Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008733.1 Hibiscus syriacus cultivar Beakdansim tig00111806_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 774200
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:355863 original size:11 final size:11
Alignment explanation
Indices: 355847--355874 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
355837 TTGTTTCCTT
355847 TTATTTATTTA
1 TTATTTATTTA
355858 TTATTTATTTA
1 TTATTTATTTA
355869 TTATTT
1 TTATTT
355875 CTCATCTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:356789 original size:16 final size:16
Alignment explanation
Indices: 356768--356799 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
356758 TTTTTATGTC
356768 CGGGATATAGAGCATG
1 CGGGATATAGAGCATG
*
356784 CGGGATATAGATCATG
1 CGGGATATAGAGCATG
356800 TGGGGTAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.12, G:0.34, T:0.22
Consensus pattern (16 bp):
CGGGATATAGAGCATG
Found at i:359803 original size:110 final size:110
Alignment explanation
Indices: 359607--360176 Score: 785
Period size: 110 Copynumber: 5.2 Consensus size: 110
359597 GATGGTGGTT
* * *
359607 GCTCAACTTCACAACGAAGGGG---C-GATTGTCAACAAACAAGTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCAACTGAATGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * * *
359668 AATTTCAACTTCACATCGAATGATATTGGACTTGAGACAACATAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * * * *
359713 GCTCAACTACACAGTGAAGGGGCAACTGAATGTCAGCAAATAACTTTTCATTTTCATTTAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCAACTGAATGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
359778 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
359823 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCAACTGAATGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
359888 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
*
359933 GCTCAACTTCACAGCGAAGGGGCAACT-AACTGTCAACAAACAATTTTTCAGTTTCATTCAGAGT
1 GCTCAACTTCACAGCGAAGGGGCAACTGAA-TGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * * *
359997 CAATTTCAATTTCACAGCGAAGAATATTAGACTCGAGACAACAAAA
65 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * * *
360043 GCTTAAATTCACAGCGAAGGGGCGACTGACTATCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCAACTGAATGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
360108 AATTTCAACTTCACAGCGAAGTAAATTAGACTCGAGACAATTCA-AA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAA--CACAA
360154 GCTCAACTTCAC-GACGAAGGGGC
1 GCTCAACTTCACAG-CGAAGGGGC
360177 TTCCCAGTTT
Statistics
Matches: 413, Mismatches: 42, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
106 19 0.05
109 2 0.00
110 368 0.89
111 22 0.05
112 2 0.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.25
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCAACTGAATGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:360434 original size:240 final size:240
Alignment explanation
Indices: 360144--360656 Score: 821
Period size: 240 Copynumber: 2.1 Consensus size: 240
360134 TAGACTCGAG
* * *
360144 ACAATTCAAAGCTCAACTTCACGACGAAGGGGCTTCCCAGTTTTATTCAGAGCCACTTTCAACTT
1 ACAATTCAAAGCTCAACTTCACGACGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTT
*
360209 CACGGCAAAGGATATTGGACTTGAAACAATACAAGCTTGGATTTCAACTTCACGACAAAGGATAT
66 CACGGCAAAGGATATTGGACTTGAAACAATACAAGCTTGGATTTCAACTTAACGACAAAGGATAT
* *
360274 TCAAGTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATA
131 TCAACTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTCAACATCACGACGAAGGATA
** * *
360339 TTGTGCCAA-CTCTAGATTGGATTTCAACTTCATGATGAAGGATAT
196 TCAT-ACAACCTCTAGATTGGATTTCAACTTCACGATGAAGGATAT
*
360384 ACAATTCAAAGCTCAACTTCATGACGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTT
1 ACAATTCAAAGCTCAACTTCACGACGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTT
* ** *
360449 CAGGGTGAAGGATATTGGACTTGAAACAATACAAGCTTGGATTTCAACTTAACGACGAAGGATAT
66 CACGGCAAAGGATATTGGACTTGAAACAATACAAGCTTGGATTTCAACTTAACGACAAAGGATAT
* *
360514 TCAACTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTCAACATCATGACGAATGATA
131 TCAACTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTCAACATCACGACGAAGGATA
360579 TCATACAACCTCTAGATTGGATTTCAACTTCACGATGAAGGATAT
196 TCATACAACCTCTAGATTGGATTTCAACTTCACGATGAAGGATAT
* * * *
360624 CCAATTCAAGGCTCAACTTCACAATGAAGGGGC
1 ACAATTCAAAGCTCAACTTCACGACGAAGGGGC
360657 CATCCACAGT
Statistics
Matches: 250, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
239 3 0.01
240 247 0.99
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (240 bp):
ACAATTCAAAGCTCAACTTCACGACGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTT
CACGGCAAAGGATATTGGACTTGAAACAATACAAGCTTGGATTTCAACTTAACGACAAAGGATAT
TCAACTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTCAACATCACGACGAAGGATA
TCATACAACCTCTAGATTGGATTTCAACTTCACGATGAAGGATAT
Found at i:360683 original size:110 final size:110
Alignment explanation
Indices: 360485--360692 Score: 319
Period size: 110 Copynumber: 1.9 Consensus size: 110
360475 CAATACAAGC
*
360485 TTGGATTTCAACTTAACGACGAAGGATATTCAACTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTAACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAAGGGGCCAT
** * *
360550 CCACGATTTCAACATCATGACGAATGATATCATACAACCTCTAGA
66 CCACGATTTCAACATCACAACGAAGGAAATCATACAACCTCTAGA
* * * *
360595 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAATGAAGGGGCCAT
1 TTGGATTTCAACTTAACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAAGGGGCCAT
360660 CCAC-AGTTTCAACATCACAACGAAGGAAATCAT
66 CCACGA-TTTCAACATCACAACGAAGGAAATCAT
360693 GCTCACCAGC
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
109 1 0.01
110 87 0.99
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (110 bp):
TTGGATTTCAACTTAACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAAGGGGCCAT
CCACGATTTCAACATCACAACGAAGGAAATCATACAACCTCTAGA
Found at i:361045 original size:3 final size:3
Alignment explanation
Indices: 361018--361069 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
361008 TTTAAAAAAA
* * *
361018 ATT A-T ATT TTT ATT TTT ATTT ATT ATT ATT ATT ATT AGT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
361063 ATT ATT A
1 ATT ATT A
361070 ATATATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:362574 original size:12 final size:12
Alignment explanation
Indices: 362557--362601 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
362547 TTTAATATTC
362557 TTTTATTTTTTA
1 TTTTATTTTTTA
362569 TTTTATTTTTTA
1 TTTTATTTTTTA
*
362581 TTATATTTTTTTA
1 TTTTA-TTTTTTA
*
362594 TTTAATTT
1 TTTTATTT
362602 ATACTTTTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:362592 original size:20 final size:19
Alignment explanation
Indices: 362552--362596 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
362542 AAAATTTTAA
362552 TATTCTTTTATTTTTTATTT
1 TATT-TTTTATTTTTTATTT
362572 TATTTTTTATTATATTT-TTT
1 TATTTTTTATT-T-TTTATTT
362592 TATTT
1 TATTT
362597 AATTTATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.30
20 13 0.57
21 3 0.13
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (19 bp):
TATTTTTTATTTTTTATTT
Found at i:362597 original size:17 final size:17
Alignment explanation
Indices: 362551--362597 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
362541 CAAAATTTTA
*
362551 ATATTCTTTTATTT-TT
1 ATATTTTTTTATTTATT
362567 -TATTTTATTT-TTTATT
1 ATATTTT-TTTATTTATT
362583 ATATTTTTTTATTTA
1 ATATTTTTTTATTTA
362598 ATTTATACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 8 0.31
16 8 0.31
17 10 0.38
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (17 bp):
ATATTTTTTTATTTATT
Found at i:363882 original size:16 final size:16
Alignment explanation
Indices: 363863--363894 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
363853 ACATGTAAAC
363863 AAAATGACAAATGCAT
1 AAAATGACAAATGCAT
*
363879 AAAATGTCAAATGCAT
1 AAAATGACAAATGCAT
363895 CAACCCAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.22
Consensus pattern (16 bp):
AAAATGACAAATGCAT
Found at i:364660 original size:6 final size:6
Alignment explanation
Indices: 364645--364675 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
364635 GATAACCTCT
*
364645 TCTTCA TCTTCC TCTTCC TCTTCC TCTTCC T
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC T
364676 TTGTAGCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.45, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCC
Found at i:366164 original size:26 final size:26
Alignment explanation
Indices: 366135--366188 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
366125 AAATGATGTT
*
366135 TAAAAATTAAAATTAAAAGATGAGGA
1 TAAAAATAAAAATTAAAAGATGAGGA
* ** *
366161 TAAAGATAAAAATTGGAAGGTGAGGA
1 TAAAAATAAAAATTAAAAGATGAGGA
366187 TA
1 TA
366189 GAGTAAGGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (26 bp):
TAAAAATAAAAATTAAAAGATGAGGA
Found at i:385289 original size:18 final size:18
Alignment explanation
Indices: 385266--385307 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
385256 GGCAAGGCTG
385266 ACTCCCAGATGCTGGAGC
1 ACTCCCAGATGCTGGAGC
385284 ACTCCCAGATGCTGGAGC
1 ACTCCCAGATGCTGGAGC
385302 ACTCCC
1 ACTCCC
385308 CCGCTCGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.17
Consensus pattern (18 bp):
ACTCCCAGATGCTGGAGC
Found at i:385540 original size:43 final size:43
Alignment explanation
Indices: 385479--385565 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
385469 TTGGAGAGGA
385479 TACAGCTGTCCCGATTCCAGAAGGTTATACCTAGCCTAGTGAG
1 TACAGCTGTCCCGATTCCAGAAGGTTATACCTAGCCTAGTGAG
*
385522 TACAGCTGTCCCGATTCCATAAGGTTATACCTAGCCTAGTGAG
1 TACAGCTGTCCCGATTCCAGAAGGTTATACCTAGCCTAGTGAG
385565 T
1 T
385566 CATCAGTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (43 bp):
TACAGCTGTCCCGATTCCAGAAGGTTATACCTAGCCTAGTGAG
Found at i:391404 original size:24 final size:24
Alignment explanation
Indices: 391377--391430 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
391367 AGAATCATGG
*
391377 CTTTTGAAGGACTAAA-AGATGTGA
1 CTTTTGAAGAAC-AAATAGATGTGA
*
391401 CTTTTGAAGAACAAATAGTTGTGA
1 CTTTTGAAGAACAAATAGATGTGA
391425 CTTTTG
1 CTTTTG
391431 GTGATCCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.35
Consensus pattern (24 bp):
CTTTTGAAGAACAAATAGATGTGA
Found at i:394719 original size:24 final size:24
Alignment explanation
Indices: 394674--394734 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
394664 AATGATGGTA
*
394674 AAAGAAGAAGAATATCAAGAAAAG
1 AAAGAAGAAGAAAATCAAGAAAAG
* *
394698 AAAGATGAAGAAAAT-AAGGAAATG
1 AAAGAAGAAGAAAATCAA-GAAAAG
*
394722 GAA-AAGAAGAAAA
1 AAAGAAGAAGAAAA
394735 AGATCGGTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 11 0.35
24 20 0.65
ACGTcount: A:0.67, C:0.02, G:0.23, T:0.08
Consensus pattern (24 bp):
AAAGAAGAAGAAAATCAAGAAAAG
Found at i:398972 original size:26 final size:26
Alignment explanation
Indices: 398936--398994 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
398926 ATACTACCAT
*
398936 TGTTTTTAAAAATTCTGCATCCTATG
1 TGTTTTTAAAAATTCTGCAACCTATG
398962 TGTTTTTAAAAATTCTGCAACCTATG
1 TGTTTTTAAAAATTCTGCAACCTATG
398988 TGTTTTT
1 TGTTTTT
