Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 96 of 126
Found at i:29234937 original size:22 final size:22
Alignment explanation
Indices: 29234894--29234952 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
29234884 TGTAGTTTTC
29234894 TAGGTGAAAAGA-T-GGATGTGA
1 TAGGTG-AAAGATTAGGATGTGA
*
29234915 TAGGTGAAAGATTAGGATTTGA
1 TAGGTGAAAGATTAGGATGTGA
* *
29234937 TGGGTGAAAGGTTAGG
1 TAGGTGAAAGATTAGG
29234953 GTATTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.15
21 7 0.21
22 21 0.64
ACGTcount: A:0.34, C:0.00, G:0.39, T:0.27
Consensus pattern (22 bp):
TAGGTGAAAGATTAGGATGTGA
Found at i:29235207 original size:6 final size:6
Alignment explanation
Indices: 29235198--29235242 Score: 56
Period size: 6 Copynumber: 7.2 Consensus size: 6
29235188 AAAACAAAAC
29235198 AAAATA AAAATA AAAAT- AAAATA AAATAGTA AAAATA AATAATA A
1 AAAATA AAAATA AAAATA AAAATA AAA-A-TA AAAATA AA-AATA A
29235243 TAAAAGGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.14
6 18 0.51
7 7 0.20
8 5 0.14
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:29235212 original size:16 final size:15
Alignment explanation
Indices: 29235187--29235247 Score: 50
Period size: 17 Copynumber: 3.7 Consensus size: 15
29235177 GTTTCCCTGC
*
29235187 AAAAACAAAACAAAAT
1 AAAAATAAAA-AAAAT
29235203 AAAAATAAAAATAAAAT
1 AAAAAT-AAAA-AAAAT
29235220 AAAATAGTAAAAATAAAT
1 AAAA-A-TAAAAA-AAAT
*
29235238 AATAATAAAA
1 AAAAATAAAA
29235248 GGAAAATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 10 0.26
17 15 0.39
18 12 0.32
19 1 0.03
ACGTcount: A:0.79, C:0.03, G:0.02, T:0.16
Consensus pattern (15 bp):
AAAAATAAAAAAAAT
Found at i:29235244 original size:19 final size:19
Alignment explanation
Indices: 29235193--29235236 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
29235183 CTGCAAAAAC
*
29235193 AAAACAAAATAAAA-A-TA
1 AAAATAAAATAAAATAGTA
29235210 AAAATAAAATAAAATAGTA
1 AAAATAAAATAAAATAGTA
29235229 AAAATAAA
1 AAAATAAA
29235237 TAATAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.54
18 1 0.04
19 10 0.42
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (19 bp):
AAAATAAAATAAAATAGTA
Found at i:29235266 original size:29 final size:29
Alignment explanation
Indices: 29235198--29235266 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
29235188 AAAACAAAAC
* *
29235198 AAAATAAAAATAAAAATAAAATAAAATAGT
1 AAAATTAAAATAAAAATAAAAGAAAATA-T
* *
29235228 AAAAAT-AAATAATAATAAAAGGAAAAT-T
1 AAAATTAAAATAAAAATAAAA-GAAAATAT
29235256 AAAATTAAAAT
1 AAAATTAAAAT
29235267 GTGTATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 6 0.19
29 17 0.53
30 9 0.28
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (29 bp):
AAAATTAAAATAAAAATAAAAGAAAATAT
Found at i:29242472 original size:35 final size:34
Alignment explanation
Indices: 29242426--29242495 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 34
29242416 GTGGCTAGAG
29242426 GATCTTCTAGCGCCTTGACTAGTTGTTTTAAAGT
1 GATCTTCTAGCGCCTTGACTAGTTGTTTTAAAGT
*
29242460 NGATCTTCTAGCGCCTTGATTAGTTGTTTTAAAGT
1 -GATCTTCTAGCGCCTTGACTAGTTGTTTTAAAGT
29242495 G
1 G
29242496 GGAAGAAGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 1 0.03
35 33 0.97
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.41
Consensus pattern (34 bp):
GATCTTCTAGCGCCTTGACTAGTTGTTTTAAAGT
Found at i:29257120 original size:16 final size:18
Alignment explanation
Indices: 29257056--29257118 Score: 117
Period size: 18 Copynumber: 3.4 Consensus size: 18
29257046 GTCCTTATAT
29257056 AATTCATATATTTTTATTA
1 AATT-ATATATTTTTATTA
29257075 AATTATATATTTTTATTA
1 AATTATATATTTTTATTA
29257093 AATTATATATTTTTATTA
1 AATTATATATTTTTATTA
29257111 AATTATAT
1 AATTATAT
29257119 TTAATAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
18 40 0.91
19 4 0.09
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTATATATTTTTATTA
Found at i:29260144 original size:26 final size:26
Alignment explanation
Indices: 29260113--29260168 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
29260103 GCAAGAAGAG
*
29260113 ATGGAATCACTCCATAAGAATAGAAT
1 ATGGAATCACTCCATAAGAATAGAAC
*
29260139 ATGGAATCACTCTATAAGAATAGAAC
1 ATGGAATCACTCCATAAGAATAGAAC
29260165 ATGG
1 ATGG
29260169 GATCTAGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (26 bp):
ATGGAATCACTCCATAAGAATAGAAC
Found at i:29263439 original size:91 final size:90
Alignment explanation
Indices: 29263237--29263457 Score: 273
Period size: 90 Copynumber: 2.4 Consensus size: 90
29263227 TAGGTAACAT
* * * * * *
29263237 AATAATACACAAATTGATA-TCTTAGATATCACATTGAAAATTTTCAAAGTATAGGTACCGTATT
1 AATAATACACAAATTGATAGT-TTAGGTATCACATTGGATATTTTCAAAATACAGGTACCATATT
* *
29263301 GGACATTTATGAAAGTAAATGTACCA
65 AGACATTTATAAAAGTAAATGTACCA
*
29263327 AATAATAAACAAATTGATAGTTTAGGTATCACATTGGATATTTTCAAAATACAGGTACCATATTA
1 AATAATACACAAATTGATAGTTTAGGTATCACATTGGATATTTTCAAAATACAGGTACCATATTA
* **
29263392 GACCTTTTATAAAAGTACGTGTACCA
66 GA-CATTTATAAAAGTAAATGTACCA
* * * *
29263418 AATAATACACAAATTGGTAGTTCAAGTAACACATTGGATA
1 AATAATACACAAATTGATAGTTTAGGTATCACATTGGATA
29263458 ATTTATGAAA
Statistics
Matches: 112, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
90 57 0.51
91 55 0.49
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.32
Consensus pattern (90 bp):
AATAATACACAAATTGATAGTTTAGGTATCACATTGGATATTTTCAAAATACAGGTACCATATTA
GACATTTATAAAAGTAAATGTACCA
Found at i:29264324 original size:3 final size:3
Alignment explanation
Indices: 29264316--29264346 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
29264306 AAAAATGTTC
29264316 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
29264347 TATTAAGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:29269778 original size:28 final size:29
Alignment explanation
Indices: 29269747--29269807 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 29
29269737 GCTAACACAT
*
29269747 ACATAACATG-TTCACATTTAGGGTTCGC
1 ACATAACATGTTTCACATATAGGGTTCGC
*
29269775 ACAT-ACATGTTTCACATATAGGGTTTGC
1 ACATAACATGTTTCACATATAGGGTTCGC
29269803 ACATA
1 ACATA
29269808 TAGAGTTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.17
28 24 0.83
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (29 bp):
ACATAACATGTTTCACATATAGGGTTCGC
Found at i:29269807 original size:15 final size:15
Alignment explanation
Indices: 29269759--29269818 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
29269749 ATAACATGTT
* *
29269759 CACATTTAGGGTTCG
1 CACATATAGGGTTTG
* *
29269774 CACATACA-TGTTT-
1 CACATATAGGGTTTG
29269787 CACATATAGGGTTTG
1 CACATATAGGGTTTG
*
29269802 CACATATAGAGTTTG
1 CACATATAGGGTTTG
29269817 CA
1 CA
29269819 TGTAGGGTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
13 7 0.19
14 7 0.19
15 22 0.61
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (15 bp):
CACATATAGGGTTTG
Found at i:29269888 original size:24 final size:24
Alignment explanation
Indices: 29269833--29269988 Score: 72
Period size: 24 Copynumber: 6.6 Consensus size: 24
29269823 GGGTTCGCAT
*
29269833 ATAA-GGTTCGCATACTAAATCAC
1 ATAAGGGTTCGCATAATAAATCAC
* *
29269856 ATAATGGTTCGCATAATAAATTAC
1 ATAAGGGTTCGCATAATAAATCAC
** ** **
29269880 ATGGGGGTTCATATACAT-AATCGT
1 ATAAGGGTTCGCATA-ATAAATCAC
*** *
29269904 ACGGGGGTTCGAAT-ATGAAATC-C
1 ATAAGGGTTCGCATAAT-AAATCAC
* * *
29269927 ATAAGGGTTCGCATATTAAAACAA
1 ATAAGGGTTCGCATAATAAATCAC
* * *
29269951 ATAGGGGTTCTCATACTAAATC-C
1 ATAAGGGTTCGCATAATAAATCAC
29269974 ATAAGGGCTTC-CATA
1 ATAAGGG-TTCGCATA
29269989 TAGGGTTCGC
Statistics
Matches: 99, Mismatches: 27, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
22 2 0.02
23 28 0.28
24 67 0.68
25 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (24 bp):
ATAAGGGTTCGCATAATAAATCAC
Found at i:29270038 original size:59 final size:59
Alignment explanation
Indices: 29269962--29270126 Score: 210
Period size: 58 Copynumber: 2.8 Consensus size: 59
29269952 TAGGGGTTCT
* *
29269962 CATACTAAATC-CATAAGGGCTTCCATATAGGGTTCGCATAATATATAGTAAGAGATCA
1 CATACTAAATCATATAAGGGTTTCCATATAGGGTTCGCATAATATATAGTAAGAGATCA
* * * *
29270020 CATACTAAGTCATATAAGGGTTTGCATAT-GGGTTCGCATAATTTATGGTAAGAGATCA
1 CATACTAAATCATATAAGGGTTTCCATATAGGGTTCGCATAATATATAGTAAGAGATCA
* * * *
29270078 TATACTAAATCATATAAAAGATTTTCATATA-GGTTCGCATAATATATAG
1 CATACTAAATCATAT-AAGGGTTTCCATATAGGGTTCGCATAATATATAG
29270127 GGTTCACATA
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
58 50 0.55
59 41 0.45
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (59 bp):
CATACTAAATCATATAAGGGTTTCCATATAGGGTTCGCATAATATATAGTAAGAGATCA
Found at i:29270136 original size:18 final size:17
Alignment explanation
Indices: 29270104--29270149 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
29270094 AAAGATTTTC
* *
29270104 ATATAGGTTCGCATAAT
1 ATATAGGTTCACATAAG
29270121 ATATAGGGTTCACATAAG
1 ATATA-GGTTCACATAAG
29270139 ATATAAGGTTC
1 ATAT-AGGTTC
29270150 GTATTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 19 0.76
19 1 0.04
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.33
Consensus pattern (17 bp):
ATATAGGTTCACATAAG
Found at i:29270323 original size:16 final size:16
Alignment explanation
Indices: 29270302--29270347 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
29270292 TTCACCTAAG
*
29270302 GGGTTCGCATTCATAA
1 GGGTTCGCATACATAA
* *
29270318 GGGTTCACATACCTAA
1 GGGTTCGCATACATAA
*
29270334 GGGTTCGTATACAT
1 GGGTTCGCATACAT
29270348 GGGGTTTCGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (16 bp):
GGGTTCGCATACATAA
