Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 154 of 190
Found at i:44896602 original size:2 final size:2
Alignment explanation
Indices: 44896595--44896619 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44896585 TATACGCATT
44896595 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 T
44896620 TATTGTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44900275 original size:20 final size:20
Alignment explanation
Indices: 44900246--44900285 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
44900236 TTCACCTCAT
*
44900246 GCATCGCATCATATGCATTA
1 GCATCACATCATATGCATTA
44900266 GCATCACATCATATGCATTA
1 GCATCACATCATATGCATTA
44900286 AAGACCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (20 bp):
GCATCACATCATATGCATTA
Found at i:44908733 original size:100 final size:100
Alignment explanation
Indices: 44908333--44908743 Score: 639
Period size: 100 Copynumber: 4.1 Consensus size: 100
44908323 TTGAAAAGTA
44908333 AAAAGATTGAAGCCACAACGGCGGATCTTACTTTCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTTCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
*
44908398 CGACGGCGGATCTGGTTTCCCTGATATTGCAATT-
66 CGACGGCGGATCTGGTTTCCCTAATATTGCAATTG
* *
44908432 AAAATATTGAAGCCACAGCGGCGGATCTTACTTTCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTTCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
* *
44908497 CGACGGCGGATCTGGTTTCCCTGATATTGCAATTA
66 CGACGGCGGATCTGGTTTCCCTAATATTGCAATTG
* * * *
44908532 AAAAGATTGAAGCCACAACAGCGGATTTTACTTCCTTAGTAGTGCAGTGGAACAGATTGAAGCTA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTTCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
*
44908597 CGACGGCGGATCTGGTTTCCCTAATATTACAATTG
66 CGACGGCGGATCTGGTTTCCCTAATATTGCAATTG
* * *
44908632 AAAAGATTGAAGCCACAACGGCAGATCTTACTTTCCT-GACAGTGCGGTGGAACAGATTGAAGCT
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTTCTTAG-CAGTGCAGTGGAACAGATTGAAGCT
* * *
44908696 ACGACGGCGGATCTAGTTTCCCTAACATTGCAGTTG
65 ACGACGGCGGATCTGGTTTCCCTAATATTGCAATTG
44908732 AACAA-ATTGAAG
1 AA-AAGATTGAAG
44908744 ATTATAGATC
Statistics
Matches: 287, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
99 98 0.34
100 187 0.65
101 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTTTCTTAGCAGTGCAGTGGAACAGATTGAAGCTA
CGACGGCGGATCTGGTTTCCCTAATATTGCAATTG
Found at i:44908735 original size:50 final size:50
Alignment explanation
Indices: 44908336--44908743 Score: 288
Period size: 50 Copynumber: 8.2 Consensus size: 50
44908326 AAAAGTAAAA
* * * *
44908336 AGATTGAAGCCACAACGGCGGATCTTACTTT-CTTAGCAGTGCAGTGGAAC
1 AGATTGAAGCCACGACGGCGGATC-TAGTTTCCCTAACAGTGCAGTGGAAC
* * * * * * * *
44908386 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAAT-TAAA
1 AGATTGAAGCCACGACGGCGGATCTAGTTTCCCTAACAGTGCAGTGGAAC
* * * *
44908435 ATATTGAAGCCAC-AGCGGCGGATCTTACTTT-CTTAGCAGTGCAGTGGAAC
1 AGATTGAAGCCACGA-CGGCGGATC-TAGTTTCCCTAACAGTGCAGTGGAAC
* * * * * * ** *
44908485 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAA
1 AGATTGAAGCCACGACGGCGGATCTAGTTTCCCTAACAGTGCAGTGGAAC
* * * * * **
44908535 AGATTGAAGCCACAACAGCGGATTTTA-CTTCCTTAGTAGTGCAGTGGAAC
1 AGATTGAAGCCACGACGGCGGA-TCTAGTTTCCCTAACAGTGCAGTGGAAC
* * * * * * * *
44908585 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCTAATATTACAATTGAAA
1 AGATTGAAGCCACGACGGCGGATCTAGTTTCCCTAACAGTGCAGTGGAAC
* * * * *
44908635 AGATTGAAGCCACAACGGCAGATCTTACTTT-CCTGACAGTGCGGTGGAAC
1 AGATTGAAGCCACGACGGCGGATC-TAGTTTCCCTAACAGTGCAGTGGAAC
* * *
44908685 AGATTGAAGCTACGACGGCGGATCTAGTTTCCCTAACATTGCAGTTGAAC
1 AGATTGAAGCCACGACGGCGGATCTAGTTTCCCTAACAGTGCAGTGGAAC
*
44908735 AAATTGAAG
1 AGATTGAAG
44908744 ATTATAGATC
Statistics
Matches: 262, Mismatches: 86, Indels: 20
0.71 0.23 0.05
Matches are distributed among these distances:
48 1 0.00
49 45 0.17
50 209 0.80
51 7 0.03
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCCACGACGGCGGATCTAGTTTCCCTAACAGTGCAGTGGAAC
Found at i:44908922 original size:44 final size:45
Alignment explanation
Indices: 44908851--44908966 Score: 162
Period size: 44 Copynumber: 2.6 Consensus size: 45
44908841 TCTATCTCCC
* *
44908851 CATACTGGTGGTGGAGTAGATCGAAGAAAGCAGATCTTGTCTTCA
1 CATACTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCA
** * *
44908896 TGTACTGG-CGTGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCC
1 CATACTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCA
*
44908940 CATACTGGTGGTGAAGTAGATCGAAGA
1 CATACTGGTCGTGAAGTAGATCGAAGA
44908967 TACAAGTCTT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 38 0.63
45 22 0.37
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (45 bp):
CATACTGGTCGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCA
Found at i:44910836 original size:2 final size:2
Alignment explanation
Indices: 44910829--44910853 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44910819 TATACGCATT
44910829 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 T
44910854 TATTGTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44925750 original size:50 final size:50
Alignment explanation
Indices: 44925675--44925770 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
44925665 CACCTTCCTT
44925675 TTTAACTCAATGTCATCCATTCCCATGAAGACGCGGGCATCAATCAGTCA
1 TTTAACTCAATGTCATCCATTCCCATGAAGACGCGGGCATCAATCAGTCA
* * * *
44925725 TTTAATTCAATGTCATCCGTTCCCATGAAGATGCGGGCATCGATCA
1 TTTAACTCAATGTCATCCATTCCCATGAAGACGCGGGCATCAATCA
44925771 TGACTGAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (50 bp):
TTTAACTCAATGTCATCCATTCCCATGAAGACGCGGGCATCAATCAGTCA
Found at i:44931225 original size:34 final size:34
Alignment explanation
Indices: 44931182--44931354 Score: 301
Period size: 34 Copynumber: 5.1 Consensus size: 34
44931172 TAATAACAAA
* *
44931182 GTAAAAATTATCAAGGGAATTAAGGTTCAATGAT
1 GTAAAAATTATCAAGGGAATTAAGGTTAAATAAT
* *
44931216 GTAAAAATTATCAAGGGAATTAAGGTTCAATGAT
1 GTAAAAATTATCAAGGGAATTAAGGTTAAATAAT
44931250 GTAAAAATTATCAAGGGAATTAAGGTTAAATAAT
1 GTAAAAATTATCAAGGGAATTAAGGTTAAATAAT
44931284 GTAAAAATTATCAAGGGAATTAAGGTTAAATAAT
1 GTAAAAATTATCAAGGGAATTAAGGTTAAATAAT
*
44931318 GTAAAAATTATCAAGGGAATTAAGGTTAGATAAT
1 GTAAAAATTATCAAGGGAATTAAGGTTAAATAAT
44931352 GTA
1 GTA
44931355 CAGTAACATA
Statistics
Matches: 136, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 136 1.00
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.29
Consensus pattern (34 bp):
GTAAAAATTATCAAGGGAATTAAGGTTAAATAAT
Found at i:44939176 original size:39 final size:39
Alignment explanation
Indices: 44939122--44939200 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
44939112 GTATCAAGGC
44939122 ATGATGATAGGCCACAAAAGAATCAACACAAATAAATTA
1 ATGATGATAGGCCACAAAAGAATCAACACAAATAAATTA
44939161 ATGATGATAGGCCACAAAAGAATCAACACAAATAAATTA
1 ATGATGATAGGCCACAAAAGAATCAACACAAATAAATTA
44939200 A
1 A
44939201 GGACCCAGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.54, C:0.15, G:0.13, T:0.18
Consensus pattern (39 bp):
ATGATGATAGGCCACAAAAGAATCAACACAAATAAATTA
Found at i:44940551 original size:2 final size:2
Alignment explanation
Indices: 44940546--44940583 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
44940536 TACATATATA
*
44940546 TG TG TG TG TG TG TG TG TG TG TG CG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
44940584 AAATTTTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:44945081 original size:43 final size:41
Alignment explanation
Indices: 44945023--44945125 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 41
44945013 AATATGTCAT
44945023 AATAATATCCTATAATATCCTATTAGAAATCAAATTGCTAATA
1 AATAATATCC-ATAATATCCTATTAGAAATCAAATTGCTAA-A
** *
44945066 AATAATATCTCATAATATTTTATTAGGAATCAAATTGCTAAA
1 AATAATATC-CATAATATCCTATTAGAAATCAAATTGCTAAA
44945108 AGATAATATCCCATAATA
1 A-ATAATAT-CCATAATA
44945126 ATATCCTAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
42 2 0.04
43 50 0.93
44 2 0.04
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.35
Consensus pattern (41 bp):
AATAATATCCATAATATCCTATTAGAAATCAAATTGCTAAA
Found at i:44949406 original size:53 final size:53
Alignment explanation
Indices: 44949347--44949452 Score: 160
Period size: 53 Copynumber: 2.0 Consensus size: 53
44949337 AGTACTAATA
* *
44949347 AAAACATATTTAAACGATTTTGTTCAAGACCT-ACAACATTATGTCTTACAAAT
1 AAAACATAATTAAACAATTTTGTTCAAGA-CTGACAACATTATGTCTTACAAAT
* *
44949400 AAAACATAATTAAATAATTTTGTTCAAGACTGACAACATTGTGTCTTACAAAT
1 AAAACATAATTAAACAATTTTGTTCAAGACTGACAACATTATGTCTTACAAAT
44949453 TGAAAAATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 2 0.04
53 46 0.96
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.34
Consensus pattern (53 bp):
AAAACATAATTAAACAATTTTGTTCAAGACTGACAACATTATGTCTTACAAAT
Found at i:44954173 original size:59 final size:61
Alignment explanation
Indices: 44954104--44954220 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 61
44954094 ATAACTTTAA
* **
44954104 TATTAAATTAATATAATACTTA-T-CAAGATAAATATTATGTTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATACTTACTACAAGATAAATATTAAATTAAATTTAATATTAAATCT
* * *
44954163 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAATTTTGATATTAA
1 TATTAAATTAATAGAATACTTA-CTACAAGATAAATATTAAATTAAATTTAATATTAA
44954221 GATAATCACT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 20 0.41
61 1 0.02
62 28 0.57
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (61 bp):
TATTAAATTAATAGAATACTTACTACAAGATAAATATTAAATTAAATTTAATATTAAATCT
Found at i:44954483 original size:31 final size:31
Alignment explanation
Indices: 44954442--44954500 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
44954432 GCCCATTTTC
44954442 ATTTTAAAAAT-TTTAAAAAATTAAAAAAAGT
1 ATTTTAAAAATATTT-AAAAATTAAAAAAAGT
* *
44954473 ATTTTTAAAATATTTTAAAATTAAAAAA
1 ATTTTAAAAATATTTAAAAATTAAAAAA
44954501 TTAAAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (31 bp):
ATTTTAAAAATATTTAAAAATTAAAAAAAGT
Found at i:44954509 original size:41 final size:39
Alignment explanation
Indices: 44954454--44954625 Score: 258
Period size: 41 Copynumber: 4.3 Consensus size: 39
44954444 TTTAAAAATT
*
44954454 TTAAAAAATTAAAAAAAGTATTTTTAAAATATTTTAAAA
1 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
44954493 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
