Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 113 of 141
Found at i:33117272 original size:23 final size:24
Alignment explanation
Indices: 33117223--33117274 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
33117213 CATAGTGATG
*
33117223 TATGATTAAGATATGAAAATGTCA
1 TATGATTAAGATATGAAAATGACA
* * *
33117247 TATGATTGAGA-ATGAAATTGAGA
1 TATGATTAAGATATGAAAATGACA
33117270 TATGA
1 TATGA
33117275 AATGAAACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.33
Consensus pattern (24 bp):
TATGATTAAGATATGAAAATGACA
Found at i:33124335 original size:16 final size:17
Alignment explanation
Indices: 33124303--33124339 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
33124293 AAAATGAAAT
33124303 AAAATTAAAGAAATTAC
1 AAAATTAAAGAAATTAC
33124320 AAAA-TAAA-AAATTTAC
1 AAAATTAAAGAAA-TTAC
33124336 AAAA
1 AAAA
33124340 ATTGAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.16
16 12 0.63
17 4 0.21
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (17 bp):
AAAATTAAAGAAATTAC
Found at i:33124403 original size:22 final size:22
Alignment explanation
Indices: 33124378--33124425 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
33124368 AGTACAGAAA
**
33124378 ATTGCGAGAATAAATGTATAAG
1 ATTGCGAGAATAAATAAATAAG
* *
33124400 ATTGGGAGAATAGATAAATAAG
1 ATTGCGAGAATAAATAAATAAG
33124422 ATTG
1 ATTG
33124426 AATAAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.46, C:0.02, G:0.25, T:0.27
Consensus pattern (22 bp):
ATTGCGAGAATAAATAAATAAG
Found at i:33125563 original size:63 final size:64
Alignment explanation
Indices: 33125480--33125607 Score: 249
Period size: 63 Copynumber: 2.0 Consensus size: 64
33125470 GGGTTGGATT
33125480 GATTAAATTTTTTAGGGTTTGGTATGTTTTCGATGGATTTGGGTTGCAAAAGTCGGTTTAACTG
1 GATTAAATTTTTTAGGGTTTGGTATGTTTTCGATGGATTTGGGTTGCAAAAGTCGGTTTAACTG
33125544 GATTAAA-TTTTTAGGGTTTGGTATGTTTTCGATGGATTTGGGTTGCAAAAGTCGGTTTAACTG
1 GATTAAATTTTTTAGGGTTTGGTATGTTTTCGATGGATTTGGGTTGCAAAAGTCGGTTTAACTG
33125607 G
1 G
33125608 TTTTGCATTG
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
63 57 0.89
64 7 0.11
ACGTcount: A:0.22, C:0.06, G:0.29, T:0.43
Consensus pattern (64 bp):
GATTAAATTTTTTAGGGTTTGGTATGTTTTCGATGGATTTGGGTTGCAAAAGTCGGTTTAACTG
Found at i:33137907 original size:19 final size:19
Alignment explanation
Indices: 33137883--33137923 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
33137873 TATTTTAAAG
33137883 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
*
33137902 TTATTTGGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
33137921 TTA
1 TTA
33137924 GAATAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (19 bp):
TTATTTAGGTAGATAAATC
Found at i:33138011 original size:41 final size:41
Alignment explanation
Indices: 33137961--33138042 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
33137951 ATATTTTATT
*
33137961 TTATATTTTAGTAGTTTATTTGAATAA-GAGAATTATTTTCC
1 TTATATTTTAGTAGTTTATTAGAATAACG-GAATTATTTTCC
*
33138002 TTATTTTTTAGTAGTTTATTAGAATAACGGAATTATTTTCC
1 TTATATTTTAGTAGTTTATTAGAATAACGGAATTATTTTCC
33138043 CAATTAGGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 37 0.97
42 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.51
Consensus pattern (41 bp):
TTATATTTTAGTAGTTTATTAGAATAACGGAATTATTTTCC
Found at i:33141512 original size:15 final size:16
Alignment explanation
Indices: 33141492--33141530 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
33141482 TAATTAAGTT
33141492 AATTATAAAAAT-ATA
1 AATTATAAAAATGATA
*
33141507 AATTATTAAAATGATA
1 AATTATAAAAATGATA
33141523 ATATTATA
1 A-ATTATA
33141531 TTTTTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 11 0.55
16 4 0.20
17 5 0.25
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AATTATAAAAATGATA
Found at i:33141716 original size:16 final size:16
Alignment explanation
Indices: 33141697--33141728 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33141687 TATTTGTGTT
*
33141697 TTATGTTTAAATTTTA
1 TTATGATTAAATTTTA
33141713 TTATGATTAAATTTTA
1 TTATGATTAAATTTTA
33141729 ATTAATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
TTATGATTAAATTTTA
Found at i:33143479 original size:31 final size:31
Alignment explanation
Indices: 33143443--33143503 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
33143433 AACATGTGGC
33143443 ATAACCAGTGTTAACATACATTAACTTTTCT
1 ATAACCAGTGTTAACATACATTAACTTTTCT
*
33143474 ATAACCAGTGTTAACATACATTAATTTTTC
1 ATAACCAGTGTTAACATACATTAACTTTTC
33143504 CATCTAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (31 bp):
ATAACCAGTGTTAACATACATTAACTTTTCT
Found at i:33148425 original size:12 final size:11
Alignment explanation
Indices: 33148407--33148440 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
33148397 ATGTTTATTA
33148407 AGTTTTCTTTT
1 AGTTTTCTTTT
33148418 AGGTTTTCTTGTT
1 A-GTTTTCTT-TT
33148431 AGTTTTCTTT
1 AGTTTTCTTT
33148441 CAAATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 16 0.76
13 3 0.14
ACGTcount: A:0.09, C:0.09, G:0.15, T:0.68
Consensus pattern (11 bp):
AGTTTTCTTTT
Found at i:33166738 original size:17 final size:17
Alignment explanation
Indices: 33166713--33166752 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
33166703 TAGAATCTAG
* *
33166713 TTGTGAAAATTATTTAA
1 TTGTAAAAATTAATTAA
33166730 TTGTAAAAATTAATTAA
1 TTGTAAAAATTAATTAA
33166747 TT-TAAA
1 TTGTAAA
33166753 TTAATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (17 bp):
TTGTAAAAATTAATTAA
Found at i:33174766 original size:12 final size:12
Alignment explanation
Indices: 33174749--33174775 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
33174739 TAATTTGCAA
33174749 AATTATTAAATT
1 AATTATTAAATT
33174761 AATTATTAAATT
1 AATTATTAAATT
33174773 AAT
1 AAT
33174776 AGAAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTATTAAATT
Found at i:33175671 original size:28 final size:28
Alignment explanation
Indices: 33175638--33175705 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
33175628 CTGTTTTATT
33175638 TAAGCACTTTGGTGTTGTTCTGTTCTGA
1 TAAGCACTTTGGTGTTGTTCTGTTCTGA
** *
33175666 TAAGCACTACGGTGTTGTTCTGTTCTGT
1 TAAGCACTTTGGTGTTGTTCTGTTCTGA
33175694 TAATGCACTTTG
1 TAA-GCACTTTG
33175706 ATGCCCTCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 28 0.82
29 6 0.18
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.44
Consensus pattern (28 bp):
TAAGCACTTTGGTGTTGTTCTGTTCTGA
Found at i:33185726 original size:14 final size:13
Alignment explanation
Indices: 33185699--33185729 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
33185689 TGTTAATGTT
33185699 TTAATTAAATTAA
1 TTAATTAAATTAA
33185712 TTAATTAAGATTAA
1 TTAATTAA-ATTAA
33185726 TTAA
1 TTAA
33185730 AATATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
TTAATTAAATTAA
Found at i:33186018 original size:22 final size:20
Alignment explanation
Indices: 33185977--33186018 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
33185967 CTATTAATGA
*
33185977 GAAATTGATGAATTAGGCTT
1 GAAATTGATGAATTAAGCTT
33185997 GAAATTGATAGATATTAAGCTT
1 GAAATTGAT-GA-ATTAAGCTT
33186019 AGATCATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (20 bp):
GAAATTGATGAATTAAGCTT
Found at i:33191488 original size:30 final size:29
Alignment explanation
Indices: 33191432--33191488 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
33191422 ATAAAAGCGA
* * *
33191432 GCCTTTGTGGCTATTTCTGTTAAGGAAAT
1 GCCTTTGTGGCAATCTCTGATAAGGAAAT
33191461 GCCTTTGTGGCAAATCTCTGATAAGGAA
1 GCCTTTGTGGC-AATCTCTGATAAGGAA
33191489 TACATGTGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35
Consensus pattern (29 bp):
GCCTTTGTGGCAATCTCTGATAAGGAAAT
Found at i:33191678 original size:29 final size:29
Alignment explanation
Indices: 33191541--33191779 Score: 187
Period size: 29 Copynumber: 8.2 Consensus size: 29
33191531 CCTAAAAAAT
* **
33191541 TGCCTTTGTGGCTAATCCATGTT-AAAGGA
1 TGCCTTTGTGGC-GATCTTTGTTAAAAGGA
* * * *
33191570 AGCCTTTGCGGCGATCTCTATT-AAAGGA
1 TGCCTTTGTGGCGATCTTTGTTAAAAGGA
* * * * * *
33191598 AGACTTTGTGGCAATCTTTATTAACAGGC
1 TGCCTTTGTGGCGATCTTTGTTAAAAGGA
* *
33191627 TGCCTTTTGTGGCTATCTCTGTTAAAAGGA
1 TGCC-TTTGTGGCGATCTTTGTTAAAAGGA
* *
33191657 TGCCTTTGTGTCGATTTTTGTTAAAAGGA
1 TGCCTTTGTGGCGATCTTTGTTAAAAGGA
* * *
33191686 TACCTTTGTGGCTATCTTTGTTAAAAAGA
1 TGCCTTTGTGGCGATCTTTGTTAAAAGGA
***
33191715 TGCCTTTGTGG-GTATCTCAATTAAAAGGA
1 TGCCTTTGTGGCG-ATCTTTGTTAAAAGGA
** * *
33191744 TGCCTTTGTGGTTATCTCTGTTAAAAGAA
1 TGCCTTTGTGGCGATCTTTGTTAAAAGGA
33191773 TGCCTTT
1 TGCCTTT
33191780 ATGGTGAGAC
Statistics
Matches: 168, Mismatches: 38, Indels: 8
0.79 0.18 0.04
Matches are distributed among these distances:
28 30 0.18
29 114 0.68
30 24 0.14
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (29 bp):
TGCCTTTGTGGCGATCTTTGTTAAAAGGA
Found at i:33191723 original size:87 final size:86
Alignment explanation
Indices: 33191533--33191768 Score: 228
Period size: 87 Copynumber: 2.7 Consensus size: 86
33191523 TGGCACGACC
* *
33191533 TAAAAA-ATTGCCTTTGTGGCTAATC-CATGTT-AAAGGAAGCCTTTGCGGCGATCTCTATTAAA
1 TAAAAAGA-TGCCTTTGTGGCT-ATCTC-TGTTAAAAGGATGCCTTTGTGGCGATCTCTATTAAA
33191595 GGAAGACTTTGTGGCAATCTTTAT
63 GGAAGACTTTGTGGCAATCTTTAT
* * * * * * *
33191619 TAACAGGCTGCCTTTTGTGGCTATCTCTGTTAAAAGGATGCCTTTGTGTCGATTTTTGTTAAAAG
1 TAAAAAGATGCC-TTTGTGGCTATCTCTGTTAAAAGGATGCCTTTGTGGCGATCTCTATT-AAAG
* * *
33191684 GATA-CCTTTGTGGCTATCTTTGT
64 GA-AGACTTTGTGGCAATCTTTAT
* ** ** *
33191707 TAAAAAGATGCCTTTGTGGGTATCTCAATTAAAAGGATGCCTTTGTGGTTATCTCTGTTAAA
1 TAAAAAGATGCCTTTGTGGCTATCTCTGTTAAAAGGATGCCTTTGTGGCGATCTCTATTAAA
33191769 AGAATGCCTT
Statistics
Matches: 121, Mismatches: 23, Indels: 12
0.78 0.15 0.08
Matches are distributed among these distances:
86 18 0.15
87 71 0.59
88 31 0.26
89 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (86 bp):
TAAAAAGATGCCTTTGTGGCTATCTCTGTTAAAAGGATGCCTTTGTGGCGATCTCTATTAAAGGA
AGACTTTGTGGCAATCTTTAT
Found at i:33191769 original size:87 final size:88
Alignment explanation
Indices: 33191564--33191779 Score: 231
Period size: 87 Copynumber: 2.5 Consensus size: 88
33191554 AATCCATGTT
* * * * * * * * *
33191564 AAAGGAAGCCTTTGCGGCGATCTCTATTAAAGGAAGA-CTTTGTGGCAATCTTTATTAACAGGCT
1 AAAGGATGCCTTTGTGTCGATCTCTGTTAAAAGAATACCTTTGTGGCAATCTTTATTAAAAAGAT
**
33191628 GCCTTTTGTGGCTATCTCTGTTA
66 GCCTTTTGTGGCTATCTCAATTA
* * * * *
33191651 AAAGGATGCCTTTGTGTCGATTTTTGTTAAAAGGATACCTTTGTGGCTATCTTTGTTAAAAAGAT
1 AAAGGATGCCTTTGTGTCGATCTCTGTTAAAAGAATACCTTTGTGGCAATCTTTATTAAAAAGAT
*
33191716 GCC-TTTGTGGGTATCTCAATTA
66 GCCTTTTGTGGCTATCTCAATTA
* *
