Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 124 of 325
Found at i:39746310 original size:48 final size:48
Alignment explanation
Indices: 39746224--39746465 Score: 239
Period size: 48 Copynumber: 5.1 Consensus size: 48
39746214 GAAATCACAT
*
39746224 TCACATATTAGGATGCCAATGCCAT-ATCCCAGATATGGTCTTACATGGGA
1 TCACATATT--GATGCCAATGCCATGA-CCCAGACATGGTCTTACATGGGA
* *
39746274 TCACATATCGATGCCAATGCCATGACTCAGACATGGTCTTACATGGGA
1 TCACATATTGATGCCAATGCCATGACCCAGACATGGTCTTACATGGGA
* * * * *
39746322 TCATGCATATTGAAGCCAAT---A-G-CCTAG-CTATGATCTTACACGATG-
1 TCA--CATATTGATGCCAATGCCATGACCCAGAC-ATGGTCTTACATG-GGA
* *
39746367 TCTCATATTGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TCACATATTGATGCCAATGCCATGACCCAGACATGGTCTTACATGGGA
* * * *
39746415 TCACATTTTGATGCCAATTCCATGTCCCAGGCATGGTCTTACATGGGA
1 TCACATATTGATGCCAATGCCATGACCCAGACATGGTCTTACATGGGA
39746463 TCA
1 TCA
39746466 TGCATATCTC
Statistics
Matches: 160, Mismatches: 20, Indels: 26
0.78 0.10 0.13
Matches are distributed among these distances:
43 14 0.09
44 1 0.01
45 16 0.10
46 3 0.02
47 3 0.02
48 100 0.62
49 2 0.01
50 21 0.13
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (48 bp):
TCACATATTGATGCCAATGCCATGACCCAGACATGGTCTTACATGGGA
Found at i:39751002 original size:17 final size:17
Alignment explanation
Indices: 39750980--39751013 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39750970 TTTGTTCTTA
39750980 AGGTTCAACCAAAATTT
1 AGGTTCAACCAAAATTT
*
39750997 AGGTTCAACCAGAATTT
1 AGGTTCAACCAAAATTT
39751014 TACACTTGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (17 bp):
AGGTTCAACCAAAATTT
Found at i:39753120 original size:27 final size:26
Alignment explanation
Indices: 39753064--39753120 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
39753054 CAACCTTAAC
* * *
39753064 CCTAGGGGTATATCAGTAATTTTGCT
1 CCTAGGGGTAAATCAGTAATTTTCCA
**
39753090 CCTAGGGGTAAATTTGTAAATTTTCCA
1 CCTAGGGGTAAATCAGT-AATTTTCCA
39753117 CCTA
1 CCTA
39753121 TAAAGGTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (26 bp):
CCTAGGGGTAAATCAGTAATTTTCCA
Found at i:39755104 original size:19 final size:18
Alignment explanation
Indices: 39755067--39755110 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
39755057 ATACATACAG
39755067 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
39755084 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
39755103 TACTAATT
1 TAATAATT
39755111 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:39759806 original size:24 final size:25
Alignment explanation
Indices: 39759774--39759837 Score: 94
Period size: 24 Copynumber: 2.6 Consensus size: 25
39759764 TATAACAATT
*
39759774 CTCACATGAGTTGTGAATGT-AATG
1 CTCACATGAGTTGTGAATGTAAATA
39759798 CTCACATGAGTTGTGAATGTAAATA
1 CTCACATGAGTTGTGAATGTAAATA
* *
39759823 CTCACACGAGCTGTG
1 CTCACATGAGTTGTG
39759838 GGTCAGGATG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
24 20 0.56
25 16 0.44
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (25 bp):
CTCACATGAGTTGTGAATGTAAATA
Found at i:39767696 original size:17 final size:17
Alignment explanation
Indices: 39767674--39767710 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
39767664 ATGCACTAAC
**
39767674 ATGAAAATGTAATGACA
1 ATGAAAATCCAATGACA
39767691 ATGAAAATCCAATGACA
1 ATGAAAATCCAATGACA
39767708 ATG
1 ATG
39767711 TATACTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (17 bp):
ATGAAAATCCAATGACA
Found at i:39771502 original size:23 final size:22
Alignment explanation
Indices: 39771470--39771512 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
39771460 ATAATCCTTA
* *
39771470 CCAAATCATACTAAATCATAAG
1 CCAAATCATACCAAAACATAAG
39771492 CCAAAGTCATACCAAAACATA
1 CCAAA-TCATACCAAAACATA
39771513 TGTTTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.51, C:0.26, G:0.05, T:0.19
Consensus pattern (22 bp):
CCAAATCATACCAAAACATAAG
Found at i:39772288 original size:42 final size:43
Alignment explanation
Indices: 39772177--39772347 Score: 122
Period size: 43 Copynumber: 4.0 Consensus size: 43
39772167 AACTCATACA
* * *
39772177 ATGCCAAC-GTCCCAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGAAATCAAATATCG
* * * *
39772220 ATGCCACTATCCCATATAGGGTCTTACACGAAATCAAATAT-G
1 ATGCCACTGTCCCAGACATGGTCTTACACGAAATCAAATATCG
*
39772262 ATGTCGA-TGTCCCAGACATGGTCTTACACGTAAATCTCAAAT-T-G
1 ATG-CCACTGTCCCAGACATGGTCTTACACG-AAA--TCAAATATCG
* * **
39772306 ATTCCAAC-ATCCCAGATGTGGTCTTACACGAAAT-AACATATC
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGAAATCAA-ATATC
39772348 AGAATCCTAT
Statistics
Matches: 101, Mismatches: 17, Indels: 20
0.73 0.12 0.14
Matches are distributed among these distances:
40 2 0.02
41 3 0.03
42 26 0.26
43 40 0.40
44 24 0.24
45 6 0.06
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACACGAAATCAAATATCG
Found at i:39772297 original size:43 final size:44
Alignment explanation
Indices: 39772177--39772297 Score: 126
Period size: 43 Copynumber: 2.8 Consensus size: 44
39772167 AACTCATACA
* *
39772177 ATGCCAAC-GTCCCAGACGTGGTCTTACATGT-AATCAAATATCG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGTAAATCAAATATCG
* * * *
39772220 ATGCCACTATCCCATATAGGGTCTTACACG-AAATCAAATAT-G
1 ATGCCACTGTCCCAGACATGGTCTTACACGTAAATCAAATATCG
*
39772262 ATGTCGA-TGTCCCAGACATGGTCTTACACGTAAATC
1 ATG-CCACTGTCCCAGACATGGTCTTACACGTAAATC
39772298 TCAAATTGAT
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
42 25 0.40
43 38 0.60
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (44 bp):
ATGCCACTGTCCCAGACATGGTCTTACACGTAAATCAAATATCG
Found at i:39777323 original size:21 final size:21
Alignment explanation
Indices: 39777299--39777345 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
39777289 GAATTGGAAG
* *
39777299 AGTATGGAATTGATAAGAGTT
1 AGTATGAAAATGATAAGAGTT
*
39777320 AGTAATGAAAATGATACGAGTT
1 AGT-ATGAAAATGATAAGAGTT
39777342 AGTA
1 AGTA
39777346 CAGGTATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.43, C:0.02, G:0.26, T:0.30
Consensus pattern (21 bp):
AGTATGAAAATGATAAGAGTT
Found at i:39782503 original size:33 final size:33
Alignment explanation
Indices: 39782465--39782532 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
39782455 TTTGGCCTTC
* *
39782465 ATTTGAACACTTTTATTAATGTTGGGCCTTTAT
1 ATTTGAACACTTTTATAAATGTTAGGCCTTTAT
*
39782498 ATTTGAACACTTTTATAAATGTTAGGCTTTTAT
1 ATTTGAACACTTTTATAAATGTTAGGCCTTTAT
39782531 AT
1 AT
39782533 GACCATTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (33 bp):
ATTTGAACACTTTTATAAATGTTAGGCCTTTAT
Found at i:39783581 original size:55 final size:54
Alignment explanation
Indices: 39783494--39783748 Score: 224
Period size: 55 Copynumber: 4.8 Consensus size: 54
39783484 ATTAGGGTTT
* *
39783494 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATTGGTAAGATTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAAGATTTCTAAGGA
* * * * *
39783549 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAG-TTACTATAAGGAA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGATT--TCTAAGG-A
* * *
39783605 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGT--GAGTTCATAA-GA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGATTTC-TAAGGA
* * *
39783656 TAAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTATG-TTTC--A--A
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGATTTCTAAGGA
* * * * *
39783706 AAGGATACCACGTAAGACCATGACAAGTCATGGAAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
39783749 GTACCATTGT
Statistics
Matches: 166, Mismatches: 25, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
49 38 0.23
50 1 0.01
51 2 0.01
52 6 0.04
53 37 0.22
54 12 0.07
55 66 0.40
56 4 0.02
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGATTTCTAAGGA
Found at i:39783961 original size:16 final size:16
Alignment explanation
Indices: 39783940--39783970 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39783930 ATAAATTTGA
39783940 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
39783956 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
39783971 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:39788020 original size:25 final size:25
Alignment explanation
Indices: 39787992--39788039 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
39787982 AACAAATTTC
39787992 TCAAAAATTTATCGGGGTAAAATCG
1 TCAAAAATTTATCGGGGTAAAATCG
** * *
39788017 TCAAAGTTTTATTGGTGTAAAAT
1 TCAAAAATTTATCGGGGTAAAAT
39788040 TTGGATGAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (25 bp):
TCAAAAATTTATCGGGGTAAAATCG
Found at i:39803509 original size:12 final size:12
Alignment explanation
Indices: 39803492--39803522 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39803482 TTATGAAAAC
39803492 TACTTTTATTTT
1 TACTTTTATTTT
39803504 TACTTTTATTTT
1 TACTTTTATTTT
39803516 TA-TTTTA
1 TACTTTTA
39803523 GCAGATTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (12 bp):
TACTTTTATTTT
Found at i:39805313 original size:40 final size:40
Alignment explanation
Indices: 39805239--39805423 Score: 259
Period size: 40 Copynumber: 4.7 Consensus size: 40
39805229 AACCCAAGTA
* *
39805239 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
39805278 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* * *
39805318 CCTTCGGGACTTAGCCCAGATATAGTCAATAGCACAACTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
39805358 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-CATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
39805397 CCTTCGGGACTTAGCCCAGATATAGTC
1 CCTTCGGGACTTAGCCCGGATATAGTC
39805424 CGAATAATCA
Statistics