44954532 TTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
1 TT--AAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
*
44954573 TTTTTAAAAAATT-AAAAAAGTA-TGTAAAAATATTTTAAAA
1 ---TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
*
44954613 TTAAAAAAATAAA
1 TTAAAAAATTAAA
44954626 TATGTTTATT
Statistics
Matches: 124, Mismatches: 3, Indels: 13
0.89 0.02 0.09
Matches are distributed among these distances:
37 9 0.07
38 2 0.02
39 40 0.32
40 17 0.14
41 46 0.37
42 8 0.06
44 2 0.02
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (39 bp):
TTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:44954520 original size:11 final size:11
Alignment explanation
Indices: 44954505--44954612 Score: 72
Period size: 11 Copynumber: 10.4 Consensus size: 11
44954495 AAAAAATTAA
44954505 AAAAAGTATTTT
1 AAAAA-TATTTT
44954517 AAAAATATTTT
1 AAAAATATTTT
*
44954528 --AAA-A-TTA
1 AAAAATATTTT
* **
44954535 AAAAAAATTAA
1 AAAAATATTTT
44954546 AAAAAGTATTTT
1 AAAAA-TATTTT
44954558 AAAAATATTTT
1 AAAAATATTTT
44954569 -AAAAT-TTTT
1 AAAAATATTTT
*
44954578 AAAAA-A-TTA
1 AAAAATATTTT
*
44954587 AAAAAGTA-TGT
1 AAAAA-TATTTT
44954598 AAAAATATTTT
1 AAAAATATTTT
44954609 AAAA
1 AAAA
44954613 TTAAAAAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
7 2 0.03
8 1 0.01
9 17 0.22
10 12 0.16
11 32 0.42
12 13 0.17
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:44954543 original size:80 final size:79
Alignment explanation
Indices: 44954442--44954621 Score: 272
Period size: 80 Copynumber: 2.2 Consensus size: 79
44954432 GCCCATTTTC
** *
44954442 ATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTTAAAATATTTTAAAA-TTAAAAAATTAAA
1 ATTTT-AAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAATT-AA
*
44954506 AAAAGTATTTTAAAAAT
64 AAAAGTA-TGTAAAAAT
44954523 ATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTTTTAAAAAATTAA
1 ATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAA--TTTAAAAAATTAA
44954588 AAAAGTATGTAAAAAT
64 AAAAGTATGTAAAAAT
44954604 ATTTTAAAATTAAAAAAA
1 ATTTTAAAATTAAAAAAA
44954622 TAAATATGTT
Statistics
Matches: 92, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
80 42 0.46
81 31 0.34
82 9 0.10
83 10 0.11
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (79 bp):
ATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAATTAAAA
AAGTATGTAAAAAT
Found at i:44955312 original size:20 final size:20
Alignment explanation
Indices: 44955289--44955355 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
44955279 AAAGTATTTC
44955289 AAAAATTTATTTTAAAAATT
1 AAAAATTTATTTTAAAAATT
**
44955309 AAAAAAGTATTTTTAAAATATTT
1 AAAAATTTA-TTTTAAAA-A-TT
* **
44955332 TAAAATTT-TTAAAAAAATT
1 AAAAATTTATTTTAAAAATT
44955351 AAAAA
1 AAAAA
44955356 AGTATGTAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
19 6 0.17
20 8 0.22
21 14 0.39
22 1 0.03
23 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (20 bp):
AAAAATTTATTTTAAAAATT
Found at i:44955347 original size:33 final size:32
Alignment explanation
Indices: 44955270--44955336 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
44955260 GGGCCCGAAC
*
44955270 AAAATAAAAAAAGTATTTCAAAAATTTATTTTA
1 AAAATTAAAAAAGTATTTCAAAAA-TTATTTTA
**
44955303 AAAATTAAAAAAGTATTTTTAAAA-TATTTTA
1 AAAATTAAAAAAGTATTTCAAAAATTATTTTA
44955334 AAA
1 AAA
44955337 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 10 0.32
33 21 0.68
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.37
Consensus pattern (32 bp):
AAAATTAAAAAAGTATTTCAAAAATTATTTTA
Found at i:44955388 original size:42 final size:42
Alignment explanation
Indices: 44955302--44955388 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
44955292 AATTTATTTT
* ** ***
44955302 AAAAATTAAAAAAGTATTTTTAAAATATTTTAAAATTTTTAA
1 AAAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAAAAA
44955344 AAAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAAAAA
1 AAAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAAAAA
44955386 AAA
1 AAA
44955389 TAAATATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (42 bp):
AAAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAAAAA
Found at i:44959323 original size:18 final size:18
Alignment explanation
Indices: 44959285--44959375 Score: 60
Period size: 18 Copynumber: 4.9 Consensus size: 18
44959275 TTGATTGGAA
**
44959285 AAAAAATATTAAAAACAAT
1 AAAAAAT-TTAAAAATTAT
44959304 AAAAAATTTAAAAATTAT
1 AAAAAATTTAAAAATTAT
* *
44959322 --AACATTGTAACAACTTATT
1 AAAAAATT-TAA-AAATTA-T
**
44959341 AAAAAATGCAAAAATTAT
1 AAAAAATTTAAAAATTAT
* *
44959359 AAAAAATGTAAATATTA
1 AAAAAATTTAAAAATTA
44959376 ACAAATTATT
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
16 5 0.09
17 3 0.05
18 30 0.53
19 13 0.23
20 2 0.04
21 4 0.07
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAAAATTTAAAAATTAT
Found at i:44959963 original size:31 final size:31
Alignment explanation
Indices: 44959902--44959969 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
44959892 TGTTAATCTA
* * *
44959902 TGAACTTGGCAATTGTTCCTCTATTGGGGCT
1 TGAACTTGACAATTGTTCCTCCATTAGGGCT
*
44959933 TGAATTTGACAATTGTT-CTCACATTAGGGCT
1 TGAACTTGACAATTGTTCCTC-CATTAGGGCT
*
44959964 TCAACT
1 TGAACT
44959970 CTAGGGCTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 3 0.10
31 27 0.90
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
TGAACTTGACAATTGTTCCTCCATTAGGGCT
Found at i:44962930 original size:21 final size:21
Alignment explanation
Indices: 44962904--44962982 Score: 126
Period size: 21 Copynumber: 3.9 Consensus size: 21
44962894 GGTGGATTAA
* *
44962904 CTCTTACGAGCTTCTATTCAG
1 CTCTTATGAGCTTCTGTTCAG
44962925 CTCTTATGAGCTTCTGTTCAG
1 CTCTTATGAGCTTCTGTTCAG
44962946 CTCTTATGAGCTTCTGTTCAG
1 CTCTTATGAGCTTCTGTTCAG
44962967 CT-TT-TGAGCTTCTGTT
1 CTCTTATGAGCTTCTGTT
44962983 GGTGTATTCG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
19 12 0.21
20 2 0.04
21 42 0.75
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (21 bp):
CTCTTATGAGCTTCTGTTCAG
Found at i:44965414 original size:29 final size:29
Alignment explanation
Indices: 44965374--44965435 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
44965364 ATTTAGTCCC
* *
44965374 TTTTGTTTTTTA-TTTCGATTTCGCCCCCT
1 TTTTGGTTTTTACTTT-GATTTAGCCCCCT
*
44965403 TTTTGGTTTTTACTTTGATTTAGTCCCCT
1 TTTTGGTTTTTACTTTGATTTAGCCCCCT
44965432 TTTT
1 TTTT
44965436 AGTATTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 26 0.90
30 3 0.10
ACGTcount: A:0.08, C:0.19, G:0.11, T:0.61
Consensus pattern (29 bp):
TTTTGGTTTTTACTTTGATTTAGCCCCCT
Found at i:44965486 original size:3 final size:3
Alignment explanation
Indices: 44965457--44965560 Score: 103
Period size: 3 Copynumber: 35.7 Consensus size: 3
44965447 TATTTTCTTC
* *
44965457 ATT ATT -TT AAT A-T ATT ATC ATTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
*
44965501 ATT ATT ATT ACT ATT -TCT ATT ATT ATT ATT ATT A-T ATT ATT -TT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
44965544 ATTT ATC A-T ATT ATT AT
1 A-TT ATT ATT ATT ATT AT
44965561 ACGATAGTTT
Statistics
Matches: 85, Mismatches: 7, Indels: 18
0.77 0.06 0.16
Matches are distributed among these distances:
2 10 0.12
3 69 0.81
4 6 0.07
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:44965802 original size:15 final size:16
Alignment explanation
Indices: 44965782--44965816 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
44965772 TCACATGTAC
*
44965782 ATTTTTTATATAT-AT
1 ATTTTTTAGATATGAT
44965797 ATTTTTTAGATATGAT
1 ATTTTTTAGATATGAT
44965813 ATTT
1 ATTT
44965817 AAACGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (16 bp):
ATTTTTTAGATATGAT
Found at i:44970900 original size:21 final size:21
Alignment explanation
Indices: 44970859--44970901 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
44970849 CTACAAATGG
44970859 AAAACTGAACTATATCAATGTA
1 AAAACTGAACTATAT-AATGTA
*
44970881 AAAACTAGTACTATAT-ATGTA
1 AAAACT-GAACTATATAATGTA
44970902 GGAGTGGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 6 0.32
23 8 0.42
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (21 bp):
AAAACTGAACTATATAATGTA
Found at i:44971496 original size:21 final size:21
Alignment explanation
Indices: 44971470--44971522 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
44971460 AGTGGTGGTG
*
44971470 GTGAGATTAGTTACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
* *
44971491 GTGAGATTAGATACTGTATCG
1 GTGAGATTAGATACTGTAGCA
44971512 GTGAGATTAGA
1 GTGAGATTAGA
44971523 AACAATGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.08, G:0.30, T:0.32
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:44976978 original size:18 final size:20
Alignment explanation
Indices: 44976940--44976979 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
44976930 TACAACACGA
44976940 TTCAATTTCATATCGAATAT
1 TTCAATTTCATATCGAATAT
*
44976960 TTCAATTTTAT-TC-AATAT
1 TTCAATTTCATATCGAATAT
44976978 TT
1 TT
44976980 TCCTAAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 2 0.11
20 10 0.53
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.53
Consensus pattern (20 bp):
TTCAATTTCATATCGAATAT
Found at i:44990814 original size:20 final size:20
Alignment explanation
Indices: 44990791--44990833 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
44990781 ATTTCTCTTC
*
44990791 TTTCCTTTC-CTCTCGTCTCT
1 TTTCCTCTCTCTCTC-TCTCT
44990811 TTT-CTCTCTCTCTCTCTCT
1 TTTCCTCTCTCTCTCTCTCT
44990830 TTTC
1 TTTC
44990834 TTCCTCCCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.00, C:0.40, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTCCTCTCTCTCTCTCTCT
Found at i:44998967 original size:30 final size:31
Alignment explanation
Indices: 44998926--44998985 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
44998916 TTGGTAGTAT
*
44998926 ATTTTTTAAAATGT-T-TAATTAATTTTTAG
1 ATTTTTTAAAATATATATAATTAATTTTTAG
*
44998955 ATTTTTCTAAAATATATATTATTAATTTTTA
1 ATTTTT-TAAAATATATATAATTAATTTTTA
44998986 AAATGTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 6 0.23
30 7 0.27
31 1 0.04
32 12 0.46
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (31 bp):
ATTTTTTAAAATATATATAATTAATTTTTAG
Found at i:45002719 original size:26 final size:25
Alignment explanation