33191738 AAAGGATGCCTTTGTGGT-TATCTCTGTTAAAAGAATGCCTTT
1 AAAGGATGCCTTTGT-GTCGATCTCTGTTAAAAGAATACCTTT
33191780 ATGGTGAGAC
Statistics
Matches: 105, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
87 78 0.74
88 27 0.26
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (88 bp):
AAAGGATGCCTTTGTGTCGATCTCTGTTAAAAGAATACCTTTGTGGCAATCTTTATTAAAAAGAT
GCCTTTTGTGGCTATCTCAATTA
Found at i:33194279 original size:25 final size:25
Alignment explanation
Indices: 33194250--33194346 Score: 113
Period size: 25 Copynumber: 3.9 Consensus size: 25
33194240 GATACTCCAC
* *
33194250 AGCTCATGAGAGCATACTGATTTAT
1 AGCTCGTGAGAGCATACCGATTTAT
* *
33194275 AGCTCGTAAAAGCATACCGATTTAT
1 AGCTCGTGAGAGCATACCGATTTAT
* *
33194300 AGCTTGTGAGAGCATACCGATCTAT
1 AGCTCGTGAGAGCATACCGATTTAT
***
33194325 AGCTCGACTGAGCATACCGATT
1 AGCTCGTGAGAGCATACCGATT
33194347 CACAGCTCAT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (25 bp):
AGCTCGTGAGAGCATACCGATTTAT
Found at i:33194361 original size:25 final size:24
Alignment explanation
Indices: 33194250--33194366 Score: 85
Period size: 25 Copynumber: 4.7 Consensus size: 24
33194240 GATACTCCAC
* *
33194250 AGCTCATGAGAGCATACTGATTTAT
1 AGCTCAT-AGAGCATACCGATTCAT
* * *
33194275 AGCTCGTAAAAGCATACCGATTTAT
1 AGCTCAT-AGAGCATACCGATTCAT
**
33194300 AGCTTGTGAGAGCATACCGA-TCTAT
1 AGCTCAT-AGAGCATACCGATTC-AT
*
33194325 AGCTCGACT-GAGCATACCGATTCAC
1 AGCTC-A-TAGAGCATACCGATTCAT
33194350 AGCTCATATGAGCATAC
1 AGCTCATA-GAGCATAC
33194367 ATGTACATGA
Statistics
Matches: 75, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
23 1 0.01
24 2 0.03
25 69 0.92
26 2 0.03
27 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (24 bp):
AGCTCATAGAGCATACCGATTCAT
Found at i:33194363 original size:50 final size:50
Alignment explanation
Indices: 33194247--33194366 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
33194237 GCGGATACTC
* *
33194247 CACAGCTCATGAGAGCATACTGATTTATAGCTCGTAAAAGCATACCGATT
1 CACAGCTCATGAGAGCATACCGATCTATAGCTCGTAAAAGCATACCGATT
* * ** **
33194297 TATAGCTTGTGAGAGCATACCGATCTATAGCTCG-ACTGAGCATACCGATT
1 CACAGCTCATGAGAGCATACCGATCTATAGCTCGTA-AAAGCATACCGATT
33194347 CACAGCTCAT-ATGAGCATAC
1 CACAGCTCATGA-GAGCATAC
33194367 ATGTACATGA
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
49 2 0.04
50 54 0.96
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (50 bp):
CACAGCTCATGAGAGCATACCGATCTATAGCTCGTAAAAGCATACCGATT
Found at i:33201985 original size:25 final size:25
Alignment explanation
Indices: 33201909--33202003 Score: 86
Period size: 25 Copynumber: 3.8 Consensus size: 25
33201899 TACTCCACAT
* *
33201909 CTCGTGAGATCATACTGATTTATAG
1 CTCGTGAGAGCATACCGATTTATAG
* * * *
33201934 CTTGTAAGTGCATACCGGTTTATAG
1 CTCGTGAGAGCATACCGATTTATAG
* *
33201959 CTCGTGAGAGCATACCGATCTACAG
1 CTCGTGAGAGCATACCGATTTATAG
33201984 CTCGACT-A-AGCATACCGATT
1 CTCG--TGAGAGCATACCGATT
33202004 CACAGGTCAT
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
25 53 0.96
26 1 0.02
27 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (25 bp):
CTCGTGAGAGCATACCGATTTATAG
Found at i:33203158 original size:12 final size:13
Alignment explanation
Indices: 33203141--33203169 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
33203131 GCTGTTACAT
33203141 GGCCTAGCACAC-
1 GGCCTAGCACACA
33203153 GGCCTAGCACACA
1 GGCCTAGCACACA
33203166 GGCC
1 GGCC
33203170 CAAGTCAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.41, G:0.28, T:0.07
Consensus pattern (13 bp):
GGCCTAGCACACA
Found at i:33211401 original size:9 final size:9
Alignment explanation
Indices: 33211387--33211425 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
33211377 TATTCTATTA
33211387 TGTTTTTTT
1 TGTTTTTTT
33211396 TGTTTTTTT
1 TGTTTTTTT
33211405 TGTTCTATTTT
1 TGTT-T-TTTT
*
33211416 GGTTTTTTT
1 TGTTTTTTT
33211425 T
1 T
33211426 TCTATTGTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 17 0.65
10 2 0.08
11 7 0.27
ACGTcount: A:0.03, C:0.03, G:0.13, T:0.82
Consensus pattern (9 bp):
TGTTTTTTT
Found at i:33213883 original size:19 final size:18
Alignment explanation
Indices: 33213859--33213907 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
33213849 TGAGATTCAA
*
33213859 TTAATTTATTTTAGATTAC
1 TTAATTTAGTTT-GATTAC
*
33213878 TTAATTTAGTTTGATTAAT
1 TTAATTTAGTTTGATT-AC
33213897 TTAA-TTAGTTT
1 TTAATTTAGTTT
33213908 AATTTATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (18 bp):
TTAATTTAGTTTGATTAC
Found at i:33228771 original size:18 final size:18
Alignment explanation
Indices: 33228750--33228789 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
33228740 TTCATACAAT
*
33228750 CATAGGTTCGCATAATAA
1 CATAGGTTCACATAATAA
33228768 CATAGGTTCACATAATAA
1 CATAGGTTCACATAATAA
33228786 CATA
1 CATA
33228790 CAACATGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (18 bp):
CATAGGTTCACATAATAA
Found at i:33228775 original size:43 final size:43
Alignment explanation
Indices: 33228728--33228819 Score: 132
Period size: 43 Copynumber: 2.1 Consensus size: 43
33228718 ACATCAATAA
* *
33228728 AGGTTCACATACT-TCATACAATCATAGGTTCGCATAATAACAT
1 AGGTTCACATAATAACATACAA-CATAGGTTCGCATAATAACAT
* *
33228771 AGGTTCACATAATAACATACAACATGGGTTTGCATAATAACAT
1 AGGTTCACATAATAACATACAACATAGGTTCGCATAATAACAT
33228814 AGGTTC
1 AGGTTC
33228820 GTAGAGTAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 37 0.84
44 7 0.16
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.29
Consensus pattern (43 bp):
AGGTTCACATAATAACATACAACATAGGTTCGCATAATAACAT
Found at i:33228800 original size:25 final size:25
Alignment explanation
Indices: 33228766--33228814 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
33228756 TTCGCATAAT
33228766 AACATAGGTTCACATAATAACATAC
1 AACATAGGTTCACATAATAACATAC
* **
33228791 AACATGGGTTTGCATAATAACATA
1 AACATAGGTTCACATAATAACATA
33228815 GGTTCGTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (25 bp):
AACATAGGTTCACATAATAACATAC
Found at i:33232282 original size:43 final size:43
Alignment explanation
Indices: 33232203--33232361 Score: 178
Period size: 43 Copynumber: 3.7 Consensus size: 43
33232193 TAACAATGCT
* * * * *
33232203 ATATCCCATATATGGTCTTACATGTAATCTCGTATCGATGCCA
1 ATATCCCAGACATGGTCTTACACGAAATCTCATATCGATGCCA
* *
33232246 ATAGCCCA-ACCATGGTCTTACACGAAATCACATATCGATGCCA
1 ATATCCCAGA-CATGGTCTTACACGAAATCTCATATCGATGCCA
* * * *
33232289 ATATCGCAGACATAGTCTTACATGAATTCTCATATCGATGCC-
1 ATATCCCAGACATGGTCTTACACGAAATCTCATATCGATGCCA
* *
33232331 ATATCCCAGATATGGTCTTACACGTAATCTC
1 ATATCCCAGACATGGTCTTACACGAAATCTC
33232362 GGTAACCCTA
Statistics
Matches: 96, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
42 26 0.27
43 69 0.72
44 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.30
Consensus pattern (43 bp):
ATATCCCAGACATGGTCTTACACGAAATCTCATATCGATGCCA
Found at i:33233236 original size:18 final size:17
Alignment explanation
Indices: 33233205--33233238 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
33233195 AAAAGATGAT
33233205 ATTTTCATCATTTAATC
1 ATTTTCATCATTTAATC
*
33233222 ATTTATCATCTTTTAAT
1 ATTT-TCATCATTTAAT
33233239 ATCTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTCATCATTTAATC
Found at i:33235453 original size:309 final size:312
Alignment explanation
Indices: 33235010--33235605 Score: 748
Period size: 309 Copynumber: 1.9 Consensus size: 312
33235000 AGTATACAAC
33235010 TAATAGAGACAATAAATTGTGCATATTAAAATAAAATGTATAAAATACATTAAAATAAAGTTTTA
1 TAATAGAGACAATAAATTGTGCATATTAAAATAAAATGTATAAAATACATTAAAATAAAGTTTTA
* * *
33235075 GTTAAGTGATAAATTTAAGTTTTTAATAAAACAATTGGCGTAGGTTCAAATCTCACTATATGAAT
66 GTTAAGTGATAAATTTAAGGTTTTAATAAAACAACTGGCCTAGGTTCAAATCTCACTATATGAAT
* *
33235140 ATTTTTATTGATTTTTCTT-AAACTAAAAAGATTAAAATGTTC-TCGAATAATATAACTTATTTT
131 ATTTTTATTGATCTTTCTTGAAA-TAAAAAGACTAAAATG-TCATCGAATAATATAACTTATTTT
*
33235203 AATTACAGAAAG-ACATTTTCGTAA-TTTCTCTAACCGAGTTGGTGTCCA-ATTAACTTGTGACA
194 AATTA-AGAAAGTACATTTTCGTAATTTTC-CTAACCGAGTTGGTG-CCAGATTAACTCGTGACA
* *
33235265 CCAACTCTA-TCAAGAGCTTAAATAATATTATATAGATAGATATACAATTGATGAAGG
256 CCAACT-TAGTCAAGAACTTAAATAATAGTATATAGATAGATATACAATTGATGAAGG
* * * * * *
33235322 TAATA-AGATAATAAATTGTGCATGTTAAAAT-AAGTGTATAAACTA-ATTAAAATAATGTTTTG
1 TAATAGAGACAATAAATTGTGCATATTAAAATAAAATGTATAAAATACATTAAAATAAAGTTTTA
* * * * *
33235384 GTTGAGT-AGTAAATTTAAGGTTTTACTAATATAACTGGCACT-GGTTTAAATCTCA-TCATATG
66 GTTAAGTGA-TAAATTTAAGGTTTTAATAAAACAACTGGC-CTAGGTTCAAATCTCACT-ATATG
* * * *
33235446 CATATTTTTATTGGTCTTTGTTGAAATGAAAAGACTAAAATGTCATCGAATAATATAACTTATTT
128 AATATTTTTATTGATCTTTCTTGAAATAAAAAGACTAAAATGTCATCGAATAATATAACTTATTT
* * * * * *
33235511 TAATTAGGAAAGTTCATTTTCTTAATTTTCCTAATCGAGTTGGTGCTAGGTTAACTCGTGACACC
193 TAATTAAGAAAGTACATTTTCGTAATTTTCCTAACCGAGTTGGTGCCAGATTAACTCGTGACACC
* *
33235576 AACTTAGTTAGGAACTTAAATAATAGTATA
258 AACTTAGTCAAGAACTTAAATAATAGTATA
33235606 GATACACAAA
Statistics
Matches: 244, Mismatches: 31, Indels: 21
0.82 0.10 0.07
Matches are distributed among these distances:
308 13 0.05
309 182 0.75
310 20 0.08
311 24 0.10
312 5 0.02
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (312 bp):
TAATAGAGACAATAAATTGTGCATATTAAAATAAAATGTATAAAATACATTAAAATAAAGTTTTA
GTTAAGTGATAAATTTAAGGTTTTAATAAAACAACTGGCCTAGGTTCAAATCTCACTATATGAAT
ATTTTTATTGATCTTTCTTGAAATAAAAAGACTAAAATGTCATCGAATAATATAACTTATTTTAA
TTAAGAAAGTACATTTTCGTAATTTTCCTAACCGAGTTGGTGCCAGATTAACTCGTGACACCAAC
TTAGTCAAGAACTTAAATAATAGTATATAGATAGATATACAATTGATGAAGG
Found at i:33236302 original size:20 final size:19
Alignment explanation
Indices: 33236260--33236303 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
33236250 CTTAACATTT
* **
33236260 ACTTCTTTTATCATTTTGG
1 ACTTTTTTTATCATTTTAA
33236279 ACTTTTTTTAATCATTTTAA
1 ACTTTTTTT-ATCATTTTAA
33236299 ACTTT
1 ACTTT
33236304 AACCTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.23, C:0.14, G:0.05, T:0.59
Consensus pattern (19 bp):
ACTTTTTTTATCATTTTAA
Found at i:33245162 original size:12 final size:12
Alignment explanation
Indices: 33245145--33245169 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33245135 GGTGTTCATT
33245145 CGGTTAACCGAC
1 CGGTTAACCGAC
33245157 CGGTTAACCGAC
1 CGGTTAACCGAC
33245169 C
1 C
33245170 CGAAATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:33245342 original size:9 final size:9
Alignment explanation
Indices: 33245331--33245406 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
33245321 TTTGGTTAAA
*
33245331 AATTAACCA
1 AATTAACCG
33245340 AATTAACCG
1 AATTAACCG
33245349 AATTAACCG
1 AATTAACCG
*
33245358 AATTACCCG
1 AATTAACCG
33245367 AATTAACCG