Found at i:29270356 original size:16 final size:16
Alignment explanation
Indices: 29270337--29270405 Score: 90
Period size: 16 Copynumber: 4.5 Consensus size: 16
29270327 TACCTAAGGG
29270337 TTCGTATACATGGGGT
1 TTCGTATACATGGGGT
*
29270353 TTCGTATATATGGGGT
1 TTCGTATACATGGGGT
* *
29270369 TT-GCATACATGGGGG
1 TTCGTATACATGGGGT
29270384 TTCGTATACAT-GGGT
1 TTCGTATACATGGGGT
29270399 TT-GTATA
1 TTCGTATA
29270406 ACAGATTACC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
14 5 0.11
15 17 0.37
16 24 0.52
ACGTcount: A:0.20, C:0.10, G:0.30, T:0.39
Consensus pattern (16 bp):
TTCGTATACATGGGGT
Found at i:29270369 original size:31 final size:30
Alignment explanation
Indices: 29270334--29270405 Score: 99
Period size: 31 Copynumber: 2.4 Consensus size: 30
29270324 ACATACCTAA
* * *
29270334 GGGTTCGTATACATGGGGTTTCGTATATAT
1 GGGTTTGTATACATGGGGGTTCGTATACAT
*
29270364 GGGGTTTGCATACATGGGGGTTCGTATACAT
1 -GGGTTTGTATACATGGGGGTTCGTATACAT
29270395 GGGTTTGTATA
1 GGGTTTGTATA
29270406 ACAGATTACC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 10 0.28
31 26 0.72
ACGTcount: A:0.19, C:0.10, G:0.33, T:0.38
Consensus pattern (30 bp):
GGGTTTGTATACATGGGGGTTCGTATACAT
Found at i:29272522 original size:20 final size:20
Alignment explanation
Indices: 29272499--29272536 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29272489 AAAAAATGAA
**
29272499 ATTTAAAATTAAAGTAATAT
1 ATTTAAAAGAAAAGTAATAT
29272519 ATTTAAAAGAAAAGTAAT
1 ATTTAAAAGAAAAGTAAT
29272537 TCAACATAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (20 bp):
ATTTAAAAGAAAAGTAATAT
Found at i:29278984 original size:77 final size:77
Alignment explanation
Indices: 29278857--29279048 Score: 384
Period size: 77 Copynumber: 2.5 Consensus size: 77
29278847 GAAGGCTAGG
29278857 AATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAATCAATCAATACCATTTTTACCATAGGA
1 AATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAATCAATCAATACCATTTTTACCATAGGA
29278922 CTAGGAATTGCT
66 CTAGGAATTGCT
29278934 AATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAATCAATCAATACCATTTTTACCATAGGA
1 AATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAATCAATCAATACCATTTTTACCATAGGA
29278999 CTAGGAATTGCT
66 CTAGGAATTGCT
29279011 AATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAA
1 AATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAA
29279049 GGAGAAACTT
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 115 1.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (77 bp):
AATCATCTTTAAATTGAAGTACGAGTGGGGGAAAACAATCAATCAATACCATTTTTACCATAGGA
CTAGGAATTGCT
Found at i:29279361 original size:16 final size:17
Alignment explanation
Indices: 29279335--29279367 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
29279325 TAAATTTTTA
*
29279335 GATATAAGTGATAAAGT
1 GATATAAGTGAGAAAGT
29279352 GATA-AAGTGAGAAAGT
1 GATATAAGTGAGAAAGT
29279368 AGGGGGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.24
Consensus pattern (17 bp):
GATATAAGTGAGAAAGT
Found at i:29283446 original size:20 final size:20
Alignment explanation
Indices: 29283421--29283461 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
29283411 TAGGACTAAA
* *
29283421 TAGGAAACATTTGAAAATTT
1 TAGGAAAAAGTTGAAAATTT
29283441 TAGGAAAAAGTTGAAAATTT
1 TAGGAAAAAGTTGAAAATTT
29283461 T
1 T
29283462 GGACTGTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.34
Consensus pattern (20 bp):
TAGGAAAAAGTTGAAAATTT
Found at i:29284374 original size:40 final size:40
Alignment explanation
Indices: 29284330--29284533 Score: 237
Period size: 40 Copynumber: 5.1 Consensus size: 40
29284320 CACACTAGAT
* * * * *
29284330 AGAAGCTCATAAGAGCTGATCCACCCGAAGCACACCAGAC
1 AGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAAAC
* *
29284370 AGAAGCTCATAAGAGTTGATCCAACCGTAACATGCCAAAC
1 AGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAAAC
* * **
29284410 AGAAGATCATAAGAGTTGATTCAATAGAAACACGCCAAAC
1 AGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAAAC
* * * * *
29284450 AGTAGCTCAGAAGAGCTGATCCAACTGAAACATGCCAAAC
1 AGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAAAC
* * *
29284490 AAAAGCTCATAAGAGTTGATCCAACCGTAACACGCCTAAC
1 AGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAAAC
29284530 AGAA
1 AGAA
29284534 AGTATAACAC
Statistics
Matches: 134, Mismatches: 30, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 134 1.00
ACGTcount: A:0.42, C:0.25, G:0.18, T:0.15
Consensus pattern (40 bp):
AGAAGCTCATAAGAGTTGATCCAACCGAAACACGCCAAAC
Found at i:29293359 original size:19 final size:20
Alignment explanation
Indices: 29293332--29293371 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
29293322 GTAAATACAC
* *
29293332 ATATGTTTATAAT-TGATCA
1 ATATATTTAAAATATGATCA
29293351 ATATATTTAAAATATGATCA
1 ATATATTTAAAATATGATCA
29293371 A
1 A
29293372 CATCATATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (20 bp):
ATATATTTAAAATATGATCA
Found at i:29295537 original size:26 final size:27
Alignment explanation
Indices: 29295478--29295549 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 27
29295468 TCATAGTATA
*
29295478 GTAAAAATAAAAATAAAATAATTTTCT
1 GTAAAAATAAAAATAAAATAATTTCCT
29295505 GTAAAAAT-AAAATAAAATAATTTCCT
1 GTAAAAATAAAAATAAAATAATTTCCT
* * *
29295531 TTGAAAAACAAAAAAAAAA
1 GT-AAAAATAAAAATAAAA
29295550 CTAAGATTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 18 0.46
27 13 0.33
28 8 0.21
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (27 bp):
GTAAAAATAAAAATAAAATAATTTCCT
Found at i:29295629 original size:120 final size:122
Alignment explanation
Indices: 29295475--29295708 Score: 429
Period size: 120 Copynumber: 1.9 Consensus size: 122
29295465 AGATCATAGT
*
29295475 ATAGTAAAAATAAAAATAAAATAATTTTCTGTAAAAATAAAATAAAATAATTTCCTTTGAAAAAC
1 ATAGTAAAAATAAAAATAAAACAATTTTCTGTAAAAATAAAATAAAATAATTTCCTTTGAAAAAC
29295540 -AAAAAAAAA-ACTAAGATTCAGAAATTATAAAAAAAATTAAAATTAAGGATATTATA
66 TAAAAAAAAATACTAAGATTCAGAAATTAT-AAAAAAATTAAAATTAAGGATATTATA
29295596 ATAGTAAAAAT-AAAATAAAACAATTTTCTGTAAAAATAAAATAAAATAATTTCCTTTGAAAAAC
1 ATAGTAAAAATAAAAATAAAACAATTTTCTGTAAAAATAAAATAAAATAATTTCCTTTGAAAAAC
29295660 TAAAAAAAAATACTAAGATTCAGAAATTATAAAAAAATTAAAATTAAGG
66 TAAAAAAAAATACTAAGATTCAGAAATTATAAAAAAATTAAAATTAAGG
29295709 GTAAATTAAT
Statistics
Matches: 110, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
120 52 0.47
121 39 0.35
122 19 0.17
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (122 bp):
ATAGTAAAAATAAAAATAAAACAATTTTCTGTAAAAATAAAATAAAATAATTTCCTTTGAAAAAC
TAAAAAAAAATACTAAGATTCAGAAATTATAAAAAAATTAAAATTAAGGATATTATA
Found at i:29295657 original size:26 final size:27
Alignment explanation
Indices: 29295601--29295671 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
29295591 TTATAATAGT
* *
29295601 AAAAATAAAATAAAACAATTTTCTGT-
1 AAAAATAAAATAAAATAATTTCCTGTA
*
29295627 AAAAATAAAATAAAATAATTTCCTTTGA
1 AAAAATAAAATAAAATAATTTCCTGT-A
* *
29295655 AAAACTAAAAAAAAATA
1 AAAAATAAAATAAAATA
29295672 CTAAGATTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 23 0.61
28 15 0.39
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (27 bp):
AAAAATAAAATAAAATAATTTCCTGTA
Found at i:29295823 original size:212 final size:212
Alignment explanation
Indices: 29295591--29296019 Score: 858
Period size: 212 Copynumber: 2.0 Consensus size: 212
29295581 ATTAAGGATA
29295591 TTATAATAGTAAAAATAAAATAAAACAATTTTCTGTAAAAATAAAATAAAATAATTTCCTTTGAA
1 TTATAATAGTAAAAATAAAATAAAACAATTTTCTGTAAAAATAAAATAAAATAATTTCCTTTGAA
29295656 AAACTAAAAAAAAATACTAAGATTCAGAAATTATAAAAAAATTAAAATTAAGGGTAAATTAATTT
66 AAACTAAAAAAAAATACTAAGATTCAGAAATTATAAAAAAATTAAAATTAAGGGTAAATTAATTT
29295721 TAGAAATAAGTGCTATAAAATTAATTATGTCATAATTGAAAAAAAGACTTATTAACTGTAAAGAA
131 TAGAAATAAGTGCTATAAAATTAATTATGTCATAATTGAAAAAAAGACTTATTAACTGTAAAGAA
29295786 AAGAATAGAATATTTTC
196 AAGAATAGAATATTTTC
29295803 TTATAATAGTAAAAATAAAATAAAACAATTTTCTGTAAAAATAAAATAAAATAATTTCCTTTGAA
1 TTATAATAGTAAAAATAAAATAAAACAATTTTCTGTAAAAATAAAATAAAATAATTTCCTTTGAA
29295868 AAACTAAAAAAAAATACTAAGATTCAGAAATTATAAAAAAATTAAAATTAAGGGTAAATTAATTT
66 AAACTAAAAAAAAATACTAAGATTCAGAAATTATAAAAAAATTAAAATTAAGGGTAAATTAATTT
29295933 TAGAAATAAGTGCTATAAAATTAATTATGTCATAATTGAAAAAAAGACTTATTAACTGTAAAGAA
131 TAGAAATAAGTGCTATAAAATTAATTATGTCATAATTGAAAAAAAGACTTATTAACTGTAAAGAA
29295998 AAGAATAGAATATTTTC
196 AAGAATAGAATATTTTC
29296015 TTATA
1 TTATA
29296020 TATTTAGCAC
Statistics
Matches: 217, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
212 217 1.00
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (212 bp):
TTATAATAGTAAAAATAAAATAAAACAATTTTCTGTAAAAATAAAATAAAATAATTTCCTTTGAA
AAACTAAAAAAAAATACTAAGATTCAGAAATTATAAAAAAATTAAAATTAAGGGTAAATTAATTT
TAGAAATAAGTGCTATAAAATTAATTATGTCATAATTGAAAAAAAGACTTATTAACTGTAAAGAA
AAGAATAGAATATTTTC
Found at i:29295869 original size:26 final size:27
Alignment explanation
Indices: 29295813--29295883 Score: 81
Period size: 26 Copynumber: 2.6 Consensus size: 27
29295803 TTATAATAGT
* *
29295813 AAAAATAAAATAAAACAATTTTCTGT-
1 AAAAATAAAATAAAATAATTTCCTGTA
*
29295839 AAAAATAAAATAAAATAATTTCCTTTGA
1 AAAAATAAAATAAAATAATTTCCTGT-A
* *
29295867 AAAACTAAAAAAAAATA
1 AAAAATAAAATAAAATA
29295884 CTAAGATTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 23 0.61
28 15 0.39
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (27 bp):
AAAAATAAAATAAAATAATTTCCTGTA
Found at i:29296725 original size:43 final size:43
Alignment explanation