Indices: 45002676--45002748 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 25
45002666 TTTTTCACCC
45002676 CAATTTTACCCTGGTAAAATTTTGA
1 CAATTTTACCCTGGTAAAATTTTGA
*
45002701 CAATTTTACTCCTGGTAAAA-ATTGA
1 CAATTTTAC-CCTGGTAAAATTTTGA
* *
45002726 CGATTTTAGCCCTGATAAAATTT
1 CAATTTTA-CCCTGGTAAAATTT
45002749 CGAAAAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 29 0.71
26 12 0.29
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (25 bp):
CAATTTTACCCTGGTAAAATTTTGA
Found at i:45038357 original size:20 final size:20
Alignment explanation
Indices: 45038334--45038373 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
45038324 AAAATCACAA
45038334 ATGCTGAATTAAAAACAAGT
1 ATGCTGAATTAAAAACAAGT
45038354 ATGCTGAATTAAAAACAAGT
1 ATGCTGAATTAAAAACAAGT
45038374 GCATAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (20 bp):
ATGCTGAATTAAAAACAAGT
Found at i:45047186 original size:23 final size:21
Alignment explanation
Indices: 45047144--45047186 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
45047134 AATAGAGAAA
*
45047144 ACGAAATTTCTGGTATATGTT
1 ACGAAATTTCTGGTAGATGTT
45047165 ACGAAATTTCATTGGTAGATGT
1 ACGAAATTTC--TGGTAGATGT
45047187 CTCATTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (21 bp):
ACGAAATTTCTGGTAGATGTT
Found at i:45051056 original size:20 final size:20
Alignment explanation
Indices: 45051031--45051070 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
45051021 GATTTTGTTG
45051031 TTGTTTGAA-TCGATTCAAAA
1 TTGTTT-AACTCGATTCAAAA
*
45051051 TTGTTTAACTCGATTTAAAA
1 TTGTTTAACTCGATTCAAAA
45051071 CCCAACAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (20 bp):
TTGTTTAACTCGATTCAAAA
Found at i:45062380 original size:41 final size:39
Alignment explanation
Indices: 45062255--45062387 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 39
45062245 CTAGTTTGGT
* * *
45062255 ACCCAGTACCTCATTGGA-TAATTCGAAGTAATAAGTTGAC
1 ACCCAGTGCCTCA-TCGATTAATCCGAAGTAATAA-TTGAC
* * * *
45062295 ACCTAGTGTCTCATCGGTTAAACCGAAGT-A-AATT-AGC
1 ACCCAGTGCCTCATCGATTAATCCGAAGTAATAATTGA-C
45062332 ACCCAGTGCCTCATCGAATTAATCCGAAGTAATAGATTGAC
1 ACCCAGTGCCTCATCG-ATTAATCCGAAGTAATA-ATTGAC
*
45062373 ACCCAGTGTCTCATC
1 ACCCAGTGCCTCATC
45062388 AACTCGAAGT
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
36 1 0.01
37 17 0.23
38 13 0.18
39 4 0.05
40 20 0.27
41 18 0.24
42 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (39 bp):
ACCCAGTGCCTCATCGATTAATCCGAAGTAATAATTGAC
Found at i:45063364 original size:50 final size:51
Alignment explanation
Indices: 45063289--45063414 Score: 191
Period size: 50 Copynumber: 2.5 Consensus size: 51
45063279 CTTACGTATG
* *
45063289 ATCACTTATCACTTGTCCCTGATCAAATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTGAAGCTACCACTT
* * *
45063339 ATCACTTGCCACTAGTCACTGATCAAATAAGTGTAGCTGAAGCTACTACTT
1 ATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTGAAGCTACCACTT
*
45063390 ATCACTTGTCACTTGCCACTGATCA
1 ATCACTTGTCACTTGTCACTGATCA
45063415 GAAGTACTCA
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 34 0.51
51 33 0.49
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.31
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAAATAAGTGTAGCTGAAGCTACCACTT
Found at i:45063410 original size:51 final size:50
Alignment explanation
Indices: 45063289--45063414 Score: 182
Period size: 51 Copynumber: 2.5 Consensus size: 50
45063279 CTTACGTATG
*
45063289 ATCACTTATCACTTGTCC-CTGATCAAATAAGTGTAGCTAAGCTACCACTT
1 ATCACTTGTCACTTG-CCACTGATCAAATAAGTGTAGCTAAGCTACCACTT
* * * *
45063339 ATCACTTGCCACTAGTCACTGATCAAATAAGTGTAGCTGAAGCTACTACTT
1 ATCACTTGTCACTTGCCACTGATCAAATAAGTGTAGCT-AAGCTACCACTT
45063390 ATCACTTGTCACTTGCCACTGATCA
1 ATCACTTGTCACTTGCCACTGATCA
45063415 GAAGTACTCA
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
49 1 0.02
50 32 0.48
51 33 0.50
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.31
Consensus pattern (50 bp):
ATCACTTGTCACTTGCCACTGATCAAATAAGTGTAGCTAAGCTACCACTT
Found at i:45078418 original size:8 final size:8
Alignment explanation
Indices: 45078407--45078437 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
45078397 AATTATTCAA
45078407 TTTTTTAT
1 TTTTTTAT
45078415 TTTTTTAT
1 TTTTTTAT
45078423 TTTTTTAT
1 TTTTTTAT
45078431 TTTTTTA
1 TTTTTTA
45078438 AAATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTAT
Found at i:45078532 original size:44 final size:45
Alignment explanation
Indices: 45078481--45078569 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
45078471 ATTGTAATAC
* *
45078481 ATTTTAAATAAATTG-TTTTTTTATTTCTATTTTGAAAATTACGT
1 ATTTTAAATAAACTGTTTTTTTTATTTCTATTTTGAAAAATACGT
45078525 ATTTTAAATAAACTGTTTTTTTTATTTCTATTTTGAAAAATACGT
1 ATTTTAAATAAACTGTTTTTTTTATTTCTATTTTGAAAAATACGT
45078570 GCTTTCACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
44 14 0.33
45 28 0.67
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.55
Consensus pattern (45 bp):
ATTTTAAATAAACTGTTTTTTTTATTTCTATTTTGAAAAATACGT
Found at i:45084410 original size:30 final size:29
Alignment explanation
Indices: 45084353--45084410 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
45084343 TGATTTGAAT
*
45084353 TTTTTAAAAATATTATATAATTTTCATAA
1 TTTTTAAAAATATTATATAATTCTCATAA
*
45084382 TTTTTAATAATGATTATAT-ATTACTCATA
1 TTTTTAAAAAT-ATTATATAATT-CTCATA
45084411 TGAAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (29 bp):
TTTTTAAAAATATTATATAATTCTCATAA
Found at i:45084640 original size:36 final size:35
Alignment explanation
Indices: 45084593--45084664 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 35
45084583 CATCTCCGGA
45084593 GCTTGGCAAATAAGGAAAGTGATCTTTTGAAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTTTG-AGATAT
* *
45084629 GCTTGGCAAATATGGAAGGTGATCTTTTGAGATAT
1 GCTTGGCAAATAAGGAAAGTGATCTTTTGAGATAT
45084664 G
1 G
45084665 TGATCCTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 7 0.21
36 27 0.79
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (35 bp):
GCTTGGCAAATAAGGAAAGTGATCTTTTGAGATAT
Found at i:45085033 original size:48 final size:48
Alignment explanation
Indices: 45084962--45085056 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
45084952 TAAGGGAATT
**
45084962 CTGTTGAATCCTTTATTGTTGCAAGTTAAGCTGACTTAGGCGTTTTTA
1 CTGTTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCGTTTTTA
*
45085010 CTGTTGAATCCTTTATTACTGCAAGTTAGGCTGACTTAGGCGTTTTT
1 CTGTTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCGTTTTT
45085057 GAGCAAAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.20, C:0.16, G:0.21, T:0.43
Consensus pattern (48 bp):
CTGTTGAATCCTTTATTACTGCAAGTTAAGCTGACTTAGGCGTTTTTA
Found at i:45108119 original size:2 final size:2
Alignment explanation
Indices: 45108112--45108138 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45108102 ATTCTCATGC
45108112 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
45108139 CATTTAGATT
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:45108779 original size:119 final size:117
Alignment explanation
Indices: 45108558--45108781 Score: 283
Period size: 119 Copynumber: 1.9 Consensus size: 117
45108548 TAAATACTAT
* ** *
45108558 AAATTTTATCATACGCATATGCATGTGGAAATTACATATTTAGAACACAAATATCTTTAAAAATA
1 AAATTCTATCATACGCATATGCATGTGGAAACCACATATCTAGAACACAAATATCTTTAAAAATA
*
45108623 ACATAAAATAAATAATGAACTCTATGATTTGAAACTAATTAATAATAACTGA
66 ACATAAAATAAATAATGAAATCTATGATTTGAAACTAATTAATAATAACTGA
* * *
45108675 AAATTCTATCAT-CTGCGTATGCATGTGGAAACCACGTATCTGGAACACAAAGT-TGCATTTAAA
1 AAATTCTATCATAC-GCATATGCATGTGGAAACCACATATCTAGAACACAAA-TAT-C-TTTAAA
* * *
45108738 AATAGCATACAATAAATAATGAAATGTAT-AGTTTGAAACTAATT
62 AATAACATAAAATAAATAATGAAATCTATGA-TTTGAAACTAATT
45108782 GATGACTCTA
Statistics
Matches: 91, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
116 1 0.01
117 43 0.47
118 3 0.03
119 44 0.48
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (117 bp):
AAATTCTATCATACGCATATGCATGTGGAAACCACATATCTAGAACACAAATATCTTTAAAAATA
ACATAAAATAAATAATGAAATCTATGATTTGAAACTAATTAATAATAACTGA
Found at i:45114953 original size:5 final size:5
Alignment explanation
Indices: 45114943--45114968 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
45114933 TTAGAGGTGG
45114943 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
45114969 CGTTTACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:45115853 original size:18 final size:16
Alignment explanation
Indices: 45115836--45115865 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
45115826 TCATTTTTTA
45115836 TTAT-TTTATATATAT
1 TTATATTTATATATAT
45115851 TTATATTTATATATA
1 TTATATTTATATATA
45115866 CGTGTTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATATTTATATATAT
Found at i:45116436 original size:18 final size:18
Alignment explanation
Indices: 45116405--45116457 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
45116395 GCAATATATG
45116405 TAAAAATA-ATTTAAAATA
1 TAAAAATATA-TTAAAATA
* *
45116423 TAAAAATTTATTAATATA
1 TAAAAATATATTAAAATA
*
45116441 TAACAATATATGTAAAA
1 TAAAAATATAT-TAAAA
45116458 ACAATTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
TAAAAATATATTAAAATA
Found at i:45116591 original size:34 final size:35
Alignment explanation
Indices: 45116536--45116602 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
45116526 CAAACACCAG
*
45116536 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
45116571 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
45116603 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:45118507 original size:19 final size:19
Alignment explanation
Indices: 45118483--45118527 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
45118473 CGTCTCTTTC
* *
45118483 TGCATT-CATTTCATGCATT
1 TGCATTACATTACAT-CATA
45118502 TGCATTACATTACATCATA
1 TGCATTACATTACATCATA
45118521 TGCATTA
1 TGCATTA
45118528 AAGACTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (19 bp):
TGCATTACATTACATCATA
Found at i:45120437 original size:24 final size:25
Alignment explanation
Indices: 45120409--45120463 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
45120399 CTTACGATAA
45120409 TTTTTGAACCAA-TATTCTTTCAGTT
1 TTTTTGAA-CAATTATTCTTTCAGTT
*
45120434 TTTTTGAATAATTATTCTTTCA-TT
1 TTTTTGAACAATTATTCTTTCAGTT