Matches: 130, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 40 0.31
40 89 0.68
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:39811674 original size:27 final size:27
Alignment explanation
Indices: 39811644--39811716 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
39811634 GGGGCATTTC
39811644 AGTCATTTTACCACATAAGGG-AGAAAT
1 AGTCATTTTACCACATAAGGGTA-AAAT
* *
39811671 AGTCATTTTACCTCATATGGGTAAAAT
1 AGTCATTTTACCACATAAGGGTAAAAT
39811698 AGTCATTTTACCACA-AAGG
1 AGTCATTTTACCACATAAGG
39811717 TGGTGTAAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
26 3 0.07
27 37 0.90
28 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (27 bp):
AGTCATTTTACCACATAAGGGTAAAAT
Found at i:39815476 original size:27 final size:27
Alignment explanation
Indices: 39815452--39815522 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
39815442 TAGGGGCATT
39815452 TCAATCATTTTACCACATAAAGGCAAAA
1 TCAATCATTTTACCACATAAAGGC-AAA
*
39815480 T-AATCATTTTACCTCATAAAGGCAAA
1 TCAATCATTTTACCACATAAAGGCAAA
* *
39815506 ACAGTCATTTTACCACA
1 TCAATCATTTTACCACA
39815523 ATGGAGGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (27 bp):
TCAATCATTTTACCACATAAAGGCAAA
Found at i:39821533 original size:69 final size:70
Alignment explanation
Indices: 39821401--39821533 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 70
39821391 TAGTTTATTA
* * * * *
39821401 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
39821466 CTTAG
66 CTTAG
39821471 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
39821534 GTTATGTGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 35 0.60
70 23 0.40
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:39823060 original size:47 final size:47
Alignment explanation
Indices: 39823006--39823457 Score: 742
Period size: 47 Copynumber: 9.6 Consensus size: 47
39822996 TATTTGAATA
*
39823006 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
39823053 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
39823100 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
39823147 AATGTGAAAGTGTATATATATGTGATAACGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
39823196 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
39823243 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
39823290 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
39823337 AAAGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
39823384 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
39823431 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
39823458 TCCCGAAGGG
Statistics
Matches: 384, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 340 0.89
49 44 0.11
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:39826068 original size:27 final size:27
Alignment explanation
Indices: 39826028--39826139 Score: 104
Period size: 27 Copynumber: 4.1 Consensus size: 27
39826018 AGGAAGCGTC
**
39826028 CTGGTGGCAATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
39826055 CTGGTGGCTCTGCCACATATT-TCT-ATT
1 CTGGTGGCTCTGCCACA-ATTATCTGA-T
*
39826082 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * ** *
39826110 CTGGCGACTCTTTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
39826136 CTGG
1 CTGG
39826140 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
26 9 0.12
27 46 0.64
28 16 0.22
29 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:39826138 original size:54 final size:54
Alignment explanation
Indices: 39826028--39826139 Score: 127
Period size: 54 Copynumber: 2.1 Consensus size: 54
39826018 AGGAAGCGTC
* * *
39826028 CTGGTGGCAATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTATT
1 CTGGTGGCAATGCCACAATTATCTGATCTGGCGACTCTGCCACATATATCTATT
** * ** *
39826082 CTGGTGGCTCTGCCACGATTATCTGTATCTGGCGACTCTTTCACAT-TATCTGTT
1 CTGGTGGCAATGCCACAATTATCTG-ATCTGGCGACTCTGCCACATATATCTATT
39826136 CTGG
1 CTGG
39826140 CAGCCATGCT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
54 32 0.67
55 16 0.33
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (54 bp):
CTGGTGGCAATGCCACAATTATCTGATCTGGCGACTCTGCCACATATATCTATT
Found at i:39829085 original size:44 final size:41
Alignment explanation
Indices: 39828988--39829086 Score: 112
Period size: 40 Copynumber: 2.4 Consensus size: 41
39828978 CAATGATATT
*
39828988 TGGCACTAAGTGTGCGATTCAAAATAGCTTCGGCTATCTAA
1 TGGCACTAAGTGTGCGATCCAAAATAGCTTCGGCTATCTAA
* * *
39829029 -GGCACTAAGTGTGCGATACCGAGATAGCTTCGGTTAAT-TGAAA
1 TGGCACTAAGTGTGCGAT-CCAAAATAGCTTCGGCT-ATCT--AA
39829072 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
39829087 AGAATCATTC
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
40 17 0.35
41 14 0.29
42 2 0.04
43 2 0.04
44 14 0.29
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (41 bp):
TGGCACTAAGTGTGCGATCCAAAATAGCTTCGGCTATCTAA
Found at i:39830140 original size:32 final size:32
Alignment explanation
Indices: 39830104--39830175 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
39830094 TCTCAATTGG
* *
39830104 GCCTAGCCCATCTCAGAACCAATATCAGTTGA
1 GCCTAGCCCATATCAGAACAAATATCAGTTGA
*
39830136 GCCTAGCCCATATCAGAACAAATATCAGTTGG
1 GCCTAGCCCATATCAGAACAAATATCAGTTGA
39830168 GCCTAGCC
1 GCCTAGCC
39830176 TAGTTCAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (32 bp):
GCCTAGCCCATATCAGAACAAATATCAGTTGA
Found at i:39834131 original size:17 final size:17
Alignment explanation
Indices: 39834109--39834142 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
39834099 CACATTAAGA
39834109 GTATTTGATGAATTATC
1 GTATTTGATGAATTATC
39834126 GTATTTGATGAATTATC
1 GTATTTGATGAATTATC
39834143 TTTGAATCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (17 bp):
GTATTTGATGAATTATC
Found at i:39843514 original size:19 final size:19
Alignment explanation
Indices: 39843492--39843549 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
39843482 TTGCACTTCA
*
39843492 GTGCCTCTGTTTGACTTTG
1 GTGCCTCTGTTTCACTTTG
* *
39843511 GTGCCTCTGTTACACTTCG
1 GTGCCTCTGTTTCACTTTG
*
39843530 GTGTCTCTGGTTTCACTTTG
1 GTGCCTCT-GTTTCACTTTG
39843550 ACGCCTCTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 23 0.72
20 9 0.28
ACGTcount: A:0.07, C:0.24, G:0.24, T:0.45
Consensus pattern (19 bp):
GTGCCTCTGTTTCACTTTG
Found at i:39846312 original size:93 final size:93
Alignment explanation
Indices: 39846198--39846369 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
39846188 CGCCCATAAG
* *
39846198 CGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
39846263 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
39846291 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
39846356 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
39846370 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:39846366 original size:46 final size:46
Alignment explanation
Indices: 39846191--39846366 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
39846181 TGTAACCCGC
* * * *
39846191 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
39846237 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
39846287 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
39846330 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
39846367 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:39846385 original size:46 final size:46
Alignment explanation
Indices: 39846240--39846378 Score: 144
Period size: 47 Copynumber: 3.0 Consensus size: 46
39846230 TTCGCATCCA
39846240 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * * *
39846288 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATC
39846333 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
39846379 CTAGTGACAT
Statistics
Matches: 75, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 28 0.37
47 30 0.40
48 2 0.03
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:39851956 original size:24 final size:24
Alignment explanation
Indices: 39851929--39851976 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
39851919 TCCTAAAATC
39851929 TCTCCATAATCCACTCCTTGATTT
1 TCTCCATAATCCACTCCTTGATTT
* *
39851953 TCTCCCTAATCCTCTCCTTGATTT
1 TCTCCATAATCCACTCCTTGATTT
39851977 CCTTCACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.17, C:0.35, G:0.04, T:0.44
Consensus pattern (24 bp):
TCTCCATAATCCACTCCTTGATTT
Found at i:39858484 original size:18 final size:18
Alignment explanation
Indices: 39858454--39858494 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
39858444 TCTGTGTGGA
39858454 GCCCACAAGCCCATTT-G
1 GCCCACAAGCCCATTTCG
39858471 GCCCACACAGCCCATTTCG
1 GCCCACA-AGCCCATTTCG
39858490 GCCCA
1 GCCCA
39858495 TCGTGGCCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 7 0.32
18 9 0.41
19 6 0.27
ACGTcount: A:0.22, C:0.46, G:0.17, T:0.15
Consensus pattern (18 bp):
GCCCACAAGCCCATTTCG
Found at i:39860385 original size:42 final size:43
Alignment explanation
Indices: 39860338--39860418 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
39860328 AAAACCATGT
*
39860338 CTGGGACA-TCGGCATC-ATATATGATTCCATGTAAGACCCTAC
1 CTGGGACAGT-GGCATCGATATATGATTACATGTAAGACCCTAC
*
39860380 CTGGGACAGTGGCATCGATATTTGATTACATGTAAGACC
1 CTGGGACAGTGGCATCGATATATGATTACATGTAAGACC
39860419 TCGTCTGGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
42 14 0.40
43 21 0.60
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (43 bp):
CTGGGACAGTGGCATCGATATATGATTACATGTAAGACCCTAC
Found at i:39860427 original size:43 final size:41
Alignment explanation
Indices: 39860336--39860437 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 41
39860326 GTAAAACCAT
*
