Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 179 of 187
Found at i:53650832 original size:29 final size:29
Alignment explanation
Indices: 53650783--53650845 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
53650773 CAACGGTGCC
* *
53650783 TTCGAACCAATAACTCAGATATCACTTAG
1 TTCGAACCAACAACTCAGATACCACTTAG
* * *
53650812 TTCGAACCAACAGCTCGGATACCACTTGG
1 TTCGAACCAACAACTCAGATACCACTTAG
53650841 TTCGA
1 TTCGA
53650846 CCTTAGCTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (29 bp):
TTCGAACCAACAACTCAGATACCACTTAG
Found at i:53660784 original size:79 final size:79
Alignment explanation
Indices: 53660653--53660811 Score: 318
Period size: 79 Copynumber: 2.0 Consensus size: 79
53660643 TCCCTTATGA
53660653 TAACTTCCTAGGATTTTCAAGCCTAGGATTTAGAAACGCATAATCTATACCAACTAATCCTATTA
1 TAACTTCCTAGGATTTTCAAGCCTAGGATTTAGAAACGCATAATCTATACCAACTAATCCTATTA
53660718 TGAACTCGTATTCT
66 TGAACTCGTATTCT
53660732 TAACTTCCTAGGATTTTCAAGCCTAGGATTTAGAAACGCATAATCTATACCAACTAATCCTATTA
1 TAACTTCCTAGGATTTTCAAGCCTAGGATTTAGAAACGCATAATCTATACCAACTAATCCTATTA
53660797 TGAACTCGTATTCT
66 TGAACTCGTATTCT
53660811 T
1 T
53660812 TTGTTAATTA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (79 bp):
TAACTTCCTAGGATTTTCAAGCCTAGGATTTAGAAACGCATAATCTATACCAACTAATCCTATTA
TGAACTCGTATTCT
Found at i:53671004 original size:5 final size:5
Alignment explanation
Indices: 53670994--53671018 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53670984 GTATATATAA
53670994 AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT
53671019 TATAGTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:53671336 original size:2 final size:2
Alignment explanation
Indices: 53671329--53671355 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53671319 TTGTGATTTC
53671329 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 A
53671356 ACTTTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53674219 original size:20 final size:20
Alignment explanation
Indices: 53674185--53674226 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
53674175 AATTATTTAA
** *
53674185 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
53674205 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
53674225 AT
1 AT
53674227 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:53677722 original size:41 final size:41
Alignment explanation
Indices: 53677540--53677725 Score: 291
Period size: 41 Copynumber: 4.5 Consensus size: 41
53677530 GACTTTAAGT
*
53677540 CTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
53677581 CTAGCAGGCTAAGTGTCGATGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
53677622 CTAGCAGGCTAAGTACCGATGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * *
53677663 CTATCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
53677704 CTAGCAGGCTAATTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
53677726 ATATGTTAAA
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 133 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:53680602 original size:21 final size:21
Alignment explanation
Indices: 53680572--53680619 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
53680562 AACAAATAGA
*
53680572 AAACACAAAGAAATTCTTGTC
1 AAACAAAAAGAAATTCTTGTC
53680593 AAACAAAAAGAAATTCTTGTC
1 AAACAAAAAGAAATTCTTGTC
53680614 AAACAA
1 AAACAA
53680620 CTTTGCTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.54, C:0.17, G:0.08, T:0.21
Consensus pattern (21 bp):
AAACAAAAAGAAATTCTTGTC
Found at i:53682119 original size:20 final size:20
Alignment explanation
Indices: 53682085--53682126 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
53682075 AACTATTTAA
** *
53682085 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
53682105 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
53682125 AT
1 AT
53682127 GTATTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:53692319 original size:9 final size:9
Alignment explanation
Indices: 53692274--53692431 Score: 54
Period size: 9 Copynumber: 16.7 Consensus size: 9
53692264 ATTACATATT
*
53692274 AAAACTATA
1 AAAATTATA
*
53692283 AAAAGTA-A
1 AAAATTATA
* *
53692291 AAATTTGTA
1 AAAATTATA
*
53692300 TAAACTTATA
1 -AAAATTATA
53692310 AAAATTAT-
1 AAAATTATA
53692318 AAAATT-TA
1 AAAATTATA
*
53692326 ATAAAATATTA
1 A-AAATTA-TA
*
53692337 AAACTT-TCA
1 AAAATTAT-A
53692346 ATAAATTTATAA
1 A-AAA-TTAT-A
*
53692358 AAAAATATAA
1 AAAATTAT-A
53692368 AAATATTCATA
1 AAA-ATT-ATA
53692379 AAAACTTATA
1 AAAA-TTATA
*
53692389 AATATTATA
1 AAAATTATA
**
53692398 AAGCTTATGA
1 AAAATTAT-A
*
53692408 ATAATTATA
1 AAAATTATA
**
53692417 AAGCTTATA
1 AAAATTATA
53692426 AAAATT
1 AAAATT
53692432 TTAATAAGAG
Statistics
Matches: 110, Mismatches: 25, Indels: 28
0.67 0.15 0.17
Matches are distributed among these distances:
7 1 0.01
8 13 0.12
9 42 0.38
10 33 0.30
11 16 0.15
12 5 0.05
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (9 bp):
AAAATTATA
Found at i:53692329 original size:27 final size:26
Alignment explanation
Indices: 53692275--53692339 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
53692265 TTACATATTA
*
53692275 AAACTATAAAAAGTAAAAATTTGTAT
1 AAACTATAAAAAGTAAAAATTTGAAT
*
53692301 AAACTTATAAAAATTATAAAATTT-AAT
1 AAAC-TATAAAAAGTA-AAAATTTGAAT
* *
53692328 AAAATATTAAAA
1 AAACTATAAAAA
53692340 CTTTCAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 11 0.33
27 15 0.45
28 7 0.21
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (26 bp):
AAACTATAAAAAGTAAAAATTTGAAT
Found at i:53692398 original size:19 final size:18
Alignment explanation
Indices: 53692301--53692427 Score: 71
Period size: 19 Copynumber: 6.6 Consensus size: 18
53692291 AAATTTGTAT
*
53692301 AAACTTATAAAAATTATA
1 AAACTTATAAATATTATA
*
53692319 AAATTTAATAAA-A-TATTA
1 AAACTT-ATAAATATTA-TA
53692337 AAACTTTCAATAAAT-TTATAAA
1 AAAC-TT--ATAAATATTAT--A
* *
53692359 AAAATATAAAAATATTCATAA
1 AAACT-TATAAATATT-AT-A
53692380 AAACTTATAAATATTATA
1 AAACTTATAAATATTATA
* *
53692398 AAGCTTATGAATAATTATA
1 AAACTTATAAAT-ATTATA
*
53692417 AAGCTTATAAA
1 AAACTTATAAA
53692428 AATTTTAATA
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
17 2 0.02
18 22 0.25
19 25 0.28
20 21 0.24
21 11 0.12
22 7 0.08
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (18 bp):
AAACTTATAAATATTATA
Found at i:53692833 original size:5 final size:5
Alignment explanation
Indices: 53692823--53692847 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53692813 AAAACAAACA
53692823 TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT
53692848 AAACCTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:53694544 original size:6 final size:6
Alignment explanation
Indices: 53694499--53694528 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
53694489 AAAACTAAGA
53694499 TTAAA- TTAAAT TTAAAT TTAAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T
53694529 GAAAACTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAAAT
Found at i:53698620 original size:30 final size:30
Alignment explanation
Indices: 53698567--53698641 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
53698557 TTAGGGCCTC
* * *
53698567 AACTTCATAATTATTTTCGTATTAAGACTTA
1 AACTTGATAATT-TTTTCATATTAAAACTTA
*
53698598 AACTTGATAATTTTTTCATATTAAAACTTG
1 AACTTGATAATTTTTTCATATTAAAACTTA
* *
53698628 AATTTGATAGTTTT
1 AACTTGATAATTTT
53698642 CAAGGATTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
30 27 0.71
31 11 0.29
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.48
Consensus pattern (30 bp):
AACTTGATAATTTTTTCATATTAAAACTTA
Found at i:53701677 original size:24 final size:24
Alignment explanation
Indices: 53701642--53701690 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
53701632 GAGGATGACC
* *
53701642 CAGAATTGGCAA-TTGCTTTGATAG
1 CAGAATTAGCAACTTG-TTTCATAG
53701666 CAGAATTAGCAACTTGTTTCATAG
1 CAGAATTAGCAACTTGTTTCATAG
53701690 C
1 C
53701691 CATATCTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (24 bp):
CAGAATTAGCAACTTGTTTCATAG
Found at i:53705518 original size:19 final size:20
Alignment explanation
Indices: 53705477--53705518 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
53705467 ATTTCTATGC
* *
53705477 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
53705497 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
53705516 CAT
1 CAT
53705519 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:53710288 original size:33 final size:32
Alignment explanation
Indices: 53710206--53710315 Score: 94
Period size: 33 Copynumber: 3.3 Consensus size: 32