1 AATTAACCG
*
33245376 AATTACCCG
1 AATTAACCG
*
33245385 AATTAACTG
1 AATTAACCG
*
33245394 AATTAACCA
1 AATTAACCG
33245403 AATT
1 AATT
33245407 GAATCACTAC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 59 1.00
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:33248965 original size:28 final size:28
Alignment explanation
Indices: 33248920--33249011 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 28
33248910 TAGCATCCTG
**
33248920 ACGGACTTACCCAGTGTTTACTGTTCCA
1 ACGGACTTACCTTGTGTTTACTGTTCCA
* *
33248948 ACGGACTTACCTTTTGTTTA-T-TATCTCG
1 ACGGACTTACCTTGTGTTTACTGT-TC-CA
* * *
33248976 ATGGACTTTCCTTGTGTTTACTGTCCCA
1 ACGGACTTACCTTGTGTTTACTGTTCCA
*
33249004 ACGAACTT
1 ACGGACTT
33249012 TCCCCGTGTT
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
26 1 0.02
27 3 0.06
28 42 0.86
29 2 0.04
30 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (28 bp):
ACGGACTTACCTTGTGTTTACTGTTCCA
Found at i:33249012 original size:28 final size:28
Alignment explanation
Indices: 33248933--33249066 Score: 106
Period size: 28 Copynumber: 4.8 Consensus size: 28
33248923 GACTTACCCA
* * * *
33248933 GTGTTTACTGTTCCAACGGACTTACCTT
1 GTGTTTACTATCCCAACGAACTTTCCTT
* * * * * *
33248961 TTGTTTATTATCTCGATGGACTTTCCTT
1 GTGTTTACTATCCCAACGAACTTTCCTT
* **
33248989 GTGTTTACTGTCCCAACGAACTTTCCCC
1 GTGTTTACTATCCCAACGAACTTTCCTT
* * **
33249017 GTGTTCACTATCCCAACGAATTTTTTTT
1 GTGTTTACTATCCCAACGAACTTTCCTT
*
33249045 GTGTTTACTATCCCAATGAACT
1 GTGTTTACTATCCCAACGAACT
33249067 ATCTCTATTT
Statistics
Matches: 79, Mismatches: 27, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
28 79 1.00
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (28 bp):
GTGTTTACTATCCCAACGAACTTTCCTT
Found at i:33249326 original size:58 final size:58
Alignment explanation
Indices: 33249226--33249376 Score: 142
Period size: 58 Copynumber: 2.6 Consensus size: 58
33249216 TCATAGCATA
* * * * * * *
33249226 TTTCATCTATATTCGTACACCGTATACCTTATACTTTTTACCATGCCGCCATAACGTC
1 TTTCATCAATAGTCTTACACCATATACCTTATACCTTGTACCATGCCACCATAACGTC
* * * **
33249284 TTTCATCCATGGTCTTACACCATATACCTT-TATCCTTGTACCATGCTACCATGGCGTC
1 TTTCATCAATAGTCTTACACCATATACCTTATA-CCTTGTACCATGCCACCATAACGTC
* * **
33249342 TTTTATCAATAGTCTTACACTACGTACCTTATACC
1 TTTCATCAATAGTCTTACACCATATACCTTATACC
33249377 AGACTGCCAT
Statistics
Matches: 74, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
57 2 0.03
58 70 0.95
59 2 0.03
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.38
Consensus pattern (58 bp):
TTTCATCAATAGTCTTACACCATATACCTTATACCTTGTACCATGCCACCATAACGTC
Found at i:33250516 original size:19 final size:18
Alignment explanation
Indices: 33250494--33250596 Score: 83
Period size: 19 Copynumber: 5.8 Consensus size: 18
33250484 AATTTTTTTT
*
33250494 TAAAAATCAAAATATTATA
1 TAAAAATTAAAA-ATTATA
*
33250513 TAAAAATTTAAAAAATATA
1 TAAAAA-TTAAAAATTATA
33250532 T-AAAATTATAAAA-TATA
1 TAAAAATTA-AAAATTATA
*
33250549 T--AAA-TAAAAATTTTA
1 TAAAAATTAAAAATTATA
*
33250564 -AAAAATAAAAATATTATA
1 TAAAAATTAAAA-ATTATA
*
33250582 TAAAAATTGAAAATT
1 TAAAAATTAAAAATT
33250597 TATCATAAGT
Statistics
Matches: 69, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 4 0.06
15 5 0.07
16 6 0.09
17 12 0.17
18 16 0.23
19 21 0.30
20 5 0.07
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (18 bp):
TAAAAATTAAAAATTATA
Found at i:33250541 original size:8 final size:9
Alignment explanation
Indices: 33250509--33250552 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
33250499 ATCAAAATAT
33250509 TATATAAAAA
1 TATAT-AAAA
* *
33250519 TTTAAAAAA
1 TATATAAAA
33250528 TATATAAAA
1 TATATAAAA
33250537 T-TATAAAA
1 TATATAAAA
33250545 TATATAAA
1 TATATAAA
33250553 TAAAAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 8 0.28
9 18 0.62
10 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TATATAAAA
Found at i:33250544 original size:17 final size:18
Alignment explanation
Indices: 33250509--33250552 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
33250499 ATCAAAATAT
33250509 TATATAAAAATTTAAAAAA
1 TATAT-AAAATTTAAAAAA
*
33250528 TATATAAAA-TTATAAAA
1 TATATAAAATTTAAAAAA
33250545 TATATAAA
1 TATATAAA
33250553 TAAAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 15 0.62
18 4 0.17
19 5 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TATATAAAATTTAAAAAA
Found at i:33250558 original size:31 final size:29
Alignment explanation
Indices: 33250521--33250589 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
33250511 TATAAAAATT
* *
33250521 TAAAAAATATATAAAATTATAAAATATATAAA
1 TAAAAATTATA-AAAAATA-AAAATAT-TAAA
* *
33250553 TAAAAATTTTAAAAAATAAAAATATTATA
1 TAAAAATTATAAAAAATAAAAATATTAAA
33250582 TAAAAATT
1 TAAAAATT
33250590 GAAAATTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 11 0.33
30 7 0.21
31 6 0.18
32 9 0.27
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
TAAAAATTATAAAAAATAAAAATATTAAA
Found at i:33250575 original size:69 final size:70
Alignment explanation
Indices: 33250432--33250594 Score: 190
Period size: 69 Copynumber: 2.4 Consensus size: 70
33250422 TAAATAATTC
* * * ** *
33250432 AAAAATATT-TA-AAAAGTTCAAAAAAAATAAAAATTCTAAAATATGTAAATATAATTTTTTTTT
1 AAAAATATTATATAAAAATTCAAAAAAAATAAAAATTATAAAATATATAAATATAA-TAATTTTA
33250495 AAAAAT
65 AAAAAT
* * *
33250501 CAAAATATTATATAAAAATTTAAAAAATATATAAAATTATAAAATATATAAATA-AA-AATTTTA
1 AAAAATATTATATAAAAATTCAAAAAAAATA-AAAATTATAAAATATATAAATATAATAATTTTA
33250564 AAAAAT
65 AAAAAT
*
33250570 AAAAATATTATATAAAAATTGAAAA
1 AAAAATATTATATAAAAATTCAAAA
33250595 TTTATCATAA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
69 41 0.51
70 2 0.03
71 17 0.21
72 20 0.25
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (70 bp):
AAAAATATTATATAAAAATTCAAAAAAAATAAAAATTATAAAATATATAAATATAATAATTTTAA
AAAAT
Found at i:33250599 original size:19 final size:19
Alignment explanation
Indices: 33250502--33250604 Score: 73
Period size: 16 Copynumber: 5.7 Consensus size: 19
33250492 TTTAAAAATC
33250502 AAAATATTATATAAAAATTTA
1 AAAAT-TTATATAAAAA-TTA
*
33250523 AAAA-ATATAT-AAAATTA
1 AAAATTTATATAAAAATTA
33250540 TAAAA--TATAT--AAA-TA
1 -AAAATTTATATAAAAATTA
33250555 AAAATTT-TA-AAAAA-TA
1 AAAATTTATATAAAAATTA
*
33250571 AAAATATTATATAAAAATTG
1 AAAAT-TTATATAAAAATTA
33250591 AAAATTTATCATAA
1 AAAATTTAT-ATAA
33250605 GTTTCATTTT
Statistics
Matches: 70, Mismatches: 2, Indels: 21
0.75 0.02 0.23
Matches are distributed among these distances:
14 4 0.06
15 4 0.06
16 14 0.20
17 10 0.14
18 10 0.14
19 14 0.20
20 10 0.14
21 4 0.06
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (19 bp):
AAAATTTATATAAAAATTA
Found at i:33250657 original size:27 final size:28
Alignment explanation
Indices: 33250621--33250677 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
33250611 TTTTTTTTTC
*
33250621 AAAAACTCTAAA-TTCTAAAAATTCAAA
1 AAAAAATCTAAATTTCTAAAAATTCAAA
*
33250648 AAAAAATCTAAATTTCTAAAAATTTAAA
1 AAAAAATCTAAATTTCTAAAAATTCAAA
33250676 AA
1 AA
33250678 TTTTCTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.28
Consensus pattern (28 bp):
AAAAAATCTAAATTTCTAAAAATTCAAA
Found at i:33250887 original size:29 final size:29
Alignment explanation
Indices: 33250855--33250956 Score: 84
Period size: 30 Copynumber: 3.4 Consensus size: 29
33250845 GAAATGCATT
33250855 TTTTTAATTTTTTTAATTTTCATATAATA
1 TTTTTAATTTTTTTAATTTTCATATAATA
* * *
33250884 TTTTGATTTTTTTTAAATTTAT-ATTTACATA
1 TTTTTAATTTTTTT-AATTT-TCATATA-ATA
*
33250915 CTTTTT-A-TTTTTTATATTTTACATATGATA
1 -TTTTTAATTTTTTTA-ATTTT-CATATAATA
*
33250945 TTTTTCATTTTT
1 TTTTTAATTTTT
33250957 AAACAATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
29 19 0.33
30 23 0.40
31 11 0.19
32 4 0.07
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (29 bp):
TTTTTAATTTTTTTAATTTTCATATAATA
Found at i:33256058 original size:71 final size:71
Alignment explanation
Indices: 33255982--33256119 Score: 267
Period size: 71 Copynumber: 1.9 Consensus size: 71
33255972 ATTATATGCA
*
33255982 TTTTATTTTAGCATGATAATAGTTAATGGCTTTATATTATGGAAGAAAGAATAATTAAAAGAAGG
1 TTTTATTATAGCATGATAATAGTTAATGGCTTTATATTATGGAAGAAAGAATAATTAAAAGAAGG
33256047 AAACAT
66 AAACAT
33256053 TTTTATTATAGCATGATAATAGTTAATGGCTTTATATTATGGAAGAAAGAATAATTAAAAGAAGG
1 TTTTATTATAGCATGATAATAGTTAATGGCTTTATATTATGGAAGAAAGAATAATTAAAAGAAGG
33256118 AA
66 AA
33256120 GGAGTGATAG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (71 bp):
TTTTATTATAGCATGATAATAGTTAATGGCTTTATATTATGGAAGAAAGAATAATTAAAAGAAGG
AAACAT
Found at i:33257880 original size:47 final size:47
Alignment explanation
Indices: 33257829--33258010 Score: 222
Period size: 47 Copynumber: 3.7 Consensus size: 47
33257819 TTAGGATTCT
* *
33257829 ATGTGATGGATGTGAACA-TGCATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
33257876 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
33257923 ATGTGATGAATGTAAAAGTGTATATATGTGTATATATGTGAAAAGGCCTAATGGTCG
1 ATGTGATGAA--T----GTG-A-A-A-GTGTATATATGTGATAAGGCCTAATGGCCG
33257980 ATGTGATGAATGTGAAAGTGTATATATGTGA
1 ATGTGATGAATGTGAAAGTGTATATATGTGA
33258011 CAGGGCCGAG
Statistics
Matches: 120, Mismatches: 4, Indels: 22
0.82 0.03 0.15
Matches are distributed among these distances:
46 1 0.01
47 67 0.56
48 1 0.01
49 2 0.02
50 1 0.01
51 3 0.03
53 3 0.03
54 1 0.01
55 2 0.02
56 1 0.01
57 38 0.32
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.31
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:33257982 original size:57 final size:57
Alignment explanation
Indices: 33257893--33258009 Score: 207
Period size: 57 Copynumber: 2.1 Consensus size: 57
33257883 GAATGTGAAA
*
33257893 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTAAAAGTGTATATAT
1 GTGTATATATGTGAAAAGGCCTAATGGCCGATGTGATGAATGTAAAAGTGTATATAT
* *
33257950 GTGTATATATGTGAAAAGGCCTAATGGTCGATGTGATGAATGTGAAAGTGTATATAT
1 GTGTATATATGTGAAAAGGCCTAATGGCCGATGTGATGAATGTAAAAGTGTATATAT
33258007 GTG
1 GTG
33258010 ACAGGGCCGA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.33
Consensus pattern (57 bp):
GTGTATATATGTGAAAAGGCCTAATGGCCGATGTGATGAATGTAAAAGTGTATATAT
Found at i:33258235 original size:37 final size:36
Alignment explanation
Indices: 33258179--33258256 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 36
33258169 CCGAGCTCTA
* * *
33258179 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCC-GGT
*
33258216 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGT
33258252 AAGAC
1 AAGAC
33258257 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 8 0.22
37 29 0.78