39860336 GTCTGGGACA-TCGGCATCATATATGATTCCATGTAAGACCC
1 GTCTGGGACAGT-GGCATCATATATGATTACATGTAAGACCC
*
39860377 -TACCTGGGACAGTGGCATCGATATTTGATTACATGTAAGACCTC
1 GT--CTGGGACAGTGGCATC-ATATATGATTACATGTAAGACC-C
39860421 GTCTGGGAC-GTTGGCAT
1 GTCTGGGACAG-TGGCAT
39860438 TGTATGAGCT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
40 1 0.02
42 15 0.29
43 34 0.65
44 1 0.02
45 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (41 bp):
GTCTGGGACAGTGGCATCATATATGATTACATGTAAGACCC
Found at i:39864771 original size:27 final size:27
Alignment explanation
Indices: 39864755--39864808 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
39864745 AGCACCGACC
*
39864755 ATGGCTTATGCAATTAGAGCTCAAGAA
1 ATGGCTTATGCAATTAGAGCACAAGAA
* *
39864782 ATGGCTTATGCAATTAGATCTCAAGAA
1 ATGGCTTATGCAATTAGAGCACAAGAA
39864809 GACGCTTTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (27 bp):
ATGGCTTATGCAATTAGAGCACAAGAA
Found at i:39866331 original size:20 final size:20
Alignment explanation
Indices: 39866285--39866333 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
39866275 CATATAACCC
39866285 TTGTTTTGCAAATTTTCATGT
1 TTGTTTTG-AAATTTTCATGT
*
39866306 TT-TTTTGAAGTTTTCTAT-T
1 TTGTTTTGAAATTTTC-ATGT
39866325 TTGTTTTGA
1 TTGTTTTGA
39866334 TTTATCCCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 10 0.40
20 13 0.52
21 2 0.08
ACGTcount: A:0.16, C:0.06, G:0.14, T:0.63
Consensus pattern (20 bp):
TTGTTTTGAAATTTTCATGT
Found at i:39868973 original size:40 final size:40
Alignment explanation
Indices: 39868918--39869049 Score: 194
Period size: 40 Copynumber: 3.3 Consensus size: 40
39868908 ATTTGATGTG
*
39868918 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
1 TATCCGGACTTAAAGACCCGCAGGCTATATGCTGGAATTA
*
39868958 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
1 TATCCGGACTTAAAGACCCGCAGGCTATATGCTGGAATTA
* ** *
39868998 TACCCGGACTT-AAGGTCCGCAGGCTATGTGCTGGAATTA
1 TATCCGGACTTAAAGACCCGCAGGCTATATGCTGGAATTA
*
39869037 TAACCGGACTTAA
1 TATCCGGACTTAA
39869050 GGTCCATAGG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
39 35 0.41
40 50 0.59
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (40 bp):
TATCCGGACTTAAAGACCCGCAGGCTATATGCTGGAATTA
Found at i:39869030 original size:39 final size:39
Alignment explanation
Indices: 39868935--39869072 Score: 177
Period size: 39 Copynumber: 3.5 Consensus size: 39
39868925 GCTTAAAGAC
* * **
39868935 CCGCAGGCTATATGCTGGAATTATATCCGGGCTTAAAGAC
1 CCGCAGGCTATATGCTGGAATTATAACCGGACTT-AAGGT
*
39868975 CCGCAGGCTATATGCTGGAATTATACCCGGACTTAAGGT
1 CCGCAGGCTATATGCTGGAATTATAACCGGACTTAAGGT
*
39869014 CCGCAGGCTATGTGCTGGAATTATAACCGGACTTAAGGT
1 CCGCAGGCTATATGCTGGAATTATAACCGGACTTAAGGT
** **
39869053 CCATAGGCTACGTGCTGGAA
1 CCGCAGGCTATATGCTGGAA
39869073 ATATGTCCCG
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 57 0.64
40 32 0.36
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGCAGGCTATATGCTGGAATTATAACCGGACTTAAGGT
Found at i:39875614 original size:39 final size:39
Alignment explanation
Indices: 39875568--39875665 Score: 169
Period size: 39 Copynumber: 2.5 Consensus size: 39
39875558 GCTTAAAGAC
* *
39875568 CCGCAGGCTATATGCTGGAATTATACCCGGACTTAAGGT
1 CCGCAGGCTATGTGCTGGAATTATAACCGGACTTAAGGT
39875607 CCGCAGGCTATGTGCTGGAATTATAACCGGACTTAAGGT
1 CCGCAGGCTATGTGCTGGAATTATAACCGGACTTAAGGT
*
39875646 CCGCAGGCTACGTGCTGGAA
1 CCGCAGGCTATGTGCTGGAA
39875666 ATATGTCCCG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.23
Consensus pattern (39 bp):
CCGCAGGCTATGTGCTGGAATTATAACCGGACTTAAGGT
Found at i:39889570 original size:5 final size:6
Alignment explanation
Indices: 39889552--39889576 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
39889542 GGCCGCTCTA
39889552 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
39889577 GGGTTTTTAA
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:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:39891824 original size:13 final size:13
Alignment explanation
Indices: 39891806--39891830 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39891796 CTCGACAGGG
39891806 ACACGCCCGTGTC
1 ACACGCCCGTGTC
39891819 ACACGCCCGTGT
1 ACACGCCCGTGT
39891831 GCGATTACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.44, G:0.24, T:0.16
Consensus pattern (13 bp):
ACACGCCCGTGTC
Found at i:39899286 original size:93 final size:93
Alignment explanation
Indices: 39899174--39899344 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
39899164 GCCCCTAAGT
*
39899174 GAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCGGA-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
39899238 ACGAGTTCGGATGCCTAGTTACATCTCAC
65 ACGAGTTCGGATGCCTAGTTACATCTCAC
* *
39899267 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
39899332 CGAGTTCGGATGC
66 CGAGTTCGGATGC
39899345 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
93 72 0.97
94 2 0.03
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:39899340 original size:46 final size:46
Alignment explanation
Indices: 39899171--39899341 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
39899161 CCCGCCCCTA
* *
39899171 AGTGAACTCGGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCATCCAT
*
39899216 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-T
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGA-G-C-A-TTCGCATCCAT
*
39899264 CA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CATTCGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCATCCAT
39899309 AGGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 A-GTGAACTCGGACTCAACTCAACGAGTTCGGA
39899342 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 7, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 3 0.03
45 1 0.01
46 57 0.53
47 31 0.29
48 3 0.03
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATTCGCATCCAT
Found at i:39912037 original size:34 final size:33
Alignment explanation
Indices: 39911982--39912046 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 33
39911972 ACATATTTGT
* *
39911982 ACTGTACTGTTACTTAGATGGGCTCAGGCCCAC
1 ACTGTACTGATACTTAGATGGGCTAAGGCCCAC
*
39912015 ACTGATACTGATACTGTA-ATGGGTTAAGGCCC
1 ACTG-TACTGATACT-TAGATGGGCTAAGGCCC
39912047 TGATTGAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 4 0.15
34 21 0.78
35 2 0.07
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (33 bp):
ACTGTACTGATACTTAGATGGGCTAAGGCCCAC
Found at i:39915757 original size:40 final size:40
Alignment explanation
Indices: 39915698--39915775 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
39915688 TGGAAAAAAA
39915698 TATAACCGGGTTAACTCCCGAAGGCATTCGTGCGGGTTAT
1 TATAACCGGGTTAACTCCCGAAGGCATTCGTGCGGGTTAT
* * *
39915738 TATAACCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTT
1 TATAACCGGGTTAACTCCCGAAGGCATTCGTGCGGGTT
39915776 GTTACATCCG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (40 bp):
TATAACCGGGTTAACTCCCGAAGGCATTCGTGCGGGTTAT
Found at i:39920057 original size:18 final size:18
Alignment explanation
Indices: 39920010--39920058 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
39920000 GGCTATAGAG
39920010 GAAAAGAAGAAGAAGAGGA
1 GAAAAGAAGAAG-AGAGGA
* *
39920029 -AATAGATGAAGAGAGGA
1 GAAAAGAAGAAGAGAGGA
39920046 GAAAAGAAGAAGA
1 GAAAAGAAGAAGA
39920059 TAAAAGAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.61, C:0.00, G:0.35, T:0.04
Consensus pattern (18 bp):
GAAAAGAAGAAGAGAGGA
Found at i:39923455 original size:19 final size:19
Alignment explanation
Indices: 39923419--39923457 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39923409 TTTTCATCAT
* *
39923419 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
39923438 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
39923457 A
1 A
39923458 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:39923953 original size:20 final size:21
Alignment explanation
Indices: 39923921--39923961 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
39923911 TTACAGAGTC
*
39923921 ACCAGATACAGATATTTTGTG
1 ACCAGATACAGATAATTTGTG
39923942 ACCAGA-ACAGATAATTTGTG
1 ACCAGATACAGATAATTTGTG
39923962 GCATAGCCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (21 bp):
ACCAGATACAGATAATTTGTG
Found at i:39924126 original size:28 final size:28
Alignment explanation
Indices: 39924083--39924143 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
39924073 TTAACCCTGA
*
39924083 GGTATAAAGGTCATTTTGCATACATAGG
1 GGTATAAAGGTAATTTTGCATACATAGG
*
39924111 GGTATAATGGTAATTTTGCATACATAGG
1 GGTATAAAGGTAATTTTGCATACATAGG
39924139 GGTAT
1 GGTAT
39924144 TCTAGTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.34
Consensus pattern (28 bp):
GGTATAAAGGTAATTTTGCATACATAGG
Found at i:39929000 original size:208 final size:208
Alignment explanation
Indices: 39928640--39929264 Score: 1151
Period size: 208 Copynumber: 3.0 Consensus size: 208
39928630 AGTATGTATG
* * * * *
39928640 CCCTGTTTTCAGATGATCTGAGACACGGGCGTGTCTGGAGCCGCGTGAGGCACACGGCCTATTCA
1 CCCTGTTTTCAGATGACCTGAGACAAGGGCATGTCTGGAGCCGTGTGAGGCATACGGCCTATTCA
* *
39928705 CACGGGCGTGTGACCCTTGTATGTTTGAAATTTTTCTAAGTTTCCAAAATTATCGTATGATATCG
66 CACAGGCGTGTGACCC-TGTATGTTTGAAATTTTTCTAAGTTTCAAAAATTATCGTATGATATCG
39928770 GTTTAGTCCCGAACCACTTCTAAAGCATGTTTAAGGCCTCATAAGCCCTTATAAGGGACAATGTG
130 GTTTAGTCCCGAACCACTTCTAAAGCATGTTTAAGGCCTCATAAGCCCTTATAAGGGACAATGTG
39928835 ATTGTGTTGAATGA
195 ATTGTGTTGAATGA
*
39928849 CCCTGTTTTCAGATGACCTGAGACAAGGGCATGTCTGGAGCCGTGTGAGGCATACAGCCTATTCA
1 CCCTGTTTTCAGATGACCTGAGACAAGGGCATGTCTGGAGCCGTGTGAGGCATACGGCCTATTCA