53710196 TGGTCCAACC
** * *
53710206 ATGGTCTTACGATTAAGGTGCCATAACCCAGTT
1 ATGGTCTTAC-ATTAAAATGCCATAGCCCAGCT
* *
53710239 ATGGTCTTTTCATTAAAATGCCATGGCCCAGCT
1 ATGGTC-TTACATTAAAATGCCATAGCCCAGCT
* * *
53710272 ATGGTCTTACATTTAAACATTGCCATAGTCCAACC
1 ATGGTCTTACA-TTAAA-A-TGCCATAGCCCAGCT
53710307 ATGGTCTTA
1 ATGGTCTTA
53710316 TCCGTCAATT
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
32 4 0.06
33 34 0.55
34 4 0.06
35 20 0.32
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (32 bp):
ATGGTCTTACATTAAAATGCCATAGCCCAGCT
Found at i:53714041 original size:2 final size:2
Alignment explanation
Indices: 53714034--53714062 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
53714024 AATATACATT
53714034 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53714063 ACATAAGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53715716 original size:7 final size:8
Alignment explanation
Indices: 53715687--53715721 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
53715677 TTGAACTGGG
53715687 TTTTTTAAA
1 TTTTTT-AA
53715696 CTTTTTTAA
1 -TTTTTTAA
53715705 TTTTTTAA
1 TTTTTTAA
53715713 TTTTTTAA
1 TTTTTTAA
53715721 T
1 T
53715722 CGGACTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 2 0.08
10 6 0.24
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTTTAA
Found at i:53717951 original size:19 final size:17
Alignment explanation
Indices: 53717908--53717951 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
53717898 TTTATTGATT
*
53717908 AAAAATACGTTAATTTA
1 AAAAATAAGTTAATTTA
53717925 AAATAATAAGTGTAATTTA
1 AAA-AATAAGT-TAATTTA
53717944 ATAAAATA
1 A-AAAATA
53717952 TTAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 6 0.26
19 12 0.52
20 2 0.09
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (17 bp):
AAAAATAAGTTAATTTA
Found at i:53718702 original size:2 final size:2
Alignment explanation
Indices: 53718695--53718732 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
53718685 TTTTTATTCG
53718695 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53718733 GAACTTGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53720451 original size:19 final size:18
Alignment explanation
Indices: 53720429--53720499 Score: 51
Period size: 18 Copynumber: 3.9 Consensus size: 18
53720419 TATCATATCA
53720429 ATTTAAAATATTAATATAT
1 ATTTAAAATATTAATAT-T
*
53720448 ATTT-AAAGATTAA-ATT
1 ATTTAAAATATTAATATT
*
53720464 CTTGTGAAAATATTTAAT-TT
1 ATT-T-AAAATA-TTAATATT
*
53720484 ATTCAAAAT-TTAATAT
1 ATTTAAAATATTAATAT
53720500 ATATAATCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
16 8 0.20
17 4 0.10
18 13 0.32
19 8 0.20
20 8 0.20
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (18 bp):
ATTTAAAATATTAATATT
Found at i:53729172 original size:20 final size:21
Alignment explanation
Indices: 53729147--53729185 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
53729137 TGAAGCAAAC
53729147 ATTTAGAA-TGAAAATGAGTT
1 ATTTAGAACTGAAAATGAGTT
*
53729167 ATTTAGAACTGAAATTGAG
1 ATTTAGAACTGAAAATGAG
53729186 AAGTTTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.33
Consensus pattern (21 bp):
ATTTAGAACTGAAAATGAGTT
Found at i:53732326 original size:12 final size:12
Alignment explanation
Indices: 53732274--53732333 Score: 70
Period size: 12 Copynumber: 5.2 Consensus size: 12
53732264 AAAATTATTA
53732274 TTTTAGAATTTT
1 TTTTAGAATTTT
53732286 TTTTA-AATTTT
1 TTTTAGAATTTT
* * *
53732297 CTTTA-TATATT
1 TTTTAGAATTTT
*
53732308 CTTTAGAATTTT
1 TTTTAGAATTTT
53732320 TTTTAGAATTTT
1 TTTTAGAATTTT
53732332 TT
1 TT
53732334 AAAAATATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
11 19 0.46
12 22 0.54
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.67
Consensus pattern (12 bp):
TTTTAGAATTTT
Found at i:53733306 original size:29 final size:30
Alignment explanation
Indices: 53733259--53733317 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
53733249 GAATTGGATC
*
53733259 AAATCAAAATTTCTTGTATAAAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTGCACA
*
53733289 AAATCAAAA-TTCATGTATACAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTGCACA
53733318 TTAAACAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTGCACA
Found at i:53734743 original size:10 final size:10
Alignment explanation
Indices: 53734727--53734814 Score: 58
Period size: 10 Copynumber: 8.7 Consensus size: 10
53734717 AAATATATTT
53734727 ATTTTTTT-A
1 ATTTTTTTAA
53734736 ATTTTTTTAA
1 ATTTTTTTAA
*
53734746 A--TTTTAAA
1 ATTTTTTTAA
*
53734754 ATATTTTTAAA
1 AT-TTTTTTAA
*
53734765 ATACTTTTTTTA
1 AT--TTTTTTAA
53734777 ATTTTTTTAA
1 ATTTTTTTAA
**
53734787 A-TTTTAAAA
1 ATTTTTTTAA
53734796 TACTTTTTTTAA
1 -A-TTTTTTTAA
53734808 ATTTTTT
1 ATTTTTT
53734815 AATTTTAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
8 7 0.11
9 14 0.23
10 17 0.27
11 10 0.16
12 14 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTTTAA
Found at i:53734792 original size:30 final size:30
Alignment explanation
Indices: 53734758--53734878 Score: 140
Period size: 30 Copynumber: 4.0 Consensus size: 30
53734748 TTTAAAATAT
53734758 TTTTAAAATACTTTTTTTAATTTTTTTAAA
1 TTTTAAAATACTTTTTTTAATTTTTTTAAA
*
53734788 TTTTAAAATACTTTTTTTAAATTTTTT-AA
1 TTTTAAAATACTTTTTTTAATTTTTTTAAA
* * *
53734817 TTTTAAAATA-TTTTTAAAATACTTTTTTTAAT
1 TTTTAAAATACTTTTT---TTAATTTTTTTAAA
*
53734849 TTTTAAAATAC-TTTTTTAATATTTATTAAA
1 TTTTAAAATACTTTTTTTAAT-TTTTTTAAA
53734879 AAATGGGCTG
Statistics
Matches: 76, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
28 5 0.07
29 15 0.20
30 33 0.43
31 8 0.11
32 15 0.20
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTAAAATACTTTTTTTAATTTTTTTAAA
Found at i:53734802 original size:21 final size:21
Alignment explanation
Indices: 53734778--53734865 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 21
53734768 CTTTTTTTAA
53734778 TTTTTTTAAATTTTAAAATAC
1 TTTTTTTAAATTTTAAAATAC
*
53734799 TTTTTTTAAATTTT---TTA-
1 TTTTTTTAAATTTTAAAATAC
* **
53734816 ATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAA-A-TTTTAAAATAC
*
53734839 TTTTTTTAATTTTTAAAATAC
1 TTTTTTTAAATTTTAAAATAC
53734860 TTTTTT
1 TTTTTT
53734866 AATATTTATT
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
17 6 0.12
18 3 0.06
19 4 0.08
21 31 0.60
22 2 0.04
23 6 0.12
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTTTAAATTTTAAAATAC
Found at i:53734814 original size:41 final size:41
Alignment explanation
Indices: 53734728--53734852 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 41
53734718 AATATATTTA
*
53734728 TTTTTTTAATTTTTTTAAATTTTAAAATA--TTTTTAAAAT
1 TTTTTTTAATTTTTTTAAATTTTAAAATACTTTTTTTAAAT
53734767 ACTTTTTTTAATTTTTTTAAATTTTAAAATACTTTTTTTAAA-
1 --TTTTTTTAATTTTTTTAAATTTTAAAATACTTTTTTTAAAT
**
53734809 -TTTTTTAA-TTTTAAAATATTTTTAAAATACTTTTTTT-AAT
1 TTTTTTTAATTTTTTTAA-A-TTTTAAAATACTTTTTTTAAAT
53734849 TTTT
1 TTTT
53734853 AAAATACTTT
Statistics
Matches: 75, Mismatches: 3, Indels: 12
0.83 0.03 0.13
Matches are distributed among these distances:
38 6 0.08
39 11 0.15
40 18 0.24
41 32 0.43
43 8 0.11
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (41 bp):
TTTTTTTAATTTTTTTAAATTTTAAAATACTTTTTTTAAAT
Found at i:53734873 original size:20 final size:21
Alignment explanation
Indices: 53734829--53734873 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
53734819 TTAAAATATT
*
53734829 TTTAAAATACTTTTTTTAATT
1 TTTAAAATACTTTTTTTAATA
53734850 TTTAAAATAC-TTTTTTAATA
1 TTTAAAATACTTTTTTTAATA
53734870 TTTA
1 TTTA
53734874 TTAAAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAAAATACTTTTTTTAATA
Found at i:53734878 original size:70 final size:70
Alignment explanation
Indices: 53734733--53734878 Score: 197
Period size: 70 Copynumber: 2.1 Consensus size: 70
53734723 ATTTATTTTT
* **
53734733 TTAATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAAATTTTAAAATA
1 TTAAATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTAAAAATTTTAAAATA
*
53734798 CTTTTT
66 C-TTTA
**
53734804 TTAAATTTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTAAAATACTTTTTTAA
1 TTAAATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTAAAA-A-TTTTAAAA
53734868 TA-TTTA
64 TACTTTA
53734874 TTAAA
1 TTAAA
53734879 AAATGGGCTG
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
70 48 0.72
71 11 0.16
72 8 0.12
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (70 bp):
TTAAATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTAAAAATTTTAAAATA
CTTTA
Found at i:53738161 original size:30 final size:28
