Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, whole genome shotgun sequence
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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 61 of 100
Found at i:11067335 original size:20 final size:23
Alignment explanation
Indices: 11067298--11067348 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
11067288 AATTATATTC
11067298 TAATTTATTTGTTGATT-ATTTAA
1 TAATTT-TTTGTTGATTAATTTAA
11067321 TAATTTTTTG-T-ATTAGATTTAA
1 TAATTTTTTGTTGATTA-ATTTAA
11067343 T-ATTTT
1 TAATTTT
11067349 ATTATGCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 3 0.12
21 6 0.23
22 11 0.42
23 6 0.23
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (23 bp):
TAATTTTTTGTTGATTAATTTAA
Found at i:11068684 original size:20 final size:21
Alignment explanation
Indices: 11068655--11068703 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
11068645 ATTATACGTG
*
11068655 AATTTGTTTTAATTTTATATT
1 AATTTGTTTTAATTATATATT
*
11068676 AATTT-TTTTAATTATATTTT
1 AATTTGTTTTAATTATATATT
11068696 AATTTGTT
1 AATTTGTT
11068704 GACTATTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (21 bp):
AATTTGTTTTAATTATATATT
Found at i:11070055 original size:17 final size:16
Alignment explanation
Indices: 11070016--11070060 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
11070006 TATCATAAAG
11070016 AATAAAATT-AAAAAT
1 AATAAAATTAAAAAAT
11070031 -ATAAAAATATAAAAAAT
1 AAT-AAAAT-TAAAAAAT
11070048 AATAAAATTAAAA
1 AATAAAATTAAAA
11070061 TCATAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.08
15 5 0.19
16 6 0.23
17 11 0.42
18 2 0.08
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATAAAATTAAAAAAT
Found at i:11070449 original size:14 final size:15
Alignment explanation
Indices: 11070429--11070472 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 15
11070419 CATCATAAAG
11070429 AATAAAATTAAAAAT
1 AATAAAATTAAAAAT
11070444 -ATAAAATATAAAAAAT
1 AATAAAAT-T-AAAAAT
11070460 AATAAAATTAAAA
1 AATAAAATTAAAA
11070473 TCAATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 7 0.27
15 5 0.19
16 7 0.27
17 7 0.27
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AATAAAATTAAAAAT
Found at i:11070725 original size:412 final size:411
Alignment explanation
Indices: 11069952--11070779 Score: 1459
Period size: 412 Copynumber: 2.0 Consensus size: 411
11069942 CTAAACCATG
*
11069952 ATATTATACATTTTTATATAGATAGACGAAGTTGAAAAATTAAAAATAAATTTCTATCATAAAGA
1 ATATTATACATTTTTATATAGATAGACGAAGTTAAAAAATTAAAAATAAATTTCTATCATAAAGA
11070017 ATAAAATTAAAAATATAAAAATATAAAAAATAATAAAATTAAAATCATAATTATGGATACACAAA
66 ATAAAATTAAAAATATAAAAATATAAAAAATAATAAAATTAAAATCATAATTATGGATACACAAA
11070082 CTCAAAACTTAATTCAATTAATTTATATTTTATTTTAAAAAAATTTAATATTTAAATCTCAAAAT
131 CTCAAAACTTAATTCAATTAATTTATATTTTATTTTAAAAAAATTTAATATTTAAATCTCAAAAT
11070147 ATATAATTTTTATATTTATATTTAAAAAAAAAAAAACCCTTGTAGGAGGAGAAGTCACAGGCACT
196 ATATAATTTTTATATTTATATTT---AAAAAAAAAACCCTTGTAGGAGGAGAAGTCACAGGCACT
* **
11070212 ATTGTACCCGGGGCCCTGTGGGAAAGCTTCAATTATTTTTTTATTCACATTTCACGTGGGGGTTT
258 ATTGTACCCGGGGCCCTGTAGGAAAGCTTCAATTATTTTTTTATTCACATTTCACGCAGGGGTTT
* *
11070277 AATAGTAGTTTACATTATTTTCAATAAGCCTACCCACAGTTCCACTTTCGGTGGGTTTTCCACTA
323 AATAGTAGTTTACATTATTTTCAACAAGCCTACCCACAGTTCCACTTTCGGTGGGTTTGCCACTA
11070342 TTTATACAGATTAATAATGATGCT
388 TTTATACAGATTAATAATGATGCT
11070366 ATATTATACATTTTTATATAGATAGACGAAGTTAAAAAATTAAAAATAAATTTC-ATCATAAAGA
1 ATATTATACATTTTTATATAGATAGACGAAGTTAAAAAATTAAAAATAAATTTCTATCATAAAGA
*
11070430 ATAAAATTAAAAATAT-AAAATATAAAAAATAATAAAATTAAAATCAATTAAATAATTGTGGATA
66 ATAAAATTAAAAATATAAAAATATAAAAAATAATAAAATTAAAATC------ATAATTATGGATA
*
11070494 CACAAACTCAAAACTTAATTCCATTAATTTATATTTTATTTTAAAAAAATTTAATATTTAAATCT
125 CACAAACTCAAAACTTAATTCAATTAATTTATATTTTATTTTAAAAAAATTTAATATTTAAATCT
11070559 CAAAATATATAATTTTTATATTTATA-TT-AAAAAAAAACCCTTGTAGGAGGAGAAGTCACAGGC
190 CAAAATATATAATTTTTATATTTATATTTAAAAAAAAAACCCTTGTAGGAGGAGAAGTCACAGGC
*
11070622 ACTATTGTACCCGGGGCCCTGTAGGATAGCTTCAATTA-TTTTTTATTCACATTTCACGCAGGGG
255 ACTATTGTACCCGGGGCCCTGTAGGAAAGCTTCAATTATTTTTTTATTCACATTTCACGCAGGGG
11070686 TTTAATAGTAGTTTACATTATTTTCAACAAGCCTACCCACAGTTCCACTTTCGGTGGGTTTGCCA
320 TTTAATAGTAGTTTACATTATTTTCAACAAGCCTACCCACAGTTCCACTTTCGGTGGGTTTGCCA
11070751 CTATTTATACAGATTAATAATGATGCT
385 CTATTTATACAGATTAATAATGATGCT
11070778 AT
1 AT
11070780 CCCTCTAAAT
Statistics
Matches: 399, Mismatches: 9, Indels: 14
0.95 0.02 0.03
Matches are distributed among these distances:
412 145 0.36
413 97 0.24
414 53 0.13
417 2 0.01
418 102 0.26
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.36
Consensus pattern (411 bp):
ATATTATACATTTTTATATAGATAGACGAAGTTAAAAAATTAAAAATAAATTTCTATCATAAAGA
ATAAAATTAAAAATATAAAAATATAAAAAATAATAAAATTAAAATCATAATTATGGATACACAAA
CTCAAAACTTAATTCAATTAATTTATATTTTATTTTAAAAAAATTTAATATTTAAATCTCAAAAT
ATATAATTTTTATATTTATATTTAAAAAAAAAACCCTTGTAGGAGGAGAAGTCACAGGCACTATT
GTACCCGGGGCCCTGTAGGAAAGCTTCAATTATTTTTTTATTCACATTTCACGCAGGGGTTTAAT
AGTAGTTTACATTATTTTCAACAAGCCTACCCACAGTTCCACTTTCGGTGGGTTTGCCACTATTT
ATACAGATTAATAATGATGCT
Found at i:11071123 original size:19 final size:19
Alignment explanation
Indices: 11071099--11071135 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
11071089 ATGATAGAAT
11071099 TTTTCATATATATATATAA
1 TTTTCATATATATATATAA
11071118 TTTTCATATATATATATA
1 TTTTCATATATATATATA
11071136 CATACTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTCATATATATATATAA
Found at i:11081239 original size:33 final size:33
Alignment explanation
Indices: 11081201--11081306 Score: 112
Period size: 33 Copynumber: 3.3 Consensus size: 33
11081191 TATTACTTTA
11081201 TTATTTTTTCATTATTTGAATATAA-TT--TTAT
1 TTATTTTTT-ATTATTTGAATATAATTTAATTAT
* *
11081232 TT-TTATTTATTATTTTAATATAATTTAATTAT
1 TTATTTTTTATTATTTGAATATAATTTAATTAT
* * * *
11081264 TTATTTTTTATTGTTTGGATATAATTTGATCAT
1 TTATTTTTTATTATTTGAATATAATTTAATTAT
11081297 TTACTTTTTT
1 TTA-TTTTTT
11081307 TTTTTAAGAT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
29 14 0.23
30 7 0.11
31 2 0.03
32 6 0.10
33 27 0.44
34 6 0.10
ACGTcount: A:0.27, C:0.03, G:0.05, T:0.65
Consensus pattern (33 bp):
TTATTTTTTATTATTTGAATATAATTTAATTAT
Found at i:11081251 original size:29 final size:30
Alignment explanation
Indices: 11081197--11081275 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
11081187 TGACTATTAC
11081197 TTTATTATTT-TTTCATTATTTGAATATAAT
1 TTTATTATTTATTT-ATTATTTGAATATAAT
*
11081227 TTTATT-TTTATTTATTATTTTAATATAAT
1 TTTATTATTTATTTATTATTTGAATATAAT
* *
11081256 TTAATTATTTATTTTTTATT
1 TTTATTATTTATTTATTATT
11081276 GTTTGGATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 23 0.52
30 21 0.48
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (30 bp):
TTTATTATTTATTTATTATTTGAATATAAT
Found at i:11084666 original size:17 final size:16
Alignment explanation
Indices: 11084627--11084669 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
11084617 CAATCGATTC
11084627 AAAATAAAATGATAAG
1 AAAATAAAATGATAAG
*
11084643 AACAATAACATGATAAAG
1 AA-AATAAAATGAT-AAG
*
11084661 TAAATAAAA
1 AAAATAAAA
11084670 AATGTTTGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 2 0.09
17 16 0.73
18 4 0.18
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (16 bp):
AAAATAAAATGATAAG
Found at i:11086367 original size:20 final size:21
Alignment explanation
Indices: 11086320--11086370 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
11086310 TCCAAAATTA
11086320 ATAAAAT-TATATTTTTTAAAT
1 ATAAAATAT-TATTTTTTAAAT
11086341 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
11086362 AT-AAATATT
1 ATAAAATATT
11086371 TAAAAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.24
21 21 0.72
22 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:11086379 original size:30 final size:30
Alignment explanation
Indices: 11086343--11086399 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
11086333 TTTTAAATAT
* *
11086343 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATTATTATATAAATATAAATATTTA
*
11086373 AAAATATTATTATATAAATATATATAT
1 AAAATATTATTATATAAATATAAATAT
11086400 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
AAAATATTATTATATAAATATAAATATTTA
Found at i:11093393 original size:17 final size:17
Alignment explanation
Indices: 11093360--11093393 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11093350 AAAGTATCAA
**
11093360 TATTTACATTTTTATTG
1 TATTTACATTTACATTG
11093377 TATTTACATTTACATTG
1 TATTTACATTTACATTG