398995 CTTGTAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (26 bp):
TGTTTTTAAAAATTCTGCAACCTATG
Found at i:399049 original size:20 final size:20
Alignment explanation
Indices: 399024--399062 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
399014 TCTGTGCACT
399024 TAGTATCGATATTGTTCATA
1 TAGTATCGATATTGTTCATA
399044 TAGTATCGATATTGTTCAT
1 TAGTATCGATATTGTTCAT
399063 CCAATACCGA
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:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (20 bp):
TAGTATCGATATTGTTCATA
Found at i:399073 original size:20 final size:20
Alignment explanation
Indices: 399030--399074 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
399020 CACTTAGTAT
* * *
399030 CGATATTGTTCATATAGTAT
1 CGATATTGTTCATACAATAC
*
399050 CGATATTGTTCATCCAATAC
1 CGATATTGTTCATACAATAC
399070 CGATA
1 CGATA
399075 CTACTATAGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (20 bp):
CGATATTGTTCATACAATAC
Found at i:399135 original size:20 final size:20
Alignment explanation
Indices: 399106--399145 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
399096 GTCAAGTTTG
399106 CCTTGAAGTATCGATACTAC
1 CCTTGAAGTATCGATACTAC
*
399126 CCTTGGAGTATCGATACTAC
1 CCTTGAAGTATCGATACTAC
399146 TCGACGGTTT
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:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (20 bp):
CCTTGAAGTATCGATACTAC
Found at i:403871 original size:116 final size:116
Alignment explanation
Indices: 403704--403920 Score: 407
Period size: 116 Copynumber: 1.9 Consensus size: 116
403694 TTCACCTTAC
*
403704 ATCATTTGCATTGAGATTTTGTTGGGAAGGATGGTGTGGACTTGTGCTTACAACTTTTGAAAGGT
1 ATCATTTGCATTGAGATCTTGTTGGGAAGGATGGTGTGGACTTGTGCTTACAACTTTTGAAAGGT
403769 TATCTTGATATGTGGTCTACAAGATTGTCTCTAAAGCACTTGCTAGCTTCT
66 TATCTTGATATGTGGTCTACAAGATTGTCTCTAAAGCACTTGCTAGCTTCT
*
403820 ATCATTTGCATTGAGATCTTGTTGGGAAGGATGTTGTGGACTTGTGCTTACAACTTTTGAAAGGT
1 ATCATTTGCATTGAGATCTTGTTGGGAAGGATGGTGTGGACTTGTGCTTACAACTTTTGAAAGGT
*
403885 TATCTTGATATGTGGTCTATAAGATTGTCTCTAAAG
66 TATCTTGATATGTGGTCTACAAGATTGTCTCTAAAG
403921 TGCTTGTTCA
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 98 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (116 bp):
ATCATTTGCATTGAGATCTTGTTGGGAAGGATGGTGTGGACTTGTGCTTACAACTTTTGAAAGGT
TATCTTGATATGTGGTCTACAAGATTGTCTCTAAAGCACTTGCTAGCTTCT
Found at i:404343 original size:11 final size:11
Alignment explanation
Indices: 404302--404357 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
404292 CTTTCATTTG
*
404302 ATTATTATTTTT
1 ATTATTA-TTAT
*
404314 ATTATTAATAAT
1 ATTATT-ATTAT
*
404326 TTTATTATTAT
1 ATTATTATTAT
404337 ATTATTATTAT
1 ATTATTATTAT
404348 ATTATTATTA
1 ATTATTATTA
404358 AATAATAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
11 24 0.63
12 13 0.34
13 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTATTATTAT
Found at i:404375 original size:3 final size:3
Alignment explanation
Indices: 404302--404357 Score: 64
Period size: 3 Copynumber: 19.3 Consensus size: 3
404292 CTTTCATTTG
* *
404302 ATT ATT ATT TTT ATT ATT AATA ATT -TT ATT ATT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
404346 A-T ATT ATT ATT A
1 ATT ATT ATT ATT A
404358 AATAATAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 6 0.13
3 37 0.82
4 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:409798 original size:55 final size:55
Alignment explanation
Indices: 409714--409825 Score: 170
Period size: 55 Copynumber: 2.0 Consensus size: 55
409704 TACTAAAAAC
* * * *
409714 ATGCAACATTCTACATATATCAAGATGTACAATTGATGCACTTATGTCTATATAT
1 ATGCAACACTCTACATATATAAAGATGTACAATTGATGCACTTATATATATATAT
* *
409769 ATGCAACACTCTACATATATAAAGATGTACATTTGATGCACTTTTATATATATAT
1 ATGCAACACTCTACATATATAAAGATGTACAATTGATGCACTTATATATATATAT
409824 AT
1 AT
409826 ATATATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (55 bp):
ATGCAACACTCTACATATATAAAGATGTACAATTGATGCACTTATATATATATAT
Found at i:409820 original size:2 final size:2
Alignment explanation
Indices: 409813--409866 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
409803 GATGCACTTT
409813 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
409855 TA TA TA TA TA TA
1 TA TA TA TA TA TA
409867 GATGGGATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:413962 original size:61 final size:63
Alignment explanation
Indices: 413897--414058 Score: 175
Period size: 73 Copynumber: 2.4 Consensus size: 63
413887 CAATCCCTAC
* *
413897 AACAAACATATAAAATATTCACTACATCA-CG-GTACTCAAACCCAGGACCTTAAAAAATAAA
1 AACAAACATATAAAATATTCACTACATCATAGAGTACTCAAACCCAAGACCTTAAAAAATAAA
*
413958 AACAATCATATAAAATATTCACTACATTTGGGATGACATAGTAGTACTCAAACCCAAGACCTTAA
1 AACAAACATATAAAATATTCACTAC-------AT--CATAG-AGTACTCAAACCCAAGACCTTAA
* *
414023 ATAATAAC
56 AAAATAAA
414031 AACAAACATATAAAATATTCACTACATC
1 AACAAACATATAAAATATTCACTACATC
414059 CGGGGTGACA
Statistics
Matches: 83, Mismatches: 6, Indels: 21
0.75 0.05 0.19
Matches are distributed among these distances:
61 24 0.29
64 1 0.01
66 2 0.02
68 2 0.02
70 2 0.02
71 1 0.01
73 51 0.61
ACGTcount: A:0.49, C:0.21, G:0.07, T:0.23
Consensus pattern (63 bp):
AACAAACATATAAAATATTCACTACATCATAGAGTACTCAAACCCAAGACCTTAAAAAATAAA
Found at i:414021 original size:73 final size:73
Alignment explanation
Indices: 413920--414156 Score: 248
Period size: 73 Copynumber: 3.2 Consensus size: 73
413910 AATATTCACT
*
413920 ACAT-CACGGTACTCAAACCCAGGACCTTAAAAAATAAAAACAATCATATAAAATATTCACTACA
1 ACATACAC-GTACTCAAACCCAAGACCTTAAAAAATAAAAACAATCATATAAAATATTCACTACA
413984 TTTGGGATG
65 TTTGGGATG
* * * *
413993 ACATAGTA-GTACTCAAACCCAAGACCTTAAATAATAACAACAAACATATAAAATATTCACTACA
1 ACATA-CACGTACTCAAACCCAAGACCTTAAAAAATAAAAACAATCATATAAAATATTCACTACA
** *
414057 TCCGGGGTG
65 TTTGGGATG
** * * * *
414066 ACATACACGGTACTCAAGTCCAAGATCTCAAAGAATAACAAAAAAT-ATATAAAATATTCACTAC
1 ACATACAC-GTACTCAAACCCAAGACCTTAAAAAATAA-AAACAATCATATAAAATATTCACTAC
*
414130 ATTT-AGAGTG
64 ATTTGGGA-TG
*
414140 ACATACGCGGTACTCAA
1 ACATACAC-GTACTCAA
414157 TTCCGAGACC
Statistics
Matches: 136, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
72 1 0.01
73 68 0.50
74 62 0.46
75 5 0.04
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (73 bp):
ACATACACGTACTCAAACCCAAGACCTTAAAAAATAAAAACAATCATATAAAATATTCACTACAT
TTGGGATG
Found at i:414117 original size:74 final size:74
Alignment explanation
Indices: 413920--414178 Score: 283
Period size: 74 Copynumber: 3.5 Consensus size: 74
413910 AATATTCACT
* * * *
413920 ACAT-CACGGTACTCAAACCCAGGACCTTAAAAAATAA-AAACAATCATATAAAATATTCACTAC
1 ACATACACGGTACTCAAACCCAAGACCTCAAAGAATAACAAAAAAT-ATATAAAATATTCACTAC
*
413983 ATTTGGGATG
65 ATTTGGGGTG
* * * * *
413993 ACATAGTA--GTACTCAAACCCAAGACCTTAAATAATAACAACAAACATATAAAATATTCACTAC
1 ACATA-CACGGTACTCAAACCCAAGACCTCAAAGAATAACAAAAAATATATAAAATATTCACTAC
**
414056 ATCCGGGGTG
65 ATTTGGGGTG
** *
414066 ACATACACGGTACTCAAGTCCAAGATCTCAAAGAATAACAAAAAATATATAAAATATTCACTACA
1 ACATACACGGTACTCAAACCCAAGACCTCAAAGAATAACAAAAAATATATAAAATATTCACTACA
* *
414131 TTTAGAGTG
66 TTTGGGGTG
* ** *
414140 ACATACGCGGTACTCAATTCCGAGACCTCAAAGAATAAC
1 ACATACACGGTACTCAAACCCAAGACCTCAAAGAATAAC
414179 TACAAATCAC
Statistics
Matches: 156, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
72 1 0.01
73 61 0.39
74 93 0.60
75 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22
Consensus pattern (74 bp):
ACATACACGGTACTCAAACCCAAGACCTCAAAGAATAACAAAAAATATATAAAATATTCACTACA
TTTGGGGTG
Found at i:414597 original size:2 final size:2
Alignment explanation
Indices: 414590--414614 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
414580 AAAATTACAA
414590 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 A
414615 AAAATAAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:419082 original size:2 final size:2
Alignment explanation
Indices: 419075--419103 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
419065 ACAAACTTTC
419075 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 T
419104 CATCTTAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:420079 original size:15 final size:15
Alignment explanation
Indices: 420059--420096 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
420049 ACCGCTCCTC
420059 TCTCTCTTCTCTCAT
1 TCTCTCTTCTCTCAT
420074 TCTCTCTTCTCTCAT
1 TCTCTCTTCTCTCAT
420089 TCTCTCTT
1 TCTCTCTT
420097 TTTTTCAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.05, C:0.39, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTCTCTTCTCTCAT
Found at i:420869 original size:3 final size:3
Alignment explanation
Indices: 420829--420879 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
420819 GTAAGGGCCT
* *
420829 ATA ATA A-A ATA AAA ATA AAA ATA A-A ATA GATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -AT-A ATA ATA ATA ATA
420874 ATA ATA
1 ATA ATA
420880 GTAACAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 4 0.10
3 31 0.77
4 4 0.10
5 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (3 bp):
ATA
Found at i:424606 original size:67 final size:67
Alignment explanation
Indices: 424498--424628 Score: 262
Period size: 67 Copynumber: 2.0 Consensus size: 67
424488 ATGCCCTGGC
424498 AAGTTAATAATAAAAGTAATGCATCTTCGTCCAATTCTAACTCCCTTGAAGCTTCATTGCAGGAG
1 AAGTTAATAATAAAAGTAATGCATCTTCGTCCAATTCTAACTCCCTTGAAGCTTCATTGCAGGAG
424563 GT
66 GT
424565 AAGTTAATAATAAAAGTAATGCATCTTCGTCCAATTCTAACTCCCTTGAAGCTTCATTGCAGGA
1 AAGTTAATAATAAAAGTAATGCATCTTCGTCCAATTCTAACTCCCTTGAAGCTTCATTGCAGGA
424629 ATTTATAGCC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (67 bp):
AAGTTAATAATAAAAGTAATGCATCTTCGTCCAATTCTAACTCCCTTGAAGCTTCATTGCAGGAG
GT
Found at i:432211 original size:35 final size:35
Alignment explanation
Indices: 432165--432234 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
432155 TCTAAAGAAA
432165 TGGCGACCTTAAGAGTTTTTGTGATTCCAGAGTCT
1 TGGCGACCTTAAGAGTTTTTGTGATTCCAGAGTCT
*
432200 TGGCGATCTTAAGAGTTTTTGTGATTCCAGAGTCT
1 TGGCGACCTTAAGAGTTTTTGTGATTCCAGAGTCT
432235 GAAGAAGAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.39
Consensus pattern (35 bp):
TGGCGACCTTAAGAGTTTTTGTGATTCCAGAGTCT
Found at i:440916 original size:140 final size:140
Alignment explanation
Indices: 440661--441256 Score: 691
Period size: 140 Copynumber: 4.3 Consensus size: 140
440651 TAAACTAATC
* * * * * *
440661 AACATTTCTAATGGAGAGTTTATAATGAGAAGAAATCATCTGATAGAGGGAGAATAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCATAA
* * * * * * *
440726 TAAGAAGAACTTGATCAACCTTCGCTCGATTCATCGCATCTGGAGTTGAATCAGTGACGCCTCAC
66 TGAGAAGAACTTGTTCAACATTTGCTCGATTCATCGCATATGGAGTTGAATCAATGAAGCCTCAC
440791 TT-ATGGGATT
131 TTGA-GGGATT
* * *
440801 AATATTTCCAATGGAGAGTTTATAATGAGAGGAACTCATCCGATAGAGAGAGAAAAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCATAA
* * * *
440866 TGAGAAGAACTTGTTCAACATTTTCTCGATTTATTGCATATGGAGTTGAATCAACGAAGCCTCAC
66 TGAGAAGAACTTGTTCAACATTTGCTCGATTCATCGCATATGGAGTTGAATCAATGAAGCCTCAC
440931 TTGAGGGATT
131 TTGAGGGATT
* * *
440941 AACATTTCCAAAT-GAGAGCTCATAATGAGAAGAACTCATCAGATAGA-AGGATAAAAAGTTCAT
1 AACATTTCC-AATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGA-GAGAAAAAGTTCAT