Alignment explanation
Indices: 53738127--53738221 Score: 102
Period size: 29 Copynumber: 3.3 Consensus size: 28
53738117 AAATATTTAT
53738127 TTTTTAAATTTTAAAATATTTTTAAAATA
1 TTTTTAAATTTTAAAATA-TTTTAAAATA
*
53738156 CTTTTTTAATTTTAAAATATTTTAAAATA
1 -TTTTTAAATTTTAAAATATTTTAAAATA
* ***
53738185 TTTTAAAATACTTTTTTA-ATTTTAAAATA
1 TTTTTAAAT--TTTAAAATATTTTAAAATA
53738214 TTTTTAAA
1 TTTTTAAA
53738222 ATACTTTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
28 7 0.12
29 28 0.50
30 21 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTTTAAATTTTAAAATATTTTAAAATA
Found at i:53738168 original size:39 final size:39
Alignment explanation
Indices: 53738125--53738282 Score: 183
Period size: 39 Copynumber: 4.3 Consensus size: 39
53738115 ATAAATATTT
53738125 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
**
53738164 ATTTTAAAATATTTTAAAATA-TTTTAAAATAC-------
1 ATTTTTTAA-ATTTTAAAATATTTTTAAAATACTTTTTTA
53738196 -TTTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATAC-TTTTTTA
* *
53738234 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
*
53738273 AATTTTTAAA
1 ATTTTTTAAA
53738283 ATAAATTTTT
Statistics
Matches: 100, Mismatches: 7, Indels: 24
0.76 0.05 0.18
Matches are distributed among these distances:
29 11 0.11
30 12 0.12
31 4 0.04
39 38 0.38
40 35 0.35
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (39 bp):
ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:53738180 original size:40 final size:42
Alignment explanation
Indices: 53738135--53738275 Score: 222
Period size: 40 Copynumber: 3.5 Consensus size: 42
53738125 ATTTTTTAAA
53738135 TTTTAAAATA-TTTTTAAAATACTTTTTTAATTTTAAAATA-
1 TTTTAAAATACTTTTTAAAATACTTTTTTAATTTTAAAATAT
53738175 TTTTAAAATA--TTTTAAAATACTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTAAAATACTTTTTTAATTTTAAAATAT
**
53738215 TTTTAAAATACTTTTTTTAAT--TTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTAAAATACTTTTTTAATTTTAAAATAT
53738255 TTTTAAAATACTTTTTAAAAT
1 TTTTAAAATACTTTTTAAAAT
53738276 TTTTAAAATA
Statistics
Matches: 94, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
39 29 0.31
40 58 0.62
42 7 0.07
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (42 bp):
TTTTAAAATACTTTTTAAAATACTTTTTTAATTTTAAAATAT
Found at i:53738200 original size:69 final size:70
Alignment explanation
Indices: 53738127--53738285 Score: 241
Period size: 69 Copynumber: 2.3 Consensus size: 70
53738117 AAATATTTAT
53738127 TTTTTAAATTTTAAAATATTTTTAAAATAC-TTTTTTAATTTTAAAATATTTTAAAATA-TTTTA
1 TTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTAAAA-ATTTTAAAATATTTTTA
53738190 AAATAC
65 AAATAC
* ***
53738196 TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAA
1 TTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTAAAAATTTTAAAATATTTTTAA
53738261 AATAC
66 AATAC
53738266 TTTTTAAAATTTTTAAAATA
1 TTTTT-AAA-TTTTAAAATA
53738286 AATTTTTGGT
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
69 40 0.49
70 29 0.36
71 2 0.02
72 10 0.12
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (70 bp):
TTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTAAAAATTTTAAAATATTTTTAA
AATAC
Found at i:53738222 original size:30 final size:30
Alignment explanation
Indices: 53738174--53738238 Score: 114
Period size: 31 Copynumber: 2.2 Consensus size: 30
53738164 ATTTTAAAAT
53738174 ATTTTAAAATATTTTAAAATAC-TTTTTTA
1 ATTTTAAAATATTTTAAAATACTTTTTTTA
53738203 ATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTAAAATA-TTTTAAAATACTTTTTTTA
53738234 ATTTT
1 ATTTT
53738239 TTTAATTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.32
30 11 0.32
31 12 0.35
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTTTAAAATATTTTAAAATACTTTTTTTA
Found at i:53738269 original size:29 final size:29
Alignment explanation
Indices: 53738215--53738272 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
53738205 TTTAAAATAT
** *
53738215 TTTTAAAATACTTTTTTTAATTTTTTTAA
1 TTTTAAAATACTTTTTAAAATCTTTTTAA
53738244 TTTTAAAATA-TTTTTAAAATACTTTTTAA
1 TTTTAAAATACTTTTTAAAAT-CTTTTTAA
53738273 AATTTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTAAAATACTTTTTAAAATCTTTTTAA
Found at i:53738291 original size:21 final size:23
Alignment explanation
Indices: 53738242--53738291 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
53738232 TAATTTTTTT
53738242 AATTTTAAAATATTTTTAAAAT-
1 AATTTTAAAATATTTTTAAAATA
* *
53738264 ACTTTTTAAA-ATTTTTAAAATA
1 AATTTTAAAATATTTTTAAAATA
53738286 AATTTT
1 AATTTT
53738292 TGGTATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
AATTTTAAAATATTTTTAAAATA
Found at i:53749741 original size:21 final size:21
Alignment explanation
Indices: 53749717--53749756 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
53749707 TAACTCTAAC
53749717 ATTTATAAAA-TTTATAATTAA
1 ATTT-TAAAACTTTATAATTAA
*
53749738 ATTTTAAAACTTTTTAATT
1 ATTTTAAAACTTTATAATT
53749757 CTTAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTTAAAACTTTATAATTAA
Found at i:53754014 original size:24 final size:24
Alignment explanation
Indices: 53753961--53754030 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
53753951 TAAAATCGTT
*
53753961 TAATTTATTATATATTATTATCTTA
1 TAATTTATTATACATTATTAT-TTA
* *
53753986 -GATTTATTATGCATTATTATTTA
1 TAATTTATTATACATTATTATTTA
*
53754009 TAATTTATCA-ACATTATTATTT
1 TAATTTATTATACATTATTATTT
53754031 TAAATTCATC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
23 14 0.37
24 24 0.63
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (24 bp):
TAATTTATTATACATTATTATTTA
Found at i:53754036 original size:23 final size:24
Alignment explanation
Indices: 53753962--53754057 Score: 79
Period size: 24 Copynumber: 4.0 Consensus size: 24
53753952 AAAATCGTTT
* * *
53753962 AATTTATTATATATTATTATCTTA
1 AATTTATCATACATTATTATTTTA
* * *
53753986 GATTTATTATGCATTATTA-TTTA
1 AATTTATCATACATTATTATTTTA
53754009 TAATTTATCA-ACATTATTATTTTA
1 -AATTTATCATACATTATTATTTTA
* *
53754033 AATTCATCATTAACATTAATATTTT
1 AATTTATCA-T-ACATTATTATTTT
53754058 TAATCATGTA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
23 19 0.33
24 27 0.47
26 12 0.21
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.54
Consensus pattern (24 bp):
AATTTATCATACATTATTATTTTA
Found at i:53754857 original size:30 final size:30
Alignment explanation
Indices: 53754811--53754934 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
53754801 TTTTATTATG
*
53754811 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
53754842 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
53754872 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
53754902 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
53754932 CCA
1 CCA
53754935 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:53754866 original size:15 final size:15
Alignment explanation
Indices: 53754821--53754928 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
53754811 CCAATATCTC
53754821 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
53754836 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
53754851 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
53754866 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
53754881 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
53754896 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
53754911 GATACCCATATCTTT
1 GATACCCATATCTTT
53754926 GAT
1 GAT
53754929 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:53759632 original size:30 final size:30
Alignment explanation
Indices: 53759598--53759709 Score: 190
Period size: 30 Copynumber: 3.7 Consensus size: 30
53759588 CCAATATCTC
53759598 GATACCCATATCTTTGACTTTCTAATATTT
1 GATACCCATATCTTTGACTTTCTAATATTT
53759628 GATACCCATATCTTTGACTTT-TCAATATTT
1 GATACCCATATCTTTGACTTTCT-AATATTT
*
53759658 GATACCCATATCTTTGACTTTCTATTATTT
1 GATACCCATATCTTTGACTTTCTAATATTT
*
53759688 GATACCCATATCTTTGATTTTC
1 GATACCCATATCTTTGACTTTC
53759710 CATAAATATG
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
29 1 0.01
30 76 0.97
31 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.47
Consensus pattern (30 bp):
GATACCCATATCTTTGACTTTCTAATATTT
Found at i:53759643 original size:15 final size:15
Alignment explanation
Indices: 53759598--53759705 Score: 60
Period size: 15 Copynumber: 7.2 Consensus size: 15
53759588 CCAATATCTC
53759598 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
53759613 GACTTTCTA-ATATTT
1 GA-TACCCATATCTTT
53759628 GATACCCATATCTTT
1 GATACCCATATCTTT
*** *
53759643 GACTTTTCA-ATATTT
1 GA-TACCCATATCTTT
