Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 159 of 284
Found at i:53328723 original size:53 final size:55
Alignment explanation
Indices: 53328623--53328761 Score: 194
Period size: 53 Copynumber: 2.6 Consensus size: 55
53328613 AGCATGGCTG
* *
53328623 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* *
53328677 CCAGAACAGATATATGTGGCAGAGCCACC-GAT-CAGATATTTGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
53328730 CCAGATCAGATATTTGTGGCATAGCCACCAGA
1 CCAGAACAGATATATGTGGCAGAGCCACCAGA
53328762 ACGCTTCCTC
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
53 45 0.59
54 17 0.22
55 14 0.18
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (55 bp):
CCAGAACAGATATATGTGGCAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:53330329 original size:43 final size:43
Alignment explanation
Indices: 53330281--53330365 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
53330271 AGCTATGATG
*
53330281 AAAAAAGATGGACAAAATTTTGTTCTTTTCACCCCTTTTTCTA
1 AAAAAAGATGGACAAAACTTTGTTCTTTTCACCCCTTTTTCTA
53330324 AAAAAAGATGGACAAAACTTTGTTCTTTTCACCCCTTTTTCT
1 AAAAAAGATGGACAAAACTTTGTTCTTTTCACCCCTTTTTCT
53330366 TTTAATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (43 bp):
AAAAAAGATGGACAAAACTTTGTTCTTTTCACCCCTTTTTCTA
Found at i:53330461 original size:26 final size:26
Alignment explanation
Indices: 53330424--53330504 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 26
53330414 CATGAAATTC
53330424 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
53330450 TTATCATAAAACACTTACCTAACCC-
1 TTATCATGAAACATTTACCTAACCCA
* *
53330475 --ATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
53330499 TTATCA
1 TTATCA
53330505 ATTTGTATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
23 19 0.41
26 27 0.59
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:53335887 original size:20 final size:19
Alignment explanation
Indices: 53335862--53335906 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
53335852 TGATTCTAAC
*
53335862 TAATTTTGAATAGTTTCATT
1 TAATTTTCAAT-GTTTCATT
* *
53335882 TAATTTTCAATTTTTCTTT
1 TAATTTTCAATGTTTCATT
53335901 TAATTT
1 TAATTT
53335907 GAACTTAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (19 bp):
TAATTTTCAATGTTTCATT
Found at i:53338405 original size:73 final size:73
Alignment explanation
Indices: 53338322--53338462 Score: 264
Period size: 73 Copynumber: 1.9 Consensus size: 73
53338312 GTTTATTTCA
*
53338322 ATTGAGATTGAGATTATGAATAACATAAGTGGCTAACTCCCTTAGGGGGTATTAACGAATGGATG
1 ATTGAGATTGAGATTATGAATAACATAAGTGGCTAACTCCCTTAGGGGATATTAACGAATGGATG
53338387 GGATTAAG
66 GGATTAAG
*
53338395 ATTGAGATTGAGATTATGAATAACATAAGTGGCTAACTCTCTTAGGGGATATTAACGAATGGATG
1 ATTGAGATTGAGATTATGAATAACATAAGTGGCTAACTCCCTTAGGGGATATTAACGAATGGATG
53338460 GGA
66 GGA
53338463 ACGTGATTAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (73 bp):
ATTGAGATTGAGATTATGAATAACATAAGTGGCTAACTCCCTTAGGGGATATTAACGAATGGATG
GGATTAAG
Found at i:53340352 original size:21 final size:21
Alignment explanation
Indices: 53340326--53340386 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
53340316 CGACAGATAA
53340326 GTGCCTAAAACGACACACAAG
1 GTGCCTAAAACGACACACAAG
* * **
53340347 GTGCCTGATACGACACATGAG
1 GTGCCTAAAACGACACACAAG
53340368 GTGCCTAAAATACGACACA
1 GTGCCT-AAA-ACGACACA
53340387 TAAAGTGTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 23 0.72
22 1 0.03
23 8 0.25
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (21 bp):
GTGCCTAAAACGACACACAAG
Found at i:53340399 original size:44 final size:41
Alignment explanation
Indices: 53340313--53340400 Score: 104
Period size: 44 Copynumber: 2.1 Consensus size: 41
53340303 CCTGAGCAGT
* *
53340313 ATACGACAGATAAGTGCCTAAAACGACACACAAGGTGCCTG
1 ATACGACACATAAGTGCCTAAAACGACACACAAAGTGCCTG
* * *
53340354 ATACGACACATGAGGTGCCTAAAATACGACACATAAAGTGTCTG
1 ATACGACACAT-AAGTGCCT-AAA-ACGACACACAAAGTGCCTG
53340398 ATA
1 ATA
53340401 TATGACACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
41 10 0.26
42 7 0.18
43 3 0.08
44 19 0.49
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTAAAACGACACACAAAGTGCCTG
Found at i:53341304 original size:17 final size:17
Alignment explanation
Indices: 53341270--53341307 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
53341260 ACTGAATTTC
53341270 AATTCAATTTATACCCT
1 AATTCAATTTATACCCT
*
53341287 AATTCCAATTTA-ATCCT
1 AATT-CAATTTATACCCT
53341304 AATT
1 AATT
53341308 AACTCATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTCAATTTATACCCT
Found at i:53341589 original size:9 final size:9
Alignment explanation
Indices: 53341575--53341599 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53341565 ATATATTAGT
53341575 TAATAATGA
1 TAATAATGA
53341584 TAATAATGA
1 TAATAATGA
53341593 TAATAAT
1 TAATAAT
53341600 AATTATAATA
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (9 bp):
TAATAATGA
Found at i:53349920 original size:12 final size:13
Alignment explanation
Indices: 53349896--53349926 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
53349886 TACAAATGTA
53349896 TCATTTCCCATTT
1 TCATTTCCCATTT
53349909 TCATTT-CCATTT
1 TCATTTCCCATTT
53349921 TCATTT
1 TCATTT
53349927 TAAGAAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (13 bp):
TCATTTCCCATTT
Found at i:53351848 original size:18 final size:20
Alignment explanation
Indices: 53351813--53351851 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
53351803 ATAAATTATA
53351813 ATTAAATATAGATTATATATT
1 ATTAAATATAGA-TATATATT
53351834 ATTAAAT-TAGA-ATATATT
1 ATTAAATATAGATATATATT
53351852 TAAATGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
ATTAAATATAGATATATATT
Found at i:53357783 original size:33 final size:33
Alignment explanation
Indices: 53357745--53357812 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
53357735 TTCACTATAG
*
53357745 ATAGAGATACCTACGATCTATTTCTCTTACTTC
1 ATAGAGATACATACGATCTATTTCTCTTACTTC
53357778 ATAGAGATACATACGATCTATTTCTCTTACTTC
1 ATAGAGATACATACGATCTATTTCTCTTACTTC
53357811 AT
1 AT
53357813 TGTTTTCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (33 bp):
ATAGAGATACATACGATCTATTTCTCTTACTTC
Found at i:53360859 original size:26 final size:25
Alignment explanation
Indices: 53360837--53360941 Score: 80
Period size: 23 Copynumber: 4.3 Consensus size: 25
53360827 GTCATGATCG
53360837 GTAAGCTCCTACTGAGCTGATGAACA
1 GTAAGCT-CTACTGAGCTGATGAACA
* *
53360863 GTATGCTCTATTGAGCTGA--AACA
1 GTAAGCTCTACTGAGCTGATGAACA
* **
53360886 GTAAACTCTAAAGAGC---TGAACA
1 GTAAGCTCTACTGAGCTGATGAACA
53360908 GTAAGCTCTTAC-GAGCTGAT-ATATCA
1 GTAAGCTC-TACTGAGCTGATGA-A-CA
53360934 GTAAGCTC
1 GTAAGCTC
53360942 ATACAAGCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
22 15 0.24
23 18 0.29
24 1 0.02
25 13 0.21
26 16 0.25
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (25 bp):
GTAAGCTCTACTGAGCTGATGAACA
Found at i:53360894 original size:23 final size:23
Alignment explanation
Indices: 53360837--53360941 Score: 86
Period size: 22 Copynumber: 4.3 Consensus size: 23
53360827 GTCATGATCG
*
53360837 GTAAGCTCCTACTGAGCTGATGAACA
1 GTAAGCT-CTAATGAGCTGA--AACA
* *
53360863 GTATGCTCTATTGAGCTGAAACA
1 GTAAGCTCTAATGAGCTGAAACA
* *
53360886 GTAAACTCTAAAGAGCTG-AACA
1 GTAAGCTCTAATGAGCTGAAACA
* *
53360908 GTAAGCTCTTACGAGCTGATATATCA
1 GTAAGCTCTAATGAGCTGA-A-A-CA
53360934 GTAAGCTC
1 GTAAGCTC
53360942 ATACAAGCTT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
22 19 0.29
23 18 0.27
24 1 0.02
25 12 0.18
26 16 0.24
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (23 bp):
GTAAGCTCTAATGAGCTGAAACA
Found at i:53362974 original size:40 final size:40
Alignment explanation
Indices: 53362918--53362993 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
53362908 TGCGCAATGC
* * *
53362918 ACCAAATGGTCGCAACATCTTATTCATCATTAAACTATGT
1 ACCAAATGGTCACAACATCTCATACATCATTAAACTATGT
53362958 ACCAAATGGTCACAACATCTCATACATCATTAAACT
1 ACCAAATGGTCACAACATCTCATACATCATTAAACT
53362994 CCAAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.29
Consensus pattern (40 bp):
ACCAAATGGTCACAACATCTCATACATCATTAAACTATGT
Found at i:53366686 original size:50 final size:50
Alignment explanation
Indices: 53366613--53366990 Score: 357
Period size: 50 Copynumber: 7.5 Consensus size: 50
53366603 GTGAGTCATG
*
53366613 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCACA
* ** * * * *
53366663 TGTGTAGTACTAAGTGCAGGCTACTATGCATACCTG-TTAACTTCGATCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGA--TAGGTCACA
* * * * * * **
53366714 TGTGTAGTACTAAGTGCAAGCTACTACGTGAATCAGATGGTTAAGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCACA
* * *
53366764 TGTGTCGTACTAAGTGCAGGCTACTACGTGT-CCTAGATTGATAGGCCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-AGATTGATAGGTCACA
* * * * * * *
53366814 TGTGTAGTACTAAGTGCAGGCTATTATGTGTACCCG-TTAACTTTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGA--TAGGTCACA
* * * * * **
53366865 TGTGTAGTACTAAGTGCAGGCTACTACATGTATCAGATGGTTAAGTCATG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCACA
* * **
53366915 TGTGTAGTACTAAGTGCAGGATACTATGTGTACCAGATTGATAGGTTGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCACA
53366965 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
53366991 TACGTACCAG
Statistics
Matches: 252, Mismatches: 68, Indels: 16
0.75 0.20 0.05
Matches are distributed among these distances:
49 7 0.03
50 171 0.68
51 72 0.29
52 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCACA
Found at i:53366998 original size:151 final size:151
Alignment explanation
Indices: 53366606--53366998 Score: 635
Period size: 151 Copynumber: 2.6 Consensus size: 151
53366596 ATCCGTTGTG
53366606 AGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGT
1 AGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGT
* *
53366671 ACTAAGTGCAGGCTACTATGCATACCTGTTAACTTCGATCACATGTGTAGTACTAAGTGCAAGCT
66 ACTAAGTGCAGGCTACTATGCGTACCCGTTAACTTCGATCACATGTGTAGTACTAAGTGCAAGCT
*
53366736 ACTACGTGAATCAGATGGTTA
131 ACTACATGAATCAGATGGTTA
* *
53366757 AGTCATGTGTGTCGTACTAAGTGCAGGCTACTACGTGT-CCTAGATTGATAGGCCGCATGTGTAG