* * * *
441004 AATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCACATATGGAGTTGAATTAGTGAAGCCTC
64 AATGAGAAGAACTTGTTCAACATTTGCTCGATTCATCGCATATGGAGTTGAATCAATGAAGCCTC
441069 ACTTGAGGGATT
129 ACTTGAGGGATT
* * * **
441081 AACATTTCCAATGGAGAGATCAAAATGAGAAGAACTCATCCGAT-GAGGGAGAATGAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCATAA
* * * ** * * * *
441145 TGA-AAAATACTTGTTCAAACA-TAGTTTAATTTATCGCATATGGATTTGAATCAAAGACGCCTC
66 TGAGAAGA-ACTTGTTC-AACATTTGCTCGATTCATCGCATATGGAGTTGAATCAATGAAGCCTC
*
441208 ACTTGAGGGATC
129 ACTTGAGGGATT
* * * *
441220 AATATTTCTAGTAGAGAGTTCATAATGAGAAGAACTC
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTC
441257 GCAGCTTTAA
Statistics
Matches: 390, Mismatches: 59, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
138 3 0.01
139 103 0.26
140 280 0.72
141 4 0.01
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (140 bp):
AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCATAA
TGAGAAGAACTTGTTCAACATTTGCTCGATTCATCGCATATGGAGTTGAATCAATGAAGCCTCAC
TTGAGGGATT
Found at i:441517 original size:25 final size:23
Alignment explanation
Indices: 441489--441540 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
441479 AAAAACCCAA
* *
441489 ACCCGAATACCCAAAGCAAGATCTG
1 ACCCGAA-ACCCAAACCAA-ACCTG
441514 ACCCGAAACCCAAACCAAACCTG
1 ACCCGAAACCCAAACCAAACCTG
441537 ACCC
1 ACCC
441541 AGAGCCTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 8 0.32
24 10 0.40
25 7 0.28
ACGTcount: A:0.40, C:0.40, G:0.12, T:0.08
Consensus pattern (23 bp):
ACCCGAAACCCAAACCAAACCTG
Found at i:444471 original size:130 final size:130
Alignment explanation
Indices: 444194--444597 Score: 423
Period size: 130 Copynumber: 3.1 Consensus size: 130
444184 ACAGTGTTCT
* * ** * *
444194 AGGGTAGATCAGATCTGGAGACTTTGATT-ATTTCACTAATCTTTAAGGAAGATTTAATCGGGGT
1 AGGGTAGATCAGATCTAGAGACTTTGATTCACTTCACTGCTCTTCAAGGAAGATTGAATCGGGGT
*
444258 TGATTTGAC-T-A--TTCTTCA-TAGAAGATCAAATCTAAATAAATGGATATGCTCTGCTGCGTT
66 TGATTT-ACTTCACTTTCTTCAGT-GAAGATCAAATCTAAATAAATGGATATGCTCTGCTGCATT
*
444318 CT
129 CC
* * * *
444320 AGGGTAGTTTAGATCTAGAGACTTTGATTCACTTCACTGCTCTTCATGCAAGATTGAATCGGGGT
1 AGGGTAGATCAGATCTAGAGACTTTGATTCACTTCACTGCTCTTCAAGGAAGATTGAATCGGGGT
* *
444385 TGATTTACTTCACTGTTCCTCAGTGAATATCAAATCTGAAA-AAA-GGATATGCTCCT-CTGCAT
66 TGATTTACTTCACT-TTCTTCAGTGAAGATCAAATCT-AAATAAATGGATATGCT-CTGCTGCAT
444447 TCC
128 TCC
* * * * *
444450 AGGGTAGGTCAAATCTAGAGACTTTGATTCACTTCACTGCTTTTCAGGGAAGATTGAATCAGGGT
1 AGGGTAGATCAGATCTAGAGACTTTGATTCACTTCACTGCTCTTCAAGGAAGATTGAATCGGGGT
* * * * ** *
444515 TGATTTGCTTCACTATTCTTCAGGGAAGATCAAATATGAGGA-AAATATATATGCTCTGCTTCAT
66 TGATTTACTTCACT-TTCTTCAGTGAAGATCAAATCT-A-AATAAATGGATATGCTCTGCTGCAT
*
444579 TCT
128 TCC
444582 AGGGTAGATCAGATCT
1 AGGGTAGATCAGATCT
444598 GGAAACCTTG
Statistics
Matches: 232, Mismatches: 34, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
126 28 0.12
127 35 0.15
128 1 0.00
130 107 0.46
131 29 0.12
132 32 0.14
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (130 bp):
AGGGTAGATCAGATCTAGAGACTTTGATTCACTTCACTGCTCTTCAAGGAAGATTGAATCGGGGT
TGATTTACTTCACTTTCTTCAGTGAAGATCAAATCTAAATAAATGGATATGCTCTGCTGCATTCC
Found at i:445867 original size:18 final size:17
Alignment explanation
Indices: 445846--445909 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 17
445836 TTAAACCCCC
*
445846 TTTTATTTTATATTCTTTT
1 TTTTTTTTTATATTC--TT
445865 TTTATTTTTTATATT-TT
1 TTT-TTTTTTATATTCTT
* *
445882 ATATTTTTT-TATTCTT
1 TTTTTTTTTATATTCTT
445898 TTGTTTTTTTAT
1 TT-TTTTTTTAT
445910 CTTCAGGCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
15 4 0.11
16 9 0.25
17 9 0.25
18 1 0.03
19 3 0.08
20 10 0.28
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTTTTTTATATTCTT
Found at i:445881 original size:15 final size:15
Alignment explanation
Indices: 445846--445909 Score: 62
Period size: 16 Copynumber: 4.4 Consensus size: 15
445836 TTAAACCCCC
445846 TTTTATTTTATA-TT
1 TTTTATTTTATATTT
*
445860 CTTT-TTTTAT-TTT
1 TTTTATTTTATATTT
*
445873 TTATATTTTATATTT
1 TTTTATTTTATATTT
* *
445888 TTTTATTCTTTTGTTT
1 TTTTATT-TTATATTT
445904 TTTTAT
1 TTTTAT
445910 CTTCAGGCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
13 10 0.25
14 9 0.22
15 9 0.22
16 12 0.30
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTATTTTATATTT
Found at i:456805 original size:19 final size:19
Alignment explanation
Indices: 456763--456806 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
456753 TATTAATGAA
*
456763 TAAAATGCAATGCGAAAAG
1 TAAAATGCAATGAGAAAAG
456782 T-AAATGCAATGTAG-AAAG
1 TAAAATGCAATG-AGAAAAG
456800 TAAAATG
1 TAAAATG
456807 TAGATGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.20
Consensus pattern (19 bp):
TAAAATGCAATGAGAAAAG
Found at i:460644 original size:345 final size:342
Alignment explanation
Indices: 460148--460830 Score: 1028
Period size: 345 Copynumber: 2.0 Consensus size: 342
460138 AATTTAAAAT
**
460148 TTATTAAAACAACATTTTAAGGTATGCGTACCAAAAATTAATTTTGAAGTTAATTACGCTAGGAA
1 TTATTAAAACAACATTTTAAGGTATGCGTACCAAAAATTAATTCGGAAGTTAATTACGCTAGGAA
* * * * *
460213 AGGATTAGCACCCCCACAACGCCCTAAATCGGTACCTAGTCGATTAATTAGTTGTCTTTGCAGTG
66 AGGATTAGCACCCCCACAAAGCCCTAAATCGGCACCTAGTCGATTAATTAGTTGTCTCTACAATG
*
460278 AATCCTACAAATTCAAATTTAATTTAATTTAAGATTCCTTTTAAAACACATTCCTTGAATTTTAG
131 AATCCTACAAATTCAAATTTAATTTAATTTAAGATCCCTTTTAAAACACATTCCTTGAATTTTAG
*
460343 GAC-GAAACAC-AACAATATTTAATTATTTCCTATCGAGAAGAAAAAGCCTCTCATGCCGTAAAG
196 GACGGAAA-ACGAA-AATATTTAACTATTTCCTATCGAGAAGAAAAAGCCTCTCATGCCGTAAAG
* * * *
460406 CACCCATTTCTTAATCCAATCGAAATAAGGAAATATTACTATTTCGTTCGAAAGTTCATTAATAA
259 CACCCATTTCTTAATCCAATCAAAATAAGGAAATATTACTATTCCATTCAAAAGTTCATTAATAA
460471 TTCAAGTTTCAAATGTAAA
324 TTCAAGTTTCAAATGTAAA
* * * *
460490 TTATTAAAACAACATTTTAAGGTATGCGTACCAAAAATTTAGTTCGGCAGTTGATTATGCGTAGG
1 TTATTAAAACAACATTTTAAGGTATGCGTACCAAAAA-TTAATTCGGAAGTTAATTACGC-TAGG
* *
460555 GAATGATTAGCACCCCCTACAAAGCCCTAAATCGGCACCTAGTCGATTAATTAGTTGTCTCTACA
64 AAAGGATTAGCACCCCC-ACAAAGCCCTAAATCGGCACCTAGTCGATTAATTAGTTGTCTCTACA
* ** * *
460620 ATGAATCTTACATGTTCTAATTTAATTTAATTTAAGATCCCTTTTTAAACACATTCCTTGAATTT
128 ATGAATCCTACAAATTCAAATTTAATTTAATTTAAGATCCCTTTTAAAACACATTCCTTGAATTT
* * * *
460685 TAGGACGGAAAACGAAAATCTTTAACTATTTCCTATCGAGAAGAAAAGGTCTCTCATGCCTTAAA
193 TAGGACGGAAAACGAAAATATTTAACTATTTCCTATCGAGAAGAAAAAGCCTCTCATGCCGTAAA
* *
460750 GCATCCATTTCTTAATCCAATCAAAATAAGGAAATATTACTATTCCATTCAAAATTTCATTAATA
258 GCACCCATTTCTTAATCCAATCAAAATAAGGAAATATTACTATTCCATTCAAAAGTTCATTAATA
*
460815 ATTCAAGTTTTAAATG
323 ATTCAAGTTTCAAATG
460831 CATGAAAAAT
Statistics
Matches: 305, Mismatches: 31, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
342 37 0.12
343 16 0.05
344 19 0.06
345 227 0.74
346 6 0.02
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (342 bp):
TTATTAAAACAACATTTTAAGGTATGCGTACCAAAAATTAATTCGGAAGTTAATTACGCTAGGAA
AGGATTAGCACCCCCACAAAGCCCTAAATCGGCACCTAGTCGATTAATTAGTTGTCTCTACAATG
AATCCTACAAATTCAAATTTAATTTAATTTAAGATCCCTTTTAAAACACATTCCTTGAATTTTAG
GACGGAAAACGAAAATATTTAACTATTTCCTATCGAGAAGAAAAAGCCTCTCATGCCGTAAAGCA
CCCATTTCTTAATCCAATCAAAATAAGGAAATATTACTATTCCATTCAAAAGTTCATTAATAATT
CAAGTTTCAAATGTAAA
Found at i:463054 original size:12 final size:12
Alignment explanation
Indices: 463034--463074 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
463024 AAGGGCCTGT
463034 AATAAAATAGAA
1 AATAAAATAGAA
463046 ACA-AAAATA-AA
1 A-ATAAAATAGAA
463057 AATAAAATAGATA
1 AATAAAATAGA-A
463070 AATAA
1 AATAA
463075 TCATAGTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 1 0.04
11 9 0.36
12 8 0.32
13 7 0.28
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (12 bp):
AATAAAATAGAA
Found at i:465853 original size:21 final size:21
Alignment explanation
Indices: 465828--465868 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
465818 GAACAAAGAG
465828 AACATTAGATA-TGGTTTGAAC
1 AACATT-GATATTGGTTTGAAC
*
465849 AACATTGCTATTGGTTTGAA
1 AACATTGATATTGGTTTGAA
465869 TTATTACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (21 bp):
AACATTGATATTGGTTTGAAC
Found at i:468369 original size:32 final size:32
Alignment explanation
Indices: 468309--468401 Score: 93
Period size: 32 Copynumber: 2.9 Consensus size: 32
468299 ATTCACGAGA
* *
468309 GGGA-TTCGCCTGGAATGCATGGCAACACCGTT
1 GGGAGTTCG-CTGGAAAGCATGGCGACACCGTT
*
468341 GGGAG-TCGCTTGGAACAGC-TGGCGACACCTTT
1 GGGAGTTCGC-TGGAA-AGCATGGCGACACCGTT
* *
468373 GGGTGTTGGCTGGAAAGCATGGCGACACC
1 GGGAGTTCGCTGGAAAGCATGGCGACACC
468402 CTTTGGTATC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
31 4 0.08
32 42 0.82
33 5 0.10
ACGTcount: A:0.20, C:0.24, G:0.35, T:0.20
Consensus pattern (32 bp):
GGGAGTTCGCTGGAAAGCATGGCGACACCGTT
Found at i:468419 original size:32 final size:30
Alignment explanation
Indices: 468318--468433 Score: 90
Period size: 32 Copynumber: 3.7 Consensus size: 30
468308 AGGGATTCGC
* * * *
468318 CTGGAATGCATGGCAACACCGTTGGGAGTCG
1 CTGGAAAGCATGGCGACACCTTTGGTA-TCG
* *
468349 CTTGGAACAGC-TGGCGACACCTTTGGGTGTTGG
1 C-TGGAA-AGCATGGCGACACCTTT-GGT-ATCG
468382 CTGGAAAGCATGGCGACACCCTTTGGTATCG
1 CTGGAAAGCATGGCGACA-CCTTTGGTATCG
* *
468413 CATGGAAGGGATGGCGACACC
1 C-TGGAAAGCATGGCGACACC
468434 AATTGTACTG
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
31 9 0.13
32 47 0.69
33 12 0.18
ACGTcount: A:0.22, C:0.23, G:0.34, T:0.21
Consensus pattern (30 bp):
CTGGAAAGCATGGCGACACCTTTGGTATCG
Found at i:470557 original size:31 final size:30
Alignment explanation
Indices: 470514--470609 Score: 156
Period size: 31 Copynumber: 3.1 Consensus size: 30
470504 TACAATACAA
470514 TCCCCAACATTTAGTCCGTTTGCAATATAG
1 TCCCCAACATTTAGTCCGTTTGCAATATAG
*
470544 TCCCCTAACATTTAGTCTGTTTGCAATATAG
1 TCCCC-AACATTTAGTCCGTTTGCAATATAG
*
470575 TCCCCCAACATTTAGTCCGTTTGCAATATGG
1 T-CCCCAACATTTAGTCCGTTTGCAATATAG
470606 TCCC
1 TCCC
470610 TGACCTAACT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
30 8 0.13
31 49 0.80
32 4 0.07
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (30 bp):
TCCCCAACATTTAGTCCGTTTGCAATATAG
Found at i:471789 original size:32 final size:32
Alignment explanation
Indices: 471742--471811 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
471732 AGTTCATGTT
*
471742 GATTATGGGACTGATATATCATGAACGAATTG
1 GATTTTGGGACTGATATATCATGAACGAATTG
*
471774 GATTTTGGGATTGATATATCATGAACGAATTG
1 GATTTTGGGACTGATATATCATGAACGAATTG
471806 GATTTT
1 GATTTT
471812 TTTACATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.37
Consensus pattern (32 bp):
GATTTTGGGACTGATATATCATGAACGAATTG
Found at i:472537 original size:30 final size:31
Alignment explanation
Indices: 472502--472570 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
472492 TCAGGGACCA
472502 TATTGCAAAC-GACTAAATGTTGG-GAGACTG
1 TATTGCAAACGGACTAAATGTTGGAG-GACTG
*
472532 TATTGCAAACGGACTAAATGTTGGAGGATTG
1 TATTGCAAACGGACTAAATGTTGGAGGACTG
472563 TATTGCAA
1 TATTGCAA
472571 GTTTTAAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 10 0.28
31 25 0.69
32 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (31 bp):
TATTGCAAACGGACTAAATGTTGGAGGACTG
