGCCAAGCAAAAGAGGATC
60523886 AA
1 AA
60523888 GCCACAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (37 bp):
AATGATCTGATTTTGTTTGGCCAAGCAAAAGAGGATC
Found at i:60536738 original size:27 final size:28
Alignment explanation
Indices: 60536704--60536788 Score: 109
Period size: 27 Copynumber: 2.9 Consensus size: 28
60536694 AAAGTTAATT
60536704 TTTAATTTTATTTTATTTTATTTTT-AA
1 TTTAATTTTATTTTATTTTATTTTTAAA
60536731 TTTAATTTTATTTTATTTTATTTTTGTAAAA
1 TTTAATTTTATTTTATTTTA-TTTT-T-AAA
*
60536762 TTTAATTTTTAATTTAATTTTATTTTT
1 TTTAA-TTTT-ATTTTATTTTATTTTT
60536789 GTAAACTTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
27 20 0.39
28 4 0.08
29 1 0.02
31 8 0.16
32 8 0.16
33 10 0.20
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (28 bp):
TTTAATTTTATTTTATTTTATTTTTAAA
Found at i:60536750 original size:43 final size:43
Alignment explanation
Indices: 60536703--60536787 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
60536693 GAAAGTTAAT
*** *
60536703 TTTTAATTTTATTTTATTTTATTTTTAATTTAATTTTATTTTA
1 TTTTAATTTTATAAAATTTAATTTTTAATTTAATTTTATTTTA
* *
60536746 TTTTATTTTTGTAAAATTTAATTTTTAATTTAATTTTATTTT
1 TTTTAATTTTATAAAATTTAATTTTTAATTTAATTTTATTTT
60536788 TGTAAACTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (43 bp):
TTTTAATTTTATAAAATTTAATTTTTAATTTAATTTTATTTTA
Found at i:60536769 original size:5 final size:5
Alignment explanation
Indices: 60536703--60536754 Score: 68
Period size: 5 Copynumber: 9.8 Consensus size: 5
60536693 GAAAGTTAAT
*
60536703 TTTTAA TTTTA TTTTA TTTTA TTTTTAA TTTAA TTTTA TTTTA TTTTA
1 TTTT-A TTTTA TTTTA TTTTA -TTTT-A TTTTA TTTTA TTTTA TTTTA
60536751 TTTT
1 TTTT
60536755 TGTAAAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
5 30 0.71
6 11 0.26
7 1 0.02
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:60536788 original size:6 final size:6
Alignment explanation
Indices: 60536698--60536787 Score: 59
Period size: 5 Copynumber: 15.3 Consensus size: 6
60536688 TTCCCGAAAG
*
60536698 TTAATTT TTAATT TT-ATT TT-ATT TTATTT TTAA-T TTAATT TT-ATT
1 TTAA-TT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT
* *
60536743 TT-ATT TTATTTT TGTAAAAT TTAATTT TTAA-T TTAATT TT-ATT TT
1 TTAATT TTA-ATT T-T-AATT TTAA-TT TTAATT TTAATT TTAATT TT
60536788 TGTAAACTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
5 35 0.51
6 17 0.25
7 13 0.19
8 3 0.04
9 1 0.01
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (6 bp):
TTAATT
Found at i:60539167 original size:9 final size:9
Alignment explanation
Indices: 60539153--60539189 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
60539143 TATAGTTTGA
60539153 TATTCGAAT
1 TATTCGAAT
60539162 TATTCGAAT
1 TATTCGAAT
*
60539171 TATTCGAGT
1 TATTCGAAT
60539180 TATTCGAAT
1 TATTCGAAT
60539189 T
1 T
60539190 CAAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:60541732 original size:43 final size:45
Alignment explanation
Indices: 60541671--60541821 Score: 140
Period size: 43 Copynumber: 3.5 Consensus size: 45
60541661 CAACGCCAAC
*
60541671 GTCCCAGA-AGTGGTCTTACATGTAATCAAATAATC-ATGCCACT
1 GTCCCAGACAGTGGTCTTACACGTAATCAAATAATCAATGCCACT
* * * *
60541714 GTCCCAGACAG-GGTCTTACACATAATCATAT-A-CAACGCCAAT
1 GTCCCAGACAGTGGTCTTACACGTAATCAAATAATCAATGCCACT
* ** *
60541756 GTCCCAAACA-TGGTCTTACACGTAAATCTCA-AATCGATGCCAACT
1 GTCCCAGACAGTGGTCTTACACGT-AATCAAATAATCAATGCC-ACT
60541801 -TCCCAGAC-GTGGTCTTACACG
1 GTCCCAGACAGTGGTCTTACACG
60541822 ATATCACATT
Statistics
Matches: 87, Mismatches: 13, Indels: 15
0.76 0.11 0.13
Matches are distributed among these distances:
41 1 0.01
42 27 0.31
43 31 0.36
44 26 0.30
45 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (45 bp):
GTCCCAGACAGTGGTCTTACACGTAATCAAATAATCAATGCCACT
Found at i:60541772 original size:42 final size:42
Alignment explanation
Indices: 60541659--60541776 Score: 114
Period size: 43 Copynumber: 2.8 Consensus size: 42
60541649 CAAAAGCTCG
* * **
60541659 TACAACGCCAACGTCCCAGAA-GTGGTCTTACATGTAATCAAA
1 TACAACGCCAATGTCCCA-AACATGGTCTTACACATAATCAAA
* * * * *
60541701 TA-ATCATGCCACTGTCCCAGACAGGGTCTTACACATAATCATA
1 TACA--ACGCCAATGTCCCAAACATGGTCTTACACATAATCAAA
60541744 TACAACGCCAATGTCCCAAACATGGTCTTACAC
1 TACAACGCCAATGTCCCAAACATGGTCTTACAC
60541777 GTAAATCTCA
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
41 1 0.02
42 28 0.47
43 29 0.49
44 1 0.02
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (42 bp):
TACAACGCCAATGTCCCAAACATGGTCTTACACATAATCAAA
Found at i:60544151 original size:19 final size:20
Alignment explanation
Indices: 60544103--60544151 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
60544093 CACACAGAAG
60544103 CGGTGTTGCAACATCCGAAT
1 CGGTGTTGCAACATCCGAAT
** *
60544123 CTTATGTTGCAACAT-CTAAT
1 C-GGTGTTGCAACATCCGAAT
60544143 CGGTGTTGC
1 CGGTGTTGC
60544152 GGCATCCGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
19 6 0.26
20 6 0.26
21 11 0.48
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
CGGTGTTGCAACATCCGAAT
Found at i:60545858 original size:14 final size:14
Alignment explanation
Indices: 60545839--60545865 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
60545829 TTGGGAAATT
60545839 AATTAATTTATTAA
1 AATTAATTTATTAA
60545853 AATTAATTTATTA
1 AATTAATTTATTA
60545866 TGTTTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATTAATTTATTAA
Found at i:60546790 original size:37 final size:37
Alignment explanation
Indices: 60546739--60546809 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
60546729 TTGTGCACAA
* *
60546739 CACTCATCAATATAACTGAAGTAAAATGTGTGCCTAG
1 CACTAATCAATATAACTAAAGTAAAATGTGTGCCTAG
*
60546776 CACTAATCAGTATAACTAAAGTAAAATGTGTGCC
1 CACTAATCAATATAACTAAAGTAAAATGTGTGCC
60546810 CAACACTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (37 bp):
CACTAATCAATATAACTAAAGTAAAATGTGTGCCTAG
Found at i:60556861 original size:30 final size:30
Alignment explanation
Indices: 60556826--60556889 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
60556816 CAAAACAGGT
* *
60556826 TGAGAAGATTGTAGGGTTGATGAAGGTGCA
1 TGAGAAGATTGGACGGTTGATGAAGGTGCA
*
60556856 TGAGAAGATTGGACTGTTGATGAAGGTGCA
1 TGAGAAGATTGGACGGTTGATGAAGGTGCA
60556886 TGAG
1 TGAG
60556890 CTGTCAAAGA
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:0.30, C:0.05, G:0.39, T:0.27
Consensus pattern (30 bp):
TGAGAAGATTGGACGGTTGATGAAGGTGCA
Found at i:60562308 original size:15 final size:16
Alignment explanation
Indices: 60562282--60562311 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
60562272 TAAAAATAAT
60562282 TATGTGTTAAAATTTA
1 TATGTGTTAAAATTTA
60562298 TATGT-TTAAAATTT
1 TATGTGTTAAAATTT
60562312 TGAATGAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (16 bp):
TATGTGTTAAAATTTA
Found at i:60563059 original size:23 final size:24
Alignment explanation
Indices: 60563033--60563077 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