1 AGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACC-AGATTGATAGGTCGCATGTGTAG
* * * * *
53366821 TACTAAGTGCAGGCTATTATGTGTACCCGTTAACTTTGATCACGTGTGTAGTACTAAGTGCAGGC
65 TACTAAGTGCAGGCTACTATGCGTACCCGTTAACTTCGATCACATGTGTAGTACTAAGTGCAAGC
*
53366886 TACTACATGTATCAGATGGTTA
130 TACTACATGAATCAGATGGTTA
* * *
53366908 AGTCATGTGTGTAGTACTAAGTGCAGGATACTATGTGTACCAGATTGATAGGTTGCATGTGTAGT
1 AGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGT
*
53366973 ACTAAGTGCAGGCTACTATACGTACC
66 ACTAAGTGCAGGCTACTATGCGTACC
53366999 AGAGAGCTTC
Statistics
Matches: 221, Mismatches: 19, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
150 2 0.01
151 217 0.98
152 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (151 bp):
AGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGT
ACTAAGTGCAGGCTACTATGCGTACCCGTTAACTTCGATCACATGTGTAGTACTAAGTGCAAGCT
ACTACATGAATCAGATGGTTA
Found at i:53367217 original size:16 final size:16
Alignment explanation
Indices: 53367196--53367227 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53367186 AAGATAGAAT
53367196 AAGTGAAATTATGTAA
1 AAGTGAAATTATGTAA
*
53367212 AAGTGAAATTTTGTAA
1 AAGTGAAATTATGTAA
53367228 TAAAACAATT
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:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (16 bp):
AAGTGAAATTATGTAA
Found at i:53367859 original size:181 final size:181
Alignment explanation
Indices: 53367555--53367882 Score: 505
Period size: 181 Copynumber: 1.8 Consensus size: 181
53367545 TCTGAAAGCT
* * * * *
53367555 GTACCATGAGATAAATAATTTTTAGTGAAGAGAGGTCGGAACTGTCAGATAGTGAAATAGTGGTA
1 GTACCATGAGATAAATAATTTTTACTGAAGAGAGGTCAGAACTATCAGACAGTGAAAAAGTGGTA
* * *
53367620 TCCTTAATGAATAAACTATACTAATTTGCTAAACCAAAAATTCTGAAAATTTTATGGTAATAATA
66 TCCTTAATGAATAAACTATACTAATTGGCTAAACCAAAAATTCTAAAAATTTTATGGTAAGAATA
*
53367685 TATGTGATTCTAGTTTTTTTGGAAAATTATTAGTTCTCAATTTAGAGTCTC
131 TATATGATTCTAGTTTTTTTGGAAAATTATTAGTTCTCAATTTAGAGTCTC
*
53367736 GTACCATGAGATAAATAATTTTTACTGAAGAGAGGTCAGAACTATCGGACAGTGAAACAAG-GGT
1 GTACCATGAGATAAATAATTTTTACTGAAGAGAGGTCAGAACTATCAGACAGTGAAA-AAGTGGT
* * * * *
53367800 ATCTTTAATGAATAAATTGTACTTATTGGCTAGACCAAAAATTCTAAAAATTTTATGGTAAGAAT
65 ATCCTTAATGAATAAACTATACTAATTGGCTAAACCAAAAATTCTAAAAATTTTATGGTAAGAAT
53367865 ATATATGATTCTAGTTTT
130 ATATATGATTCTAGTTTT
53367883 ATATAAAATT
Statistics
Matches: 131, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
181 129 0.98
182 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (181 bp):
GTACCATGAGATAAATAATTTTTACTGAAGAGAGGTCAGAACTATCAGACAGTGAAAAAGTGGTA
TCCTTAATGAATAAACTATACTAATTGGCTAAACCAAAAATTCTAAAAATTTTATGGTAAGAATA
TATATGATTCTAGTTTTTTTGGAAAATTATTAGTTCTCAATTTAGAGTCTC
Found at i:53371975 original size:41 final size:41
Alignment explanation
Indices: 53371872--53372024 Score: 175
Period size: 41 Copynumber: 3.7 Consensus size: 41
53371862 TACCATACCA
* * * * *
53371872 ATGCCATATCCCAAATATAGTCTTACATG-GGATCTCGTAACG
1 ATGCCATATCCCAGATATGGTCTTACACGAAG-TCTCAT-ACG
* *
53371914 ATGCCAATAGCCCAGCTATGGTCTTACACGAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAGTCTCATA-CG
*
53371957 AT-CCATATCCCAGATATGGTCTTACACGAAGTCTTATACTG
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATAC-G
53371998 ATGCCATATCCCAGATATGGTCTTACA
1 ATGCCATATCCCAGATATGGTCTTACA
53372025 GGTAGTCTTA
Statistics
Matches: 96, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
40 1 0.01
41 34 0.35
42 32 0.33
43 28 0.29
44 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (41 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATACG
Found at i:53372018 original size:42 final size:42
Alignment explanation
Indices: 53371872--53372034 Score: 170
Period size: 42 Copynumber: 3.9 Consensus size: 42
53371862 TACCATACCA
* * * * ** *
53371872 ATGCCATATCCCAAATATAGTCTTACATG-GGATCTCGTAACG
1 ATGCCATATCCCAGATATGGTCTTACACGAAG-TCTTATATCG
* * *
53371914 ATGCCAATAGCCCAGCTATGGTCTTACACGAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAGTCTTATATCG
53371957 AT-CCATATCCCAGATATGGTCTTACACGAAGTCTTATA-CTG
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTTATATC-G
* *
53371998 ATGCCATATCCCAGATATGGTCTTACAGGTAGTCTTA
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTTA
53372035 GTAAGCCTAT
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
40 1 0.01
41 34 0.33
42 39 0.38
43 29 0.28
44 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTTATATCG
Found at i:53376592 original size:46 final size:46
Alignment explanation
Indices: 53376540--53376715 Score: 171
Period size: 46 Copynumber: 3.8 Consensus size: 46
53376530 TGGTTGAGCA
*
53376540 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * * * *
53376586 TTCGAACTTGTTGAGTTGAGTTCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
53376633 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
**
53376679 -CCTGAGTTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
53376716 GTGGGTTACA
Statistics
Matches: 104, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
43 6 0.06
45 5 0.05
46 60 0.58
47 25 0.24
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:53376696 original size:93 final size:93
Alignment explanation
Indices: 53376537--53376707 Score: 256
Period size: 93 Copynumber: 1.8 Consensus size: 93
53376527 GGATGGTTGA
* *
53376537 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTTCGAACTTGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCTCGAACTTGTTGAGT
*
53376602 TGAGTTCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
53376630 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC-CTG-AGTTCGTTGA
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCTC-GAACTT-GTTGA
53376693 GTTGAGTCCGAGTTC
64 GTTGAGTCCGAGTTC
53376708 ACTTATGGGT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
92 4 0.06
93 66 0.94
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCTCGAACTTGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:53380160 original size:39 final size:41
Alignment explanation
Indices: 53380065--53380248 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 41
53380055 TTGAATGATG
*
53380065 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
53380104 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
*
53380144 TCCGGGCTAAG-CCCGAAGGCATTTGTCCG-AGATACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
53380183 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* *
53380223 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
53380249 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 10, Indels: 19
0.81 0.06 0.12
Matches are distributed among these distances:
39 54 0.43
40 60 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:53380270 original size:79 final size:79
Alignment explanation
Indices: 53380117--53380281 Score: 194
Period size: 79 Copynumber: 2.1 Consensus size: 79
53380107 GGACTAAGAT
* **
53380117 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTCCGAGATACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGATACTAA
*
53380182 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
53380196 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGA-G
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGA-GATA
* *
53380258 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
53380275 CCGAAGG
1 CCGAAGG
53380282 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
78 3 0.04
79 45 0.61
80 24 0.32
81 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGATACTAA
ATCCGGGTTAAATC
Found at i:53382416 original size:44 final size:43
Alignment explanation
Indices: 53382368--53382524 Score: 149
Period size: 43 Copynumber: 3.7 Consensus size: 43
53382358 ATATTTTTCG
*
53382368 TGTAAGACCATGTCTGGGACATTGGCATCA-ATTTATGATTTACA
1 TGTAAGACCATGTCTGAGACATTGGCATCATA-TT-TGATTTACA
* * * * **
53382412 TGTAAGACCATGTCTGGGACATCGGTATCGTATTTGATTT-TG
1 TGTAAGACCATGTCTGAGACATTGGCATCATATTTGATTTACA
* * *
53382454 TGTAAGACCCTGTCTGAGATAATGGCATCGATATTTGA-TTACA
1 TGTAAGACCATGTCTGAGACATTGGCATC-ATATTTGATTTACA
* * *
53382497 TATAAGACCACGTCTGAGACGTTGGCAT
1 TGTAAGACCATGTCTGAGACATTGGCAT
53382525 TGTACGAGCT
Statistics
Matches: 90, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
42 25 0.28
43 35 0.39
44 29 0.32
45 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (43 bp):
TGTAAGACCATGTCTGAGACATTGGCATCATATTTGATTTACA
Found at i:53382727 original size:20 final size:20
Alignment explanation
Indices: 53382690--53382727 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53382680 ATTTGTGAAC
*
53382690 ATATGGAATATGTTTGTATT
1 ATATGGAATATGTATGTATT
53382710 ATATGGAA-ATGTGATGTA
1 ATATGGAATATGT-ATGTA
53382728 CATATGAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (20 bp):
ATATGGAATATGTATGTATT
Found at i:53393424 original size:42 final size:43
Alignment explanation
Indices: 53393364--53393459 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 43
53393354 TATGATTTAT
* * *
53393364 GTGTAAGACCATGTCTGGGACATTAGCATCG-TATTTGATTTC
1 GTGTAAGACCATGCCTGGGACAGTAGCATCGATATTTGATTAC
* *
53393406 GTGTAAGACCCTGCCTGGGACAGTGGCATCGATATTTGATTAC
1 GTGTAAGACCATGCCTGGGACAGTAGCATCGATATTTGATTAC
*
53393449 ATGTAAGACCA
1 GTGTAAGACCA
53393460 CATCTGGGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 27 0.59
43 19 0.41
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCATGCCTGGGACAGTAGCATCGATATTTGATTAC
Found at i:53393467 original size:43 final size:43
Alignment explanation
Indices: 53393319--53393477 Score: 144
Period size: 43 Copynumber: 3.7 Consensus size: 43
53393309 ATGTGTTTTT
* * *
53393319 CATGTAGGACCACGTCTGGGACATTGTCATCAAT-TTATGATTTA
1 CATGTAAGACCACGTCTGGGACATTGGCATCGATATT-TGA-TTA
** * * *
53393363 TGTGTAAGACCATGTCTGGGACATTAGCATCG-TATTTGATTT
1 CATGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTA
* * *
53393405 CGTGTAAGACC-CTGCCTGGGACAGTGGCATCGATATTTGATTA
1 CATGTAAGACCAC-GTCTGGGACATTGGCATCGATATTTGATTA
* **
53393448 CATGTAAGACCACATCTGGGATGTTGGCAT
1 CATGTAAGACCACGTCTGGGACATTGGCAT
53393478 TGTACGAGCT
Statistics
Matches: 91, Mismatches: 20, Indels: 9
0.76 0.17 0.08
Matches are distributed among these distances:
42 28 0.31