11093394 AATATTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.59
Consensus pattern (17 bp):
TATTTACATTTACATTG
Found at i:11104510 original size:100 final size:100
Alignment explanation
Indices: 11104337--11104532 Score: 365
Period size: 100 Copynumber: 2.0 Consensus size: 100
11104327 TTAAATATGA
* *
11104337 AAGATTACCTAATTATAACTTAAACAAAATTAAACAAAATGTCACTAACAAGGTATAATGTAAAC
1 AAGATTACCTAATTATAACCTAAACAAAATTAAACAAAATGCCACTAACAAGGTATAATGTAAAC
11104402 CCAAGCGTGCAAGAATAAACTAAACATGTAAATGC
66 CCAAGCGTGCAAGAATAAACTAAACATGTAAATGC
*
11104437 AAGATTACCTAATTATAACCTAAACAGAATTAAACAAAATGCCACTAACAAGGTATAATGTAAAC
1 AAGATTACCTAATTATAACCTAAACAAAATTAAACAAAATGCCACTAACAAGGTATAATGTAAAC
11104502 CCAAGCGTGCAAGAATAAACTAAACATGTAA
66 CCAAGCGTGCAAGAATAAACTAAACATGTAA
11104533 TTATGCAAAA
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 93 1.00
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (100 bp):
AAGATTACCTAATTATAACCTAAACAAAATTAAACAAAATGCCACTAACAAGGTATAATGTAAAC
CCAAGCGTGCAAGAATAAACTAAACATGTAAATGC
Found at i:11108363 original size:40 final size:40
Alignment explanation
Indices: 11108305--11108421 Score: 162
Period size: 40 Copynumber: 2.9 Consensus size: 40
11108295 TTGAAATTAA
* * *
11108305 AAAAAACTCCTTTGACCAGAGGTAACAAACTTTAAATGTT
1 AAAAAGCTCCTTTAACCAGAGGCAACAAACTTTAAATGTT
* * *
11108345 AAAAAGCTCCTCTCACCAGAAGCAACAAACTTTAAATGTT
1 AAAAAGCTCCTTTAACCAGAGGCAACAAACTTTAAATGTT
* *
11108385 AAAAAGCTTCTTTAACCAAAGGCAACAAACTTTAAAT
1 AAAAAGCTCCTTTAACCAGAGGCAACAAACTTTAAAT
11108422 TAAAATCTGA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 67 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (40 bp):
AAAAAGCTCCTTTAACCAGAGGCAACAAACTTTAAATGTT
Found at i:11120902 original size:10 final size:11
Alignment explanation
Indices: 11120854--11120906 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
11120844 CAAAATATCA
*
11120854 ATTATTATTATT
1 ATTATTGTT-TT
11120866 ATTATT-TTTT
1 ATTATTGTTTT
11120876 ATTAATT-TTTT
1 ATT-ATTGTTTT
11120887 ATTATTGTTTT
1 ATTATTGTTTT
11120898 A-TATTGTTT
1 ATTATTGTTT
11120907 AAATGAATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
10 16 0.41
11 17 0.44
12 6 0.15
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.72
Consensus pattern (11 bp):
ATTATTGTTTT
Found at i:11121217 original size:19 final size:17
Alignment explanation
Indices: 11121179--11121211 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
11121169 AATTATTTCC
11121179 ATTAAATAATTATTATT
1 ATTAAATAATTATTATT
11121196 ATTAAA-AATTATTATT
1 ATTAAATAATTATTATT
11121212 TATATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTAAATAATTATTATT
Found at i:11121327 original size:24 final size:25
Alignment explanation
Indices: 11121299--11121392 Score: 102
Period size: 25 Copynumber: 3.8 Consensus size: 25
11121289 ACCAGTAATA
* *
11121299 ATAAAAAATAACAATAATAAT-ATC
1 ATAAAAAATAACAATAAAAATCAAC
11121323 ATAAAAAATAAC-ATAAAAATCAAC
1 ATAAAAAATAACAATAAAAATCAAC
* *
11121347 ATAAAAAAATAAAAATAAAAATCAAA
1 AT-AAAAAATAACAATAAAAATCAAC
* * *
11121373 ACAAAAAATAAAAACAAAAA
1 ATAAAAAATAACAATAAAAA
11121393 GAAAAGGAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
23 7 0.11
24 16 0.26
25 26 0.43
26 12 0.20
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.16
Consensus pattern (25 bp):
ATAAAAAATAACAATAAAAATCAAC
Found at i:11121328 original size:23 final size:24
Alignment explanation
Indices: 11121299--11121383 Score: 91
Period size: 24 Copynumber: 3.5 Consensus size: 24
11121289 ACCAGTAATA
* *
11121299 ATAAAAAATAACAATAATAAT-ATC
1 ATAAAAAATAAC-ATAAAAATCAAC
11121323 ATAAAAAATAACATAAAAATCAAC
1 ATAAAAAATAACATAAAAATCAAC
* *
11121347 ATAAAAAAATAAAAATAAAAATCAAA
1 AT-AAAAAAT-AACATAAAAATCAAC
*
11121373 ACAAAAAATAA
1 ATAAAAAATAA
11121384 AAACAAAAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
23 7 0.13
24 18 0.34
25 14 0.26
26 14 0.26
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (24 bp):
ATAAAAAATAACATAAAAATCAAC
Found at i:11121332 original size:12 final size:12
Alignment explanation
Indices: 11121299--11121354 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
11121289 ACCAGTAATA
11121299 ATAAAAAATAAC
1 ATAAAAAATAAC
* *
11121311 A-ATAATAATATC
1 ATA-AAAAATAAC
11121323 ATAAAAAATAAC
1 ATAAAAAATAAC
11121335 AT-AAAAATCAAC
1 ATAAAAAAT-AAC
11121347 ATAAAAAA
1 ATAAAAAA
11121355 ATAAAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
11 7 0.19
12 23 0.64
13 6 0.17
ACGTcount: A:0.71, C:0.09, G:0.00, T:0.20
Consensus pattern (12 bp):
ATAAAAAATAAC
Found at i:11121366 original size:5 final size:6
Alignment explanation
Indices: 11121351--11121397 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
11121341 ATCAACATAA
* *
11121351 AAAAAT AAAAAT AAAAAT CAAAACA- AAAAAT AAAAAC AAAAAG AAAA
1 AAAAAT AAAAAT AAAAAT -AAAA-AT AAAAAT AAAAAT AAAAAT AAAA
11121398 GGAAAAACCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
5 1 0.03
6 30 0.83
7 4 0.11
8 1 0.03
ACGTcount: A:0.83, C:0.06, G:0.02, T:0.09
Consensus pattern (6 bp):
AAAAAT
Found at i:11121366 original size:12 final size:11
Alignment explanation
Indices: 11121325--11121397 Score: 56
Period size: 12 Copynumber: 6.0 Consensus size: 11
11121315 ATAATATCAT
*
11121325 AAAAAATAACA
1 AAAAAATAAAA
*
11121336 TAAAAATCAACATA
1 AAAAAAT-AA-A-A
11121350 AAAAAATAAAA
1 AAAAAATAAAA
11121361 ATAAAAATCAAAA
1 A-AAAAAT-AAAA
11121374 CAAAAAATAAAA
1 -AAAAAATAAAA
*
11121386 ACAAAAAGAAAA
1 A-AAAAATAAAA
11121398 GGAAAAACCT
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
11 9 0.18
12 22 0.43
13 12 0.24
14 8 0.16
ACGTcount: A:0.79, C:0.08, G:0.01, T:0.11
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:11121386 original size:13 final size:13
Alignment explanation
Indices: 11121350--11121392 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
11121340 AATCAACATA
11121350 AAAAAATAAAAA-
1 AAAAAATAAAAAC
* *
11121362 TAAAAATCAAAAC
1 AAAAAATAAAAAC
11121375 AAAAAATAAAAAC
1 AAAAAATAAAAAC
11121388 AAAAA
1 AAAAA
11121393 GAAAAGGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.84, C:0.07, G:0.00, T:0.09
Consensus pattern (13 bp):
AAAAAATAAAAAC
Found at i:11121760 original size:18 final size:18
Alignment explanation
Indices: 11121730--11121766 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
11121720 TTCCAGATTT
11121730 CGATGTCGAAAAATTCAA
1 CGATGTCGAAAAATTCAA
11121748 CGATCGTCGAAAAATTCAA
1 CGAT-GTCGAAAAATTCAA
11121767 ACATTTCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (18 bp):
CGATGTCGAAAAATTCAA
Found at i:11121785 original size:51 final size:51
Alignment explanation
Indices: 11121655--11121773 Score: 132
Period size: 51 Copynumber: 2.3 Consensus size: 51
11121645 AACGGCATCG
* * * * * *
11121655 AAAAATTCAAAGA-TCCCTGATTTTGATGGTTGAAAAATTCAACGGTCACCA
1 AAAAATTCAAACATTTCCAGATTTCGAT-GTCGAAAAATTCAACGATCACCA
* ** *
11121706 AAAAATTCAAACTTTTCCAGATTTCGATGTCGAAAAATTCAACGATCGTCG
1 AAAAATTCAAACATTTCCAGATTTCGATGTCGAAAAATTCAACGATCACCA
11121757 AAAAATTCAAACATTTC
1 AAAAATTCAAACATTTC
11121774 TAGTTTCCGA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
51 45 0.80
52 11 0.20
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (51 bp):
AAAAATTCAAACATTTCCAGATTTCGATGTCGAAAAATTCAACGATCACCA
Found at i:11121794 original size:51 final size:51
Alignment explanation
Indices: 11121687--11121795 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 51
11121677 TTGATGGTTG
* * * *
11121687 AAAAATTCAACGGTCACCAAAAAATTCAAACTTTTCCAGATTTCGATGTCG
1 AAAAATTCAACGATCACCAAAAAATTCAAACATTTCCAGATTTCGATGACC
** * *
11121738 AAAAATTCAACGATCGTCGAAAAATTCAAACATTTCTAG-TTTCCGATGACC
1 AAAAATTCAACGATCACCAAAAAATTCAAACATTTCCAGATTT-CGATGACC
*
11121789 CAAAATT
1 AAAAATT
11121796 TTTTTTGAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
50 3 0.06
51 45 0.94
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (51 bp):
AAAAATTCAACGATCACCAAAAAATTCAAACATTTCCAGATTTCGATGACC
Found at i:11122252 original size:23 final size:21
Alignment explanation
Indices: 11122222--11122266 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 21
11122212 TGTTTTAAAG
11122222 ATTAATAATAATAATAAACAAA
1 ATTAATAATAATAATAAA-AAA
11122244 ATTATATAATAATAATAAAAAA
1 ATTA-ATAATAATAATAAAAAA
11122266 A
1 A
11122267 GAACAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
ATTAATAATAATAATAAAAAA
Found at i:11123546 original size:21 final size:21
Alignment explanation
Indices: 11123513--11123553 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11123503 TTTGAGATGA