Indices: 29296636--29296727 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
29296626 CTTGTGGTTG
* * * *
29296636 CTTCCTTTTTTGTTGTTTCTTGGTTGTGGTTGCTTCCATGTTA
1 CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTGCTTCCACGTAA
** **
29296679 CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTTTTTTTACGTAA
1 CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTGCTTCCACGTAA
29296722 CTTCCT
1 CTTCCT
29296728 CTGTCTTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.07, C:0.17, G:0.18, T:0.58
Consensus pattern (43 bp):
CTTCCTTTTTTGTCGTTTCTTGGTAGTGGTTGCTTCCACGTAA
Found at i:29297342 original size:21 final size:22
Alignment explanation
Indices: 29297304--29297345 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
29297294 AATAAATGAA
**
29297304 AAGAAAAATTTTATCCACAACC
1 AAGAAAAATTACATCCACAACC
29297326 AAGAAAAATTACA-CCACAAC
1 AAGAAAAATTACATCCACAAC
29297346 TGGCAAGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.55, C:0.24, G:0.05, T:0.17
Consensus pattern (22 bp):
AAGAAAAATTACATCCACAACC
Found at i:29312706 original size:75 final size:74
Alignment explanation
Indices: 29312623--29312762 Score: 174
Period size: 75 Copynumber: 1.9 Consensus size: 74
29312613 AATATACATA
* * * * *
29312623 CATAATCAAAACTTTCACAT-ACATATATAAATTTCATACTTAAATTCATTACAAGAACATATAC
1 CATAATC-AAAC-CTCACATAACATATATAAATGTCATACCTAAATTCAATAAAAGAACATATAC
29312687 ACATAATCTTG
64 ACATAATCTTG
* * *
29312698 CATAATCAAACCTCATATAAACTTATATAAATGTCCTACCTAAATTCAATAAAAGAACATATACA
1 CATAATCAAACCTCACAT-AACATATATAAATGTCATACCTAAATTCAATAAAAGAACATATACA
29312763 TATATGTAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
73 5 0.09
74 4 0.07
75 46 0.84
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (74 bp):
CATAATCAAACCTCACATAACATATATAAATGTCATACCTAAATTCAATAAAAGAACATATACAC
ATAATCTTG
Found at i:29313038 original size:12 final size:12
Alignment explanation
Indices: 29313021--29313074 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
29313011 CTCAAAAACT
29313021 TATATATATACA
1 TATATATATACA
*
29313033 TATATATATTCGAA
1 TATATATATAC--A
*
29313047 TATTATACATACA
1 TA-TATATATACA
29313060 TATATATATACA
1 TATATATATACA
29313072 TAT
1 TAT
29313075 CTTTGTCTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 22 0.63
13 3 0.09
14 3 0.09
15 7 0.20
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (12 bp):
TATATATATACA
Found at i:29313549 original size:15 final size:15
Alignment explanation
Indices: 29313529--29313560 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
29313519 CAAAATAAGC
29313529 TAGTTTAAATATAAT
1 TAGTTTAAATATAAT
29313544 TAGTTTAAATATAAT
1 TAGTTTAAATATAAT
29313559 TA
1 TA
29313561 CATTCAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (15 bp):
TAGTTTAAATATAAT
Found at i:29317515 original size:30 final size:30
Alignment explanation
Indices: 29317456--29317535 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
29317446 ACACAAAGTG
*
29317456 CTTGGAAACTATAA-CACTAGTACATAGTA
1 CTTGGAAACTATAATCACCAGTACATAGTA
* * *
29317485 CTTGGAAACTGTAATCACCGGTATATAGTA
1 CTTGGAAACTATAATCACCAGTACATAGTA
* *
29317515 CCTGGAAACTAAAATCACCAG
1 CTTGGAAACTATAATCACCAG
29317536 CACCTAGTGC
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 13 0.31
30 29 0.69
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (30 bp):
CTTGGAAACTATAATCACCAGTACATAGTA
Found at i:29321269 original size:6 final size:6
Alignment explanation
Indices: 29321254--29321328 Score: 87
Period size: 6 Copynumber: 12.5 Consensus size: 6
29321244 GCAAATGAAT
* * * * * *
29321254 CATTTA CATTTC CATTTT CATTTT CATTTC CATTTC CGTTTT CATTTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
*
29321302 CATTTC CATTTC CATTTT CATTTC CAT
1 CATTTC CATTTC CATTTC CATTTC CAT
29321329 ATCTAATTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.17, C:0.25, G:0.01, T:0.56
Consensus pattern (6 bp):
CATTTC
Found at i:29321276 original size:18 final size:18
Alignment explanation
Indices: 29321254--29321328 Score: 96
Period size: 18 Copynumber: 4.2 Consensus size: 18
29321244 GCAAATGAAT
* *
29321254 CATTTACATTTCCATTTT
1 CATTTTCATTTCCATTTC
29321272 CATTTTCATTTCCATTTC
1 CATTTTCATTTCCATTTC
* *
29321290 CGTTTTCATTTTCATTTC
1 CATTTTCATTTCCATTTC
* *
29321308 CATTTCCATTTTCATTTC
1 CATTTTCATTTCCATTTC
29321326 CAT
1 CAT
29321329 ATCTAATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.17, C:0.25, G:0.01, T:0.56
Consensus pattern (18 bp):
CATTTTCATTTCCATTTC
Found at i:29321281 original size:24 final size:24
Alignment explanation
Indices: 29321253--29321324 Score: 126
Period size: 24 Copynumber: 3.0 Consensus size: 24
29321243 TGCAAATGAA
*
29321253 TCATTTACATTTCCATTTTCATTT
1 TCATTTCCATTTCCATTTTCATTT
*
29321277 TCATTTCCATTTCCGTTTTCATTT
1 TCATTTCCATTTCCATTTTCATTT
29321301 TCATTTCCATTTCCATTTTCATTT
1 TCATTTCCATTTCCATTTTCATTT
29321325 CCATATCTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.17, C:0.24, G:0.01, T:0.58
Consensus pattern (24 bp):
TCATTTCCATTTCCATTTTCATTT
Found at i:29332081 original size:21 final size:21
Alignment explanation
Indices: 29332055--29332111 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
29332045 TTATCGCTTT
*
29332055 CCACACGGGCGTGTGCCTTAGA
1 CCACACGGGCGTGTGCCTCA-A
* *
29332077 -CACACGGTCGTGTTCCTCAA
1 CCACACGGGCGTGTGCCTCAA
*
29332097 CCACATGGGCGTGTG
1 CCACACGGGCGTGTG
29332112 AGTTAGCCAC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.18, C:0.32, G:0.30, T:0.21
Consensus pattern (21 bp):
CCACACGGGCGTGTGCCTCAA
Found at i:29332240 original size:21 final size:21
Alignment explanation
Indices: 29332216--29332263 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
29332206 CACATGGGCG
29332216 TGTGTCTCAGCCACACGGCCA
1 TGTGTCTCAGCCACACGGCCA
* **
29332237 TGTGCCTTTGCCACACGGCCA
1 TGTGTCTCAGCCACACGGCCA
29332258 TGTGTC
1 TGTGTC
29332264 ACTCTCCGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.35, G:0.25, T:0.25
Consensus pattern (21 bp):
TGTGTCTCAGCCACACGGCCA
Found at i:29335516 original size:3 final size:3
Alignment explanation
Indices: 29335510--29335537 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
29335500 GACCACCACA
29335510 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
29335538 CGACAATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:29350038 original size:54 final size:51
Alignment explanation
Indices: 29349902--29350059 Score: 183
Period size: 51 Copynumber: 3.0 Consensus size: 51
29349892 ATTTTTTTTG
* * * * * *
29349902 GGTGTTGGCACACTAATGGCTGGCACCCTTGTACCAGATTTTAAAAAAATT
1 GGTGCTGGGACACTAATAGCCGGCACTCTTGTACCAGATTTAAAAAAAATT
* *
29349953 GGTGCTGGGACACTAATGGCCGACA-TCCTTGTACCAGAATTTAAAAAAAAATT
1 GGTGCTGGGACACTAATAGCCGGCACT-CTTGTACCAG-ATTT-AAAAAAAATT
* *
29350006 GGATGCTGGGACACTGATAGCCGGCACTCTTGTATCAGATTTAAAAAAAATT
1 GG-TGCTGGGACACTAATAGCCGGCACTCTTGTACCAGATTTAAAAAAAATT
29350058 GG
1 GG
29350060 GGTGTCGAGA
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
51 31 0.34
52 16 0.17
53 15 0.16
54 29 0.32
55 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (51 bp):
GGTGCTGGGACACTAATAGCCGGCACTCTTGTACCAGATTTAAAAAAAATT
Found at i:29350072 original size:53 final size:52
Alignment explanation
Indices: 29349899--29350084 Score: 207
Period size: 53 Copynumber: 3.5 Consensus size: 52
29349889 AAAATTTTTT
* * * * *
29349899 TTGGGTGTTGGCACACTAATGGCTGGCACCCTTGTACCAGATTTTAAAAAAA
1 TTGGGTGCTGGGACACTAATGGCCGGCACTCTTGTACCAGATTTAAAAAAAA
*
29349951 TT-GGTGCTGGGACACTAATGGCCGACA-TCCTTGTACCAGAATTTAAAAAAAAA
1 TTGGGTGCTGGGACACTAATGGCCGGCACT-CTTGTACCAG-ATTT-AAAAAAAA
* * * *
29350004 TTGGATGCTGGGACACTGATAGCCGGCACTCTTGTATCAGATTTAAAAAAAA
1 TTGGGTGCTGGGACACTAATGGCCGGCACTCTTGTACCAGATTTAAAAAAAA
*
29350056 TTGGGGTG-TCGAGACACTAATGGCCGGCA
1 TT-GGGTGCT-GGGACACTAATGGCCGGCA
29350085 ACCACTTAGT
Statistics
Matches: 112, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
51 31 0.28
52 17 0.15
53 33 0.29
54 30 0.27
55 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (52 bp):
TTGGGTGCTGGGACACTAATGGCCGGCACTCTTGTACCAGATTTAAAAAAAA
Found at i:29353349 original size:28 final size:29
Alignment explanation
Indices: 29353325--29353385 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
29353315 CATTTTTATT
29353325 TTTTATTAC-TTTATTT-ATTTATTTTAAC
1 TTTTA-TACTTTTATTTAATTTATTTTAAC
*
29353353 TTTTATACTTTTATTTAATTTAATTTACAC
1 TTTTATACTTTTATTTAATTTATTTTA-AC
29353383 TTT
1 TTT
29353386 ATTTATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 3 0.10
28 12 0.41
29 9 0.31
30 5 0.17
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTATACTTTTATTTAATTTATTTTAAC
Found at i:29353396 original size:16 final size:15
Alignment explanation
Indices: 29353338--29353409 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 15
29353328 TATTACTTTA
29353338 TTTATTTATTTTAAC
1 TTTATTTATTTTAAC
*
29353353 TTT-TATACTTTT-A-
1 TTTATTTA-TTTTAAC
*
29353366 TTTAATTTAATTTACAC
1 TTT-ATTTATTTTA-AC
29353383 TTTATTTATTTT-AC
1 TTTATTTATTTTAAC
*
29353397 TCTATTTCATTTT
1 TTTATTT-ATTTT
29353410 GTAATAAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
13 3 0.07
14 15 0.33
15 15 0.33
16 9 0.20
17 3 0.07
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTATTTATTTTAAC
Found at i:29358428 original size:9 final size:9
Alignment explanation
Indices: 29358414--29358444 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29358404 GTTAAACGAA
29358414 TCGAGTTAT
1 TCGAGTTAT