43 35 0.38
44 28 0.31
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
CATGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTA
Found at i:53393655 original size:19 final size:19
Alignment explanation
Indices: 53393631--53393686 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
53393621 GAATATGTAT
53393631 ATATGTGTGAACATATGGA
1 ATATGTGTGAACATATGGA
* **
53393650 ATATGTTTGTATTATATGGA
1 ATATGTGTG-AACATATGGA
*
53393670 A-ATGTGATGTACATATG
1 ATATGTG-TGAACATATG
53393687 AGCAAATGGT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.39
Consensus pattern (19 bp):
ATATGTGTGAACATATGGA
Found at i:53393680 original size:20 final size:20
Alignment explanation
Indices: 53393643--53393680 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53393633 ATGTGTGAAC
*
53393643 ATATGGAATATGTTTGTATT
1 ATATGGAATATGTATGTATT
53393663 ATATGGAA-ATGTGATGTA
1 ATATGGAATATGT-ATGTA
53393681 CATATGAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (20 bp):
ATATGGAATATGTATGTATT
Found at i:53398749 original size:15 final size:16
Alignment explanation
Indices: 53398729--53398758 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53398719 AAGATCTTAT
53398729 AATCATAA-CTTACTC
1 AATCATAACCTTACTC
53398744 AATCATAACCTTACT
1 AATCATAACCTTACT
53398759 AAGGGTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (16 bp):
AATCATAACCTTACTC
Found at i:53398998 original size:43 final size:43
Alignment explanation
Indices: 53398945--53399094 Score: 214
Period size: 43 Copynumber: 3.5 Consensus size: 43
53398935 ATTCCAGATG
* * *
53398945 TGGTTTTACATAGAA-TCTCGTATCGATGCCAATAGCCCAGCTA
1 TGGTCTTACAT-GAAGTCTCATATCAATGCCAATAGCCCAGCTA
53398988 TGGTCTTACATGAAGTCTCATATCAATGCCAATAGCCCAGCTA
1 TGGTCTTACATGAAGTCTCATATCAATGCCAATAGCCCAGCTA
* * *
53399031 TGGTCTTACATGAAGTCTCATATCAATGCC-ATATCCTAGATA
1 TGGTCTTACATGAAGTCTCATATCAATGCCAATAGCCCAGCTA
*
53399073 TGGTCTTACACGAAGTCTCATA
1 TGGTCTTACATGAAGTCTCATA
53399095 CTGATGCCGT
Statistics
Matches: 99, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
42 33 0.33
43 66 0.67
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (43 bp):
TGGTCTTACATGAAGTCTCATATCAATGCCAATAGCCCAGCTA
Found at i:53399088 original size:42 final size:42
Alignment explanation
Indices: 53398921--53399126 Score: 209
Period size: 43 Copynumber: 4.9 Consensus size: 42
53398911 CACACGGTGC
* * * * *
53398921 CATACCAATGCCATATTCCAGATGTGGTTTTACATAGAA-TCT
1 CATATCAATGCCATATCCCAGATATGGTCTTACA-CGAAGTCT
* * * * *
53398963 CGTATCGATGCCAATAGCCCAGCTATGGTCTTACATGAAGTCT
1 CATATCAATGCC-ATATCCCAGATATGGTCTTACACGAAGTCT
* * *
53399006 CATATCAATGCCAATAGCCCAGCTATGGTCTTACATGAAGTCT
1 CATATCAATGCC-ATATCCCAGATATGGTCTTACACGAAGTCT
*
53399049 CATATCAATGCCATATCCTAGATATGGTCTTACACGAAGTCT
1 CATATCAATGCCATATCCCAGATATGGTCTTACACGAAGTCT
* * *
53399091 CATA-CTGATGCCGTATCCCAAATATGGTCTTACACG
1 CATATC-AATGCCATATCCCAGATATGGTCTTACACG
53399127 TAGCCTTAGT
Statistics
Matches: 142, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.01
42 68 0.48
43 73 0.51
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (42 bp):
CATATCAATGCCATATCCCAGATATGGTCTTACACGAAGTCT
Found at i:53399102 original size:85 final size:85
Alignment explanation
Indices: 53398921--53399124 Score: 207
Period size: 85 Copynumber: 2.4 Consensus size: 85
53398911 CACACGGTGC
* ** * * * * * *
53398921 CATACCAATGCCATATTCCAGATGTGGTTTTACATAGAATCTCGTATCGATGCCAATAGCCCAGC
1 CATATCAATGCCATAGCCCAAATATGGTCTTACATAGAATCTCATATCAATGCCAATAGCCCAGA
*
53398986 TATGGTCTTACATGAAGTCT
66 TATGGTCTTACACGAAGTCT
** * *
53399006 CATATCAATGCCAATAGCCCAGCTATGGTCTTACAT-GAAGTCTCATATCAATGCC-ATATCCTA
1 CATATCAATGCC-ATAGCCCAAATATGGTCTTACATAGAA-TCTCATATCAATGCCAATAGCCCA
53399069 GATATGGTCTTACACGAAGTCT
64 GATATGGTCTTACACGAAGTCT
* * *
53399091 CATA-CTGATGCCGTATCCCAAATATGGTCTTACA
1 CATATC-AATGCCATAGCCCAAATATGGTCTTACA
53399125 CGTAGCCTTA
Statistics
Matches: 99, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
84 19 0.19
85 49 0.49
86 31 0.31
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (85 bp):
CATATCAATGCCATAGCCCAAATATGGTCTTACATAGAATCTCATATCAATGCCAATAGCCCAGA
TATGGTCTTACACGAAGTCT
Found at i:53400681 original size:24 final size:23
Alignment explanation
Indices: 53400645--53400690 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
53400635 TTTGGAGAAT
53400645 TTTGTGTTTAGGTTCTGAAGGTTC
1 TTTGTGTTTAGGTTCTG-AGGTTC
*
53400669 TTTGT-TTTGAGGTTTTGAGGTT
1 TTTGTGTTT-AGGTTCTGAGGTT
53400691 TAGTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.11, C:0.04, G:0.30, T:0.54
Consensus pattern (23 bp):
TTTGTGTTTAGGTTCTGAGGTTC
Found at i:53401212 original size:18 final size:16
Alignment explanation
Indices: 53401185--53401230 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
53401175 TTTAAAGAGT
53401185 TTTATTTTTACTAAAAT-
1 TTTATTTTT--TAAAATA
*
53401202 TATATTTTTTAAAATA
1 TTTATTTTTTAAAATA
53401218 TTTATTTTTTAAA
1 TTTATTTTTTAAA
53401231 TAAGAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 6 0.23
16 12 0.46
17 8 0.31
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATTTTTTAAAATA
Found at i:53401223 original size:16 final size:15
Alignment explanation
Indices: 53401155--53401230 Score: 61
Period size: 17 Copynumber: 4.9 Consensus size: 15
53401145 AAAAATATCT
53401155 TTTTATTTTTT---A
1 TTTTATTTTTTAAAA
53401167 TTTT-TTATTTTAAAGA
1 TTTTATT-TTTTAAA-A
53401183 GTTTTATTTTTACTAAAA
1 -TTTTATTTTT--TAAAA
*
53401201 TTATATTTTTTAAAA
1 TTTTATTTTTTAAAA
53401216 TATTTATTTTTTAAA
1 T-TTTATTTTTTAAA
53401231 TAAGAAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
11 2 0.04
12 8 0.15
15 6 0.12
16 13 0.25
17 16 0.31
18 3 0.06
19 4 0.08
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (15 bp):
TTTTATTTTTTAAAA
Found at i:53401673 original size:10 final size:10
Alignment explanation
Indices: 53401658--53401720 Score: 58
Period size: 10 Copynumber: 6.4 Consensus size: 10
53401648 TAACATTGAA
53401658 TTTTATAAAT
1 TTTTATAAAT
*
53401668 TTTTATAATT
1 TTTTATAAAT
53401678 TTTTAT-AAT
1 TTTTATAAAT
* *
53401687 TTTAATGAAT
1 TTTTATAAAT
**
53401697 TTTTAT-CTT
1 TTTTATAAAT
53401706 TTTTAATAAAT
1 TTTT-ATAAAT
53401717 TTTT
1 TTTT
53401721 TATTTTTTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
9 12 0.29
10 25 0.60
11 5 0.12
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:53401683 original size:20 final size:19
Alignment explanation
Indices: 53401667--53401746 Score: 67
Period size: 19 Copynumber: 4.2 Consensus size: 19
53401657 ATTTTATAAA
* *
53401667 TTTTTATAATTTTTTATAA
1 TTTTTATAAATTTTTATAT
* * *
53401686 TTTTAATGAATTTTTATCT
1 TTTTTATAAATTTTTATAT
53401705 TTTTTAATAAATTTTT-TAT
1 TTTTT-ATAAATTTTTATAT
53401724 TTTTTA-AGAATTATTT-TAT
1 TTTTTATA-AATT-TTTATAT
53401743 TTTT
1 TTTT
53401747 GACATTGTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
17 1 0.02
18 5 0.10
19 35 0.70
20 9 0.18
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTTATAAATTTTTATAT
Found at i:53401726 original size:19 final size:19
Alignment explanation
Indices: 53401674--53401746 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
53401664 AAATTTTTAT
*
53401674 AATTTTTTATAATTTTAATG
1 AATTTTTTAT-TTTTTAATG
* *
53401694 AATTTTTATCTTTTTTAATA
1 AATTTTT-TATTTTTTAATG
53401714 AATTTTTTATTTTTTAA-G
1 AATTTTTTATTTTTTAATG
53401732 AATTATTTTATTTTT
1 AATT-TTTTATTTTT
53401747 GACATTGTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.09
19 19 0.41
20 21 0.46
21 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (19 bp):
AATTTTTTATTTTTTAATG
Found at i:53404833 original size:2 final size:2
Alignment explanation
Indices: 53404826--53404852 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53404816 TCCAGGTTTG
53404826 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
53404853 ATCTAGTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:53408178 original size:16 final size:16
Alignment explanation
Indices: 53408123--53408170 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
53408113 TGTTTAGTTC
*
53408123 ACTGTAATGAAATAGA
1 ACTGTAATAAAATAGA
*
53408139 ACTGTAATAAAATAAA
1 ACTGTAATAAAATAGA
*
53408155 ACAGTAATAAAATAGA
1 ACTGTAATAAAATAGA
53408171 GTTGTAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.23
Consensus pattern (16 bp):
ACTGTAATAAAATAGA
Found at i:53408268 original size:15 final size:16
Alignment explanation
Indices: 53408248--53408283 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
53408238 TTATTAAATT
53408248 TATAATTAAAT-ATAA
1 TATAATTAAATAATAA
53408263 TATAA-TAAATAATAA
1 TATAATTAAATAATAA
53408278 -ATAATT
1 TATAATT
53408284 TGATCAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TATAATTAAATAATAA
Found at i:53409804 original size:9 final size:8
Alignment explanation
Indices: 53409776--53409801 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
53409766 AAAAATAATG
53409776 AAGGAAAA
1 AAGGAAAA
53409784 AAGGAAAA
1 AAGGAAAA
53409792 AAGGAAAA
1 AAGGAAAA
53409800 AA
1 AA
53409802 AGGGTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AAGGAAAA
Found at i:53410078 original size:48 final size:48
Alignment explanation
Indices: 53410006--53410125 Score: 181
Period size: 48 Copynumber: 2.5 Consensus size: 48
53409996 AGGTGTTCCG
* *
53410006 ATCCCTTTGTTCTTGGC-CCTAGCCACCG-TTCGGATTCCCATAATCTCT
1 ATCCCTTTGTTCTCGACTCC-AGCCACCGCTT-GGATTCCCATAATCTCT
*
53410054 ATCCCTTTGTTCTCGACTCCAGCCACCGCTTGGATTCCTATAATCTCT
1 ATCCCTTTGTTCTCGACTCCAGCCACCGCTTGGATTCCCATAATCTCT
53410102 ATCCCTTTGTTCTCGACTCCAGCC
1 ATCCCTTTGTTCTCGACTCCAGCC
53410126 GCCNNNNNNN
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
48 63 0.94
49 4 0.06
ACGTcount: A:0.15, C:0.37, G:0.13, T:0.35
Consensus pattern (48 bp):
ATCCCTTTGTTCTCGACTCCAGCCACCGCTTGGATTCCCATAATCTCT
Found at i:53413036 original size:10 final size:9
Alignment explanation
Indices: 53413021--53413045 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
53413011 TTTAATATTA
53413021 AATTTTTTT
1 AATTTTTTT
53413030 AATTTTTTT
1 AATTTTTTT
53413039 AATTTTT
1 AATTTTT
53413046 AATTTTAAGT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