60563023 ATATCCTCAC
*
60563033 ATGGAGTGTAG-GGTTGGATGGAG
1 ATGGAGTGTAGAGGCTGGATGGAG
*
60563056 ATGGTGTGTAGAGGCTGGATGG
1 ATGGAGTGTAGAGGCTGGATGG
60563078 GTAGGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.20, C:0.02, G:0.51, T:0.27
Consensus pattern (24 bp):
ATGGAGTGTAGAGGCTGGATGGAG
Found at i:60563591 original size:6 final size:6
Alignment explanation
Indices: 60563580--60563617 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
60563570 AAGCTTTCGC
60563580 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AA
60563618 ACTTTTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:60563651 original size:18 final size:18
Alignment explanation
Indices: 60563622--60563669 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
60563612 TAAAAAACTT
*
60563622 TTTGAAATTGAATAATGA
1 TTTGAAAATGAATAATGA
* *
60563640 TTTGTAAATGAATAATGT
1 TTTGAAAATGAATAATGA
60563658 TTTGAAAATGAA
1 TTTGAAAATGAA
60563670 CGACAAGGCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.40
Consensus pattern (18 bp):
TTTGAAAATGAATAATGA
Found at i:60564017 original size:25 final size:25
Alignment explanation
Indices: 60563989--60564054 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
60563979 ACTGTCCTTT
* *
60563989 ATAGTATATCCTGAAACTGCTATAG
1 ATAGTATATACTGAAACTACTATAG
*
60564014 ATAGTATATACTGAGACTACTATAG
1 ATAGTATATACTGAAACTACTATAG
60564039 ATAG-ACTATACTGAAA
1 ATAGTA-TATACTGAAA
60564055 ACACTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
24 1 0.03
25 35 0.97
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (25 bp):
ATAGTATATACTGAAACTACTATAG
Found at i:60566471 original size:18 final size:18
Alignment explanation
Indices: 60566427--60566474 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
60566417 AATAAAAATA
60566427 AATGTTTTGAAATTGAAT
1 AATGTTTTGAAATTGAAT
* *
60566445 AACGATTTGTAAA-TGAAT
1 AATGTTTTG-AAATTGAAT
60566463 AATGTTTTGAAA
1 AATGTTTTGAAA
60566475 ACGAACGACA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 3 0.12
18 19 0.76
19 3 0.12
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.40
Consensus pattern (18 bp):
AATGTTTTGAAATTGAAT
Found at i:60574707 original size:45 final size:44
Alignment explanation
Indices: 60574614--60574793 Score: 195
Period size: 45 Copynumber: 4.0 Consensus size: 44
60574604 CAGATACACG
* * * * * * *
60574614 GTGG-ATCAGCACATAGC-ACCACCCTTATAGTTAATGATACTCG
1 GTGGAATCAGCACACAACAACCACCTTTATAATCAATG-TACCCA
* *
60574657 GTGGAATCAGCACATAGA-AACCACCTTCATAATCAATAGTACCCA
1 GTGGAATCAGCACACA-ACAACCACCTTTATAATCAAT-GTACCCA
*
60574702 GTGGAATCAGCACACAACAACCACCTTTATAATCAATGATACCCG
1 GTGGAATCAGCACACAACAACCACCTTTATAATCAATG-TACCCA
*
60574747 GTGGAATCAGCACACAACAACCACCTTTATAATTAATGGTACCCA
1 GTGGAATCAGCACACAACAACCACCTTTATAATCAAT-GTACCCA
60574792 GT
1 GT
60574794 ACACGTAGTA
Statistics
Matches: 118, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
43 4 0.03
44 13 0.11
45 99 0.84
46 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (44 bp):
GTGGAATCAGCACACAACAACCACCTTTATAATCAATGTACCCA
Found at i:60574749 original size:90 final size:88
Alignment explanation
Indices: 60574614--60574793 Score: 236
Period size: 90 Copynumber: 2.0 Consensus size: 88
60574604 CAGATACACG
* * * * * *
60574614 GTGGATCAGCACATAGCACCACCCTTATAGTTAATGATACTCGGTGGAATCAGCACATAGA-AAC
1 GTGGATCAGCACACAACACCACCCTTATAATCAATGATACCCGGTGGAATCAGCACACA-ACAAC
60574678 CACCTTCATAATCAATAGTACCCA
65 CACCTTCATAATCAATAGTACCCA
*
60574702 GTGGAATCAGCACACAACAACCACCTTTATAATCAATGATACCCGGTGGAATCAGCACACAACAA
1 GTGG-ATCAGCACACAAC-ACCACCCTTATAATCAATGATACCCGGTGGAATCAGCACACAACAA
* * *
60574767 CCACCTTTATAATTAATGGTACCCA
64 CCACCTTCATAATCAATAGTACCCA
60574792 GT
1 GT
60574794 ACACGTAGTA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
88 4 0.05
89 12 0.15
90 63 0.80
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (88 bp):
GTGGATCAGCACACAACACCACCCTTATAATCAATGATACCCGGTGGAATCAGCACACAACAACC
ACCTTCATAATCAATAGTACCCA
Found at i:60580672 original size:39 final size:39
Alignment explanation
Indices: 60580618--60580794 Score: 264
Period size: 39 Copynumber: 4.5 Consensus size: 39
60580608 AACATGTTTC
* *
60580618 TGAGTATTGTAATATATGCTTGAATGATATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
60580657 TGAGTATTATGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
*
60580696 TGAGTATTGTGATATATGCTTGAATGTTTTGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
** * *
60580735 TTTGTATTGTGATATATACTTGAATGTTGTGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
* *
60580774 TGTGTAATGTGATATATGCTT
1 TGAGTATTGTGATATATGCTT
60580795 TAAAGTGAAT
Statistics
Matches: 126, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 126 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.47
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
Found at i:60580730 original size:22 final size:22
Alignment explanation
Indices: 60580666--60580775 Score: 78
Period size: 22 Copynumber: 5.4 Consensus size: 22
60580656 ATGAGTATTA
*
60580666 TGATATATGCTTGAATGTTATG
1 TGATATATGCTTGAATGTTTTG
* *
60580688 TGAT-TAT--ATG-A-GTATTG
1 TGATATATGCTTGAATGTTTTG
60580705 TGATATATGCTTGAATGTTTTG
1 TGATATATGCTTGAATGTTTTG
* *
60580727 TGAT-TAT-ATT---TGTATTG
1 TGATATATGCTTGAATGTTTTG
* *
60580744 TGATATATACTTGAATGTTGTG
1 TGATATATGCTTGAATGTTTTG
60580766 TGATTATATG
1 TGA-TATATG
60580776 TGTAATGTGA
Statistics
Matches: 66, Mismatches: 11, Indels: 21
0.67 0.11 0.21
Matches are distributed among these distances:
17 18 0.27
18 7 0.11
19 4 0.06
20 4 0.06
21 7 0.11
22 21 0.32
23 5 0.08
ACGTcount: A:0.26, C:0.03, G:0.22, T:0.49
Consensus pattern (22 bp):
TGATATATGCTTGAATGTTTTG
Found at i:60580809 original size:23 final size:23
Alignment explanation
Indices: 60580779--60580832 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
60580769 TTATATGTGT
*
60580779 AATGTGATATATGCTTTAAAGTG
1 AATGTGATATATGCTTAAAAGTG
60580802 AATGTGATATATGCTTAAAAGTG
1 AATGTGATATATGCTTAAAAGTG
60580825 AATGTGAT
1 AATGTGAT
60580833 TATAATATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (23 bp):
AATGTGATATATGCTTAAAAGTG
Found at i:60580813 original size:39 final size:40
Alignment explanation
Indices: 60580618--60580814 Score: 219
Period size: 39 Copynumber: 5.0 Consensus size: 40
60580608 AACATGTTTC
*
60580618 TGAGTATTGTAATATATGCTTGAA--TGATATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTGA-ATGTGATTATA
* *
60580657 TGAGTATTATGATATATGCTTGAATGT-TATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTGAATGTGATTATA
**
60580696 TGAGTATTGTGATATATGCTTGAATGT-TTTGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTGAATGTGATTATA
** *
60580735 TTTGTATTGTGATATATACTTGAATGTTG--TGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATG-TGAATGTGATTATA
* * * *
60580774 TGTGTAATGTGATATATGCTTTAAAGTGAATGTGA-TATA