*
29358423 TCGAGTTAA
1 TCGAGTTAT
29358432 TCGAGTTAT
1 TCGAGTTAT
29358441 TCGA
1 TCGA
29358445 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:29358762 original size:30 final size:31
Alignment explanation
Indices: 29358728--29358787 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
29358718 AAACCTTTTA
*
29358728 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
29358758 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
29358788 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:29364049 original size:20 final size:20
Alignment explanation
Indices: 29364007--29364053 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
29363997 CTACCCACAT
*
29364007 TAGGGCTCTAAATCTAGTGC
1 TAGGGCTCTAAATCTACTGC
29364027 TAGGGCTCTAAATCTGACT-C
1 TAGGGCTCTAAATCT-ACTGC
29364047 TAGGGCT
1 TAGGGCT
29364054 TGGCCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (20 bp):
TAGGGCTCTAAATCTACTGC
Found at i:29365748 original size:25 final size:24
Alignment explanation
Indices: 29365717--29365775 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
29365707 TTTGTTTATG
29365717 TTTTAATT-TTATGTGATTTAATAA
1 TTTTAATTATTATGTG-TTTAATAA
* *
29365741 TTATTAATTAATTTTGTGTTTCATAA
1 TT-TTAATT-ATTATGTGTTTAATAA
29365767 TTTTAATTA
1 TTTTAATTA
29365776 GGTACAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
25 12 0.40
26 9 0.30
27 6 0.20
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (24 bp):
TTTTAATTATTATGTGTTTAATAA
Found at i:29365751 original size:29 final size:25
Alignment explanation
Indices: 29365719--29365775 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 25
29365709 TGTTTATGTT
29365719 TTAATTTTATGTGATTTAATAATTATTAA
1 TTAA-TTT-TGTG-TTTAATAATT-TTAA
*
29365748 TTAATTTTGTGTTTCATAATTTTAA
1 TTAATTTTGTGTTTAATAATTTTAA
29365773 TTA
1 TTA
29365776 GGTACAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 7 0.26
26 9 0.33
27 4 0.15
28 3 0.11
29 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (25 bp):
TTAATTTTGTGTTTAATAATTTTAA
Found at i:29365919 original size:20 final size:20
Alignment explanation
Indices: 29365894--29365943 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
29365884 AAAAAGGCCA
29365894 AGCCCTAG-AGCCAGATTTGG
1 AGCCCTAGCA-CCAGATTTGG
*
29365914 AGCCCTAGCACTAGATTTGG
1 AGCCCTAGCACCAGATTTGG
*
29365934 AGCCCCAGCA
1 AGCCCTAGCA
29365944 TGGGTAGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.18
Consensus pattern (20 bp):
AGCCCTAGCACCAGATTTGG
Found at i:29373977 original size:16 final size:16
Alignment explanation
Indices: 29373956--29373986 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29373946 TGACGGTTCT
29373956 AAATTTAGCAAAGATG
1 AAATTTAGCAAAGATG
29373972 AAATTTAGCAAAGAT
1 AAATTTAGCAAAGAT
29373987 TGCAGAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (16 bp):
AAATTTAGCAAAGATG
Found at i:29374432 original size:24 final size:24
Alignment explanation
Indices: 29374405--29374457 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
29374395 TGCAATCGAT
*
29374405 AGGGTGAAGAGAGGAGCTGTGGAA
1 AGGGTGAAGAAAGGAGCTGTGGAA
29374429 AGGGTGAAGAAAGGAGCTGTGGAA
1 AGGGTGAAGAAAGGAGCTGTGGAA
29374453 AGGGT
1 AGGGT
29374458 TTCAAAGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.34, C:0.04, G:0.49, T:0.13
Consensus pattern (24 bp):
AGGGTGAAGAAAGGAGCTGTGGAA
Found at i:29376323 original size:168 final size:168
Alignment explanation
Indices: 29376045--29376376 Score: 601
Period size: 168 Copynumber: 2.0 Consensus size: 168
29376035 ATTTGATACG
*
29376045 CCGTGTCCTAATGTATTGGACATGACATGTTGATTCCTCGAGATGAGAATTTTTAAAATAATAAT
1 CCGTGTCCTAATGTATTGGACACGACATGTTGATTCCTCGAGATGAGAATTTTTAAAATAATAAT
* * *
29376110 AATGGCAATATTTGATATTTAGGAATTTTGTGAAATTGAGCCCTAACTTACTGGGTTTTGATTTT
66 AAAGGCAATATTCGATATTTAGGAATTTTGTGAAATCGAGCCCTAACTTACTGGGTTTTGATTTT
29376175 CTGATTTGACCCAAATGATCAGATGTCCTTCTCACACA
131 CTGATTTGACCCAAATGATCAGATGTCCTTCTCACACA
* * *
29376213 CCGTGTCCTAATGTATTGGACACGACATGTTGATTTCTTGAGATGAGAATTTTTAAAGTAATAAT
1 CCGTGTCCTAATGTATTGGACACGACATGTTGATTCCTCGAGATGAGAATTTTTAAAATAATAAT
29376278 AAAGGCAATATTCGATATTTAGGAATTTTGTGAAATCGAGCCCTAACTTACTGGGTTTTGATTTT
66 AAAGGCAATATTCGATATTTAGGAATTTTGTGAAATCGAGCCCTAACTTACTGGGTTTTGATTTT
29376343 CTGATTTGACCCAAATGATCAGATGTCCTTCTCA
131 CTGATTTGACCCAAATGATCAGATGTCCTTCTCA
29376377 AAAATGCATA
Statistics
Matches: 157, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
168 157 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (168 bp):
CCGTGTCCTAATGTATTGGACACGACATGTTGATTCCTCGAGATGAGAATTTTTAAAATAATAAT
AAAGGCAATATTCGATATTTAGGAATTTTGTGAAATCGAGCCCTAACTTACTGGGTTTTGATTTT
CTGATTTGACCCAAATGATCAGATGTCCTTCTCACACA
Found at i:29380383 original size:31 final size:32
Alignment explanation
Indices: 29380341--29380431 Score: 139
Period size: 31 Copynumber: 2.8 Consensus size: 32
29380331 GTTCAGATTC
29380341 AAAAAAAATCAAAATCAAAGTCAAAAAGAAG-
1 AAAAAAAATCAAAATCAAAGTCAAAAAGAAGA
*
29380372 AAAAAAGATCAAAATCAAAGTCAAAAAGAAGAA
1 AAAAAAAATCAAAATCAAAGTCAAAAAGAAG-A
*
29380405 AAAGAAAAACCAAAATCAAAGTCAAAA
1 AAA-AAAAATCAAAATCAAAGTCAAAA
29380432 TGAAAATGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
31 30 0.56
33 3 0.06
34 21 0.39
ACGTcount: A:0.70, C:0.11, G:0.10, T:0.09
Consensus pattern (32 bp):
AAAAAAAATCAAAATCAAAGTCAAAAAGAAGA
Found at i:29380437 original size:31 final size:31
Alignment explanation
Indices: 29380344--29380444 Score: 123
Period size: 31 Copynumber: 3.2 Consensus size: 31
29380334 CAGATTCAAA
29380344 AAAAATCAAAATCAAAGTCAAAAAGAAGAAA-
1 AAAAATCAAAATCAAAGTCAAAAAGAA-AAAG
*
29380375 AAAGATCAAAATCAAAGTCAAAAAGAAGAAAAAG
1 AAAAATCAAAATCAAAGTC--AAA-AAGAAAAAG
* * *
29380409 AAAAACCAAAATCAAAGTCAAAATGAAAATG
1 AAAAATCAAAATCAAAGTCAAAAAGAAAAAG
29380440 AAAAA
1 AAAAA
29380445 GAGAGAAGAA
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
31 30 0.49
32 3 0.05
33 6 0.10
34 22 0.36
ACGTcount: A:0.69, C:0.10, G:0.11, T:0.10
Consensus pattern (31 bp):
AAAAATCAAAATCAAAGTCAAAAAGAAAAAG
Found at i:29381365 original size:13 final size:14
Alignment explanation
Indices: 29381347--29381380 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
29381337 TTTGAGTCAA
*
29381347 AAAAATGAAAATG-
1 AAAAATGAAAAAGT
29381360 AAAAATGAAAAAGT
1 AAAAATGAAAAAGT
29381374 AAAAATG
1 AAAAATG
29381381 GAGACGCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
AAAAATGAAAAAGT
Found at i:29382770 original size:87 final size:87
Alignment explanation
Indices: 29382615--29382910 Score: 403
Period size: 87 Copynumber: 3.4 Consensus size: 87
29382605 AACAGATCAG
*
29382615 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCAAAAACAAAGCCTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTC
29382680 CATCGGTTGCAGTGGAGCGGGT
66 CATCGGTTGCAGTGGAGCGGGT
* * * * * *
29382702 TAAAAATATCAGATCTTGCCTTCCTGCATTAACAGCAAAGCATATCAAAAACAAAGACTTGCCTC
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTC
29382767 CATCGGTTGCAGTGGAGCGGGT
66 CATCGGTTGCAGTGGAGCGGGT
* * ** * *
29382789 TAAAGATAGCAGATCTTGCCTTCCTGCACTGACAGCGAAGTAGATTGAAGACACCAGCCTTGCCT
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACA-AAGCCTTGCCT
* **
29382854 CCCTCGGTTGCAGTGGAGTAGGT
65 CCATCGGTTGCAGTGGAGCGGGT
* * * *
29382877 TGAATATAGCAGATCTTGCCTTCCCGCATCGACA
1 TAAAGATAGCAGATCTTGCCTTCCTGCATTGACA
29382911 ATGAAGTAGA
Statistics
Matches: 181, Mismatches: 27, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
87 123 0.68
88 58 0.32
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (87 bp):
TAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCAAAAACAAAGCCTTGCCTC
CATCGGTTGCAGTGGAGCGGGT
Found at i:29382895 original size:44 final size:44
Alignment explanation
Indices: 29382759--29382897 Score: 120
Period size: 44 Copynumber: 3.2 Consensus size: 44
29382749 AAAACAAAGA
* ** *
29382759 CTTGCCTCCATCGGTTGCAGTGGAGCGGGTTAAAGATAGCAGAT
1 CTTGCCTCCCTCGGTTGCAGTGGAGTAGGTTGAAGATAGCAGAT
* ** * * * * * *
29382803 CTTGCCTTCCT-GCACTGACAGCGAAGTAGATTGAAGACACCAG-C
1 CTTGCCTCCCTCG-GTTG-CAGTGGAGTAGGTTGAAGATAGCAGAT
*
29382847 CTTGCCTCCCTCGGTTGCAGTGGAGTAGGTTGAATATAGCAGAT
1 CTTGCCTCCCTCGGTTGCAGTGGAGTAGGTTGAAGATAGCAGAT
29382891 CTTGCCT
1 CTTGCCT
29382898 TCCCGCATCG
Statistics
Matches: 68, Mismatches: 23, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
43 20 0.29
44 30 0.44
45 18 0.26
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.26
Consensus pattern (44 bp):
CTTGCCTCCCTCGGTTGCAGTGGAGTAGGTTGAAGATAGCAGAT
Found at i:29383298 original size:44 final size:44
Alignment explanation
Indices: 29383178--29383317 Score: 136
Period size: 44 Copynumber: 3.1 Consensus size: 44
29383168 TGTAAGGAAA
* * *
29383178 CAGATTGAAGCCGGTAATCCTATCTCCCTGAGATTACAGTGGAA
1 CAGATTGAAGCCAGTAATCCTATCTACCTGAGATTACAGTGGAG
* ** ** * * * *
29383222 TAGACCGAAGATATTCAAATCTTATCTACCTGAGATTATAGCGGAG
1 CAGATTGAAGCCAGT--AATCCTATCTACCTGAGATTACAGTGGAG
*
29383268 CAGATTGAAGCCAGTAATCCTATCTTCCTGAGATTACAGTGGAG
1 CAGATTGAAGCCAGTAATCCTATCTACCTGAGATTACAGTGGAG
*
29383312 CGGATT
1 CAGATT
29383318 AAAAGGATCT
Statistics
Matches: 71, Mismatches: 23, Indels: 4
0.72 0.23 0.04
Matches are distributed among these distances:
44 38 0.54
46 33 0.46
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
CAGATTGAAGCCAGTAATCCTATCTACCTGAGATTACAGTGGAG
Found at i:29388285 original size:16 final size:17
Alignment explanation
Indices: 29388249--29388289 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