AATTTTTTT
Found at i:53413271 original size:19 final size:20
Alignment explanation
Indices: 53413247--53413284 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
53413237 TCTCATTTTT
53413247 TATTTGTTTTT-TGTTTTAA
1 TATTTGTTTTTATGTTTTAA
53413266 TATTTGTTTTTATGTTTTA
1 TATTTGTTTTTATGTTTTA
53413285 GATGTACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.16, C:0.00, G:0.11, T:0.74
Consensus pattern (20 bp):
TATTTGTTTTTATGTTTTAA
Found at i:53420379 original size:59 final size:62
Alignment explanation
Indices: 53420308--53420424 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 62
53420298 ATCACTTTAA
* * * *
53420308 TATTAAATTAATATAATATTTATC-A-A-GATAAATATTAGATTAAATTTAATATTAAAGCT
1 TATTAAAATAATAGAATATTTATCTACATGATAAACATTAAATTAAATTTAATATTAAAGCT
*
53420367 TATTAAAATAATAGAATATTTATCTACATGATAAACATTAAATTAATTTTAATATTAA
1 TATTAAAATAATAGAATATTTATCTACATGATAAACATTAAATTAAATTTAATATTAA
53420425 GATAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 22 0.44
60 1 0.02
61 1 0.02
62 26 0.52
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (62 bp):
TATTAAAATAATAGAATATTTATCTACATGATAAACATTAAATTAAATTTAATATTAAAGCT
Found at i:53421790 original size:15 final size:15
Alignment explanation
Indices: 53421766--53421797 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
53421756 TATGCATGTA
*
53421766 AAATATAAAAGACAT
1 AAATACAAAAGACAT
53421781 AAATACAAAAGACAT
1 AAATACAAAAGACAT
53421796 AA
1 AA
53421798 TGGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:53422980 original size:23 final size:23
Alignment explanation
Indices: 53422953--53423004 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
53422943 CCTTAGGGGA
* * *
53422953 GATTAACGAGTGGATGGGGACGT
1 GATTAACGAATGGAAGGGGACAT
*
53422976 GATTAACGAATGGAAGGGGATAT
1 GATTAACGAATGGAAGGGGACAT
53422999 GATTAA
1 GATTAA
53423005 TGAAGGATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.06, G:0.37, T:0.23
Consensus pattern (23 bp):
GATTAACGAATGGAAGGGGACAT
Found at i:53441216 original size:57 final size:57
Alignment explanation
Indices: 53441153--53441282 Score: 179
Period size: 57 Copynumber: 2.3 Consensus size: 57
53441143 AAAATTTTGA
* *
53441153 AAAGGTAAGCCTTTGTGGCAAACCTGTTAAAGGACAAACTTTATGGCAAAACTCTGG
1 AAAGGTAAGCCTTTGTGGCAAACCTGTTAAAGGACAAACTTTATGACAAAAATCTGG
* * ** * * *
53441210 AAAGGTAGGCCTTTATGGTGAACCTGTTAAAGGATAACCTTTGTGACAAAAATCTGG
1 AAAGGTAAGCCTTTGTGGCAAACCTGTTAAAGGACAAACTTTATGACAAAAATCTGG
53441267 AAAGGTAAGCCTTTGT
1 AAAGGTAAGCCTTTGT
53441283 AATAAACTCT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (57 bp):
AAAGGTAAGCCTTTGTGGCAAACCTGTTAAAGGACAAACTTTATGACAAAAATCTGG
Found at i:53448136 original size:53 final size:53
Alignment explanation
Indices: 53448056--53448162 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
53448046 CGAATCTGCC
53448056 ACTATGATTTGTGGCAAATCAGTGACAGACACAAGCTGATGGCATAGTCGTGT
1 ACTATGATTTGTGGCAAATCAGTGACAGACACAAGCTGATGGCATAGTCGTGT
*
53448109 ACTATGATTTGTGGCAAATCAGTGACAGACACAAGCTGATGGCATAGTTGTGT
1 ACTATGATTTGTGGCAAATCAGTGACAGACACAAGCTGATGGCATAGTCGTGT
53448162 A
1 A
53448163 GGTACTGTGT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (53 bp):
ACTATGATTTGTGGCAAATCAGTGACAGACACAAGCTGATGGCATAGTCGTGT
Found at i:53450748 original size:48 final size:48
Alignment explanation
Indices: 53450685--53450910 Score: 319
Period size: 48 Copynumber: 4.7 Consensus size: 48
53450675 CTCGCACACT
* * *
53450685 AAGTGCTCATATCATGGCCCGAAGCCAACTCAATATATCTCACACCCG
1 AAGTGCTAATATCATGGCCCGAAGCCAAATCAATATAACTCACACCCG
* *
53450733 AAGTGCTAATATCATGGCCCAAAGCCAAATCAATA-AAGCTCGCACCCG
1 AAGTGCTAATATCATGGCCCGAAGCCAAATCAATATAA-CTCACACCCG
* * **
53450781 AAGTGCCAATATCATGGCCCGAAGCCAAATCAATGTAACTTGCACCCG
1 AAGTGCTAATATCATGGCCCGAAGCCAAATCAATATAACTCACACCCG
** *
53450829 AAGTGCTAATATCATGGCCTAAAGTCAAATCAATATAACTCACACCCG
1 AAGTGCTAATATCATGGCCCGAAGCCAAATCAATATAACTCACACCCG
*
53450877 AAGTGCTAATAACATGGCCCGAAGCCAAATCAAT
1 AAGTGCTAATATCATGGCCCGAAGCCAAATCAAT
53450911 GTATCTCCTA
Statistics
Matches: 156, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
47 1 0.01
48 153 0.98
49 2 0.01
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.19
Consensus pattern (48 bp):
AAGTGCTAATATCATGGCCCGAAGCCAAATCAATATAACTCACACCCG
Found at i:53453897 original size:48 final size:45
Alignment explanation
Indices: 53453754--53453928 Score: 165
Period size: 47 Copynumber: 3.8 Consensus size: 45
53453744 GTAAGGTGCT
* * *
53453754 GATGCCATGTCCCAGACATGGTCTTACACTAACTATCATCTCGTAGCC
1 GATG-CATGTCCCAGACATGGTCTTACACTAGCTCTCATCT-GT-GTC
* * *
53453802 GATGCATGTTCCAGACAT-GTCTTACACTAGCACTCGTCTTGATGTC
1 GATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATC-TG-TGTC
* * *
53453848 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTAATCATGTGGTC
1 GATG-CATGTCCCAGACATGGTCTTACACTAGCTCTCATC-TGT-GTC
* *
53453896 GATGCATGTCCCAGACAT-TTCTCACACTAGCTC
1 GATGCATGTCCCAGACATGGTCTTACACTAGCTC
53453929 ACAATAACCC
Statistics
Matches: 105, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
46 35 0.33
47 41 0.39
48 29 0.28
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.30
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTGTGTC
Found at i:53453923 original size:94 final size:94
Alignment explanation
Indices: 53453754--53453926 Score: 240
Period size: 94 Copynumber: 1.8 Consensus size: 94
53453744 GTAAGGTGCT
* *
53453754 GATGCCATGTCCCAGACATGGTCTTACACTAACTATCATCTCGTAGCCGATGCATGTTCCAGACA
1 GATGCCATGTCCCAGACATGGTCTTACACTAACTATAATCTCGTAGCCGATGCATGTCCCAGACA
*
53453819 TGTCTTACACTAGCACTCGTCTTGATGTC
66 TGTCTCACACTAGCACTCGTCTTGATGTC
* ** * * *
53453848 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTAATCAT-GTGGTCGATGCATGTCCCAGAC
1 GATGCCATGTCCCAGACATGGTCTTACACTAACTATAATC-TCGTAGCCGATGCATGTCCCAGAC
*
53453912 ATTTCTCACACTAGC
65 ATGTCTCACACTAGC
53453927 TCACAATAAC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
94 67 0.99
95 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (94 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAACTATAATCTCGTAGCCGATGCATGTCCCAGACA
TGTCTCACACTAGCACTCGTCTTGATGTC
Found at i:53455880 original size:21 final size:19
Alignment explanation
Indices: 53455838--53455881 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
53455828 TAGATATTTC
* *
53455838 TTTTGAACCCTCAAATCAA
1 TTTTGAACACTCAAAACAA
53455857 TTTTGAACACTCATAAAACAA
1 TTTTGAACACTC--AAAACAA
53455878 TTTT
1 TTTT
53455882 CAAAGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
21 10 0.48
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (19 bp):
TTTTGAACACTCAAAACAA
Found at i:53457143 original size:137 final size:135
Alignment explanation
Indices: 53456942--53457217 Score: 534
Period size: 137 Copynumber: 2.0 Consensus size: 135
53456932 ATTCAAGCTC
53456942 AGTTCATTTACTACCTAGACTCCAAATAGGTAGAATGGCACCCAGACACTTTTAGATGAGACTTG
1 AGTTCATTTACTACCTAGACTCCAAATAGGTAGAATGGCACCCAGACACTTTTAGATGAGACTTG
53457007 ACAGTAATGCAAATGCGTAAGAAACTAAAAGAATCAGTAAAAGAAACGTAGAATTGATATTAAAA
66 ACAGTAATGCAAATGCGTAAGAAACTAAAAGAATCAGTAAAAGAAACGTAGAATTGATATTAAAA
53457072 CAAGAGA
131 C--GAGA
53457079 AGTTCATTTACTACCTAGACTCCAAATAGGTAGAATGGCACCCAGACACTTTTAGATGAGACTTG
1 AGTTCATTTACTACCTAGACTCCAAATAGGTAGAATGGCACCCAGACACTTTTAGATGAGACTTG
53457144 ACAGTAATGCAAATGCGTAAGAAACTAAAAGAATCAGTAAAAGAAACGTAGAATTGATATTAAAA
66 ACAGTAATGCAAATGCGTAAGAAACTAAAAGAATCAGTAAAAGAAACGTAGAATTGATATTAAAA
53457209 CGAGA
131 CGAGA
53457214 AGTT
1 AGTT
53457218 TCGGAATAAG
Statistics
Matches: 139, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
135 8 0.06
137 131 0.94
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.23
Consensus pattern (135 bp):
AGTTCATTTACTACCTAGACTCCAAATAGGTAGAATGGCACCCAGACACTTTTAGATGAGACTTG
ACAGTAATGCAAATGCGTAAGAAACTAAAAGAATCAGTAAAAGAAACGTAGAATTGATATTAAAA
CGAGA
Found at i:53461395 original size:12 final size:12
Alignment explanation
Indices: 53461378--53461403 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53461368 TAGGTAAAGA
53461378 ATATATATAGTT
1 ATATATATAGTT
53461390 ATATATATAGTT
1 ATATATATAGTT
53461402 AT
1 AT
53461404 GGTTAGCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATATATAGTT
Found at i:53463712 original size:13 final size:13
Alignment explanation
Indices: 53463694--53463719 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53463684 CATCGGACCT
53463694 TCAACTCATGCAA
1 TCAACTCATGCAA
53463707 TCAACTCATGCAA
1 TCAACTCATGCAA
53463720 CTGCCATGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
TCAACTCATGCAA
Found at i:53467540 original size:21 final size:21
Alignment explanation
Indices: 53467514--53467554 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53467504 CGAGTGGATC
53467514 AGCTCTTACAAGCTTCTGTTA
1 AGCTCTTACAAGCTTCTGTTA
* *
53467535 AGCTCTTTCGAGCTTCTGTT
1 AGCTCTTACAAGCTTCTGTT
53467555 GGCAGACTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (21 bp):
AGCTCTTACAAGCTTCTGTTA
Found at i:53469131 original size:21 final size:21
Alignment explanation
Indices: 53469105--53469155 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
53469095 CGGGTGGATT
*
53469105 AGCTCTTACAAGCTTCTGTTC
1 AGCTCTTACAAGCTTCTATTC
*
53469126 AGCTCTTTCAAGCTTCTATTC
1 AGCTCTTACAAGCTTCTATTC
53469147 AGCTCTTAC
1 AGCTCTTAC
53469156 GTGTTCAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.29, G:0.12, T:0.39
Consensus pattern (21 bp):
AGCTCTTACAAGCTTCTATTC
Found at i:53474562 original size:27 final size:26
Alignment explanation
Indices: 53474520--53474633 Score: 113
Period size: 27 Copynumber: 4.2 Consensus size: 26
53474510 AGCATGGCTG
* * *
53474520 CCAGAATAGATCTTGTGACAGAGTCA
1 CCAGAATAGATATTGTGGCAGAGCCA
53474546 CCAGACATAGATATTGTGGCAGAGCCA
1 CCAGA-ATAGATATTGTGGCAGAGCCA
* *
53474573 CCAGAAACAGGTATTTGTGGCAGAGCCA
1 CCAG-AATAGATA-TTGTGGCAGAGCCA
* *
53474601 CCAG-ATCAGATATTTATGGCAGAGCCG
1 CCAGAAT-AGATA-TTGTGGCAGAGCCA
53474628 CCAGAA
1 CCAGAA
53474634 CGCTTCCTCT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
26 6 0.08
27 48 0.65
28 20 0.27
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.19