39928914 CACAGGCGTGTGACCCTGTATGTTTGAAATTTTTCTAAGTTTCAAAAATTATCGTATGATATCGG
66 CACAGGCGTGTGACCCTGTATGTTTGAAATTTTTCTAAGTTTCAAAAATTATCGTATGATATCGG
* *
39928979 TTTAGTCCTGAACCACTTCTAAAGCATGTTTAAGGCCTCACAAGCCCTTATAAGGGACAATGTGA
131 TTTAGTCCCGAACCACTTCTAAAGCATGTTTAAGGCCTCATAAGCCCTTATAAGGGACAATGTGA
39929044 TTGTGTTGAATGA
196 TTGTGTTGAATGA
39929057 CCCTGTTTTCAGATGACCTGAGACAAGGGCATGTCTGGAGCCGTGTGAGGCATACGGCCTATTCA
1 CCCTGTTTTCAGATGACCTGAGACAAGGGCATGTCTGGAGCCGTGTGAGGCATACGGCCTATTCA
39929122 CACAGGCGTGTGACCCTGTATGTTTGAAATTTTTCTAAGTTTCAAAAATTATCGTATGATATCGG
66 CACAGGCGTGTGACCCTGTATGTTTGAAATTTTTCTAAGTTTCAAAAATTATCGTATGATATCGG
39929187 TTTAGTCCCGAACCACTTCTAAAGCATGTTTAAGGCCTCATAAGCCCTTATAAGGGACAATGTGA
131 TTTAGTCCCGAACCACTTCTAAAGCATGTTTAAGGCCTCATAAGCCCTTATAAGGGACAATGTGA
39929252 TTGTGTTGAATGA
196 TTGTGTTGAATGA
39929265 TTTATGAGAA
Statistics
Matches: 403, Mismatches: 13, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
208 329 0.82
209 74 0.18
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (208 bp):
CCCTGTTTTCAGATGACCTGAGACAAGGGCATGTCTGGAGCCGTGTGAGGCATACGGCCTATTCA
CACAGGCGTGTGACCCTGTATGTTTGAAATTTTTCTAAGTTTCAAAAATTATCGTATGATATCGG
TTTAGTCCCGAACCACTTCTAAAGCATGTTTAAGGCCTCATAAGCCCTTATAAGGGACAATGTGA
TTGTGTTGAATGA
Found at i:39935099 original size:20 final size:20
Alignment explanation
Indices: 39935057--39935106 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
39935047 TACATATTAT
* * *
39935057 CACTATTCATGATTTGACTC
1 CACTATTCATGACTTAACCC
*
39935077 CACTGTTCATGACTTAACCC
1 CACTATTCATGACTTAACCC
39935097 CACTATTCAT
1 CACTATTCAT
39935107 AGAACTGACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.30, G:0.08, T:0.36
Consensus pattern (20 bp):
CACTATTCATGACTTAACCC
Found at i:39941116 original size:34 final size:34
Alignment explanation
Indices: 39941054--39941173 Score: 141
Period size: 34 Copynumber: 3.5 Consensus size: 34
39941044 TTACAGTGTT
* ** * *
39941054 ATTTTGTGTGCTATATGAATTACCTCTTACGAGC
1 ATTTGGTGTGCTGGATGGATTAGCTCTTACGAGC
* * *
39941088 ATTTGGTGTGATGGATGGATTAGGTCTTATGAGC
1 ATTTGGTGTGCTGGATGGATTAGCTCTTACGAGC
* *
39941122 ATTTGGTGTGCTTGATGGATTAGCTCATACGAGC
1 ATTTGGTGTGCTGGATGGATTAGCTCTTACGAGC
*
39941156 ATCTGGTGTGCTGGATGG
1 ATTTGGTGTGCTGGATGG
39941174 TTAACCGTGT
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 71 1.00
ACGTcount: A:0.20, C:0.12, G:0.30, T:0.38
Consensus pattern (34 bp):
ATTTGGTGTGCTGGATGGATTAGCTCTTACGAGC
Found at i:39941351 original size:27 final size:26
Alignment explanation
Indices: 39941304--39941369 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
39941294 GTTTTGATTG
* *
39941304 ACAGGAATTCTGATAATAACCTTATTC
1 ACAGGAACTCTGATAAGAACCTTA-TC
39941331 ACAGGAACTCT-ATCAAGAACCTTATC
1 ACAGGAACTCTGAT-AAGAACCTTATC
*
39941357 GCTAGGAACTCTG
1 AC-AGGAACTCTG
39941370 TTCAGGATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 5 0.15
27 28 0.85
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (26 bp):
ACAGGAACTCTGATAAGAACCTTATC
Found at i:39945159 original size:27 final size:26
Alignment explanation
Indices: 39945122--39945236 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
39945112 AGCATGGCTG
* *
39945122 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
39945148 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
39945176 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
39945203 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
39945230 CCAGAAC
1 CCAGAAC
39945237 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:39945181 original size:54 final size:54
Alignment explanation
Indices: 39945122--39945236 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
39945112 AGCATGGCTG
*
39945122 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
39945176 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
39945230 CCAGAAC
1 CCAGAAC
39945237 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:39952592 original size:26 final size:26
Alignment explanation
Indices: 39952556--39952665 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
39952546 CATGAAATTC
39952556 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
39952582 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
39952608 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
39952634 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
39952660 TTATCA
1 TTATCA
39952666 ATTTGTACCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:39954958 original size:40 final size:39
Alignment explanation
Indices: 39954893--39954978 Score: 127
Period size: 40 Copynumber: 2.2 Consensus size: 39
39954883 TATATATATA
*
39954893 TAGCCGAAGCTATCTCAAATTGCACACCAAGTGCCACTTT
1 TAGCCGAAGCTATCTCAAATCGCACACCAAGTGCCA-TTT
* * *
39954933 TAGCCGAAGCTATTTCGAATCGCACACTAAGTGCCATTT
1 TAGCCGAAGCTATCTCAAATCGCACACCAAGTGCCATTT
39954972 TAGCCGA
1 TAGCCGA
39954979 TAAGTCGTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 10 0.24
40 32 0.76
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (39 bp):
TAGCCGAAGCTATCTCAAATCGCACACCAAGTGCCATTT
Found at i:39958333 original size:25 final size:25
Alignment explanation
Indices: 39958303--39958352 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
39958293 CACAATCACA
39958303 TAGTTTACTCCAAGCAAATTAACAT
1 TAGTTTACTCCAAGCAAATTAACAT
39958328 TAGTTTACTCCAAGCAAATTAACAT
1 TAGTTTACTCCAAGCAAATTAACAT
39958353 ACTTATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (25 bp):
TAGTTTACTCCAAGCAAATTAACAT
Found at i:39958988 original size:43 final size:43
Alignment explanation
Indices: 39958940--39959050 Score: 152
Period size: 43 Copynumber: 2.6 Consensus size: 43
39958930 TCCTAGATAT
* * *
39958940 GGTCTTACATGTTATCACATATCGATGCCACTGTCCCACACAG
1 GGTCTTACATGTAATCACATATCGATGCCAATGTCCCAAACAG
* * *
39958983 GGTCTTACATGAAATCACA-ATACAATGCCAATGTCCCAAACAT
1 GGTCTTACATGTAATCACATAT-CGATGCCAATGTCCCAAACAG
39959026 GGTCTTACATGTAATCACATATCGA
1 GGTCTTACATGTAATCACATATCGA
39959051 GTCGAGTCAT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 2 0.03
43 54 0.93
44 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.27
Consensus pattern (43 bp):
GGTCTTACATGTAATCACATATCGATGCCAATGTCCCAAACAG
Found at i:39959077 original size:46 final size:49
Alignment explanation
Indices: 39959007--39959182 Score: 155
Period size: 50 Copynumber: 3.6 Consensus size: 49
39958997 TCACAATACA
* *
39959007 ATGCCAATGTCCCAAACATGGTCTTACA-TGTAATCAC-ATATCGAGTC-G
1 ATGCC-ATGTCCCAGACATGGTCTTACACTG-AATCACTATATCGAGGCTG
* * *
39959055 A-GTCATGTCCCAGACATGGTCTTACACTGACTCTCTTATATCGAGGCTG
1 ATGCCATGTCCCAGACATGGTCTTACACTGAATCAC-TATATCGAGGCTG
* ** * * * * *
39959104 ATGCCATATCCCAGACATGGTCTTACACTGGCTCTCCTCTTTCCG-TGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGAATC-ACTATAT-CGAGGCTG
39959154 ATGCCATGTCCCAGACATGGTCTTACACT
1 ATGCCATGTCCCAGACATGGTCTTACACT
39959183 AGCTCACATG
Statistics
Matches: 107, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
46 25 0.23
47 4 0.04
48 10 0.09
49 2 0.02
50 63 0.59
51 3 0.03
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.29
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGAATCACTATATCGAGGCTG
Found at i:39959124 original size:50 final size:50
Alignment explanation
Indices: 39959062--39959182 Score: 163
Period size: 50 Copynumber: 2.4 Consensus size: 50
39959052 TCGAGTCATG
* *
39959062 TCCCAGACATGGTCTTACACTGACTCTCTTATAT-CGAGGCTGATGCCATA
1 TCCCAGACATGGTCTTACACTGACTCTCCTATATCCG-GGCCGATGCCATA
* * * * *
39959112 TCCCAGACATGGTCTTACACTGGCTCTCCTCTTTCCGTGCCGATGCCATG
1 TCCCAGACATGGTCTTACACTGACTCTCCTATATCCGGGCCGATGCCATA
39959162 TCCCAGACATGGTCTTACACT
1 TCCCAGACATGGTCTTACACT
39959183 AGCTCACATG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
50 61 0.97
51 2 0.03
ACGTcount: A:0.20, C:0.32, G:0.18, T:0.30
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACACTGACTCTCCTATATCCGGGCCGATGCCATA
Found at i:39962434 original size:46 final size:46
Alignment explanation
Indices: 39962384--39962557 Score: 221
Period size: 46 Copynumber: 3.8 Consensus size: 46
39962374 GTTGAGCATT
39962384 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
* *
39962430 CGAACTCGTTGAGTTGAGTCCGAGTTC-CTGA--GATG-TAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TC
* *
39962477 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
* *
39962523 CGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39962558 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 8, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 61 0.55
47 29 0.26
48 4 0.04
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
Found at i:39962543 original size:93 final size:93
Alignment explanation
Indices: 39962379--39962549 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
39962369 GGATGGTTGA
* * *
39962379 GCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39962444 TGAGTCCGAGTTCCTGAGATGTAACTAG
66 TGAGTCCGAGTTCCTGAGATGTAACTAG
*
39962472 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
39962537 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
39962550 GCTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCCTGAGATGTAACTAG
Found at i:39968715 original size:40 final size:40
Alignment explanation
Indices: 39968671--39968891 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
39968661 GCTCCTCGTT
* *
39968671 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
39968711 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
39968751 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
*
39968790 CAAATGCCTTC-GG-CTTAG-CCGGAT-TAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