29388239 TTTGCTAAGG
*
29388249 GAAATAAATGGAAAGAA
1 GAAAAAAATGGAAAGAA
*
29388266 GAAAAAAATGTAAA-AA
1 GAAAAAAATGGAAAGAA
29388282 GAAAAAAA
1 GAAAAAAA
29388290 GTAGGGTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (17 bp):
GAAAAAAATGGAAAGAA
Found at i:29392482 original size:18 final size:19
Alignment explanation
Indices: 29392461--29392502 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
29392451 TGGTTAATTT
29392461 TTAATTAAGCTA-GTTTAA
1 TTAATTAAGCTAGGTTTAA
*
29392479 TTAATTTAGCTATGGTTTAA
1 TTAATTAAGCTA-GGTTTAA
29392499 TTAA
1 TTAA
29392503 GCTAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
20 10 0.48
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (19 bp):
TTAATTAAGCTAGGTTTAA
Found at i:29393161 original size:9 final size:9
Alignment explanation
Indices: 29393147--29393222 Score: 59
Period size: 9 Copynumber: 8.4 Consensus size: 9
29393137 TAAACAATAT
29393147 TTTTTATAA
1 TTTTTATAA
*
29393156 TTTTTATAC
1 TTTTTATAA
29393165 TTTTTAATAA
1 TTTTT-ATAA
* *
29393175 TTTTAATAC
1 TTTTTATAA
29393184 TTTTT-T-A
1 TTTTTATAA
*
29393191 TTTTTAAATA
1 TTTTTATA-A
*
29393201 TTTTTTTGAA
1 TTTTTAT-AA
29393211 TTTTTA-AA
1 TTTTTATAA
29393219 TTTT
1 TTTT
29393223 AAAAAATTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
7 5 0.10
8 7 0.13
9 20 0.38
10 19 0.37
11 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:29393168 original size:19 final size:19
Alignment explanation
Indices: 29393142--29393191 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
29393132 AAACTTAAAC
29393142 AATA-TTTTTTATAATTTT
1 AATACTTTTTTATAATTTT
* *
29393160 TATACTTTTTAATAATTTT
1 AATACTTTTTTATAATTTT
29393179 AATACTTTTTTAT
1 AATACTTTTTTAT
29393192 TTTTAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 3 0.11
19 24 0.89
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (19 bp):
AATACTTTTTTATAATTTT
Found at i:29393187 original size:28 final size:26
Alignment explanation
Indices: 29393142--29393197 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
29393132 AAACTTAAAC
* *
29393142 AATATTTTTTATAATTTTTATACTTTTT
1 AATAATTTTAATAATTTTT-TA-TTTTT
*
29393170 AATAATTTTAATACTTTTTTATTTTT
1 AATAATTTTAATAATTTTTTATTTTT
29393196 AA
1 AA
29393198 ATATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.28
27 2 0.08
28 16 0.64
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (26 bp):
AATAATTTTAATAATTTTTTATTTTT
Found at i:29393649 original size:22 final size:21
Alignment explanation
Indices: 29393618--29393662 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
29393608 TACACCAAAA
*
29393618 TAGGCTTTTAGCGGCGCTTTTT
1 TAGGCCTTTAGCGGCG-TTTTT
29393640 TAGGCCTTTAGCGGCGTTTTT
1 TAGGCCTTTAGCGGCGTTTTT
29393661 TA
1 TA
29393663 ACGCCACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.11, C:0.18, G:0.27, T:0.44
Consensus pattern (21 bp):
TAGGCCTTTAGCGGCGTTTTT
Found at i:29393894 original size:43 final size:43
Alignment explanation
Indices: 29393733--29393937 Score: 256
Period size: 42 Copynumber: 4.8 Consensus size: 43
29393723 GCGTCGCTAA
* * *
29393733 CTTTAGCGGCGCTTTTCCCATAAACGCCGCTAAAGACCATGAT
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* *
29393776 CTTTAGCGGCGC--TTCCCTACAAATGCCACTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCC-ACAAACGCCGCTAAAGACCAAGAC
* *
29393818 CTTTAGCGGCGC-TTCCCCACAAACGTCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* * * *
29393860 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGA-TATTGAG
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCA-AGAC
29393903 CTTTAGCGGCGCTTTTTCCCACAAACGCCGCTAAA
1 CTTTAGCGGCGC-TTTTCCCACAAACGCCGCTAAA
29393938 AATATATCTT
Statistics
Matches: 141, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
41 5 0.04
42 64 0.45
43 50 0.35
44 22 0.16
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.22
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:29393965 original size:16 final size:16
Alignment explanation
Indices: 29393935--29393964 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29393925 AAACGCCGCT
29393935 AAAAATATATCTTTTA
1 AAAAATATATCTTTTA
29393951 AAAAATATAT-TTTT
1 AAAAATATATCTTTT
29393965 TTCAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAAATATATCTTTTA
Found at i:29394276 original size:43 final size:43
Alignment explanation
Indices: 29394210--29394300 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
29394200 ACATATGCAA
* * * *
29394210 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
29394253 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
29394296 -GTAAT
1 GGTAAT
29394301 GAACTCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:29398920 original size:41 final size:41
Alignment explanation
Indices: 29398863--29398982 Score: 215
Period size: 41 Copynumber: 3.0 Consensus size: 41
29398853 TCAAAAGCGG
29398863 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
*
29398904 GCATTAGCGGCGCTTATTCAAAAATGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
*
29398945 GAATTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGGCCC
1 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCC
29398983 CAAAAACTCA
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
40 22 0.29
41 54 0.71
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.18
Consensus pattern (41 bp):
GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
Found at i:29399168 original size:41 final size:40
Alignment explanation
Indices: 29399058--29399151 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
29399048 AATGCTTATT
* *
29399058 TTTAGCGGCGTTTCTA-AAAAGCGCCGCTAATGCTCGACC
1 TTTAGTGGCGTTTTTATAAAAGCGCCGCTAATGCTCGACC
* **
29399097 TTTAGTGGCGTTTTTATAAAAGCGCCGCTAATGCTTGATT
1 TTTAGTGGCGTTTTTATAAAAGCGCCGCTAATGCTCGACC
29399137 TTTAGTGGCGTTTTT
1 TTTAGTGGCGTTTTT
29399152 TGTCCAAACG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 14 0.29
40 35 0.71
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (40 bp):
TTTAGTGGCGTTTTTATAAAAGCGCCGCTAATGCTCGACC
Found at i:29399174 original size:12 final size:12
Alignment explanation
Indices: 29399157--29399182 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29399147 TTTTTTGTCC
29399157 AAACGCCGCTAA
1 AAACGCCGCTAA
29399169 AAACGCCGCTAA
1 AAACGCCGCTAA
29399181 AA
1 AA
29399183 GCCTATTTTG
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:29399288 original size:21 final size:21
Alignment explanation
Indices: 29399247--29399294 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
29399237 ATTATTGTAC
* *
29399247 GTATATTTCTAATATTATATT
1 GTATATTTCTAACAATATATT
29399268 GTATATTTCTAACACAT-TATT
1 GTATATTTCTAACA-ATATATT
*
29399289 ATATAT
1 GTATAT
29399295 ATATACTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.52
Consensus pattern (21 bp):
GTATATTTCTAACAATATATT
Found at i:29411177 original size:93 final size:93
Alignment explanation
Indices: 29411067--29412025 Score: 1857
Period size: 93 Copynumber: 10.3 Consensus size: 93
29411057 GCCCCTAAGT
* * *
29411067 GAACTC-AGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGA-ACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
29411131 ACGAGTTTGGATGCCTAGTTACATCTCAC
65 ACGAGTTTGGATGCCTAGTTACATCTCAC
29411160 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29411225 CGAGTTTGGATGCCTAGTTACATCTCAC
66 CGAGTTTGGATGCCTAGTTACATCTCAC
29411253 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29411318 CGAGTTTGGATGCCTAGTTACATCTCAC
66 CGAGTTTGGATGCCTAGTTACATCTCAC
29411346 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29411411 CGAGTTTGGATGCCTAGTTACATCTCAC
66 CGAGTTTGGATGCCTAGTTACATCTCAC
29411439 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29411504 CGAGTTTGGATGCCTAGTTACATCTCAC
66 CGAGTTTGGATGCCTAGTTACATCTCAC
29411532 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29411597 CGAGTTTGGATGCCTAGTTACATCTCAC
66 CGAGTTTGGATGCCTAGTTACATCTCAC
29411625 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29411690 CGAGTTTGGATGCCTAGTTACATCTCAC
66 CGAGTTTGGATGCCTAGTTACATCTCAC
29411718 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29411783 CGAGTTTGGATGCCTAGTTACATCTCAC
66 CGAGTTTGGATGCCTAGTTACATCTCAC
29411811 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29411876 CGAGTTTGGATGCCTAGTTACATCTCAC
66 CGAGTTTGGATGCCTAGTTACATCTCAC
29411904 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
29411969 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTTGGATGCCTAGTTACATCTCAC
*
29411997 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGAACTCAACTCAACGAGTTCGGA
29412026 TGCTCAACCA
Statistics
Matches: 860, Mismatches: 5, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
93 859 1.00
94 1 0.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (93 bp):
GAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTTGGATGCCTAGTTACATCTCAC
Found at i:29412485 original size:30 final size:30
Alignment explanation
Indices: 29412451--29412510 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
29412441 ATTTAATACG
29412451 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
29412481 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
29412511 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:29416666 original size:15 final size:15
Alignment explanation
Indices: 29416642--29416693 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
29416632 ACACTAAAAC
*
29416642 ATAT-AAACAAGGAA