Consensus pattern (26 bp):
CCAGAATAGATATTGTGGCAGAGCCA
Found at i:53474597 original size:28 final size:28
Alignment explanation
Indices: 53474532--53474633 Score: 118
Period size: 27 Copynumber: 3.7 Consensus size: 28
53474522 AGAATAGATC
* * * *
53474532 TTGTGACAGAGTCACCAGACATAGATA-
1 TTGTGGCAGAGCCACCAGAAACAGATAT
*
53474559 TTGTGGCAGAGCCACCAGAAACAGGTAT
1 TTGTGGCAGAGCCACCAGAAACAGATAT
*
53474587 TTGTGGCAGAGCCACCAG-ATCAGATAT
1 TTGTGGCAGAGCCACCAGAAACAGATAT
* *
53474614 TTATGGCAGAGCCGCCAGAA
1 TTGTGGCAGAGCCACCAGAA
53474634 CGCTTCCTCT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 45 0.70
28 19 0.30
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (28 bp):
TTGTGGCAGAGCCACCAGAAACAGATAT
Found at i:53494585 original size:21 final size:21
Alignment explanation
Indices: 53494561--53494635 Score: 57
Period size: 21 Copynumber: 3.5 Consensus size: 21
53494551 AATTTTCCCT
*
53494561 TTTCTTTTATTTCTTTTTTCC
1 TTTCTCTTATTTCTTTTTTCC
*
53494582 TTTCTCCTATTTCGTTTTCACTTCC
1 TTTCTCTTATTTC-TTTT---TTCC
53494607 TTT-TCTT-TTTCTTTCTTT-C
1 TTTCTCTTATTTCTTT-TTTCC
*
53494626 TTTCTTTTAT
1 TTTCTCTTAT
53494636 ATTTTATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
19 4 0.09
20 5 0.12
21 12 0.28
22 7 0.16
23 5 0.12
24 3 0.07
25 7 0.16
ACGTcount: A:0.05, C:0.23, G:0.01, T:0.71
Consensus pattern (21 bp):
TTTCTCTTATTTCTTTTTTCC
Found at i:53494710 original size:25 final size:24
Alignment explanation
Indices: 53494663--53494719 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
53494653 ATTATTATTA
* *
53494663 TATTATATTATTTTAATATATACAT
1 TATTATATTAATTTAATAAATAC-T
**
53494688 TATTATATTAATTTCTTAAATACT
1 TATTATATTAATTTAATAAATACT
*
53494712 AATTATAT
1 TATTATAT
53494720 AATATATGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 8 0.30
25 19 0.70
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTATATTAATTTAATAAATACT
Found at i:53498132 original size:45 final size:43
Alignment explanation
Indices: 53497974--53498131 Score: 171
Period size: 45 Copynumber: 3.7 Consensus size: 43
53497964 ATATCATACA
*
53497974 ATGCCAACGTCCCAGACATGGTCTTACATGCT-ATCAC-ATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACA--CTAATCACAATATCG
* * * *
53498017 ATGCCACTGTTCCAGACAGGGTCTTACACGAATCA-AATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACACTAATCACAATATCG
** *
53498058 ATGCTGATGTCCCAGACATGGTCTTACACATAACCACATATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACAC-TAATCACA-ATATCG
*
53498103 ATGCCAATGTCCCAGACAAGGTCTTACAC
1 ATGCCAATGTCCCAGACATGGTCTTACAC
53498132 AAGAACACAT
Statistics
Matches: 94, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
41 27 0.29
42 11 0.12
43 25 0.27
44 3 0.03
45 28 0.30
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACTAATCACAATATCG
Found at i:53503317 original size:41 final size:42
Alignment explanation
Indices: 53503267--53503376 Score: 141
Period size: 41 Copynumber: 2.6 Consensus size: 42
53503257 ACTGAGATTA
*
53503267 CGTGTAAGACCATATCTGGGATATGGAATCGATATGAGA-CT
1 CGTGTAAGACCATATCTGGGATATGGAATCGATACGAGATCT
* * * *
53503308 CGTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGATTT
1 CGTGTAAGACCATATCTGGGATA-TGGAATCGATACGAGATCT
* *
53503351 CATGTAAGACCATATCTAGGATATGG
1 CGTGTAAGACCATATCTGGGATATGG
53503377 CATTGGTATG
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 21 0.36
42 17 0.29
43 20 0.34
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGGGATATGGAATCGATACGAGATCT
Found at i:53503378 original size:42 final size:42
Alignment explanation
Indices: 53503260--53503379 Score: 152
Period size: 42 Copynumber: 2.9 Consensus size: 42
53503250 TAGGGTTACT
* * *
53503260 GAGATTACGTGTAAGACCATATCTGGGATATGGAATCGATAT
1 GAGATTTCGTGTAAGACCATATCTGGGATATGGCATCGATAC
* * *
53503302 GAGA-CTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATAC
1 GAGATTTCGTGTAAGACCATATCTGGGATA-TGGCATCGATAC
* *
53503344 GAGATTTCATGTAAGACCATATCTAGGATATGGCAT
1 GAGATTTCGTGTAAGACCATATCTGGGATATGGCAT
53503380 TGGTATGGTA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 21 0.32
42 24 0.37
43 20 0.31
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (42 bp):
GAGATTTCGTGTAAGACCATATCTGGGATATGGCATCGATAC
Found at i:53506591 original size:48 final size:48
Alignment explanation
Indices: 53506487--53506602 Score: 151
Period size: 48 Copynumber: 2.4 Consensus size: 48
53506477 TTTGGGTGAT
* * * **
53506487 ATGTGTGCCAGTCTAAGACCATGTCTGGGACATGGCATTGGCCACATT
1 ATGTGAGCCAGTATAAGACCATGTCTGGGACATGACATTGGCCACAGC
* * * *
53506535 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGACATTGGCCTCGGC
1 ATGTGAGCCAGTATAAGACCATGTCTGGGACATGACATTGGCCACAGC
53506583 ATGTGAGCCAGTATAAGACC
1 ATGTGAGCCAGTATAAGACC
53506603 CTTTTTGGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.23
Consensus pattern (48 bp):
ATGTGAGCCAGTATAAGACCATGTCTGGGACATGACATTGGCCACAGC
Found at i:53534147 original size:9 final size:9
Alignment explanation
Indices: 53534133--53534245 Score: 61
Period size: 9 Copynumber: 11.8 Consensus size: 9
53534123 ATGACATGTG
53534133 ATAAAAAAT
1 ATAAAAAAT
53534142 ATAAAAAAT
1 ATAAAAAAT
*
53534151 A-AAAATCA-
1 ATAAAA-AAT
*
53534159 ATAAAAATT
1 ATAAAAAAT
53534168 ATAAAAAAT
1 ATAAAAAAT
*
53534177 ATTAAGAAATT
1 A-TAA-AAAAT
*
53534188 ATTAAAAAT
1 ATAAAAAAT
53534197 -TAGAACAAATTT
1 ATA-AA-AAA--T
*
53534209 ATAAAAATT
1 ATAAAAAAT
53534218 ATAAAAAAATT
1 AT-AAAAAA-T
*
53534229 ATAAAATAT
1 ATAAAAAAT
53534238 ATCAAAAA
1 AT-AAAAA
53534246 GGCTCTTTAA
Statistics
Matches: 79, Mismatches: 12, Indels: 25
0.68 0.10 0.22
Matches are distributed among these distances:
8 6 0.08
9 36 0.46
10 22 0.28
11 10 0.13
12 3 0.04
13 2 0.03
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:53534174 original size:10 final size:10
Alignment explanation
Indices: 53534161--53534234 Score: 71
Period size: 10 Copynumber: 7.3 Consensus size: 10
53534151 AAAAATCAAT
53534161 AAAAATTATA
1 AAAAATTATA
53534171 AAAAA-TATTA
1 AAAAATTA-TA
* *
53534181 AGAAATTATT
1 AAAAATTATA
*
53534191 AAAAATTAGA
1 AAAAATTATA
*
53534201 ACAAATT-TA
1 AAAAATTATA
53534210 TAAAAATTATAA
1 -AAAAATTAT-A
53534222 AAAAATTATA
1 AAAAATTATA
53534232 AAA
1 AAA
53534235 TATATCAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
9 3 0.06
10 35 0.69
11 12 0.24
12 1 0.02
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (10 bp):
AAAAATTATA
Found at i:53534176 original size:20 final size:19
Alignment explanation
Indices: 53534133--53534234 Score: 79
Period size: 20 Copynumber: 5.3 Consensus size: 19
53534123 ATGACATGTG
53534133 ATAAAAAAT-ATAAAAA--
1 ATAAAAAATAATAAAAATT
53534149 AT-AAAAATCAATAAAAATT
1 ATAAAAAAT-AATAAAAATT
*
53534168 ATAAAAAATATTAAGAAATT
1 ATAAAAAATAATAA-AAATT
* * *
53534188 ATTAAAAATTAGAACAAATTT
1 ATAAAAAATAATAA-AAA-TT
53534209 ATAAAAATTATAA-AAAAATT
1 ATAAAAA--ATAATAAAAATT
53534229 ATAAAA
1 ATAAAA
53534235 TATATCAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
15 6 0.09
16 2 0.03
17 7 0.10
19 6 0.09
20 32 0.46
21 11 0.16
22 2 0.03
23 3 0.04
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
ATAAAAAATAATAAAAATT
Found at i:53534491 original size:10 final size:10
Alignment explanation
Indices: 53534471--53534523 Score: 60
Period size: 9 Copynumber: 5.7 Consensus size: 10
53534461 TTATAATTTC
*
53534471 TTTTCTATAT
1 TTTTATATAT
*
53534481 TTCTATATA-
1 TTTTATATAT
53534490 TTTTATA-AT
1 TTTTATATAT
53534499 TTTTATA-AT
1 TTTTATATAT
53534508 TTTTA-ATAT
1 TTTTATATAT
53534517 TTTTATA
1 TTTTATA
53534524 GCTTTTATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 2 0.05
9 27 0.73
10 8 0.22
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTATATAT
Found at i:53534502 original size:9 final size:9
Alignment explanation
Indices: 53534490--53534570 Score: 65
Period size: 9 Copynumber: 8.7 Consensus size: 9
53534480 TTTCTATATA
53534490 TTTTATAAT
1 TTTTATAAT
53534499 TTTTATAAT
1 TTTTATAAT
53534508 TTTTA-ATAT
1 TTTTATA-AT
**
53534517 TTTTATAGC
1 TTTTATAAT
*
53534526 TTTTATTAAAA
1 TTTTA-T-AAT
*
53534537 TTTAATAAT
1 TTTTATAAT
*
53534546 TTTTATAAC
1 TTTTATAAT
*
53534555 TTTTATTGAT
1 TTTTA-TAAT
53534565 TTTTAT
1 TTTTAT
53534571 TTTTATCATT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
8 1 0.02
9 41 0.72
10 10 0.18
11 5 0.09
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:53534569 original size:29 final size:28
Alignment explanation
Indices: 53534485--53534569 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 28
53534475 CTATATTTCT
*
53534485 ATATATTTTATAATTTTTA-TAATTTTTA
1 ATAT-TTTTATAACTTTTATTAATTTTTA
* **
53534513 ATATTTTTATAGCTTTTATTAAAATTTA
1 ATATTTTTATAACTTTTATTAATTTTTA
*
53534541 ATAATTTTTATAACTTTTATTGATTTTTA
1 AT-ATTTTTATAACTTTTATTAATTTTTA
53534570 TTTTTATCAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 12 0.26
28 13 0.28
29 22 0.47
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (28 bp):
ATATTTTTATAACTTTTATTAATTTTTA
Found at i:53534872 original size:92 final size:90
Alignment explanation
Indices: 53534697--53534881 Score: 212
Period size: 92 Copynumber: 2.0 Consensus size: 90
53534687 TTGTTTTTTT
* * * * *
53534697 TTTTGAAAAATTTTGAGGGCCTTTTTGATACATTTTGAAAGTTCAAGTACCCAATTGAATGTAAA
1 TTTTGAAAAAATTTGAAGGCCTTTTTAATACATTTTGAAAGTTCAAGTACCCAAGTGAATGAAAA
*
53534762 AAAAAAAGCATGGGCTTAATTGCTTC
66 AAAAAAAGCA-GGACTTAATTGCTTC
* * * * *
53534788 TTTTGAAAAAAATTTGAAGGTCTTTTTAATATATTTTGAAAGTTTAAGTACTCAAGTGAGTGCAA
1 TTTTG-AAAAAATTTGAAGGCCTTTTTAATACATTTTGAAAGTTCAAGTACCCAAGTGAATG-AA
53534853 GAAAACAAAAAG-A-GACTTAATTGCTTC
64 -AAAA-AAAAAGCAGGACTTAATTGCTTC
53534880 TT
1 TT
53534882 CTTCTTCTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
91 5 0.06
92 62 0.78
93 1 0.01
94 5 0.06
95 6 0.08
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (90 bp):
TTTTGAAAAAATTTGAAGGCCTTTTTAATACATTTTGAAAGTTCAAGTACCCAAGTGAATGAAAA
AAAAAAAGCAGGACTTAATTGCTTC
Found at i:53538440 original size:46 final size:45
Alignment explanation
Indices: 53538301--53538519 Score: 183
Period size: 46 Copynumber: 4.7 Consensus size: 45
53538291 TATCCGTGCT
* * * *