39968826 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
39968867 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39968892 CATCATTCAA
Statistics
Matches: 161, Mismatches: 12, Indels: 16
0.85 0.06 0.08
Matches are distributed among these distances:
36 25 0.16
37 5 0.03
38 12 0.07
39 38 0.24
40 70 0.43
41 11 0.07
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:39968851 original size:115 final size:120
Alignment explanation
Indices: 39968671--39968891 Score: 294
Period size: 115 Copynumber: 1.9 Consensus size: 120
39968661 GCTCCTCGTT
*
39968671 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
39968736 ATTTAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
66 ATATAGTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* * **
39968790 CAAATGCCTTC-GG-CTTAG-CCGGAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* *
39968850 GATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
65 GATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
39968892 CATCATTCAA
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
114 3 0.03
115 46 0.51
116 24 0.27
117 4 0.04
118 2 0.02
119 11 0.12
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:39974486 original size:32 final size:32
Alignment explanation
Indices: 39974445--39974508 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
39974435 CATGATAGCC
39974445 TCGGACGAAACACATTCCCGAGCGTATTTGCT
1 TCGGACGAAACACATTCCCGAGCGTATTTGCT
39974477 TCGGACGAAACACATTCCCGAGCGTATTTGCT
1 TCGGACGAAACACATTCCCGAGCGTATTTGCT
39974509 AAGTCTAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (32 bp):
TCGGACGAAACACATTCCCGAGCGTATTTGCT
Found at i:39979920 original size:40 final size:40
Alignment explanation
Indices: 39979842--39979950 Score: 186
Period size: 40 Copynumber: 2.8 Consensus size: 40
39979832 GGACTTAACC
* *
39979842 CGCACAAATGCCTTCGG-GCTTAG-CCGGAATTAGTATCT
1 CGCACAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCT
39979880 CGCACAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCT
1 CGCACAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCT
39979920 CGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 CGCACAAATGCCTTCGGATCTTAGTCCGGAT
39979951 ATGGTCACTT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
38 17 0.25
39 5 0.07
40 45 0.67
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (40 bp):
CGCACAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCT
Found at i:39979973 original size:40 final size:40
Alignment explanation
Indices: 39979843--39979989 Score: 162
Period size: 40 Copynumber: 3.7 Consensus size: 40
39979833 GACTTAACCC
* *
39979843 GCACAAATGCCTTCGG-GCTTAG-CCGGA-ATTAGTATCTC
1 GCACAAATGCCTTCGGATCTTAGTCCGGATA-TAGTATCTA
* *
39979881 GCACAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTC
1 GCACAAATGCCTTCGGATCTTAGTCCGGATATAGTATCTA
*
39979921 GCACAAATGCCTTCGGATCTTAGTCCGGATATGGTCA-CTTA
1 GCACAAATGCCTTCGGATCTTAGTCCGGATATAGT-ATC-TA
*
39979962 GCACAAA-GCCTTCGGGA-CTTAGCCCGGA
1 GCACAAATGCCTTC-GGATCTTAGTCCGGA
39979990 CATCATTCAA
Statistics
Matches: 97, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
38 16 0.16
39 5 0.05
40 64 0.66
41 12 0.12
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (40 bp):
GCACAAATGCCTTCGGATCTTAGTCCGGATATAGTATCTA
Found at i:39992821 original size:14 final size:14
Alignment explanation
Indices: 39992802--39992828 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39992792 CACAATTGGT
39992802 AAAATTTTCATATC
1 AAAATTTTCATATC
39992816 AAAATTTTCATAT
1 AAAATTTTCATAT
39992829 AACCTTCCTA
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:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAATTTTCATATC
Found at i:40000939 original size:26 final size:26
Alignment explanation
Indices: 40000910--40000967 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
40000900 TGGTACAAAT
40000910 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
40000936 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
40000962 TGATAA
1 TGATAA
40000968 GAATTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:40004751 original size:50 final size:50
Alignment explanation
Indices: 40004671--40004797 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 50
40004661 CCGTGAGTAA
* *
40004671 TGAGATCCCATATAAGACCATGTCTAGGACATGGAATTGGCATCAATATG
1 TGAGATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCAATATG
* * ***
40004721 TGAGATCCCATGTAAGAGCATGTCTGGGACATGGCATTGGCATTGGTATG
1 TGAGATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCAATATG
* *
40004771 T--GATCCTATGTAAGACCATATCTGGGA
1 TGAGATCCCATGTAAGACCATGTCTGGGA
40004798 TATGACCTTG
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
48 23 0.34
50 44 0.66
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (50 bp):
TGAGATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCAATATG
Found at i:40004795 original size:48 final size:49
Alignment explanation
Indices: 40004673--40004812 Score: 156
Period size: 50 Copynumber: 2.9 Consensus size: 49
40004663 GTGAGTAATG
* * *
40004673 AGATCCCATATAAGACCATGTCTAGGACATGGAATTGGCATCAATATGT
1 AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGT
* ***
40004722 GAGATCCCATGTAAGAGCATGTCTGGGACATGGCATTGGCATTGGTATGT
1 -AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGT
* * * * *
40004772 -GATCCTATGTAAGACCATATCTGGGATATGACCTTGGCATC
1 AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
40004813 TTATTATGTG
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
48 34 0.45
50 42 0.55
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (49 bp):
AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCAATATGT
Found at i:40007726 original size:9 final size:9
Alignment explanation
Indices: 40007712--40007806 Score: 136
Period size: 9 Copynumber: 10.6 Consensus size: 9
40007702 TTTATACAAA
40007712 TAATTCGGT
1 TAATTCGGT
40007721 TAATTCGGT
1 TAATTCGGT
*
40007730 TAATTTGGT
1 TAATTCGGT
* *
40007739 TAATTTGGG
1 TAATTCGGT
40007748 TAATTCGGT
1 TAATTCGGT
*
40007757 TAATTCGGG
1 TAATTCGGT
40007766 TAATTCGGT
1 TAATTCGGT
* *
40007775 TAATTTGAT
1 TAATTCGGT
40007784 TAATTCGGT
1 TAATTCGGT
40007793 TAATTCGGT
1 TAATTCGGT
40007802 TAATT
1 TAATT
40007807 TTATACTTAT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 76 1.00
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.46
Consensus pattern (9 bp):
TAATTCGGT
Found at i:40008848 original size:46 final size:45
Alignment explanation
Indices: 40008786--40008957 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 45
40008776 TCTCGTAACT
* *
40008786 GATGAATGTCCTAGACATGTCTTACACTAGCTTACGTCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTT-CGTCTCGAGGCC
* * *
40008832 GATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGC-TTCGTCTCGAGGCC
* * * * * * *
40008878 AATGCCATGTTCCAAACATGGTCTTACACTGGCTCTCATAAT-GTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTAGCT-TCGT-CTCGAGGCC
40008926 GATGCATGTCCCAGACATGTCTTACACTAGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCT
40008958 CACACAAGTG
Statistics
Matches: 102, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
46 55 0.54
47 25 0.25
48 21 0.21
49 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTTCGTCTCGAGGCC
Found at i:40013241 original size:20 final size:20
Alignment explanation
Indices: 40013212--40013257 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
40013202 AGCACATGTA
* *
40013212 TTCATAAAATTTCAAAATTT
1 TTCATTAAATTTCAAAACTT
* *
40013232 TTCATTAAATTTTACAACTT
1 TTCATTAAATTTCAAAACTT
40013252 TTCATT
1 TTCATT
40013258 TTAATCCCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (20 bp):
TTCATTAAATTTCAAAACTT
Found at i:40028292 original size:9 final size:9
Alignment explanation
Indices: 40028278--40028334 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
40028268 TTTTGATAAC
40028278 ATGATATGT
1 ATGATATGT
*
40028287 ATGATATGCAC
1 ATGATATG--T
*
40028298 ATGACATGT
1 ATGATATGT
*
40028307 ATGATATGCAC
1 ATGATATG--T
40028318 ATGATATGT
1 ATGATATGT
40028327 ATGATATG
1 ATGATATG
40028335 CACACGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:40028301 original size:20 final size:20
Alignment explanation
Indices: 40028276--40028338 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
40028266 GATTTTGATA
40028276 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
40028296 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
40028316 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
40028336 ACA
1 ACA
40028339 CGAGATGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:40028511 original size:22 final size:24
Alignment explanation
Indices: 40028392--40028517 Score: 188
Period size: 24 Copynumber: 5.4 Consensus size: 24
40028382 GAGGAAGTGC
*
40028392 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
40028416 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
40028440 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
40028464 -AAAGGGATTATG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
40028486 AAAAGGGCTT-TG-CCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
40028508 AAAAGAGGCT
1 AAAAG-GGCT
40028518 AGGCCTCCAG
Statistics
Matches: 97, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
22 27 0.28
23 23 0.24
24 47 0.48
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:40028758 original size:31 final size:31
Alignment explanation
Indices: 40028723--40028786 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