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (36 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGT
Found at i:33288675 original size:116 final size:116
Alignment explanation
Indices: 33288471--33288700 Score: 406
Period size: 116 Copynumber: 2.0 Consensus size: 116
33288461 TACCCTTACT
* *
33288471 AGGGTATCGATACTGAGCACTTTTCAAGAAAATTTTTAAGAAATAGAATCTCAAGATACTAGACT
1 AGGGTATCGATACTGAGCACTTTTCAAGAAAATTTTTAAGAAACAGAATCTCAAGATACCAGACT
*
33288536 AAAGTATCAATACTTTATATTAGAGTATCAATGCATAAAAAAGTTATCATA
66 AAAGTATCAATACTTTATATTAGAGTATCAATGCATAAAAAAGGTATCATA
* *
33288587 AGGGTATCGATACTTAGCACTTTTCAAGAAAATTTTTAAGAAACAGAATCTCAAGATTCCAGACT
1 AGGGTATCGATACTGAGCACTTTTCAAGAAAATTTTTAAGAAACAGAATCTCAAGATACCAGACT
*
33288652 AAAGTATCAATATTTTATATTAGAGTATCAATGCATAAAAAAGGTATCA
66 AAAGTATCAATACTTTATATTAGAGTATCAATGCATAAAAAAGGTATCA
33288701 CTACAATTAT
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 108 1.00
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.31
Consensus pattern (116 bp):
AGGGTATCGATACTGAGCACTTTTCAAGAAAATTTTTAAGAAACAGAATCTCAAGATACCAGACT
AAAGTATCAATACTTTATATTAGAGTATCAATGCATAAAAAAGGTATCATA
Found at i:33295708 original size:46 final size:45
Alignment explanation
Indices: 33295637--33295727 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 45
33295627 TCTAAGCTCG
* * *
33295637 ACTTACCTCTTTGTTGCGTGGTCATGGTGGTGCGAGGAGTTTACA
1 ACTTACCTCTTTGCTGCGTAGTCATGGTAGTGCGAGGAGTTTACA
*
33295682 ACTTTCCTCTCTTGCTGCGTAGTCATGGTAGTGCGAGGAGTTTACA
1 ACTTACCTCT-TTGCTGCGTAGTCATGGTAGTGCGAGGAGTTTACA
33295728 CTCCTCCTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 9 0.22
46 32 0.78
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.35
Consensus pattern (45 bp):
ACTTACCTCTTTGCTGCGTAGTCATGGTAGTGCGAGGAGTTTACA
Found at i:33304582 original size:43 final size:43
Alignment explanation
Indices: 33304535--33304631 Score: 140
Period size: 43 Copynumber: 2.3 Consensus size: 43
33304525 TACTAGGCTT
* *
33304535 GAAGCCCGATATCATTTCACCGGCAATATAGCCTGCTAGGCCC
1 GAAGCCCGATATCATCTCACCAGCAATATAGCCTGCTAGGCCC
* * *
33304578 GAAGCCCGATATTATCTCACCAGCATTATAGCTTGCTAGGCCC
1 GAAGCCCGATATCATCTCACCAGCAATATAGCCTGCTAGGCCC
*
33304621 GAAGCTCGATA
1 GAAGCCCGATA
33304632 ATATTATTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.23
Consensus pattern (43 bp):
GAAGCCCGATATCATCTCACCAGCAATATAGCCTGCTAGGCCC
Found at i:33307348 original size:40 final size:40
Alignment explanation
Indices: 33307293--33307371 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
33307283 ATCAAGGAAG
*
33307293 ATTGACTGAATATTACTTCTTCTGCAATGCCTATTTTAGT
1 ATTGACTGAATATTACTTCTTCTCCAATGCCTATTTTAGT
33307333 ATTGACTGAATATTACTTCTTCTCCAATGCCTATTTTAG
1 ATTGACTGAATATTACTTCTTCTCCAATGCCTATTTTAG
33307372 GCTTTGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.44
Consensus pattern (40 bp):
ATTGACTGAATATTACTTCTTCTCCAATGCCTATTTTAGT
Found at i:33310414 original size:14 final size:14
Alignment explanation
Indices: 33310395--33310439 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
33310385 ATCTAAAAAG
*
33310395 AAAATAAAAGTAAA
1 AAAATAAAAATAAA
33310409 AAAATAAAAATAAA
1 AAAATAAAAATAAA
* *
33310423 TAAAGAAAAATTAAA
1 AAAATAAAAA-TAAA
33310438 AA
1 AA
33310440 TCATATCTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (14 bp):
AAAATAAAAATAAA
Found at i:33310832 original size:17 final size:17
Alignment explanation
Indices: 33310795--33310832 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
33310785 AAATAGATAA
**
33310795 AAAAGAAATAAATAACT
1 AAAAGAAATAAATAAAG
33310812 AAAAGAAATAAATAAAG
1 AAAAGAAATAAATAAAG
33310829 AAAA
1 AAAA
33310833 ATAAACAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (17 bp):
AAAAGAAATAAATAAAG
Found at i:33322414 original size:80 final size:80
Alignment explanation
Indices: 33322320--33322479 Score: 302
Period size: 80 Copynumber: 2.0 Consensus size: 80
33322310 TTTATAATGA
*
33322320 ATTTCCAAAGTCGGAAAAGGGAATCCAGAAATCGCTCTGGCCCTGTTTCACAAGAGTTTAATTAT
1 ATTTCCAAAGTCGGAAAAGGGAATCCAGAAATCGCTCTGGCCCTGTTTCACAAGAGTTTAATTAC
33322385 CTCCTAACATACAGC
66 CTCCTAACATACAGC
*
33322400 ATTTCCAAAGTCGGAACAGGGAATCCAGAAATCGCTCTGGCCCTGTTTCACAAGAGTTTAATTAC
1 ATTTCCAAAGTCGGAAAAGGGAATCCAGAAATCGCTCTGGCCCTGTTTCACAAGAGTTTAATTAC
33322465 CTCCTAACATACAGC
66 CTCCTAACATACAGC
33322480 TCATACGGTC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (80 bp):
ATTTCCAAAGTCGGAAAAGGGAATCCAGAAATCGCTCTGGCCCTGTTTCACAAGAGTTTAATTAC
CTCCTAACATACAGC
Found at i:33323534 original size:27 final size:26
Alignment explanation
Indices: 33323517--33323586 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 26
33323507 ATATTAAGTC
*
33323517 CGCACACTCAGTTCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
33323544 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
33323572 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
33323587 GTACAATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:33323579 original size:28 final size:28
Alignment explanation
Indices: 33323517--33323614 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
33323507 ATATTAAGTC
* *
33323517 CGCACACTCAGTTCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
33323544 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
33323572 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
33323601 CGCACACTTAGTGC
1 CGCACACTTAGTGC
33323615 CAATCTCATG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 21 0.33
28 23 0.37
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:33324078 original size:14 final size:14
Alignment explanation
Indices: 33324059--33324088 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
33324049 TGGGCATACT
33324059 TATGTATATATATA
1 TATGTATATATATA
33324073 TATGTATATATATA
1 TATGTATATATATA
33324087 TA
1 TA
33324089 CTTCGGAATG
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TATGTATATATATA
Found at i:33329568 original size:20 final size:20
Alignment explanation
Indices: 33329543--33329582 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
33329533 GCATTGCTTG
*
33329543 AAAAAACACCTTT-GGGAGA
1 AAAAAAAACCTTTGGGGAGA
*
33329562 AAAAAAAACTTTTGGGGAGA
1 AAAAAAAACCTTTGGGGAGA
33329582 A
1 A
33329583 GCTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.50, C:0.10, G:0.23, T:0.17
Consensus pattern (20 bp):
AAAAAAAACCTTTGGGGAGA
Found at i:33329790 original size:21 final size:21
Alignment explanation
Indices: 33329761--33329810 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
33329751 GTATTCTTAG
33329761 TTAAGAGTGGTAAATAACTCAA
1 TTAA-AGTGGTAAATAACTCAA
*
33329783 TTAAAGTGGTAAATAACTTAA
1 TTAAAGTGGTAAATAACTCAA
33329804 TTAAAGT
1 TTAAAGT
33329811 AAATATTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (21 bp):
TTAAAGTGGTAAATAACTCAA
Found at i:33333353 original size:22 final size:20
Alignment explanation
Indices: 33333325--33333365 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
33333315 TTCTACGTAA
33333325 AATTTTTGTGTTCGATTTTTTC
1 AATTTTTGTGTT--ATTTTTTC
*
33333347 AATTTTTTTGTTATTTTTT
1 AATTTTTGTGTTATTTTTT
33333366 TGTTCGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.15, C:0.05, G:0.10, T:0.71
Consensus pattern (20 bp):
AATTTTTGTGTTATTTTTTC
Found at i:33337140 original size:4 final size:4
Alignment explanation
Indices: 33337131--33337156 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
33337121 ACCCAAACAC
33337131 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
33337157 AACCTTGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:33337218 original size:22 final size:22
Alignment explanation
Indices: 33337190--33337251 Score: 99
Period size: 22 Copynumber: 2.8 Consensus size: 22
33337180 CCTTTGTTGG
33337190 CCACCCACCTTAGCCACCAACT
1 CCACCCACCTTAGCCACCAACT
33337212 CCACCCACCTTAGCCACCAACT
1 CCACCCACCTTAGCCACCAACT
*
33337234 CCA-CCACCCTTGGCCACC
1 CCACCCA-CCTTAGCCACC
33337252 TAAACCACCC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 3 0.08
22 35 0.92
ACGTcount: A:0.24, C:0.56, G:0.06, T:0.13
Consensus pattern (22 bp):
CCACCCACCTTAGCCACCAACT
Found at i:33337508 original size:18 final size:19
Alignment explanation
Indices: 33337472--33337528 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 19
33337462 ACTATTACTA
*
33337472 TTATATATTAGTGTATATTT
1 TTATATA-TAGTATATATTT
*
33337492 TTATGTATA-TATATA-TT
1 TTATATATAGTATATATTT
33337509 TTATATATAGTAT-TATTT
1 TTATATATAGTATATATTT
33337527 TT
1 TT
33337529 TATTACTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 12 0.38
18 12 0.38
19 2 0.06
20 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
TTATATATAGTATATATTT
Found at i:33337632 original size:14 final size:14
Alignment explanation
Indices: 33337613--33337644 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
33337603 GTATTTCTAT
33337613 TATATACATATATA
1 TATATACATATATA
*
33337627 TATATACATTTATA
1 TATATACATATATA
33337641 TATA
1 TATA
33337645 GTATTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (14 bp):
TATATACATATATA
Found at i:33349993 original size:132 final size:132
Alignment explanation
Indices: 33349751--33351095 Score: 2127
Period size: 132 Copynumber: 10.2 Consensus size: 132
33349741 TGAAGTCATT
* * * *
33349751 AAAGTAGATCTTGTCTTCATGTATTGGCGTGAAGCAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
* *
33349816 TATTGATAGGAAGTGGATCCAGGATGCAGATCTTGTCTTCCCATATTTGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
33349881 AG
131 AG
* *
33349883 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGGTAGCAGATCCTATCTTTCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
* * *
33349948 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGCCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
33350013 AG
131 AG
* *
33350015 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
*
33350080 TATTGATAGGAAGTGGATCCAGGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
33350145 AG
131 AG
* * *
33350147 AAAGCAGATCTTGTCTTCATGAATTGGCGTAAAGTAGATCGAAGGA-AGCAAATCCTATCTTTCT
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAA-GATAGCAGATCCTATCTTCCT
* *
33350211 ATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
65 ATATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
33350276 CAG
130 CAG
* * *
33350279 AAAGCAGATCTTGTCTTCATGAATTGGCGTAAAGTAGATCGAAGGTAGCAGATCCTATCTTTCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
* * *
33350344 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTATTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
33350409 AG
131 AG
* * * *