45120458 TTTTTG
1 TTTTTG
45120464 GATTTTCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.60
Consensus pattern (25 bp):
TTTTTGAACAATTATTCTTTCAGTT
Found at i:45121708 original size:17 final size:16
Alignment explanation
Indices: 45121679--45121717 Score: 69
Period size: 17 Copynumber: 2.4 Consensus size: 16
45121669 GGAGGATTTT
45121679 TTATATTATTTAATAA
1 TTATATTATTTAATAA
45121695 TTATATTCATTTAATAA
1 TTATATT-ATTTAATAA
45121712 TTATAT
1 TTATAT
45121718 AAATATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTATTTAATAA
Found at i:45128681 original size:28 final size:27
Alignment explanation
Indices: 45128649--45128703 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
45128639 TTATTATATT
*
45128649 TTTTATTTACTAAAATATTATAAAAAAA
1 TTTTATTTACCAAAATA-TATAAAAAAA
45128677 TTTTATTTACCAAAATATATAAAAAAA
1 TTTTATTTACCAAAATATATAAAAAAA
45128704 CAGAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (27 bp):
TTTTATTTACCAAAATATATAAAAAAA
Found at i:45128782 original size:27 final size:27
Alignment explanation
Indices: 45128744--45128821 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
45128734 AGCTAATCAC
*
45128744 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
* *
45128771 ATTGGCGGCACCAATGGTGCCAATGTG
1 ATTGGCGGCACCAATGGTGCCAAAGAG
45128798 ATTGGCGGCACCAATGGTGCCAAA
1 ATTGGCGGCACCAATGGTGCCAAA
45128822 AGGACTAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.28, C:0.23, G:0.32, T:0.17
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGAG
Found at i:45129256 original size:18 final size:19
Alignment explanation
Indices: 45129217--45129275 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
45129207 ATTTTATATT
45129217 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
45129236 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
45129254 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
45129273 TTA
1 TTA
45129276 CTTAATTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:45129978 original size:28 final size:28
Alignment explanation
Indices: 45129938--45130007 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
45129928 TTTTTCTGTT
45129938 TTTTTGAT-ATATTTTAGTAAATAAAAAA
1 TTTTT-ATAATATTTTAGTAAATAAAAAA
*
45129966 TTTTTATAATATTTTGGTAAATAAAAAA
1 TTTTTATAATATTTTAGTAAATAAAAAA
**
45129994 -AGTTATAATATTTT
1 TTTTTATAATATTTT
45130008 GGTTATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 14 0.37
28 24 0.63
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (28 bp):
TTTTTATAATATTTTAGTAAATAAAAAA
Found at i:45130008 original size:27 final size:28
Alignment explanation
Indices: 45129946--45130010 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
45129936 TTTTTTTGAT
* **
45129946 ATATTTTAGTAAATAAAAAATTTTTATA
1 ATATTTTGGTAAATAAAAAATAGTTATA
45129974 ATATTTTGGTAAATAAAAAA-AGTTATA
1 ATATTTTGGTAAATAAAAAATAGTTATA
45130001 ATATTTTGGT
1 ATATTTTGGT
45130011 TATTTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 15 0.44
28 19 0.56
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAATAGTTATA
Found at i:45130675 original size:29 final size:29
Alignment explanation
Indices: 45130633--45130691 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
45130623 GGAGGAGGAG
45130633 TAAGATTAATGAAAGGTATCTCCTTTTGT
1 TAAGATTAATGAAAGGTATCTCCTTTTGT
45130662 TAAGATTAATGAAAGGTATCTCCTTTTGT
1 TAAGATTAATGAAAGGTATCTCCTTTTGT
45130691 T
1 T
45130692 TTCTTCCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (29 bp):
TAAGATTAATGAAAGGTATCTCCTTTTGT
Found at i:45143626 original size:20 final size:20
Alignment explanation
Indices: 45143601--45143639 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
45143591 AGAGGCTTTT
45143601 CTTTGTTCTCAAAAGGTTCG
1 CTTTGTTCTCAAAAGGTTCG
45143621 CTTTGTTCTCAAAAGGTTC
1 CTTTGTTCTCAAAAGGTTC
45143640 TATGTCAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.41
Consensus pattern (20 bp):
CTTTGTTCTCAAAAGGTTCG
Found at i:45150320 original size:340 final size:340
Alignment explanation
Indices: 45149700--45150381 Score: 1364
Period size: 340 Copynumber: 2.0 Consensus size: 340
45149690 TAGGCCAAGG
45149700 ACATGGGTGAAATTGCCAGGAAGAGAAAAAGAAAGTTGGTGGAAAAATAAAGAGAGGAGAGTTAG
1 ACATGGGTGAAATTGCCAGGAAGAGAAAAAGAAAGTTGGTGGAAAAATAAAGAGAGGAGAGTTAG
45149765 TGGATGGTGGACTATGGTGGCTACAGGCTTGCTTCATGGCAGTGGCTTCATTTTGGGCTTGTGGC
66 TGGATGGTGGACTATGGTGGCTACAGGCTTGCTTCATGGCAGTGGCTTCATTTTGGGCTTGTGGC
45149830 GTCTAAGAGAATGGGAGAATAATGAGATTTTTTTTTATGTCAGTTTAACATATCCATGCACACGT
131 GTCTAAGAGAATGGGAGAATAATGAGATTTTTTTTTATGTCAGTTTAACATATCCATGCACACGT
45149895 AACTAATATTACATTCCTATGTTTAAGATTTGATCCTTTTATGCAAATAGGAATATGTTTATGAT
196 AACTAATATTACATTCCTATGTTTAAGATTTGATCCTTTTATGCAAATAGGAATATGTTTATGAT
45149960 TTTATCAGACTATGCAAATAGGATGAAATACGTTGAAATTTAAAGCTTGTTGGATAAAATATGTT
261 TTTATCAGACTATGCAAATAGGATGAAATACGTTGAAATTTAAAGCTTGTTGGATAAAATATGTT
45150025 GTGATGTACTCCTCC
326 GTGATGTACTCCTCC
45150040 ACATGGGTGAAATTGCCAGGAAGAGAAAAAGAAAGTTGGTGGAAAAATAAAGAGAGGAGAGTTAG
1 ACATGGGTGAAATTGCCAGGAAGAGAAAAAGAAAGTTGGTGGAAAAATAAAGAGAGGAGAGTTAG
45150105 TGGATGGTGGACTATGGTGGCTACAGGCTTGCTTCATGGCAGTGGCTTCATTTTGGGCTTGTGGC
66 TGGATGGTGGACTATGGTGGCTACAGGCTTGCTTCATGGCAGTGGCTTCATTTTGGGCTTGTGGC
45150170 GTCTAAGAGAATGGGAGAATAATGAGATTTTTTTTTATGTCAGTTTAACATATCCATGCACACGT
131 GTCTAAGAGAATGGGAGAATAATGAGATTTTTTTTTATGTCAGTTTAACATATCCATGCACACGT
45150235 AACTAATATTACATTCCTATGTTTAAGATTTGATCCTTTTATGCAAATAGGAATATGTTTATGAT
196 AACTAATATTACATTCCTATGTTTAAGATTTGATCCTTTTATGCAAATAGGAATATGTTTATGAT
45150300 TTTATCAGACTATGCAAATAGGATGAAATACGTTGAAATTTAAAGCTTGTTGGATAAAATATGTT
261 TTTATCAGACTATGCAAATAGGATGAAATACGTTGAAATTTAAAGCTTGTTGGATAAAATATGTT
45150365 GTGATGTACTCCTCC
326 GTGATGTACTCCTCC
45150380 AC
1 AC
45150382 TTTCTCAACT
Statistics
Matches: 342, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
340 342 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (340 bp):
ACATGGGTGAAATTGCCAGGAAGAGAAAAAGAAAGTTGGTGGAAAAATAAAGAGAGGAGAGTTAG
TGGATGGTGGACTATGGTGGCTACAGGCTTGCTTCATGGCAGTGGCTTCATTTTGGGCTTGTGGC
GTCTAAGAGAATGGGAGAATAATGAGATTTTTTTTTATGTCAGTTTAACATATCCATGCACACGT
AACTAATATTACATTCCTATGTTTAAGATTTGATCCTTTTATGCAAATAGGAATATGTTTATGAT
TTTATCAGACTATGCAAATAGGATGAAATACGTTGAAATTTAAAGCTTGTTGGATAAAATATGTT
GTGATGTACTCCTCC
Found at i:45151521 original size:41 final size:40
Alignment explanation
Indices: 45151476--45151577 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 40
45151466 TGATTCAGTA
*
45151476 CACCGACACTTAGCCTGCTAGACATATAGTCTGAAATATTT
1 CACCGGCA-TTAGCCTGCTAGACATATAGTCTGAAATATTT
* * *
45151517 CACCGGCATTAAGCCTGCTAGACATTTAGTCTGAAGTGTTT
1 CACCGGCATT-AGCCTGCTAGACATATAGTCTGAAATATTT
*
45151558 CACCGGCAATAAGCCTGCTA
1 CACCGGC-ATTAGCCTGCTA
45151578 AGCGCTAAGC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 2 0.04
41 50 0.93
42 2 0.04
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (40 bp):
CACCGGCATTAGCCTGCTAGACATATAGTCTGAAATATTT
Found at i:45151592 original size:41 final size:41
Alignment explanation
Indices: 45151487--45151592 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
45151477 ACCGACACTT
* * * *
45151487 AGCCTGCTAGACA-TATAGTCTGAAATATTTCACCGGCATTA
1 AGCCTGCTAGACACTA-AGCCTGAAGTGTTTCACCGGCAATA
* * *
45151528 AGCCTGCTAGACATTTAGTCTGAAGTGTTTCACCGGCAATA
1 AGCCTGCTAGACACTAAGCCTGAAGTGTTTCACCGGCAATA
*
45151569 AGCCTGCTA-AGCGCTAAGCCTGAA
1 AGCCTGCTAGA-CACTAAGCCTGAA
45151593 AATCTCAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.02
41 53 0.96
42 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACACTAAGCCTGAAGTGTTTCACCGGCAATA
Found at i:45152715 original size:13 final size:13
Alignment explanation
Indices: 45152697--45152721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45152687 CAATCAAATG
45152697 CACACAAAATAAA
1 CACACAAAATAAA
45152710 CACACAAAATAA
1 CACACAAAATAA
45152722 TATTAAAATA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:45157653 original size:15 final size:14
Alignment explanation
Indices: 45157627--45157675 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
45157617 AGTTTTAAAA
45157627 ATAAAGAATTAAATT
1 ATAAA-AATTAAATT
* *
45157642 ATGATAAATTAAATG
1 AT-AAAAATTAAATT
45157657 ATAAAAATTAAATT
1 ATAAAAATTAAATT
*
45157671 TTAAA
1 ATAAA
45157676 TTTGAACATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 14 0.50
15 12 0.43
16 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (14 bp):
ATAAAAATTAAATT
Found at i:45161922 original size:23 final size:23
Alignment explanation
Indices: 45161896--45161939 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
45161886 TTTTATTAAA
*
45161896 TTTGTATATAAATTTTGATTTTT
1 TTTGTATATAAATTTTAATTTTT
* *
45161919 TTTGTATTTTAATTTTAATTT
1 TTTGTATATAAATTTTAATTT
45161940 GACATGTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (23 bp):
TTTGTATATAAATTTTAATTTTT
Found at i:45168244 original size:13 final size:13
Alignment explanation
Indices: 45168226--45168255 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
45168216 ATAATATTTT
*
45168226 TTTATTTTTAGAA
1 TTTATTATTAGAA
45168239 TTTATTATTAGAA
1 TTTATTATTAGAA
45168252 TTTA
1 TTTA
45168256 ACTTTCCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (13 bp):
TTTATTATTAGAA
Found at i:45168635 original size:16 final size:16
Alignment explanation
Indices: 45168606--45168648 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
45168596 CCGATATAAT
*
45168606 AAATATATTT-ATTTTT
1 AAATAT-TTTAATTTTA
*
45168622 AAATTTTTTAATTTTA
1 AAATATTTTAATTTTA
45168638 AAATATTTTAA
1 AAATATTTTAA
45168649 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 3 0.13
16 20 0.87
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAATATTTTAATTTTA
Found at i:45168667 original size:37 final size:40
Alignment explanation
Indices: 45168626--45168701 Score: 122
Period size: 37 Copynumber: 2.0 Consensus size: 40
45168616 ATTTTTAAAT
45168626 TTTTTAATTTTAAAATA-TTTT-AAATA-TTTTTTTATTA
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATTA
*
45168663 TTTTTAATTTTAAGATATTTTTAAAATACTTTTTTTATT
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATT
45168702 TTTAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
37 16 0.46
38 4 0.11
39 5 0.14
40 10 0.29