40028713 CGATTACAGT
40028723 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
40028754 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
40028785 AA
1 AA
40028787 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:40036281 original size:25 final size:25
Alignment explanation
Indices: 40036252--40036299 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
40036242 TTATAACATG
* *
40036252 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
40036277 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
40036300 GTTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:40036350 original size:9 final size:9
Alignment explanation
Indices: 40036338--40036394 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
40036328 TTTGATAGAC
40036338 ATGATATGT
1 ATGATATGT
*
40036347 ATGATATGCAC
1 ATGATATG--T
*
40036358 ATGACATGT
1 ATGATATGT
*
40036367 ATGATATGCAC
1 ATGATATG--T
40036378 ATGATATGT
1 ATGATATGT
40036387 ATGATATG
1 ATGATATG
40036395 CACACGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:40036361 original size:20 final size:20
Alignment explanation
Indices: 40036336--40036398 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
40036326 ATTTTGATAG
40036336 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
40036356 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
40036376 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
40036396 ACA
1 ACA
40036399 CGAGATGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:40036478 original size:24 final size:24
Alignment explanation
Indices: 40036451--40036556 Score: 133
Period size: 24 Copynumber: 4.4 Consensus size: 24
40036441 GGAGGAAGTG
*
40036451 CAAAAGGGCTTATGCCCCAGCTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
40036475 CAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
40036499 -TAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* * *
40036522 TAAAAGGGCTTTTGCCCCAATTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
40036546 TAAAAGAGGCT
1 CAAAAG-GGCT
40036557 AGGCCTCCAG
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
23 21 0.29
24 48 0.66
25 4 0.05
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:40036527 original size:47 final size:47
Alignment explanation
Indices: 40036453--40036549 Score: 167
Period size: 47 Copynumber: 2.1 Consensus size: 47
40036443 AGGAAGTGCA
*
40036453 AAAGGGCTTATGCCCCAGCTATCAAAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGCTATCAAAAGGGCTTTTGCCCCAATTATT
* *
40036500 AAAGGGCTTATGCCCCAGTTATTAAAAGGGCTTTTGCCCCAATTATT
1 AAAGGGCTTATGCCCCAGCTATCAAAAGGGCTTTTGCCCCAATTATT
40036547 AAA
1 AAA
40036550 AGAGGCTAGG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (47 bp):
AAAGGGCTTATGCCCCAGCTATCAAAAGGGCTTTTGCCCCAATTATT
Found at i:40036799 original size:31 final size:31
Alignment explanation
Indices: 40036764--40036827 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
40036754 CGATTACAGT
40036764 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
40036795 AAAGGCTTCGGCCCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
40036826 AA
1 AA
40036828 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:40041606 original size:49 final size:48
Alignment explanation
Indices: 40041534--40041706 Score: 179
Period size: 49 Copynumber: 3.6 Consensus size: 48
40041524 TGTTGTGTGT
*
40041534 CAGTGTAAGACCTGTCTGGGACATGGCATCGACATTGATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC-TTGATAGATGAAAGC
* * * * * *
40041583 CAGTGTAAGACTTGTTTGGGACATGGCATCAGTCTCGATATATGAAAGT
1 CAGTGTAAGACCTGTCTGGGACATGGCATC-GACTTGATAGATGAAAGC
* * * **
40041632 TAGTGTAAAACCTGTCTGGGACATGGCATCGACTTTA-ATG-TGCTAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACTTGATA-GATGAAAGC
*
40041679 CAGTGTAAGACCATGTCTAGGACATGGC
1 CAGTGTAAGACC-TGTCTGGGACATGGC
40041707 GTCAACATCT
Statistics
Matches: 100, Mismatches: 21, Indels: 7
0.78 0.16 0.05
Matches are distributed among these distances:
47 15 0.15
48 18 0.18
49 65 0.65
50 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.27
Consensus pattern (48 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGACTTGATAGATGAAAGC
Found at i:40041654 original size:142 final size:136
Alignment explanation
Indices: 40041398--40041657 Score: 315
Period size: 142 Copynumber: 1.9 Consensus size: 136
40041388 TATGTGCGCT
*
40041398 AGTGTAAGACATTATGAGACATGCATCGACATTGAGACGAGAGCTAATGTAAGACATGTATGGGA
1 AGTGTAAGACATTATGAGACATGCATCGACATTGAGACGAGAGCCAATGTAAGACATGTATGGGA
* * *
40041463 CATGCATCAGCCTCAGGATATACAAGCTAGTGTAAGACTTGTCTAGGACATGGTGTCAGTTTGTT
66 CATGCATCAGCCTCA-GATATAAAAGCTAGTGTAAAACCTGTCTAGGACATGGTGTCAGTTTGTT
40041528 GTGTGTC
130 GTGTGTC
* * * * * * *
40041535 AGTGTAAGACCTGTCTGGGACATGGCATCGACATTGATAGATGAGAGCCAGTGTAAGACTTGTTT
1 AGTGTAAGACAT-TATGAGACAT-GCATCGACATTG--AGACGAGAGCCAATGTAAGACATGTAT
* * *
40041600 GGGACATGGCATCAGTCTC-GATATATGAAAGTTAGTGTAAAACCTGTCTGGGACATGG
62 GGGACAT-GCATCAGCCTCAGATATA--AAAGCTAGTGTAAAACCTGTCTAGGACATGG
40041658 CATCGACTTT
Statistics
Matches: 102, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
137 11 0.11
138 8 0.08
139 12 0.12
140 6 0.06
141 29 0.28
142 36 0.35
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.27
Consensus pattern (136 bp):
AGTGTAAGACATTATGAGACATGCATCGACATTGAGACGAGAGCCAATGTAAGACATGTATGGGA
CATGCATCAGCCTCAGATATAAAAGCTAGTGTAAAACCTGTCTAGGACATGGTGTCAGTTTGTTG
TGTGTC
Found at i:40059234 original size:49 final size:49
Alignment explanation
Indices: 40059169--40059297 Score: 163
Period size: 49 Copynumber: 2.6 Consensus size: 49
40059159 TGTTGTGTGT
*
40059169 CAGTGTAAGACCTGTCTGAGACATGGCATCGACAC-CGATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGAGACATGGCATCGAC-CTCGATAGATGAAAGC
* * * * *
40059218 CAGTGTAAGACTTGTCTGGGACATGGCATCAACCTCGATATATGAAAGT
1 CAGTGTAAGACCTGTCTGAGACATGGCATCGACCTCGATAGATGAAAGC
*
40059267 CAGTGTAAGACCTGTCT-AGGACATAGCATCG
1 CAGTGTAAGACCTGTCTGA-GACATGGCATCG
40059298 GCTTTAATAT
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 1 0.01
49 67 0.99
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.22
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGAGACATGGCATCGACCTCGATAGATGAAAGC
Found at i:40084620 original size:30 final size:30
Alignment explanation
Indices: 40084586--40084646 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40084576 TCCTTAACTC
40084586 AAACTTTTACAAAATTAAAATTTTGCCCCT
1 AAACTTTTACAAAATTAAAATTTTGCCCCT
* * * * *
40084616 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTACAAAATTAAAATTTTGCCCCT
40084646 A
1 A
40084647 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (30 bp):
AAACTTTTACAAAATTAAAATTTTGCCCCT
Found at i:40085522 original size:5 final size:5
Alignment explanation
Indices: 40085496--40085583 Score: 58
Period size: 5 Copynumber: 16.8 Consensus size: 5
40085486 AATCCTCCTT
*
40085496 TTTTA -TTTA TTCTTA TTTTTA TTTTA -TTTA TTTTA TTTTAA TTTTTC
1 TTTTA TTTTA TT-TTA -TTTTA TTTTA TTTTA TTTTA TTTT-A -TTTTA
*
40085543 TTTTGA TTTTTA TTTTCA TTTCAA TTTTA --TTA TTTTA TTTT
1 TTTT-A -TTTTA TTTT-A TTT-TA TTTTA TTTTA TTTTA TTTT
40085584 GAAAGACATA
Statistics
Matches: 67, Mismatches: 4, Indels: 24
0.71 0.04 0.25
Matches are distributed among these distances:
3 3 0.04
4 8 0.12
5 30 0.45
6 16 0.24
7 10 0.15
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:40085522 original size:21 final size:20
Alignment explanation
Indices: 40085496--40085540 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
40085486 AATCCTCCTT
*
40085496 TTTTATTTATTCTTATTTTTA
1 TTTTATTTATT-TTATTTTAA
40085517 TTTTATTTATTTTATTTTAA
1 TTTTATTTATTTTATTTTAA
40085537 TTTT
1 TTTT
40085541 TCTTTTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTATTTATTTTATTTTAA
Found at i:40085541 original size:21 final size:22
Alignment explanation
Indices: 40085495--40085541 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
40085485 GAATCCTCCT
*
40085495 TTTTTATTTATTCTTATTTTTA
1 TTTTTATTTATTCTTATTTTAA
40085517 -TTTTATTTATT-TTATTTTAA
1 TTTTTATTTATTCTTATTTTAA
40085537 TTTTT
1 TTTTT
40085542 CTTTTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTATTTATTCTTATTTTAA
Found at i:40085553 original size:7 final size:6
Alignment explanation
Indices: 40085501--40085563 Score: 54
Period size: 6 Copynumber: 10.2 Consensus size: 6
40085491 TCCTTTTTTA
* * * * *
40085501 TTTATT CTTATT TTTATT TTATTTAT TTTATT TTAATT TTTCTT TTGATT
1 TTTATT TTTATT TTTATT TT-TAT-T TTTATT TTTATT TTTATT TTTATT
*
40085551 TTTATT TTCATT T
1 TTTATT TTTATT T
40085564 CAATTTTATT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
6 37 0.84
7 4 0.09
8 3 0.07
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:40085563 original size:12 final size:11
Alignment explanation
Indices: 40085495--40085583 Score: 60
Period size: 12 Copynumber: 7.9 Consensus size: 11
40085485 GAATCCTCCT
40085495 TTTTTA-TTTA
1 TTTTTATTTTA
*
40085505 TTCTTATTTT-
1 TTTTTATTTTA
40085515 TATTTTA-TTTA
1 T-TTTTATTTTA
40085526 -TTTTATTTTAA
1 TTTTTATTTT-A
*
40085537 TTTTTCTTTTGA
1 TTTTTATTTT-A
40085549 TTTTTATTTTCA
1 TTTTTATTTT-A
**
40085561 TTTCAATTTTA
1 TTTTTATTTTA
40085572 TTATTTTATTTT
1 -T-TTTTATTTT
40085584 GAAAGACATA
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
9 5 0.08
10 12 0.20
11 9 0.15
12 28 0.46
13 7 0.11
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.75
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:40088510 original size:21 final size:22
Alignment explanation
Indices: 40088476--40088517 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