33350411 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGGTAGCAGATCCTATGTTTCTT
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
* * *
33350476 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGGAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
33350541 AG
131 AG
* * * * *
33350543 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTCGATCAAAGATAGCAGGTCCTATCTTCCGA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
*
33350608 TATTGATAGGAAGTGGATCCAGGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
33350673 AG
131 AG
* * * * *
33350675 AAAGCAGATCTTATCTTCATGAATTGGCGTAAAGTAGATCGAAGGTAGCAGATCCTATCTTTCTT
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
* *
33350740 TATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
33350805 AG
131 AG
* *
33350807 AAAGCAGATCTTGTCTTCACGTATTGGCGTGAAGTAGATCGAAGATAGCACG-TCCTATCTTCCT
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCA-GATCCTATCTTCCT
*
33350871 ATATTGATAGGAAGTGGATCCAATATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
65 ATATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG
33350936 CAG
130 CAG
* * *
33350939 AAAGCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGAAGATAGCAGGTCCTATCTTCCTA
1 AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
* * * *
33351004 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATTGA
66 TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
33351069 AG
131 AG
** * *
33351071 ATTGCAGATCTTGCCTTCCTGTATT
1 AAAGCAGATCTTGTCTTCATGTATT
33351096 TGGCAGCGAA
Statistics
Matches: 1127, Mismatches: 82, Indels: 8
0.93 0.07 0.01
Matches are distributed among these distances:
131 2 0.00
132 1122 1.00
133 3 0.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (132 bp):
AAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAGATCGAAGATAGCAGATCCTATCTTCCTA
TATTGATAGGAAGTGGATCCAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGC
AG
Found at i:33351212 original size:134 final size:135
Alignment explanation
Indices: 33351061--33351365 Score: 540
Period size: 136 Copynumber: 2.3 Consensus size: 135
33351051 GGTGGTGAAG
*
33351061 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCAAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCAAAGATGGCAGAT
33351126 TTTACCTCCC-TGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCAG
66 TTTACCTCCCGTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCAG
33351190 TGGAA
131 TGGAA
*
33351195 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCGAAGATGGCAGAT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCAAAGATGGCAGAT
* *
33351260 TTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATCTGGCA
66 TTTACCTCCC-GTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCA
33351325 GTGGAA
130 GTGGAA
* *
33351331 TAGATTGAAGATTGCAGATCCTGCCTTCCTATATT
1 TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATT
33351366 GGTAGGAAGT
Statistics
Matches: 163, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
134 73 0.45
136 90 0.55
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (135 bp):
TAGATTGAAGATTGCAGATCTTGCCTTCCTGTATTAGGCAGCGAAGCAGATCAAAGATGGCAGAT
TTTACCTCCCGTGACCACAGTGGAGTACATTGAAGCCGATAACTCTATCTCACTGTATCTGGCAG
TGGAA
Found at i:33351551 original size:43 final size:40
Alignment explanation
Indices: 33351504--33351674 Score: 137
Period size: 40 Copynumber: 4.2 Consensus size: 40
33351494 CTTGGGCAAC
*
33351504 AGTGGAATAGATCGAAGATTACAATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATCG--CATTA-AATCTTATCTCCCTAAGCAGT
* *
33351547 AGTGGAGTAGATCGCATTAAGTCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATCGCATTAAATCTTATCTCCCTAAGCAGT
** *** ** * *
33351587 AGTGGAGCAGATAAAACCACAGATCTTATTTCCCTAAGCAAT
1 AGTGGAATAGATCGCATTA-A-ATCTTATCTCCCTAAGCAGT
* * * *
33351629 AGT-GAAGCAGATCGCATCAAGTCTTATCTCCCTAAGTAGT
1 AGTGGAA-TAGATCGCATTAAATCTTATCTCCCTAAGCAGT
33351669 AGTGGA
1 AGTGGA
33351675 GCAGACTAAA
Statistics
Matches: 103, Mismatches: 21, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
40 52 0.50
41 10 0.10
42 28 0.27
43 13 0.13
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (40 bp):
AGTGGAATAGATCGCATTAAATCTTATCTCCCTAAGCAGT
Found at i:33351580 original size:40 final size:40
Alignment explanation
Indices: 33351528--33351679 Score: 196
Period size: 40 Copynumber: 3.8 Consensus size: 40
33351518 AAGATTACAA
* *
33351528 TCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGCATTAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
*** *
33351568 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAACCACAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCA-AG
* * *
33351609 ATCTTATTTCCCTAAGCAATAGTGAAGCAGATCGCATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
*
33351650 TCTTATCTCCCTAAGTAGTAGTGGAGCAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGA
33351680 CTAAAAACAC
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
40 58 0.62
41 4 0.04
42 31 0.33
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCATCAAG
Found at i:33351622 original size:82 final size:83
Alignment explanation
Indices: 33351526--33351695 Score: 261
Period size: 82 Copynumber: 2.1 Consensus size: 83
33351516 CGAAGATTAC
* * * *
33351526 AATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGCATTAAGTCTTATCTCCCTAAGCAGTAGTG
1 AATCTTATCTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTG
*
33351591 GAGCAGA-TAAAACCACA
66 GAGCAGACTAAAAACACA
* * *
33351608 GATCTTATTTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGTAGTAGTG
1 AATCTTATCTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTG
33351673 GAGCAGACTAAAAACACA
66 GAGCAGACTAAAAACACA
33351691 AATCT
1 AATCT
33351696 CATCCCCATG
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
82 65 0.83
83 13 0.17
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (83 bp):
AATCTTATCTCCCTAAGCAATAGTGAAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTG
GAGCAGACTAAAAACACA
Found at i:33351632 original size:42 final size:42
Alignment explanation
Indices: 33351527--33351695 Score: 157
Period size: 40 Copynumber: 4.1 Consensus size: 42
33351517 GAAGATTACA
* *** **
33351527 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGCATTA-AG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAAACACAG
*
33351568 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAACCACAG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAAACACAG
* * * *** *
33351609 ATCTTATTTCCCTAAGCAATAGTGAAGCAGATCGCATCA-AG
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAAACACAG
* *
33351650 -TCTTATCTCCCTAAGTAGTAGTGGAGCAGACTAAAAACACAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGA-TAAAAACACAG
33351692 ATCT
1 ATCT
33351696 CATCCCCATG
Statistics
Matches: 101, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
40 58 0.57
41 8 0.08
42 32 0.32
43 3 0.03
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (42 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATAAAAACACAG
Found at i:33352050 original size:22 final size:22
Alignment explanation
Indices: 33352022--33352083 Score: 99
Period size: 22 Copynumber: 2.8 Consensus size: 22
33352012 CCTTTGTTGG
33352022 CCACCCACCTTAGCCACCAACT
1 CCACCCACCTTAGCCACCAACT
33352044 CCACCCACCTTAGCCACCAACT
1 CCACCCACCTTAGCCACCAACT
*
33352066 CCA-CCACCCTTGGCCACC
1 CCACCCA-CCTTAGCCACC
33352084 TAAACCACCC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 3 0.08
22 35 0.92
ACGTcount: A:0.24, C:0.56, G:0.06, T:0.13
Consensus pattern (22 bp):
CCACCCACCTTAGCCACCAACT
Found at i:33352212 original size:22 final size:23
Alignment explanation
Indices: 33352165--33352213 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
33352155 GTTTTTGGTT
33352165 TTTTGGAGAAGGATTGTTCTTTG
1 TTTTGGAGAAGGATTGTTCTTTG
* * *
33352188 TTTTGGAGGAGG-TTTTTTTTTG
1 TTTTGGAGAAGGATTGTTCTTTG
33352210 TTTT
1 TTTT
33352214 TTGAGGTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.12, C:0.02, G:0.29, T:0.57
Consensus pattern (23 bp):
TTTTGGAGAAGGATTGTTCTTTG
Found at i:33352214 original size:23 final size:23
Alignment explanation
Indices: 33352164--33352228 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
33352154 GGTTTTTGGT
* * *
33352164 TTTTTGGAGAAGGATTGTTCTTTG
1 TTTTTGGAGGAGG-TTTTTTTTTG
33352188 -TTTTGGAGGAGGTTTTTTTTTG
1 TTTTTGGAGGAGGTTTTTTTTTG
* *
33352210 TTTTTTGAGG-TGTTTTTTT
1 TTTTTGGAGGAGGTTTTTTT
33352229 GTAAAAAAGG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.11, C:0.02, G:0.28, T:0.60
Consensus pattern (23 bp):
TTTTTGGAGGAGGTTTTTTTTTG
Found at i:33352573 original size:3 final size:3
Alignment explanation
Indices: 33352559--33352644 Score: 60
Period size: 3 Copynumber: 29.3 Consensus size: 3
33352549 GAGCTTTGTT
* *
33352559 TTA TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
33352603 TT- TCTCA TGTA TATA TTA TT- TT- TTA -TA TTA TTA TTA -TA TTA T
1 TTA T-T-A T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
33352645 ATATGCCCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 12 0.18
3 48 0.71
4 6 0.09
5 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:33352601 original size:18 final size:18
Alignment explanation
Indices: 33352559--33352648 Score: 83
Period size: 18 Copynumber: 4.7 Consensus size: 18
33352549 GAGCTTTGTT
*
33352559 TTATTATTTTATTATTTTTA
1 TTATTA-TTTA-TATTATTA
*
33352579 CTATTATTTATATTATTA
1 TTATTATTTATATTATTA
*
33352597 TTATTATTTCTCATGTATATA
1 TTATTATTTAT-AT-TAT-TA
*
33352618 TTATTTTTTATATTATTA
1 TTATTATTTATATTATTA
33352636 TTA-TATTATATAT
1 TTATTATT-TATAT
33352649 GCCCTCTCCA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
17 3 0.05
18 26 0.44
19 9 0.15
20 10 0.17
21 11 0.19
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (18 bp):
TTATTATTTATATTATTA
Found at i:33352886 original size:18 final size:19
Alignment explanation
Indices: 33352850--33352906 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 19
33352840 ACTATTACTA
*
33352850 TTATATATTAGTGTATATTT
1 TTATATA-TAGTATATATTT
*
33352870 TTATGTATA-TATATA-TT
1 TTATATATAGTATATATTT
33352887 TTATATATAGTAT-TATTT
1 TTATATATAGTATATATTT
33352905 TT
1 TT
33352907 TATTACTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
17 12 0.38
18 12 0.38
19 2 0.06
20 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (19 bp):
TTATATATAGTATATATTT
Found at i:33353008 original size:12 final size:12
Alignment explanation
Indices: 33352991--33353020 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
33352981 GTATTTCTAT
33352991 TATATACATATA