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (40 bp):
TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTATTA
Found at i:45168695 original size:28 final size:27
Alignment explanation
Indices: 45168642--45168695 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
45168632 ATTTTAAAAT
** * *
45168642 ATTTTAAATATTTTTTTATTATTTTTA
1 ATTTTAAATATTTTTAAAATACTTTTA
45168669 ATTTTAAGATATTTTTAAAATACTTTT
1 ATTTTAA-ATATTTTTAAAATACTTTT
45168696 TTTATTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (27 bp):
ATTTTAAATATTTTTAAAATACTTTTA
Found at i:45168715 original size:20 final size:20
Alignment explanation
Indices: 45168678--45168731 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
45168668 AATTTTAAGA
* * **
45168678 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAAAAATTTTGG
45168698 TATTTTTAAAAAAATTTTGG
1 TATTTTTAAAAAAATTTTGG
45168718 TATTTATTAAAAAA
1 TATTT-TTAAAAAA
45168732 TGGGTCGGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (20 bp):
TATTTTTAAAAAAATTTTGG
Found at i:45169361 original size:27 final size:27
Alignment explanation
Indices: 45169323--45169380 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
45169313 AAAGTGGGTT
45169323 ATTTATACATGCTGTAGTGGGTCTGTA
1 ATTTATACATGCTGTAGTGGGTCTGTA
45169350 ATTTATACATGCTGTAGTGGGTCTGTA
1 ATTTATACATGCTGTAGTGGGTCTGTA
45169377 ATTT
1 ATTT
45169381 GTTTTCATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.22, C:0.10, G:0.24, T:0.43
Consensus pattern (27 bp):
ATTTATACATGCTGTAGTGGGTCTGTA
Found at i:45171582 original size:22 final size:22
Alignment explanation
Indices: 45171541--45171639 Score: 89
Period size: 23 Copynumber: 4.5 Consensus size: 22
45171531 GAAGATGAAA
**
45171541 CTGGAAATTG-TTACATTTGTT
1 CTGGAAATTGTTTTGATTTGTT
* *
45171562 -TTGATATTGTTCTTGATTTGTT
1 CTGGAAATTGTT-TTGATTTGTT
45171584 CTGGAAATTGTTTTGA-TTGTCT
1 CTGGAAATTGTTTTGATTTGT-T
45171606 ACTGGAAATTGTTTTGA-TTGTCT
1 -CTGGAAATTGTTTTGATTTGT-T
45171629 GCTGGAAATTG
1 -CTGGAAATTG
45171640 AATTTGTTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
20 7 0.11
21 5 0.08
22 13 0.20
23 41 0.62
ACGTcount: A:0.20, C:0.08, G:0.22, T:0.49
Consensus pattern (22 bp):
CTGGAAATTGTTTTGATTTGTT
Found at i:45171610 original size:23 final size:22
Alignment explanation
Indices: 45171567--45171639 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 22
45171557 TTGTTTTGAT
45171567 ATTGTTCTTGATTTGT-TCTGGAA
1 ATTGTT-TTGA-TTGTCTCTGGAA
45171590 ATTGTTTTGATTGTCTACTGGAA
1 ATTGTTTTGATTGTCT-CTGGAA
45171613 ATTGTTTTGATTGTCTGCTGGAA
1 ATTGTTTTGATTGTCT-CTGGAA
45171636 ATTG
1 ATTG
45171640 AATTTGTTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
21 4 0.09
22 5 0.11
23 38 0.81
ACGTcount: A:0.19, C:0.08, G:0.23, T:0.49
Consensus pattern (22 bp):
ATTGTTTTGATTGTCTCTGGAA
Found at i:45172870 original size:25 final size:25
Alignment explanation
Indices: 45172836--45172941 Score: 119
Period size: 25 Copynumber: 4.2 Consensus size: 25
45172826 TACATCAATA
45172836 ATTAAAATAAGGACTTTAATATTTT
1 ATTAAAATAAGGACTTTAATATTTT
* *
45172861 ATTAAAATAAGGAC--TAATCA-ATA
1 ATTAAAATAAGGACTTTAAT-ATTTT
45172884 ATTAAAATAAGGACTTTAATATTTT
1 ATTAAAATAAGGACTTTAATATTTT
* *
45172909 ATTAAAAATCAAGAAATTTAATATTTT
1 ATT-AAAAT-AAGGACTTTAATATTTT
*
45172936 AATAAA
1 ATTAAA
45172942 GAAATTTAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
23 19 0.28
24 2 0.03
25 22 0.32
26 8 0.12
27 17 0.25
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.38
Consensus pattern (25 bp):
ATTAAAATAAGGACTTTAATATTTT
Found at i:45172887 original size:23 final size:23
Alignment explanation
Indices: 45172829--45172898 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
45172819 AAAAAATTAC
45172829 ATCAATAATTAAAATAAGGACTTTA
1 ATCAATAATTAAAATAAGGAC--TA
* *
45172854 AT-ATTTTATTAAAATAAGGACTA
1 ATCA-ATAATTAAAATAAGGACTA
45172877 ATCAATAATTAAAATAAGGACT
1 ATCAATAATTAAAATAAGGACT
45172899 TTAATATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 20 0.51
24 2 0.05
25 17 0.44
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (23 bp):
ATCAATAATTAAAATAAGGACTA
Found at i:45176648 original size:90 final size:92
Alignment explanation
Indices: 45176516--45176712 Score: 299
Period size: 90 Copynumber: 2.2 Consensus size: 92
45176506 TTGATTTTAG
** *
45176516 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAACAAATTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* *
45176581 ATTTAATATTAATTATTTTAAAATATA
66 ATGTAATAATAATTATTTTAAAATATA
* *
45176608 TAAATTCATATAA-AA-AAATTATTATCAATAATTTTATGAAATTATATATTATTATTAAATTAT
1 TAAATTCATATAAGAACAAATTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
*
45176671 ATGTAATAATAATTATTTTAAATTATA
66 ATGTAATAATAATTATTTTAAAATATA
*
45176698 AAAATTCATATAAGA
1 TAAATTCATATAAGA
45176713 TAATTTATTA
Statistics
Matches: 95, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
90 79 0.83
91 3 0.03
92 13 0.14
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (92 bp):
TAAATTCATATAAGAACAAATTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
ATGTAATAATAATTATTTTAAAATATA
Found at i:45176654 original size:46 final size:46
Alignment explanation
Indices: 45176516--45176756 Score: 139
Period size: 47 Copynumber: 5.3 Consensus size: 46
45176506 TTGATTTTAG
* *
45176516 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATA
1 TAAATTCATATAA-AA-AATTTATTATTAATAATTTTATGAAATTATA
* * * *
45176564 TATCATT-AT-TAAATTATATTTAATATTAATTATTTTA--AAA-TATA
1 TA-AATTCATATAAA--AAATTTATTATTAATAATTTTATGAAATTATA
* *
45176608 TAAATTCATATAAAAAAATTATTATCAATAATTTTATGAAATTATA
1 TAAATTCATATAAAAAATTTATTATTAATAATTTTATGAAATTATA
** * *
45176654 T--ATT-AT-TATTAAATTATATGTAATAATAATTATT-TTAAATTATA
1 TAAATTCATATAAAAAATT-TAT-TATTAATAATT-TTATGAAATTATA
* * * *
45176698 AAAATTCATATAAGATAATTTATTAGTT-ATAATTATT-TTAAATTTTA
1 TAAATTCATATAA-AAAATTTATTA-TTAATAATT-TTATGAAATTATA
45176745 TTAAA-TCATATA
1 -TAAATTCATATA
45176757 TTTTAATTAA
Statistics
Matches: 150, Mismatches: 25, Indels: 37
0.71 0.12 0.17
Matches are distributed among these distances:
42 6 0.04
43 25 0.17
44 29 0.19
45 12 0.08
46 9 0.06
47 48 0.32
48 14 0.09
49 7 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (46 bp):
TAAATTCATATAAAAAATTTATTATTAATAATTTTATGAAATTATA
Found at i:45176691 original size:26 final size:28
Alignment explanation
Indices: 45176536--45176697 Score: 82
Period size: 28 Copynumber: 5.6 Consensus size: 28
45176526 TAAGAACATT
* *
45176536 TTATTATTAAGAATTTTATGAAATTATATA
1 TTATTATT-A-AATTATATGAAATAATATA
* ** *
45176566 TCATTATTAAATTATATTTAATATTA-A
1 TTATTATTAAATTATATGAAATAATATA
* *
45176593 TTATT-TTAAAATATAT-AAATTCATATAAAAAAA
1 TTATTATTAAATTATATGAAA-T-A-AT----ATA
* * *
45176626 TTATTATCAATAATTTTATGAAATTATATA
1 TTATTAT-TA-AATTATATGAAATAATATA
*
45176656 TTATTATTAAATTATATGTAATAATA-A
1 TTATTATTAAATTATATGAAATAATATA
45176683 TTATT-TTAAATTATA
1 TTATTATTAAATTATA
45176698 AAAATTCATA
Statistics
Matches: 101, Mismatches: 19, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
25 2 0.02
26 21 0.21
27 12 0.12
28 27 0.27
29 2 0.02
30 16 0.16
32 1 0.01
33 6 0.06
34 3 0.03
35 1 0.01
36 7 0.07
37 3 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
TTATTATTAAATTATATGAAATAATATA
Found at i:45176695 original size:44 final size:43
Alignment explanation
Indices: 45176556--45176741 Score: 128
Period size: 44 Copynumber: 4.1 Consensus size: 43
45176546 GAATTTTATG
* *
45176556 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATAATTATTAAATTATA-TTAATAATAATTATTTT
* * * *
45176600 AAAATATATA-AATTCATATAAA-AAAATTATTATCAATAATT-TTATG
1 AAATTATATATAATT-AT-TAAATTATATTA--AT-AATAATTATT-TT
*
45176646 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATAATTATTAAATTATAT-TAATAATAATTATTTT
* * * *
45176690 AAATTATA-AAAATTCATATAAGATAATTTATTAGTTATAATTATTTT
1 AAATTATATATAATT-AT-TAA-AT--TATATTAATAATAATTATTTT
45176737 AAATT
1 AAATT
45176742 TTATTAAATC
Statistics
Matches: 111, Mismatches: 16, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
43 10 0.09
44 31 0.28
45 19 0.17
46 23 0.21
47 24 0.22
48 4 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (43 bp):
AAATTATATATAATTATTAAATTATATTAATAATAATTATTTT
Found at i:45176904 original size:25 final size:26
Alignment explanation
Indices: 45176872--45176926 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
45176862 TTATTAAATT
*
45176872 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
45176897 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
45176922 A-ATAT
1 ATATAT
45176927 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:45177157 original size:16 final size:16
Alignment explanation
Indices: 45177136--45177173 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
45177126 TTGATTTGCT
*
45177136 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
45177152 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
45177168 AATACA
1 ATTACA
45177174 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:45192385 original size:5 final size:5
Alignment explanation
Indices: 45192375--45192414 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
45192365 TTCTTCGTGT
*
45192375 TTTTA TTTTA TTTTA -TTTA TTTTA TCTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
45192415 ATATATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:45192399 original size:19 final size:19
Alignment explanation
Indices: 45192375--45192411 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
45192365 TTCTTCGTGT
*
45192375 TTTTATTTTATTTTATTTA
1 TTTTATCTTATTTTATTTA
45192394 TTTTATCTTATTTTATTT
1 TTTTATCTTATTTTATTT
45192412 TATATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATCTTATTTTATTTA
Found at i:45193101 original size:20 final size:20
Alignment explanation
Indices: 45193073--45193122 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 20
45193063 AGCAAAGTCA
45193073 AAGAAAAAAACAGCAAGCAAA-
1 AAGAAAAAAA-A-CAAGCAAAG
45193094 AAGCAAAAAAAACAAGCAAAG
1 AAG-AAAAAAAACAAGCAAAG
45193115 AAGAAAAA
1 AAGAAAAA
45193123 GAGAAGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 13 0.48
21 7 0.26
22 7 0.26
ACGTcount: A:0.74, C:0.12, G:0.14, T:0.00
Consensus pattern (20 bp):
AAGAAAAAAAACAAGCAAAG