40088466 TTCTCTCTGC
40088476 TTTAAATAAATTAGTTAATTAG
1 TTTAAATAAATTAGTTAATTAG
40088498 TTTAAAT-AATTAGTTAATTA
1 TTTAAATAAATTAGTTAATTA
40088518 AAACAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTTAAATAAATTAGTTAATTAG
Found at i:40096469 original size:18 final size:18
Alignment explanation
Indices: 40096446--40096483 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
40096436 GTAGGTTTCC
*
40096446 AAAAATGGAAATGGAAAT
1 AAAAATGAAAATGGAAAT
40096464 AAAAATGAAAATGGAAAT
1 AAAAATGAAAATGGAAAT
40096482 AA
1 AA
40096484 TCTATTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (18 bp):
AAAAATGAAAATGGAAAT
Found at i:40097949 original size:38 final size:38
Alignment explanation
Indices: 40097906--40097982 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
40097896 CTTAAGTGGC
*
40097906 ATCATTTTAGTGATGATAGCACTACATGATGCGTTTAT
1 ATCATTTTAGTGATGATAGCACTACATAATGCGTTTAT
40097944 ATCATTTTAGTGATGATAGCACTACATAATGCGTTTAT
1 ATCATTTTAGTGATGATAGCACTACATAATGCGTTTAT
40097982 A
1 A
40097983 CTTATTTGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (38 bp):
ATCATTTTAGTGATGATAGCACTACATAATGCGTTTAT
Found at i:40101766 original size:20 final size:20
Alignment explanation
Indices: 40101741--40101788 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
40101731 GGTCACACAT
40101741 GCCCGTGTGGCTTGGGACAC
1 GCCCGTGTGGCTTGGGACAC
40101761 GCCCGTGTGGCTTGGGACAC
1 GCCCGTGTGGCTTGGGACAC
40101781 GCCCGTGT
1 GCCCGTGT
40101789 CCTCAGCCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.08, C:0.31, G:0.40, T:0.21
Consensus pattern (20 bp):
GCCCGTGTGGCTTGGGACAC
Found at i:40111068 original size:147 final size:147
Alignment explanation
Indices: 40110705--40111126 Score: 630
Period size: 146 Copynumber: 2.9 Consensus size: 147
40110695 GTTTTTTTTA
* *
40110705 TTATAATTTGTTTATGTTATTGAATGAAGTTAAGTTTAAATGTTTTTGATTGTACGGTAATGCTC
1 TTATAATTTTTTTATGTTATTGAATGAAGTTAAGTTTAAATGTTTCTGATTGTACGGTAATGCTC
* * * *** *
40110770 TATGACCTTAAATCGGTGATGGATATGGGTTAGAGGAGTTACAGGCCACTTCACTCTTTGCTAAT
66 TATGACCCTAAACCGGCGACAAATATGGGTTAGAGGTGTTACAGGCCACTTCACTCTTTGCTAAT
40110835 GTACGCATATATTTTGT
131 GTACGCATATATTTTGT
*
40110852 TTATAA-TTTTTTATGTTATTGAATGAAGTTAAGTTTATATGTTTCTGATTGTACGGTAATGCTC
1 TTATAATTTTTTTATGTTATTGAATGAAGTTAAGTTTAAATGTTTCTGATTGTACGGTAATGCTC
* * *
40110916 TATGACCCTAAACCGACGACAAATATGGGTTAGAGGTGTTATAGGCCACTTCTCTCTTTGCTAAT
66 TATGACCCTAAACCGGCGACAAATATGGGTTAGAGGTGTTACAGGCCACTTCACTCTTTGCTAAT
** *
40110981 GTATTCATATGTTTTGT
131 GTACGCATATATTTTGT
*
40110998 TTATAATTTTTTTATGTTATTGAGTGAAGTTAAGTTTAAATGTTTCTGATTGTACGGTAATGCTC
1 TTATAATTTTTTTATGTTATTGAATGAAGTTAAGTTTAAATGTTTCTGATTGTACGGTAATGCTC
* * * * * *
40111063 TATGACCCTAAACTGGGGACAAACATGGGTTAGAGGTGTTACAGGCTACTTCGCTCTTTACTAA
66 TATGACCCTAAACCGGCGACAAATATGGGTTAGAGGTGTTACAGGCCACTTCACTCTTTGCTAA
40111127 CTTTTCAGTA
Statistics
Matches: 248, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
146 130 0.52
147 118 0.48
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (147 bp):
TTATAATTTTTTTATGTTATTGAATGAAGTTAAGTTTAAATGTTTCTGATTGTACGGTAATGCTC
TATGACCCTAAACCGGCGACAAATATGGGTTAGAGGTGTTACAGGCCACTTCACTCTTTGCTAAT
GTACGCATATATTTTGT
Found at i:40119055 original size:27 final size:27
Alignment explanation
Indices: 40119014--40119298 Score: 346
Period size: 27 Copynumber: 10.6 Consensus size: 27
40119004 CCAAACTGTT
*
40119014 TAAAATTATCGAAATACCCTC-GATTTG
1 TAAAATTACCGAAATACCCTCAG-TTTG
* *
40119041 TAAAATTACCAAAATACCCTCAATTTG
1 TAAAATTACCGAAATACCCTCAGTTTG
* * *
40119068 TAAAATTACCAAAATACCCCCAATTTG
1 TAAAATTACCGAAATACCCTCAGTTTG
* *
40119095 TAAAATTACTGAAATACCCTTAGTTTG
1 TAAAATTACCGAAATACCCTCAGTTTG
*
40119122 TAAAATTACTGAAATACCCTCAGTTTG
1 TAAAATTACCGAAATACCCTCAGTTTG
*
40119149 TAAAATTATCGAAATACCCTC-GATTTG
1 TAAAATTACCGAAATACCCTCAG-TTTG
**
40119176 TAAAATTACTAAAATACCC-CAGTTTG
1 TAAAATTACCGAAATACCCTCAGTTTG
40119202 TAAAATTACCGAAATACCAC-CAGTTTG
1 TAAAATTACCGAAATACC-CTCAGTTTG
* * * *
40119229 CAAAACTATCGAAATACCCT-AATTTG
1 TAAAATTACCGAAATACCCTCAGTTTG
* *
40119255 TAAAATTACCAAAATAACCTCAGTTTG
1 TAAAATTACCGAAATACCCTCAGTTTG
40119282 TAAAATTACCGAAATAC
1 TAAAATTACCGAAATAC
40119299 ATCTATAGGG
Statistics
Matches: 223, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
26 43 0.19
27 180 0.81
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.30
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTCAGTTTG
Found at i:40119239 original size:80 final size:80
Alignment explanation
Indices: 40119037--40119298 Score: 366
Period size: 80 Copynumber: 3.3 Consensus size: 80
40119027 ATACCCTCGA
* * * * *
40119037 TTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCCAATTTGTAAAATT
1 TTTGTAAAATTACCGAAATACCCTCAGTTTGTAAAATTATCGAAATACCCTCAATTTGTAAAATT
* *
40119102 ACTGAAATACCCTTAG
66 ACTAAAATACCC-CAG
* *
40119118 TTTGTAAAATTACTGAAATACCCTCAGTTTGTAAAATTATCGAAATACCCTCGATTTGTAAAATT
1 TTTGTAAAATTACCGAAATACCCTCAGTTTGTAAAATTATCGAAATACCCTCAATTTGTAAAATT
40119183 ACTAAAATACCCCAG
66 ACTAAAATACCCCAG
* *
40119198 TTTGTAAAATTACCGAAATACCAC-CAGTTTGCAAAACTATCGAAATACCCT-AATTTGTAAAAT
1 TTTGTAAAATTACCGAAATACC-CTCAGTTTGTAAAATTATCGAAATACCCTCAATTTGTAAAAT
* *
40119261 TACCAAAATAACCTCAG
65 TACTAAAAT-ACCCCAG
40119278 TTTGTAAAATTACCGAAATAC
1 TTTGTAAAATTACCGAAATAC
40119299 ATCTATAGGG
Statistics
Matches: 164, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
79 19 0.12
80 75 0.46
81 70 0.43
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (80 bp):
TTTGTAAAATTACCGAAATACCCTCAGTTTGTAAAATTATCGAAATACCCTCAATTTGTAAAATT
ACTAAAATACCCCAG
Found at i:40119722 original size:27 final size:27
Alignment explanation
Indices: 40119662--40119736 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
40119652 TTGTTTATGG
*
40119662 CTTTGTGCAAATCATATTTACTAGTGG
1 CTTTGTGCAAATCATATTTACTAGTGA
* * *
40119689 CTATGTGCATATCATATTTA-TTGATGA
1 CTTTGTGCAAATCATATTTACTAG-TGA
*
40119716 CTTTGTGTC-GATCATATTTAC
1 CTTTGTG-CAAATCATATTTAC
40119737 CCATGGCTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.05
27 36 0.92
28 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (27 bp):
CTTTGTGCAAATCATATTTACTAGTGA
Found at i:40123278 original size:27 final size:27
Alignment explanation
Indices: 40123245--40123427 Score: 174
Period size: 27 Copynumber: 6.8 Consensus size: 27
40123235 GGAAAATCAG
* *
40123245 TCATTTTACCTTATAGGGGCATTACAA
1 TCATTTTACCCTATAGGGGTATTACAA
* * * *
40123272 TAATTTTACCCTACAGGGATATTACAG
1 TCATTTTACCCTATAGGGGTATTACAA
* *
40123299 TCATTTTACCCTATAGGGGTATTTCGA
1 TCATTTTACCCTATAGGGGTATTACAA
* **
40123326 TCATTTTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCTATAGGGGTATTACAA
* * *
40123353 TCATTTTACCTTAT-GAGGGTATTTCAG
1 TCATTTTACCCTATAG-GGGTATTACAA
* **
40123380 TCATTTTACCCTAT-GAGGGTATTTCGG
1 TCATTTTACCCTATAG-GGGTATTACAA
40123407 TCATTTTACCCTAT-GGGGTAT
1 TCATTTTACCCTATAGGGGTAT
40123428 CTCGGTCACC
Statistics
Matches: 138, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
26 7 0.05
27 131 0.95
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (27 bp):
TCATTTTACCCTATAGGGGTATTACAA
Found at i:40123306 original size:54 final size:52
Alignment explanation
Indices: 40123241--40123427 Score: 212
Period size: 54 Copynumber: 3.5 Consensus size: 52
40123231 GTAGGGAAAA
* * * *
40123241 TCAGTCATTTTACCTTATAGGGGCATTACAATAATTTTACCCTACAGGGATATT
1 TCAGTCATTTTACCCTAT-GGGGTATTTCAATCATTTTACCCTACAGGG-TATT
* * *
40123295 ACAGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATAGGGGTATT
1 TCAGTCATTTTACCCTAT-GGGGTATTTCAATCATTTTACCCTACA-GGGTATT
* * * *
40123349 TCGGTCATTTTACCTTATGAGGGTATTTCAGTCATTTTACCCTATGAGGGTATT
1 TCAGTCATTTTACCCTATG-GGGTATTTCAATCATTTTACCCTA-CAGGGTATT
*
40123403 TCGGTCATTTTACCCTATGGGGTAT
1 TCAGTCATTTTACCCTATGGGGTAT
40123428 CTCGGTCACC
Statistics
Matches: 116, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
53 7 0.06
54 105 0.91
55 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.40
Consensus pattern (52 bp):
TCAGTCATTTTACCCTATGGGGTATTTCAATCATTTTACCCTACAGGGTATT
Found at i:40123335 original size:81 final size:81
Alignment explanation
Indices: 40123245--40123424 Score: 231
Period size: 81 Copynumber: 2.2 Consensus size: 81
40123235 GGAAAATCAG
*
40123245 TCATTTTACCTTATAGGGGCATTACAATAATTTTACCCTA-CAGGGATATTACAGTCATTTTACC
1 TCATTTTACCCTATAGGGGCATTACAATAATTTTACCCTATCAGGG-TATTACAGTCATTTTACC
40123309 CTAT-AGGGGTATTTCGA
65 CTATGA-GGGTATTTCGA
* * ** * * * *
40123326 TCATTTTACCCTATAGGGGTATTTCGGTCATTTTACCTTATGAGGGTATTTCAGTCATTTTACCC
1 TCATTTTACCCTATAGGGGCATTACAATAATTTTACCCTATCAGGGTATTACAGTCATTTTACCC
*
40123391 TATGAGGGTATTTCGG
66 TATGAGGGTATTTCGA
40123407 TCATTTTACCCTAT-GGGG
1 TCATTTTACCCTATAGGGG
40123425 TATCTCGGTC
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
80 4 0.05
81 78 0.90
82 5 0.06
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.39
Consensus pattern (81 bp):
TCATTTTACCCTATAGGGGCATTACAATAATTTTACCCTATCAGGGTATTACAGTCATTTTACCC
TATGAGGGTATTTCGA
Found at i:40125500 original size:15 final size:15
Alignment explanation
Indices: 40125458--40125501 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
40125448 TGTCAAAATC
*
40125458 AAACAAATGAAAATAT
1 AAACAAAT-AAAATAG
*
40125474 AAA-AATTAAAATAG
1 AAACAAATAAAATAG
40125488 AAACAAATAAAATA
1 AAACAAATAAAATA
40125502 AATGGTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 9 0.38
15 12 0.50
16 3 0.12
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.18
Consensus pattern (15 bp):
AAACAAATAAAATAG