53759658 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
53759673 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
53759688 GATACCCATATCTTT
1 GATACCCATATCTTT
53759703 GAT
1 GAT
53759706 TTTCCATAAA
Statistics
Matches: 63, Mismatches: 24, Indels: 12
0.64 0.24 0.12
Matches are distributed among these distances:
14 10 0.16
15 43 0.68
16 10 0.16
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.46
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:53767953 original size:26 final size:25
Alignment explanation
Indices: 53767897--53767946 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
53767887 AGAGGCCAAG
53767897 ACTAGTTTTTGCATGTAAGCCACAT
1 ACTAGTTTTTGCATGTAAGCCACAT
53767922 ACTAGTTTTTGCATGTAAGCCACAT
1 ACTAGTTTTTGCATGTAAGCCACAT
53767947 TATTAGTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (25 bp):
ACTAGTTTTTGCATGTAAGCCACAT
Found at i:53771301 original size:29 final size:29
Alignment explanation
Indices: 53771267--53771322 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
53771257 CGCGGAAAAT
53771267 GGCCCATTCCGGTAAATAGTT-AAAAAACC
1 GGCCCATTCCGGTAAATA-TTGAAAAAACC
*
53771296 GGCCCATTTCGGTAAATATTGAAAAAA
1 GGCCCATTCCGGTAAATATTGAAAAAA
53771323 ATGGGCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (29 bp):
GGCCCATTCCGGTAAATATTGAAAAAACC
Found at i:53776362 original size:21 final size:20
Alignment explanation
Indices: 53776322--53776453 Score: 122
Period size: 21 Copynumber: 6.3 Consensus size: 20
53776312 CAGATACGCC
53776322 AACAGAAGCTCAAA-AGCTG
1 AACAGAAGCTCAAAGAGCTG
53776341 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCA-AAGAGCTG
* * * *
53776362 AATAGAAACTCATAAAAGTTG
1 AACAGAAGCTCA-AAGAGCTG
*
53776383 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTC-AAAGAGCTG
* *
53776404 AACAGAAGCCCCGAAAGAGCTA
1 AACAGAAG-CTC-AAAGAGCTG
* *
53776426 AATAGAAGCTCGAAAGAGCTA
1 AACAGAAGCTC-AAAGAGCTG
53776447 AACAGAA
1 AACAGAA
53776454 AGTAAAACAC
Statistics
Matches: 94, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
19 12 0.13
20 2 0.02
21 63 0.67
22 17 0.18
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (20 bp):
AACAGAAGCTCAAAGAGCTG
Found at i:53781230 original size:21 final size:23
Alignment explanation
Indices: 53781206--53781248 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
53781196 ATCATATTAT
53781206 AAACAAT-TTTA-AAAATGTTTA
1 AAACAATATTTATAAAATGTTTA
*
53781227 AAACAATATTTATAAAGTGTTT
1 AAACAATATTTATAAAATGTTT
53781249 TACCCTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 8 0.42
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (23 bp):
AAACAATATTTATAAAATGTTTA
Found at i:53801972 original size:47 final size:47
Alignment explanation
Indices: 53801921--53802046 Score: 137
Period size: 47 Copynumber: 2.7 Consensus size: 47
53801911 AAAATTGTAG
* * *
53801921 CCCTTGAA-CAATTATTGTGAAAGTCAATTTGTTTGGCTTAATAGTAT
1 CCCTTGAAGCAATT-TTGTGAAAGCCAATTTGTTTGACGTAATAGTAT
* * * * *
53801968 CCCTTAAAGGAGTTTTATGGAAGCCAATTTGTTTGACGTAATAGTAT
1 CCCTTGAAGCAATTTTGTGAAAGCCAATTTGTTTGACGTAATAGTAT
* * *
53802015 CCCTTGAAGTAATTTTGTGAAATCCAAGTTGT
1 CCCTTGAAGCAATTTTGTGAAAGCCAATTTGT
53802047 ATAATATGAT
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
47 60 0.95
48 3 0.05
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.38
Consensus pattern (47 bp):
CCCTTGAAGCAATTTTGTGAAAGCCAATTTGTTTGACGTAATAGTAT
Found at i:53809381 original size:15 final size:16
Alignment explanation
Indices: 53809355--53809385 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
53809345 AAATGTAAGT
53809355 TTTAATAATATATAAA
1 TTTAATAATATATAAA
53809371 TTTAA-AATATATAAA
1 TTTAATAATATATAAA
53809386 AATATTACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAATAATATATAAA
Found at i:53848723 original size:16 final size:17
Alignment explanation
Indices: 53848693--53848725 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53848683 GACTATACAT
*
53848693 AAAATTTTAATAAATAA
1 AAAATATTAATAAATAA
53848710 AAAATATTAA-AAATAA
1 AAAATATTAATAAATAA
53848726 TATAAGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATATTAATAAATAA
Found at i:53851169 original size:50 final size:50
Alignment explanation
Indices: 53851111--53851286 Score: 205
Period size: 50 Copynumber: 3.5 Consensus size: 50
53851101 TTATGAAATG
* *
53851111 TCCCATGTAAGACCATGTATGGGACATGGCATTGGCACCGATATAAGAAC
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGATATAAGAAC
** * * *
53851161 TCTTATGTAAGACCATATCTGGGACATGACATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGATATAAGAAC
* * *
53851211 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--G-TACAGAAAAC
1 TCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGATATA-AGAAC
* *
53851259 ATCCCATGTAAGACTATGTCTGGGACAT
1 -TCCCATGTAAGACCATATCTGGGACAT
53851287 AACTTTGGCA
Statistics
Matches: 106, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
47 2 0.02
48 5 0.05
49 24 0.23
50 75 0.71
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATATCTGGGACATGGCATTGGCACCGATATAAGAAC
Found at i:53851512 original size:12 final size:12
Alignment explanation
Indices: 53851495--53851526 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
53851485 ATGAGTTATT
*
53851495 TAAGTAAGCAAG
1 TAAGTAAACAAG
53851507 TAAGTAAACAAG
1 TAAGTAAACAAG
53851519 TAAGTAAA
1 TAAGTAAA
53851527 GAAGCGAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (12 bp):
TAAGTAAACAAG
Found at i:53855237 original size:31 final size:31
Alignment explanation
Indices: 53855180--53855238 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
53855170 ATCATAAAAT
* *
53855180 TATTTGAAAGTTTTCATTTAAATCACTAAAC
1 TATTTGAAACTTTTCATTCAAATCACTAAAC
*
53855211 TATTTGAAAACTTTT-ATTCAAGTCACTA
1 TATTTG-AAACTTTTCATTCAAATCACTA
53855239 GTTACTTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 17 0.71
32 7 0.29
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (31 bp):
TATTTGAAACTTTTCATTCAAATCACTAAAC
Found at i:53855916 original size:17 final size:18
Alignment explanation
Indices: 53855885--53855921 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
53855875 TGATTGGCCC
*
53855885 AATTATAAAATTATTAAA
1 AATTATAAAAATATTAAA
53855903 AATTA-AAAAATATTAAA
1 AATTATAAAAATATTAAA
53855920 AA
1 AA
53855922 AGTTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTATAAAAATATTAAA
Found at i:53858951 original size:15 final size:15
Alignment explanation
Indices: 53858933--53858961 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53858923 AATTTGATCA
53858933 ATTTTAATTTTTTTT
1 ATTTTAATTTTTTTT
53858948 ATTTTAATTTTTTT
1 ATTTTAATTTTTTT
53858962 CTAAATGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
ATTTTAATTTTTTTT
Found at i:53860442 original size:13 final size:13
Alignment explanation
Indices: 53860424--53860448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53860414 TTCGAGAGTT
53860424 ATTAATATTTATA
1 ATTAATATTTATA
53860437 ATTAATATTTAT
1 ATTAATATTTAT
53860449 TTACATGTCG
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:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTAATATTTATA
Found at i:53869703 original size:2 final size:2
Alignment explanation
Indices: 53869696--53869732 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
53869686 TGTCATACTT
53869696 TA TA 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 TA TA T
53869733 TATTATTATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53878266 original size:26 final size:27
Alignment explanation
Indices: 53878237--53878295 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
53878227 CCTAAAAATC
53878237 AACTTTTTG-AAACCTTAAAGGAAGTT
1 AACTTTTTGTAAACCTTAAAGGAAGTT
* **
53878263 AAC-TTTTGTCATTCTTAAAGGAAGTT
1 AACTTTTTGTAAACCTTAAAGGAAGTT
*
53878289 GACTTTT
1 AACTTTT
53878296 GTTCATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 5 0.19
26 19 0.70
27 3 0.11
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (27 bp):
AACTTTTTGTAAACCTTAAAGGAAGTT
Found at i:53878999 original size:2 final size:2
Alignment explanation
Indices: 53878992--53879054 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
53878982 GAAAATTCTC
*
53878992 AT AT AT AT GT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53879033 AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
53879055 GTACTACAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
1 2 0.04
2 55 0.96
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53883069 original size:15 final size:15
Alignment explanation