1 TATATACATATA
*
33353003 TATATACATTTA
1 TATATACATATA
33353015 TATATA
1 TATATA
33353021 GTATTATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (12 bp):
TATATACATATA
Found at i:33358276 original size:93 final size:93
Alignment explanation
Indices: 33358159--33358425 Score: 280
Period size: 93 Copynumber: 2.9 Consensus size: 93
33358149 ACATCTAAAT
* *
33358159 CGATGCCATGTCCCAGACAGGTCTTACATTGGCTCTCATCTATC-AGTG-TCAATGCCATGTCCC
1 CGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATATCGAG-GCT-AATG-CATGTCCC
33358222 AGACAGGTCTTACACT-GACACATGTC-AA-GC
63 AGACAGGTCTTACACTAG-C-CATGTCTAATGC
* * * *
33358252 CGATGCCATGTCCCAGATAGGTCTTACACTAGCT-TGCATATCTCGAGGCTGATGCATGTCCCAG
1 CGATGCCATGTCCCAGACAGGTCTTACACTGGCTCT-CATATATCGAGGCTAATGCATGTCCCAG
* **
33358316 ACATGTCTTACACTAGCTTTGTCTTAATGC
65 ACAGGTCTTACACTAGCCATGTC-TAATGC
* **
33358346 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-AT-GTGGCCGATGCATGTCCCAG
1 CGATGCCATGTCCCAGACA-GGTCTTACACTGGCTCTCATATATCGAGGCTAATGCATGTCCCAG
* *
33358409 ACATGTCTTACATTAGC
65 ACAGGTCTTACACTAGC
33358426 ACACATCCAT
Statistics
Matches: 150, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
91 4 0.03
92 25 0.17
93 78 0.52
94 24 0.16
95 18 0.12
96 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (93 bp):
CGATGCCATGTCCCAGACAGGTCTTACACTGGCTCTCATATATCGAGGCTAATGCATGTCCCAGA
CAGGTCTTACACTAGCCATGTCTAATGC
Found at i:33358324 original size:48 final size:47
Alignment explanation
Indices: 33358159--33358425 Score: 201
Period size: 48 Copynumber: 5.7 Consensus size: 47
33358149 ACATCTAAAT
* * * * * * *
33358159 CGATGCCATGTCCCAGACAGGTCTTACATTGGCTCTCATCTATCAGTGT
1 CGATGCCATGTCCCAGACATGTCTTACACTAGCT-TCATATCTGAG-GC
* * * * *
33358208 CAATGCCATGTCCCAGACAGGTCTTACACT-GAC-ACATGTC--AAGC
1 CGATGCCATGTCCCAGACATGTCTTACACTAG-CTTCATATCTGAGGC
* *
33358252 CGATGCCATGTCCCAGATAGGTCTTACACTAGCTTGCATATCTCGAGGC
1 CGATGCCATGTCCCAGACATGTCTTACACTAGCTT-CATATCT-GAGGC
* * * *
33358301 TGATG-CATGTCCCAGACATGTCTTACACTAGCTT--TGTCTTAATGC
1 CGATGCCATGTCCCAGACATGTCTTACACTAGCTTCATATC-TGAGGC
* * *
33358346 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-ATGTGGC
1 CGATGCCATGTCCCAGACAT-GTCTTACACTAGCT-TCATATCTGAGGC
*
33358394 CGATG-CATGTCCCAGACATGTCTTACATTAGC
1 CGATGCCATGTCCCAGACATGTCTTACACTAGC
33358426 ACACATCCAT
Statistics
Matches: 178, Mismatches: 27, Indels: 29
0.76 0.12 0.12
Matches are distributed among these distances:
44 30 0.17
45 12 0.07
46 31 0.17
47 31 0.17
48 37 0.21
49 36 0.20
50 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.28
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGTCTTACACTAGCTTCATATCTGAGGC
Found at i:33361382 original size:27 final size:28
Alignment explanation
Indices: 33361306--33361420 Score: 94
Period size: 27 Copynumber: 4.1 Consensus size: 28
33361296 AGCATGGCTG
* * *
33361306 CCAGATACAGA-AA-ATGTGACAGAGTCA
1 CCAGA-ACAGAGAATATGTGGCAGTGCCA
* * *
33361333 CCAGATACAGATATTTTGTGGCAGTGCCA
1 CCAGA-ACAGAGAATATGTGGCAGTGCCA
*
33361362 CCAGAACAG-GAATATGTGGCAGAGCCA
1 CCAGAACAGAGAATATGTGGCAGTGCCA
* *
33361389 CCAGAACAGATAATTTGTGGCA-TAGCCA
1 CCAGAACAGAGAATATGTGGCAGT-GCCA
33361417 CCAG
1 CCAG
33361421 GACGATTCCT
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
27 34 0.47
28 23 0.32
29 15 0.21
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (28 bp):
CCAGAACAGAGAATATGTGGCAGTGCCA
Found at i:33361416 original size:28 final size:28
Alignment explanation
Indices: 33361331--33361420 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 28
33361321 GTGACAGAGT
*
33361331 CACCAGATACAGATATTTTGTGGCAGT-GC
1 CACCAGA-ACAGATAATTTGTGGCA-TAGC
* * *
33361360 CACCAGAACAG-GAATATGTGGCAGAGC
1 CACCAGAACAGATAATTTGTGGCATAGC
33361387 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCATAGC
33361415 CACCAG
1 CACCAG
33361421 GACGATTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 22 0.42
28 23 0.44
29 7 0.13
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.19
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCATAGC
Found at i:33361418 original size:55 final size:56
Alignment explanation
Indices: 33361306--33361420 Score: 155
Period size: 55 Copynumber: 2.1 Consensus size: 56
33361296 AGCATGGCTG
* *
33361306 CCAGATACAGAAAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGTGCCA
1 CCAGATACAGAAAATGTGACAGAGCCACCAGATACAGATAATTTGTGGCAGTGCCA
* *
33361362 CCAGA-ACAGGAATATGTGGCAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
1 CCAGATACA-GAAAATGTGACAGAGCCACCAGATACAGATAATTTGTGGCAGT-GCCA
33361417 CCAG
1 CCAG
33361421 GACGATTCCT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
54 1 0.02
55 27 0.51
56 25 0.47
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (56 bp):
CCAGATACAGAAAATGTGACAGAGCCACCAGATACAGATAATTTGTGGCAGTGCCA
Found at i:33361573 original size:28 final size:28
Alignment explanation
Indices: 33361526--33361590 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
33361516 AAATTAACCC
*
33361526 TAGGGGTATAGAGGTCATTTTGCATACA
1 TAGGGGTATAGAGGTAATTTTGCATACA
33361554 TAGGGGTATA-ATGGTAATTTTGCATACA
1 TAGGGGTATAGA-GGTAATTTTGCATACA
33361582 TAGGGGTAT
1 TAGGGGTAT
33361591 TCTAGTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 34 0.97
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTGCATACA
Found at i:33361860 original size:16 final size:16
Alignment explanation
Indices: 33361839--33361880 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
33361829 CAAAATACTG
33361839 GCTTTTCGGCATTTCA
1 GCTTTTCGGCATTTCA
* *
33361855 GCTTTTCAGCATTTCG
1 GCTTTTCGGCATTTCA
33361871 GCTTTTCGGC
1 GCTTTTCGGC
33361881 TTTTGCCGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.10, C:0.26, G:0.21, T:0.43
Consensus pattern (16 bp):
GCTTTTCGGCATTTCA
Found at i:33361861 original size:8 final size:8
Alignment explanation
Indices: 33361838--33361884 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
33361828 CCAAAATACT
33361838 GGCTTTTC
1 GGCTTTTC
*
33361846 GGCATTTC
1 GGCTTTTC
*
33361854 AGCTTTTC
1 GGCTTTTC
* *
33361862 AGCATTTC
1 GGCTTTTC
33361870 GGCTTTTC
1 GGCTTTTC
33361878 GGCTTTT
1 GGCTTTT
33361885 GCCGATGTAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.09, C:0.23, G:0.21, T:0.47
Consensus pattern (8 bp):
GGCTTTTC
Found at i:33369268 original size:27 final size:28
Alignment explanation
Indices: 33369226--33369306 Score: 85
Period size: 27 Copynumber: 2.9 Consensus size: 28
33369216 GTCACCAGAT
* *
33369226 ACAGATATTTTGTGGCAGTGCCACCAAA
1 ACAGATAATATGTGGCAGTGCCACCAAA
* * *
33369254 ATAGA-AATATGTGGCAGAGCCACCAGA
1 ACAGATAATATGTGGCAGTGCCACCAAA
*
33369281 ACAGATAATTTGTGGCA-TAGCCACCA
1 ACAGATAATATGTGGCAGT-GCCACCA
33369307 GGAGCTTCCT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
27 22 0.51
28 21 0.49
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (28 bp):
ACAGATAATATGTGGCAGTGCCACCAAA
Found at i:33369293 original size:55 final size:55
Alignment explanation
Indices: 33369201--33369306 Score: 153
Period size: 55 Copynumber: 1.9 Consensus size: 55
33369191 TGCCAGATAC
* *
33369201 AGAAAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCACCAAAAT
1 AGAAAATGTGACAGAGCCACCAGATACAGATAATTTGTGGCA-TAGCCACCAAAAT
*
33369256 AGAAATATGTGGCAGAGCCACCAGA-ACAGATAATTTGTGGCATAGCCACCA
1 AGAAA-ATGTGACAGAGCCACCAGATACAGATAATTTGTGGCATAGCCACCA
33369307 GGAGCTTCCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
54 1 0.02
55 28 0.61
56 17 0.37
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (55 bp):
AGAAAATGTGACAGAGCCACCAGATACAGATAATTTGTGGCATAGCCACCAAAAT
Found at i:33369297 original size:28 final size:28
Alignment explanation
Indices: 33369207--33369307 Score: 114
Period size: 28 Copynumber: 3.6 Consensus size: 28
33369197 ATACAGAAAA
* * *
33369207 TGTGACAGAGTCACCAGATACAGATATTT
1 TGTGGCAGAGCCACCAGA-ACAGATAATT
* * * *
33369236 TGTGGCAGTGCCACCAAAATAGA-AATA
1 TGTGGCAGAGCCACCAGAACAGATAATT
33369263 TGTGGCAGAGCCACCAGAACAGATAATT
1 TGTGGCAGAGCCACCAGAACAGATAATT
*
33369291 TGTGGCATAGCCACCAG
1 TGTGGCAGAGCCACCAG
33369308 GAGCTTCCTC
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
27 22 0.37
28 23 0.39
29 14 0.24
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.21
Consensus pattern (28 bp):
TGTGGCAGAGCCACCAGAACAGATAATT
Found at i:33369459 original size:28 final size:28
Alignment explanation
Indices: 33369412--33369476 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
33369402 AAATTAACAC
*
33369412 TAGGGGTATAGAGGTCATTTTGCATACA
1 TAGGGGTATAGAGGTAATTTTGCATACA
33369440 TAGGGGTATA-ATGGTAATTTTGCATACA
1 TAGGGGTATAGA-GGTAATTTTGCATACA
33369468 TAGGGGTAT
1 TAGGGGTAT
33369477 TCTAGTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 34 0.97
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTGCATACA
Found at i:33369739 original size:8 final size:8
Alignment explanation
Indices: 33369723--33369770 Score: 62
Period size: 8 Copynumber: 6.0 Consensus size: 8
33369713 CCCAAAATAC
33369723 CGGCTTTT
1 CGGCTTTT
*
33369731 CGGCATTT
1 CGGCTTTT
33369739 CGGCTTTT
1 CGGCTTTT
33369747 CGG-TATTT
1 CGGCT-TTT
*
33369755 CAGCTTTT
1 CGGCTTTT
33369763 CGGCTTTT
1 CGGCTTTT
33369771 GTCGATCTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
7 1 0.03
8 32 0.94
9 1 0.03
ACGTcount: A:0.06, C:0.23, G:0.23, T:0.48
Consensus pattern (8 bp):
CGGCTTTT
Found at i:33369744 original size:16 final size:16
Alignment explanation
Indices: 33369723--33369766 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
33369713 CCCAAAATAC
33369723 CGGCTTTTCGGCATTT
1 CGGCTTTTCGGCATTT
*
33369739 CGGCTTTTCGGTATTT
1 CGGCTTTTCGGCATTT
*
33369755 CAGCTTTTCGGC
1 CGGCTTTTCGGC
33369767 TTTTGTCGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.07, C:0.25, G:0.25, T:0.43
Consensus pattern (16 bp):
CGGCTTTTCGGCATTT
Found at i:33374674 original size:47 final size:46
Alignment explanation
Indices: 33374625--33375267 Score: 435
Period size: 47 Copynumber: 13.5 Consensus size: 46
33374615 ATTGACGGTT
* * *
33374625 AAGGATACCATGTAAGACCATGTCAAGACATGGCATCGGCATTGATT
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGCATAGA-C
** *
33374672 AAGGACT-CCATGTAAGACCACATCAAGATATGGCATTGGCACTAAGAC
1 AAGGA-TACCATGTAAGACCATGTCAAGACATGGCATTGGCA-T-AGAC
* *** *
33374720 AGGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTA-AGAC
1 AAGGATACCATGTAAGACCATGTCAAG-ACATGGCA-TTGGCATAGAC
*** * * *
33374767 AAGGATACCATGTAAGACCATGTTTGGAACATAGCATTTGGTA-AGAT
1 AAGGATACCATGTAAGACCATGTCAAG-ACATGGCA-TTGGCATAGAC
* * *