1 ATATAAAACAAAGAA
*
29416656 ATATAAAACAAATAA
1 ATATAAAACAAAGAA
* *
29416671 ATAAAAAACAAAAAAA
1 ATATAAAAC-AAAGAA
29416687 ATATAAA
1 ATATAAA
29416694 GTTTTACCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 4 0.13
15 16 0.52
16 11 0.35
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (15 bp):
ATATAAAACAAAGAA
Found at i:29417451 original size:23 final size:25
Alignment explanation
Indices: 29417406--29417471 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 25
29417396 TATTTTTGTA
* **
29417406 TGTATACTATCCTATATTTATATTCT
1 TGTATACTA-CATATATACATATTCT
*
29417432 TG-ATACTAC-TATATACATATTTT
1 TGTATACTACATATATACATATTCT
*
29417455 TGTATATTACATATATA
1 TGTATACTACATATATA
29417472 TGTTTTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 13 0.38
24 7 0.21
25 12 0.35
26 2 0.06
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (25 bp):
TGTATACTACATATATACATATTCT
Found at i:29419008 original size:24 final size:24
Alignment explanation
Indices: 29418980--29419028 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
29418970 CCAAAATAAC
29418980 AATTAATTTTTATATAAACTTTTA
1 AATTAATTTTTATATAAACTTTTA
29419004 AATTAATTTTTATATAAACTTTTA
1 AATTAATTTTTATATAAACTTTTA
29419028 A
1 A
29419029 CAAATATACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
AATTAATTTTTATATAAACTTTTA
Found at i:29419026 original size:12 final size:12
Alignment explanation
Indices: 29418987--29419027 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
29418977 AACAATTAAT
29418987 TTTTATATAAAC
1 TTTTATATAAAC
* * *
29418999 TTTTAAATTAAT
1 TTTTATATAAAC
29419011 TTTTATATAAAC
1 TTTTATATAAAC
29419023 TTTTA
1 TTTTA
29419028 ACAAATATAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (12 bp):
TTTTATATAAAC
Found at i:29419690 original size:41 final size:41
Alignment explanation
Indices: 29419633--29419850 Score: 330
Period size: 41 Copynumber: 5.3 Consensus size: 41
29419623 GTTATATGAC
* *
29419633 TTTTAGTGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTAGT
* *
29419674 TTTTAGCGGCGTTTTACCAAAAGCGCGGCTAATGCTCTATT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTAGT
* * * * *
29419715 TTTTGGCAGCGTTTTACCAAAAGCGCCCCTAATGTTCTATT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTAGT
* *
29419756 TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTAGT
29419797 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTA-T
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTAGT
29419837 TTTTAGCGGCGTTT
1 TTTTAGCGGCGTTT
29419851 CGAAATTGCT
Statistics
Matches: 159, Mismatches: 18, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 15 0.09
41 144 0.91
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.35
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTAGT
Found at i:29421948 original size:31 final size:32
Alignment explanation
Indices: 29421875--29421954 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
29421865 AAATTTTAGT
* *
29421875 TTGTTGGATTTTGAAATTATTATGTCTGGAAT
1 TTGTTGGATATTGAAATTATTATGTCTGGAAC
* * *
29421907 TTGTTAGATATTGAATTTATTATGT-T-TAAGC
1 TTGTTGGATATTGAAATTATTATGTCTGGAA-C
29421938 TTGTTGGATATTGAAAT
1 TTGTTGGATATTGAAAT
29421955 AATTGACAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 2 0.05
31 16 0.40
32 22 0.55
ACGTcount: A:0.28, C:0.03, G:0.20, T:0.50
Consensus pattern (32 bp):
TTGTTGGATATTGAAATTATTATGTCTGGAAC
Found at i:29422711 original size:17 final size:16
Alignment explanation
Indices: 29422679--29422734 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 16
29422669 TAAAAAATAG
*
29422679 AAATTAAAAATCAAAAA
1 AAATAAAAAAT-AAAAA
29422696 TAAATAAAAAATAAAAA
1 -AAATAAAAAATAAAAA
29422713 AAA-ACACACAAATAAAAA
1 AAATA-A-A-AAATAAAAA
29422731 AAAT
1 AAAT
29422735 CTACATACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
15 1 0.03
16 4 0.12
17 6 0.18
18 22 0.67
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (16 bp):
AAATAAAAAATAAAAA
Found at i:29428839 original size:15 final size:16
Alignment explanation
Indices: 29428819--29428857 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
29428809 TAAGGTTTTA
29428819 AGGGTTTTTAT-AGTT
1 AGGGTTTTTATAAGTT
*
29428834 AGGGTTTTTTATAATTT
1 AGGG-TTTTTATAAGTT
29428851 AGGGTTT
1 AGGGTTT
29428858 ATGGTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 10 0.48
17 7 0.33
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.54
Consensus pattern (16 bp):
AGGGTTTTTATAAGTT
Found at i:29428844 original size:16 final size:17
Alignment explanation
Indices: 29428819--29428857 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
29428809 TAAGGTTTTA
29428819 AGGG-TTTTTAT-AGTT
1 AGGGTTTTTTATAAGTT
*
29428834 AGGGTTTTTTATAATTT
1 AGGGTTTTTTATAAGTT
29428851 AGGGTTT
1 AGGGTTT
29428858 ATGGTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 7 0.33
17 10 0.48
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.54
Consensus pattern (17 bp):
AGGGTTTTTTATAAGTT
Found at i:29428887 original size:24 final size:25
Alignment explanation
Indices: 29428833--29428890 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
29428823 TTTTTATAGT
*
29428833 TAGGG-TTTTTTATAATTTAGGGTT
1 TAGGGTTTTTTTATAATTTAGGGTA
* **
29428857 TATGGTTTTTTTATGTTTTAGGG-A
1 TAGGGTTTTTTTATAATTTAGGGTA
29428881 TAGGGTTTTT
1 TAGGGTTTTT
29428891 AGGATTTAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.17, C:0.00, G:0.26, T:0.57
Consensus pattern (25 bp):
TAGGGTTTTTTTATAATTTAGGGTA
Found at i:29428898 original size:22 final size:22
Alignment explanation
Indices: 29428864--29428910 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
29428854 GTTTATGGTT
* *
29428864 TTTTTATGTTTTAGGGATAGGG
1 TTTTTAGGATTTAGGGATAGGG
* *
29428886 TTTTTAGGATTTAGGGTTGGGG
1 TTTTTAGGATTTAGGGATAGGG
29428908 TTT
1 TTT
29428911 ATAAAAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.34, T:0.51
Consensus pattern (22 bp):
TTTTTAGGATTTAGGGATAGGG
Found at i:29429027 original size:16 final size:17
Alignment explanation
Indices: 29428998--29429030 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
29428988 ATTAGGGTTA
29428998 ATTGATTAAAATTAGGG
1 ATTGATTAAAATTAGGG
29429015 ATTGATT-AAATTAGGG
1 ATTGATTAAAATTAGGG
29429031 TTTAAGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.36
Consensus pattern (17 bp):
ATTGATTAAAATTAGGG
Found at i:29430223 original size:26 final size:26
Alignment explanation
Indices: 29430187--29430238 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
29430177 TACCCAACCC
29430187 CTACACGACACTCCGTTAGTGGATGG
1 CTACACGACACTCCGTTAGTGGATGG
*
29430213 CTACACGACACTCTGTTAGTGGATGG
1 CTACACGACACTCCGTTAGTGGATGG
29430239 GACATGTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (26 bp):
CTACACGACACTCCGTTAGTGGATGG
Found at i:29433142 original size:18 final size:18
Alignment explanation
Indices: 29433121--29433155 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29433111 AAAAGGAAAC
*
29433121 ATATAAGGGTTAGGATAT
1 ATATAAGGGCTAGGATAT
29433139 ATATAAGGGCTAGGATA
1 ATATAAGGGCTAGGATA
29433156 CGCACCTAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.29, T:0.29
Consensus pattern (18 bp):
ATATAAGGGCTAGGATAT
Found at i:29434808 original size:48 final size:46
Alignment explanation
Indices: 29434754--29434888 Score: 164
Period size: 48 Copynumber: 2.8 Consensus size: 46
29434744 ATGCAAACAT
29434754 CATAAATGAAAAAAAAATCAAGTAGTATTGAAATTTTAATTATAA-TTG
1 CATAAATGAAAAAAAAATCAA-TAGTATTGAAA-TTTAATTA-AATTTG
*
29434802 CATAAATGAAAAAAATATCAAATAGTATTGCAAATTTAATTAAATTTG
1 CATAAATGAAAAAAAAATC-AATAGTATTG-AAATTTAATTAAATTTG
* * *
29434850 CGTAAATTAAGAAAAAATCGAATAGTATTGAAAATTTAA
1 CATAAATGAAAAAAAAATC-AATAGTATTG-AAATTTAA
29434889 AATTATCACT
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
47 2 0.03
48 70 0.91
49 5 0.06
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (46 bp):
CATAAATGAAAAAAAAATCAATAGTATTGAAATTTAATTAAATTTG
Found at i:29435068 original size:21 final size:23
Alignment explanation
Indices: 29435022--29435070 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
29435012 TTAAACAAAT
*
29435022 AAAA-TTGTTAGAATTTTTGTAG
1 AAAATTTGATAGAATTTTTGTAG
29435044 -AAATTTGATAGAA-TTTTG-AG
1 AAAATTTGATAGAATTTTTGTAG
29435064 AAAATTT
1 AAAATTT
29435071 CAATGAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 14 0.58
22 8 0.33
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (23 bp):
AAAATTTGATAGAATTTTTGTAG
Found at i:29436837 original size:144 final size:144
Alignment explanation
Indices: 29436673--29437088 Score: 656
Period size: 144 Copynumber: 2.9 Consensus size: 144
29436663 AACAGTCTTG
*
29436673 TTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTCGTTGTACCTTTAAAGCAAC
1 TTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTCGTTGTACCTTCAAAGCAAC
* * * * *
29436738 AAACTTAATGGATCTATTCCACAAGAAATTGGTAGATTAAGGAATTTGGTTGCATTCGATCTATC
66 CAACTTAATGGATCCATTCCACAAGAAATTGGGAGACTAAAGAATTTGGTTGCATTCGATCTATC
29436803 CTACAATAGGCTTA
131 CTACAATAGGCTTA
*
29436817 TTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTCGTTGTTCCTTCAAAGCAAC
1 TTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTCGTTGTACCTTCAAAGCAAC
* *
29436882 CAACTTAATGGATCCATTCCACAAGAAATTGGGAGCCTAAAGAATTTGGTTGC-TCTGGATCTAT
66 CAACTTAATGGATCCATTCCACAAGAAATTGGGAGACTAAAGAATTTGGTTGCAT-TCGATCTAT
* * *
29436946 CCTCCAATAGTCTTG
130 CCTACAATAGGCTTA
* * *
29436961 TTGGTCCAATCCCATCTTCTATCAGCAACTTAACTAATCATGCCTCGTTGTACCTTCAAAGCAAC