Found at i:40132793 original size:52 final size:52
Alignment explanation
Indices: 40132711--40132814 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
40132701 ATATGTATGC
* *
40132711 GGCATCCGAGCTTATTGAGTTGGTCTGAGTTCATAATGGATGCGATACATGT
1 GGCATCCGAGCTCATTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGT
*
40132763 GGCATCTGAGCTCATTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGT
1 GGCATCCGAGCTCATTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGT
40132815 AATTGGGTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (52 bp):
GGCATCCGAGCTCATTGAGTTGGTCCGAGTTCATAATGGATGCGATACATGT
Found at i:40134875 original size:43 final size:43
Alignment explanation
Indices: 40134778--40134943 Score: 147
Period size: 43 Copynumber: 3.9 Consensus size: 43
40134768 ATCGAGATGC
* *
40134778 GATTACATGTAAGACCATGTCTAGCACATTGGCATTG-TATTGT
1 GATTACATGTAAGACCATGTCTAGGACATTGGCATTGTTA-TAT
* * * *
40134821 GTTTACGTGTAAGACAATGTCTGGGACATTGGCATTGTTATAT
1 GATTACATGTAAGACCATGTCTAGGACATTGGCATTGTTATAT
* * * * *** * *
40134864 GATTTCATGTAAGGCCACGTCTGGGTTGTTGGCATCGATATAT
1 GATTACATGTAAGACCATGTCTAGGACATTGGCATTGTTATAT
* * *
40134907 GATGACATGTAAGACCATATCTAGGATA-TGGCATTGT
1 GATTACATGTAAGACCATGTCTAGGACATTGGCATTGT
40134944 ACGAGCTCTA
Statistics
Matches: 95, Mismatches: 27, Indels: 3
0.76 0.22 0.02
Matches are distributed among these distances:
42 7 0.07
43 86 0.91
44 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTAGGACATTGGCATTGTTATAT
Found at i:40144982 original size:27 final size:27
Alignment explanation
Indices: 40144951--40145030 Score: 101
Period size: 27 Copynumber: 3.0 Consensus size: 27
40144941 AAGGGGGTGG
40144951 TCCATCGAGATAGTAAACATGTGGTAA
1 TCCATCGAGATAGTAAACATGTGGTAA
* *
40144978 TCCATC-ATGACAGTAAACATGTGGTAT
1 TCCATCGA-GATAGTAAACATGTGGTAA
*
40145005 TCTATCG-GTATAGTAAACATGTGGTA
1 TCCATCGAG-ATAGTAAACATGTGGTA
40145031 GTTTGTCGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
26 2 0.04
27 44 0.96
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (27 bp):
TCCATCGAGATAGTAAACATGTGGTAA
Found at i:40145049 original size:54 final size:54
Alignment explanation
Indices: 40144959--40145089 Score: 133
Period size: 54 Copynumber: 2.4 Consensus size: 54
40144949 GGTCCATCGA
* * *
40144959 GATAGTAAACATGTGGTAATCCATCATGACAGTAAACAT-GTGGTATTCTA-TCGG
1 GATAGTAAACATGTGGTAGTTCATCATGACAGTAAACATAG-GGTAGTCTACT-GG
* ** *
40145013 TATAGTAAACATGTGGTAGTTTGTCGA-GACATTAAACATAGGGTAGTCTACTGG
1 GATAGTAAACATGTGGTAGTTCATC-ATGACAGTAAACATAGGGTAGTCTACTGG
* *
40145067 GACAGTAAAAATGTGGTAGTTCA
1 GATAGTAAACATGTGGTAGTTCA
40145090 CCGGGACAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
54 59 0.95
55 3 0.05
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (54 bp):
GATAGTAAACATGTGGTAGTTCATCATGACAGTAAACATAGGGTAGTCTACTGG
Found at i:40145095 original size:27 final size:28
Alignment explanation
Indices: 40144986--40145104 Score: 104
Period size: 27 Copynumber: 4.4 Consensus size: 28
40144976 AATCCATCAT
*
40144986 GACAGTAAACATGTGGTA-TTCTATCGG
1 GACAGTAAACATGTGGTAGTTCTACCGG
* * ** *
40145013 TATAGTAAACATGTGGTAGTT-TGTCGA
1 GACAGTAAACATGTGGTAGTTCTACCGG
* *
40145040 GACATTAAACATAG-GGTAG-TCTACTGG
1 GACAGTAAACAT-GTGGTAGTTCTACCGG
*
40145067 GACAGTAAAAATGTGGTAGTTC-ACCGG
1 GACAGTAAACATGTGGTAGTTCTACCGG
*
40145094 GACAATAAACA
1 GACAGTAAACA
40145105 CAAGAATGTC
Statistics
Matches: 71, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
26 2 0.03
27 64 0.90
28 5 0.07
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.27
Consensus pattern (28 bp):
GACAGTAAACATGTGGTAGTTCTACCGG
Found at i:40151687 original size:6 final size:6
Alignment explanation
Indices: 40151673--40151715 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
40151663 ATAAGGTCTC
* *
40151673 TTTAAT TTTATT TTTATT TTCATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT T
40151716 GGGGATTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:40153638 original size:23 final size:23
Alignment explanation
Indices: 40153608--40153709 Score: 95
Period size: 22 Copynumber: 4.5 Consensus size: 23
40153598 CAACTCATTG
40153608 GAGCTTACTGTTTTAGCTCG-TA
1 GAGCTTACTGTTTTAGCTCGATA
*
40153630 TGAGCTTACT-ATTTAGCTCGATA
1 -GAGCTTACTGTTTTAGCTCGATA
* * *
40153653 GAACTTACTG-TTCAGCTCAATA
1 GAGCTTACTGTTTTAGCTCGATA
** *
40153675 GAGCTTACCATTTCAGCTC-ATTA
1 GAGCTTACTGTTTTAGCTCGA-TA
40153698 GAGCTTACTGTT
1 GAGCTTACTGTT
40153710 CATCAACTCA
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
22 35 0.53
23 31 0.47
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (23 bp):
GAGCTTACTGTTTTAGCTCGATA
Found at i:40153887 original size:19 final size:20
Alignment explanation
Indices: 40153863--40153920 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
40153853 TACCGATCAT
40153863 ATGAAT-AAGCTA-TGTTGAA
1 ATGAATGAA-CTATTGTTGAA
*
40153882 ATGAATGAATTATTGTTGAA
1 ATGAATGAACTATTGTTGAA
* *
40153902 ATGAATGAATTACTGTTGA
1 ATGAATGAACTATTGTTGA
40153921 TACAGATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 8 0.23
20 27 0.77
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (20 bp):
ATGAATGAACTATTGTTGAA
Found at i:40153900 original size:20 final size:20
Alignment explanation
Indices: 40153875--40153920 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
40153865 GAATAAGCTA
*
40153875 TGTTGAAATGAATGAATTAT
1 TGTTGAAATGAATGAATTAC
40153895 TGTTGAAATGAATGAATTAC
1 TGTTGAAATGAATGAATTAC
40153915 TGTTGA
1 TGTTGA
40153921 TACAGATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.39
Consensus pattern (20 bp):
TGTTGAAATGAATGAATTAC
Found at i:40153932 original size:20 final size:20
Alignment explanation
Indices: 40153906--40154001 Score: 115
Period size: 20 Copynumber: 4.8 Consensus size: 20
40153896 GTTGAAATGA
40153906 ATGAATTACTGTTGA-TACAG
1 ATGAATTACTGTT-ATTACAG
* *
40153926 ATAAATTACTGTTATTACTG
1 ATGAATTACTGTTATTACAG
*
40153946 ATGAATTACTGTTATTACTG
1 ATGAATTACTGTTATTACAG
40153966 ATGAATTACTGGTTA-TACAG
1 ATGAATTACT-GTTATTACAG
*
40153986 ATGAACTACTAGTTAT
1 ATGAATTACT-GTTAT
40154002 ATGAATGAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
19 1 0.01
20 62 0.93
21 4 0.06
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (20 bp):
ATGAATTACTGTTATTACAG
Found at i:40153952 original size:60 final size:60
Alignment explanation
Indices: 40153886--40154001 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 60
40153876 GTTGAAATGA
* *
40153886 ATGAATTATTGTTGA-AATGAATGAATTACT-GTTGATACAGATAAATTACT-GTTATTACTG
1 ATGAATTACTGTT-ATAATG-ATGAATTACTGGTT-ATACAGATAAACTACTAGTTATTACTG
* *
40153946 ATGAATTACTGTTATTACTGATGAATTACTGGTTATACAGATGAACTACTAGTTAT
1 ATGAATTACTGTTA-TAATGATGAATTACTGGTTATACAGATAAACTACTAGTTAT
40154002 ATGAATGAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
59 1 0.02
60 36 0.75
61 11 0.23
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (60 bp):
ATGAATTACTGTTATAATGATGAATTACTGGTTATACAGATAAACTACTAGTTATTACTG
Found at i:40153955 original size:11 final size:11
Alignment explanation
Indices: 40153906--40153976 Score: 55
Period size: 11 Copynumber: 7.0 Consensus size: 11
40153896 GTTGAAATGA
40153906 ATGAATTACTG
1 ATGAATTACTG
* *
40153917 TTG-A-TACAG
1 ATGAATTACTG
*
40153926 ATAAATTACTG
1 ATGAATTACTG
*
40153937 -T-TATTACTG
1 ATGAATTACTG
40153946 ATGAATTACTG
1 ATGAATTACTG
*
40153957 -T-TATTACTG
1 ATGAATTACTG
40153966 ATGAATTACTG
1 ATGAATTACTG
40153977 GTTATACAGA
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
9 19 0.42
10 6 0.13
11 20 0.44
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (11 bp):
ATGAATTACTG
Found at i:40157589 original size:37 final size:37
Alignment explanation
Indices: 40157539--40157617 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
40157529 TTATTACGAA
* *
40157539 GTCTTACCCGGACATAA-TCTCCACACGAAGTTACCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCACCGG
* * *
40157576 GTCTTACTCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCACCGG
40157613 GTCTT
1 GTCTT
40157618 TAGAGCTCGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 34 0.94
38 2 0.06
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCACCGG
Found at i:40157853 original size:47 final size:47
Alignment explanation
Indices: 40157736--40158208 Score: 804
Period size: 47 Copynumber: 10.1 Consensus size: 47
40157726 CCCTTCGGGA
* * * * * * *
40157736 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
40157783 C-CGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40157829 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40157876 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40157923 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40157970 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40158017 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40158064 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40158111 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40158158 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40158205 CTTA
1 CTTA
40158209 CTATCATTTC
Statistics
Matches: 404, Mismatches: 21, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
46 37 0.09
47 367 0.91
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40167254 original size:11 final size:11
Alignment explanation
Indices: 40167238--40167262 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40167228 ATATCTAGAA
40167238 TTCTCTTCATT
1 TTCTCTTCATT
40167249 TTCTCTTCATT
1 TTCTCTTCATT
40167260 TTC
1 TTC
40167263 ATTAACTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Done.