Found at i:45193220 original size:7 final size:7
Alignment explanation
Indices: 45193205--45193271 Score: 55
Period size: 7 Copynumber: 8.7 Consensus size: 7
45193195 GGCTGAACGG
*
45193205 AGAAGAA
1 AGAAAAA
45193212 AGAAAAA
1 AGAAAAA
45193219 AGAAAAGA
1 AGAAAA-A
45193227 AGAAAGAA
1 AGAAA-AA
45193235 AGAAGAAA
1 AGAA-AAA
45193243 CAGAGAAGAA
1 -AGA-AA-AA
45193253 AGAAGAAA
1 AGAA-AAA
45193261 A-AAAAA
1 AGAAAAA
45193267 AGAAA
1 AGAAA
45193272 GGAAAAAGGG
Statistics
Matches: 51, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
6 4 0.08
7 17 0.33
8 17 0.33
9 10 0.20
10 3 0.06
ACGTcount: A:0.76, C:0.01, G:0.22, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:45193223 original size:11 final size:11
Alignment explanation
Indices: 45193207--45193279 Score: 74
Period size: 11 Copynumber: 6.3 Consensus size: 11
45193197 CTGAACGGAG
45193207 AAGAAAGAAAA
1 AAGAAAGAAAA
*
45193218 AAGAAAAGAAGA
1 AAG-AAAGAAAA
45193230 AAGAAAGAAGAA
1 AAGAAAGAA-AA
*
45193242 ACAGAGAAGAAAG
1 A-AGA-AAGAAAA
*
45193255 AAGAAAAAAAA
1 AAGAAAGAAAA
*
45193266 AAGAAAGGAAA
1 AAGAAAGAAAA
45193277 AAG
1 AAG
45193280 GGGAAAGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
11 26 0.51
12 15 0.29
13 5 0.10
14 5 0.10
ACGTcount: A:0.75, C:0.01, G:0.23, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAAA
Found at i:45193253 original size:18 final size:19
Alignment explanation
Indices: 45193205--45193272 Score: 88
Period size: 18 Copynumber: 3.7 Consensus size: 19
45193195 GGCTGAACGG
*
45193205 AGAAGAAAGAAAAAAGAAA
1 AGAAGAAAGAAAGAAGAAA
45193224 AGAAGAAAGAAAGAAGAAA
1 AGAAGAAAGAAAGAAGAAA
45193243 CAG-AG-AAGAAAGAAGAAA
1 -AGAAGAAAGAAAGAAGAAA
*
45193261 A-AAAAAAGAAAG
1 AGAAGAAAGAAAG
45193273 GAAAAAGGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
17 2 0.05
18 20 0.45
19 20 0.45
20 2 0.05
ACGTcount: A:0.75, C:0.01, G:0.24, T:0.00
Consensus pattern (19 bp):
AGAAGAAAGAAAGAAGAAA
Found at i:45193289 original size:4 final size:4
Alignment explanation
Indices: 45193207--45193272 Score: 54
Period size: 4 Copynumber: 17.8 Consensus size: 4
45193197 CTGAACGGAG
* *
45193207 AAGA AAGA AA-A AAGA AA-A GAAGA AAGA AAG- AAGA AACA GAG- AAGA
1 AAGA AAGA AAGA AAGA AAGA -AAGA AAGA AAGA AAGA AAGA AAGA AAGA
*
45193252 AAG- AAGA AA-A AAAA AAGA AAG
1 AAGA AAGA AAGA AAGA AAGA AAG
45193273 GAAAAAGGGG
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
3 15 0.30
4 34 0.68
5 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:45193421 original size:21 final size:22
Alignment explanation
Indices: 45193395--45193452 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
45193385 CAAAATAGAA
*
45193395 AAAGAAA-CAGCAGAAAAAAAG
1 AAAGAAAGAAGCAGAAAAAAAG
45193416 AAAGAAAGAAGCAG-AAAAAAG
1 AAAGAAAGAAGCAGAAAAAAAG
45193437 AAGAAGAAAGAAGCAG
1 -A-AAGAAAGAAGCAG
45193453 TCCAGCAGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 14 0.42
22 6 0.18
23 13 0.39
ACGTcount: A:0.69, C:0.07, G:0.24, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAGCAGAAAAAAAG
Found at i:45193438 original size:13 final size:14
Alignment explanation
Indices: 45193413--45193448 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
45193403 AGCAGAAAAA
45193413 AAGAAAGAAAGAAG
1 AAGAAAGAAAGAAG
*
45193427 CAGAAA-AAAGAAG
1 AAGAAAGAAAGAAG
45193440 AAGAAAGAA
1 AAGAAAGAA
45193449 GCAGTCCAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.72, C:0.03, G:0.25, T:0.00
Consensus pattern (14 bp):
AAGAAAGAAAGAAG
Found at i:45193446 original size:23 final size:23
Alignment explanation
Indices: 45193386--45193452 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
45193376 AAAAAAAACC
* * *
45193386 AAAATAGAAAAAGAAA-CAGCAG
1 AAAAAAGAAGAAGAAAGAAGCAG
45193408 -AAAAA-AAGAAAGAAAGAAGCAG
1 AAAAAAGAAG-AAGAAAGAAGCAG
45193430 AAAAAAGAAGAAGAAAGAAGCAG
1 AAAAAAGAAGAAGAAAGAAGCAG
45193453 TCCAGCAGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.05
21 10 0.26
22 5 0.13
23 18 0.47
24 3 0.08
ACGTcount: A:0.70, C:0.06, G:0.22, T:0.01
Consensus pattern (23 bp):
AAAAAAGAAGAAGAAAGAAGCAG
Found at i:45193650 original size:13 final size:14
Alignment explanation
Indices: 45193634--45193663 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
45193624 TGGGTAAATT
45193634 TTTTA-TCCATTTA
1 TTTTAGTCCATTTA
45193647 TTTTAGTCCATTTA
1 TTTTAGTCCATTTA
45193661 TTT
1 TTT
45193664 AAATATTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.20, C:0.13, G:0.03, T:0.63
Consensus pattern (14 bp):
TTTTAGTCCATTTA
Found at i:45194066 original size:17 final size:17
Alignment explanation
Indices: 45194039--45194084 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
45194029 AAAAAAATCG
45194039 TGTTTCAAAAATTT-TCA
1 TGTTTC-AAAATTTCTCA
*
45194056 TGTCTTCAAAATTTCTCG
1 TGT-TTCAAAATTTCTCA
45194074 TGTTTCAAAAT
1 TGTTTCAAAAT
45194085 AATAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (17 bp):
TGTTTCAAAATTTCTCA
Found at i:45194170 original size:17 final size:18
Alignment explanation
Indices: 45194142--45194233 Score: 52
Period size: 16 Copynumber: 5.3 Consensus size: 18
45194132 TTCTTTTTTA
45194142 AAAAATTC-CGTG-TTTC
1 AAAAATTCTCGTGATTTC
***
45194158 AAAAATTCTCGTGAATAAAA
1 AAAAATTCTCGTG-AT-TTC
*
45194178 AAAAATT-TCGTGTTTTC
1 AAAAATTCTCGTGATTTC
* *
45194195 -AAAATTCCCGTG-TTTGA
1 AAAAATTCTCGTGATTT-C
*
45194212 AAAAATT-TCGTGTTTTC
1 AAAAATTCTCGTGATTTC
45194229 AAAAA
1 AAAAA
45194234 AAAATTTCTC
Statistics
Matches: 57, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
16 17 0.30
17 17 0.30
18 10 0.18
19 6 0.11
20 7 0.12
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (18 bp):
AAAAATTCTCGTGATTTC
Found at i:45194215 original size:36 final size:34
Alignment explanation
Indices: 45194141--45194232 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 34
45194131 TTTCTTTTTT
* *
45194141 AAAAAATTCCGTG-TTTCAAAAATTCTCGTGAATAAA
1 AAAAAATTTCGTGTTTTC-AAAATTCCCGTGAAT--A
** *
45194177 AAAAAATTTCGTGTTTTCAAAATTCCCGTGTTTG
1 AAAAAATTTCGTGTTTTCAAAATTCCCGTGAATA
45194211 AAAAAATTTCGTGTTTTCAAAA
1 AAAAAATTTCGTGTTTTCAAAA
45194233 AAAAATTTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
34 22 0.44
36 24 0.48
37 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (34 bp):
AAAAAATTTCGTGTTTTCAAAATTCCCGTGAATA
Found at i:45194289 original size:19 final size:19
Alignment explanation
Indices: 45194266--45194553 Score: 103
Period size: 18 Copynumber: 15.4 Consensus size: 19
45194256 TTTGATGTTA
45194266 TCGTGTTTTCAAAAAATTC
1 TCGTGTTTTCAAAAAATTC
* * * * *
45194285 CCGTG-TTTGACAAATTTT
1 TCGTGTTTTCAAAAAATTC
45194303 TC-TGTTTTCAAAAAATTC
1 TCGTGTTTTCAAAAAATTC
* *
45194321 TCGTGTTTTCAAAATTTTCATGTTT
1 TCGTGTTTTCAAAA-----A-ATTC
45194346 TCGTGTTTTCAAAAAATTC
1 TCGTGTTTTCAAAAAATTC
*
45194365 TCGTGTTTTTAAAAAAAATT-
1 TCGTG-TTTT-CAAAAAATTC
***
45194385 TCGTG-TTT-AAAAAAAAA
1 TCGTGTTTTCAAAAAATTC
* *
45194402 TCATGTTTTC--AAAATTT
1 TCGTGTTTTCAAAAAATTC
* *
45194419 TCGTGTTTTC-AAAATTTT
1 TCGTGTTTTCAAAAAATTC
45194437 TCGTG---TCAAAAAAATTC
1 TCGTGTTTTC-AAAAAATTC
* * * *
45194454 TCATG-TATCGAAAATTTC
1 TCGTGTTTTCAAAAAATTC
45194472 -CGTGTTTTCAAAAAAAAATT-
1 TCGTGTTTTC---AAAAAATTC
*
45194492 TCGTG-TTTC-AAAGA-TC
1 TCGTGTTTTCAAAAAATTC
*
45194508 TTCGTGTTTTCAAAAATTATTA
1 -TCGTGTTTTCAAAAA--ATTC
*
45194530 TTGTG-TTTC--AAAATTC
1 TCGTGTTTTCAAAAAATTC
45194546 TCGTGTTT
1 TCGTGTTT
45194554 AAAAACAAAA
Statistics
Matches: 200, Mismatches: 38, Indels: 64
0.66 0.13 0.21
Matches are distributed among these distances:
15 3 0.01
16 17 0.09
17 39 0.19
18 55 0.28
19 27 0.14
20 18 0.09
21 23 0.12
22 1 0.00
24 1 0.00
25 16 0.08
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (19 bp):
TCGTGTTTTCAAAAAATTC
Found at i:45194309 original size:36 final size:36
Alignment explanation
Indices: 45194269--45194347 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
45194259 GATGTTATCG
*
45194269 TGTTTTCAAAAAATTCCCGTGTTTGACAAATTTTTC-
1 TGTTTTCAAAAAATTCCCGTGTTT-ACAAAATTTTCA
* *
45194305 TGTTTTCAAAAAATTCTCGTGTTTTCAAAATTTTCA
1 TGTTTTCAAAAAATTCCCGTGTTTACAAAATTTTCA
45194341 TGTTTTC
1 TGTTTTC
45194348 GTGTTTTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 9 0.23
36 30 0.77
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (36 bp):
TGTTTTCAAAAAATTCCCGTGTTTACAAAATTTTCA
Found at i:45194371 original size:27 final size:25
Alignment explanation
Indices: 45194321--45194373 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
45194311 CAAAAAATTC
*
45194321 TCGTGTTTTCAAAATTTTCATGTTT
1 TCGTGTTTTCAAAATTCTCATGTTT
*
45194346 TCGTGTTTTCAAAAAATTCTCGTGTTT
1 TCGTGTTTTC--AAAATTCTCATGTTT
45194373 T
1 T
45194374 TAAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.42
27 14 0.58
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53
Consensus pattern (25 bp):
TCGTGTTTTCAAAATTCTCATGTTT
Found at i:45194379 original size:20 final size:19
Alignment explanation
Indices: 45194344--45194402 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
45194334 ATTTTCATGT
*
45194344 TTTCGTG-TTTTCAAAAAA
1 TTTCGTGTTTTTAAAAAAA
45194362 TTCTCGTGTTTTTAAAAAAAA
1 TT-TCGTGTTTTT-AAAAAAA
**
45194383 TTTCGTGTTTAAAAAAAAA
1 TTTCGTGTTTTTAAAAAAA
45194402 T
1 T
45194403 CATGTTTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 2 0.06
19 13 0.37
20 12 0.34
21 8 0.23
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (19 bp):
TTTCGTGTTTTTAAAAAAA
Found at i:45194439 original size:18 final size:17
Alignment explanation
Indices: 45194405--45194553 Score: 77
Period size: 17 Copynumber: 8.3 Consensus size: 17
45194395 AAAAAAATCA
45194405 TGTTTTCAAAATTTTCG
1 TGTTTTCAAAATTTTCG
45194422 TGTTTTCAAAATTTTTCG
1 TGTTTTCAAAA-TTTTCG
**** * *
45194440 TGTCAAAAAAATTCTCA
1 TGTTTTCAAAATTTTCG
* *
45194457 TG-TATCGAAAATTTCCG
1 TGTTTTC-AAAATTTTCG
*
45194474 TGTTTTCAAAAAAAAATTTCG
1 TGTTTTC----AAAATTTTCG
*
45194495 TG-TTTCAAAGATCTTCG
1 TGTTTTCAAA-ATTTTCG
**
45194512 TGTTTTCAAAAATTATTAT
1 TGTTTTC-AAAATT-TTCG
*
45194531 TGTGTTTCAAAATTCTCG
1 TGT-TTTCAAAATTTTCG
45194549 TGTTT
1 TGTTT
45194554 AAAAACAAAA
Statistics
Matches: 97, Mismatches: 24, Indels: 22
0.68 0.17 0.15
Matches are distributed among these distances:
16 4 0.04
17 35 0.36
18 26 0.27
19 14 0.14
20 8 0.08
21 10 0.10