1 TTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTCGTTGTACCTTCAAAGCAAC
* *
29437026 CAAC-TAATGGATCCATCCCACAAGAAATTGGGAGACTAAAGAATTTGGTTGCATTTGATCTAT
66 CAACTTAATGGATCCATTCCACAAGAAATTGGGAGACTAAAGAATTTGGTTGCATTCGATCTAT
29437089 AGACTAAGGA
Statistics
Matches: 251, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
143 55 0.22
144 196 0.78
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (144 bp):
TTGGTCCAATCCCATCTTCTGTCAGCAACTTAACCAATCTTGCCTCGTTGTACCTTCAAAGCAAC
CAACTTAATGGATCCATTCCACAAGAAATTGGGAGACTAAAGAATTTGGTTGCATTCGATCTATC
CTACAATAGGCTTA
Found at i:29437093 original size:31 final size:31
Alignment explanation
Indices: 29437058--29437119 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
29437048 AGAAATTGGG
*
29437058 AGACTAAAGAATTTGGTTGCATTTGATCTAT
1 AGACTAAAGAATTTGGTTGCATTCGATCTAT
*
29437089 AGACTAAGGAATTTGGTTGCATTCGATCTAT
1 AGACTAAAGAATTTGGTTGCATTCGATCTAT
29437120 CCTACAGTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.37
Consensus pattern (31 bp):
AGACTAAAGAATTTGGTTGCATTCGATCTAT
Found at i:29437349 original size:144 final size:144
Alignment explanation
Indices: 29437089--29437421 Score: 463
Period size: 144 Copynumber: 2.3 Consensus size: 144
29437079 TTTGATCTAT
* *
29437089 AGACTAAGGAATTTGGTTGCATTCGATCTATCCTACAGTAGGCTTGTTGGTCCAATCCCATCTTC
1 AGACTAAGGAATTTGGTTGCATTGGATCTATCCTACAATAGGCTTGTTGGTCCAATCCCATCTTC
* * *
29437154 TGTCAGCAACTTAACCAATCTTGCCTCGCTGTTCCTTCAAAGCAACAAACTTAATGGATGCATTC
66 TGTCAGCAACTTAACCAATCTTACCTCGCTGCTCCTTCAAAGCAACAAACTTAATGGATCCATTC
29437219 CA-AATGAAATTAGA
131 CACAA-GAAATTAGA
* *
29437233 AGACTAAGGAATTTGGTTGAATTGGATCTATCCT-CTAATAGTCTTGTTGGTCCAATCCCATCTT
1 AGACTAAGGAATTTGGTTGCATTGGATCTATCCTAC-AATAGGCTTGTTGGTCCAATCCCATCTT
* * * * * *
29437297 TTGTCAGCTACTTAACCGATCTTACCTCGTTGCTCCTTCAATGCAACAAACTTAATGGATCCGTT
65 CTGTCAGCAACTTAACCAATCTTACCTCGCTGCTCCTTCAAAGCAACAAACTTAATGGATCCATT
* * *
29437362 CCACAAGAGATTGGG
130 CCACAAGAAATTAGA
* * *
29437377 AGACTAACGAATTTGGTTGCATTGGATCTATCTTTCAATAGGCTT
1 AGACTAAGGAATTTGGTTGCATTGGATCTATCCTACAATAGGCTT
29437422 TCAGGTCACA
Statistics
Matches: 166, Mismatches: 20, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
143 1 0.01
144 162 0.98
145 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (144 bp):
AGACTAAGGAATTTGGTTGCATTGGATCTATCCTACAATAGGCTTGTTGGTCCAATCCCATCTTC
TGTCAGCAACTTAACCAATCTTACCTCGCTGCTCCTTCAAAGCAACAAACTTAATGGATCCATTC
CACAAGAAATTAGA
Found at i:29452845 original size:26 final size:26
Alignment explanation
Indices: 29452816--29452870 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
29452806 AGGCCCATAA
29452816 GTCTTTATAATGTTATTTACAAAATT
1 GTCTTTATAATGTTATTTACAAAATT
*
29452842 GTCTTTGTAATGTTATTTACAAAATT
1 GTCTTTATAATGTTATTTACAAAATT
29452868 GTC
1 GTC
29452871 GTGAAAGTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (26 bp):
GTCTTTATAATGTTATTTACAAAATT
Found at i:29471952 original size:43 final size:45
Alignment explanation
Indices: 29471880--29472002 Score: 128
Period size: 43 Copynumber: 2.8 Consensus size: 45
29471870 ATCGAGATGC
* *** * *
29471880 GATTACATGTAAGACCATGTCTAAAACATTGGCATTG-T-ATTGA
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAATCGA
*
29471923 GATTACGTGTAAGAACATGTCTGGGACATTGGCATCGTTAATCGA
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAATCGA
* * *
29471968 G-TT-CGTGTAAGACCCTGTCTGGGATAGTGGCATCG
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCG
29472003 ATATGGGTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
43 59 0.88
44 3 0.04
45 5 0.07
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (45 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAATCGA
Found at i:29480218 original size:15 final size:15
Alignment explanation
Indices: 29480178--29480223 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
29480168 TTTTTACAAA
29480178 TAATATCTA-ATTATT
1 TAATATCTATA-TATT
*
29480193 T-GTATCATATATATT
1 TAATATC-TATATATT
29480208 TAATATCTATATATT
1 TAATATCTATATATT
29480223 T
1 T
29480224 CCAACAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 4 0.15
15 17 0.65
16 5 0.19
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (15 bp):
TAATATCTATATATT
Found at i:29483368 original size:10 final size:11
Alignment explanation
Indices: 29483348--29483372 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29483338 TGCCAATTTC
29483348 TTTCTTTTTTT
1 TTTCTTTTTTT
29483359 TTTCTTTTTTT
1 TTTCTTTTTTT
29483370 TTT
1 TTT
29483373 ATTATCAAAC
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:29483607 original size:31 final size:32
Alignment explanation
Indices: 29483561--29483625 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
29483551 TTATTTATAC
29483561 TTTTATAATTTTAAAA-AGATTAAA-T-TAATT
1 TTTTATAATTTTAAAAGAGA-TAAAGTATAATT
*
29483591 TTTTATCATTTTTAAAAGAGATAAAGTATAATT
1 TTTTAT-AATTTTAAAAGAGATAAAGTATAATT
29483624 TT
1 TT
29483626 ATTTTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 6 0.20
31 13 0.43
32 4 0.13
33 7 0.23
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (32 bp):
TTTTATAATTTTAAAAGAGATAAAGTATAATT
Found at i:29483898 original size:34 final size:35
Alignment explanation
Indices: 29483860--29483927 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
29483850 TTCAATTTTA
29483860 GAAAGTGAT-AATTATCATTCAATAAATACATTTC
1 GAAAGTGATAAATTATCATTCAATAAATACATTTC
* **
29483894 GAAAGTGATAAATTATTATTCAATGGATACATTT
1 GAAAGTGATAAATTATCATTCAATAAATACATTT
29483928 TCATGAGACA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 9 0.30
35 21 0.70
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.37
Consensus pattern (35 bp):
GAAAGTGATAAATTATCATTCAATAAATACATTTC
Found at i:29500376 original size:16 final size:16
Alignment explanation
Indices: 29500356--29500394 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
29500346 TGAGGTAGGA
29500356 CTGTAATTGAATAGAG
1 CTGTAATTGAATAGAG
*
29500372 TTGTAATTGAATAGAG
1 CTGTAATTGAATAGAG
29500388 CTGTAAT
1 CTGTAAT
29500395 CAGTAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (16 bp):
CTGTAATTGAATAGAG
Found at i:29502369 original size:21 final size:19
Alignment explanation
Indices: 29502327--29502369 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
29502317 TTTTATTTGG
**
29502327 AACTGTAGTAATTTCAGTT
1 AACTGTAGTAATTTCAAAT
29502346 AACTGTAGTAATCCTTCAAAT
1 AACTGTAGTAAT--TTCAAAT
29502367 AAC
1 AAC
29502370 CTTATTACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.60
21 8 0.40
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (19 bp):
AACTGTAGTAATTTCAAAT
Found at i:29506824 original size:46 final size:45
Alignment explanation
Indices: 29506757--29507097 Score: 200
Period size: 46 Copynumber: 7.8 Consensus size: 45
29506747 ATTATACAGG
*
29506757 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAA-TTCAGA
* * * *
29506803 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAGGATAGT-A-A
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGA-ATTCAGA
* * * * * *
29506847 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG------GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCAGA
* * * *
29506886 TCTTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--A-CA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGAATTCAGA
*
29506927 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAA-TTCAGA
* * * *
29506973 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCA-GA
* * * * **
29507016 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGAT-TAA-AATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGATCAAAGAAT-TCAGA
* * * *
29507060 TCTTATCTCCCTGAGATTATAGCGGAGCAGATCGAAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGA
29507098 CACTATCTTA
Statistics
Matches: 228, Mismatches: 42, Indels: 50
0.71 0.13 0.16
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 23 0.10
40 1 0.00
41 27 0.12
42 7 0.03
43 29 0.13
44 59 0.26
45 6 0.03
46 73 0.32
47 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (45 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCAGA
Found at i:29507037 original size:43 final size:43
Alignment explanation
Indices: 29506927--29507130 Score: 164
Period size: 43 Copynumber: 4.7 Consensus size: 43
29506917 TCACATCAGG
* * * * *
29506927 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA---C-TA
29506973 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
* * * * * * **
29507016 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGAT-TAAAATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCGAAGA-CA-CTA
*
29507060 TCTTATCTCCCTGAGATTATAGCGGAGCAGATCGAAGACACTA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
* *
29507103 TCTTATCTCCCCGA-AGTTACAGTGGAGC
1 TCTTATCTCCCTGAGA-TTACAGCGGAGC
29507131 GGATTAAAGG
Statistics
Matches: 126, Mismatches: 25, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
42 5 0.04
43 53 0.42
44 29 0.23
45 4 0.03
46 34 0.27
47 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
Found at i:29507061 original size:87 final size:83
Alignment explanation
Indices: 29506970--29507175 Score: 306
Period size: 87 Copynumber: 2.4 Consensus size: 83
29506960 AAAGAATTTC
*
29506970 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCCGAAGTTA
29507035 CAGTGGAGCGGATTAAAATAAG
66 CAGTGGAGCGGATT---A-AAG
* *
29507057 AGATCTTATCTCCCTGAGATTATAGCGGAGCAGATCGAAGACACTATCTTATCTCCCCGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCCGAAGTTA
29507122 CAGTGGAGCGGATTAAAG
66 CAGTGGAGCGGATTAAAG
* * * *
29507140 -GATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCG
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCG
29507176 CATCAAGTCT
Statistics
Matches: 111, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
82 31 0.28
83 3 0.03
84 1 0.01
87 76 0.68
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (83 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCCGAAGTTA
CAGTGGAGCGGATTAAAG
Found at i:29507073 original size:44 final size:42
Alignment explanation
Indices: 29506970--29507163 Score: 119
Period size: 43 Copynumber: 4.6 Consensus size: 42
29506960 AAAGAATTTC
* * * * *
29506970 AGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAGACA
1 AGATCTTATCTCCCTGAAG-TTACAGTGGAGCGGAT-TAAAAAA
** *
29507013 CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAA
1 AGATCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAA-AA
* * * * * *
29507056 GAGATCTTATCTCCCTG-AGATTATAGCGGAGCAGATCGAAGACA
1 -AGATCTTATCTCCCTGAAG-TTACAGTGGAGCGGAT-TAAAAAA
** *
29507100 CTATCTTATCTCCCCGAAGTTACAGTGGAGCGGATT---AAA
1 AGATCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAAA
* * *
29507139 GGATCTTATCTCTCTGAGGTTACAG
1 AGATCTTATCTCCCTGAAGTTACAG
29507164 CAGAGTAGAT
Statistics
Matches: 115, Mismatches: 30, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
39 22 0.19
42 3 0.03
43 56 0.49
44 31 0.27
45 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (42 bp):
AGATCTTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAAA
Found at i:29508239 original size:3 final size:3
Alignment explanation
Indices: 29508173--29508230 Score: 64
Period size: 3 Copynumber: 19.3 Consensus size: 3
29508163 GTACTTTTGC
* * *
29508173 TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT TAT TAT CAT CT-T TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
*
29508218 TAT TAT TAG TAT T
1 TAT TAT TAT TAT T
29508231 GGTATTATTG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 1 0.02
3 44 0.98
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:29508687 original size:18 final size:18
Alignment explanation
Indices: 29508666--29508702 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29508656 TACACCTATA
*
29508666 TATATATGTACATATTTT
1 TATATATATACATATTTT
*
29508684 TATATATATGCATATTTT
1 TATATATATACATATTTT
29508702 T
1 T
29508703 TTTCTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (18 bp):
TATATATATACATATTTT
Found at i:29508689 original size:20 final size:18
Alignment explanation
Indices: 29508664--29508702 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
29508654 TATACACCTA
29508664 TATATATATGTACATATTTT
1 TATATATATG--CATATTTT
29508684 TATATATATGCATATTTT
1 TATATATATGCATATTTT
29508702 T
1 T
29508703 TTTCTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (18 bp):
TATATATATGCATATTTT
Found at i:29516368 original size:18 final size:16
Alignment explanation
Indices: 29516334--29516366 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29516324 TATATATATA
29516334 TATATATACATATTTT
1 TATATATACATATTTT
*
29516350 TATATATGCATATTTT
1 TATATATACATATTTT
29516366 T
1 T
29516367 TTTATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
TATATATACATATTTT
Found at i:29517807 original size:17 final size:17
Alignment explanation
Indices: 29517785--29517819 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29517775 TTTTCCTCTC
29517785 TTTTTTTAA-ATATTTAT
1 TTTTTTTAACAT-TTTAT
29517802 TTTTTTTAACATTTTAT
1 TTTTTTTAACATTTTAT
29517819 T
1 T
29517820 AGACCTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTTAACATTTTAT
Found at i:29522523 original size:25 final size:24
Alignment explanation
Indices: 29522487--29522558 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 24
29522477 AGGTAATAAA
29522487 TTTTATAA-AATTTTAAAAATTATAT
1 TTTTA-AATAATTTT-AAAATTATAT
29522512 TTTTAAATAA-TTT--AATTATAT
1 TTTTAAATAATTTTAAAATTATAT
**
29522533 TTTTATTTAATTTTAAGAATTATAT
1 TTTTAAATAATTTTAA-AATTATAT
29522558 T
1 T
29522559 AATTGATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
21 16 0.40
22 3 0.08
24 5 0.12
25 16 0.40
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (24 bp):
TTTTAAATAATTTTAAAATTATAT
Found at i:29522887 original size:31 final size:31
Alignment explanation
Indices: 29522849--29522908 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
29522839 GTTTAAGAAA
* * * *
29522849 CCCTTATTTGAGCATTTTTTAAAATGTTTGG
1 CCCTTATTTGAACACTTTTAAAAAGGTTTGG
29522880 CCCTTATTTGAACACTTTTAAAAAGGTTT
1 CCCTTATTTGAACACTTTTAAAAAGGTTT
29522909 ATCTTTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (31 bp):
CCCTTATTTGAACACTTTTAAAAAGGTTTGG
Found at i:29527404 original size:13 final size:13
Alignment explanation
Indices: 29527386--29527410 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29527376 TACAAAACAT
29527386 CAAGCCCAAATTA
1 CAAGCCCAAATTA
29527399 CAAGCCCAAATT
1 CAAGCCCAAATT
29527411 TAAAACCTAT
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:0.44, C:0.32, G:0.08, T:0.16
Consensus pattern (13 bp):
CAAGCCCAAATTA
Found at i:29529614 original size:22 final size:21
Alignment explanation
Indices: 29529583--29529627 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
29529573 TACACCAAAA
*
29529583 TAGGCTTTTAGCGGCGCTTTTT
1 TAGGCCTTTAGCGGCG-TTTTT
29529605 TAGGCCTTTAGCGGCGTTTTT
1 TAGGCCTTTAGCGGCGTTTTT
29529626 TA
1 TA
29529628 ACGCCACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.11, C:0.18, G:0.27, T:0.44
Consensus pattern (21 bp):
TAGGCCTTTAGCGGCGTTTTT
Found at i:29529859 original size:43 final size:43
Alignment explanation
Indices: 29529698--29529902 Score: 256
Period size: 42 Copynumber: 4.8 Consensus size: 43
29529688 GCGTCGCTAA
* * *
29529698 CTTTAGCGGCGCTTTTCCCATAAACGCCGCTAAAGACCATGAT
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* *
29529741 CTTTAGCGGCGC--TTCCCTACAAATGCCACTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCC-ACAAACGCCGCTAAAGACCAAGAC
* *
29529783 CTTTAGCGGCGC-TTCCCCACAAACGTCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
* * * *
29529825 CTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGA-TATTGAG
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCA-AGAC
29529868 CTTTAGCGGCGCTTTTTCCCACAAACGCCGCTAAA
1 CTTTAGCGGCGC-TTTTCCCACAAACGCCGCTAAA
29529903 AATATATCGT
Statistics
Matches: 141, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
41 5 0.04
42 64 0.45
43 50 0.35
44 22 0.16
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.22
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
Found at i:29530237 original size:43 final size:43
Alignment explanation
Indices: 29530171--29530261 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
29530161 ATATATGCAA
* * * *
29530171 GGTAATAAAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
29530214 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
29530257 -GTAAT
1 GGTAAT
29530262 GAACTCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 5 0.12
43 38 0.88
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:29535181 original size:41 final size:41
Alignment explanation
Indices: 29535124--29535368 Score: 382
Period size: 41 Copynumber: 6.0 Consensus size: 41
29535114 TCAAAAGCGG
* *
29535124 GCATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGGCCCAA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
*
29535165 GCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
*
29535206 GCATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
* *
29535247 GCATTAGCGGCGCTTCTTCACAAACGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
* * *
29535288 GCATTAGTGGCGCTTATTCAAAAACGCCGCTAAAGGCCCGT
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
* *
29535329 GAATTAGCGGCGCTTTTTTTAAAAACGCCGCTAAAGGCCC
1 GCATTAGCGGCGC-TTTTTCAAAAACGCCGCTAAAGGCCC
29535369 CAAAACTCAG
Statistics
Matches: 188, Mismatches: 15, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
41 164 0.87
42 24 0.13
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (41 bp):
GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGA
Found at i:29535550 original size:41 final size:41
Alignment explanation
Indices: 29535422--29535554 Score: 141
Period size: 40 Copynumber: 3.3 Consensus size: 41
29535412 CACTTTTTGG
* **
29535422 AAAA-CGCCGGTAATGCTT-ATTTTTAGCGGCGTTTTCCA-
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTAT
* ** *
29535460 AAAAGCGCCGCTAATGCTCGACCTTTAGCAGCG-TTTTTAT
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTAT
*
29535500 AAAAGCGCCGCTAATGCTTGATTTTTAGTGGCGTTTTTTAT
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTAT
*
29535541 CCAAA-CGCCGCTAA
1 -AAAAGCGCCGCTAA
29535555 AAACGCCGCT
Statistics
Matches: 77, Mismatches: 13, Indels: 7
0.79 0.13 0.07
Matches are distributed among these distances:
38 4 0.05
39 16 0.21
40 38 0.49
41 16 0.21
42 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (41 bp):
AAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGTTTTTTAT
Found at i:29535560 original size:12 final size:12
Alignment explanation
Indices: 29535543--29535568 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29535533 TTTTTTATCC
29535543 AAACGCCGCTAA
1 AAACGCCGCTAA
29535555 AAACGCCGCTAA
1 AAACGCCGCTAA
29535567 AA
1 AA
29535569 GCCTATTTTG
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Done.