11123513 AGGGATCAATTGGTT-TTGAT
1 AGGGATCAATTGGTTCTTGAT
*
11123533 AGGGAATCGATTGGTTCTTGA
1 AGGG-ATCAATTGGTTCTTGA
11123554 ATTTCACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 10 0.56
22 4 0.22
ACGTcount: A:0.24, C:0.07, G:0.32, T:0.37
Consensus pattern (21 bp):
AGGGATCAATTGGTTCTTGAT
Found at i:11126471 original size:29 final size:30
Alignment explanation
Indices: 11126417--11126490 Score: 141
Period size: 29 Copynumber: 2.5 Consensus size: 30
11126407 TATTTTCTAT
11126417 TAAAAATATTATTTTACTCATAAATCATAA
1 TAAAAATATTATTTTACTCATAAATCATAA
11126447 TAAAAATATTATTTTACTCA-AAATCATAA
1 TAAAAATATTATTTTACTCATAAATCATAA
11126476 TAAAAATATTATTTT
1 TAAAAATATTATTTT
11126491 CTATACATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 24 0.55
30 20 0.45
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (30 bp):
TAAAAATATTATTTTACTCATAAATCATAA
Found at i:11126906 original size:25 final size:26
Alignment explanation
Indices: 11126858--11126906 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
11126848 GAAATTTTCA
*
11126858 AATCATTTTCAAAAATAGATTTTATT
1 AATCATTTTCAAAAATAGAATTTATT
*
11126884 AATC-TTTTCAAAAATATAATTTA
1 AATCATTTTCAAAAATAGAATTTA
11126907 AAATATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (26 bp):
AATCATTTTCAAAAATAGAATTTATT
Found at i:11126944 original size:14 final size:14
Alignment explanation
Indices: 11126927--11126957 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11126917 TATTTTTTAT
11126927 TTTTATAAAACATA
1 TTTTATAAAACATA
*
11126941 TTTTATAAAATATA
1 TTTTATAAAACATA
11126955 TTT
1 TTT
11126958 AAAAAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTATAAAACATA
Found at i:11127526 original size:19 final size:19
Alignment explanation
Indices: 11127482--11127535 Score: 83
Period size: 21 Copynumber: 2.8 Consensus size: 19
11127472 CGACCCGAAA
11127482 TTAATA-AAATATTATTTT
1 TTAATATAAATATTATTTT
11127500 TTAAAATATAAATATTATTTT
1 TT--AATATAAATATTATTTT
11127521 TTAATATAAATATTA
1 TTAATATAAATATTA
11127536 AAAATATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 2 0.06
19 13 0.39
20 4 0.12
21 14 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAATATAAATATTATTTT
Found at i:11127589 original size:19 final size:21
Alignment explanation
Indices: 11127546--11127591 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
11127536 AAAATATATT
*
11127546 ATAAATAATATAAATAAATAA
1 ATAATTAATATAAATAAATAA
*
11127567 ATAATTAAT-TAATTAAA-AA
1 ATAATTAATATAAATAAATAA
11127586 ATAATT
1 ATAATT
11127592 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
20 7 0.30
21 8 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAATTAATATAAATAAATAA
Found at i:11132453 original size:18 final size:19
Alignment explanation
Indices: 11132410--11132455 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
11132400 AAGGGCTGGA
11132410 ATTTAT-AAATTAATTAAT
1 ATTTATAAAATTAATTAAT
* *
11132428 A-TTCTAAAATT-ATTATT
1 ATTTATAAAATTAATTAAT
11132445 ATTTATAAAAT
1 ATTTATAAAAT
11132456 GTTATCCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTATAAAATTAATTAAT
Found at i:11133085 original size:22 final size:23
Alignment explanation
Indices: 11133051--11133093 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
11133041 ATTTATATAT
* *
11133051 TTTTTATTTTATACAGTTATTTC
1 TTTTTATTATATAAAGTTATTTC
11133074 TTTTTA-TATATAAAGTTATT
1 TTTTTATTATATAAAGTTATT
11133094 AAATTTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (23 bp):
TTTTTATTATATAAAGTTATTTC
Found at i:11135952 original size:21 final size:21
Alignment explanation
Indices: 11135900--11135953 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
11135890 ATTTTTATTC
*
11135900 ATTTTTATTTTA-GATTTTTT
1 ATTTTTATTTTATCATTTTTT
*
11135920 A-TTTCATATTTATCATTTTTT
1 ATTTTTAT-TTTATCATTTTTT
11135941 ATTTTTATTTTAT
1 ATTTTTATTTTAT
11135954 GGTCTATCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 5 0.18
20 5 0.18
21 13 0.46
22 5 0.18
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (21 bp):
ATTTTTATTTTATCATTTTTT
Found at i:11138198 original size:64 final size:65
Alignment explanation
Indices: 11138117--11138250 Score: 155
Period size: 64 Copynumber: 2.1 Consensus size: 65
11138107 TTTTTAAGGA
* * * *
11138117 AAAGTTAAAAGTTTCAATTTTCCTTGAAAAT-AATTTTCTAAAAAATATTTTTTAGA-AAAAATT
1 AAAGTTAAAAGTATCAATTTTCCTCGAAAATAAAGTTTC-AAAAAATATATTTTAGAGAAAAATT
11138180 G
65 G
* * ** * *
11138181 AAAGTTGAAAGTATCAATTTTTCTCGAAGTTAAAGTTTCAAAAAATATATTTTGGAGAAAAGTTG
1 AAAGTTAAAAGTATCAATTTTCCTCGAAAATAAAGTTTCAAAAAATATATTTTAGAGAAAAATTG
11138246 AAAGT
1 AAAGT
11138251 ATCAATTTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
64 40 0.69
65 18 0.31
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (65 bp):
AAAGTTAAAAGTATCAATTTTCCTCGAAAATAAAGTTTCAAAAAATATATTTTAGAGAAAAATTG
Found at i:11151798 original size:21 final size:21
Alignment explanation
Indices: 11151766--11151870 Score: 129
Period size: 21 Copynumber: 5.0 Consensus size: 21
11151756 TACAAGACGT
*
11151766 CACAACAGCTTCCAGTTCAAA
1 CACAATAGCTTCCAGTTCAAA
*
11151787 CATAATAGCTTCCAGTTCAAA
1 CACAATAGCTTCCAGTTCAAA
*
11151808 CACAATAGCTTCCAATTCAAA
1 CACAATAGCTTCCAGTTCAAA
* * * *
11151829 CACAACAACTTCCAGCTCAAT
1 CACAATAGCTTCCAGTTCAAA
* *
11151850 CACAATAGCTTTCAGCTCAAA
1 CACAATAGCTTCCAGTTCAAA
11151871 AAATATTGTC
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.39, C:0.30, G:0.08, T:0.23
Consensus pattern (21 bp):
CACAATAGCTTCCAGTTCAAA
Found at i:11152539 original size:17 final size:15
Alignment explanation
Indices: 11152494--11152540 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 15
11152484 ATGAAATAAT
11152494 AAAATAT-TAACAA-
1 AAAATATATAACAAC
*
11152507 ATAATATATAACAAC
1 AAAATATATAACAAC
11152522 AAAATATAATAACTAAC
1 AAAATAT-ATAAC-AAC
11152539 AA
1 AA
11152541 TATGTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 6 0.21
16 5 0.18
17 5 0.18
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATATATAACAAC
Found at i:11157848 original size:51 final size:51
Alignment explanation
Indices: 11157793--11157892 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 51
11157783 GAAGCTGAAG
* * *
11157793 AATGATGTTAATATTGAGGACTTAAAATTAATAAAAGACATTGAGCTGATT
1 AATGATGTTAATATTAAGGACTTAAAATTAACAAAAGACAGTGAGCTGATT
* *
11157844 AATGATGTTAATGTTAAGGACTTAAAATTAGCAAAAGACAGTGAGCTGA
1 AATGATGTTAATATTAAGGACTTAAAATTAACAAAAGACAGTGAGCTGA
11157893 AGCTAAAGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (51 bp):
AATGATGTTAATATTAAGGACTTAAAATTAACAAAAGACAGTGAGCTGATT
Found at i:11159035 original size:15 final size:15
Alignment explanation
Indices: 11159017--11159050 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
11159007 ATTCGAAGAA
11159017 GAAAGCTAAATAGAT
1 GAAAGCTAAATAGAT
* *
11159032 GAAAGTTAAATGGAT
1 GAAAGCTAAATAGAT
11159047 GAAA
1 GAAA
11159051 ACAGGTGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.24, T:0.21
Consensus pattern (15 bp):
GAAAGCTAAATAGAT
Found at i:11159297 original size:42 final size:43
Alignment explanation
Indices: 11159250--11159332 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
11159240 TAAACCTGAC
* *
11159250 CCCGACCCGAAACCGA-TATTTCAA-AAAATAAATCCGACCTAA
1 CCCGACCCGAAACCCATTATTTCAAGAAAA-AAACCCGACCTAA
*
11159292 CCCGACCCGAAACCCATTTTTTCAAGAAAAAAACCCGACCT
1 CCCGACCCGAAACCCATTATTTCAAGAAAAAAACCCGACCT
11159333 TAAATGATCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 15 0.42
43 17 0.47
44 4 0.11
ACGTcount: A:0.40, C:0.34, G:0.10, T:0.17
Consensus pattern (43 bp):
CCCGACCCGAAACCCATTATTTCAAGAAAAAAACCCGACCTAA
Found at i:11160141 original size:23 final size:22
Alignment explanation
Indices: 11160091--11160133 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
11160081 TTTTAACTTA
*
11160091 AAAAAACTAAAAAAAGTTAAAG
1 AAAAAACTAAAAAAAGTGAAAG
11160113 AAAAAACTAAAAAAA-TGAAAG
1 AAAAAACTAAAAAAAGTGAAAG
11160134 GGAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.74, C:0.05, G:0.09, T:0.12
Consensus pattern (22 bp):
AAAAAACTAAAAAAAGTGAAAG
Found at i:11160750 original size:17 final size:17
Alignment explanation
Indices: 11160710--11160752 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
11160700 TTAACTAGAT
11160710 AAAAAAATTAAAAATCCA
1 AAAAAAATTAAAAAT-CA
*
11160728 AGAAAAATTAAACAAT-A
1 AAAAAAATTAAA-AATCA
11160745 AAAAAAAT
1 AAAAAAAT
11160753 AAGGTGCTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 8 0.36
18 11 0.50
19 3 0.14
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAAAAATTAAAAATCA
Found at i:11160927 original size:29 final size:28
Alignment explanation
Indices: 11160873--11160932 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
11160863 ATAAATTAGT
*
11160873 ATAATATTTTCATTAAAGTAAGATATTAA
1 ATAATATTTTCATTAAAGTAACATA-TAA
11160902 ATAATAATTTT-ATTAATA-TAACATATAA
1 ATAAT-ATTTTCATTAA-AGTAACATATAA
11160930 ATA
1 ATA
11160933 TTAAATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 6 0.21
29 16 0.57
30 6 0.21
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (28 bp):
ATAATATTTTCATTAAAGTAACATATAA
Found at i:11160971 original size:12 final size:12
Alignment explanation
Indices: 11160927--11160973 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
11160917 ATATAACATA
11160927 TAAATAT-TAAAT
1 TAAATATAT-AAT
*
11160939 TAAATAAATAAT
1 TAAATATATAAT
*
11160951 TAAAAATATAAT
1 TAAATATATAAT
*
11160963 TATATATATAA
1 TAAATATATAA
11160974 ATACACTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 28 0.97
13 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAATATATAAT
Found at i:11161191 original size:18 final size:18
Alignment explanation
Indices: 11161170--11161204 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11161160 AATTTATTTG
*
11161170 ATTAAAAAAAGTAAAAAA
1 ATTAAAAAAACTAAAAAA
*
11161188 ATTAATAAAACTAAAAA
1 ATTAAAAAAACTAAAAA
11161205 TGTGGTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (18 bp):
ATTAAAAAAACTAAAAAA
Found at i:11164674 original size:75 final size:75
Alignment explanation
Indices: 11164550--11164696 Score: 267
Period size: 75 Copynumber: 2.0 Consensus size: 75
11164540 ATGGTAAGTG
* * *
11164550 TCTGAATGATCACCAAGCTATTGCATCACTATACTTTCGTTATTTAAGATGAAAATAGTGTTTTT
1 TCTGAATGATCACCAAGCTACTGCATCACTATACTCTCGTTATTAAAGATGAAAATAGTGTTTTT
11164615 TGATGTTGCC
66 TGATGTTGCC
11164625 TCTGAATGATCACCAAGCTACTGCATCACTATACTCTCGTTATTAAAGATGAAAATAGTGTTTTT
1 TCTGAATGATCACCAAGCTACTGCATCACTATACTCTCGTTATTAAAGATGAAAATAGTGTTTTT
11164690 TGATGTT
66 TGATGTT
11164697 TTTGTAGGGA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (75 bp):
TCTGAATGATCACCAAGCTACTGCATCACTATACTCTCGTTATTAAAGATGAAAATAGTGTTTTT
TGATGTTGCC
Found at i:11164939 original size:72 final size:72
Alignment explanation
Indices: 11164822--11164963 Score: 248
Period size: 72 Copynumber: 2.0 Consensus size: 72
11164812 GATGAAGATG
*
11164822 AGGTAAATGTGGTCAAGACCATACTCAAATCTGCAAGAGTCCTGGAGAGAATTGAACTTGGCTCT
1 AGGTAAATGTGGTCAAGACCATACTCAAATCTGCAAGAGTCCTGGAGAGAATTGAACCTGGCTCT
11164887 AAGAATA
66 AAGAATA
* * *
11164894 AGGTAAGTGTGGTCAAGACTATACTGAAATCTGCAAGAGTCCTGGAGAGAATTGAACCTGGCTCT
1 AGGTAAATGTGGTCAAGACCATACTCAAATCTGCAAGAGTCCTGGAGAGAATTGAACCTGGCTCT
11164959 AAGAA
66 AAGAA
11164964 GGAAAACAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.23
Consensus pattern (72 bp):
AGGTAAATGTGGTCAAGACCATACTCAAATCTGCAAGAGTCCTGGAGAGAATTGAACCTGGCTCT
AAGAATA
Found at i:11167259 original size:1 final size:1
Alignment explanation
Indices: 11167253--11167289 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
11167243 GATCAAAGAT
11167253 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11167290 CAAATTATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11182297 original size:8 final size:8
Alignment explanation
Indices: 11182284--11182331 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
11182274 ATGAACAGGT
11182284 ATATATAC
1 ATATATAC
11182292 ATATATAC
1 ATATATAC
*
11182300 ATATAAAC
1 ATATATAC
* *
11182308 AT-TGTAT
1 ATATATAC
*
11182315 ATATATAT
1 ATATATAC
11182323 ATATATAC
1 ATATATAC
11182331 A
1 A
11182332 CACACATATG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
7 4 0.12
8 29 0.88
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (8 bp):
ATATATAC
Found at i:11188763 original size:14 final size:14
Alignment explanation
Indices: 11188744--11188770 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11188734 TTAAACTTTG
11188744 TAATTAAAAGTTAC
1 TAATTAAAAGTTAC
11188758 TAATTAAAAGTTA
1 TAATTAAAAGTTA
11188771 GGTTCCCATT
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:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (14 bp):
TAATTAAAAGTTAC
Found at i:11194390 original size:31 final size:31
Alignment explanation
Indices: 11194349--11194407 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
11194339 CCTTAAATAA
* *
11194349 TTGTTGCATAAACAGATATTTTGTAAAAGGT
1 TTGTTCCATAAACAGATATTCTGTAAAAGGT
* *
11194380 TTGTTCCATAAATAGCTATTCTGTAAAA
1 TTGTTCCATAAACAGATATTCTGTAAAA
11194408 TAATCTTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (31 bp):
TTGTTCCATAAACAGATATTCTGTAAAAGGT
Found at i:11197752 original size:19 final size:19
Alignment explanation
Indices: 11197730--11197768 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
11197720 TTTCTTAATG
11197730 GCCCCTTCTTTAATCATGT
1 GCCCCTTCTTTAATCATGT
11197749 GCCCCTTCTTTAATCATGT
1 GCCCCTTCTTTAATCATGT
11197768 G
1 G
11197769 TTATACATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.31, G:0.13, T:0.41
Consensus pattern (19 bp):
GCCCCTTCTTTAATCATGT
Found at i:11199996 original size:26 final size:26
Alignment explanation
Indices: 11199965--11200015 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
11199955 TGCAATTTCT
11199965 TTTTAG-ATTTATTCATTTTCAAAAGG
1 TTTTAGTATTT-TTCATTTTCAAAAGG
*
11199991 TTTTAGTATTTTTTATTTTCAAAAG
1 TTTTAGTATTTTTCATTTTCAAAAG
11200016 TATAAGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (26 bp):
TTTTAGTATTTTTCATTTTCAAAAGG
Found at i:11200191 original size:6 final size:6
Alignment explanation
Indices: 11200157--11200190 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
11200147 TTTAATTTAA
* *
11200157 TTTTGC TTTTGC TTTTGC TTTTTC TTTTTC TTTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTT
11200191 TTGTGGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (6 bp):
TTTTGC
Found at i:11202564 original size:25 final size:23
Alignment explanation
Indices: 11202536--11202590 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
11202526 AAACTTGAAT
*
11202536 GCAATAAATGAAAAAGTGACATGTG
1 GCAA-AAAGGAAAAA-TGACATGTG
*
11202561 GCAAAAAGGAATAATGACATGTG
1 GCAAAAAGGAAAAATGACATGTG
*
11202584 GTAAAAA
1 GCAAAAA
11202591 AAGATTGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 15 0.56
24 8 0.30
25 4 0.15
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
GCAAAAAGGAAAAATGACATGTG
Found at i:11204138 original size:2 final size:2
Alignment explanation
Indices: 11204131--11204167 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11204121 AACTGTTATC
11204131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11204168 CGTACACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11204903 original size:24 final size:24
Alignment explanation
Indices: 11204875--11204926 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
11204865 GGAACTCGGC
11204875 TTTTGCTTTAATTT-TTTTTACTCT
1 TTTTGCTTT-ATTTCTTTTTACTCT
* *
11204899 TTTTGCTTTCTTTCTTTTTTCTCT
1 TTTTGCTTTATTTCTTTTTACTCT
11204923 TTTT
1 TTTT
11204927 CATCTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (24 bp):
TTTTGCTTTATTTCTTTTTACTCT
Found at i:11204934 original size:24 final size:24
Alignment explanation
Indices: 11204886--11204939 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
11204876 TTTGCTTTAA
*
11204886 TTTTTTTTACTCTTTTTGCTTTCT
1 TTTTTTTTACTCTTTTTGCTCTCT
11204910 TTCTTTTTT-CTCTTTTT-CATCTCT
1 TT-TTTTTTACTCTTTTTGC-TCTCT
11204934 TTTTTT
1 TTTTTT
11204940 ACTTTTTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 5 0.19
24 16 0.59
25 6 0.22
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.76
Consensus pattern (24 bp):
TTTTTTTTACTCTTTTTGCTCTCT
Found at i:11204959 original size:20 final size:20
Alignment explanation
Indices: 11204911--11204949 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
11204901 TTGCTTTCTT
11204911 TCTTTTTTCT-CTTTTTCATC
1 TCTTTTTT-TACTTTTTCATC
11204931 TCTTTTTTTACTTTTTCAT
1 TCTTTTTTTACTTTTTCAT
11204950 TTTATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.72
Consensus pattern (20 bp):
TCTTTTTTTACTTTTTCATC
Found at i:11205184 original size:20 final size:19
Alignment explanation
Indices: 11205161--11205203 Score: 77
Period size: 20 Copynumber: 2.2 Consensus size: 19
11205151 AATTAATTAA
11205161 TTAATTTTATATTTATATAT
1 TTAATTTTATATTTATAT-T
11205181 TTAATTTTATATTTATATT
1 TTAATTTTATATTTATATT
11205200 TTAA
1 TTAA
11205204 AAATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTAATTTTATATTTATATT
Found at i:11209836 original size:4 final size:4
Alignment explanation
Indices: 11209827--11209885 Score: 55
Period size: 4 Copynumber: 13.8 Consensus size: 4
11209817 AAAAGAATAA
* *
11209827 AAAT AAAT AAAT AAGT AAAT AAGAT AAAT AAAT GCAAT AAAATT AAAT
1 AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT -AAAT -AAA-T AAAT
*
11209875 GAAT AAAT AAA
1 AAAT AAAT AAA
11209886 AATAAAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
4 32 0.71
5 12 0.27
6 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:11217285 original size:18 final size:18
Alignment explanation
Indices: 11217264--11217298 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11217254 TTTTGAAAAA
*
11217264 TTATTTTGTTTACTTTTG
1 TTATTTTATTTACTTTTG
*
11217282 TTATTTTATTTAGTTTT
1 TTATTTTATTTACTTTT
11217299 CATGATGCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (18 bp):
TTATTTTATTTACTTTTG
Found at i:11218549 original size:14 final size:14
Alignment explanation
Indices: 11218518--11218551 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
11218508 CCATAATCAT
11218518 AATAAATAAAATAC
1 AATAAATAAAATAC
11218532 AATAACATAAAATA-
1 AATAA-ATAAAATAC
11218546 AATAAA
1 AATAAA
11218552 AGCAGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 10 0.53
15 8 0.42
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (14 bp):
AATAAATAAAATAC
Found at i:11220033 original size:50 final size:50
Alignment explanation
Indices: 11219973--11220077 Score: 174
Period size: 50 Copynumber: 2.1 Consensus size: 50
11219963 TCATAATCAG
*
11219973 TTCAACCATTAAACCACAAAATCGGATCTTGGATTCTCAAAATTGAGATC
1 TTCAACCATTAAACCACAAAATCGGATATTGGATTCTCAAAATTGAGATC
* * *
11220023 TTCAATCATTAAACCACAAAATCGGATATTTGATTCTCCAAATTGAGATC
1 TTCAACCATTAAACCACAAAATCGGATATTGGATTCTCAAAATTGAGATC
11220073 TTCAA
1 TTCAA
11220078 ATTCCCACAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.30
Consensus pattern (50 bp):
TTCAACCATTAAACCACAAAATCGGATATTGGATTCTCAAAATTGAGATC
Found at i:11223153 original size:2 final size:2
Alignment explanation
Indices: 11223148--11223180 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11223138 TGTGTGTGTG
11223148 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11223181 TAATATGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11227284 original size:110 final size:111
Alignment explanation
Indices: 11227170--11227371 Score: 300
Period size: 110 Copynumber: 1.8 Consensus size: 111
11227160 TTCTACCATT
* *
11227170 TTTTAGAATACTTTAGAAAATTTCTTTATATGAATATTTTTAA-TAAAATCACCACTTGTGACTT
1 TTTTAGAATACTTTAGAAAATATCTTTATATAAATATTTTTAATTAAAATCACCACTTGTGACTT
11227234 TATTGTTT-TTAATAATGCTTTTTTTATTCTGAAATGTTTCTAACAC
66 TATTGTTTATTAATAAT-CTTTTTTTATTCTGAAATGTTTCTAACAC
* * * * *
11227280 TTTTATAATATTTTAGAAAATATCTTTGTGTAAATATTTTTAATTAAAATCACCACTTGTGATTT
1 TTTTAGAATACTTTAGAAAATATCTTTATATAAATATTTTTAATTAAAATCACCACTTGTGACTT
* *
11227345 TATTTTTTATTAATAATTTTTTTTTAT
66 TATTGTTTATTAATAATCTTTTTTTAT
11227372 GTTTATGTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
110 37 0.46
111 36 0.44
112 8 0.10
ACGTcount: A:0.32, C:0.08, G:0.07, T:0.52
Consensus pattern (111 bp):
TTTTAGAATACTTTAGAAAATATCTTTATATAAATATTTTTAATTAAAATCACCACTTGTGACTT
TATTGTTTATTAATAATCTTTTTTTATTCTGAAATGTTTCTAACAC
Found at i:11227728 original size:7 final size:7
Alignment explanation
Indices: 11227718--11227789 Score: 53
Period size: 7 Copynumber: 10.3 Consensus size: 7
11227708 AATATTTAAA
11227718 AAAATAT
1 AAAATAT
11227725 AAAATAT
1 AAAATAT
11227732 AAAATAT
1 AAAATAT
**
11227739 TTAA-A-
1 AAAATAT
11227744 AAAATAT
1 AAAATAT
*
11227751 AAATTA-
1 AAAATAT
11227757 AAAATATTT
1 AAAATA--T
11227766 AAAAAATAT
1 --AAAATAT
11227775 AAAATAT
1 AAAATAT
11227782 AAAA-AT
1 AAAATAT
11227788 AA
1 AA
11227790 TAAATAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
5 2 0.04
6 11 0.21
7 32 0.62
9 1 0.02
11 6 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAATAT
Found at i:11227754 original size:25 final size:26
Alignment explanation
Indices: 11227719--11227785 Score: 111
Period size: 24 Copynumber: 2.7 Consensus size: 26
11227709 ATATTTAAAA
11227719 AAATATAAAATATAAAATATTTAAAA
1 AAATATAAAATATAAAATATTTAAAA
*
11227745 AAATATAAATTA-AAAATATTT-AAA
1 AAATATAAAATATAAAATATTTAAAA
11227769 AAATATAAAATATAAAA
1 AAATATAAAATATAAAA
11227786 ATAATAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 14 0.37
25 13 0.34
26 11 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (26 bp):
AAATATAAAATATAAAATATTTAAAA
Found at i:11227795 original size:15 final size:15
Alignment explanation
Indices: 11227717--11227793 Score: 57
Period size: 15 Copynumber: 4.7 Consensus size: 15
11227707 AAATATTTAA
11227717 AAAAATATAAAATAT
1 AAAAATATAAAATAT
* *
11227732 AAAATATTTAAAAAAAT
1 AAAA-ATAT-AAAATAT
*
11227749 ATAAAT-TAAAAATATTT
1 AAAAATAT-AAAATA--T
11227766 AAAAAATATAAAATAT
1 -AAAAATATAAAATAT
11227782 AAAAATAATAAA
1 AAAAAT-ATAAA
11227794 TAAATAAGAG
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
15 17 0.34
16 11 0.22
17 10 0.20
18 11 0.22
19 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATATAAAATAT
Found at i:11227799 original size:26 final size:27
Alignment explanation
Indices: 11227699--11227788 Score: 145
Period size: 26 Copynumber: 3.5 Consensus size: 27
11227689 CCCTAAATTA
11227699 AAAAT-TAAAAATATTTAAAAAAATAT
1 AAAATATAAAAATATTTAAAAAAATAT
11227725 AAAATAT-AAAATATTTAAAAAAATAT
1 AAAATATAAAAATATTTAAAAAAATAT
11227751 -AAAT-TAAAAATATTT-AAAAAATAT
1 AAAATATAAAAATATTTAAAAAAATAT
11227775 AAAATATAAAAATA
1 AAAATATAAAAATA
11227789 ATAAATAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.17
25 17 0.28
26 32 0.53
27 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAATATAAAAATATTTAAAAAAATAT
Found at i:11227799 original size:50 final size:51
Alignment explanation
Indices: 11227700--11227799 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 51
11227690 CCTAAATTAA
*
11227700 AAATTAAAAATATTTAAAAAAATATAAAATATAAAATATTTAAAAAAATAT
1 AAATTAAAAATATTTAAAAAAATATAAAATATAAAATATATAAAAAAATAT
*
11227751 AAATTAAAAATATTT-AAAAAATATAAAATATAAAA-ATAATAAATAAATA
1 AAATTAAAAATATTTAAAAAAATATAAAATATAAAATAT-ATAAAAAAATA
11227800 AGAGAAGAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
49 2 0.04
50 29 0.63
51 15 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (51 bp):
AAATTAAAAATATTTAAAAAAATATAAAATATAAAATATATAAAAAAATAT
Found at i:11227800 original size:24 final size:25
Alignment explanation
Indices: 11227699--11227800 Score: 104
Period size: 26 Copynumber: 4.1 Consensus size: 25
11227689 CCCTAAATTA
*
11227699 AAAAT-TAAAAATATTTAAAAAAAT
1 AAAATATAAAAATATATAAAAAAAT
*
11227723 ATAAA-ATATAAAATATTTAAAAAAAT
1 A-AAATATA-AAAATATATAAAAAAAT
*
11227749 ATAAAT-TAAAAATATTTAAAAAATAT
1 A-AAATATAAAAATATATAAAAAA-AT
*
11227775 AAAATATAAAAATA-ATAAATAAAT
1 AAAATATAAAAATATATAAAAAAAT
11227799 AA
1 AA
11227801 GAGAAGAGAA
Statistics
Matches: 70, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
24 5 0.07
25 30 0.43
26 35 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAATATAAAAATATATAAAAAAAT
Found at i:11229152 original size:42 final size:43
Alignment explanation
Indices: 11229100--11229273 Score: 165
Period size: 43 Copynumber: 4.0 Consensus size: 43
11229090 TTTTTTTTTT
* * * * *
11229100 AATTTGAAAGGCTCCTCTAAGTAGAGACTCGATAATTTTTG-A
1 AATTTAAAAAGCTCCTCTAAGCAGAGACTTGATAACTTTTGAA
* * * *
11229142 AATTTAAAAGGTTCCTCTAAGCAGAGACTTAACAACTTTTGAAA
1 AATTTAAAAAGCTCCTCTAAGCAGAGACTTGATAACTTTTG-AA
* *
11229186 AATTTAAAAAGCTCATCTAAGCA-AAAGCTTGATAACTTTTGAA
1 AATTTAAAAAGCTCCTCTAAGCAGAGA-CTTGATAACTTTTGAA
* * *
11229229 AATTAAAAAAGCTCCTCTAAGAATA-AGCTTGATAACTTTTAGAA
1 AATTTAAAAAGCTCCTCTAAGCAGAGA-CTTGATAACTTTT-GAA
11229273 A
1 A
11229274 TTAAAATATT
Statistics
Matches: 111, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
42 34 0.31
43 39 0.35
44 38 0.34
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (43 bp):
AATTTAAAAAGCTCCTCTAAGCAGAGACTTGATAACTTTTGAA
Found at i:11235521 original size:20 final size:20
Alignment explanation
Indices: 11235498--11235558 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
11235488 ATTTGATTTG
*
11235498 TTTTGATTTTTTCTATT-TTA
1 TTTTGATTTTAT-TATTATTA
*
11235518 TTTTTATTTTATTATTATTA
1 TTTTGATTTTATTATTATTA
*
11235538 TTTTCATCTTTAATTATTATT
1 TTTTGAT-TTT-ATTATTATT
11235559 TTACTCATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.11
20 19 0.54
21 3 0.09
22 9 0.26