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (17 bp):
TGTTTTCAAAATTTTCG
Found at i:45194500 original size:20 final size:22
Alignment explanation
Indices: 45194464--45194503 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
45194454 TCATGTATCG
45194464 AAAATTTCCGTGTTTTCAAAAA
1 AAAATTTCCGTGTTTTCAAAAA
45194486 AAAATTT-CGTG-TTTCAAA
1 AAAATTTCCGTGTTTTCAAA
45194504 GATCTTCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (22 bp):
AAAATTTCCGTGTTTTCAAAAA
Found at i:45194536 original size:38 final size:37
Alignment explanation
Indices: 45194344--45194553 Score: 104
Period size: 37 Copynumber: 5.7 Consensus size: 37
45194334 ATTTTCATGT
*
45194344 TTTCGTGTTTTCAAAAAATTCTCGTGTTTT-TAAAAAAAA
1 TTTCGTG-TTTC--AAAATTCTCGTGTTTTCAAAAAAAAA
* *** * *
45194383 TTTCGTGTTTAAAAAAAAATCATGTTTTC----AAAAT
1 TTTCGTGTTT-CAAAATTCTCGTGTTTTCAAAAAAAAA
*
45194417 TTTCGTGTTTTCAAAATTTTTCGTG---TC--AAAAAAA
1 TTTCGTG-TTTCAAAA-TTCTCGTGTTTTCAAAAAAAAA
* *
45194451 TTCTCATGTATCGAAAATT-TCCGTGTTTTCAAAAAAAAA
1 TT-TCGTGTTTC-AAAATTCT-CGTGTTTTCAAAAAAAAA
**
45194490 TTTCGTGTTTCAAAGA-TCTTCGTGTTTTC-AAAAATTA
1 TTTCGTGTTTCAAA-ATTC-TCGTGTTTTCAAAAAAAAA
*
45194527 TTATTGTGTTTCAAAATTCTCGTGTTT
1 TT-TCGTGTTTCAAAATTCTCGTGTTT
45194554 AAAAACAAAA
Statistics
Matches: 133, Mismatches: 19, Indels: 40
0.69 0.10 0.21
Matches are distributed among these distances:
32 2 0.02
33 1 0.01
34 30 0.23
35 15 0.11
37 35 0.26
38 33 0.25
39 17 0.13
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (37 bp):
TTTCGTGTTTCAAAATTCTCGTGTTTTCAAAAAAAAA
Found at i:45195329 original size:34 final size:34
Alignment explanation
Indices: 45195286--45195354 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
45195276 GATGTTAAAT
*
45195286 TTACTCATAGATCCGGATAGATCAAATATGGAGC
1 TTACTCATAGATCCGGATAGATCAAATACGGAGC
*
45195320 TTACTCATAGATCTGGATAGATCAAATACGGAGC
1 TTACTCATAGATCCGGATAGATCAAATACGGAGC
45195354 T
1 T
45195355 ATATCGAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (34 bp):
TTACTCATAGATCCGGATAGATCAAATACGGAGC
Found at i:45197295 original size:140 final size:140
Alignment explanation
Indices: 45197043--45197455 Score: 530
Period size: 140 Copynumber: 3.0 Consensus size: 140
45197033 GTCGGCACAA
* * * * *
45197043 TGTTGGACAAAGCTGACTTTTATTTAAGTGTTGCCTTAGGCATGCATATCTCAGCCTTTATACAA
1 TGTTGGACAAAGTTGACTTTTATTTAAGCGTTGTCTTAGGCATGCATATCCCAACCTTTATACAA
* * * *
45197108 AGA-TTGGGTCAAAGCGTATGCCGGCAAGTCTATCCCAACACTTAGGAAAGTGTTGGCCCAAAAG
66 AGAGTT-GGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGACCCAAAAG
*
45197172 TGT-TGACATAG
130 TGTCGGA-ATAG
*
45197183 TGTTGGACAAAATTGACTTTTATTTAAGCGTTGTCTTAGGCATGCATATCCCAACCTTTATACAA
1 TGTTGGACAAAGTTGACTTTTATTTAAGCGTTGTCTTAGGCATGCATATCCCAACCTTTATACAA
* * * * *
45197248 AGAGTTGACCAAGGTGTATGTCGGTAAGTCTATCCGAACACTTAGGAAAGTGTCGACCCAAAAGT
66 AGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGACCCAAAAGT
45197313 GTCGGAATAG
131 GTCGGAATAG
* * * *
45197323 TATTGGATAAAGTCGA-TTCTTATTTAAGCATT-TCCTTAGGCATGCATATCCCAAGCC-TTATA
1 TGTTGGACAAAGTTGACTT-TTATTTAAGCGTTGT-CTTAGGCATGCATATCCCAA-CCTTTATA
* * **
45197385 CAAAGAGTTGGCCAAAACGTATGTTGGCAAGTCTATCCCAACACTTAAAAAAGTGTCGACCCAAA
63 CAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGACCCAAA
45197450 AGTGTC
128 AGTGTC
45197456 ACCTTAAGAC
Statistics
Matches: 238, Mismatches: 30, Indels: 10
0.86 0.11 0.04
Matches are distributed among these distances:
139 3 0.01
140 229 0.96
141 6 0.03
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (140 bp):
TGTTGGACAAAGTTGACTTTTATTTAAGCGTTGTCTTAGGCATGCATATCCCAACCTTTATACAA
AGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGACCCAAAAGT
GTCGGAATAG
Found at i:45197774 original size:8 final size:8
Alignment explanation
Indices: 45197761--45197826 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
45197751 CACAAAATAT
45197761 ATATTATA
1 ATATTATA
45197769 ATATTATA
1 ATATTATA
45197777 ATATTAT-
1 ATATTATA
*
45197784 ATGTTA-A
1 ATATTATA
*
45197791 TTATTA-A
1 ATATTATA
*
45197798 GTATATATATT
1 --ATAT-TATA
45197809 ATATTAT-
1 ATATTATA
45197816 ATATTATA
1 ATATTATA
45197824 ATA
1 ATA
45197827 AGTAAATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
7 17 0.36
8 21 0.45
9 7 0.15
10 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (8 bp):
ATATTATA
Found at i:45197811 original size:7 final size:7
Alignment explanation
Indices: 45197758--45197823 Score: 53
Period size: 7 Copynumber: 8.6 Consensus size: 7
45197748 GGCCACAAAA
45197758 TATATAT
1 TATATAT
45197765 TATAATAT
1 TAT-ATAT
45197773 TATAATAT
1 TAT-ATAT
*
45197781 TATATGT
1 TATATAT
45197788 TA-ATTAT
1 TATA-TAT
45197795 TAAGTATAT
1 T-A-TATAT
45197804 ATATTATAT
1 -TA-TATAT
45197813 TATATAT
1 TATATAT
45197820 TATA
1 TATA
45197824 ATAAGTAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
6 1 0.02
7 20 0.40
8 18 0.36
9 9 0.18
10 2 0.04
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (7 bp):
TATATAT
Found at i:45197836 original size:30 final size:32
Alignment explanation
Indices: 45197768--45197836 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
45197758 TATATATTAT
* *
45197768 AATATTATAATATTATATGTTAATTATTAAGTA
1 AATA-TATAATATTATATATTAATTAATAAGTA
* *
45197801 TATATATTATATTATATATT-A-TAATAAGTA
1 AATATATAATATTATATATTAATTAATAAGTA
45197831 AATATA
1 AATATA
45197837 ATAAATAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 13 0.42
31 1 0.03
32 14 0.45
33 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (32 bp):
AATATATAATATTATATATTAATTAATAAGTA
Found at i:45198627 original size:15 final size:15
Alignment explanation
Indices: 45198607--45198656 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
45198597 TGATGAATTT
45198607 ATTGAATTTATATTG
1 ATTGAATTTATATTG
45198622 ATTGAATTGGTATATAT-
1 ATTGAATT--TATAT-TG
*
45198639 ATTGAATATATATTG
1 ATTGAATTTATATTG
45198654 ATT
1 ATT
45198657 ATTTGAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
17 12 0.40
18 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:45198697 original size:29 final size:28
Alignment explanation
Indices: 45198639--45198702 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
45198629 TGGTATATAT
*
45198639 ATTGAATATATATTGATTATTTGAATTGA
1 ATTGAATATATATTGA-TATTTGAAGTGA
*
45198668 ATTGAATATATGTTG-TATTTGAAAAGTGA
1 ATTGAATATATATTGATATTTG--AAGTGA
45198697 ATTGAA
1 ATTGAA
45198703 ACCCTATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 6 0.19
29 25 0.81
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (28 bp):
ATTGAATATATATTGATATTTGAAGTGA
Found at i:45198783 original size:41 final size:38
Alignment explanation
Indices: 45198737--45198867 Score: 99
Period size: 41 Copynumber: 3.3 Consensus size: 38
45198727 GTCGGATGTA
45198737 GATGAGACACTAGGTGTTAATTTACTACTTCGGATTAATTC
1 GATGAGACACT-GGTGTTAATTTA-TACTTCGGATT-ATTC
* ** * **
45198778 GATGAGGCACTGGGTGCCAATTTAT--TTCGGTTTAGCC
1 GATGAGACACT-GGTGTTAATTTATACTTCGGATTATTC
*
45198815 GATGAGACACTGAGTGTCT-ATTTATTACTTCGAATTATTC
1 GATGAGACACTG-GTGT-TAATTTA-TACTTCGGATTATTC
45198855 GATGATG-CACTGG
1 GATGA-GACACTGG
45198868 GTGCCAAACT
Statistics
Matches: 70, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
36 1 0.01
37 20 0.29
38 8 0.11
39 1 0.01
40 19 0.27
41 21 0.30
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (38 bp):
GATGAGACACTGGTGTTAATTTATACTTCGGATTATTC
Found at i:45201668 original size:96 final size:96
Alignment explanation
Indices: 45201504--45201697 Score: 275
Period size: 96 Copynumber: 2.0 Consensus size: 96
45201494 TATTATCTAT
* * * *
45201504 ATATATGTAATGAGTAACTAAGCTTTACTCGTATAGTATTCAATATGTTATCCAGTCTTTTGCAA
1 ATATATATAATGAGTAACTAAGCTTTACTCGTATAATATTCAATATGTTATCCAGTCTATTACAA
45201569 CAAAATGGGGG-CACCGCCTCACATTTCGATC
66 CAAAA-GGGGGACACCGCCTCACATTTCGATC
* *
45201600 ATATATATAATGAGTAACTAAGCTTTACTCTTATAATATTCAATATTTTATCCAGAT-TATTACA
1 ATATATATAATGAGTAACTAAGCTTTACTCGTATAATATTCAATATGTTATCCAG-TCTATTACA
* * *
45201664 ACAAAAGGGGGATATCGCCTTACATTTCGATC
65 ACAAAAGGGGGACACCGCCTCACATTTCGATC
45201696 AT
1 AT
45201698 CGCTTCATAC
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
95 5 0.06
96 81 0.93
97 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.35
Consensus pattern (96 bp):
ATATATATAATGAGTAACTAAGCTTTACTCGTATAATATTCAATATGTTATCCAGTCTATTACAA
CAAAAGGGGGACACCGCCTCACATTTCGATC
Found at i:45206446 original size:42 final size:42
Alignment explanation
Indices: 45206370--45206567 Score: 245
Period size: 42 Copynumber: 4.7 Consensus size: 42
45206360 GTGCTAAACA
* ** *
45206370 GAAACCCATAAGGGTTGAA-TGGAAGCTCGTAAGAGCTGAATG
1 GAAACCCATAAGGGTTAAACT-GAAGCTCAAAAGAGCTGAACG
* *** * *
45206412 AAAATTGATAAGGGTTAAATTGAAGCTTAAAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
* *
45206454 GAAACTCAGAAGGGTTAAACTGAAGCTCAAAAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACTGAAGCTC-AAAAGAGCTGAACG
45206497 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
* *
45206539 GAAATCCATAAGGGTTAAACTGAAACTCA
1 GAAACCCATAAGGGTTAAACTGAAGCTCA
45206568 TATGAGTTAA
Statistics
Matches: 135, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
42 94 0.70
43 41 0.30
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
Found at i:45206569 original size:21 final size:21
Alignment explanation
Indices: 45206454--45206569 Score: 81
Period size: 21 Copynumber: 5.5 Consensus size: 21
45206444 GAGCTGAACG
*
45206454 GAAACTCAGAAGGGTTAAACT
1 GAAACTCATAAGGGTTAAACT
* * * * * *
45206475 GAAGCTCAAAAAGAGCTGAACG
1 GAAACTC-ATAAGGGTTAAACT
*
45206497 GAAACCCATAAGGGTTAAACT
1 GAAACTCATAAGGGTTAAACT
* * * * * *
45206518 GAAGCTCAAAAGAGCTGAACG
1 GAAACTCATAAGGGTTAAACT
45206539 GAAA-TCCATAAGGGTTAAACT
1 GAAACT-CATAAGGGTTAAACT
45206560 GAAACTCATA
1 GAAACTCATA
45206570 TGAGTTAACA
Statistics
Matches: 66, Mismatches: 26, Indels: 6
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.02
21 50 0.76
22 15 0.23
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.16
Consensus pattern (21 bp):
GAAACTCATAAGGGTTAAACT
Found at i:45206879 original size:45 final size:46
Alignment explanation
Indices: 45206793--45206880 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
45206783 ATTTCAATTT
* * * *
45206793 ATAATTTAACGATATTTCATTTTTTTTAACAATATGCTAAATATATA