Indices: 53883026--53883073 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
53883016 ACGTGTGTCG
* *
53883026 AAATATATTTTACAA
1 AAATATAATTTAAAA
* *
53883041 AAATA-AAATGAAAA
1 AAATATAATTTAAAA
53883055 AAATATAATTTAAAA
1 AAATATAATTTAAAA
53883070 AAAT
1 AAAT
53883074 CTAAAAATCA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (15 bp):
AAATATAATTTAAAA
Found at i:53884818 original size:7 final size:7
Alignment explanation
Indices: 53884806--53884830 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53884796 AATTCAGTAC
53884806 TTTTATA
1 TTTTATA
53884813 TTTTATA
1 TTTTATA
53884820 TTTTATA
1 TTTTATA
53884827 TTTT
1 TTTT
53884831 TTTATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTATA
Found at i:53886401 original size:24 final size:25
Alignment explanation
Indices: 53886369--53886415 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
53886359 CTTTCAAGTT
*
53886369 AAATTAAAT-AAATATTTTGAATTC
1 AAATTAAATCAAATAATTTGAATTC
*
53886393 AAATTAAATCATATAATTTGAAT
1 AAATTAAATCAAATAATTTGAAT
53886416 AATTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (25 bp):
AAATTAAATCAAATAATTTGAATTC
Found at i:53906096 original size:27 final size:27
Alignment explanation
Indices: 53906066--53906128 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
53906056 GTCTATGATT
53906066 ATATATATATTACGGGAATCAATAATC
1 ATATATATATTACGGGAATCAATAATC
* * * * *
53906093 ATATATATATTATGGGGATTAATTATT
1 ATATATATATTACGGGAATCAATAATC
53906120 ATATATATA
1 ATATATATA
53906129 GTTTTTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (27 bp):
ATATATATATTACGGGAATCAATAATC
Found at i:53907783 original size:29 final size:28
Alignment explanation
Indices: 53907722--53907786 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
53907712 TGCTTTGTAT
*
53907722 ATTTAAAATTTAGTCTTCATTTTTTTAT
1 ATTTAAAATTTAGTCTTCATTTTTTTAA
*
53907750 TTTTAGAAATTTAGTC-T-ATTTATTTTCAA
1 ATTTA-AAATTTAGTCTTCATTT-TTTT-AA
53907779 ATTTAAAA
1 ATTTAAAA
53907787 ATTCAGAGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 4 0.13
28 12 0.39
29 15 0.48
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (28 bp):
ATTTAAAATTTAGTCTTCATTTTTTTAA
Found at i:53912354 original size:15 final size:14
Alignment explanation
Indices: 53912329--53912361 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
53912319 AATCAGCAGC
53912329 AAGAAAAG-A-AAA
1 AAGAAAAGAAGAAA
53912341 AAGAAAAGAAGAAA
1 AAGAAAAGAAGAAA
53912355 AAGAAAA
1 AAGAAAA
53912362 ATACATCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 1 0.05
14 10 0.53
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAGAAA
Found at i:53913240 original size:18 final size:18
Alignment explanation
Indices: 53913217--53913253 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
53913207 TCATCATTAT
53913217 TATTAGTATTAT-TATTTA
1 TATTAGT-TTATATATTTA
53913235 TATTAGTTTATATATTTA
1 TATTAGTTTATATATTTA
53913253 T
1 T
53913254 CTACATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TATTAGTTTATATATTTA
Found at i:53916833 original size:45 final size:45
Alignment explanation
Indices: 53916766--53916941 Score: 230
Period size: 45 Copynumber: 4.0 Consensus size: 45
53916756 GTGTATTGAG
* **
53916766 TATCATTGGTTATAAAGGTGGTTGCTATGTGCTGATTCCACCGGG
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
* *
53916811 TACCATTGATTATAAAGGTGGTTGCTATGTGCTGACTCCACCGAA
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
* * ** *
53916856 AATCATTAAAAATAAAGGTGGTTGTTATGTGCTGATTCCACCGAA
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
* *
53916901 TATAATTGATTATAAGGGTGG-TGCTATGTGCTGA-TCCACCG
1 TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCG
53916942 TGTAACGGTT
Statistics
Matches: 112, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 7 0.06
44 12 0.11
45 93 0.83
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (45 bp):
TATCATTGATTATAAAGGTGGTTGCTATGTGCTGATTCCACCGAA
Found at i:53916921 original size:90 final size:88
Alignment explanation
Indices: 53916777--53916941 Score: 258
Period size: 90 Copynumber: 1.9 Consensus size: 88
53916767 ATCATTGGTT
** *
53916777 ATAAAGGTGGTTGCTATGTGCTGATTCCACCGGGTACCATTGATTATAAAGGTGGTTGCTATGTG
1 ATAAAGGTGGTTGCTATGTGCTGATTCCACCGAATACAATTGATTATAAAGGTGG-TGCTATGTG
53916842 CTGACTCCACCGAAAATCATTAAAA
65 CTGA-TCCACCGAAAATCATTAAAA
* * *
53916867 ATAAAGGTGGTTGTTATGTGCTGATTCCACCGAATATAATTGATTATAAGGGTGGTGCTATGTGC
1 ATAAAGGTGGTTGCTATGTGCTGATTCCACCGAATACAATTGATTATAAAGGTGGTGCTATGTGC
53916932 TGATCCACCG
66 TGATCCACCG
53916942 TGTAACGGTT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
88 7 0.10
89 13 0.19
90 49 0.71
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (88 bp):
ATAAAGGTGGTTGCTATGTGCTGATTCCACCGAATACAATTGATTATAAAGGTGGTGCTATGTGC
TGATCCACCGAAAATCATTAAAA
Found at i:53920087 original size:7 final size:7
Alignment explanation
Indices: 53920077--53920101 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53920067 CTAATATAAG
53920077 TTTTACA
1 TTTTACA
53920084 TTTTACA
1 TTTTACA
53920091 TTTTACA
1 TTTTACA
53920098 TTTT
1 TTTT
53920102 TTGAAAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTACA
Found at i:53927390 original size:2 final size:2
Alignment explanation
Indices: 53927383--53927420 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
53927373 ATAAATTGTA
53927383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53927421 CGTTGATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53928288 original size:34 final size:34
Alignment explanation
Indices: 53928240--53928321 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
53928230 TAAGAGTTAG
**
53928240 CTTTCCTCTTTTATGATCCTAAGTTCAAACCATT
1 CTTTCCTCTTTTATGATCCTAAGTTCAAAAAATT
*
53928274 CTTTTCTCTTTTATGATCCTAAGTTCAAAAAATT
1 CTTTCCTCTTTTATGATCCTAAGTTCAAAAAATT
53928308 CTTTCCTCTTTTAT
1 CTTTCCTCTTTTAT
53928322 TTTGAGAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.49
Consensus pattern (34 bp):
CTTTCCTCTTTTATGATCCTAAGTTCAAAAAATT
Found at i:53929468 original size:29 final size:30
Alignment explanation
Indices: 53929434--53929500 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
53929424 ATAGGGGCTG
* * *
53929434 GATCAAATTT-GTCCCTCTATTATTAAATA
1 GATCAAATTTAGTCACTATATTATTAAAAA
*
53929463 GATC-AATTTAGTCATTATATTATTAAAAA
1 GATCAAATTTAGTCACTATATTATTAAAAA
53929492 GAATCAAAT
1 G-ATCAAAT
53929501 AAGATCAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 5 0.16
29 20 0.65
30 3 0.10
31 3 0.10
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (30 bp):
GATCAAATTTAGTCACTATATTATTAAAAA
Found at i:53931060 original size:25 final size:25
Alignment explanation
Indices: 53931032--53931090 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
53931022 ATGAATTAAC
*
53931032 AAAATATATAAAGTAT-ATTTTATAT
1 AAAATATATAAA-TATGAGTTTATAT
* *
53931057 AAAATAAATAAATATGCGTTTATAT
1 AAAATATATAAATATGAGTTTATAT
*
53931082 AAAAAATAT
1 AAAATATAT
53931091 GTACATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 3 0.11
25 25 0.89
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (25 bp):
AAAATATATAAATATGAGTTTATAT
Found at i:53933044 original size:50 final size:50
Alignment explanation
Indices: 53932886--53933322 Score: 322
Period size: 50 Copynumber: 8.9 Consensus size: 50
53932876 GTGTCGCCTG
* * *
53932886 GAAGTAAGATTCACCGTTGTGGCTTCGATCTTTTAAATTGTAATGTCGGG
1 GAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGTCGGA
** * * * * * ** * *
53932936 GAAGCGAGACTCGCCATTGTAGCTTCAATCTGTTCCACTGC-A--TCGCCA
1 GAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGTCG-GA
*
53932984 GAAGTAAGATTCGCCGTTATGGCTTCGATCTTTTAAATTGCAATGTCGGA
1 GAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGTCGGA
* * * *** *
53933034 GAAGTGAGATTCGCCGTTGTAGCTTCAATCTGTTT-CGCTGC-A--TCGCCA
1 GAAGTAAGATTCGCCGTTGTGGCTTCGATCT-TTTAAATTGCAATGTCG-GA
*
53933082 GAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATATCGGA
1 GAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGTCGGA
* * * * * **** * *
53933132 GAAGTGAGATTCGTCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCTG-
1 GAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-GTCGGA
53933181 GAAGTAAGATTCGCCGTTGTGGCATT-GATCTTTTAAATTGCAATGTCGGA
1 GAAGTAAGATTCGCCGTTGTGGC-TTCGATCTTTTAAATTGCAATGTCGGA
* * * * * **** * *
53933231 GAAGTGAGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGC-ATCGCCTG-
1 GAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT-GTCGGA
*
53933280 GAAGTAAGATTCGCCGTTGTGGCTTCGGTCTTTTAAATTGCAA