1 TGAGTATTGTGATATATGCTTGAATGTGAATGTGATTATA
60580813 TG
1 TG
60580815 CTTAAAAGTG
Statistics
Matches: 139, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
38 2 0.01
39 130 0.94
40 6 0.04
41 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.22, T:0.46
Consensus pattern (40 bp):
TGAGTATTGTGATATATGCTTGAATGTGAATGTGATTATA
Found at i:60584228 original size:18 final size:20
Alignment explanation
Indices: 60584205--60584245 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
60584195 CTATTTTTAG
*
60584205 AAATTG-AATATA-CTATTT
1 AAATTGAAATATATATATTT
60584223 AAATTGAAATATATATATTT
1 AAATTGAAATATATATATTT
60584243 AAA
1 AAA
60584246 AATGAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 6 0.30
20 8 0.40
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (20 bp):
AAATTGAAATATATATATTT
Found at i:60584251 original size:21 final size:19
Alignment explanation
Indices: 60584211--60584261 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
60584201 TTAGAAATTG
*
60584211 AATATACTATTTAAATTGAA
1 AATATA-TATTTAAAATGAA
60584231 ATATATATATTTAAAAATGAA
1 A-ATATATATTT-AAAATGAA
60584252 AATA-ATATTT
1 AATATATATTT
60584262 GAATGATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 6 0.21
20 9 0.32
21 13 0.46
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (19 bp):
AATATATATTTAAAATGAA
Found at i:60589207 original size:93 final size:93
Alignment explanation
Indices: 60589060--60589233 Score: 296
Period size: 93 Copynumber: 1.9 Consensus size: 93
60589050 GCTTCTTGTG
** * *
60589060 TGAATGTTGATGATGAGAAGACTCCTGTTGCATCTCCAACAGGTTCATCTGCTGAAAGGAAGTTA
1 TGAATGTTGATGATGAGAAGAAGCCAGTTGCATCTCCAACAGGTTCATCAGCTGAAAGGAAGTTA
60589125 ACTCCTGTAGCTGGTGGTTCATCATGTA
66 ACTCCTGTAGCTGGTGGTTCATCATGTA
60589153 TGAATGTTGATGATG-GAATGAAGCCAGTTGCATCTCCAACAGGTTCATCAGCTGAAAGGAAGTT
1 TGAATGTTGATGATGAGAA-GAAGCCAGTTGCATCTCCAACAGGTTCATCAGCTGAAAGGAAGTT
60589217 AACTCCTGTAGCTGGTG
65 AACTCCTGTAGCTGGTG
60589234 AGGTTTTGTT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 3 0.04
93 73 0.96
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (93 bp):
TGAATGTTGATGATGAGAAGAAGCCAGTTGCATCTCCAACAGGTTCATCAGCTGAAAGGAAGTTA
ACTCCTGTAGCTGGTGGTTCATCATGTA
Found at i:60608717 original size:28 final size:28
Alignment explanation
Indices: 60608668--60608744 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
60608658 CGCCAGAAAA
* * *
60608668 GGAAAGTCTACTTAA-GAGTATCTTACGT
1 GGAAAGTCCAC-TAAGGACTATCGTACGT
*
60608696 GGAAAGTCCACTAAGGACTATCGTATGT
1 GGAAAGTCCACTAAGGACTATCGTACGT
* *
60608724 GGAATGTCCGCTAAGGACTAT
1 GGAAAGTCCACTAAGGACTAT
60608745 TTGTTCTGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 3 0.07
28 39 0.93
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (28 bp):
GGAAAGTCCACTAAGGACTATCGTACGT
Found at i:60608760 original size:28 final size:28
Alignment explanation
Indices: 60608695--60608762 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
60608685 GTATCTTACG
* *
60608695 TGGAAAGTCCACTAAGGACTATCGTATG
1 TGGAAAGTCCGCTAAGGACTATCGTATC
* *
60608723 TGGAATGTCCGCTAAGGACTATTTGT-TC
1 TGGAAAGTCCGCTAAGGACTA-TCGTATC
*
60608751 TGTAAAGTCCGC
1 TGGAAAGTCCGC
60608763 CAAGAGCTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 30 0.91
29 3 0.09
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (28 bp):
TGGAAAGTCCGCTAAGGACTATCGTATC
Found at i:60608948 original size:15 final size:15
Alignment explanation
Indices: 60608928--60608958 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
60608918 GTTATGTAAG
60608928 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
60608943 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
60608958 T
1 T
60608959 ATGTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:60613281 original size:15 final size:15
Alignment explanation
Indices: 60613261--60613291 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
60613251 GTTATGTAAG
60613261 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
*
60613276 TGAAAGGTTAAGAGT
1 TGAAAGGTCAAGAGT
60613291 T
1 T
60613292 ATGTTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:60616511 original size:21 final size:21
Alignment explanation
Indices: 60616487--60616527 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
60616477 AAAATCCCCC
60616487 AAGAAAAAAACAAGAAAAATG
1 AAGAAAAAAACAAGAAAAATG
* **
60616508 AAGAAGAAAGGAAGAAAAAT
1 AAGAAAAAAACAAGAAAAAT
60616528 CCCAACAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (21 bp):
AAGAAAAAAACAAGAAAAATG
Found at i:60618136 original size:8 final size:8
Alignment explanation
Indices: 60618087--60618160 Score: 53
Period size: 8 Copynumber: 9.1 Consensus size: 8
60618077 AAAAAGATAT
60618087 TAAAAA-A
1 TAAAAATA
*
60618094 TAAATATA
1 TAAAAATA
*
60618102 TATAAATA
1 TAAAAATA
**
60618110 TAAAACCA
1 TAAAAATA
60618118 TAATAAA-A
1 TAA-AAATA
60618126 TAAAAATA
1 TAAAAATA
60618134 TAAAAATAA
1 TAAAAAT-A
*
60618143 CAAAAATTA
1 TAAAAA-TA
*
60618152 TGAAAATA
1 TAAAAATA
60618160 T
1 T
60618161 TTTCTCATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
7 8 0.15
8 30 0.58
9 13 0.25
10 1 0.02
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.26
Consensus pattern (8 bp):
TAAAAATA
Found at i:60618136 original size:16 final size:16
Alignment explanation
Indices: 60618076--60618136 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
60618066 ATAAAAATCC
* *
60618076 TAAAAAGATATTAAAA
1 TAAAAATATAATAAAA
60618092 -AATAAATATATATAAATA
1 TAA-AAATATA-ATAAA-A
**
60618110 TAAAACCATAATAAAA
1 TAAAAATATAATAAAA
60618126 TAAAAATATAA
1 TAAAAATATAA
60618137 AAATAACAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
15 2 0.06
16 16 0.46
17 9 0.26
18 6 0.17
19 2 0.06
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (16 bp):
TAAAAATATAATAAAA
Found at i:60622523 original size:16 final size:16
Alignment explanation
Indices: 60622502--60622532 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
60622492 AAGATAGTAC
60622502 CTTTAATAAAATTTAT
1 CTTTAATAAAATTTAT
60622518 CTTTAATAAAATTTA
1 CTTTAATAAAATTTA
60622533 CAAATGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
CTTTAATAAAATTTAT
Found at i:60622743 original size:18 final size:19
Alignment explanation
Indices: 60622720--60622757 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
60622710 GCCTTTATGG
*
60622720 TTGTTATAAATAA-AAAAA
1 TTGTTATAAAAAATAAAAA
60622738 TTGTTATAAAAAATAAAAA
1 TTGTTATAAAAAATAAAAA
60622757 T
1 T
60622758 AAAATGTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
TTGTTATAAAAAATAAAAA
Found at i:60625145 original size:3 final size:3
Alignment explanation
Indices: 60625137--60625307 Score: 342
Period size: 3 Copynumber: 57.0 Consensus size: 3
60625127 TTAGGTCTTT
60625137 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