Found at i:473048 original size:12 final size:11
Alignment explanation
Indices: 473012--473049 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
473002 TATGTATCTG
473012 ATTTTAAAT-T
1 ATTTTAAATAT
*
473022 TTTTTAAATAT
1 ATTTTAAATAT
473033 ATTTTAAATAT
1 ATTTTAAATAT
473044 AATTTT
1 -ATTTT
473050 TATCCTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 8 0.33
11 11 0.46
12 5 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTTAAATAT
Found at i:474228 original size:17 final size:17
Alignment explanation
Indices: 474208--474243 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
474198 TTTAAAAATT
*
474208 ATTAAAAAATATAATAA
1 ATTAAAAAATATAAAAA
*
474225 ATTATAAAATATAAAAA
1 ATTAAAAAATATAAAAA
474242 AT
1 AT
474244 ATTTCAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTAAAAAATATAAAAA
Found at i:475773 original size:3 final size:3
Alignment explanation
Indices: 475765--475864 Score: 193
Period size: 3 Copynumber: 33.7 Consensus size: 3
475755 CTCAGTACCT
475765 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
475812 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
475860 TTA TT
1 TTA TT
475865 GATGCTTGGA
Statistics
Matches: 96, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 94 0.98
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:475941 original size:32 final size:32
Alignment explanation
Indices: 475899--475965 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
475889 AGCACTGGCT
475899 CTACACTAGATTATGCTCTTTACTTGTGGCCA
1 CTACACTAGATTATGCTCTTTACTTGTGGCCA
*
475931 CTACATTAGATTATGCTCTTTACTTGTGGCCA
1 CTACACTAGATTATGCTCTTTACTTGTGGCCA
475963 CTA
1 CTA
475966 TTCATACATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (32 bp):
CTACACTAGATTATGCTCTTTACTTGTGGCCA
Found at i:476407 original size:16 final size:17
Alignment explanation
Indices: 476377--476408 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
476367 ATATTTATTT
476377 ATATAAAATATAATATA
1 ATATAAAATATAATATA
476394 ATATAAAA-ATAATAT
1 ATATAAAATATAATAT
476409 TGAGATCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:476498 original size:17 final size:17
Alignment explanation
Indices: 476478--476510 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
476468 AAAAATTAAA
476478 AAATATTTTA-AATAATT
1 AAAT-TTTTACAATAATT
476495 AAATTTTTACAATAAT
1 AAATTTTTACAATAAT
476511 ATCATTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTTTTACAATAATT
Found at i:476572 original size:16 final size:16
Alignment explanation
Indices: 476527--476573 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
476517 TATCACCTCA
476527 TAAAATTATAAAATGAT
1 TAAAATTATAAAAT-AT
* *
476544 TAATA-TATTAAATAT
1 TAAAATTATAAAATAT
476559 TAAAATTATAAAATA
1 TAAAATTATAAAATA
476574 ATTTTAACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 6 0.24
16 15 0.60
17 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAAATTATAAAATAT
Found at i:489101 original size:31 final size:31
Alignment explanation
Indices: 488952--489130 Score: 189
Period size: 31 Copynumber: 5.8 Consensus size: 31
488942 AAATTACGCG
** * *
488952 TTTAGTATTTAAATTATTAGTTTTAATTCGT
1 TTTAGTACATAAACTATTAGTTTTGATTCGT
* ** *
488983 TTTAATATTTAAACTATTAATTTTGATTCGT
1 TTTAGTACATAAACTATTAGTTTTGATTCGT
* * *
489014 TTTAATACTTAAACTATTAGTTTTGATTTGT
1 TTTAGTACATAAACTATTAGTTTTGATTCGT
*
489045 TTTAGTACATAAACTATTAATTTTGATTCGT
1 TTTAGTACATAAACTATTAGTTTTGATTCGT
* * * *
489076 TTTAGTACATAAACTATCAGCTTTGATCCAT
1 TTTAGTACATAAACTATTAGTTTTGATTCGT
*
489107 TTTAGTACCTAAACT-TTCAGTTTT
1 TTTAGTACATAAACTATT-AGTTTT
489131 TTCAAAACCA
Statistics
Matches: 128, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
30 1 0.01
31 127 0.99
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (31 bp):
TTTAGTACATAAACTATTAGTTTTGATTCGT
Found at i:491165 original size:15 final size:15
Alignment explanation
Indices: 491145--491174 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
491135 ATTAAAATCA
*
491145 GTTTTTTTATAACCG
1 GTTTTTTTAAAACCG
491160 GTTTTTTTAAAACCG
1 GTTTTTTTAAAACCG
491175 AAACCGATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (15 bp):
GTTTTTTTAAAACCG
Found at i:492351 original size:59 final size:59
Alignment explanation
Indices: 492252--492368 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 59
492242 ACTATAACCA
* * * * *
492252 TCAGTTTAAATTGGTTCTTAAACTTTTGAATATTCCAATTTTATCCCTAAAATATGACT
1 TCAGTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCATCCCTAAAATATGACT
* *
492311 TCAGTCTAAATTAGTCCTTAAACTTTT-AGACATTCTAATTTCATCCCTAAACTATGAC
1 TCAGTCTAAATTAGTCCTTAAACTTTTGA-ACATTCCAATTTCATCCCTAAAATATGAC
492369 CCTCAATTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 1 0.02
59 49 0.98
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (59 bp):
TCAGTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCATCCCTAAAATATGACT
Found at i:492627 original size:56 final size:58
Alignment explanation
Indices: 492565--492715 Score: 144
Period size: 60 Copynumber: 2.6 Consensus size: 58
492555 GGAATCTTCA
** * * *
492565 AAAAGTTTGGGGACCAATTTAGAAT-G-TCGTAGTTTGGGGATGAAATTGAAATGTTT
1 AAAAGTTTGACGACCAATTTAGAATGGATCATAGTTTAGGGATGAAATTGAAATATTT
* * *
492621 AGAAGTTTGACGACTAATTTAGAATGGTAATCATAGTTTAGGGATGAAATTGGAATATTT
1 AAAAGTTTGACGACCAATTTAGAATGG--ATCATAGTTTAGGGATGAAATTGAAATATTT
* * * *
492681 AAAAGTTTAAGGATCAATTTAAAATAAGGATCATA
1 AAAAGTTTGACGACCAATTTAGAAT--GGATCATA
492716 CTTTGAGGAT
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
56 21 0.28
57 1 0.01
60 51 0.68
62 2 0.03
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.33
Consensus pattern (58 bp):
AAAAGTTTGACGACCAATTTAGAATGGATCATAGTTTAGGGATGAAATTGAAATATTT
Found at i:497177 original size:51 final size:51
Alignment explanation
Indices: 497118--497218 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
497108 TCAGGGGGAG
* *
497118 AGTTACAAGGAATTTTAGCATGTTCAAACCGATATTTCTTTACAGCCTATT
1 AGTTACAAGGAATTTCAACATGTTCAAACCGATATTTCTTTACAGCCTATT
*
497169 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCTAT
1 AGTTACAAGGAATTTCAACATGTTCAAACCGATATTTCTTTACAGCCTAT
497219 CCTTTCCTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (51 bp):
AGTTACAAGGAATTTCAACATGTTCAAACCGATATTTCTTTACAGCCTATT
Found at i:499447 original size:14 final size:14
Alignment explanation
Indices: 499430--499474 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
499420 TAACAGAATT
499430 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
*
499444 GTCTGTTTTCTGCAGA
1 GTCTGTTTTCT--ACA
499460 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
499474 G
1 G
499475 AACTCAATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 14 0.52
16 13 0.48
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:499464 original size:16 final size:15
Alignment explanation
Indices: 499430--499475 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
499420 TAACAGAATT
*
499430 GTCTGTTTTCT-ACA
1 GTCTGTTTTCTCAGA
499444 GTCTGTTTTCTGCAGA
1 GTCTGTTTTCT-CAGA
499460 GTCTGTTTTCTACAGA
1 GTCTGTTTTCT-CAGA
499476 ACTCAATGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 11 0.39
16 17 0.61
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.46
Consensus pattern (15 bp):
GTCTGTTTTCTCAGA
Found at i:514828 original size:25 final size:25
Alignment explanation
Indices: 514794--514847 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
514784 ACCATCTTCA
*
514794 ATCTCGTACATAACACACTCCTTTC
1 ATCTCGTACACAACACACTCCTTTC
*
514819 ATCTCTTACACAACACACTCCTTTC
1 ATCTCGTACACAACACACTCCTTTC
514844 ATCT
1 ATCT
514848 TCAATCTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.37, G:0.02, T:0.33
Consensus pattern (25 bp):
ATCTCGTACACAACACACTCCTTTC
Found at i:517596 original size:12 final size:12
Alignment explanation
Indices: 517571--517603 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
517561 CAAACTATTA
517571 GTAAA-TAA-GG
1 GTAAACTAATGG
517581 GTAAACTAATGG
1 GTAAACTAATGG
517593 GTAAACTAATG
1 GTAAACTAATG
517604 ATTTTATCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 5 0.24
11 3 0.14
12 13 0.62
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.24
Consensus pattern (12 bp):
GTAAACTAATGG
Found at i:518529 original size:20 final size:19
Alignment explanation
Indices: 518506--518546 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
518496 TACAAATTTG
*
518506 AAAAATTAACAATTTTTTTA
1 AAAAATT-ACAATTTTTATA
*
518526 AAAAATTTCAATTTTTATA
1 AAAAATTACAATTTTTATA
518545 AA
1 AA
518547 CTACACTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAAATTACAATTTTTATA
Found at i:518681 original size:16 final size:16
Alignment explanation
Indices: 518629--518681 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
518619 TGAATGAAAA
*
518629 TTTTTAATTAAA-TTT
1 TTTTTAATTAAAGATT
*
518644 TATTTTAATTAAAAGCTAT
1 T-TTTTAATT-AAAGAT-T
518663 TTTTTAATTAAAGATT
1 TTTTTAATTAAAGATT
518679 TTT
1 TTT
518682 CATTTTTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 1 0.03
16 12 0.38
17 8 0.25
18 9 0.28
19 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (16 bp):
TTTTTAATTAAAGATT
Found at i:518708 original size:17 final size:17
Alignment explanation
Indices: 518686--518718 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
518676 ATTTTTCATT
*
518686 TTTGTTTACATGTTTTA
1 TTTGTTTACATATTTTA
518703 TTTGTTTACATATTTT
1 TTTGTTTACATATTTT
518719 TCAAAGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.67
Consensus pattern (17 bp):
TTTGTTTACATATTTTA
Found at i:520759 original size:554 final size:554
Alignment explanation
Indices: 519710--520823 Score: 2210
Period size: 554 Copynumber: 2.0 Consensus size: 554
519700 AGAACATTGG
519710 CGGTAGACACCTTTGGATATCCGACTCATAATAAGGGATCCAATCAAACTGTCAAAAGTATTATG
1 CGGTAGACACCTTTGGATATCCGACTCATAATAAGGGATCCAATCAAACTGTCAAAAGTATTATG
519775 TTAGTATAATTAAACAATTACTATTAAAAATTCAAAGTTAATGCAAAAAATATTAAAATTTACCG
66 TTAGTATAATTAAACAATTACTATTAAAAATTCAAAGTTAATGCAAAAAATATTAAAATTTACCG
519840 CATGTCTACCGGTGATATCAATCTTCATCCGAATATCTACTTTGGTTGCACCCTATAACTTTGTA
131 CATGTCTACCGGTGATATCAATCTTCATCCGAATATCTACTTTGGTTGCACCCTATAACTTTGTA
519905 TCGGTTATTCGGTGTCCCCATCTAAAAAAATACATAATTTATTATCATTTTAAAAATATTTAAAT
196 TCGGTTATTCGGTGTCCCCATCTAAAAAAATACATAATTTATTATCATTTTAAAAATATTTAAAT
519970 AAATATTATAAAATATCAAAACCTTAAATATAGGAATTTACCTTGCGACAAGAGGAAACTTCATA
261 AAATATTATAAAATATCAAAACCTTAAATATAGGAATTTACCTTGCGACAAGAGGAAACTTCATA
520035 GGAACGGATGTAATAAGCGTAAAAAACCGGAGACGATACCACGCCCATGATTGGAGCAAAACTAA
326 GGAACGGATGTAATAAGCGTAAAAAACCGGAGACGATACCACGCCCATGATTGGAGCAAAACTAA
520100 ACAGTCCGCTACATCTGCTTTTTTTCCTATAACCACTATGGTCGCCTTACAAAGTTCATGATACA
391 ACAGTCCGCTACATCTGCTTTTTTTCCTATAACCACTATGGTCGCCTTACAAAGTTCATGATACA
520165 AAAAAGCCAAAATTGCATAACCCAACTATATTGGCGACATACAAGGAAATCATTCAATACCGGAA
456 AAAAAGCCAAAATTGCATAACCCAACTATATTGGCGACATACAAGGAAATCATTCAATACCGGAA
520230 GATATTGGGTGTGCACCAAATTGCCCGATTTATC
521 GATATTGGGTGTGCACCAAATTGCCCGATTTATC
520264 CGGTAGACACCTTTGGATATCCGACTCATAATAAGGGATCCAATCAAACTGTCAAAAGTATTATG
1 CGGTAGACACCTTTGGATATCCGACTCATAATAAGGGATCCAATCAAACTGTCAAAAGTATTATG