53538301 GATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATCTCATAGTC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTTAT-GCC
* * * *
53538347 GATGCATGTCCCAGACATGTCTTACACTGGCT-TACGTCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATCT-TATGCC
*
53538393 GATGCATGTCTCAGACATGTCTTACACTAGCTCTCATCTTAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTT-ATGCC
** * * * ** *
53538439 GATGTCATGTCCTGGACATGGTCTTACATTGGCTCTTATAATATGGTC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATCTTAT-GCC
53538487 GATGCATGTCCCAGACATGTCTTACACTAGCTC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTC
53538520 ACACAAGTGA
Statistics
Matches: 140, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
44 10 0.07
45 15 0.11
46 65 0.46
47 27 0.19
48 23 0.16
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTTATGCC
Found at i:53538497 original size:140 final size:142
Alignment explanation
Indices: 53538163--53538514 Score: 383
Period size: 140 Copynumber: 2.5 Consensus size: 142
53538153 CCAATGCAAC
*
53538163 GTCCTAGACATGGTCTTACACTGGCTCATATCTCAAGTCGATGCCATGTCCCAGACATGGTCTTA
1 GTCCTAGACATGGTCTTACACTGGCTCATATAT--AGTCGATG-CATGTCCCAGACAT-GTCTTA
* *
53538228 CATTGACTATCGTCATCGAGGCCAACGCCATGTCCCAAACATGGTCTCACATTAGCTCTTACATA
62 CACTGACTATCGTCATCGAGGCCAACGCCATGTCCCAAACATGGTCTCACACTAGCTCTTACATA
** *
53538293 TCCGTGCTGATGCCAT
127 TCAATGCCGATGCCAT
* * * *
53538309 GTCCCAGACATGGTCTTACACTGACACATCTCATAGTCGATGCATGTCCCAGACATGTCTTACAC
1 GTCCTAGACATGGTCTTACACTGGCTCATAT-ATAGTCGATGCATGTCCCAGACATGTCTTACAC
* * * * * * * *
53538374 TGGCT-TACGTC-TCGAGGCCGATG-CATGTCTCAGACAT-GTCTTACACTAGCTC-T-CATCTT
65 TGACTAT-CGTCATCGAGGCCAACGCCATGTCCCAAACATGGTCTCACACTAGCTCTTACATATC
*
53538433 AATGCCGATGTCAT
129 AATGCCGATGCCAT
* * *
53538447 GTCCTGGACATGGTCTTACATTGGCTCTTATAATATGGTCGATGCATGTCCCAGACATGTCTTAC
1 GTCCTAGACATGGTCTTACACTGGCTC--AT-ATATAGTCGATGCATGTCCCAGACATGTCTTAC
53538512 ACT
63 ACT
53538515 AGCTCACACA
Statistics
Matches: 175, Mismatches: 26, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
138 36 0.21
139 1 0.01
140 48 0.27
141 13 0.07
142 11 0.06
143 16 0.09
144 14 0.08
145 8 0.05
146 27 0.15
147 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (142 bp):
GTCCTAGACATGGTCTTACACTGGCTCATATATAGTCGATGCATGTCCCAGACATGTCTTACACT
GACTATCGTCATCGAGGCCAACGCCATGTCCCAAACATGGTCTCACACTAGCTCTTACATATCAA
TGCCGATGCCAT
Found at i:53541770 original size:19 final size:20
Alignment explanation
Indices: 53541732--53541770 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
53541722 TATTCTCGCC
* *
53541732 ATTTAATAGATTTTATTTTG
1 ATTTAATAGATATAATTTTG
53541752 ATTTAAT-GATATAATTTTG
1 ATTTAATAGATATAATTTTG
53541771 TTTCGGGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (20 bp):
ATTTAATAGATATAATTTTG
Found at i:53541810 original size:59 final size:59
Alignment explanation
Indices: 53541703--53541814 Score: 170
Period size: 59 Copynumber: 1.9 Consensus size: 59
53541693 ACGTAATAAA
* * * *
53541703 ATAATTTTGTTTCGGGATTTATTCTCGCCATTTAATAGATTTTATTTTGATTTAATGAT
1 ATAATTTTGTTTCGGGATTTAATCTCGCCATTTAATAAAATTGATTTTGATTTAATGAT
* *
53541762 ATAATTTTGTTTCGGGATTTAATCTTGCCATTTAATAAAATTGGTTTTGATTT
1 ATAATTTTGTTTCGGGATTTAATCTCGCCATTTAATAAAATTGATTTTGATTT
53541815 TATTTCAGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.26, C:0.08, G:0.14, T:0.52
Consensus pattern (59 bp):
ATAATTTTGTTTCGGGATTTAATCTCGCCATTTAATAAAATTGATTTTGATTTAATGAT
Found at i:53548799 original size:47 final size:47
Alignment explanation
Indices: 53548741--53548862 Score: 199
Period size: 47 Copynumber: 2.6 Consensus size: 47
53548731 GCATTGGCAC
53548741 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
53548788 TAAGACAAGGATACCATGTAAGACCATCTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* * * *
53548835 TAAGATAAGTATATCAAGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
53548863 CCAAGGCATG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:53548964 original size:55 final size:54
Alignment explanation
Indices: 53548852--53549257 Score: 266
Period size: 55 Copynumber: 7.4 Consensus size: 54
53548842 AGTATATCAA
* * * *
53548852 GTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC-AAGGAAATCAT
1 GTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAAGG-TACCAT
* * * *
53548906 GTAATACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAATGTCCCAT
1 GTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGCAAAGGTACCAT
* * *
53548961 GTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAA-G-ACAGGATACCAT
1 GTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAAGG-TACCAT
**** *** *
53549013 GTAAGACCATGTTTGGAACATGGCATT--TG-GTAAGATAAGG---ATGT--CAT
1 GTAAGACCATGCCAAG-ACATGGCATTGATGAGTTCTATAAGGCAAAGGTACCAT
* * * * *
53549060 GTAAGACCATGCCAAGGCATGGCATTGATAACTTCTATAAGGCAAGGAAATCATGTAAGAAATCA
1 GTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC-----AA--A-G---G-TACCA
53549125 T
54 T
* *
53549126 GTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCAT
1 GTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGCAAAGGTACCAT
* * *
53549181 GTAAGACCATGCCAAGGCATGGCATTGGA-GAGTTC-ATTAGGC-AAGGATACCAC
1 GTAAGACCATGCCAAGACATGGCATT-GATGAGTTCTATAAGGCAAAGG-TACCAT
*
53549234 GTAAGACCATGTCAAGACATGGCA
1 GTAAGACCATGCCAAGACATGGCA
53549258 ATGGTAAGTT
Statistics
Matches: 274, Mismatches: 49, Indels: 59
0.72 0.13 0.15
Matches are distributed among these distances:
46 9 0.03
47 15 0.05
48 1 0.00
49 8 0.03
50 4 0.01
51 9 0.03
52 23 0.08
53 45 0.16
54 32 0.12
55 74 0.27
56 6 0.02
59 2 0.01
60 1 0.00
62 2 0.01
63 1 0.00
66 33 0.12
67 9 0.03
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.23
Consensus pattern (54 bp):
GTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAAGGTACCAT
Found at i:53549020 original size:208 final size:213
Alignment explanation
Indices: 53548788--53549243 Score: 715
Period size: 208 Copynumber: 2.1 Consensus size: 213
53548778 TGGCATTTGG
*
53548788 TAAGACAAGGATACCATGTAAGACCATCTTTGGAACATGGCATTTGGTAAGATAAGTATATCAAG
1 TAAGACAAGGATACCATGTAAGACCATCTTTGGAACATGGCATTTGGTAAGATAAGGATATCAAG
*
53548853 TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGT-A-A-T-ACC
66 TAAGACCATGCCAAGGCATGGCATTGATAACTTCTATAAGGCAAGGAAATCATGTAACAGTAACC
*
53548914 ATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAATGTCCCATGTAAGACCATGCCAAGGC
131 ATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCATGTAAGACCATGCCAAGGC
*
53548979 ATGGCATTGGTGAGTTCA
196 ATGGCATTGGAGAGTTCA
* * *
53548997 TAAGAC-AGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATGTCATG
1 TAAGACAAGGATACCATGTAAGACCATCTTTGGAACATGGCATTTGGTAAGATAAGGATATCAAG
53549061 TAAGACCATGCCAAGGCATGGCATTGATAACTTCTATAAGGCAAGGAAATCATGTAAGAAATCAT
66 TAAGACCATGCCAAGGCATGGCATTGATAACTTCTATAAGGCAAGGAAATCATGT----AA-CA-
53549126 GTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCATGTAAGACCAT
125 GT-A-ACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCATGTAAGACCAT
53549191 GCCAAGGCATGGCATTGGAGAGTTCA
188 GCCAAGGCATGGCATTGGAGAGTTCA
* * *
53549217 TTAGGCAAGGATACCACGTAAGACCAT
1 TAAGACAAGGATACCATGTAAGACCAT
53549244 GTCAAGACAT
Statistics
Matches: 224, Mismatches: 10, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
208 108 0.48
209 6 0.03
213 1 0.00
215 1 0.00
217 1 0.00
220 88 0.39
221 19 0.08
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (213 bp):
TAAGACAAGGATACCATGTAAGACCATCTTTGGAACATGGCATTTGGTAAGATAAGGATATCAAG
TAAGACCATGCCAAGGCATGGCATTGATAACTTCTATAAGGCAAGGAAATCATGTAACAGTAACC
ATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCATGTAAGACCATGCCAAGGC
ATGGCATTGGAGAGTTCA
Found at i:53549074 original size:99 final size:101
Alignment explanation
Indices: 53548788--53549119 Score: 391
Period size: 101 Copynumber: 3.2 Consensus size: 101
53548778 TGGCATTTGG
* * * *
53548788 TAAGACAAGGATACCATGTAAGACCATCTTTGGAACATGGCATTTGGTAAGATAAGTATATCAAG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATGTCATG
53548853 TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
66 TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
* * * * *** **
53548889 TAAGGCAAGGAAATCATGTAATACCATGTCAAG-ACATGGCATTGATGAGTTACTATAAGGCAAA
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATT--TG-G-TAAGATAAGG---A
* *
53548953 TGTCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-A
59 TGT--CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
53548997 TAAGAC-AGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATGTCATG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATGTCATG
*
53549061 TAAGACCATGCCAAGGCATGGCATTGATAACTTCTA
66 TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
* * *
53549097 TAAGGCAAGGAAATCATGTAAGA
1 TAAGACAAGGATACCATGTAAGA
53549120 AATCATGTAA
Statistics
Matches: 189, Mismatches: 30, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
99 35 0.19
100 16 0.08
101 43 0.23
102 2 0.01
103 1 0.01
104 15 0.08
105 1 0.01
106 2 0.01
107 23 0.12
108 16 0.08
109 35 0.19
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (101 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGATAAGGATGTCATG
TAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
Found at i:53549123 original size:12 final size:12
Alignment explanation
Indices: 53549106--53549131 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53549096 ATAAGGCAAG
53549106 GAAATCATGTAA
1 GAAATCATGTAA
53549118 GAAATCATGTAA
1 GAAATCATGTAA
53549130 GA
1 GA
53549132 CCATGTCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (12 bp):
GAAATCATGTAA
Found at i:53549238 original size:53 final size:55
Alignment explanation
Indices: 53549126--53549257 Score: 173
Period size: 53 Copynumber: 2.4 Consensus size: 55
53549116 AAGAAATCAT
* *
53549126 GTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTCCCAT
1 GTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTACCAC
* * *
53549181 GTAAGACCATGCCAAGGCATGGCATTGGA-GAGTT-C-ATTAGGC-AAGGATACCAC
1 GTAAGACCATGTCAAGACATGGCATT-GATGAGTTACTATAAGGCAAAGG-TACCAC
53549234 GTAAGACCATGTCAAGACATGGCA
1 GTAAGACCATGTCAAGACATGGCA
53549258 ATGGTAAGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