1 ATAATTTAACAATATTTCA-TTTTTTCAAAAATATACTAAATATATA
*
45206840 ATAATTTAACAATATTTCA-TTTTTCAAAAATATATTAAATA
1 ATAATTTAACAATATTTCATTTTTTCAAAAATATACTAAATA
45206881 CGTAACATCA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 18 0.50
47 18 0.50
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (46 bp):
ATAATTTAACAATATTTCATTTTTTCAAAAATATACTAAATATATA
Found at i:45208695 original size:31 final size:32
Alignment explanation
Indices: 45208639--45208723 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 32
45208629 TCATATACTA
*
45208639 AATAAAATAATAAAATATCTCATTAAA-ATATT
1 AATAAAATAATAAAATATCTAATTAAATA-ATT
**
45208671 AATAAAATAAT-ATTTATCTAATTAAATAATT
1 AATAAAATAATAAAATATCTAATTAAATAATT
45208702 -ATAAAATATCATCAAAATATCT
1 AATAAAATA--AT-AAAATATCT
45208724 CTAATATCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
30 8 0.19
31 15 0.35
32 14 0.33
34 6 0.14
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.36
Consensus pattern (32 bp):
AATAAAATAATAAAATATCTAATTAAATAATT
Found at i:45213744 original size:3 final size:3
Alignment explanation
Indices: 45213736--45213766 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
45213726 CCTACGATTG
*
45213736 ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
45213767 GTTGCATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:45216496 original size:170 final size:169
Alignment explanation
Indices: 45216198--45217458 Score: 1801
Period size: 170 Copynumber: 7.4 Consensus size: 169
45216188 AAAATAAATG
*
45216198 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGCGACCCGGGTTCGATCCCCGG
1 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
* * * *
45216263 CAACGGCGATTATAAATTTTTTCCTATCAAAAGAAGTTTTTGGATTTCTGGTCAAATTCCAGATA
66 CAACGGCGATTATTAATTTTTTCCTATCAAAAAAAGTTTTTGGATTTCTGGACAAACTCCAGATA
*
45216328 TTGCATGCGTAAAATATTAGAAAACTACCGAAAAATAGCA
131 TTGCATG-GTAAAATATTAGAAAACTACCGAAAAATAACA
* * * *
45216368 CGTCGTTCTAGTATAGTGGTGAGTATTCCCGCCTGTCGCGCGGGTGACCCGGGTTCGATCCCTGG
1 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
* *
45216433 CAACGGCGATTATTAATATTTTCCTATCAAAAAAAGATTTTGGATTTCTGGACAAACTCCAGATA
66 CAACGGCGATTATTAATTTTTTCCTATCAAAAAAAGTTTTTGGATTTCTGGACAAACTCCAGATA
*
45216498 TTGCATGGGTAAAATGTTAGAAAACTACCGAAAAATAACA
131 TTGCAT-GGTAAAATATTAGAAAACTACCGAAAAATAACA
45216538 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
1 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
* * *
45216603 CAACGGCGAATT-TTAATTATTTTCCTATCATATAAAGTTTTTAGATTTCTGGACAAACTCCAGA
66 CAACGGCG-ATTATTAATT-TTTTCCTATCAAAAAAAGTTTTTGGATTTCTGGACAAACTCCAGA
* *
45216667 TATTGCGTGGATAAAATACTAGAAAACTACCG-AAAATCAACA
129 TATTGCATGG-TAAAATATTAGAAAACTACCGAAAAAT-AACA
45216709 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
1 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
** *
45216774 CAACGGCGATTATTAATTTTTTCCTATCAAAAACGGTTTTTGGTTTTCTGGACAAACTCCAGATA
66 CAACGGCGATTATTAATTTTTTCCTATCAAAAAAAGTTTTTGGATTTCTGGACAAACTCCAGATA
* * *
45216839 CTGCATGGCTAAAATGTTAGAAAACTACCGAAAACTAACA
131 TTGCATGG-TAAAATATTAGAAAACTACCGAAAAATAACA
45216879 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGAT-CCCGG
1 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
* * *
45216943 CAACGGCGATTGTTAAGTTTTTCCTATCAAAAAAAGTTTTTGGATTTTTGGACAAACTCCAGATA
66 CAACGGCGATTATTAATTTTTTCCTATCAAAAAAAGTTTTTGGATTTCTGGACAAACTCCAGATA
* * * **
45217008 TTGCATGGCTAAAATGTTAGAAAACTACGGAAAATTAAGG
131 TTGCATGG-TAAAATATTAGAAAACTACCGAAAAATAACA
* **
45217048 AGTC---GTAGTATAGTGGTGAATATTCCCGCCTGTCACGCGGGTGACCCGTTTTCGATCCCCGG
1 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
* *
45217110 CAACGGCGATTGTTAAGTTTTTTTCCTATCAAAAAAAGTTTTTGGATTTTTGGACAAACTCCAGA
66 CAACGGCGATTATTAA--TTTTTTCCTATCAAAAAAAGTTTTTGGATTTCTGGACAAACTCCAGA
* * *
45217175 TATTGCATGGGTAAAATATTAGAAAACAACTG-GAAATCAACA
129 TATTGCAT-GGTAAAATATTAGAAAACTACCGAAAAAT-AACA
* **
45217217 A---GTTGTAGTATAGTGGTAAGTATTCCCGTTTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
1 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
* * * *
45217279 GAACGGCGATTATTAGTGGTTTTCCTATCAAATAAAGTTTTTGGATTTCTGGACAAACTCCAGAT
66 CAACGGCGATTATTAAT-TTTTTCCTATCAAAAAAAGTTTTTGGATTTCTGGACAAACTCCAGAT
45217344 ATTGCATCGGTAAAATATTAGAAAACTACCG-AAAATCAACA
130 ATTGCAT-GGTAAAATATTAGAAAACTACCGAAAAAT-AACA
* * * * *
45217385 AGTTGTAGTA-TAGTGGTGGTGAGTAATCCCAG-CTGTCACGCGGGTGACCCGTGTTCGATCCCC
1 AGTCGTTGTAGTA-TAGTGGTGAGTATTCCC-GCCTGTCACGCGGGTGACCCGGGTTCGATCCCC
*
45217448 GGTAACGGCGA
64 GGCAACGGCGA
45217459 CTAACTTTTT
Statistics
Matches: 988, Mismatches: 82, Indels: 41
0.89 0.07 0.04
Matches are distributed among these distances:
166 49 0.05
167 22 0.02
168 85 0.09
169 243 0.25
170 372 0.38
171 216 0.22
172 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (169 bp):
AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
CAACGGCGATTATTAATTTTTTCCTATCAAAAAAAGTTTTTGGATTTCTGGACAAACTCCAGATA
TTGCATGGTAAAATATTAGAAAACTACCGAAAAATAACA
Found at i:45216824 original size:341 final size:339
Alignment explanation
Indices: 45216198--45217458 Score: 1837
Period size: 341 Copynumber: 3.7 Consensus size: 339
45216188 AAAATAAATG
*
45216198 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGCGACCCGGGTTCGATCCCCGG
1 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
* * * *
45216263 CAACGGCGATTATAAATTTTTTCCTATCAAAAGAAGTTTTTGGATTTCTGGTCAAATTCCAGATA
66 CAACGGCGATTATTAATTTTTTCCTATCAAAAAAAGTTTTTGGATTTCTGGACAAACTCCAGATA
* * *
45216328 TTGCATGCGTAAAATATTAGAAAACTACCGAAAAAT-AGCACGTCGTTCTAGTATAGTGGTGAGT
131 TTGCATG-GTAAAATATTAGAAAACTACCG-AAAATCAACAAGTCGTTGTAGTATAGTGGTGAGT
* * *
45216392 ATTCCCGCCTGTCGCGCGGGTGACCCGGGTTCGATCCCTGGCAACGGCGATTATTAATATTTTCC
194 ATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGATTATTAATTTTTTCC
* *
45216457 TATCAAAAAAAGATTTTGGATTTCTGGACAAACTCCAGATATTGCATGGGTAAAATGTTAGAAAA
259 TATCAAAAAAAGTTTTTGGTTTTCTGGACAAACTCCAGATATTGCATGGGTAAAATGTTAGAAAA
45216522 CTACCGAAAAATAACA
324 CTACCGAAAAATAACA
45216538 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
1 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
* * *
45216603 CAACGGCGAATT-TTAATTATTTTCCTATCATATAAAGTTTTTAGATTTCTGGACAAACTCCAGA
66 CAACGGCG-ATTATTAATT-TTTTCCTATCAAAAAAAGTTTTTGGATTTCTGGACAAACTCCAGA
* *
45216667 TATTGCGTGGATAAAATACTAGAAAACTACCGAAAATCAACAAGTCGTTGTAGTATAGTGGTGAG
129 TATTGCATGG-TAAAATATTAGAAAACTACCGAAAATCAACAAGTCGTTGTAGTATAGTGGTGAG
45216732 TATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGATTATTAATTTTTTC
193 TATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGATTATTAATTTTTTC
** * *
45216797 CTATCAAAAACGGTTTTTGGTTTTCTGGACAAACTCCAGATACTGCATGGCTAAAATGTTAGAAA
258 CTATCAAAAAAAGTTTTTGGTTTTCTGGACAAACTCCAGATATTGCATGGGTAAAATGTTAGAAA
*
45216862 ACTACCGAAAACTAACA
323 ACTACCGAAAAATAACA
45216879 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGAT-CCCGG
1 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
* * *
45216943 CAACGGCGATTGTTAAGTTTTTCCTATCAAAAAAAGTTTTTGGATTTTTGGACAAACTCCAGATA
66 CAACGGCGATTATTAATTTTTTCCTATCAAAAAAAGTTTTTGGATTTCTGGACAAACTCCAGATA
* * * ** *
45217008 TTGCATGGCTAAAATGTTAGAAAACTACGGAAAATTAAGGAGTC---GTAGTATAGTGGTGAATA
131 TTGCATGG-TAAAATATTAGAAAACTACCGAAAATCAACAAGTCGTTGTAGTATAGTGGTGAGTA
** *
45217070 TTCCCGCCTGTCACGCGGGTGACCCGTTTTCGATCCCCGGCAACGGCGATTGTTAAGTTTTTTTC
195 TTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGATTATTAA--TTTTTTC
*
45217135 CTATCAAAAAAAGTTTTTGGATTTT-TGGACAAACTCCAGATATTGCATGGGTAAAATATTAGAA
258 CTATCAAAAAAAGTTTTTGG-TTTTCTGGACAAACTCCAGATATTGCATGGGTAAAATGTTAGAA
* * *
45217199 AACAACTG-GAAATCAACA
322 AACTACCGAAAAAT-AACA
* **
45217217 A---GTTGTAGTATAGTGGTAAGTATTCCCGTTTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
1 AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
* * * *
45217279 GAACGGCGATTATTAGTGGTTTTCCTATCAAATAAAGTTTTTGGATTTCTGGACAAACTCCAGAT
66 CAACGGCGATTATTAAT-TTTTTCCTATCAAAAAAAGTTTTTGGATTTCTGGACAAACTCCAGAT
* * *
45217344 ATTGCATCGGTAAAATATTAGAAAACTACCGAAAATCAACAAGTTGTAGTA-TAGTGGTGGTGAG
130 ATTGCAT-GGTAAAATATTAGAAAACTACCGAAAATCAACAAGTCGTTGTAGTA-TAGTGGTGAG
* * *
45217408 TAATCCCAG-CTGTCACGCGGGTGACCCGTGTTCGATCCCCGGTAACGGCGA
193 TATTCCC-GCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGA
45217459 CTAACTTTTT
Statistics
Matches: 834, Mismatches: 70, Indels: 34
0.89 0.07 0.04
Matches are distributed among these distances:
335 52 0.06
336 88 0.11
337 83 0.10
338 74 0.09
339 88 0.11
340 158 0.19
341 291 0.35
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (339 bp):
AGTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGG
CAACGGCGATTATTAATTTTTTCCTATCAAAAAAAGTTTTTGGATTTCTGGACAAACTCCAGATA
TTGCATGGTAAAATATTAGAAAACTACCGAAAATCAACAAGTCGTTGTAGTATAGTGGTGAGTAT
TCCCGCCTGTCACGCGGGTGACCCGGGTTCGATCCCCGGCAACGGCGATTATTAATTTTTTCCTA
TCAAAAAAAGTTTTTGGTTTTCTGGACAAACTCCAGATATTGCATGGGTAAAATGTTAGAAAACT
ACCGAAAAATAACA
Found at i:45225238 original size:100 final size:95
Alignment explanation
Indices: 45225054--45225250 Score: 304
Period size: 100 Copynumber: 2.0 Consensus size: 95
45225044 CGGGCAGTTG
*
45225054 CTGCTCTATCTACACAACCAAGAAAACTTAGTAAAGAAGTAAGTAGCAAATAAGGTAGCTACTCT
1 CTGCTCTATCTACACAACCAAGAAAACCTAGTAAAGAAGTAAGTAGCAAATAAGGTAGCTACTCT
45225119 TCCATGATTCTCTCTTGTTTAAACGTGTAA
66 TCCATGATTCTCTCTTGTTTAAACGTGTAA
* * * *
45225149 CTGCTCTATCTACACAACCAAGGAAACCTAGTAAAGAAGTAAGAAAAGTAGCAATTAAGTTGGCT
1 CTGCTCTATCTACACAACCAAGAAAACCTAGTAAAGAAGT-----AAGTAGCAAATAAGGTAGCT
45225214 ACTCTTCCATGATTCTCTCTTGTTTAAACGTGTAA
61 ACTCTTCCATGATTCTCTCTTGTTTAAACGTGTAA
45225249 CT
1 CT
45225251 TTGTTGTTGA
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
95 38 0.41
100 54 0.59
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (95 bp):
CTGCTCTATCTACACAACCAAGAAAACCTAGTAAAGAAGTAAGTAGCAAATAAGGTAGCTACTCT
TCCATGATTCTCTCTTGTTTAAACGTGTAA
Found at i:45227167 original size:2 final size:2
Alignment explanation
Indices: 45227160--45227208 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
45227150 ATCCAAGTAT
45227160 TA TA 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 TA TA
45227202 TCA TA TA
1 T-A TA TA
45227209 AACATTCAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.