520329 TTAGTATAATTAAACAATTACTATTAAAAATTCAAAGTTAATGCAAAAAATATTAAAATTTACCG
66 TTAGTATAATTAAACAATTACTATTAAAAATTCAAAGTTAATGCAAAAAATATTAAAATTTACCG
520394 CATGTCTACCGGTGATATCAATCTTCATCCGAATATCTACTTTGGTTGCACCCTATAACTTTGTA
131 CATGTCTACCGGTGATATCAATCTTCATCCGAATATCTACTTTGGTTGCACCCTATAACTTTGTA
520459 TCGGTTATTCGGTGTCCCCATCTAAAAAAATACATAATTTATTATCATTTTAAAAATATTTAAAT
196 TCGGTTATTCGGTGTCCCCATCTAAAAAAATACATAATTTATTATCATTTTAAAAATATTTAAAT
*
520524 AAATATTATAAAATATCAAAACTTTAAATATAGGAATTTACCTTGCGACAAGAGGAAACTTCATA
261 AAATATTATAAAATATCAAAACCTTAAATATAGGAATTTACCTTGCGACAAGAGGAAACTTCATA
*
520589 GGAACGGATGTAATAAGCGTAAAAAACGGGAGACGATACCACGCCCATGATTGGAGCAAAACTAA
326 GGAACGGATGTAATAAGCGTAAAAAACCGGAGACGATACCACGCCCATGATTGGAGCAAAACTAA
520654 ACAGTCCGCTACATCTGCTTTTTTTCCTATAACCACTATGGTCGCCTTACAAAGTTCATGATACA
391 ACAGTCCGCTACATCTGCTTTTTTTCCTATAACCACTATGGTCGCCTTACAAAGTTCATGATACA
520719 AAAAAGCCAAAATTGCATAACCCAACTATATTGGCGACATACAAGGAAATCATTCAATACCGGAA
456 AAAAAGCCAAAATTGCATAACCCAACTATATTGGCGACATACAAGGAAATCATTCAATACCGGAA
520784 GATATTGGGTGTGCACCAAATTGCCCGATTTATC
521 GATATTGGGTGTGCACCAAATTGCCCGATTTATC
520818 CGGTAG
1 CGGTAG
520824 CAAGATCCCT
Statistics
Matches: 558, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
554 558 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (554 bp):
CGGTAGACACCTTTGGATATCCGACTCATAATAAGGGATCCAATCAAACTGTCAAAAGTATTATG
TTAGTATAATTAAACAATTACTATTAAAAATTCAAAGTTAATGCAAAAAATATTAAAATTTACCG
CATGTCTACCGGTGATATCAATCTTCATCCGAATATCTACTTTGGTTGCACCCTATAACTTTGTA
TCGGTTATTCGGTGTCCCCATCTAAAAAAATACATAATTTATTATCATTTTAAAAATATTTAAAT
AAATATTATAAAATATCAAAACCTTAAATATAGGAATTTACCTTGCGACAAGAGGAAACTTCATA
GGAACGGATGTAATAAGCGTAAAAAACCGGAGACGATACCACGCCCATGATTGGAGCAAAACTAA
ACAGTCCGCTACATCTGCTTTTTTTCCTATAACCACTATGGTCGCCTTACAAAGTTCATGATACA
AAAAAGCCAAAATTGCATAACCCAACTATATTGGCGACATACAAGGAAATCATTCAATACCGGAA
GATATTGGGTGTGCACCAAATTGCCCGATTTATC
Found at i:521068 original size:28 final size:28
Alignment explanation
Indices: 521028--521084 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
521018 GTACTAATAT
521028 TGTAAGGCTATCCAAGCTTCTTCAATGA
1 TGTAAGGCTATCCAAGCTTCTTCAATGA
521056 TGTAAGGCTATCCAAGCTTCTTCAATGA
1 TGTAAGGCTATCCAAGCTTCTTCAATGA
521084 T
1 T
521085 AAAGAAGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (28 bp):
TGTAAGGCTATCCAAGCTTCTTCAATGA
Found at i:527678 original size:28 final size:28
Alignment explanation
Indices: 527638--527701 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
527628 CAACTGCATT
* *
527638 TCCATCTATTGCACCATCAGATCATCAC
1 TCCATCTCTTGCACCAACAGATCATCAC
527666 TCCATCTCTTGCACCAACAGATCATCAC
1 TCCATCTCTTGCACCAACAGATCATCAC
527694 TCCATCTC
1 TCCATCTC
527702 CACCTTCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.27, C:0.39, G:0.06, T:0.28
Consensus pattern (28 bp):
TCCATCTCTTGCACCAACAGATCATCAC
Found at i:533950 original size:277 final size:271
Alignment explanation
Indices: 533379--533871 Score: 702
Period size: 277 Copynumber: 1.8 Consensus size: 271
533369 GTTTATGATG
* * *
533379 AAATTGAAATGTTCAAAAGTGTGAGGACTAATTTAGAATGATATTCATAGTTTAGGGATAAAATT
1 AAATTGAAATGTTCAAAACTGTGAGGACTAATTTAGAATAATATTCATAGTTTAGGAATAAAATT
* * *
533444 GGAACATTTAACAATTTAAAGACTAATTTAAAATGAGAATGATACTTTGAGAATATATGATGCAA
66 GGAACATTTAACAATTTAAAGACTAATTTAAAACGAGAATCATACTTTGAGAACATATGATGCAA
* *
533509 TTAACTCCTAGAAAAATATCCCTTTTTAATAATTTGTTATCATTTAAGATAATATTTTAGGTTGT
131 TTAACTCCTAGAAAAATATCCCCTTTAAATAATTTGTTATCATTTAAGATAATATTTTAGGTTGT
* * * ** *
533574 AATCTAAAATGTTCTATATTTTGGGAACAATTCTGGTTGCAACCTAAACTGTTACATGAGTTTTG
196 AATCTAAAATGTTATAAAGTTT--GAACAATAATGGTT-CAA-CTAAACTGTAACA-GAGTTTTG
* *
533639 AAATCGATTTAAAGTTA
256 AAAAC-ATTAAAAGTTA
*
533656 AAATTGAAATGTTCAAAACTGTGAGGACTAATTTAGAATAATATTCATAGTTTAGGAATGAAATT
1 AAATTGAAATGTTCAAAACTGTGAGGACTAATTTAGAATAATATTCATAGTTTAGGAATAAAATT
* * * * *
533721 GTAACTTTTAATAATTTAGAGACTAATTTAAAACGAGAATCATACTTTGAGAACATTTGATGCAA
66 GGAACATTTAACAATTTAAAGACTAATTTAAAACGAGAATCATACTTTGAGAACATATGATGCAA
*
533786 TTAACTCCTAG-AAAAT-TCCTCCTTTAAATACTTTGTTATCATTTAAGATAATATTTTAGGTTG
131 TTAACTCCTAGAAAAATATCC-CCTTTAAATAATTTGTTATCATTTAAGATAATATTTTAGGTTG
533849 TAATCTAAAATGTTATAAAGTTT
195 TAATCTAAAATGTTATAAAGTTT
533872 AACCTAAAAT
Statistics
Matches: 197, Mismatches: 18, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
275 3 0.02
276 65 0.33
277 129 0.65
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (271 bp):
AAATTGAAATGTTCAAAACTGTGAGGACTAATTTAGAATAATATTCATAGTTTAGGAATAAAATT
GGAACATTTAACAATTTAAAGACTAATTTAAAACGAGAATCATACTTTGAGAACATATGATGCAA
TTAACTCCTAGAAAAATATCCCCTTTAAATAATTTGTTATCATTTAAGATAATATTTTAGGTTGT
AATCTAAAATGTTATAAAGTTTGAACAATAATGGTTCAACTAAACTGTAACAGAGTTTTGAAAAC
ATTAAAAGTTA
Found at i:536222 original size:17 final size:17
Alignment explanation
Indices: 536189--536221 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
536179 TGATCCCACG
536189 AATTTCTTTCTTCTTTT
1 AATTTCTTTCTTCTTTT
*
536206 AATTT-TTTTTTCTTTT
1 AATTTCTTTCTTCTTTT
536222 TCAAATTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (17 bp):
AATTTCTTTCTTCTTTT
Found at i:540199 original size:16 final size:16
Alignment explanation
Indices: 540119--540193 Score: 123
Period size: 16 Copynumber: 4.7 Consensus size: 16
540109 TGATGCTCTA
540119 AATCATTCAGCATTTG
1 AATCATTCAGCATTTG
540135 AATCATTCAGCATTTG
1 AATCATTCAGCATTTG
540151 AATCATTCAGCATTTG
1 AATCATTCAGCATTTG
* *
540167 AATCATTCAGTATTTA
1 AATCATTCAGCATTTG
*
540183 AATTATTCAGC
1 AATCATTCAGC
540194 GTTTAATTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 55 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (16 bp):
AATCATTCAGCATTTG
Found at i:541851 original size:25 final size:22
Alignment explanation
Indices: 541822--541867 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
541812 ATTTTAACTC
541822 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
541847 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
541868 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:542840 original size:89 final size:90
Alignment explanation
Indices: 542727--542927 Score: 255
Period size: 90 Copynumber: 2.2 Consensus size: 90
542717 ACAGATTTGG
* * * * *
542727 TCCACTGCTCCTCAGGGAAGATCAAATCTGA-AAAAGGGATATGCTT-TGCTTCTCTTCAGGGTA
1 TCCACTGCTCTTCAGGGAAGATCAAATCTCATAAAAGGGATATG-TTCTGCTGCCCTTAAGGGTA
*
542790 GATTAGATCTAAAAACATTGATTCA-
65 GATAAGATCTAAAAACATTGATTCAC
* *
542815 TACCACTGCTCTTCAGGGAAGATCAAATCTCATAAAGGGGATCTGTTCTGCTGCCCTTAAGGGTA
1 T-CCACTGCTCTTCAGGGAAGATCAAATCTCATAAAAGGGATATGTTCTGCTGCCCTTAAGGGTA
* **
542880 GATAAGATTTGGAAACATTGATTCAC
65 GATAAGATCTAAAAACATTGATTCAC
*
542906 TCCAGTGCTCTTCAGGGAAGAT
1 TCCACTGCTCTTCAGGGAAGAT
542928 TGAATCGAGT
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
88 1 0.01
89 30 0.31
90 65 0.67
91 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (90 bp):
TCCACTGCTCTTCAGGGAAGATCAAATCTCATAAAAGGGATATGTTCTGCTGCCCTTAAGGGTAG
ATAAGATCTAAAAACATTGATTCAC
Found at i:542943 original size:41 final size:41
Alignment explanation
Indices: 542897--542974 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
542887 TTTGGAAACA
* * *
542897 TTGATTCACTCCAGTGCTCTTCAGGGAAGATTGAATCGAGT
1 TTGATTCACTCCACTGCTCTTCAAGGAAGATTAAATCGAGT
** *
542938 TTGATTTGCTTCACTGCTCTTCAAGGAAGATTAAATC
1 TTGATTCACTCCACTGCTCTTCAAGGAAGATTAAATC
542975 TGAGAAAGGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (41 bp):
TTGATTCACTCCACTGCTCTTCAAGGAAGATTAAATCGAGT
Found at i:542960 original size:131 final size:130
Alignment explanation
Indices: 542818--543057 Score: 365
Period size: 131 Copynumber: 1.8 Consensus size: 130
542808 TGATTCATAC
* * * *
542818 CACTGCTCTTCAGGGAAGATCAAATCTCATAAAGGGGATCTGTTCTGCTGCC-CTTAAGGGTAGA
1 CACTGCTCTTCAAGGAAGATCAAATCTCAGAAAGGGGATCTGCTCTGCT-CCTCTTAAGGGTAAA
*
542882 TAAGATTTGGAAACATTGATTCACTCCAGTGCTCTTCAGGGAAGATTGAATCGAGTTTGATTTGC
65 TAAGATTTGGAAACATTGATTCACTCCACTGCTCTT-AGGGAAGATTGAATCGAGTTTGATTTGC
542947 TT
129 TT
* * *
542949 CACTGCTCTTCAAGGAAGATTAAATCTGAGAAAGGGGATCTGCTCTGCTCCTCTTCAGGGTAAAT
1 CACTGCTCTTCAAGGAAGATCAAATCTCAGAAAGGGGATCTGCTCTGCTCCTCTTAAGGGTAAAT
* *
543014 CAGATTTGGAAACGTTGATTCACTCCACTGCTCTTAGGGAAGAT
66 AAGATTTGGAAACATTGATTCACTCCACTGCTCTTAGGGAAGAT
543058 CAGATCTGAG
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
130 11 0.11
131 87 0.89
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (130 bp):
CACTGCTCTTCAAGGAAGATCAAATCTCAGAAAGGGGATCTGCTCTGCTCCTCTTAAGGGTAAAT
AAGATTTGGAAACATTGATTCACTCCACTGCTCTTAGGGAAGATTGAATCGAGTTTGATTTGCTT
Found at i:543048 original size:45 final size:44
Alignment explanation
Indices: 542999--543142 Score: 114
Period size: 45 Copynumber: 3.2 Consensus size: 44
542989 TGCTCTGCTC
*
542999 CTCTTCAGGGTAAATCAGATTTGGAAACGTTGATTCACTCCACTG
1 CTCTTCAGGGTAAATCAGATCTGGAAA-GTTGATTCACTCCACTG
** *** *
543044 CTCTT-AGGG-AAGATCAGATCTGAGAAAGGGGA-TCTACTCTGTTT
1 CTCTTCAGGGTAA-ATCAGATCTG-GAAAGTTGATTC-ACTCCACTG
* * * * *
543088 CTTTTCAGGGTATATCAGATCCGAAAAATTTGATTCACTCCACTG
1 CTCTTCAGGGTAAATCAGATCTG-GAAAGTTGATTCACTCCACTG
543133 CTCTTCAGGG
1 CTCTTCAGGG
543143 AAGATTGAAT
Statistics
Matches: 74, Mismatches: 19, Indels: 12
0.70 0.18 0.11
Matches are distributed among these distances:
43 4 0.05
44 25 0.34
45 42 0.57
46 3 0.04
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (44 bp):
CTCTTCAGGGTAAATCAGATCTGGAAAGTTGATTCACTCCACTG
Found at i:543055 original size:220 final size:220
Alignment explanation
Indices: 542654--543199 Score: 634
Period size: 220 Copynumber: 2.5 Consensus size: 220
542644 ATTGCTCTTC
* * * *
542654 AGGGTAGATTAGATTTGGAAACGTTGATTCACTCCACTGCTCTTCAGGGTAGATTGAATCGAGAC
1 AGGGTAGATAAGATTTGGAAACATTGATTCACTCCACTGCTCTTCAGGGAAGATTGAATCGAGAT
* * * * * * * *
542719 AGATTTGGTCCACTGCTCCTCAGGGAAGATCAAATCTGAAAAAGGGATATGCTTTGCTTCTCTTC
66 TGATTTGCTTCACTGCTCTTCAAGGAAGATTAAATCTGAAAAAGGGATATGCTCTGCTCCTCTTC
* * *
542784 AGGGTAGATTAGATCTAAAAACATTGATTCATACCACTGCTCTTCAGGGAAGATCAAATCTCATA
131 AGGGTAAATCAGATCTAAAAACATTGATTCATACCACTGCTCTTCAGGGAAGATCAAATCTCAGA
**
542849 AAGGGGATCTGTTCTGCTGCCCTTA
196 AAGGGGATCTACTCTGCTGCCCTTA
* *
542874 AGGGTAGATAAGATTTGGAAACATTGATTCACTCCAGTGCTCTTCAGGGAAGATTGAATCGAGTT
1 AGGGTAGATAAGATTTGGAAACATTGATTCACTCCACTGCTCTTCAGGGAAGATTGAATCGAGAT
* *
542939 TGATTTGCTTCACTGCTCTTCAAGGAAGATTAAATCTGAGAAAGGGGATCTGCTCTGCTCCTCTT
66 TGATTTGCTTCACTGCTCTTCAAGGAAGATTAAATCTGA-AAAAGGGATATGCTCTGCTCCTCTT
* ** * * *
543004 CAGGGTAAATCAGATTTGGAAACGTTGATTCACT-CCACTGCTCTT-AGGGAAGATCAGATCTGA
130 CAGGGTAAATCAGATCTAAAAACATTGATTCA-TACCACTGCTCTTCAGGGAAGATCAAATCTCA
* * ** *
543067 GAAAGGGGATCTACTCTGTTTCTTTTC
194 GAAAGGGGATCTACTCTGCTGCCCTTA
* * ** * * *
543094 AGGGTATATCAGA-TCCGAAAAATTTGATTCACTCCACTGCTCTTCAGGGAAGATTGAATCGGGC
1 AGGGTAGATAAGATTTGGAAACA-TTGATTCACTCCACTGCTCTTCAGGGAAGATTGAATCGAGA
* * * *
543158 TTGATTTGTTTCTCTTG-TCTTCAA-GAAGATTTAATTTGAAAA
65 TTGATTTGCTTCAC-TGCTCTTCAAGGAAGATTAAATCTGAAAA
543200 TTAAACATTA
Statistics
Matches: 278, Mismatches: 44, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
218 3 0.01
219 19 0.07
220 195 0.70
221 60 0.22