1 GAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAA
53933323 ACTATGGTTT
Statistics
Matches: 285, Mismatches: 85, Indels: 34
0.71 0.21 0.08
Matches are distributed among these distances:
47 9 0.03
48 62 0.22
49 73 0.26
50 132 0.46
51 9 0.03
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (50 bp):
GAAGTAAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGTCGGA
Found at i:53933218 original size:197 final size:197
Alignment explanation
Indices: 53932843--53933322 Score: 757
Period size: 197 Copynumber: 2.4 Consensus size: 197
53932833 CGAGGAAATA
** ** *
53932843 AGATTCGCCGTTGCGGCTTCAATCTGTTCCGCTGTGTCGCCTGGAAGTAAGATTCACCGTTGTGG
1 AGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGG
* * *
53932908 CTTCGATCTTTTAAATTGTAATGTCGGGGAAGCGAGACTCGCCATTGTAGCTTCAATCTGTTCCA
66 CTTCGATCTTTTAAATTGCAATATCGGAGAAGCGAGACTCGCCATTGTAGCTTCAATCTGTTCCA
53932973 CTGCATCGCCAGAAGTAAGATTCGCCGTTATGGCTTCGATCTTTTAAATTGCAATGTCGGAGAAG
131 CTGCATCGCCAGAAGTAAGATTCGCCGTTATGGCTTCGATCTTTTAAATTGCAATGTCGGAGAAG
53933038 TG
196 TG
* *
53933040 AGATTCGCCGTTGTAGCTTCAATCTGTTTCGCTGCATCGCC-AGAAGTAAGATTCGCCGTTGTGG
1 AGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGG
* * * * *
53933104 CTTCGATCTTTTAAATTGCAATATCGGAGAAGTGAGATTCGTCGTTGTAGCTTCAATCTGTTCCG
66 CTTCGATCTTTTAAATTGCAATATCGGAGAAGCGAGACTCGCCATTGTAGCTTCAATCTGTTCCA
* *
53933169 CTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGGCATT-GATCTTTTAAATTGCAATGTCGGAGA
131 CTGCATCGCC-AGAAGTAAGATTCGCCGTTATGGC-TTCGATCTTTTAAATTGCAATGTCGGAGA
53933233 AGTG
194 AGTG
*
53933237 AGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGG
1 AGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGG
*
53933302 CTTCGGTCTTTTAAATTGCAA
66 CTTCGATCTTTTAAATTGCAA
53933323 ACTATGGTTT
Statistics
Matches: 259, Mismatches: 21, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
196 88 0.34
197 127 0.49
198 44 0.17
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (197 bp):
AGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGG
CTTCGATCTTTTAAATTGCAATATCGGAGAAGCGAGACTCGCCATTGTAGCTTCAATCTGTTCCA
CTGCATCGCCAGAAGTAAGATTCGCCGTTATGGCTTCGATCTTTTAAATTGCAATGTCGGAGAAG
TG
Found at i:53933234 original size:99 final size:99
Alignment explanation
Indices: 53932843--53933322 Score: 759
Period size: 98 Copynumber: 4.9 Consensus size: 99
53932833 CGAGGAAATA
** ** *
53932843 AGATTCGCCGTTGCGGCTTCAATCTGTTCCGCTGTGTCGCCTGGAAGTAAGATTCACCGTTGTGG
1 AGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGG
* * *
53932908 CTTCGATCTTTTAAATTGTAATGTCGGGGAAGCG
66 CTTCGATCTTTTAAATTGCAATGTCGGAGAAGTG
* * * * *
53932942 AGACTCGCCATTGTAGCTTCAATCTGTTCCACTGCATCGCC-AGAAGTAAGATTCGCCGTTATGG
1 AGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGG
53933006 CTTCGATCTTTTAAATTGCAATGTCGGAGAAGTG
66 CTTCGATCTTTTAAATTGCAATGTCGGAGAAGTG
* *
53933040 AGATTCGCCGTTGTAGCTTCAATCTGTTTCGCTGCATCGCC-AGAAGTAAGATTCGCCGTTGTGG
1 AGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGG
*
53933104 CTTCGATCTTTTAAATTGCAATATCGGAGAAGTG
66 CTTCGATCTTTTAAATTGCAATGTCGGAGAAGTG
*
53933138 AGATTCGTCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGG
1 AGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGG
53933203 CATT-GATCTTTTAAATTGCAATGTCGGAGAAGTG
66 C-TTCGATCTTTTAAATTGCAATGTCGGAGAAGTG
*
53933237 AGATTCACCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGG
1 AGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGG
*
53933302 CTTCGGTCTTTTAAATTGCAA
66 CTTCGATCTTTTAAATTGCAA
53933323 ACTATGGTTT
Statistics
Matches: 352, Mismatches: 26, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
98 184 0.52
99 166 0.47
100 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (99 bp):
AGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTCGCCGTTGTGG
CTTCGATCTTTTAAATTGCAATGTCGGAGAAGTG
Found at i:53934658 original size:16 final size:15
Alignment explanation
Indices: 53934637--53934676 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
53934627 CTCCCTCTTT
*
53934637 TTTTTTCAGTGCCCCC
1 TTTTTTCAATG-CCCC
*
53934653 TTTTTTGAATGCCCC
1 TTTTTTCAATGCCCC
53934668 TTTTTTCAA
1 TTTTTTCAA
53934677 GTGAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.12, C:0.28, G:0.10, T:0.50
Consensus pattern (15 bp):
TTTTTTCAATGCCCC
Found at i:53937677 original size:19 final size:19
Alignment explanation
Indices: 53937650--53937760 Score: 168
Period size: 19 Copynumber: 5.8 Consensus size: 19
53937640 AATCATATCT
53937650 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* ** *
53937669 TCAAAGATTATACATCATA
1 TCTAAGATTGCATATCATA
53937688 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
53937707 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
53937726 TCTACGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
53937745 TATAAGATTGCATATC
1 TCTAAGATTGCATATC
53937761 CTCAAAAATT
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 81 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:53948510 original size:3 final size:3
Alignment explanation
Indices: 53948502--53948563 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
53948492 AATAAATAGG
53948502 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53948550 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
53948564 GGACCAATTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:53954093 original size:18 final size:18
Alignment explanation
Indices: 53954054--53954094 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
53954044 GCCTGATGGT
* *
53954054 TCTTCTCCATCATCTTCC
1 TCTTCTCCATCATCATCA
53954072 TCTTCTCCATCATCATCA
1 TCTTCTCCATCATCATCA
53954090 TCTTC
1 TCTTC
53954095 CAAAGCTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.41, G:0.00, T:0.44
Consensus pattern (18 bp):
TCTTCTCCATCATCATCA
Found at i:53954609 original size:3 final size:3
Alignment explanation
Indices: 53954603--53954634 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
53954593 TCAAGACAGG
53954603 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
53954635 GAAGAACAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:53960777 original size:43 final size:39
Alignment explanation
Indices: 53960659--53960775 Score: 101
Period size: 43 Copynumber: 2.8 Consensus size: 39
53960649 GAGAAAACGC
**
53960659 CGCTATAGAACATGACCTTTAGCGGCGTTTCCCATAAAAA
1 CGCTATAGAACATGACCTTTAGCGGCGTTTTAC-TAAAAA
* * *
53960699 CACTTATAAAGAACATTACCTGTAGCGATGC-TTTTACTAAAAA
1 CGC-TAT--AGAACATGACCTTTAGCG--GCGTTTTACTAAAAA
53960742 TGGCGCTATAGAACATGACCTTTAGCGGCGTTTT
1 ---CGCTATAGAACATGACCTTTAGCGGCGTTTT
53960776 TAGTAAAAGC
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
40 2 0.03
41 5 0.08
42 4 0.07
43 38 0.63
44 4 0.07
45 5 0.08
46 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (39 bp):
CGCTATAGAACATGACCTTTAGCGGCGTTTTACTAAAAA
Found at i:53960808 original size:43 final size:43
Alignment explanation
Indices: 53960761--53960946 Score: 205
Period size: 43 Copynumber: 4.3 Consensus size: 43
53960751 AGAACATGAC
* *
53960761 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGTTAAATGTCATGTT
1 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTAAAGGTCATGTT
* * * * *
53960804 CTTTAGCTGCATTTGTGAG-AAAAGAGCCACTAAAGGTCATGTT
1 CTTTAGCGGCGTTT-TTAGTAAAAGCGCCGCTAAAGGTCATGTT
* * * *
53960847 CTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTAAAGGTCATGTT
** * *
53960890 CTTTAGCAACATTTTTAATAAAAGCGCCGCTAAA-GTCCATGTT
1 CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTAAAGGT-CATGTT
53960933 CTTTAGCGGCGTTT
1 CTTTAGCGGCGTTT
53960947 GTGGGAAAAT
Statistics
Matches: 114, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
42 3 0.03
43 108 0.95
44 3 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTAGTAAAAGCGCCGCTAAAGGTCATGTT
Found at i:53960854 original size:86 final size:86
Alignment explanation
Indices: 53960764--53960955 Score: 242
Period size: 86 Copynumber: 2.2 Consensus size: 86
53960754 ACATGACCTT
* * * * ** *
53960764 TAGCGGCGTTTTTAGTAAAAGCGCCGTTAAATGTCATGTTCTTTAGCTGCATTTGTGAGAAAAGA
1 TAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCAACATTTGTAAGAAAAGA
53960829 GCCACTAAAGGT-CATGTTCTA
66 GCCACTAAA-GTCCATGTTCTA
* * * *
53960850 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCAACATTTTTAATAAAAGC
1 TAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCAACATTTGTAAGAAAAGA
* *
53960915 GCCGCTAAAGTCCATGTTCTT
66 GCCACTAAAGTCCATGTTCTA
*
53960936 TAGCGGCGTTTGTGGGAAAA
1 TAGCGGCGTTTGTAGGAAAA
53960956 TACCACTAAC