52 4 0.06
53 32 0.47
54 1 0.01
55 29 0.43
56 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (55 bp):
GTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGTACCAC
Found at i:53549497 original size:9 final size:9
Alignment explanation
Indices: 53549480--53549516 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
53549470 TGAGTTTTTG
53549480 AATTCGAAT
1 AATTCGAAT
*
53549489 AACTCGAAT
1 AATTCGAAT
*
53549498 AATTCGAAC
1 AATTCGAAT
53549507 AATTCGAAT
1 AATTCGAAT
53549516 A
1 A
53549517 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (9 bp):
AATTCGAAT
Found at i:53550761 original size:25 final size:25
Alignment explanation
Indices: 53550733--53550786 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
53550723 GAGATGTTGT
53550733 AGGTATGTAAGCAAGCTATTAAGTA
1 AGGTATGTAAGCAAGCTATTAAGTA
53550758 AGGTATGTAAGCAAGCTATTAAGTA
1 AGGTATGTAAGCAAGCTATTAAGTA
53550783 AGGT
1 AGGT
53550787 GTCTTTTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.28
Consensus pattern (25 bp):
AGGTATGTAAGCAAGCTATTAAGTA
Found at i:53567677 original size:35 final size:37
Alignment explanation
Indices: 53567602--53567692 Score: 114
Period size: 35 Copynumber: 2.5 Consensus size: 37
53567592 ATAATCTTTA
* * *
53567602 ATGATATGCAATCTTAAATATGATATGCAATCTTAAAT
1 ATGATA-GCAATCTTAGATATAATATGCAATATTAAAT
*
53567640 ATGATA-CAATCTTAGATATAAT-TGCAATATTAGAT
1 ATGATAGCAATCTTAGATATAATATGCAATATTAAAT
53567675 ATGATATGCAATCTTAGA
1 ATGATA-GCAATCTTAGA
53567693 AGATATGATT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
35 17 0.36
36 14 0.30
37 10 0.21
38 6 0.13
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (37 bp):
ATGATAGCAATCTTAGATATAATATGCAATATTAAAT
Found at i:53567691 original size:19 final size:19
Alignment explanation
Indices: 53567602--53567692 Score: 125
Period size: 19 Copynumber: 4.9 Consensus size: 19
53567592 ATAATCTTTA
*
53567602 ATGATATGCAATCTTAAAT
1 ATGATATGCAATCTTAGAT
*
53567621 ATGATATGCAATCTTAAAT
1 ATGATATGCAATCTTAGAT
53567640 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
* *
53567657 ATAAT-TGCAATATTAGAT
1 ATGATATGCAATCTTAGAT
53567675 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
53567693 AGATATGATT
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
17 14 0.22
18 14 0.22
19 36 0.56
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:53567714 original size:23 final size:22
Alignment explanation
Indices: 53567602--53567716 Score: 80
Period size: 19 Copynumber: 5.9 Consensus size: 22
53567592 ATAATCTTTA
53567602 ATGATATGCAATCTT--AA-AT
1 ATGATATGCAATCTTAGAAGAT
53567621 ATGATATGCAATCTT--AA-AT
1 ATGATATGCAATCTTAGAAGAT
53567640 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
* *
53567657 ATAAT-TGCAATATT---AGAT
1 ATGATATGCAATCTTAGAAGAT
53567675 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
53567697 ATGATTTTGTAATCTTAGAA
1 ATGA-TATGCAATCTTAGAA
53567717 ATTTAATTTG
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.01
17 13 0.16
18 14 0.17
19 33 0.40
22 8 0.10
23 13 0.16
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:53568241 original size:20 final size:20
Alignment explanation
Indices: 53568177--53568241 Score: 53
Period size: 20 Copynumber: 3.1 Consensus size: 20
53568167 ATTCTATTTA
53568177 TTCATTTTTTTAGTG-TATGT
1 TTCATTTTTTTA-TGCTATGT
* *
53568197 CATTTATCTTATTTATGC-ATAGT
1 --TTCAT-TTTTTTATGCTAT-GT
53568220 TTCATTTTTTTATGCTATGT
1 TTCATTTTTTTATGCTATGT
53568240 TT
1 TT
53568242 AATTATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
20 13 0.37
21 6 0.17
22 8 0.23
23 8 0.23
ACGTcount: A:0.18, C:0.09, G:0.11, T:0.62
Consensus pattern (20 bp):
TTCATTTTTTTATGCTATGT
Found at i:53575647 original size:107 final size:107
Alignment explanation
Indices: 53575524--53576060 Score: 1029
Period size: 107 Copynumber: 5.0 Consensus size: 107
53575514 TAAACAAAAA
* * *
53575524 ATTAGTTTAACAAAACAATGATATGTTAAGTTAGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAGTGATATATTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
53575589 AATTGTATTAAAATTTTTGTTAATTACTCTATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTATAAAATTTTTG
53575631 ATTAGTTTAACAAAACAGTGATATATTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAGTGATATATTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
53575696 AATTGTATTAAAATTTTTGTTAATTACTCTATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTATAAAATTTTTG
53575738 ATTAGTTTAACAAAACAGTGATATATTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAGTGATATATTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
53575803 AATTGTATTAAAATTTTTGTTAATTACTCTATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTATAAAATTTTTG
53575845 ATTAGTTTAACAAAACAGTGATATATTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAGTGATATATTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
53575910 AATTGTATTAAAATTTTTGTTAATTACTCTATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCTATAAAATTTTTG
53575952 ATTAGTTTAACAAAACAGTGATATATTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
1 ATTAGTTTAACAAAACAGTGATATATTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
*
53576017 AATTGTATTAAATTTTTTGTTAATTACTCTGATAAAATTTTTG
66 AATTGTATTAAAATTTTTGTTAATTACTCT-ATAAAATTTTTG
53576060 A
1 A
53576061 CCTGTTTTTT
Statistics
Matches: 425, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
107 412 0.97
108 13 0.03
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (107 bp):
ATTAGTTTAACAAAACAGTGATATATTAAGTTGGAATAAGTTTTAAATAATAAAATTTCTAACAA
AATTGTATTAAAATTTTTGTTAATTACTCTATAAAATTTTTG
Found at i:53577922 original size:4 final size:4
Alignment explanation
Indices: 53577913--53577960 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
53577903 TTTTTAAGTT
*
53577913 TTTA TTTA TTTA TTT- TTTAA GTT- TTTA TTTA -TT- TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA
53577958 TTT
1 TTT
53577961 TATATAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 9 0.24
4 26 0.70
5 2 0.05
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:53577932 original size:23 final size:23
Alignment explanation
Indices: 53577902--53577946 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
53577892 TTCTTTTTTC
53577902 TTTTTTAAGTTTTTATTTATTTA
1 TTTTTTAAGTTTTTATTTATTTA
53577925 TTTTTTAAGTTTTTATTTATTT
1 TTTTTTAAGTTTTTATTTATTT
53577947 TTATTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTTTTAAGTTTTTATTTATTTA
Found at i:53577947 original size:10 final size:10
Alignment explanation
Indices: 53577911--53577956 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
53577901 CTTTTTTAAG
53577911 TTTTTATTTA
1 TTTTTATTTA
*
53577921 TTTATTTTTTAA
1 TTT-TTATTT-A
53577933 GTTTTTATTTA
1 -TTTTTATTTA
53577944 TTTTTATTTA
1 TTTTTATTTA
53577954 TTT
1 TTT
53577957 ATTTTATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
10 16 0.52
11 6 0.19
12 6 0.19
13 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:53577963 original size:23 final size:23
Alignment explanation
Indices: 53577905--53577953 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
53577895 TTTTTTCTTT
*
53577905 TTTAAGTTTTTATTTATTTATTT
1 TTTAAGTTTTTATTTATTTATTA
53577928 TTTAAGTTTTTATTTATTT-TTA
1 TTTAAGTTTTTATTTATTTATTA
53577950 TTTA
1 TTTA
53577954 TTTATTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (23 bp):
TTTAAGTTTTTATTTATTTATTA
Found at i:53578042 original size:24 final size:22
Alignment explanation
Indices: 53577956--53578043 Score: 72
Period size: 22 Copynumber: 3.8 Consensus size: 22
53577946 TTTATTTATT
*
53577956 TATTTTATATAAA-ATTTTAAATG
1 TATTTT-TA-AAATATTTTAAATA
* *
53577979 TATATTTGAAATATTTTATAATA
1 TATTTTTAAAATATTTTA-AATA
53578002 TTAATTTTTAAAA-ATTTTAAATA
1 -T-ATTTTTAAAATATTTTAAATA
53578025 TATTTTTTAAAATTATTTT
1 TA-TTTTTAAAA-TATTTT
53578044 TTTAAAAATT
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
21 4 0.08
22 17 0.32
23 12 0.23
24 12 0.23
25 8 0.15
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTTTTAAAATATTTTAAATA
Found at i:53578062 original size:22 final size:22
Alignment explanation
Indices: 53578031--53578088 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
53578021 AATATATTTT
53578031 TTAAA-ATTATTTTTTTAAAAA
1 TTAAATATTATTTTTTTAAAAA
**
53578052 TTAAATATTA-TTTTTTAAATT
1 TTAAATATTATTTTTTTAAAAA
53578073 TTAAATATATATTTTT
1 TTAAATAT-TATTTTT
53578089 AATAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 22 0.69
22 6 0.19
23 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTAAATATTATTTTTTTAAAAA
Found at i:53578072 original size:34 final size:35
Alignment explanation
Indices: 53577989--53578070 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 35
53577979 TATATTTGAA
* * *
53577989 ATATTTTATAATATTA-ATTTTTAAAAATTTTAAAT
1 ATATTTTTTAAAATTATTTTTTTAAAAA-TTTAAAT
53578024 ATATTTTTTAAAATTATTTTTTTAAAAA-TTAAAT
1 ATATTTTTTAAAATTATTTTTTTAAAAATTTAAAT
53578058 ATTATTTTTTAAA
1 A-TATTTTTTAAA
53578071 TTTTAAATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 7 0.17
35 25 0.60
36 10 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (35 bp):
ATATTTTTTAAAATTATTTTTTTAAAAATTTAAAT
Found at i:53578098 original size:21 final size:22
Alignment explanation
Indices: 53578034--53578095 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 22
53578024 ATATTTTTTA
*
53578034 AAAT-TATTTTTTTAA-AAATT
1 AAATATATATTTTTAATAAATT
53578054 AAATAT-TATTTTT--TAAATTTT
1 AAATATATATTTTTAATAAA--TT
53578075 AAATATATATTTTTAATAAAT
1 AAATATATATTTTTAATAAAT
53578096 AAAACATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
19 3 0.09
20 10 0.29
21 9 0.26
22 8 0.24
24 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AAATATATATTTTTAATAAATT
Found at i:53578183 original size:11 final size:11
Alignment explanation
Indices: 53578151--53578221 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 11
53578141 TTGTTTTATA
53578151 ATATTTTAAATGT
1 ATATTTTAAA--T
*
53578164 ATATCTTAAAT
1 ATATTTTAAAT
53578175 ATATTTT-AAT
1 ATATTTTAAAT
* *
53578185 TTGTTTTATAAT
1 ATATTTTA-AAT
53578197 -T-TTTTAAAT
1 ATATTTTAAAT
53578206 AT-TTTTAAAAT