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTTGATTTTATTATTATTA
Found at i:11235553 original size:22 final size:20
Alignment explanation
Indices: 11235511--11235558 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
11235501 TGATTTTTTC
*
11235511 TATT-TTATTTTTATTTTAT
1 TATTATTATTTTCATTTTAT
11235530 TATTATTATTTTCATCTTTAAT
1 TATTATTATTTTCAT-TTT-AT
11235552 TATTATT
1 TATTATT
11235559 TTACTCATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 4 0.16
20 9 0.36
21 3 0.12
22 9 0.36
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTATTATTTTCATTTTAT
Found at i:11235641 original size:12 final size:13
Alignment explanation
Indices: 11235619--11235647 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
11235609 TTTTATGAAT
11235619 TTTATTTTATTTA
1 TTTATTTTATTTA
11235632 TTTA-TTTATTTA
1 TTTATTTTATTTA
11235644 TTTA
1 TTTA
11235648 AAAATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:11236607 original size:13 final size:12
Alignment explanation
Indices: 11236575--11236639 Score: 69
Period size: 13 Copynumber: 5.3 Consensus size: 12
11236565 AAAACTGTTT
11236575 AAATATATTAAA
1 AAATATATTAAA
*
11236587 AATTTATATTAAA
1 AA-ATATATTAAA
*
11236600 ATAATATATAAAA
1 A-AATATATTAAA
11236613 AAATAT-TTAAA
1 AAATATATTAAA
* *
11236624 AAATAAATTTAA
1 AAATATATTAAA
11236636 AAAT
1 AAAT
11236640 CAATTGATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
11 9 0.20
12 15 0.34
13 19 0.43
14 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAATATATTAAA
Found at i:11246282 original size:10 final size:10
Alignment explanation
Indices: 11246269--11246353 Score: 50
Period size: 10 Copynumber: 8.4 Consensus size: 10
11246259 TTTCGAAAAT
11246269 AAATTTTTAA
1 AAATTTTTAA
11246279 AAATTTTTAA
1 AAATTTTTAA
** *
11246289 AGGTTTTCAAGAA
1 AAATTTT---TAA
* *
11246302 TAAATATTTAG
1 -AAATTTTTAA
*
11246313 AAATCTTTAA
1 AAATTTTTAA
*
11246323 AAATTTTCAA
1 AAATTTTTAA
11246333 AAA--TTT-A
1 AAATTTTTAA
11246340 AAATTTTTAA
1 AAATTTTTAA
11246350 AAAT
1 AAAT
11246354 AAATAATCGA
Statistics
Matches: 55, Mismatches: 13, Indels: 14
0.67 0.16 0.17
Matches are distributed among these distances:
7 4 0.07
8 2 0.04
9 3 0.05
10 39 0.71
11 1 0.02
13 2 0.04
14 4 0.07
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (10 bp):
AAATTTTTAA
Found at i:11246305 original size:34 final size:34
Alignment explanation
Indices: 11246254--11246353 Score: 101
Period size: 34 Copynumber: 2.9 Consensus size: 34
11246244 AATGTGATTT
* * *
11246254 AAAACTTTCGAAAATAAATTTTTAAAAATTTTTA
1 AAAATTTTCAAAAATAAATTTTTAAAAATCTTTA
** * * *
11246288 AAGGTTTTCAAGAATAAATATTTAGAAATCTTTA
1 AAAATTTTCAAAAATAAATTTTTAAAAATCTTTA
11246322 AAAATTTTCAAAAATTTAAAATTTTTAAAAAT
1 AAAATTTTCAAAAA--T-AAATTTTTAAAAAT
11246354 AAATAATCGA
Statistics
Matches: 50, Mismatches: 13, Indels: 3
0.76 0.20 0.05
Matches are distributed among these distances:
34 37 0.74
36 1 0.02
37 12 0.24
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (34 bp):
AAAATTTTCAAAAATAAATTTTTAAAAATCTTTA
Found at i:11246828 original size:20 final size:21
Alignment explanation
Indices: 11246790--11246829 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11246780 TTTAATTTTG
*
11246790 TTTTTGATTTTGATTAAATTA
1 TTTTTGATTTTGATAAAATTA
*
11246811 TTTTTTATTTTG-TAAAATT
1 TTTTTGATTTTGATAAAATT
11246830 TTGATTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTTTGATTTTGATAAAATTA
Found at i:11246950 original size:34 final size:34
Alignment explanation
Indices: 11246912--11246994 Score: 107
Period size: 34 Copynumber: 2.4 Consensus size: 34
11246902 TTATATTTTA
*
11246912 AAAAACTTATAAAAA-TATTCAAAAATATAAA-TC
1 AAAAACTTTTAAAAACTATTC-AAAATATAAATTC
*
11246945 TAAAAACTTTTAAAAACTATTCGAAATATAAATTC
1 -AAAAACTTTTAAAAACTATTCAAAATATAAATTC
*
11246980 AAAAAATTTTAAAAA
1 AAAAACTTTTAAAAA
11246995 ATGTAAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 37 0.84
35 7 0.16
ACGTcount: A:0.60, C:0.08, G:0.01, T:0.30
Consensus pattern (34 bp):
AAAAACTTTTAAAAACTATTCAAAATATAAATTC
Found at i:11247051 original size:79 final size:81
Alignment explanation
Indices: 11246920--11247071 Score: 202
Period size: 79 Copynumber: 1.9 Consensus size: 81
11246910 TAAAAAACTT
*
11246920 ATAAAAATATTCAAAAATATAAATCTAAAAACTTTTAAAAACTATTCGAAATATAAATTCAAAAA
1 ATAAAAATATTCAAAAATACAAATCTAAAAACTTTTAAAAACTATTCGAAATATAAATTCAAAAA
11246985 ATTTTAAAAAATGTAA
66 ATTTTAAAAAATGTAA
* * * * **
11247001 ATAAAACT-TTCAAAAATACAAATTTAAAAA-TTTTAAAAA-TTTTTGAAAATATAAATTTGAAA
1 ATAAAAATATTCAAAAATACAAATCTAAAAACTTTTAAAAACTATTCG-AAATATAAATTCAAAA
*
11247063 ACTTTTAAA
65 AATTTTAAA
11247072 GCTTTTAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
78 4 0.06
79 31 0.50
80 20 0.32
81 7 0.11
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.34
Consensus pattern (81 bp):
ATAAAAATATTCAAAAATACAAATCTAAAAACTTTTAAAAACTATTCGAAATATAAATTCAAAAA
ATTTTAAAAAATGTAA
Found at i:11247091 original size:34 final size:33
Alignment explanation
Indices: 11247002--11247104 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 33
11246992 AAAATGTAAA
* *
11247002 TAAAACTTTCAAAAATACAAATTT-AAAAATTT
1 TAAAACTTTTAAAAATATAAATTTGAAAAATTT
* * *
11247034 TAAAAATTTTTGAAAATATAAATTTGAAAACTTT
1 T-AAAACTTTTAAAAATATAAATTTGAAAAATTT
* *
11247068 TAAAGCTTTTAAAAATATAAAATTG-AAAATTT
1 TAAAACTTTTAAAAATATAAATTTGAAAAATTT
*
11247100 AAAAA
1 TAAAA
11247105 GAATAAGTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
32 10 0.18
33 39 0.68
34 8 0.14
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (33 bp):
TAAAACTTTTAAAAATATAAATTTGAAAAATTT
Found at i:11255851 original size:30 final size:29
Alignment explanation
Indices: 11255793--11255848 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
11255783 ATAGGTTTTG
11255793 AAACGGGTTACTTAGAAAAACAAAAAACA
1 AAACGGGTTACTTAGAAAAACAAAAAACA
11255822 AAACGGGTTACTTAGAAAAACAAAAAA
1 AAACGGGTTACTTAGAAAAACAAAAAA
11255849 ACACGGTCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.59, C:0.12, G:0.14, T:0.14
Consensus pattern (29 bp):
AAACGGGTTACTTAGAAAAACAAAAAACA
Found at i:11264455 original size:20 final size:20
Alignment explanation
Indices: 11264432--11264470 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11264422 TAGTTAGAAG
* *
11264432 ATTGATGTATTGTATTCAAC
1 ATTGATGCAGTGTATTCAAC
11264452 ATTGATGCAGTGTATTCAA
1 ATTGATGCAGTGTATTCAA
11264471 TGTATGCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTGATGCAGTGTATTCAAC
Found at i:11267485 original size:3 final size:3
Alignment explanation
Indices: 11267477--11267505 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
11267467 TTAGTTTTAT
11267477 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
11267506 TTGTCTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11268357 original size:14 final size:14
Alignment explanation
Indices: 11268338--11268367 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11268328 CAACGAAGGA
11268338 ATACATAAACAACT
1 ATACATAAACAACT
11268352 ATACATAAACAACT
1 ATACATAAACAACT
11268366 AT
1 AT
11268368 TAATCTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (14 bp):
ATACATAAACAACT
Found at i:11280168 original size:23 final size:23
Alignment explanation
Indices: 11280134--11280178 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
11280124 TAAAATTATT
*
11280134 TTTTATTAAAAAATATCATTTTA
1 TTTTATTAAAAAATATAATTTTA
11280157 TTTTATCT-AAAAATATAATTTT
1 TTTTAT-TAAAAAATATAATTTT
11280179 TTTATAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTATTAAAAAATATAATTTTA
Found at i:11305873 original size:22 final size:20
Alignment explanation
Indices: 11305848--11305893 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
11305838 ATTATCAAAA
* *
11305848 TTAAAATTATGATTTATTTAAT
1 TTAAAATAAT-ATTT-TTAAAT
11305870 TTAAAATAATATTTTTAAAT
1 TTAAAATAATATTTTTAAAT
11305890 TTAA
1 TTAA
11305894 TCATTTTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 4 0.18
22 9 0.41
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTAAAATAATATTTTTAAAT
Found at i:11305892 original size:20 final size:22
Alignment explanation
Indices: 11305839--11305893 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
11305829 ATTTTTGAAA
* * *
11305839 TTATCAAAATTAAAATTATGAT
1 TTATTAAATTTAAAATAATGAT
*
11305861 TTATTTAATTTAAAATAAT-AT
1 TTATTAAATTTAAAATAATGAT
11305882 TT-TTAAATTTAA
1 TTATTAAATTTAA
11305894 TCATTTTGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 9 0.32
21 4 0.14
22 15 0.54
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTATTAAATTTAAAATAATGAT
Found at i:11306305 original size:98 final size:99
Alignment explanation
Indices: 11306121--11306319 Score: 355
Period size: 98 Copynumber: 2.0 Consensus size: 99
11306111 GAGTAGACTG
*
11306121 GATTTTTCAATTAGAAAATTTAGGCTCCAAGTTGAATAATTTAAGCAGACAGGATTGCAATTTCT
1 GATTTTTCAATTAGAAAATTTAGGCTCCAAGTTGAATAATTTAAGCAGACAGGATTGAAATTTCT
*
11306186 TCATATATCTCAATCTTACAACAGTAACTGCTAA
66 TCATATATCTCAATCTGACAACAGTAACTGCTAA
**
11306220 GATTTTTCAATTAGAAAATTTAGGCTCCAAGTTGAATAA-TTGGGCAGACAGGATTGAAATTTCT
1 GATTTTTCAATTAGAAAATTTAGGCTCCAAGTTGAATAATTTAAGCAGACAGGATTGAAATTTCT
11306284 TCATATATCTCAATCTGACAACAGTAACTGCTAA
66 TCATATATCTCAATCTGACAACAGTAACTGCTAA
11306318 GA
1 GA
11306320 AAGAAGTTGG
Statistics
Matches: 96, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
98 57 0.59
99 39 0.41
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (99 bp):
GATTTTTCAATTAGAAAATTTAGGCTCCAAGTTGAATAATTTAAGCAGACAGGATTGAAATTTCT
TCATATATCTCAATCTGACAACAGTAACTGCTAA
Found at i:11306847 original size:29 final size:29
Alignment explanation
Indices: 11306790--11306848 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
11306780 TGTGGGTTAA
* *
11306790 TATTGAATTTTGTCATTATATTTTAAATT
1 TATTGAATTTTATCATTATACTTTAAATT
* *
11306819 TATTGAATTTTATCATTTTACTTTCAATT
1 TATTGAATTTTATCATTATACTTTAAATT
11306848 T
1 T
11306849 CGTTGAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (29 bp):
TATTGAATTTTATCATTATACTTTAAATT
Found at i:11307134 original size:31 final size:30
Alignment explanation
Indices: 11307080--11307155 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 30
11307070 GTCCTATAAC
*
11307080 CAATAAAATTGAAAGCATAGTGGCAAAGTT
1 CAATAAAATTGAAAGCATAGTGGCAAAATT
* *
11307110 CAATAAAATTTGATAGTATAGTGGCAAAATT
1 CAATAAAA-TTGAAAGCATAGTGGCAAAATT
**
11307141 CAAGGAAATTGAAAG
1 CAATAAAATTGAAAG
11307156 AAGAGTGATA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 14 0.36
31 25 0.64
ACGTcount: A:0.47, C:0.08, G:0.20, T:0.25
Consensus pattern (30 bp):
CAATAAAATTGAAAGCATAGTGGCAAAATT
Found at i:11320425 original size:16 final size:15
Alignment explanation
Indices: 11320406--11320472 Score: 64
Period size: 16 Copynumber: 4.3 Consensus size: 15
11320396 ATTCTTAACA
11320406 AAAATAAATAAATAAT
1 AAAATAAATAAA-AAT
* * *
11320422 AAAATTAGTAAAATT
1 AAAATAAATAAAAAT
11320437 GAAAATAAATAAAAAT
1 -AAAATAAATAAAAAT
11320453 AAAATATAA-AATAAAT
1 AAAATA-AATAA-AAAT
11320469 AAAA
1 AAAA
11320473 ATCAGAGCCA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
15 10 0.24
16 32 0.76
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
AAAATAAATAAAAAT
Found at i:11320446 original size:32 final size:29
Alignment explanation
Indices: 11320406--11320464 Score: 91
Period size: 32 Copynumber: 1.9 Consensus size: 29
11320396 ATTCTTAACA
11320406 AAAATAAATAAATAATAAAATTAGTAAAATTG
1 AAAATAAATAAA-AATAAAA-TA-TAAAATTG
11320438 AAAATAAATAAAAATAAAATATAAAAT
1 AAAATAAATAAAAATAAAATATAAAAT
11320465 AAATAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 6 0.22
30 2 0.07
31 7 0.26
32 12 0.44
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.25
Consensus pattern (29 bp):
AAAATAAATAAAAATAAAATATAAAATTG
Found at i:11320463 original size:22 final size:22
Alignment explanation
Indices: 11320430--11320474 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
11320420 ATAAAATTAG
11320430 TAAAATTGAAAATAAATAAAAA
1 TAAAATTGAAAATAAATAAAAA
11320452 TAAAATAT-AAAATAAATAAAAA
1 TAAAAT-TGAAAATAAATAAAAA
11320474 T
1 T
11320475 CAGAGCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAAATTGAAAATAAATAAAAA
Found at i:11321333 original size:3 final size:3
Alignment explanation
Indices: 11321325--11321462 Score: 146
Period size: 3 Copynumber: 48.3 Consensus size: 3
11321315 AAAGAAAAGA
11321325 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
11321373 AAT AAT AAT -AT ACT -AT AAT AAT AAT AAT -AT AAT -AT AGT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
11321416 GAT -AT AAT ACT AGT AAC AAT AAT -AC AAT AAT AAT AAC AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11321462 A
1 A
11321463 GCAGTAATAA
Statistics
Matches: 113, Mismatches: 15, Indels: 14
0.80 0.11 0.10
Matches are distributed among these distances:
2 11 0.10
3 102 0.90
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11325516 original size:21 final size:21
Alignment explanation
Indices: 11325492--11325532 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
11325482 AGTAGTGAAT
* * *
11325492 ATGAGATTAATTATTATAATG
1 ATGAAATTAAATACTATAATG
11325513 ATGAAATTAAATACTATAAT
1 ATGAAATTAAATACTATAAT
11325533 AATATGGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (21 bp):
ATGAAATTAAATACTATAATG
Found at i:11325705 original size:10 final size:10
Alignment explanation
Indices: 11325684--11325716 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
11325674 TATTTGTAAA
11325684 ATTAATAAATT
1 ATTAA-AAATT
11325695 ATTAAAAATT
1 ATTAAAAATT
11325705 ATT-AAAATT
1 ATTAAAAATT
11325714 ATT
1 ATT
11325717 TTATATCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 8 0.36
11 5 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:11325781 original size:50 final size:52
Alignment explanation
Indices: 11325699--11325795 Score: 137
Period size: 50 Copynumber: 1.9 Consensus size: 52
11325689 TAAATTATTA
*
11325699 AAAATTATTAAAATTATTTTATATCAAGTAAT-ATTTTAATT-AATAAATTG
1 AAAATTATTAAAATTATTTTATATCAAATAATAATTTTAATTGAATAAATTG
* *
11325749 AAAA-TATTAAAATTATTTTTATTTCAAATAATAATTTTTATTGAATA
1 AAAATTATTAAAATTA-TTTTATATCAAATAATAATTTTAATTGAATA
11325796 TTTAAATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
49 11 0.27
50 18 0.44
51 8 0.20
52 4 0.10
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (52 bp):
AAAATTATTAAAATTATTTTATATCAAATAATAATTTTAATTGAATAAATTG
Found at i:11326747 original size:3 final size:3
Alignment explanation
Indices: 11326739--11326772 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
11326729 TTGTGCTAAC
11326739 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
11326773 TATTATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:11326777 original size:3 final size:3
Alignment explanation
Indices: 11326771--11326797 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11326761 AATAATAATA
11326771 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
11326798 GTTTCTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:11327023 original size:11 final size:10
Alignment explanation
Indices: 11326954--11327033 Score: 56
Period size: 10 Copynumber: 7.8 Consensus size: 10
11326944 TTTTTTTAAA
11326954 TTCTAAAAACTT
1 TTCTAAAAA--T
*
11326966 TTTTAAAAAT
1 TTCTAAAAAT
*
11326976 TT-TTAAAAT
1 TTCTAAAAAT
*
11326985 TTCTGAAAAT
1 TTCTAAAAAT
*
11326995 TTC-AAAACAA
1 TTCTAAAA-AT
*
11327005 TTCTAAAATT
1 TTCTAAAAAT
11327015 TTCTAAAAACT
1 TTCTAAAAA-T
*
11327026 TTCCAAAA
1 TTCTAAAA
11327034 GACTAAAATA
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
9 11 0.20
10 24 0.44
11 12 0.22
12 8 0.15
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.40
Consensus pattern (10 bp):
TTCTAAAAAT
Found at i:11327298 original size:37 final size:37
Alignment explanation
Indices: 11327257--11327327 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
11327247 TTTTTGAAAA
* *
11327257 TTTTTGAAAATTTAAAAAAAATAAAAAATTCTAATTT
1 TTTTTAAAAAATTAAAAAAAATAAAAAATTCTAATTT
* * *
11327294 TTTTTAAAAAATTAAAAAAATTGAACAATTCTAA
1 TTTTTAAAAAATTAAAAAAAATAAAAAATTCTAA
11327328 AAATTCTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (37 bp):
TTTTTAAAAAATTAAAAAAAATAAAAAATTCTAATTT
Found at i:11327679 original size:19 final size:19
Alignment explanation
Indices: 11327657--11327707 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
11327647 TAAATCTTCA
*
11327657 TTTTTTAAATTTTTTG-GAT
1 TTTTTTAAA-ATTTTGAGAT
*
11327676 TTTTGTAAAATTTTGAGAT
1 TTTTTTAAAATTTTGAGAT
*
11327695 TTTTTGAAAATTT
1 TTTTTTAAAATTT
11327708 GTAACTTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (19 bp):
TTTTTTAAAATTTTGAGAT
Found at i:11327782 original size:12 final size:11
Alignment explanation
Indices: 11327752--11327792 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 11
11327742 AATTTTTGAA
11327752 TTTTTTAAA--
1 TTTTTTAAATT
11327761 TTTTTTAAATT
1 TTTTTTAAATT
11327772 TTTTTTGAAATT
1 TTTTTT-AAATT
11327784 TTCTTTTAA
1 TT-TTTTAA
11327793 TAATGATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.32
11 6 0.21
12 9 0.32
13 4 0.14