60625185 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
60625233 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
60625281 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
60625308 TTAACAGTAA
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 168 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:60627464 original size:3 final size:3
Alignment explanation
Indices: 60627456--60627502 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
60627446 AGTAGGTGAC
60627456 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
60627503 AATTAACAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:60630767 original size:16 final size:18
Alignment explanation
Indices: 60630730--60630767 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
60630720 AATGACTTGG
60630730 AAATGAAATTATGTATTTC
1 AAATGAAATTA-GTATTTC
60630749 AAATGAAATTA-TA-TTC
1 AAATGAAATTAGTATTTC
60630765 AAA
1 AAA
60630768 AATAGAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 2 0.11
19 11 0.58
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37
Consensus pattern (18 bp):
AAATGAAATTAGTATTTC
Found at i:60633950 original size:27 final size:27
Alignment explanation
Indices: 60633894--60633950 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
60633884 GTCTCGACGA
* *
60633894 ACTACCCCATGTTTACCGTTTCGGTAG
1 ACTACCCCATGTTTACCATTTCGATAG
** *
60633921 ACTACCCTGTGTTTACCATTTCGATCG
1 ACTACCCCATGTTTACCATTTCGATAG
60633948 ACT
1 ACT
60633951 TTATTGGTCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (27 bp):
ACTACCCCATGTTTACCATTTCGATAG
Found at i:60637413 original size:22 final size:20
Alignment explanation
Indices: 60637363--60637413 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 20
60637353 ATTAAAAATC
60637363 ATTAAAATTATTTAAAAAAGGA
1 ATTAAAATTATTTAAAAAA--A
*
60637385 ATAAAAATTACATTTAAAAAAA
1 ATTAAAATT--ATTTAAAAAAA
60637407 ATTAAAA
1 ATTAAAA
60637414 ATAAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 15 0.60
24 10 0.40
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (20 bp):
ATTAAAATTATTTAAAAAAA
Found at i:60637559 original size:22 final size:24
Alignment explanation
Indices: 60637518--60637566 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
60637508 ATGATTTAAC
* *
60637518 AAAAAAATATAAATTCAAAGATTA
1 AAAAAAATATAAATTAAAAGACTA
60637542 AAAAAAAT-TAAA-TAAAAGACTA
1 AAAAAAATATAAATTAAAAGACTA
60637564 AAA
1 AAA
60637567 TATATAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 11 0.48
23 4 0.17
24 8 0.35
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (24 bp):
AAAAAAATATAAATTAAAAGACTA
Found at i:60639886 original size:17 final size:17
Alignment explanation
Indices: 60639860--60639898 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
60639850 TCATATTTGA
*
60639860 TTTTTTTAAA-TTTAAT
1 TTTTTTTAAAGTTAAAT
60639876 TTTTATTTAAAGTTAAAT
1 TTTT-TTTAAAGTTAAAT
60639894 TTTTT
1 TTTTT
60639899 AACAATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTTTTAAAGTTAAAT
Found at i:60643118 original size:15 final size:15
Alignment explanation
Indices: 60643098--60643130 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
60643088 TGTTTTGATC
*
60643098 AAAAGAAATGAAATG
1 AAAAGAAATGAAAAG
60643113 AAAAGAAATGAAAAG
1 AAAAGAAATGAAAAG
60643128 AAA
1 AAA
60643131 TAAAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (15 bp):
AAAAGAAATGAAAAG
Found at i:60643137 original size:9 final size:10
Alignment explanation
Indices: 60643102--60643139 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
60643092 TTGATCAAAA
*
60643102 GAAATGAAAT
1 GAAAAGAAAT
60643112 GAAAAGAAAT
1 GAAAAGAAAT
60643122 GAAAAGAAAT
1 GAAAAGAAAT
60643132 -AAAAGAAA
1 GAAAAGAAA
60643140 AAGGAAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (10 bp):
GAAAAGAAAT
Found at i:60647164 original size:16 final size:16
Alignment explanation
Indices: 60647136--60647170 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
60647126 ACATAATCAA
60647136 ACTTAGTTATTTAAAT
1 ACTTAGTTATTTAAAT
60647152 ACTTACGTT-TTTAAAT
1 ACTTA-GTTATTTAAAT
60647168 ACT
1 ACT
60647171 AAAGGTGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (16 bp):
ACTTAGTTATTTAAAT
Found at i:60647452 original size:15 final size:15
Alignment explanation
Indices: 60647429--60647460 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
60647419 TTTTTTAATC
*
60647429 AAAAGAAATGAAATG
1 AAAAAAAATGAAATG
60647444 AAAAAAAATGAAATG
1 AAAAAAAATGAAATG
60647459 AA
1 AA
60647461 GAGGAAAATG
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:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (15 bp):
AAAAAAAATGAAATG
Found at i:60649113 original size:48 final size:49
Alignment explanation
Indices: 60649013--60649127 Score: 135
Period size: 48 Copynumber: 2.4 Consensus size: 49
60649003 GCTGTATAAT
* *
60649013 GGGAAGCTCTTGAGAGCCAATTATCCAGAAGCTCATACGAGCCATAAAC
1 GGGAAGCTCATGAGAGCCAAATATCCAGAAGCTCATACGAGCCATAAAC
* * * * *
60649062 GGGAAGCTCAAGAGAGCCAAAT-TCGATAAGCTCATGCGAGCCA-ATATC
1 GGGAAGCTCATGAGAGCCAAATATCCAGAAGCTCATACGAGCCATA-AAC
*
60649110 GGGAAGCTCGTGAGAGCC
1 GGGAAGCTCATGAGAGCC
60649128 TATTATCGGG
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
47 1 0.02
48 36 0.64
49 19 0.34
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (49 bp):
GGGAAGCTCATGAGAGCCAAATATCCAGAAGCTCATACGAGCCATAAAC
Found at i:60649116 original size:24 final size:24
Alignment explanation
Indices: 60649013--60649151 Score: 104
Period size: 24 Copynumber: 5.7 Consensus size: 24
60649003 GCTGTATAAT
*
60649013 GGGAAGCTCTTGAGAGCCAATTATC
1 GGGAAGCTCATGAGAGCCAA-TATC
** *
60649038 CAGAAGCTCAT-ACGAGCC-ATAAAC
1 GGGAAGCTCATGA-GAGCCAAT-ATC
*
60649062 GGGAAGCTCAAGAGAGCCAA-ATTC
1 GGGAAGCTCATGAGAGCCAATA-TC
** *
60649086 GATAAGCTCATGCGAGCCAATATC
1 GGGAAGCTCATGAGAGCCAATATC
* *
60649110 GGGAAGCTCGTGAGAGCCTATTATC
1 GGGAAGCTCATGAGAGCC-AATATC
* *
60649135 GGGACGCTCATAAGAGC
1 GGGAAGCTCATGAGAGC
60649152 TGTGGTGTGT
Statistics
Matches: 87, Mismatches: 20, Indels: 14
0.72 0.17 0.12
Matches are distributed among these distances:
23 2 0.02
24 50 0.57
25 35 0.40
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (24 bp):
GGGAAGCTCATGAGAGCCAATATC
Found at i:60651102 original size:47 final size:47
Alignment explanation
Indices: 60651027--60651209 Score: 215
Period size: 47 Copynumber: 3.9 Consensus size: 47
60651017 GGGGTGTGAC
* * * * * *
60651027 AATTAAATAATTTAATCATGAACGTGATAAATGGAAAAATAAAAATA
1 AATTAAATGATATAATCATCAACATGATAAGTGGAATAATAAAAATA
*
60651074 AATTAAATGATATAATCATCAACATGATAAGTGGTATAATAAAAATA
1 AATTAAATGATATAATCATCAACATGATAAGTGGAATAATAAAAATA
* * ** ** *
60651121 AATTAAACGATATAATCATCGATGTGATAAGTGTCATGATAAAAATA
1 AATTAAATGATATAATCATCAACATGATAAGTGGAATAATAAAAATA
*
60651168 AATTAAATGATATAATCAT-AGACATGATAAGTGGCATAATAA
1 AATTAAATGATATAATCATCA-ACATGATAAGTGGAATAATAA