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 2 0.02
86 90 0.98
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (86 bp):
TAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCAACATTTGTAAGAAAAGA
GCCACTAAAGTCCATGTTCTA
Found at i:53962993 original size:6 final size:6
Alignment explanation
Indices: 53962982--53963017 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
53962972 TAATACACTA
53962982 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
1 ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT ACTAAT
53963018 TAATCCGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ACTAAT
Found at i:53965261 original size:42 final size:43
Alignment explanation
Indices: 53965209--53965294 Score: 113
Period size: 42 Copynumber: 2.0 Consensus size: 43
53965199 ACATGTTATA
* *
53965209 ATATATCGATGCCACTATCCCAGAC-TGGGTCTTACACGAAATC
1 ATATATCGATGCCAATATCCCAGACAT-AGTCTTACACGAAATC
* *
53965252 ATATA-CGATGCCAATGTCCCATACATAGTCTTACACGAAATC
1 ATATATCGATGCCAATATCCCAGACATAGTCTTACACGAAATC
53965294 A
1 A
53965295 CACCTCAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 32 0.84
43 6 0.16
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.26
Consensus pattern (43 bp):
ATATATCGATGCCAATATCCCAGACATAGTCTTACACGAAATC
Found at i:53969028 original size:29 final size:30
Alignment explanation
Indices: 53968995--53969064 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
53968985 CTAAGTTATC
53968995 TTAAATCTTAAAAT-AA-AA-AAAAATTAGGA
1 TTAAATC-TAAAATAAATAATAAAAATT-GGA
*
53969024 TTAAAACTAAAATAAATAATAAAAATTGGA
1 TTAAATCTAAAATAAATAATAAAAATTGGA
*
53969054 TTAAATATAAA
1 TTAAATCTAAA
53969065 GATATCAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 6 0.17
29 8 0.23
30 14 0.40
31 7 0.20
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (30 bp):
TTAAATCTAAAATAAATAATAAAAATTGGA
Found at i:53969482 original size:5 final size:5
Alignment explanation
Indices: 53969472--53969496 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53969462 TATTATTAGT
53969472 ATACA ATACA ATACA ATACA ATACA
1 ATACA ATACA ATACA ATACA ATACA
53969497 TGCCAAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
ATACA
Found at i:53973378 original size:29 final size:29
Alignment explanation
Indices: 53973336--53973391 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
53973326 AGCAAAATAT
53973336 TTATAAAATTAAAAATA-TGTTATAAAAGC
1 TTATAAAATTAAAAATATTGTT-TAAAAGC
* *
53973365 TTATCAAATTAAAATTATTGTTTAAAA
1 TTATAAAATTAAAAATATTGTTTAAAA
53973392 ATATGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (29 bp):
TTATAAAATTAAAAATATTGTTTAAAAGC
Found at i:53973650 original size:5 final size:5
Alignment explanation
Indices: 53973640--53973664 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53973630 AAGTTCAAAG
53973640 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
53973665 GAGAGAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:53974983 original size:34 final size:33
Alignment explanation
Indices: 53974936--53975027 Score: 130
Period size: 34 Copynumber: 2.7 Consensus size: 33
53974926 GATTCCAATT
* *
53974936 TTTAGGGGAAAAATAAGGGATTTTGGGGTTATGG
1 TTTA-GGGAAAAATAAGAGATTTTAGGGTTATGG
53974970 TTTAGGGATAAAATAAGAGATTTTAGGGTTATGG
1 TTTAGGGA-AAAATAAGAGATTTTAGGGTTATGG
*
53975004 TTTAGGGGGAAAATAAGAGATTTT
1 TTTA-GGGAAAAATAAGAGATTTT
53975028 TAGCATAGTA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
33 4 0.08
34 46 0.87
35 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.33, T:0.34
Consensus pattern (33 bp):
TTTAGGGAAAAATAAGAGATTTTAGGGTTATGG
Found at i:53975179 original size:41 final size:41
Alignment explanation
Indices: 53975086--53975206 Score: 143
Period size: 41 Copynumber: 3.0 Consensus size: 41
53975076 CAGCGTTTTG
* * * *
53975086 ATAAACGCCGCTAATGCTTGACTTTTTGCAGCGTTTTTCTC
1 ATAAACGCCGCTACTGCTTGACCTTTTGCGGCATTTTTCTC
* * * *
53975127 GTAAGCGCCGCTACCGCTTGACCTTTTGCGGCATTTTTCTT
1 ATAAACGCCGCTACTGCTTGACCTTTTGCGGCATTTTTCTC
* * *
53975168 ATAAACACCGCTACTGCTTTACCTATTGCGGCATTTTTC
1 ATAAACGCCGCTACTGCTTGACCTTTTGCGGCATTTTTC
53975207 CGTTAGTGCC
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.37
Consensus pattern (41 bp):
ATAAACGCCGCTACTGCTTGACCTTTTGCGGCATTTTTCTC
Found at i:53978753 original size:14 final size:15
Alignment explanation
Indices: 53978729--53978757 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
53978719 TTGTTAATAT
53978729 CCATTTGTCTGCAAA
1 CCATTTGTCTGCAAA
53978744 CCATTT-TCTGCAAA
1 CCATTTGTCTGCAAA
53978758 ATTGTGCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (15 bp):
CCATTTGTCTGCAAA
Found at i:53981071 original size:14 final size:14
Alignment explanation
Indices: 53981036--53981080 Score: 72
Period size: 14 Copynumber: 3.1 Consensus size: 14
53981026 TTAAATGTAT
*
53981036 ATAAATATTTAAAA
1 ATAAATATATAAAA
53981050 ATATAATATATAAAA
1 ATA-AATATATAAAA
53981065 ATAAATATATAAAA
1 ATAAATATATAAAA
53981079 AT
1 AT
53981081 GTAGAAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAATATATAAAA
Found at i:53981300 original size:12 final size:12
Alignment explanation
Indices: 53981270--53981317 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
53981260 ACATTTATAT
*
53981270 TGTTTAATATTG
1 TGTTTAATATTA
53981282 T-TTTAATATTA
1 TGTTTAATATTA
53981293 TGTTTAATATTA
1 TGTTTAATATTA
*
53981305 TATTTAATATTA
1 TGTTTAATATTA
53981317 T
1 T
53981318 TTATAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
11 10 0.30
12 23 0.70
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (12 bp):
TGTTTAATATTA
Found at i:53981315 original size:24 final size:24
Alignment explanation
Indices: 53981255--53981317 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
53981245 TAAAACTTTT
*
53981255 ATATTACATTT-ATA-T-TGTTTA
1 ATATTATATTTAATATTATGTTTA
*
53981276 ATATTGT-TTTAATATTATGTTTA
1 ATATTATATTTAATATTATGTTTA
53981299 ATATTATATTTAATATTAT
1 ATATTATATTTAATATTAT
53981318 TTATAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 3 0.09
21 8 0.23
22 1 0.03
23 12 0.34
24 11 0.31
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.59
Consensus pattern (24 bp):
ATATTATATTTAATATTATGTTTA
Found at i:53981520 original size:19 final size:19
Alignment explanation
Indices: 53981508--53981559 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
53981498 TTTTTCTAGA
53981508 TTTTATATATTTTTTGAAT
1 TTTTATATATTTTTTGAAT
**
53981527 TTTTATATATTTATTTCCAT
1 TTTTATATATTT-TTTGAAT
53981547 TTTTATAT-TTTTT
1 TTTTATATATTTTT
53981560 AATGTGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 2 0.07
19 15 0.50
20 13 0.43
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTATATATTTTTTGAAT
Found at i:53993749 original size:12 final size:12
Alignment explanation
Indices: 53993732--53993804 Score: 53
Period size: 12 Copynumber: 5.9 Consensus size: 12
53993722 GTTATAATAC
53993732 TTTATTTTATAT
1 TTTATTTTATAT
53993744 TTTATTTT-TAT
1 TTTATTTTATAT
*
53993755 TTT-TATTACTAT
1 TTTATTTTA-TAT
53993767 TTCTATTTCTAT-T
1 TT-TATTT-TATAT
**
53993780 ACTATTCTTATAT
1 TTTATT-TTATAT
53993793 TTTATTATTATA
1 TTTATT-TTATA
53993805 ATGGTGATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
10 3 0.06
11 6 0.13
12 20 0.43
13 13 0.28
14 3 0.06
15 2 0.04
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTTTATAT
Found at i:53993767 original size:18 final size:18
Alignment explanation
Indices: 53993732--53993799 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
53993722 GTTATAATAC
*
53993732 TTTATTTTATATT-TTATT
1 TTTATTTT-TATTACTATT
53993750 TTTATTTTTATTACTATT
1 TTTATTTTTATTACTATT
* *
53993768 TCTATTTCTATTACTATT
1 TTTATTTTTATTACTATT
*
53993786 CTTATATTTTATTA
1 TTTAT-TTTTATTA
53993800 TTATAATGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
17 4 0.10
18 31 0.74
19 7 0.17
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTTTTATTACTATT
Found at i:53995834 original size:21 final size:21
Alignment explanation
Indices: 53995805--53995846 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53995795 CTAAGTACAT
* *
53995805 GGGCATGTGGAGTAGCCACAC
1 GGGCATGTGGAATAGACACAC
*
53995826 GGGCGTGTGGAATAGACACAC
1 GGGCATGTGGAATAGACACAC
53995847 AATCTGGGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.38, T:0.14
Consensus pattern (21 bp):
GGGCATGTGGAATAGACACAC
Found at i:53997013 original size:18 final size:18
Alignment explanation
Indices: 53996990--53997024 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53996980 AGCCTAGTAC
53996990 CCAAAC-TAAAGCCCAAAA
1 CCAAACTTAAA-CCCAAAA