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (11 bp):
TTTTTTAAATT
Found at i:11327785 original size:9 final size:9
Alignment explanation
Indices: 11327656--11327775 Score: 62
Period size: 9 Copynumber: 12.8 Consensus size: 9
11327646 TTAAATCTTC
11327656 ATTTTTTAA
1 ATTTTTTAA
**
11327665 ATTTTTTGG
1 ATTTTTTAA
11327674 ATTTTTGTAA
1 ATTTTT-TAA
* * *
11327684 AATTTTGAG
1 ATTTTTTAA
11327693 ATTTTTTGAA
1 ATTTTTT-AA
* *
11327703 AATTTGTAA
1 ATTTTTTAA
* *
11327712 CTTTCCTT-A
1 ATTT-TTTAA
*
11327721 ATTTTTAAGA
1 ATTTTTTA-A
*
11327731 ATTTTTAAAAA
1 ATTTTT--TAA
* *
11327742 AATTTTTGA
1 ATTTTTTAA
11327751 ATTTTTTAA
1 ATTTTTTAA
11327760 ATTTTTTAA
1 ATTTTTTAA
11327769 ATTTTTT
1 ATTTTTT
11327776 TTGAAATTTT
Statistics
Matches: 80, Mismatches: 24, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
8 1 0.01
9 51 0.64
10 20 0.25
11 6 0.08
12 2 0.03
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.58
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:11328741 original size:22 final size:23
Alignment explanation
Indices: 11328712--11328778 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 23
11328702 CTGTGGGTTC
11328712 AAAA-AATTTTATTTATTAAAT-
1 AAAATAATTTTATTTATTAAATA
* **
11328733 TAAATAATTATT-TTTATTATCTA
1 AAAATAATT-TTATTTATTAAATA
11328756 AAAATAATTTGTAATTTATTAAA
1 AAAATAATTT-T-ATTTATTAAA
11328779 AATTTTGATT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
21 3 0.09
22 13 0.38
23 11 0.32
25 7 0.21
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (23 bp):
AAAATAATTTTATTTATTAAATA
Found at i:11333085 original size:41 final size:44
Alignment explanation
Indices: 11333035--11333115 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
11333025 ACCCCTCTGC
**
11333035 CATTGTTTCAAA-T-AAAAAAA-GAGTTTACACGCAACCTCTCG
1 CATTGTTTCAAATTAAAAAAAATGAGCATACACGCAACCTCTCG
*
11333076 CATTTTTTCAAATTAAAAAAAATGAGCATACACGCAACCT
1 CATTGTTTCAAATTAAAAAAAATGAGCATACACGCAACCT
11333116 TTGACACATG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 11 0.32
42 1 0.03
43 7 0.21
44 15 0.44
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (44 bp):
CATTGTTTCAAATTAAAAAAAATGAGCATACACGCAACCTCTCG
Found at i:11344907 original size:15 final size:15
Alignment explanation
Indices: 11344887--11344918 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
11344877 CCTTTCCTCC
11344887 ACACACTCTTCAAAG
1 ACACACTCTTCAAAG
11344902 ACACACTCTTCAAAG
1 ACACACTCTTCAAAG
11344917 AC
1 AC
11344919 TTAGCCTTTT
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:0.41, C:0.34, G:0.06, T:0.19
Consensus pattern (15 bp):
ACACACTCTTCAAAG
Found at i:11345963 original size:18 final size:19
Alignment explanation
Indices: 11345928--11345963 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
11345918 TATTTAATAT
11345928 TAAAATATGATATAAATTA
1 TAAAATATGATATAAATTA
*
11345947 TAAAATAT-ATTTAAATT
1 TAAAATATGATATAAATT
11345964 TTTTACATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAAATATGATATAAATTA
Found at i:11346560 original size:9 final size:9
Alignment explanation
Indices: 11346523--11346600 Score: 57
Period size: 9 Copynumber: 8.6 Consensus size: 9
11346513 TTTACATGTT
11346523 TATATTAAA
1 TATATTAAA
* *
11346532 TTAAAATAAA
1 -TATATTAAA
**
11346542 TATAAAAAA
1 TATATTAAA
*
11346551 TATGTTAAA
1 TATATTAAA
*
11346560 TGTATTAAA
1 TATATTAAA
11346569 TATATTAAA
1 TATATTAAA
*
11346578 TGTATTAAA
1 TATATTAAA
* *
11346587 CATGTTAAA
1 TATATTAAA
*
11346596 CATAT
1 TATAT
11346601 ATTAGTATAA
Statistics
Matches: 53, Mismatches: 15, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
9 46 0.87
10 7 0.13
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (9 bp):
TATATTAAA
Found at i:11346569 original size:18 final size:18
Alignment explanation
Indices: 11346548--11346595 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
11346538 TAAATATAAA
11346548 AAATATGTTAAATGTATT
1 AAATATGTTAAATGTATT
*
11346566 AAATATATTAAATGTATT
1 AAATATGTTAAATGTATT
*
11346584 AAACATGTTAAA
1 AAATATGTTAAA
11346596 CATATATTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (18 bp):
AAATATGTTAAATGTATT
Found at i:11346743 original size:18 final size:18
Alignment explanation
Indices: 11346722--11346766 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
11346712 TTAAATACAT
*
11346722 ATATAATTATTTTATATC
1 ATATAATTATATTATATC
*
11346740 ATATAATCATATTATATC
1 ATATAATTATATTATATC
*
11346758 TTA-AATTAT
1 ATATAATTAT
11346767 CAAATTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATAATTATATTATATC
Found at i:11350824 original size:179 final size:179
Alignment explanation
Indices: 11350517--11350875 Score: 664
Period size: 179 Copynumber: 2.0 Consensus size: 179
11350507 ATAAGTTTTC
* *
11350517 TGCTATTATGCAATAGCTACATTTATATAGCAAATTACCAATCCCCATCAAAATCTTTTTTTGGT
1 TGCTATTATGCAATAGCTACATTTATATACCAAATTACCAATCCCCATCAAAATCTTTGTTTGGT
*
11350582 ACAGGATAGCTAGTATAACTTGAAGAATTTCTGCACAGAACATAGACAAAGCAGGATAAAAAACA
66 ACAGGATAGCTAGTATAACTTGAAGAATTTCTGCACAGAACATAGACAAAGCAGGACAAAAAACA
* *
11350647 CCCAGAACAAGAATATTAGCCCCTATTGTTTTTGAGTAGGAATCCTTCA
131 CCCAGAACAAGAATATTAGCCCCTACTGTTTTTGAGTAGCAATCCTTCA
11350696 TGCTATTATGCAATAGCTACATTTATATACCAAATTACCAATCCCCATCAAAATCTTTGTTTGGT
1 TGCTATTATGCAATAGCTACATTTATATACCAAATTACCAATCCCCATCAAAATCTTTGTTTGGT
*
11350761 ACAGGATAGCTAGTATAACTTGAAGAATTTCTGCACAGCACATAGACAAAGCAGGACAAAAAACA
66 ACAGGATAGCTAGTATAACTTGAAGAATTTCTGCACAGAACATAGACAAAGCAGGACAAAAAACA
11350826 CCCAGAACAAGAATATTAGCCCCTACTGTTTTTGAGTAGCAATCCTTCA
131 CCCAGAACAAGAATATTAGCCCCTACTGTTTTTGAGTAGCAATCCTTCA
11350875 T
1 T
11350876 TCCAATCATT
Statistics
Matches: 174, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
179 174 1.00
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.28
Consensus pattern (179 bp):
TGCTATTATGCAATAGCTACATTTATATACCAAATTACCAATCCCCATCAAAATCTTTGTTTGGT
ACAGGATAGCTAGTATAACTTGAAGAATTTCTGCACAGAACATAGACAAAGCAGGACAAAAAACA
CCCAGAACAAGAATATTAGCCCCTACTGTTTTTGAGTAGCAATCCTTCA
Found at i:11354046 original size:22 final size:20
Alignment explanation
Indices: 11354004--11354049 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
11353994 ATGAATATAC
* *
11354004 TTTATATATAATAGTTCATT
1 TTTATATATAACAGTTAATT
11354024 TTTATATATTAACAGTGTAATT
1 TTTATATA-TAACAGT-TAATT
11354046 TTTA
1 TTTA
11354050 ATTTTACAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 6 0.27
22 8 0.36
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (20 bp):
TTTATATATAACAGTTAATT
Found at i:11357491 original size:10 final size:9
Alignment explanation
Indices: 11357409--11357492 Score: 50
Period size: 9 Copynumber: 9.3 Consensus size: 9
11357399 AATTTTCTAA
*
11357409 AAAAAATCC
1 AAAAAATTC
*
11357418 ATAAAATTC
1 AAAAAATTC
11357427 AAAAAAATT-
1 -AAAAAATTC
* *
11357436 -AAATATTT
1 AAAAAATTC
*
11357444 AAAAAATTA
1 AAAAAATTC
11357453 AAAAAATT-
1 AAAAAATTC
*
11357461 ATGAAAACTT-
1 A--AAAAATTC
11357471 AAAAAATTC
1 AAAAAATTC
11357480 AAAAAATCTC
1 AAAAAAT-TC
11357490 AAA
1 AAA
11357493 TTTTTAATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
7 6 0.10
8 7 0.12
9 28 0.47
10 19 0.32
ACGTcount: A:0.65, C:0.08, G:0.01, T:0.25
Consensus pattern (9 bp):
AAAAAATTC
Found at i:11357499 original size:27 final size:25
Alignment explanation
Indices: 11357420--11357486 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 25
11357410 AAAAATCCAT
11357420 AAAATTCAAAAAAATTAAATATTTAA
1 AAAATTC-AAAAAATTAAATATTTAA
* * *
11357446 AAAATTAAAAAAATTATGAAAACTTAA
1 AAAATTCAAAAAATTA--AATATTTAA
11357473 AAAATTCAAAAAAT
1 AAAATTCAAAAAAT
11357487 CTCAAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 9 0.26
26 6 0.17
27 20 0.57
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.27
Consensus pattern (25 bp):
AAAATTCAAAAAATTAAATATTTAA
Found at i:11357512 original size:29 final size:29
Alignment explanation
Indices: 11357436--11357540 Score: 83
Period size: 27 Copynumber: 3.7 Consensus size: 29
11357426 CAAAAAAATT
* * *
11357436 AAATATTTAA-AAAATTAAAAAAATTATGA
1 AAAT-TTTAATAAAAATAAAAAAATTCTAA
* * * *
11357465 AAA-CTTAA-AAAATTCAAAAAA-TCTCA
1 AAATTTTAATAAAAATAAAAAAATTCTAA
* *
11357491 AATTTTTAATAACAACTAAAAAAATTCTAA
1 AAATTTTAATAA-AAATAAAAAAATTCTAA
11357521 AAATTTTAATAAAAATAAAA
1 AAATTTTAATAAAAATAAAA
11357541 TGTTAATAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
26 5 0.08
27 20 0.33
28 2 0.03
29 19 0.31
30 15 0.25
ACGTcount: A:0.63, C:0.07, G:0.01, T:0.30
Consensus pattern (29 bp):
AAATTTTAATAAAAATAAAAAAATTCTAA
Done.