60651210 CCACTAGAAG
Statistics
Matches: 115, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
47 115 1.00
ACGTcount: A:0.52, C:0.07, G:0.13, T:0.29
Consensus pattern (47 bp):
AATTAAATGATATAATCATCAACATGATAAGTGGAATAATAAAAATA
Found at i:60653235 original size:32 final size:32
Alignment explanation
Indices: 60653191--60653270 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 32
60653181 CTGTGTGTTA
* *
60653191 GGCCATGTGGGACACACATG-CTGGACCTTTTG
1 GGCCATGTGGGACACAC-GGACTGAACCTTTTG
*
60653223 GGTCATGTGGGACACACGGACTGAACCTTTTG
1 GGCCATGTGGGACACACGGACTGAACCTTTTG
*
60653255 GGCCATGTGGGCCACA
1 GGCCATGTGGGACACA
60653271 TGGGCATGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 1 0.02
32 41 0.98
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.23
Consensus pattern (32 bp):
GGCCATGTGGGACACACGGACTGAACCTTTTG
Found at i:60656176 original size:6 final size:6
Alignment explanation
Indices: 60656165--60656191 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
60656155 CAGATTTTTT
60656165 TTTGGG TTTGGG TTTGGG TTTGGG TTT
1 TTTGGG TTTGGG TTTGGG TTTGGG TTT
60656192 TTTGTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.44, T:0.56
Consensus pattern (6 bp):
TTTGGG
Found at i:60672897 original size:41 final size:41
Alignment explanation
Indices: 60672840--60672945 Score: 176
Period size: 41 Copynumber: 2.6 Consensus size: 41
60672830 AATGAGATAA
* *
60672840 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
*
60672881 TTCAGACTATACGTCTAGCAGGCTTGACGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
*
60672922 TTCGGACTTTACGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
60672946 AATTGCCAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
Found at i:60675380 original size:2 final size:2
Alignment explanation
Indices: 60675333--60675363 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
60675323 CATTTATCAG
60675333 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60675364 TTGTATATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60679748 original size:13 final size:13
Alignment explanation
Indices: 60679719--60679782 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
60679709 TTTAACATTG
*
60679719 CTTTTAATAAA-TG
1 CTTTTAA-AAAGTA
60679732 CTTTTAAAAAGTA
1 CTTTTAAAAAGTA
**
60679745 CTTTGGAAAAGTGA
1 CTTTTAAAAAGT-A
*
60679759 -TTTTAGAAAGTA
1 CTTTTAAAAAGTA
60679771 CTTTTAAAAAGT
1 CTTTTAAAAAGT
60679783 TTGGTTTAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
12 4 0.10
13 36 0.88
14 1 0.02
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (13 bp):
CTTTTAAAAAGTA
Found at i:60679780 original size:26 final size:26
Alignment explanation
Indices: 60679719--60679782 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
60679709 TTTAACATTG
*
60679719 CTTTTAATAAA-TGCTTTTAAAAAGTA
1 CTTTTAA-AAAGTGATTTTAAAAAGTA
** *
60679745 CTTTGGAAAAGTGATTTTAGAAAGTA
1 CTTTTAAAAAGTGATTTTAAAAAGTA
60679771 CTTTTAAAAAGT
1 CTTTTAAAAAGT
60679783 TTGGTTTAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
25 3 0.10
26 28 0.90
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.39
Consensus pattern (26 bp):
CTTTTAAAAAGTGATTTTAAAAAGTA
Found at i:60681479 original size:21 final size:21
Alignment explanation
Indices: 60681453--60681493 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
60681443 ATTTTCCCTT
60681453 TCTCCTTTCTCTTCTAAGCAA
1 TCTCCTTTCTCTTCTAAGCAA
*
60681474 TCTCCTTTCTCTTTTAAGCA
1 TCTCCTTTCTCTTCTAAGCA
60681494 TATTTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.32, G:0.05, T:0.46
Consensus pattern (21 bp):
TCTCCTTTCTCTTCTAAGCAA
Found at i:60681731 original size:15 final size:15
Alignment explanation
Indices: 60681711--60681740 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
60681701 ATCAAATTGT
*
60681711 TTGTTGAAGCTTCCA
1 TTGTTGAAGATTCCA
60681726 TTGTTGAAGATTCCA
1 TTGTTGAAGATTCCA
60681741 GAAAATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (15 bp):
TTGTTGAAGATTCCA
Found at i:60690050 original size:4 final size:4
Alignment explanation
Indices: 60690041--60690068 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
60690031 TCTTGAGCCA
60690041 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
60690069 GTGTTGAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:60696698 original size:8 final size:8
Alignment explanation
Indices: 60696674--60696714 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
60696664 ATGCAATGCT
60696674 TATGCATG
1 TATGCATG
*
60696682 CATGCATG
1 TATGCATG
60696690 TATGCATG
1 TATGCATG
*
60696698 TATGTATG
1 TATGCATG
*
60696706 TATGTATG
1 TATGCATG
60696714 T
1 T
60696715 GTACAAACCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (8 bp):
TATGCATG
Found at i:60696710 original size:12 final size:12
Alignment explanation
Indices: 60696674--60696714 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
60696664 ATGCAATGCT
*
60696674 TATGCATGCATG
1 TATGTATGCATG
*
60696686 CATGTATGCATG
1 TATGTATGCATG
*
60696698 TATGTATGTATG
1 TATGTATGCATG
60696710 TATGT
1 TATGT
60696715 GTACAAACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (12 bp):
TATGTATGCATG
Found at i:60704261 original size:107 final size:107
Alignment explanation
Indices: 60704075--60704289 Score: 367
Period size: 107 Copynumber: 2.0 Consensus size: 107
60704065 TGTTCCCTCG
*
60704075 CCATGAAACCGTTCAATTAAATGAGAGTAATTTTATTTTTTGGAAGCATCAAATAAATTTGATTC
1 CCATGAAACCATTCAATTAAATGAGAGTAATTTTATTTTTTGGAAGCATCAAATAAATTTGATTC
* *
60704140 CTGAAGGATATGGAATGACGGGTTACATTTTAGAAACTCTAT
66 CTAAAGGATATGGAATGACGAGTTACATTTTAGAAACTCTAT
*
60704182 CCATGAAACTATTCAATTAAATGAGAGTAATTTTATTTTTTGGAAGCATCAAATAAATTTGATTC
1 CCATGAAACCATTCAATTAAATGAGAGTAATTTTATTTTTTGGAAGCATCAAATAAATTTGATTC
* * *
60704247 CTAAAGGGTATGGAATGACGAGTTACATTTTGGGAACTCTAT
66 CTAAAGGATATGGAATGACGAGTTACATTTTAGAAACTCTAT
60704289 C
1 C
60704290 TATTCCAGCA
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 101 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (107 bp):
CCATGAAACCATTCAATTAAATGAGAGTAATTTTATTTTTTGGAAGCATCAAATAAATTTGATTC
CTAAAGGATATGGAATGACGAGTTACATTTTAGAAACTCTAT
Found at i:60708613 original size:33 final size:33
Alignment explanation
Indices: 60708575--60708706 Score: 120
Period size: 33 Copynumber: 3.7 Consensus size: 33
60708565 ATGTGAAAGG
*
60708575 GGTTGCTAAGTGCTGATTCCCTGAATTACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
* * * *
60708608 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A-ATT--A-CTG--GT
*
60708649 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
*
60708682 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
60708707 TAACGGATAA
Statistics
Matches: 79, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
33 39 0.49
34 6 0.08
35 3 0.04
36 3 0.04
38 2 0.03
39 3 0.04
40 3 0.04