222 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (220 bp):
AGGGTAGATAAGATTTGGAAACATTGATTCACTCCACTGCTCTTCAGGGAAGATTGAATCGAGAT
TGATTTGCTTCACTGCTCTTCAAGGAAGATTAAATCTGAAAAAGGGATATGCTCTGCTCCTCTTC
AGGGTAAATCAGATCTAAAAACATTGATTCATACCACTGCTCTTCAGGGAAGATCAAATCTCAGA
AAGGGGATCTACTCTGCTGCCCTTA
Found at i:543069 original size:89 final size:90
Alignment explanation
Indices: 542949--543147 Score: 274
Period size: 89 Copynumber: 2.2 Consensus size: 90
542939 TGATTTGCTT
* * *
542949 CACTGCTCTTCAAGGAAGATTAAATCTGAGAAAGGGGATCTGCTCTGCTCCTCTTCAGGGTAAAT
1 CACTGCTCTTCAGGGAAGATCAAATCTGAGAAAGGGGATCTACTCTGCTCCTCTTCAGGGTAAAT
** * *
543014 CAGATTTGGAAACGTTGATTCACTC
66 CAGATCCGAAAAAGTTGATTCACTC
* * * * *
543039 CACTGCTCTT-AGGGAAGATCAGATCTGAGAAAGGGGATCTACTCTGTTTCTTTTCAGGGTATAT
1 CACTGCTCTTCAGGGAAGATCAAATCTGAGAAAGGGGATCTACTCTGCTCCTCTTCAGGGTAAAT
*
543103 CAGATCCGAAAAATTTGATTCACTC
66 CAGATCCGAAAAAGTTGATTCACTC
543128 CACTGCTCTTCAGGGAAGAT
1 CACTGCTCTTCAGGGAAGAT
543148 TGAATCGGGC
Statistics
Matches: 95, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
89 76 0.80
90 19 0.20
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (90 bp):
CACTGCTCTTCAGGGAAGATCAAATCTGAGAAAGGGGATCTACTCTGCTCCTCTTCAGGGTAAAT
CAGATCCGAAAAAGTTGATTCACTC
Found at i:544471 original size:20 final size:20
Alignment explanation
Indices: 544446--544507 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
544436 TTGAACCTCC
544446 TTTTATTAATTATTTTTCTT
1 TTTTATTAATTATTTTTCTT
544466 TTTTATTAATTAATTTTT-TT
1 TTTTATTAATT-ATTTTTCTT
*
544486 CTTTT-TT--TTTTTTTTCTT
1 -TTTTATTAATTATTTTTCTT
544504 TTTT
1 TTTT
544508 TATTTTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 9 0.24
18 4 0.11
20 15 0.39
21 10 0.26
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTATTAATTATTTTTCTT
Found at i:544483 original size:1 final size:1
Alignment explanation
Indices: 544479--544530 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
544469 TATTAATTAA
* * * * * *
544479 TTTTTTTCTTTTTTTTTTTTTTCTTTTTTTATTTTTTATTTCTTATTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
544531 CATTTTGTTT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:544488 original size:23 final size:23
Alignment explanation
Indices: 544447--544536 Score: 92
Period size: 23 Copynumber: 3.9 Consensus size: 23
544437 TGAACCTCCT
544447 TTTATTAATTATTTTTCTTTTTTA
1 TTTATTAATT-TTTTTCTTTTTTA
* *
544471 TTAATTAATTTTTTTCTTTTTTT
1 TTTATTAATTTTTTTCTTTTTTA
* ** *
544494 TTTTTTTCTTTTTTTATTTTTTA
1 TTTATTAATTTTTTTCTTTTTTA
* *
544517 TTTCTT-ATTTTTTTCATTTT
1 TTTATTAATTTTTTTCTTTTT
544537 GTTTCTTCTT
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
22 11 0.20
23 34 0.63
24 9 0.17
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTATTAATTTTTTTCTTTTTTA
Found at i:544492 original size:8 final size:8
Alignment explanation
Indices: 544479--544515 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
544469 TATTAATTAA
544479 TTTTTTTC
1 TTTTTTTC
544487 TTTTTTT-
1 TTTTTTTC
544494 TTTTTTTC
1 TTTTTTTC
*
544502 TTTTTTTA
1 TTTTTTTC
544510 TTTTTT
1 TTTTTT
544516 ATTTCTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.03, C:0.05, G:0.00, T:0.92
Consensus pattern (8 bp):
TTTTTTTC
Found at i:544497 original size:15 final size:15
Alignment explanation
Indices: 544479--544536 Score: 71
Period size: 15 Copynumber: 3.8 Consensus size: 15
544469 TATTAATTAA
544479 TTTTTTTCTTTTTTT
1 TTTTTTTCTTTTTTT
544494 TTTTTTTCTTTTTTT
1 TTTTTTTCTTTTTTT
* * * *
544509 ATTTTTTATTTCTTA
1 TTTTTTTCTTTTTTT
544524 TTTTTTTCATTTT
1 TTTTTTTC-TTTT
544537 GTTTCTTCTT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
15 32 0.91
16 3 0.09
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTTTTCTTTTTTT
Found at i:544505 original size:21 final size:20
Alignment explanation
Indices: 544478--544530 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 20
544468 TTATTAATTA
544478 ATTT-TTTTCTTTTTTTTTTT
1 ATTTCTTTT-TTTTTTTTTTT
*
544498 -TTTC-TTTTTTTATTTTTT
1 ATTTCTTTTTTTTTTTTTTT
544516 ATTTCTTATTTTTTT
1 ATTTCTT-TTTTTTT
544531 CATTTTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 10 0.37
19 10 0.37
20 1 0.04
21 6 0.22
ACGTcount: A:0.08, C:0.06, G:0.00, T:0.87
Consensus pattern (20 bp):
ATTTCTTTTTTTTTTTTTTT
Found at i:544536 original size:7 final size:7
Alignment explanation
Indices: 544458--544529 Score: 53
Period size: 7 Copynumber: 10.7 Consensus size: 7
544448 TTATTAATTA
*
544458 TTTTTCT
1 TTTTTAT
544465 TTTTTAT
1 TTTTTAT
* *
544472 TAATTAAT
1 T-TTTTAT
544480 TTTTT-T
1 TTTTTAT
*
544486 CTTTT-T
1 TTTTTAT
544492 TTTTT-T
1 TTTTTAT
*
544498 TTTCT-T
1 TTTTTAT
544504 TTTTTAT
1 TTTTTAT
544511 TTTTTAT
1 TTTTTAT
*
544518 TTCTTAT
1 TTTTTAT
544525 TTTTT
1 TTTTT
544530 TCATTTTGTT
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
6 20 0.38
7 27 0.52
8 5 0.10
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTAT
Found at i:544549 original size:46 final size:46
Alignment explanation
Indices: 544458--544549 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 46
544448 TTATTAATTA
* * * *
544458 TTTTTCTTTTTTATTAATTAATTTTTTTCTTTTTTTTTTTTTTCTT
1 TTTTTATTTTTTATTAATTAATTTTTTTCTTTTGTTTCTTCTTCTT
**
544504 TTTTTATTTTTTATTTCTT-ATTTTTTTCATTTTGTTTCTTCTTCTT
1 TTTTTATTTTTTATTAATTAATTTTTTTC-TTTTGTTTCTTCTTCTT
544550 CAGGCAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 9 0.23
46 30 0.77
ACGTcount: A:0.10, C:0.09, G:0.01, T:0.80
Consensus pattern (46 bp):
TTTTTATTTTTTATTAATTAATTTTTTTCTTTTGTTTCTTCTTCTT
Found at i:548188 original size:109 final size:109
Alignment explanation
Indices: 548028--548230 Score: 268
Period size: 109 Copynumber: 1.9 Consensus size: 109
548018 GCAAGGATCG
* * *
548028 AAGTTGTTATTTACCCGTTTTAAGCATGCTATATATATTTTTAGGATATTTGATGTTTAGTGTCC
1 AAGTTGTTATTTACCCATTTTAAGCATACTATATATATTTTTAGGATATTTGATGTTTAGT-CCC
*
548093 CA-TAGTTTA-GCGTGTTTTTGTATATTGGTCACCTATAGGGACCA
65 CATTA-TTTAGGCGTGTTTTTGCATATTGGTCACCTATAGGGACCA
* * * * *
548137 AAGTTGTTATTTACCCATTTTCATGCATATTATGTA-ATTTTTGGGATATTTGTTGTTTAGTCCC
1 AAGTTGTTATTTACCCATTTT-AAGCATACTATATATATTTTTAGGATATTTGATGTTTAGTCCC
*
548201 CATTATTTAGGCGTGTTTTTGCATTTTGGT
65 CATTATTTAGGCGTGTTTTTGCATATTGGT
548231 TATGTGTAGT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
108 8 0.10
109 63 0.78
110 10 0.12
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (109 bp):
AAGTTGTTATTTACCCATTTTAAGCATACTATATATATTTTTAGGATATTTGATGTTTAGTCCCC
ATTATTTAGGCGTGTTTTTGCATATTGGTCACCTATAGGGACCA
Found at i:548601 original size:24 final size:24
Alignment explanation
Indices: 548574--548620 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
548564 AGTTCGATTA
* *
548574 GCATTTTG-TTTTATTTTAATTTTT
1 GCATGTTGCTTTTATGTT-ATTTTT
548598 GCATGTTGCTTTTATGTTATTTT
1 GCATGTTGCTTTTATGTTATTTT
548621 ATTTTAGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.15, C:0.06, G:0.13, T:0.66
Consensus pattern (24 bp):
GCATGTTGCTTTTATGTTATTTTT
Found at i:549245 original size:131 final size:131
Alignment explanation
Indices: 549055--549580 Score: 781
Period size: 131 Copynumber: 4.0 Consensus size: 131
549045 ATAAGTAACA
* * *
549055 CTCGAATTAATATTGAA-CTTTAGGACGAAATAGT-A-ATCTCTTTCATTTCGATTGGAGTAATA
1 CTCGAATCAATATT-AATTTTTAAGACGAAATAGTGATATCTC-TTCATTTCGATTGGAGTAATA
* * *
549117 AATGAATGCTTTAAGGTATGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTT
64 AATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTT
549182 TCT
129 TCT
* * * *
549185 CTAGAATCAATATTTATTTTTAAGATGAAATAGTGATATCTCTTCATTTCGATTGTAGTAATAAA
1 CTCGAATCAATATTAATTTTTAAGACGAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAA
549250 TGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
66 TGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
549315 T
131 T
* * *
549316 CTCGAATCAATATTGATTTATAAGACGAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAG
1 CTCGAATCAATATTAATTTTTAAGACGAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAA
* * * *
549381 TGATTTCTTTAAGGCATGAGAGGTCATTTATTTTCGATTGAAAATAATTAGATATTATCGTTTTC
66 TGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
549446 T
131 T
* * * * *
549447 CTCGAATCAATATTGAATTTTT-AGACGAAATAGTGACATCTCTTCATTTCAATTAGTGTAACAA
1 CTCGAATCAATATT-AATTTTTAAGACGAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAA
* *
549511 ATGACTGCTTTAAGGCATGAGAGGTCATTTATTTTCGATTGGAAATAATTAGATATTATCATTTT
65 ATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTT
549576 CT
130 CT
549578 CTC
1 CTC
549581 TTAAAATCCA
Statistics
Matches: 360, Mismatches: 32, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
129 1 0.00
130 26 0.07
131 323 0.90
132 10 0.03
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (131 bp):
CTCGAATCAATATTAATTTTTAAGACGAAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAA
TGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTC
T
Found at i:553474 original size:15 final size:16
Alignment explanation
Indices: 553447--553477 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
553437 TCAAGAGCAA
553447 AGGTGAGTTATTTGTT
1 AGGTGAGTTATTTGTT
553463 AGGTGA-TTATTTGTT
1 AGGTGAGTTATTTGTT
553478 GAATTTAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (16 bp):
AGGTGAGTTATTTGTT
Found at i:554052 original size:24 final size:24
Alignment explanation
Indices: 554025--554081 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
554015 GTATTGGTAT
554025 CGATACCCTCAGCTAGGGTAGTAC
1 CGATACCCTCAGCTAGGGTAGTAC
*
554049 CGATACCATCAGCTAGGGTAGTAC
1 CGATACCCTCAGCTAGGGTAGTAC
**
554073 TAATACCCT
1 CGATACCCT
554082 ATAGTGGGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (24 bp):
CGATACCCTCAGCTAGGGTAGTAC
Found at i:555168 original size:20 final size:20
Alignment explanation
Indices: 555143--555187 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
555133 ATACAGTTGT
555143 ACGTGGACAGCTGGCTCTGC
1 ACGTGGACAGCTGGCTCTGC
555163 ACGTGGACAGCTGGCTCTGC
1 ACGTGGACAGCTGGCTCTGC
555183 ACGTG
1 ACGTG
555188 AAATGATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.29, G:0.36, T:0.20
Consensus pattern (20 bp):
ACGTGGACAGCTGGCTCTGC
Found at i:555593 original size:15 final size:15
Alignment explanation
Indices: 555570--555611 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
555560 CTCACTTCCC
555570 TTTGATGTTATTTTA
1 TTTGATGTTATTTTA
*
555585 TTTGCTGTTATTTTA
1 TTTGATGTTATTTTA
*
555600 TTT-ATTTTATTT
1 TTTGATGTTATTT
555612 GTGGGTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (15 bp):
TTTGATGTTATTTTA
Found at i:555742 original size:24 final size:24
Alignment explanation
Indices: 555697--555746 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
555687 TGGTGGTTGG
555697 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
555721 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
555745 TT
1 TT
555747 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:561200 original size:15 final size:15
Alignment explanation
Indices: 561177--561218 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
561167 CTCACTTCCC
561177 TTTGATGTTATTTTA
1 TTTGATGTTATTTTA
*
561192 TTTGCTGTTATTTTA