33374814 AAGGATATCATGTAAGACCATGCCAATG-CATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAA-GACATGGCATTG----G--C-AT-AGAC
* * * * *
33374868 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATCGGCATTGATT
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGCATAGA-C
** *
33374915 AAGGACT-CCATGTAAGACCACATCAAGATATGGCATTGGCACTAAGAC
1 AAGGA-TACCATGTAAGACCATGTCAAGACATGGCATTGGCA-T-AGAC
* *** *
33374963 AGGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTA-AGAC
1 AAGGATACCATGTAAGACCATGTCAAG-ACATGGCA-TTGGCATAGAC
*** *
33375010 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTA-AGAC
1 AAGGATACCATGTAAGACCATGTCAAG-ACATGGCA-TTGGCATAGAC
*** *
33375057 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTA-AGAC
1 AAGGATACCATGTAAGACCATGTCAAG-ACATGGCA-TTGGCATAGAC
*** *
33375104 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTA-AGAC
1 AAGGATACCATGTAAGACCATGTCAAG-ACATGGCA-TTGGCATAGAC
*** *
33375151 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTA-AGAC
1 AAGGATACCATGTAAGACCATGTCAAG-ACATGGCA-TTGGCATAGAC
*** *
33375198 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTA-AGAC
1 AAGGATACCATGTAAGACCATGTCAAG-ACATGGCA-TTGGCATAGAC
33375245 AAGGATACCATGTAAGACCATGT
1 AAGGATACCATGTAAGACCATGT
33375268 TTGGAACATG
Statistics
Matches: 523, Mismatches: 49, Indels: 48
0.84 0.08 0.08
Matches are distributed among these distances:
45 3 0.01
46 7 0.01
47 403 0.77
48 43 0.08
49 19 0.04
50 11 0.02
52 1 0.00
53 1 0.00
54 35 0.07
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (46 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGCATAGAC
Found at i:33375063 original size:243 final size:235
Alignment explanation
Indices: 33374625--33375278 Score: 892
Period size: 243 Copynumber: 2.7 Consensus size: 235
33374615 ATTGACGGTT
*
33374625 AAGGATACCATGTAAGACCATGTCAAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGAC
1 AAGGAAACCATGTAAGACCATGTCAAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGAC
33374690 CACATCAAGATATGGCATTGGCACTAAGACAGGGATACCATGTAAGACCATGTTTGGAACATGGC
66 CACATCAAGATATGGCATTGGCACTAAGACAGGGATACCATGTAAGACCATGTTTGGAACATGGC
* *
33374755 ATTTGGTAAGACAAGGATACCATGTAAGACCATGTTTGGAACATAGCATTTGGTAAGATAAGGAT
131 ATTTGGTAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGACAAGGAT
* *
33374820 ATCATGTAAGACCATGCCAAT-G-CATGGCATTGATAAGTTCTATAAGGC
196 ACCATGTAAGACCATG--AATGGACATGGCATT--T--G----ATAAGAC
*
33374868 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGAC
1 AAGGAAACCATGTAAGACCATGTCAAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGAC
33374933 CACATCAAGATATGGCATTGGCACTAAGACAGGGATACCATGTAAGACCATGTTTGGAACATGGC
66 CACATCAAGATATGGCATTGGCACTAAGACAGGGATACCATGTAAGACCATGTTTGGAACATGGC
33374998 ATTTGGTAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGACAAGGAT
131 ATTTGGTAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGACAAGGAT
** *
33375063 ACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGAC
196 ACCATGTAAGACCATGAATGG-ACATGGCATTTGATAAGAC
* *** * * * *
33375104 AAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTA-AGA-CAAGGA-TACCATGTAA
1 AAGGAAACCATGTAAGACCATGTCAAG-ACATGGCA-TCGGCATTGATTAAGGACT-CCATGTAA
** *** * *
33375166 GACCATGTTTGGAACATGGCATTTGG---TAAGACAAGGATACCATGTAAGACCATGTTTGGAAC
63 GACCACATCAAG-ATATGGCA-TTGGCACTAAGACAGGGATACCATGTAAGACCATGTTTGGAAC
33375228 ATGGCATTTGGTAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGG
126 ATGGCATTTGGTAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGG
33375279 TGTTAAGTGA
Statistics
Matches: 378, Mismatches: 25, Indels: 24
0.89 0.06 0.06
Matches are distributed among these distances:
235 87 0.23
236 47 0.12
237 17 0.04
238 8 0.02
240 1 0.00
241 1 0.00
242 2 0.01
243 206 0.54
244 9 0.02
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (235 bp):
AAGGAAACCATGTAAGACCATGTCAAGACATGGCATCGGCATTGATTAAGGACTCCATGTAAGAC
CACATCAAGATATGGCATTGGCACTAAGACAGGGATACCATGTAAGACCATGTTTGGAACATGGC
ATTTGGTAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGACAAGGAT
ACCATGTAAGACCATGAATGGACATGGCATTTGATAAGAC
Found at i:33375268 original size:47 final size:47
Alignment explanation
Indices: 33374714--33375278 Score: 714
Period size: 47 Copynumber: 11.9 Consensus size: 47
33374704 GCATTGGCAC
*
33374714 TAAGACAGGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
33374761 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATAGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* * ** *
33374808 TAAGATAAGGATATCATGTAAGACCATG---CCAATGCATGGCATTGATAAGTTCTA
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAA--CATGGCATT--T--G----G
* * * *** *
33374862 TAAGGCAAGGAAATCATGTAAGACCATGTCAAG-ACATGGCA-TCGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* * * ** *** *
33374907 CATTGATTAAGGACT-CCATGTAAGACCACATCAAG-ATATGGCA-TTGG
1 TA-AGA-CAAGGA-TACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
33374954 CACTAAGACAGGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 ---TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
33375004 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
33375051 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
33375098 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
33375145 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
33375192 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
33375239 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGG
33375279 TGTTAAGTGA
Statistics
Matches: 460, Mismatches: 36, Indels: 44
0.85 0.07 0.08
Matches are distributed among these distances:
44 2 0.00
45 1 0.00
46 9 0.02
47 378 0.82
48 20 0.04
49 10 0.02
50 6 0.01
53 1 0.00
54 32 0.07
56 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.25
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:33382425 original size:54 final size:54
Alignment explanation
Indices: 33382341--33382459 Score: 148
Period size: 54 Copynumber: 2.2 Consensus size: 54
33382331 TCCTCACTCG
* *
33382341 TGTAACTCACTAAGTTGCCTCACACGCCCGTGTGCCAGGCCATATACTAGGCCA
1 TGTAACTCACTAAGTTGCCACACACGCCCGTGTGCCAAGCCATATACTAGGCCA
* * * * * * **
33382395 TGTAACTCTCTTAGTTGCCACACACTCCCGTGTTCCAAGCCATGTGCTAGGCTG
1 TGTAACTCACTAAGTTGCCACACACGCCCGTGTGCCAAGCCATATACTAGGCCA
33382449 TGTAACTCACT
1 TGTAACTCACT
33382460 GACTTGGAAC
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (54 bp):
TGTAACTCACTAAGTTGCCACACACGCCCGTGTGCCAAGCCATATACTAGGCCA
Found at i:33391704 original size:9 final size:9
Alignment explanation
Indices: 33391690--33391714 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
33391680 ACCATTTGCT
33391690 GATAAATAA
1 GATAAATAA
33391699 GATAAATAA
1 GATAAATAA
33391708 GATAAAT
1 GATAAAT
33391715 GTAGTTCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (9 bp):
GATAAATAA
Found at i:33394069 original size:14 final size:14
Alignment explanation
Indices: 33394050--33394076 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33394040 AAGGAAGAAA
33394050 AAGAGAAATAAATT
1 AAGAGAAATAAATT
33394064 AAGAGAAATAAAT
1 AAGAGAAATAAAT
33394077 AATGTAAAAA
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:0.67, C:0.00, G:0.15, T:0.19
Consensus pattern (14 bp):
AAGAGAAATAAATT
Found at i:33394597 original size:22 final size:22
Alignment explanation
Indices: 33394556--33394612 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
33394546 TTTTAATTAT
33394556 ATTTATTA-TTAACAAAATTTA
1 ATTTATTATTTAACAAAATTTA
*
33394577 GTTTATTATTTAA-AAATATTTA
1 ATTTATTATTTAACAAA-ATTTA
33394599 ATTTAACTTATTTA
1 ATTT-A-TTATTTA
33394613 TTTTTAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 10 0.33
22 12 0.40
23 1 0.03
24 7 0.23
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTATTATTTAACAAAATTTA
Found at i:33396419 original size:12 final size:12
Alignment explanation
Indices: 33396402--33396432 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
33396392 GAAGCAGGGG
33396402 AGAAAAAGCGAA
1 AGAAAAAGCGAA
*
33396414 AGAAAAAGGGAA
1 AGAAAAAGCGAA
33396426 AGAAAAA
1 AGAAAAA
33396433 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGCGAA
Found at i:33406700 original size:3 final size:3
Alignment explanation
Indices: 33406692--33406716 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
33406682 GTTGTGGCGT
33406692 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
33406717 AAATTAGGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:33406747 original size:6 final size:6
Alignment explanation
Indices: 33406736--33406760 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
33406726 GAGGAATTAA
33406736 GGTTAG GGTTAG GGTTAG GGTTAG G
1 GGTTAG GGTTAG GGTTAG GGTTAG G
33406761 AATGGGGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTTAG
Found at i:33406941 original size:3 final size:3
Alignment explanation
Indices: 33406935--33406977 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
33406925 GGAGAAGAAA
* * *
33406935 TTG TTG TTG TTG TTG CTG TTG TTG TTG TTG TTG CTG TTT TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
33406978 AAGAGAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.05, G:0.30, T:0.65
Consensus pattern (3 bp):
TTG
Found at i:33406995 original size:3 final size:3
Alignment explanation
Indices: 33406987--33407018 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
33406977 TAAGAGAAAT
33406987 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
33407019 TTGATGATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:33410158 original size:50 final size:50
Alignment explanation
Indices: 33410043--33410280 Score: 199
Period size: 50 Copynumber: 4.7 Consensus size: 50
33410033 ATACCAAAGT
** * ** * **
33410043 CATGTCCCAGACATGGTCTTACATGGGATGTTTTTTGT-ATTGCCAATGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGC
* * * * ** *
33410092 TATATCCCAGATATGGTCTTACATTGGAGTTCTCATATCGGTGCCCATGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGC
*** * *
33410142 CATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAACGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGC
* * *
33410192 CATGTCCCAGACATGGTCTTACATGAGACCTCTCATAACCTCAATGATGCCGATGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTGCCAATGC
*
33410248 CATGTCCCAGACATGGTCTTACATGGGATCTCT
1 CATGTCCCAGACATGGTCTTACATGGGACCTCT
33410281 TTACCCAAAT
Statistics
Matches: 147, Mismatches: 35, Indels: 7
0.78 0.19 0.04
Matches are distributed among these distances:
49 28 0.19
50 78 0.53
53 2 0.01
56 39 0.27
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAATGC
Found at i:33420267 original size:16 final size:16