41 20 0.25
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.30
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATTACTGGT
Found at i:60708692 original size:74 final size:75
Alignment explanation
Indices: 60708496--60708705 Score: 320
Period size: 75 Copynumber: 2.8 Consensus size: 75
60708486 TGATTCCCCC
* * *
60708496 AAGGGGTTGCTAAGTGCTGATTTCTC-AA-CACATTGGTGGTTGCTAAGTGCTAATCCCACCGTA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCAC--TGGTGGTTGCTAAGTGCTGATCCCACCGTA
60708559 TCTTAAATGTGA
64 TCTTAAATGTGA
* *
60708571 AAGGGGTTGCTAAGTGCTGATTCCCTGAATTACTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
60708636 TTAAATGTG-
66 TTAAATGTGA
60708645 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAAT-CCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTG-ATCCCACCG
60708706 ATAACGGATA
Statistics
Matches: 125, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
74 56 0.45
75 65 0.52
76 2 0.02
77 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
TTAAATGTGA
Found at i:60714582 original size:26 final size:25
Alignment explanation
Indices: 60714545--60714636 Score: 96
Period size: 26 Copynumber: 3.5 Consensus size: 25
60714535 GTACATAGTA
*
60714545 CCTGCTTAAATATACACTGGCTCAAAG
1 CCTGC-TAAATA-ACACTGGCTCAAGG
*
60714572 CCTGCTAAATAAC-CATCAGCTCAAGG
1 CCTGCTAAATAACAC-T-GGCTCAAGG
*
60714598 CCTGCTAAATAACAACTGGCTCGAGG
1 CCTGCTAAATAAC-ACTGGCTCAAGG
*
60714624 CTTGCTAAATAAC
1 CCTGCTAAATAAC
60714637 CACCAGCTCA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
24 1 0.02
25 3 0.05
26 45 0.80
27 6 0.11
28 1 0.02
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (25 bp):
CCTGCTAAATAACACTGGCTCAAGG
Found at i:60714630 original size:52 final size:53
Alignment explanation
Indices: 60714545--60714652 Score: 148
Period size: 52 Copynumber: 2.1 Consensus size: 53
60714535 GTACATAGTA
*
60714545 CCTGCTTAAATATACACTGGCTCAAAGCCTGCTAAATAACCATCAGCTCAAGG
1 CCTGCTTAAATATACACTGGCTCAAAGCCTGCTAAATAACCACCAGCTCAAGG
* * * *
60714598 CCTGC-TAAATA-ACAACTGGCTCGAGGCTTGCTAAATAACCACCAGCTCAATG
1 CCTGCTTAAATATAC-ACTGGCTCAAAGCCTGCTAAATAACCACCAGCTCAAGG
60714650 CCT
1 CCT
60714653 ATTTTTTCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 2 0.04
52 42 0.86
53 5 0.10
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (53 bp):
CCTGCTTAAATATACACTGGCTCAAAGCCTGCTAAATAACCACCAGCTCAAGG
Found at i:60714645 original size:26 final size:26
Alignment explanation
Indices: 60714564--60714652 Score: 106
Period size: 26 Copynumber: 3.4 Consensus size: 26
60714554 ATATACACTG
* *
60714564 GCTCAAAGCCTGCTAAATAACCATCA
1 GCTCAAGGCCTGCTAAATAACCACCA
* **
60714590 GCTCAAGGCCTGCTAAATAACAACTG
1 GCTCAAGGCCTGCTAAATAACCACCA
* *
60714616 GCTCGAGGCTTGCTAAATAACCACCA
1 GCTCAAGGCCTGCTAAATAACCACCA
*
60714642 GCTCAATGCCT
1 GCTCAAGGCCT
60714653 ATTTTTTCGA
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (26 bp):
GCTCAAGGCCTGCTAAATAACCACCA
Found at i:60727434 original size:12 final size:12
Alignment explanation
Indices: 60727404--60727436 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
60727394 ATAATATTTT
60727404 AAAATT-ATATA
1 AAAATTAATATA
60727415 AAAA-TAATATA
1 AAAATTAATATA
60727426 AAAATTAATAT
1 AAAATTAATAT
60727437 GGGCGAGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:60727657 original size:14 final size:15
Alignment explanation
Indices: 60727638--60727667 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
60727628 TTTAACTTAG
60727638 ATCTAAATTT-TAAA
1 ATCTAAATTTCTAAA
60727652 ATCTAAATTTCTAAA
1 ATCTAAATTTCTAAA
60727667 A
1 A
60727668 ATGAAAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
ATCTAAATTTCTAAA
Found at i:60735866 original size:28 final size:27
Alignment explanation
Indices: 60735818--60735881 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
60735808 CTTTAGAATG
* *
60735818 CGCCACGAAGGCATTCCTTTCCATAGAT
1 CGCCACAAAGGCATTCATTT-CATAGAT
60735846 CGCCACAAAGGC-TTCAATTTCATAGAT
1 CGCCACAAAGGCATTC-ATTTCATAGAT
* *
60735873 TGTCACAAA
1 CGCCACAAA
60735882 AGTTTTCGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 17 0.55
28 14 0.45
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (27 bp):
CGCCACAAAGGCATTCATTTCATAGAT
Found at i:60737444 original size:27 final size:27
Alignment explanation
Indices: 60737414--60737477 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
60737404 CTATCGTGAT
*
60737414 AGTAAACACAGGATAATCC-GCTAGGAC
1 AGTAAACACAGGATAATCCATC-AGGAC
* *
60737441 AGTAAACACGGGATGATCCATCAGGAC
1 AGTAAACACAGGATAATCCATCAGGAC
60737468 AGTAAACACA
1 AGTAAACACA
60737478 AAAAATCCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14
Consensus pattern (27 bp):
AGTAAACACAGGATAATCCATCAGGAC
Found at i:60742097 original size:1 final size:1
Alignment explanation
Indices: 60742093--60742126 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
60742083 TATATATATG
60742093 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
60742127 GTATTTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:60756084 original size:19 final size:18
Alignment explanation
Indices: 60756055--60756099 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
60756045 TTTATTTATT
* *
60756055 AAAATAATAATTTTATAA
1 AAAACAATAATCTTATAA
*
60756073 ATAAACAATAATCTTATAT
1 A-AAACAATAATCTTATAA
60756092 AAAACAAT
1 AAAACAAT
60756100 TTAAGCGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAACAATAATCTTATAA
Found at i:60758652 original size:20 final size:20
Alignment explanation
Indices: 60758629--60758670 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
60758619 CATGTGGGGT
60758629 TAAAAACACCCACCCATCCC
1 TAAAAACACCCACCCATCCC
*
60758649 TAAAAACACCCATCCATCCC
1 TAAAAACACCCACCCATCCC
60758669 TA
1 TA
60758671 CACACCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.45, G:0.00, T:0.14
Consensus pattern (20 bp):
TAAAAACACCCACCCATCCC
Found at i:60762761 original size:23 final size:23
Alignment explanation
Indices: 60762735--60762819 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
60762725 ATATTCACGG
*
60762735 ACATGTTCATTTAAC-TTAATCGA
1 ACATGTTCA-TGAACATTAATCGA
* *
60762758 ACATGTTCACGAACATTAAACGA
1 ACATGTTCATGAACATTAATCGA
*
60762781 ACATGTTCATGAACATATAATTGA
1 ACATGTTCATGAACAT-TAATCGA
*
60762805 ACATGTTCACGAACA
1 ACATGTTCATGAACA
60762820 ACATTAATAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 3 0.06
23 31 0.58
24 19 0.36
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (23 bp):
ACATGTTCATGAACATTAATCGA
Found at i:60762772 original size:12 final size:12
Alignment explanation
Indices: 60762755--60762819 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
60762745 TTAACTTAAT
60762755 CGAACATGTTCA
1 CGAACATGTTCA
**
60762767 CGAACAT-TAAA
1 CGAACATGTTCA
60762778 CGAACATGTTCA
1 CGAACATGTTCA
* * *
60762790 TGAACAT-ATAA
1 CGAACATGTTCA
*