53997008 CCAAACTTAAACCCAAA
1 CCAAACTTAAACCCAAA
53997025 CCTACCCCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.54, C:0.34, G:0.03, T:0.09
Consensus pattern (18 bp):
CCAAACTTAAACCCAAAA
Found at i:54000142 original size:23 final size:24
Alignment explanation
Indices: 54000089--54000147 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 24
54000079 ATGTTTTGTA
* *
54000089 TTTTATTTAATATTAGTATACTTAT
1 TTTTATTTAATATTAATATAC-AAT
54000114 TTTTATTTAATATTAATATA-AAT
1 TTTTATTTAATATTAATATACAAT
54000137 TTTTATTTAAT
1 TTTTATTTAAT
54000148 TAGATTTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 13 0.41
25 19 0.59
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTATTTAATATTAATATACAAT
Found at i:54000758 original size:29 final size:29
Alignment explanation
Indices: 54000708--54000767 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
54000698 TAATGTTCTT
* ** * *
54000708 ATCTCCCCAAGTATCTTGCTTCTTCTGAA
1 ATCTCCCCAAATAAATTCCTTCCTCTGAA
54000737 ATCTCCCCAAATAAATTCCTTCCTCTGAA
1 ATCTCCCCAAATAAATTCCTTCCTCTGAA
54000766 AT
1 AT
54000768 TTCCATGTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.27, C:0.32, G:0.07, T:0.35
Consensus pattern (29 bp):
ATCTCCCCAAATAAATTCCTTCCTCTGAA
Found at i:54003879 original size:23 final size:23
Alignment explanation
Indices: 54003849--54003895 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
54003839 AATGAGAAGT
54003849 ATGAGGTAGACTGTGGATTAGGC
1 ATGAGGTAGACTGTGGATTAGGC
54003872 ATGAGGTAGACTGTGGATTAGGC
1 ATGAGGTAGACTGTGGATTAGGC
54003895 A
1 A
54003896 ACAAGCATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.09, G:0.38, T:0.26
Consensus pattern (23 bp):
ATGAGGTAGACTGTGGATTAGGC
Found at i:54004944 original size:23 final size:24
Alignment explanation
Indices: 54004902--54004954 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
54004892 GAACTCGTTA
*
54004902 TTTTTGCACATGTTATTTTTTAAT
1 TTTTTACACATGTTATTTTTTAAT
54004926 TTTTTACACATGTTA-TTTTTAAT
1 TTTTTACACATGTTATTTTTTAAT
54004949 TTTTTA
1 TTTTTA
54004955 TTTAAAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.23, C:0.08, G:0.06, T:0.64
Consensus pattern (24 bp):
TTTTTACACATGTTATTTTTTAAT
Found at i:54007094 original size:14 final size:14
Alignment explanation
Indices: 54007077--54007104 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54007067 GTTTAAAATT
54007077 TTTAATTAATTAAA
1 TTTAATTAATTAAA
54007091 TTTAATTAATTAAA
1 TTTAATTAATTAAA
54007105 AATCTATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:54007445 original size:31 final size:30
Alignment explanation
Indices: 54007385--54007454 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
54007375 AGAGTGATTA
**
54007385 AAATAGAAACGATCTAAAATGTGCGTGACT
1 AAATAGAAACGATCTAAAATGTGAATGACT
* * *
54007415 GAAATAGAAATGATTTAAAATGTTAATGACT
1 -AAATAGAAACGATCTAAAATGTGAATGACT
*
54007446 AAATTGAAA
1 AAATAGAAA
54007455 ACATTCATAG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 8 0.24
31 25 0.76
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (30 bp):
AAATAGAAACGATCTAAAATGTGAATGACT
Found at i:54009169 original size:19 final size:17
Alignment explanation
Indices: 54009135--54009177 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
54009125 CTTCTCTTTT
* *
54009135 TTTATTTTTTTTAATTCA
1 TTTATTTTATTCAATT-A
54009153 TTCTATTTTATTCAATTA
1 TT-TATTTTATTCAATTA
54009171 TTTATTT
1 TTTATTT
54009178 ATTGTCTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 5 0.23
19 12 0.55
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATTTTATTCAATTA
Found at i:54013922 original size:68 final size:68
Alignment explanation
Indices: 54013782--54013925 Score: 166
Period size: 68 Copynumber: 2.1 Consensus size: 68
54013772 TTAATCACTT
*
54013782 TAATATTAAATTAATATAATACTTATGAAGATAAATATTAAATTTAACTTAATATAAGATAATCA
1 TAATATTAAATTAATAAAATACTTATGAAGATAAATATTAAATTTAACTTAATATAAGATAATCA
***
54013847 CTT
66 AAA
* * * * *
54013850 TAATATTAAATTAATAAAATA-TTATTAAGATAAGTATTGAATTTAATTTAATATTAA-ATTTAT
1 TAATATTAAATTAATAAAATACTTATGAAGATAAATATTAAATTTAACTTAATA-TAAGA-TAAT
*
54013913 TAAAA
64 CAAAA
54013918 TAATATTA
1 TAATATTA
54013926 TTTTTTAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
67 29 0.45
68 35 0.55
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (68 bp):
TAATATTAAATTAATAAAATACTTATGAAGATAAATATTAAATTTAACTTAATATAAGATAATCA
AAA
Found at i:54015726 original size:18 final size:19
Alignment explanation
Indices: 54015705--54015742 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
54015695 AAAAAAATTT
54015705 AAAG-TTATGAAAATA-AAA
1 AAAGATTAT-AAAATAGAAA
54015723 AAAGATTATAAAATAGAAA
1 AAAGATTATAAAATAGAAA
54015742 A
1 A
54015743 TTGAGAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AAAGATTATAAAATAGAAA
Found at i:54019651 original size:17 final size:18
Alignment explanation
Indices: 54019622--54019655 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
54019612 ATTTTTAATA
54019622 TTTTAATACATTTATTTC
1 TTTTAATACATTTATTTC
54019640 TTTTAATA-ATTTATTT
1 TTTTAATACATTTATTT
54019656 AATCATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTAATACATTTATTTC
Found at i:54022403 original size:24 final size:24
Alignment explanation
Indices: 54022351--54022405 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
54022341 AAACTCATGC
* * *
54022351 GAGCCAATAACGGGTAGCTCCGAA
1 GAGCCATTAACGGGAAGCTCCAAA
*
54022375 GAGCCATTAACGGGAAGCTCTAAA
1 GAGCCATTAACGGGAAGCTCCAAA
*
54022399 TAGCCAT
1 GAGCCAT
54022406 ATGTCGGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.16
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCCAAA
Found at i:54022979 original size:10 final size:11
Alignment explanation
Indices: 54022956--54022984 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
54022946 GAATTTAACA
54022956 TCAATTCATAT
1 TCAATTCATAT
54022967 TCAATTC-TAT
1 TCAATTCATAT
54022977 TCAATTCA
1 TCAATTCA
54022985 CATCCTAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (11 bp):
TCAATTCATAT
Found at i:54027240 original size:17 final size:16
Alignment explanation
Indices: 54027218--54027251 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
54027208 AAGTATAGGG
*
54027218 GCAAAAATATAATTTTT
1 GCAAAAAAAT-ATTTTT
54027235 GCAAAAAAATATTTTT
1 GCAAAAAAATATTTTT
54027251 G
1 G
54027252 GGCTGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (16 bp):
GCAAAAAAATATTTTT
Found at i:54027673 original size:51 final size:52
Alignment explanation
Indices: 54027557--54027677 Score: 192
Period size: 52 Copynumber: 2.3 Consensus size: 52
54027547 ACTAGTGACT
54027557 CAAGTGTGGTACTATGTGAAAGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAAGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
* *
54027609 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGGTAGCTTTGG-CTA
1 CAAGTGTGGTACTATGTGAAAGCCACTTTGTGAAGAAAGATAGCTTTGGTC-A
*
54027660 CAAGGGTGGTACTATGTG
1 CAAGTGTGGTACTATGTG
54027678 CAGGTCACCG
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
50 1 0.02
51 30 0.46
52 34 0.52
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (52 bp):
CAAGTGTGGTACTATGTGAAAGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
Found at i:54028039 original size:14 final size:14
Alignment explanation
Indices: 54028020--54028047 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54028010 TAGAAGAAAT
54028020 GGTGTAAGCAAGAG
1 GGTGTAAGCAAGAG
54028034 GGTGTAAGCAAGAG
1 GGTGTAAGCAAGAG
54028048 AATTTCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.43, T:0.14
Consensus pattern (14 bp):
GGTGTAAGCAAGAG
Found at i:54038974 original size:19 final size:19
Alignment explanation
Indices: 54038945--54038993 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 19
54038935 TCATTTCTCT
54038945 TTTTCTATTCATTCTGTTCA
1 TTTT-TATTCATTCTGTTCA
54038965 TTTTTATTCATTCTGTTCA
1 TTTTTATTCATTCTGTTCA
*
54038984 TTTCTATTCA
1 TTTTTATTCA
54038994 AACACAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.16, C:0.18, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTTATTCATTCTGTTCA
Found at i:54052624 original size:31 final size:31
Alignment explanation
Indices: 54052589--54052648 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
54052579 ATTGTCACTA
*
54052589 AACTA-TTCAAAAGTTTTCATTTAAGTCATTG
1 AACTATTTCAAAA-TTTTCACTTAAGTCATTG
*
54052620 AACTATTTGAAAATTTTCACTTAAGTCAT
1 AACTATTTCAAAATTTTCACTTAAGTCAT
54052649 CAAGCTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (31 bp):
AACTATTTCAAAATTTTCACTTAAGTCATTG
Done.