Alignment explanation
Indices: 33420246--33420279 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33420236 TTCACAAAAA
33420246 TTACCAATGAGGTAAT
1 TTACCAATGAGGTAAT
* *
33420262 TTACCAGTGGGGTAAT
1 TTACCAATGAGGTAAT
33420278 TT
1 TT
33420280 TATAATTTCT
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:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (16 bp):
TTACCAATGAGGTAAT
Found at i:33420353 original size:25 final size:26
Alignment explanation
Indices: 33420315--33420366 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
33420305 AAGTTGTAAG
33420315 TAAAAAAATATCTTTAGA-AATTTTC
1 TAAAAAAATATCTTTAGAGAATTTTC
* *
33420340 TAAAATAATCTCTTTAGAGAATTTTC
1 TAAAAAAATATCTTTAGAGAATTTTC
33420366 T
1 T
33420367 TTCTACAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (26 bp):
TAAAAAAATATCTTTAGAGAATTTTC
Found at i:33420506 original size:16 final size:16
Alignment explanation
Indices: 33420487--33420524 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
33420477 AAATTAATAT
33420487 AATATTTATCAAGATA
1 AATATTTATCAAGATA
33420503 AATATTTATCAAGATA
1 AATATTTATCAAGATA
33420519 AATATT
1 AATATT
33420525 AGATTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (16 bp):
AATATTTATCAAGATA
Found at i:33423370 original size:63 final size:62
Alignment explanation
Indices: 33423296--33423416 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 62
33423286 TACCCCTAGA
*
33423296 GAAGGTGTTGATACAAGGAATGATT-ACGTGTGTTATGGTGCTTGTGTAAAATAAACTGATGCT
1 GAAGGTATTGATACAAGGAATGATTAAC--GTGTTATGGTGCTTGTGTAAAATAAACTGATGCT
** * * *
33423359 GAAGGTATTGATGTAGGGAATGATTGAACGTGTTGTGTTGCTTGTGTAAAATAAACTG
1 GAAGGTATTGATACAAGGAATGATT-AACGTGTTATGGTGCTTGTGTAAAATAAACTG
33423417 GGTTAGTACA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
63 48 0.96
65 2 0.04
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.34
Consensus pattern (62 bp):
GAAGGTATTGATACAAGGAATGATTAACGTGTTATGGTGCTTGTGTAAAATAAACTGATGCT
Found at i:33427559 original size:12 final size:12
Alignment explanation
Indices: 33427537--33427565 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
33427527 TAAATGTCTT
33427537 TAAAA-TAGTAA
1 TAAAATTAGTAA
33427548 TAAAATTAGTAA
1 TAAAATTAGTAA
33427560 TAAAAT
1 TAAAAT
33427566 AAAAGTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (12 bp):
TAAAATTAGTAA
Found at i:33430126 original size:75 final size:75
Alignment explanation
Indices: 33429982--33430127 Score: 202
Period size: 75 Copynumber: 1.9 Consensus size: 75
33429972 GACAGCATTG
* * *
33429982 AATGTGAGCCCAGCTTTAGTTGGATAAACCAACAATGTTTGCGCCCAACGCTAGTTGGGTATACC
1 AATGTGAGCCCAGCTTTAGTTGGATAAACCAACAATGTTTGCGCCCAACGCTAGTCGGATAAACC
33430047 GATGATAATA
66 GATGATAATA
* ** * * * *
33430057 AATGTGAGCCCAGCTTTAGTTGGATGAACCAACGGTGTTTGTGCTCAGCGCTAGTCGGATAAACT
1 AATGTGAGCCCAGCTTTAGTTGGATAAACCAACAATGTTTGCGCCCAACGCTAGTCGGATAAACC
33430122 GATGAT
66 GATGAT
33430128 TGTGTGCCCA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (75 bp):
AATGTGAGCCCAGCTTTAGTTGGATAAACCAACAATGTTTGCGCCCAACGCTAGTCGGATAAACC
GATGATAATA
Found at i:33433161 original size:31 final size:31
Alignment explanation
Indices: 33433082--33433150 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
33433072 GTTACAAAAT
33433082 AGTCATTAAACTATTCGAAAGTTTTCATTTA
1 AGTCATTAAACTATTCGAAAGTTTTCATTTA
**
33433113 AGTCATTAAACTATTCGAAAGTTTTTGTTTA
1 AGTCATTAAACTATTCGAAAGTTTTCATTTA
33433144 AGTCATT
1 AGTCATT
33433151 GTATTATTCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (31 bp):
AGTCATTAAACTATTCGAAAGTTTTCATTTA
Found at i:33433519 original size:43 final size:43
Alignment explanation
Indices: 33433374--33433713 Score: 309
Period size: 43 Copynumber: 8.0 Consensus size: 43
33433364 TTTCTCACGT
** * * * *
33433374 AAACGCCGCTAAAGAACATGATCTTTAGCAGCAC-TTTACCA-C
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTA-TAGC
* ** *
33433416 AAACGCCGCTAAAGATCATGACCTTTAGCGGCG--TTTAAAG-
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGC
*
33433456 ATAAGTGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAAG-
1 A-AA-CGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTAT-AGC
* * * *
33433501 AAACACCGCTAAATGTCATGTTTTTTAGCGACGCTTTTATAAG-
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTAT-AGC
* * * * *
33433544 AAAAGCCGTTAAAAGACATGTTCTTTAGCAGCGCTTTTATAGC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGC
* * *
33433587 AAACGCCGCTAAAGGTCATGTTCTTTAGCGACAC-TTTCTAGC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGC
* * * * *
33433629 AAACGCCGTTAAAGGCCATCTTCTTTAGCGGCGCCTTTATAGA
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGC
* *
33433672 AAACGCCACTAAAGGTCATGTTCTTCAGCGGCGCTTTTATAG
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAG
33433714 AAAAGGCCAC
Statistics
Matches: 246, Mismatches: 44, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
40 2 0.01
41 6 0.02
42 93 0.38
43 136 0.55
44 6 0.02
45 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGC
Found at i:33433580 original size:86 final size:85
Alignment explanation
Indices: 33433416--33433718 Score: 317
Period size: 85 Copynumber: 3.6 Consensus size: 85
33433406 ACTTTACCAC
* ** * * * * * *
33433416 AAACGCCGCTAAAGATCATGACCTTTAGCG--GCGTTTAAAGATAAGTGCCGCTAAAGGTCATGT
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTATAGA-AA-AGCCGTTAAAAGACATGT
33433479 TCTTTAGCGGCGCTTTTATA-A
64 TCTTTAGCGGCGCTTTTATAGA
* * *
33433500 GAAACACCGCTAAATGTCATGTTTTTTAGCGACGCTTTTATAAGAAAAGCCGTTAAAAGACATGT
1 -AAACGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTAT-AGAAAAGCCGTTAAAAGACATGT
* *
33433565 TCTTTAGCAGCGCTTTTATAGC
64 TCTTTAGCGGCGCTTTTATAGA
* * * * * *
33433587 AAACGCCGCTAAAGGTCATGTTCTTTAGCGACAC-TTTCTAGCAAACGCCGTTAAAGGCCATCTT
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTATAG-AAAAGCCGTTAAAAGACATGTT
*
33433651 CTTTAGCGGCGCCTTTATAGA
65 CTTTAGCGGCGCTTTTATAGA
* * *
33433672 AAACGCCACTAAAGGTCATGTTCTTCAGCGGCGCTTTTATAGAAAAG
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTATAGAAAAG
33433719 GCCACTAACT
Statistics
Matches: 180, Mismatches: 32, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
84 2 0.01
85 98 0.54
86 69 0.38
87 8 0.04
88 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (85 bp):
AAACGCCGCTAAAGGTCATGTTCTTTAGCGACGCTTTTATAGAAAAGCCGTTAAAAGACATGTTC
TTTAGCGGCGCTTTTATAGA
Found at i:33433714 original size:43 final size:43
Alignment explanation
Indices: 33433416--33433726 Score: 317
Period size: 43 Copynumber: 7.3 Consensus size: 43
33433406 ACTTTACCAC
* ** *
33433416 AAACGCCGCTAAAGATCATGACCTTTAGCGGCG--TTTAAAGA
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGA
**
33433457 TAAGTGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATA-A
1 -AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGA
* * * *
33433500 GAAACACCGCTAAATGTCATGTTTTTTAGCGACGCTTTTATAAGA
1 -AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTAT-AGA
* * * * *
33433545 AAA-GCCGTTAAAAGACATGTTCTTTAGCAGCGCTTTTATAGC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGA
* * * *
33433587 AAACGCCGCTAAAGGTCATGTTCTTTAGCGACAC-TTTCTAGC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGA
* * * *
33433629 AAACGCCGTTAAAGGCCATCTTCTTTAGCGGCGCCTTTATAGA
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGA
* *
33433672 AAACGCCACTAAAGGTCATGTTCTTCAGCGGCGCTTTTATAGA
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGA
* *
33433715 AAAGGCCACTAA
1 AAACGCCGCTAA
33433727 CTTTGGCAGA
Statistics
Matches: 221, Mismatches: 42, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
42 69 0.31
43 142 0.64
44 9 0.04
45 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTATAGA
Found at i:33434047 original size:21 final size:21
Alignment explanation
Indices: 33434002--33434047 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
33433992 ACTCTGCTTT
*
33434002 GCTTCCCTCGCTACTGCCTCT
1 GCTTCCCTCGCTACTGCCTCA
**
33434023 GCTTCCCTCGCTGTTGCCTCA
1 GCTTCCCTCGCTACTGCCTCA
33434044 GCTT
1 GCTT
33434048 TAAGTTGTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.43, G:0.17, T:0.35
Consensus pattern (21 bp):
GCTTCCCTCGCTACTGCCTCA
Found at i:33439515 original size:47 final size:47
Alignment explanation
Indices: 33439461--33439627 Score: 298
Period size: 47 Copynumber: 3.6 Consensus size: 47
33439451 CAAGCTATGG
*
33439461 AAGTTATGTGAGTTATGTAAGTTATGATATGATATATATAAGTTATT
1 AAGTTATGTGAGTTATGTAAGTTATGGTATGATATATATAAGTTATT
*
33439508 AAGTTATGTGAGTTATGTAAATTATGGTATGATATATATAAGTTATT
1 AAGTTATGTGAGTTATGTAAGTTATGGTATGATATATATAAGTTATT
33439555 AAGTTATGTGAGTTATGTAAGTTATGGTATGATATATATAAGTTATT
1 AAGTTATGTGAGTTATGTAAGTTATGGTATGATATATATAAGTTATT
* *
33439602 AAGTTATGTAAGTTATGTGAGTTATG
1 AAGTTATGTGAGTTATGTAAGTTATG
33439628 TAAATTATGA
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 115 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (47 bp):
AAGTTATGTGAGTTATGTAAGTTATGGTATGATATATATAAGTTATT
Found at i:33439532 original size:9 final size:9
Alignment explanation
Indices: 33439408--33439688 Score: 152
Period size: 9 Copynumber: 31.0 Consensus size: 9
33439398 TAAGTATAAT
33439408 TAAGTTATG
1 TAAGTTATG
*
33439417 TAACTTATG
1 TAAGTTATG
* * *
33439426 ATATGATATA
1 -TAAGTTATG
*
33439436 T-ATTTATG
1 TAAGTTATG
33439444 T-A-TTATG
1 TAAGTTATG
* *
33439451 CAAGCTATG
1 TAAGTTATG
*
33439460 GAAGTTATG
1 TAAGTTATG
*
33439469 TGAGTTATG
1 TAAGTTATG
33439478 TAAGTTATG
1 TAAGTTATG
* *
33439487 ATATGATATATA
1 -TAAG-T-TATG
33439499 TAAGTTAT-
1 TAAGTTATG
33439507 TAAGTTATG
1 TAAGTTATG
*
33439516 TGAGTTATG
1 TAAGTTATG
*
33439525 TAAATTATGG
1 TAAGTTAT-G
* *
33439535 TATGATATATA
1 TAAG-T-TATG
33439546 TAAGTTAT-
1 TAAGTTATG
33439554 TAAGTTATG
1 TAAGTTATG
*
33439563 TGAGTTATG
1 TAAGTTATG
33439572 TAAGTTATGG
1 TAAGTTAT-G
* *
33439582 TATGATATATA
1 TAAG-T-TATG
33439593 TAAGTTAT-
1 TAAGTTATG
33439601 TAAGTTATG
1 TAAGTTATG
33439610 TAAGTTATG
1 TAAGTTATG
*
33439619 TGAGTTATG
1 TAAGTTATG
*
33439628 TAAATTATG
1 TAAGTTATG
* *
33439637 ATATGATATATA
1 -TAAG-T-TATG
33439649 TAAGTTA-G
1 TAAGTTATG
33439657 TAAG---T-
1 TAAGTTATG
33439662 TAAGTTATG
1 TAAGTTATG
* *
33439671 TGAGTTATT
1 TAAGTTATG
33439680 TAAGTTATG
1 TAAGTTATG
33439689 GTATGAGTGA
Statistics
Matches: 206, Mismatches: 43, Indels: 46
0.70 0.15 0.16
Matches are distributed among these distances:
5 4 0.02
7 5 0.02
8 35 0.17
9 113 0.55
10 21 0.10
11 16 0.08
12 12 0.06
ACGTcount: A:0.35, C:0.01, G:0.20, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Done.