60762801 TTGAACATGTTCA
1 -CGAACATGTTCA
60762814 CGAACA
1 CGAACA
60762820 ACATTAATAA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
11 11 0.28
12 27 0.68
13 2 0.05
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.25
Consensus pattern (12 bp):
CGAACATGTTCA
Found at i:60763588 original size:19 final size:20
Alignment explanation
Indices: 60763561--60763616 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
60763551 GACAAAATTT
*
60763561 AATTTAAATATATAAATT-A
1 AATTAAAATATATAAATTAA
*
60763580 TATTAAAATATA-ACAATTACA
1 AATTAAAATATATA-AATTA-A
60763601 AATTAAAATATATAAA
1 AATTAAAATATATAAA
60763617 ATTTTATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
21 14 0.47
22 1 0.03
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTAAAATATATAAATTAA
Found at i:60764532 original size:19 final size:19
Alignment explanation
Indices: 60764500--60764553 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
60764490 AAATCTTATA
*
60764500 ATTTTTACAA-TTTTAATC
1 ATTTTTAAAATTTTTAATC
*
60764518 ATTTTTAAAATTTTTAATG
1 ATTTTTAAAATTTTTAATC
*
60764537 ATTTTCAAAATTATTTA
1 ATTTTTAAAATT-TTTA
60764554 TTATTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 9 0.29
19 18 0.58
20 4 0.13
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTTAAAATTTTTAATC
Found at i:60764644 original size:20 final size:20
Alignment explanation
Indices: 60764621--60764685 Score: 71
Period size: 19 Copynumber: 3.2 Consensus size: 20
60764611 AATTTTTACA
* *
60764621 ATTTTTTATAAAATTTTAAT
1 ATTTTTTAAAAAACTTTAAT
*
60764641 A-TTTTAAAAAAACTTT-AT
1 ATTTTTTAAAAAACTTTAAT
60764659 ATATTTTTAAATAAACTTTAAT
1 AT-TTTTTAAA-AAACTTTAAT
60764681 ATTTT
1 ATTTT
60764686 AAAATAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
18 3 0.08
19 12 0.32
20 8 0.22
21 10 0.27
22 4 0.11
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTTTAAAAAACTTTAAT
Found at i:60764698 original size:20 final size:20
Alignment explanation
Indices: 60764635--60764692 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
60764625 TTTATAAAAT
60764635 TTTAATATTTTAAAA-AAAC
1 TTTAATATTTTAAAATAAAC
*
60764654 TTTATATATTTTTAAATAAAC
1 TTTA-ATATTTTAAAATAAAC
60764675 TTTAATATTTTAAAATAA
1 TTTAATATTTTAAAATAA
60764693 TTTTTACTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 4 0.11
20 23 0.66
21 8 0.23
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTAATATTTTAAAATAAAC
Found at i:60765358 original size:18 final size:18
Alignment explanation
Indices: 60765321--60765376 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
60765311 TAAAAAATTT
*
60765321 AGAAATATATATAATCTAAA
1 AGAAATATA-A-AATATAAA
60765341 A-AACATATAAAATATAAA
1 AGAA-ATATAAAATATAAA
*
60765359 AGAATTATAAAA-ATAAA
1 AGAAATATAAAATATAAA
60765376 A
1 A
60765377 TTTTAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 6 0.19
18 15 0.47
19 5 0.16
20 6 0.19
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (18 bp):
AGAAATATAAAATATAAA
Found at i:60772233 original size:28 final size:28
Alignment explanation
Indices: 60772187--60772270 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 28
60772177 AAAAACAAAA
*
60772187 AAATTACATCTTGATCCCTAATATTTT-G
1 AAATTACA-CTTGAGCCCTAATATTTTCG
*
60772215 TAAATTACACTTGGGCCCTAA-ACTTTCTCG
1 -AAATTACACTTGAGCCCTAATA-TTT-TCG
*
60772245 AAATTACACTTTAGCCCT-ATATTTTC
1 AAATTACACTTGAGCCCTAATATTTTC
60772271 CTAAAATTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
27 3 0.06
28 17 0.36
29 26 0.55
30 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (28 bp):
AAATTACACTTGAGCCCTAATATTTTCG
Found at i:60772848 original size:12 final size:12
Alignment explanation
Indices: 60772827--60772893 Score: 73
Period size: 12 Copynumber: 5.6 Consensus size: 12
60772817 CCCGAAGAAG
60772827 AAGAAGAAAAAGA
1 AAGAA-AAAAAGA
60772840 AAG-AAAAAAGA
1 AAGAAAAAAAGA
* *
60772851 AGGAGAAAAAGA
1 AAGAAAAAAAGA
* *
60772863 GAGAAAAAAGGA
1 AAGAAAAAAAGA
*
60772875 AAGAAAAAAAAA
1 AAGAAAAAAAGA
60772887 AAGAAAA
1 AAGAAAA
60772894 TCTACAGTCG
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
11 9 0.20
12 32 0.73
13 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAGA
Found at i:60772849 original size:11 final size:11
Alignment explanation
Indices: 60772833--60772893 Score: 68
Period size: 11 Copynumber: 5.3 Consensus size: 11
60772823 GAAGAAGAAG
60772833 AAAAAGAAAGA
1 AAAAAGAAAGA
*
60772844 AAAAAGAAGGA
1 AAAAAGAAAGA
*
60772855 GAAAAAGAGAGA
1 -AAAAAGAAAGA
60772867 AAAAAGGAAAGAA
1 AAAAA-GAAAG-A
*
60772880 AAAAAAAAAGA
1 AAAAAGAAAGA
60772891 AAA
1 AAA
60772894 TCTACAGTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
11 19 0.45
12 17 0.40
13 6 0.14
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:60772857 original size:23 final size:23
Alignment explanation
Indices: 60772824--60772893 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
60772814 TGACCCGAAG
*
60772824 AAGAAGAAGAAAAAGAAAGAAAA
1 AAGAAGGAGAAAAAGAAAGAAAA
*
60772847 AAGAAGGAGAAAAAGAGAGAAAA
1 AAGAAGGAGAAAAAGAAAGAAAA
* * *
60772870 AAGGAAAGAAAAAAAAAAAGAAAA
1 AA-GAAGGAGAAAAAGAAAGAAAA
60772894 TCTACAGTCG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 23 0.57
24 17 0.43
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (23 bp):
AAGAAGGAGAAAAAGAAAGAAAA
Found at i:60772877 original size:16 final size:16
Alignment explanation
Indices: 60772833--60772892 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
60772823 GAAGAAGAAG
60772833 AAAAAGAAAGAAAAAA
1 AAAAAGAAAGAAAAAA
* *
60772849 GAAGGAGAA-AAAGAGAGAA
1 -AA--A-AAGAAAGAAAAAA
*
60772868 AAAAGGAAAGAAAAAA
1 AAAAAGAAAGAAAAAA
60772884 AAAAAGAAA
1 AAAAAGAAA
60772893 ATCTACAGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
15 1 0.03
16 17 0.52
17 2 0.06
18 2 0.06
19 9 0.27
20 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAA
Found at i:60773207 original size:21 final size:19
Alignment explanation
Indices: 60773181--60773224 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
60773171 AACATCCAGC
60773181 AAAAAAAAAAGGAAAGAGAAG
1 AAAAAAAAAAGGAAA-A-AAG
*
60773202 AAAAAAAAAGGGAAAAAAG
1 AAAAAAAAAAGGAAAAAAG
60773221 AAAA
1 AAAA
60773225 GGGCCCACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 1 0.05
21 14 0.64
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGGAAAAAAG
Found at i:60773699 original size:17 final size:17
Alignment explanation
Indices: 60773677--60774148 Score: 169
Period size: 18 Copynumber: 25.8 Consensus size: 17
60773667 ACAATTTTAA
60773677 AAAAATTGTCGTG-TTTC
1 AAAAATT-TCGTGTTTTC
* *
60773694 AAAAATTTCGAGTTTTAA
1 AAAAATTTCGTGTTTT-C
**
60773712 AAAAAAATC-TAGTTTTC
1 AAAAATTTCGT-GTTTTC
*
60773729 AAAAAAATTTC-TCATGTTTC
1 --AAAAATTTCGT-GT-TTTC
*
60773749 AAAAATTTTTGTGTTTTC
1 AAAAA-TTTCGTGTTTTC
*
60773767 AAAAATTCTCGTG-CTTC
1 AAAAATT-TCGTGTTTTC
*
60773784 AAAAATTTTCGCGTTTTC