1 ATATTTT-AAAT
53578217 ATATT
1 ATATT
53578222 ATTTTTAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
9 3 0.06
10 18 0.37
11 14 0.29
12 5 0.10
13 9 0.18
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (11 bp):
ATATTTTAAAT
Found at i:53578226 original size:16 final size:15
Alignment explanation
Indices: 53578205--53578235 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
53578195 ATTTTTTAAA
53578205 TATTTTTAAAATATAT
1 TATTTTTAAAA-ATAT
53578221 TATTTTTAAAAATAT
1 TATTTTTAAAAATAT
53578236 GAACTTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTTTAAAAATAT
Found at i:53578305 original size:51 final size:51
Alignment explanation
Indices: 53578144--53578318 Score: 131
Period size: 52 Copynumber: 3.3 Consensus size: 51
53578134 TTATTATTTG
* * **
53578144 TTTTATAATATTTTAAATGTATATCTTAAATATATTTTAATTTGT-TTTATAA
1 TTTTATAATATTTTAAATGTATATTTTTAATA-ATTTTAATTT-TAAATATAA
* * * * * * *
53578196 TTTTTTAAATATTTTTAAAATATATTATTTTTAAAAATATGAACTTTCAAAT-TTA
1 TTTTAT-AATA-TTTT-AAATGTA-TATTTTTAATAATTTTAA-TTTTAAATATAA
* *
53578251 TTTTATAATATTTTAAATGCATATTTTTAATACTTTTAATTTTAAATATAA
1 TTTTATAATATTTTAAATGTATATTTTTAATAATTTTAATTTTAAATATAA
53578302 TTTTTATAA-ATTATTAA
1 -TTTTATAATATT-TTAA
53578319 TTTTTTAAAT
Statistics
Matches: 94, Mismatches: 20, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
50 7 0.07
51 19 0.20
52 22 0.23
53 8 0.09
54 8 0.09
55 18 0.19
56 12 0.13
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.55
Consensus pattern (51 bp):
TTTTATAATATTTTAAATGTATATTTTTAATAATTTTAATTTTAAATATAA
Found at i:53578327 original size:16 final size:16
Alignment explanation
Indices: 53578290--53578332 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
53578280 ATACTTTTAA
53578290 TTTTAAA-TA-TAATT
1 TTTTAAATTATTAATT
53578304 TTTATAAATTATTAATT
1 TTT-TAAATTATTAATT
53578321 TTTTAAATTATT
1 TTTTAAATTATT
53578333 TTAAAAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.12
15 4 0.15
16 11 0.42
17 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTAAATTATTAATT
Found at i:53578375 original size:21 final size:21
Alignment explanation
Indices: 53578322--53578389 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
53578312 TTATTAATTT
* **
53578322 TTTAAATTATTTTAAAAGATA
1 TTTAAATTTTTTTAAATTATA
*
53578343 TTCAAATATTTTTTAAATTATA
1 TTTAAAT-TTTTTTAAATTATA
**
53578365 TTTAAATTTTTAAAAATTAATA
1 TTTAAATTTTTTTAAATT-ATA
53578387 TTT
1 TTT
53578390 TATTTGGTGG
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
21 15 0.39
22 23 0.61
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (21 bp):
TTTAAATTTTTTTAAATTATA
Found at i:53578394 original size:21 final size:20
Alignment explanation
Indices: 53578348--53578394 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
53578338 AGATATTCAA
*
53578348 ATATTTTTTAAATTATATTT
1 ATATTTTTAAAATTATATTT
*
53578368 AAATTTTTAAAAATTAATATTT
1 ATATTTTT-AAAATT-ATATTT
53578390 -TATTT
1 ATATTT
53578395 GGTGGAGCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 7 0.32
21 9 0.41
22 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTTTAAAATTATATTT
Found at i:53584686 original size:27 final size:26
Alignment explanation
Indices: 53584649--53584763 Score: 106
Period size: 27 Copynumber: 4.3 Consensus size: 26
53584639 AGCATGGCTG
*
53584649 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGACAGAGCCA
*
53584675 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGACAGAGCCA
53584703 CCAGAACAGATATATGT-AGCAGAGCCA
1 CCAGAACAGATA-ATGTGA-CAGAGCCA
* ** * * *
53584730 CTAGATTAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCA
53584757 CCAGAAC
1 CCAGAAC
53584764 GCTTCCTCCA
Statistics
Matches: 72, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
26 5 0.07
27 50 0.69
28 17 0.24
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGACAGAGCCA
Found at i:53584708 original size:54 final size:54
Alignment explanation
Indices: 53584649--53584763 Score: 144
Period size: 54 Copynumber: 2.1 Consensus size: 54
53584639 AGCATGGCTG
*
53584649 CCAGAACAGATA-ATGT-GACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTAG-CAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * * *
53584703 CCAGAACAGATATATGTAGCAGAGCCACTAGATTAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTAGCAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
53584757 CCAGAAC
1 CCAGAAC
53584764 GCTTCCTCCA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
54 36 0.68
55 16 0.30
56 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATATATGTAGCAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:53586419 original size:26 final size:26
Alignment explanation
Indices: 53586381--53586490 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
53586371 CATGAAATTC
53586381 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
53586407 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
53586433 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
53586459 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
53586485 TTATCA
1 TTATCA
53586491 ATTTGTACCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:53598405 original size:46 final size:46
Alignment explanation
Indices: 53598322--53598465 Score: 157
Period size: 46 Copynumber: 3.2 Consensus size: 46
53598312 TCCCATCCAC
* * * * * * *
53598322 GGTCTTATTTATCTT-TGACATGATGCCATAGTGTCTTTCAACTAT
1 GGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
53598367 GGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
1 GGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
** * * *
53598413 GGTCTTACACA-TTTCATATCAGGTTGTCATGGTATCTTTCAACCAT
1 GGTCTTATTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAACCAT
53598459 GGTCTTA
1 GGTCTTA
53598466 CACATTTCAT
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
45 17 0.20
46 68 0.80
ACGTcount: A:0.21, C:0.20, G:0.16, T:0.43
Consensus pattern (46 bp):
GGTCTTATTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCAT
Found at i:53598466 original size:46 final size:46
Alignment explanation
Indices: 53598345--53598480 Score: 175
Period size: 46 Copynumber: 3.0 Consensus size: 46
53598335 TTTGACATGA
* * * ** * *
53598345 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
53598391 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
53598437 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATTTCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
53598481 AGAGCACACT
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 4 0.05
46 76 0.95
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:53600956 original size:29 final size:30
Alignment explanation
Indices: 53600906--53600973 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
53600896 CACCCTTAAA
* * *
53600906 ATATTTTCACTATTAGTCCTTCAACTTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
53600936 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
53600965 AGTATTTAC
1 A-TATTTAC
53600974 TCCTGGGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.28, C:0.19, G:0.04, T:0.49
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:53607237 original size:16 final size:16
Alignment explanation
Indices: 53607206--53607248 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
53607196 TATAGAAAAT
*
53607206 ACAAAAAAGAAAAG-AA
1 ACAAAAAA-AACAGAAA
53607222 ACAACAAAAAACAGAAA
1 ACAA-AAAAAACAGAAA
53607239 ACAAAAAAAA
1 ACAAAAAAAA
53607249 TAAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.81, C:0.12, G:0.07, T:0.00
Consensus pattern (16 bp):
ACAAAAAAAACAGAAA
Found at i:53610342 original size:27 final size:27
Alignment explanation
Indices: 53610307--53610360 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
53610297 GTTTTGGAGG
*
53610307 AAGATTTTTCAGAAAAGCCTCCACATA
1 AAGAATTTTCAGAAAAGCCTCCACATA
*
53610334 AAGAATTTTTAGAAAAGCCTCCACATA
1 AAGAATTTTCAGAAAAGCCTCCACATA
53610361 TACTTACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (27 bp):
AAGAATTTTCAGAAAAGCCTCCACATA
Found at i:53611418 original size:23 final size:23
Alignment explanation
Indices: 53611370--53611429 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
53611360 AAGATGAGTG
* *
53611370 AACAAGAAATATTCTCTAGTGAA
1 AACAGGAAATATTCTCCAGTGAA
*
53611393 AACAGGAAATATTCTCCGGT-ACA
1 AACAGGAAATATTCTCCAGTGA-A
*
53611416 AACAGTAAATATTC
1 AACAGGAAATATTC
53611430 CCTGGCAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.25
Consensus pattern (23 bp):
AACAGGAAATATTCTCCAGTGAA
Found at i:53617788 original size:24 final size:24
Alignment explanation
Indices: 53617756--53617802 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
53617746 CTGTCAGGAG
**
53617756 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
53617780 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
53617803 GGAAATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.23
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:53619331 original size:27 final size:27
Alignment explanation
Indices: 53619225--53619331 Score: 128
Period size: 27 Copynumber: 3.9 Consensus size: 27
53619215 AGGAAGCGTC
*
53619225 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
*
53619252 CTGGTGGCTCTGCCACATATTTCTGT-T
1 CTGGTGGCTCTGCCACAT-TATCTGTAT
*
53619279 CTGGTGGCTTTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
* *
53619307 CTGGTGACTCTGTCACATTATCTGT
1 CTGGTGGCTCTGCCACATTATCTGT
53619332 TCTAGCAGCC
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
26 2 0.03
27 51 0.74
28 16 0.23
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTATCTGTAT
Found at i:53619331 original size:54 final size:54
Alignment explanation
Indices: 53619225--53619334 Score: 159
Period size: 54 Copynumber: 2.0 Consensus size: 54
53619215 AGGAAGCGTC
* *
53619225 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
53619279 CTGGTGGCTTTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
53619333 CT
1 CT
53619335 AGCAGCCATG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
54 32 0.64
55 18 0.36
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Done.