1 AAAAA-TTTCGTGTTTTC
*
60773802 AAAAATTTTCGTGTTTTAAA
1 AAAAA-TTTCGTGTTTT--C
*
60773822 AAAAATTTCGT-ATTTC
1 AAAAATTTCGTGTTTTC
*
60773838 AAAAATATTCGTGTTTTAA
1 AAAAAT-TTCGTGTTTT-C
* *
60773857 AAAAATAAAAAAAGAATCCAT-TTTTC
1 AAAAAT----------TTCGTGTTTTC
*
60773883 -AAAATCGTCGTGTTTTC
1 AAAAAT-TTCGTGTTTTC
* *
60773900 -AAAATTCCAATGTTTT-
1 AAAAATTTC-GTGTTTTC
* *
60773916 AAAAACTTCCGTATTTTC
1 AAAAA-TTTCGTGTTTTC
*
60773934 AAAAATTTCCGTGCTTTC
1 AAAAATTT-CGTGTTTTC
60773952 AAAAATCTTCGTGTTTTC
1 AAAAAT-TTCGTGTTTTC
*
60773970 AAAAATCCTCGTGTTTTC
1 AAAAAT-TTCGTGTTTTC
*
60773988 AAAAATTCCG-GTATTTC
1 AAAAATTTCGTGT-TTTC
*
60774005 AAAAATTCTCGTGTTTTT
1 AAAAATT-TCGTGTTTTC
* *
60774023 AGAACTTCTCGTGTTTT-
1 AAAAATT-TCGTGTTTTC
*
60774040 AAAAACTTCCGTGTTTTC
1 AAAAA-TTTCGTGTTTTC
* *
60774058 AAAATTTTCGTGTTTTTTT
1 AAAAATTTCGTG--TTTTC
* *
60774077 AAGAATTTTCGTG-TCTC
1 AA-AAATTTCGTGTTTTC
*
60774094 TAAAATTCTCGTGTTCTT-
1 AAAAATT-TCGTGTT-TTC
60774112 AAAAATTTTTCGTGTTTTTTAC
1 AAAAA--TTTCGTG--TTTT-C
60774134 AAAAATTTTCGTGTT
1 AAAAA-TTTCGTGTT
60774149 AAAAAAAATT
Statistics
Matches: 349, Mismatches: 57, Indels: 96
0.70 0.11 0.19
Matches are distributed among these distances:
16 19 0.05
17 94 0.27
18 141 0.40
19 43 0.12
20 24 0.07
21 10 0.03
22 5 0.01
25 5 0.01
27 4 0.01
28 4 0.01
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:60773838 original size:36 final size:34
Alignment explanation
Indices: 60773671--60773862 Score: 145
Period size: 35 Copynumber: 5.4 Consensus size: 34
60773661 TATGGTACAA
*
60773671 TTTTAAAAAAATTGTCGTGTTTCAAAAA-TTTCGAG
1 TTTTAAAAAAATT-TCGT-TTTCAAAAATTTTCGTG
* * *
60773706 TTTTAAAAAAAAATCTAGTTTTCAAAAAAATTTCTCATG
1 TTTT--AAAAAAATTTCGTTTTC--AAAAATTT-TCGTG
* ** * *
60773745 TTTCAAAAATTTTTGTGTTTTCAAAAATTCTCGTG
1 TTTTAAAAAAATTT-CGTTTTCAAAAATTTTCGTG
* * *
60773780 -CTTCAAAAATTTTCGCGTTTTCAAAAATTTTCGTG
1 TTTTAAAAAAATTT--CGTTTTCAAAAATTTTCGTG
*
60773815 TTTTAAAAAAAATTTCGTATTTCAAAAATATTCGTG
1 TTTT-AAAAAAATTTCGT-TTTCAAAAATTTTCGTG
60773851 TTTTAAAAAAAT
1 TTTTAAAAAAAT
60773863 AAAAAAAGAA
Statistics
Matches: 125, Mismatches: 21, Indels: 22
0.74 0.12 0.13
Matches are distributed among these distances:
34 9 0.07
35 42 0.34
36 32 0.26
37 28 0.22
38 8 0.06
39 6 0.05
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.42
Consensus pattern (34 bp):
TTTTAAAAAAATTTCGTTTTCAAAAATTTTCGTG
Found at i:60774016 original size:35 final size:35
Alignment explanation
Indices: 60773891--60774073 Score: 164
Period size: 35 Copynumber: 5.2 Consensus size: 35
60773881 TCAAAATCGT
*
60773891 CGTGTTTTC-AAAATTC-CAATGTTTT-AAAAACTTC
1 CGTGTTTTCAAAAATTCTC-GTGTTTTCAAAAA-TTC
* * *
60773925 CGTATTTTCAAAAATT-TCCGTGCTTTCAAAAATCTT
1 CGTGTTTTCAAAAATTCT-CGTGTTTTCAAAAAT-TC
*
60773961 CGTGTTTTCAAAAATCCTCGTGTTTTCAAAAATTC
1 CGTGTTTTCAAAAATTCTCGTGTTTTCAAAAATTC
* * *
60773996 CG-GTATTTCAAAAATTCTCGTGTTTTTAGAACTTC
1 CGTGT-TTTCAAAAATTCTCGTGTTTTCAAAAATTC
* *
60774031 TCGTGTTTT-AAAAACTTC-CGTGTTTTCAAAATTTT
1 -CGTGTTTTCAAAAA-TTCTCGTGTTTTCAAAAATTC
60774066 CGTGTTTT
1 CGTGTTTT
60774074 TTTAAGAATT
Statistics
Matches: 123, Mismatches: 16, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
34 18 0.15
35 59 0.48
36 43 0.35
37 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.44
Consensus pattern (35 bp):
CGTGTTTTCAAAAATTCTCGTGTTTTCAAAAATTC
Found at i:60774075 original size:53 final size:53
Alignment explanation
Indices: 60773910--60774130 Score: 195
Period size: 53 Copynumber: 4.1 Consensus size: 53
60773900 AAAATTCCAA
* * * * *
60773910 TGTTTTAAAAACTTC-CGTATTTTCAAAAATTTCCGTGCTTTCAAAAATCTTCG
1 TGTTTTTAGAACTTCTCGTGTTTTCAAAAA-TTCCGTGTTTTCAAAAATTTTCG
* * * * *
60773963 TGTTTTCAAAAATCCTCGTGTTTTCAAAAATTCCG-GTATTTCAAAAATTCTCG
1 TGTTTTTAGAACTTCTCGTGTTTTCAAAAATTCCGTGT-TTTCAAAAATTTTCG
60774016 TGTTTTTAGAACTTCTCGTGTTTT-AAAAACTTCCGTGTTTTC-AAAATTTTCG
1 TGTTTTTAGAACTTCTCGTGTTTTCAAAAA-TTCCGTGTTTTCAAAAATTTTCG
* * *
60774068 TGTTTTTTTAAGAA-TTTTCGTG-TCTCTAAAATTCTCGTGTTCTT-AAAAATTTTTCG
1 TG--TTTTT-AGAACTTCTCGTGTTTTCAAAAATTC-CGTGTT-TTCAAAAA-TTTTCG
60774124 TGTTTTT
1 TGTTTTT
60774131 TACAAAAATT
Statistics
Matches: 141, Mismatches: 15, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
52 17 0.12
53 64 0.45
54 42 0.30
55 10 0.07
56 8 0.06
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.47
Consensus pattern (53 bp):
TGTTTTTAGAACTTCTCGTGTTTTCAAAAATTCCGTGTTTTCAAAAATTTTCG
Found at i:60778278 original size:4 final size:4
Alignment explanation
Indices: 60778269--60778304 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
60778259 AAAAAGTTCA
60778269 TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG
60778305 GGTGAGATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:60780236 original size:19 final size:18
Alignment explanation
Indices: 60780212--60780314 Score: 56
Period size: 20 Copynumber: 5.8 Consensus size: 18
60780202 TATTTTTTCT
60780212 AAAATTAAAACATTTATAA
1 AAAATTAAAA-ATTTATAA
*
60780231 AAAATTCAAAATTTAT--
1 AAAATTAAAAATTTATAA
* *
60780247 --ATTGTAAAAAATTATAA
1 AAAAT-TAAAAATTTATAA
* *
60780264 AAACTCTAAAAAATATATAA
1 AAAAT-T-AAAAATTTATAA
*
60780284 AAAAGTT--AAATTTTTAA
1 AAAA-TTAAAAATTTATAA
*
60780301 AAATTTAAAAATTT
1 AAAATTAAAAATTT
60780315 TCTAAAATAA
Statistics
Matches: 63, Mismatches: 12, Indels: 19
0.67 0.13 0.20
Matches are distributed among these distances:
14 2 0.03
15 9 0.14
16 2 0.03
17 11 0.17
18 12 0.19
19 12 0.19
20 14 0.22
21 1 0.02
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAATTAAAAATTTATAA
Found at i:60780244 original size:18 final size:19
Alignment explanation
Indices: 60780212--60780247 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
60780202 TATTTTTTCT
60780212 AAAATTAAAACATTTATAA
1 AAAATTAAAACATTTATAA
*
60780231 AAAATTCAAA-ATTTATA
1 AAAATTAAAACATTTATA
60780248 TTGTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATTAAAACATTTATAA
Found at i:60781692 original size:23 final size:23
Alignment explanation
Indices: 60781666--60781719 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
60781656 TGATTTTTAA
*
60781666 ATTTTGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
60781689 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
60781712 ATTTAGAA
1 ATTTAGAA
60781720 AAAATCTAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:60781693 original size:13 final size:13
Alignment explanation
Indices: 60781675--60781717 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
60781665 AATTTTGAAT
60781675 TATTTAGTGATAA
1 TATTTAGTGATAA
*
60781688 TATTTA--GA-AT
1 TATTTAGTGATAA
60781698 TATTTAGTGATAA
1 TATTTAGTGATAA
60781711 TATTTAG
1 TATTTAG
60781718 AAAAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 2 0.08
13 14 0.56
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (13 bp):
TATTTAGTGATAA
Done.