1 TTTGATGTTATTTTA
*
561207 TTT-ATTTTATTT
1 TTTGATGTTATTT
561219 GTGGGTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (15 bp):
TTTGATGTTATTTTA
Found at i:561349 original size:24 final size:24
Alignment explanation
Indices: 561304--561353 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
561294 TGGTGGTTGG
561304 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
561328 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
561352 TT
1 TT
561354 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:578177 original size:2 final size:2
Alignment explanation
Indices: 578166--578909 Score: 119
Period size: 2 Copynumber: 376.0 Consensus size: 2
578156 TAAAAACAAT
* *
578166 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA AA CTA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * * *
578209 TA TA TA TA T- TA AA TA TA TA TA -A TA TA AA AA CTA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * * *
578251 TA TT TA T- TA TA TA CTA TA TA AA AA T- TA TA TA TA T- TA TG TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
578291 TA AA CTA TA TA TA CCA TG TA TA AA CTA TA GA GTT TA TA TA TGA -A
1 TA TA -TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA T-A TA
* * * *
578335 CTA T- TG CA CTA TA TA TA AA T- TA TA TA GTT TA T- TA -A TA TA
1 -TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * *
578374 AA T- TA TA CA GTT TA TA TA TA AA T- TA TA TA TGA -A T- TA TA TT
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
* * * * *
578414 TA AA TA TA TA CA AA T- TA TA TT TA TA TA T- TA TG TA TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
578452 TA TA AA T- TA TA TA TA CTA TG TA TA AA T- TA TA CA -A TT TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
578492 TA GTT TA AA TA TA AA GTA TA TA -A GTA TA TA TA TA AA CTA TA AA
1 TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA
* * * * * *
578535 T- TA TA TA TT TT TA TA TA -A TA TA CA TT TA -A AA CA 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
* *
578574 CA TA TA TA -A TA -A TA AA GTA TA -A GTA 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
* * * * *
578615 TA TA TA TA TA TA AA TA TA TA AA GTA TA T- TA TA AA GA T- TA AA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * *
578656 GTA TA TA -A GCA TA TA -A TA TA AA GCA TA TA -A GTA TA TA -A TA
1 -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA
* * *
578696 TA -A AA TA TA TA AA TA T- TA AA TA TA TA -A GTA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
578735 AA GTA TA TA TA -A CTA TA AA CTA TA TA TA TA TA TA TA TA -A GT-
1 TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* * * * * *
578776 TT TA GTA TA AA GCA TA TA TA T- TA TA TA AA GTA TA TA -A GTG TG
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA
* * * *
578818 TG TA TA TA TA TA TA TA TA TA TA TA AA GT- TT TA GTA TA AA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA
* *
578860 TA TA TA CA TA TA -A TA -A TA TA AA GTA TA -A GTA TA T- 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
578900 TA TA TA TA TA
1 TA TA TA TA TA
578910 AAGTATAATT
Statistics
Matches: 528, Mismatches: 124, Indels: 180
0.63 0.15 0.22
Matches are distributed among these distances:
1 49 0.09
2 439 0.83
3 40 0.08
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.42
Consensus pattern (2 bp):
TA
Found at i:578203 original size:9 final size:8
Alignment explanation
Indices: 578166--578245 Score: 54
Period size: 9 Copynumber: 9.5 Consensus size: 8
578156 TAAAAACAAT
578166 TATAATATA
1 TATAA-ATA
*
578175 TATATATA
1 TATAAATA
*
578183 TATATATA
1 TATAAATA
578191 TATAAACTA
1 TATAAA-TA
* *
578200 TAT-AGTT
1 TATAAATA
*
578207 TATATATA
1 TATAAATA
578215 TATTAAATA
1 TA-TAAATA
578224 TATATAATA
1 TATA-AATA
*
578233 TAAAAACTA
1 TATAAA-TA
578242 TATA
1 TATA
578246 GTTTATATTT
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
7 4 0.07
8 24 0.43
9 28 0.50
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (8 bp):
TATAAATA
Found at i:578234 original size:42 final size:42
Alignment explanation
Indices: 578165--578271 Score: 150
Period size: 42 Copynumber: 2.6 Consensus size: 42
578155 ATAAAAACAA
*
578165 TTATA-ATATA-TATATATATATATATATATAAACTATATAGT
1 TTATATATATATTATATATATATA-ATATAAAAACTATATAGT
*
578206 TTATATATATATTAAATATATATAATATAAAAACTATATAGT
1 TTATATATATATTATATATATATAATATAAAAACTATATAGT
578248 TTATAT-T-TATTATATACTATATAA
1 TTATATATATATTATATA-TATATAA
578272 AAATTATATA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
40 8 0.13
41 13 0.22
42 28 0.47
43 11 0.18
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.47
Consensus pattern (42 bp):
TTATATATATATTATATATATATAATATAAAAACTATATAGT
Found at i:578423 original size:21 final size:21
Alignment explanation
Indices: 578385--578445 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
578375 ATTATACAGT
*
578385 TTATATATAAATTATATATGAA
1 TTATATTTAAA-TATATATGAA
**
578407 TTATATTTAAATATATACAAA
1 TTATATTTAAATATATATGAA
*
578428 TTATATTTATATAT-TATG
1 TTATATTTAAATATATATG
578446 TATAATTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 2 0.06
21 21 0.64
22 10 0.30
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (21 bp):
TTATATTTAAATATATATGAA
Found at i:578449 original size:17 final size:17
Alignment explanation
Indices: 578429--578482 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
578419 ATATACAAAT
* * *
578429 TATATTTATATATTATG
1 TATAATTATAAATTATA
578446 TATAATTATAAATTATA
1 TATAATTATAAATTATA
578463 TATACTATGTATAAATTATA
1 TATA--AT-TATAAATTATA
578483 CAATTTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 18 0.58
19 2 0.06
20 11 0.35
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (17 bp):
TATAATTATAAATTATA
Found at i:578466 original size:11 final size:11
Alignment explanation
Indices: 578344--578455 Score: 74
Period size: 11 Copynumber: 10.4 Consensus size: 11
578334 ACTATTGCAC
578344 TATATATAAAT
1 TATATATAAAT
**
578355 TATATAGTTTAT
1 TATATA-TAAAT
578367 TA-ATATAAAT
1 TATATATAAAT
*
578377 TATACAGT---T
1 TATATA-TAAAT
578386 TATATATAAAT
1 TATATATAAAT
*
578397 TATATATGAAT
1 TATATATAAAT
*
578408 TATATTTAAA-
1 TATATATAAAT
*
578418 TATATACAAAT
1 TATATATAAAT
*
578429 TATATTTATATAT
1 TATA--TATAAAT
*
578442 TATGTAT-AAT
1 TATATATAAAT
578452 TATA
1 TATA
578456 AATTATATAT
Statistics
Matches: 76, Mismatches: 16, Indels: 19
0.68 0.14 0.17
Matches are distributed among these distances:
8 1 0.01
9 6 0.08
10 18 0.24
11 37 0.49
12 6 0.08
13 8 0.11
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (11 bp):
TATATATAAAT
Found at i:578871 original size:38 final size:37
Alignment explanation
Indices: 578567--579134 Score: 161
Period size: 39 Copynumber: 15.3 Consensus size: 37
578557 CATTTAAAAC
* *
578567 ATATATACATATATAATAATAAAGTATAAGTATATATAT
1 ATATATATATATATAAT-ATAAAGTATAAGTATA-CTAT
* *
578606 ATATATATATATATATATATAAATATATAAAGTATATTAT
1 ATATATATATATATA-ATATAAA-GTAT-AAGTATACTAT
* * * * *
578646 AAAGATTAAAGTATATAAGCATATAA-TATAAAGCATA-TA-
1 ATATA-TATA-TATATAA-TATA-AAGTAT-AAGTATACTAT
* *
578685 AGTATATA-ATATAAAATATATAAATATTAA--ATA-TAT
1 A-TATATATATATATAATATA-AAGTA-TAAGTATACTAT
* *
578721 A-AGTATATA-ATATAA-AGTATA-TATAACTATAAACTAT
1 ATA-TATATATATATAATA-TAAAGTATAAGTAT--ACTAT
** *
578758 ATATATATATATATAAGT-TTTAGTATAA--A-GC-AT
1 ATATATATATATATAA-TATAAAGTATAAGTATACTAT
* **
578791 ATATAT-TATATA-AAGTATATAAGTGTGTGTATA-T--
1 ATATATATATATATAA-TATA-AAGTATAAGTATACTAT
* *
578825 --ATATATATATAT-ATATAAAGTTTTAGTATAAACTAT
1 ATATATATATATATAATATAAAGTATAAGTAT--ACTAT
* *
578861 ATATACATATA-ATAATATAAAGTATAAGTATATTAT
1 ATATATATATATATAATATAAAGTATAAGTATACTAT
* *
578897 ATATATATATATA-AAGTAT-AATTATAA--AGACTA-
1 ATATATATATATATAA-TATAAAGTATAAGTATACTAT
* *
578930 AAATATA-AGTATATAATATAAAGTATATAAAGTATA-TAC
1 ATATATATA-TATATAATATAAAG--TAT-AAGTATACTAT
*
578969 ATATAAAGTATA-AGT-ATATATAAGCTATAAAGTATA-TAT
1 ATATATA-TATATA-TAATATA-AAG-TAT-AAGTATACTAT
* * *
579008 ATATAGTTTTAGTATATAATATAAATTATAAAAGTATA-TAC
1 ATATA--TATA-TATATAATATAAAGTAT--AAGTATACTAT
* ** *
579049 ATATAAAGTATA-AGCATATAAAGTATAAAGTATAAGTAT
1 ATATATA-TATATATAATATAAAGTAT-AAGTAT-ACTAT
**
579088 ATATATGGATATA-AAGTATAAAGTATAAGTATA-TAT
1 ATATATATATATATAA-TATAAAGTATAAGTATACTAT
579124 ATATATATATA
1 ATATATATATA
579135 AAGTTTTAGT
Statistics
Matches: 407, Mismatches: 56, Indels: 135
0.68 0.09 0.23
Matches are distributed among these distances:
31 13 0.03
32 19 0.05
33 35 0.09
34 15 0.04
35 17 0.04
36 47 0.12
37 37 0.09
38 59 0.14
39 78 0.19
40 28 0.07
41 42 0.10
42 15 0.04
43 2 0.00
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (37 bp):
ATATATATATATATAATATAAAGTATAAGTATACTAT
Found at i:578916 original size:7 final size:7
Alignment explanation
Indices: 578906--579434 Score: 212
Period size: 7 Copynumber: 74.4 Consensus size: 7
578896 TATATATATA
578906 TATAAAG
1 TATAAAG
*
578913 TAT-AAT
1 TATAAAG
578919 TATAAAG
1 TATAAAG
*
578926 -ACTAAAA
1 TA-TAAAG
578933 TAT-AAG
1 TATAAAG
578939 TATATAA-
1 TATA-AAG
578946 TATAAAG
1 TATAAAG
578953 TATATAAAG
1 --TATAAAG
578962 TATATACA-
1 TATA-A-AG
578970 TATAAAG
1 TATAAAG
578977 TAT-AAG
1 TATAAAG
578983 TATATATAAG
1 --TATA-AAG
578993 CTATAAAG
1 -TATAAAG
*
579001 TATATA-
1 TATAAAG
*
579007 TATATAG
1 TATAAAG
**
579014 T-TTTAG
1 TATAAAG
579020 TATATAA-
1 TATA-AAG
*
579027 TATAAAT
1 TATAAAG
579034 TATAAAAG
1 TAT-AAAG
579042 TATATACA-
1 TATA-A-AG
579050 TATAAAG
1 TATAAAG
579057 TAT-AAG
1 TATAAAG
579063 CATATAAAG
1 --TATAAAG
579072 TATAAAG
1 TATAAAG
579079 TAT-AAG
1 TATAAAG
*
579085 TATATA-
1 TATAAAG
**
579091 TATGGA-
1 TATAAAG
579097 TATAAAG
1 TATAAAG
579104 TATAAAG
1 TATAAAG
579111 TAT-AAG
1 TATAAAG
579117 TATATATA-
1 TATA-A-AG
*
579125 TATATA-
1 TATAAAG
579131 TATAAAG
1 TATAAAG
**
579138 T-TTTAG
1 TATAAAG
579144 TATATAA-
1 TATA-AAG
579151 TATAAAG
1 TATAAAG
*
579158 TATTAAAA
1 TA-TAAAG
579166 TATATAA-
1 TATA-AAG
579173 TATAAAG
1 TATAAAG
579180 TATATAAG
1 TATA-AAG
579188 TACATATACA-
1 T--ATA-A-AG
579198 TATAAAG
1 TATAAAG
579205 TAT-AAG
1 TATAAAG
579211 TATATATA-
1 TATA-A-AG
*
579219 TATAAAC
1 TATAAAG
579226 TATAAAG
1 TATAAAG
579233 TAT-AAG
1 TATAAAG
*
579239 TATATA-
1 TATAAAG
579245 TATAAAAG
1 TAT-AAAG
579253 T-TATAAG
1 TATA-AAG
579260 TATTAAAG
1 TA-TAAAG
* *
579268 TATATAC
1 TATAAAG
579275 TATAAAG
1 TATAAAG
579282 TAT-AAG
1 TATAAAG
579288 T-TATAAG
1 TATA-AAG
579295 TATTAAA-
1 TA-TAAAG
579302 TATAAAG
1 TATAAAG
579309 TATTAAAG
1 TA-TAAAG
*
579317 TATACCA-
1 TATA-AAG
579324 TATAAAG
1 TATAAAG
579331 TATTAAAG
1 TA-TAAAG
*
579339 TATATAAA
1 TATA-AAG
579347 TATAAA-
1 TATAAAG
579353 TATTAAA-
1 TA-TAAAG
579360 TATAAAG
1 TATAAAG
*
579367 TATATATG
1 TATA-AAG
579375 TATATAAG
1 TATA-AAG
579383 TATATAA-
1 TATA-AAG
579390 TATAAAG
1 TATAAAG
*
579397 TATTAAAC
1 TA-TAAAG
579405 TATATAA-
1 TATA-AAG
579412 TAT-AAG
1 TATAAAG
579418 TATACAA-
1 TATA-AAG
579425 TATAAAG
1 TATAAAG
579432 TAT
1 TAT
579435 TACAGTATAT
Statistics
Matches: 414, Mismatches: 35, Indels: 146
0.70 0.06 0.25
Matches are distributed among these distances:
5 3 0.01
6 108 0.26
7 161 0.39
8 110 0.27
9 22 0.05
10 9 0.02
11 1 0.00
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (7 bp):
TATAAAG
Found at i:578949 original size:70 final size:69
Alignment explanation
Indices: 578755--579214 Score: 211
Period size: 69 Copynumber: 6.4 Consensus size: 69
578745 AACTATAAAC
* * * * * *
578755 TATATATATATATATAT-AAGTTTTAGTATAAAGC-ATATATATTATATAA-AGTATATAAGTGT
1 TATATATATATATATATAAAGTATAAGTATAAA-CTAAATATA-CATATAATAATATA-AAGTAT
**
578817 GTGTATA
63 AAGTATA
* * *
578824 TATATATATATATATATAAAGTTTTAGTATAAACTATATATACATATAATAATATAAAGTATAAG
1 TATATATATATATATATAAAGTATAAGTATAAACTAAATATACATATAATAATATAAAGTATAAG
578889 TATA
66 TATA
*
578893 T-TATATATATATATATAAAGTATAATTATAAAGACTAAAATATA-AGTAT-ATAATATAAAGTA
1 TATATATATATATATATAAAGTATAAGTAT-AA-ACT-AAATATACA-TATAATAATATAAAG--
578955 TATAAAGTATA
60 TAT-AAGTATA
* * * * * * ** *
578966 TACATATAAAGTATA-AGTATA-TATAAGCTATAAAGTATATATATATAGTTTTAGTATATAA-T
1 TATATATATA-TATATA-TAAAGTATAAG-TATAAACTAAATATACATA-TAATAATATA-AAGT
*
579028 ATAAAT-TA
61 ATAAGTATA
* * *
579036 TA-AAAGTATATACATATAAAGTATAAGCATATAAAGTATAAAGTATA-AGTATATATATGGATA
1 TATATA-TATATATATATAAAGTATAAG--TATAAA--CTAAA-TATACA-TATA-ATA---ATA
579099 TAAAGTATAAAGTATAA
55 TAAAGTAT-AAGTAT-A
* * *
579116 GTATATATATATATATATAAAGTTTTAGTAT--A-T-AATATAAAGTATTAA-AATATATAA-TA
1 -TATATATATATATATATAAAGTATAAGTATAAACTAAATATACA-TA-TAATAATATA-AAGTA
579175 TAAAGTATA
62 T-AAGTATA
* *
579184 TA-AGTACATATACATATAAAGTATAAGTATA
1 TATA-TATATATATATATAAAGTATAAGTATA
579215 TATATATAAA
Statistics
Matches: 313, Mismatches: 37, Indels: 83
0.72 0.09 0.19
Matches are distributed among these distances:
66 1 0.00
67 24 0.08
68 26 0.08
69 60 0.19
70 58 0.19
71 18 0.06
72 19 0.06
73 24 0.08
74 31 0.10
75 12 0.04
76 2 0.01
77 8 0.03
78 3 0.01
79 4 0.01
80 1 0.00
81 20 0.06
82 2 0.01
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (69 bp):
TATATATATATATATATAAAGTATAAGTATAAACTAAATATACATATAATAATATAAAGTATAAG
TATA
Found at i:578957 original size:22 final size:22
Alignment explanation
Indices: 578652--579451 Score: 320
Period size: 22 Copynumber: 36.8 Consensus size: 22
578642 TTATAAAGAT
*
578652 TAAAGTATATAAGCATATAATA
1 TAAAGTATATAAGTATATAATA
*
578674 TAAAGCATATAAGTATATAATA
1 TAAAGTATATAAGTATATAATA
* *
578696 TAAAATATATAAATAT-TAAATA
1 TAAAGTATATAAGTATAT-AATA
*
578718 TATAAGTATATAA-TATAAAGTATA
1 TA-AAGTATATAAGTATATA--ATA
* *
578742 TATAACTATA-AACTATAT-ATA
1 TA-AAGTATATAAGTATATAATA
* * *
578763 TATA-TATATAAGT-TTTAGTA
1 TAAAGTATATAAGTATATAATA
*
578783 TAAAGCATAT-A-TAT-T-ATA
1 TAAAGTATATAAGTATATAATA
* * *
578801 TAAAGTATATAAGTGTGT-GTA
1 TAAAGTATATAAGTATATAATA
*
578822 TATA-TATAT-A-TATAT-ATA
1 TAAAGTATATAAGTATATAATA
*
578840 TAAAGT-T-TTAGTATA-AACTA
1 TAAAGTATATAAGTATATAA-TA
* *
578860 TATA-TACAT-A-TA-ATAATA
1 TAAAGTATATAAGTATATAATA
578878 TAAAG--TATAAGTATATTATATA
1 TAAAGTATATAAGTATA-TA-ATA
* *
578900 TATA-TATATAAAGTATA-ATTA
1 TAAAGTATAT-AAGTATATAATA
578921 TAAAGACTAAAATATAAGTATATAATA
1 TAAAG--T---ATATAAGTATATAATA
578948 TAAAGTATATAAAGTATATACATA
1 TAAAGTATAT-AAGTATATA-ATA
578972 TAAAG--TATAAGTATATATAAGCTA
1 TAAAGTATATAAG--TATATAA--TA
*
578996 TAAAGTATAT-A-TATATAGT-
1 TAAAGTATATAAGTATATAATA
**
579015 TTTAGTATATAA-TATA-AATTA
1 TAAAGTATATAAGTATATAA-TA
579036 TAAAAGTATATACA-TATA-AAGTA
1 T-AAAGTATATA-AGTATATAA-TA
*
579059 T-AAGCATATAAAGTATA-AAGTA
1 TAAAGTATAT-AAGTATATAA-TA
*
579081 T-AAGTATATATATGGATATAAAGTA
1 TAAAGTATATA-A-GTATAT-AA-TA
579106 TAAAG--TATAAGTATATATATA
1 TAAAGTATATAAGTATATA-ATA
* *
579127 TATATA-TAAAGTTTTAGTATATAATA
1 TA-A-AGT--A-TATAAGTATATAATA
*
579153 TAAAGTAT-TAAAATATATAATA
1 TAAAGTATAT-AAGTATATAATA
579175 TAAAGTATATAAGTACATATACATA
1 TAAAGTATATAAGT--ATATA-ATA
579200 TAAAG--TATAAGTATATATATA
1 TAAAGTATATAAGTATATA-ATA
* *
579221 TAAACTATA-AAGTATA-AGTA
1 TAAAGTATATAAGTATATAATA
* *
579241 TATA-TATAAAAGT-TATAAGTA
1 TAAAGTATATAAGTATATAA-TA
*
579262 TTAAAGTATAT-ACTATA-AAGTA
1 -TAAAGTATATAAGTATATAA-TA
579284 T-AAGT-TATAAGTAT-TAAATA
1 TAAAGTATATAAGTATAT-AATA
**
579304 TAAAGTAT-TAAAGTATACCATA
1 TAAAGTATAT-AAGTATATAATA
579326 TAAAGTAT-TAAAGTATATAAATA
1 TAAAGTATAT-AAGTATAT-AATA
*
579349 TAAA-TAT-TAAATATA-AAGTA
1 TAAAGTATATAAGTATATAA-TA
*
579369 TATATGTATATAAGTATATAATA
1 TA-AAGTATATAAGTATATAATA
*
579392 TAAAGTAT-TAAACTATATAATA
1 TAAAGTATAT-AAGTATATAATA
*
579414 T-AAGTATACAA-TATA-AAGTA
1 TAAAGTATATAAGTATATAA-TA
* *
579434 TTACAGTATATAAATATA
1 -TAAAGTATATAAGTATA
579452 GAGTTATATA
Statistics
Matches: 611, Mismatches: 69, Indels: 195
0.70 0.08 0.22
Matches are distributed among these distances:
17 3 0.00
18 28 0.05
19 45 0.07
20 63 0.10
21 83 0.14
22 196 0.32
23 84 0.14
24 51 0.08
25 18 0.03
26 18 0.03
27 22 0.04
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.37
Consensus pattern (22 bp):
TAAAGTATATAAGTATATAATA
Found at i:579129 original size:124 final size:120
Alignment explanation
Indices: 578939--579352 Score: 114
Period size: 124 Copynumber: 3.3 Consensus size: 120
578929 AAAATATAAG
* * *
578939 TATATAATATAAAGTATATAA-AGTATATACATATAAAGTATAAGTATATATAAGCTATAAAGTA
1 TATATAATATAAAG-ATATAAGA-CATATAAATATAAAGTATAAGTATATAT-A--TATAAACTA
* * *
579003 TATA-TATATAGT-TTTAGTATATA-ATATAAA-TTATAAAAGTATATACATATAAAGTA-TAAG
61 TAAAGTATA-AGTATATA-TATATATATATAAAGTT-T--TAGTATATA-ATATAAAGTATTAA-
*
579063 CA
119 AA
* * *
579065 TATA-AAGTATAAAG-TATAAGTATATATATGGATATAAAGTATAAAGTATA-AGTATATATA-T
1 TATATAA-TATAAAGATATAAG-ACATATA--AATATAAAGTAT-AAGTATATA-TATATAAACT
* * * *
579126 ATATA-TATAAAGT-TTTAGTATATA-ATATAAAGTATTAAAATATATAATATAAAGTATATAAG
60 ATAAAGTAT-AAGTATATA-TATATATATATAAAGT-TT-TAGTATATAATATAAAGTAT-TAA-
*
579188 TA
119 AA
* * * *
579190 CATATACATATAAAGTATAAGTATATATATATAAACTATAAAGTATAAGTATATATATA-AAAGT
1 TATATA-ATATAAAG-AT-A-TA-AGACATATAAA-TATAAAGTATAAGTATATATATATAAACT
*
579254 -TATAAGTATTAAAGTATATACTATA-A-AGTAT-AAGTTATAAGTAT-TAAATATAAAGTATTA
60 ATA-AAGTA-T-AAGTATATA-TATATATA-TATAAAGTT-TTAGTATAT-AATATAAAGTATTA
*
579314 AAG
118 AAA
** *
579317 TATACCATATAAAG-TATTAA-AGTATATAAATATAAA
1 TATATAATATAAAGATA-TAAGA-CATATAAATATAAA
579353 TATTAAATAT
Statistics
Matches: 240, Mismatches: 18, Indels: 65
0.74 0.06 0.20
Matches are distributed among these distances:
121 7 0.03
122 9 0.04
123 13 0.05
124 45 0.19
125 24 0.10
126 29 0.12
127 21 0.09
128 27 0.11
129 32 0.13
130 22 0.09
131 11 0.05
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.36
Consensus pattern (120 bp):
TATATAATATAAAGATATAAGACATATAAATATAAAGTATAAGTATATATATATAAACTATAAAG
TATAAGTATATATATATATATATAAAGTTTTAGTATATAATATAAAGTATTAAAA
Found at i:579364 original size:58 final size:57
Alignment explanation
Indices: 579096--579443 Score: 181
Period size: 57 Copynumber: 6.0 Consensus size: 57
579086 ATATATATGG
* * * * *
579096 ATATAAAGTA-TAAAGTATA-AGTATATA-TATATATATATAAAGT-TT-TAGTATATA
1 ATATAAAGTATTAAACTATATAATATA-AGTAT-TAAATATAAAGTATTAAAGTATACA
* *
579150 ATATAAAGTATTAAAATATATAATATAAAGTATATAAGTACATATACA-TA-TAAAGTATA-A
1 ATATAAAGTATTAAACTATATAATAT-AAGTAT-T-A--A-ATATAAAGTATTAAAGTATACA
* * *
579210 GTATATA-TATATAAACTATA-AAGTATAAGTA-TATATATAAA--AGTTATAAGTATTA-A
1 ATATAAAGTAT-TAAACTATATAA-TATAAGTATTAAATATAAAGTA-TTA-AAGTA-TACA
* * * * *
579266 AGTATATACTA-TAAAGTATA-AGTTATAAGTATTAAATATAAAGTATTAAAGTATACC
1 A-TATAAAGTATTAAACTATATA-ATATAAGTATTAAATATAAAGTATTAAAGTATACA
* * *
579323 ATATAAAGTATTAAAGTATATAAATATAAATATTAAATATAAAGTATATATGTATATAAGTATAT
1 ATATAAAGTATTAAACTATAT-AATATAAGTATTAAATATAAAG----TA--T-TA-AAGTATAC
579388 A
57 A
*
579389 ATATAAAGTATTAAACTATATAATATAAGTA-TACAATATAAAGTATTACAGTATA
1 ATATAAAGTATTAAACTATATAATATAAGTATTA-AATATAAAGTATTAAAGTATA
579444 TAAATATAGA
Statistics
Matches: 235, Mismatches: 24, Indels: 67
0.72 0.07 0.21
Matches are distributed among these distances:
52 1 0.00
53 6 0.03
54 12 0.05
55 13 0.06
56 35 0.15
57 43 0.18
58 27 0.11
59 13 0.06
60 19 0.08
61 14 0.06
62 2 0.01
64 3 0.01
65 20 0.09
66 27 0.11
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (57 bp):
ATATAAAGTATTAAACTATATAATATAAGTATTAAATATAAAGTATTAAAGTATACA
Found at i:579373 original size:30 final size:29
Alignment explanation
Indices: 578896--579434 Score: 188
Period size: 30 Copynumber: 18.1 Consensus size: 29
578886 AAGTATATTA
* *
578896 TATATATATATATAAAGTATAATTATAAAG
1 TATATATAAATAT-AAGTATAAATATAAAG
*
578926 -A-CTA-AAATATAAGTATATAATATAAAG
1 TATATATAAATATAAGTATA-AATATAAAG
578953 TATATA-AAGTATATACA-TATAAAGTAT-AAG
1 TATATATAA--ATATA-AGTATAAA-TATAAAG
* * *
578983 TATATATAAGCTATAAAGTATATATATATAG
1 TATATATAA-ATAT-AAGTATAAATATAAAG
*
579014 T-T-T-TAGTATATAA-TATAAATTATAAAAG
1 TATATATA-AATATAAGTATAAA-TAT-AAAG
* *
579042 TATATACATATA-AAGTATAAGCATATAAAG
1 TATATATAAATATAAGTATAA--ATATAAAG
* **
579072 TATAAAGTATAAGTATATA-TATGGATATAAAG
1 TAT--A-TATAAATATA-AGTATAAATATAAAG
* *
579104 --TATA-AAGTATAAGTAT--ATATATA-
1 TATATATAAATATAAGTATAAATATAAAG
* *
579127 TATATATAAAGTTTTAGTATATAATATAAAG
1 TATATATAAA-TATAAGTATA-AATATAAAG
*
579158 TAT-TA-AAATATATAATATAAAGTATATAAG
1 TATATATAAATATA-AGTATAAA-TATA-AAG
* * *
579188 TACATATACATATAAAGTATAAGTAT--A-
1 TATATATAAATAT-AAGTATAAATATAAAG
*
579215 TATATATAAACTATAAAGTATAAGTAT--A-
1 TATATATAAA-TAT-AAGTATAAATATAAAG
* *
579243 TATATA-AAAGTTATAAGTATTAAAGTATATAC
1 TATATATAAA--TATAAGTA-TAAA-TATAAAG
*
579275 TATAAAGTATAAGTTATAAGTATTAAATATAAAG
1 TAT--A-TATAA-ATATAAGTA-TAAATATAAAG
*
579309 TAT-TA-AAGTATACCA-TATAAAGTATTAAAG
1 TATATATAAATATA--AGTATAAA-TA-TAAAG
*
579339 --TATATAAATATAAATATTAAATATAAAG
1 TATATATAAATATAAGTA-TAAATATAAAG
**
579367 TATATATGTATATAAGTATATAATATAAAG
1 TATATATAAATATAAGTATA-AATATAAAG
579397 TATTAAACTATATAATATAAGTATACAATATAAAG
1 TA-T--A-TATA-AATATAAGTATA-AATATAAAG
579432 TAT
1 TAT
579435 TACAGTATAT
Statistics
Matches: 396, Mismatches: 45, Indels: 132
0.69 0.08 0.23
Matches are distributed among these distances:
24 6 0.02
25 5 0.01
26 24 0.06
27 43 0.11
28 62 0.16
29 38 0.10
30 92 0.23
31 37 0.09
32 25 0.06
33 7 0.02
34 17 0.04
35 38 0.10
36 2 0.01
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (29 bp):
TATATATAAATATAAGTATAAATATAAAG
Found at i:579378 original size:36 final size:36
Alignment explanation
Indices: 578568--579451 Score: 322
Period size: 36 Copynumber: 24.3 Consensus size: 36
578558 ATTTAAAACA
*
578568 TATATACATATATAATAATAAAGTAT-AAGTATAT-A-
1 TATATAAATATATAAT-ATAAA-TATAAAGTATATAAG
* *
578603 TATATATATATAT-ATATATATATAAA-TATATAAAG
1 TATATAAATATATAATATAAATATAAAGTATAT-AAG
* *
578638 TATAT---TATA-AAGATTAAAGTATATAAGCATATAA-
1 TATATAAATATATAATA-TAAA-TATA-AAGTATATAAG
** * *
578672 TATA-AAGCATATAAGTATATAATATAAAATATATAAA
1 TATATAAATATATAA-TATA-AATATAAAGTATATAAG
578709 TAT-TAAATATATAAGTATATAATATAAAGTATAT-A-
1 TATATAAATATATAA-TATA-AATATAAAGTATATAAG
* *
578744 TAACTATAAACTATAT-ATATATATATATAAGT-T-TTAG
1 T-A-TATAAA-TATATAATATAAATATA-AAGTATATAAG
** *
578781 TATA-AAGCATAT-ATAT-TATATAAAGTATATAAGTG
1 TATATAAATATATAATATAAATATAAAGTATATAA--G
* * * * *
578816 TGTGTATATATATATATATATATATAAAGT-T-TTAG
1 TATATAAATATATA-ATATAAATATAAAGTATATAAG
578851 TATA-AACTATATATACATATAATAATATAAAG--TATAAG
1 TATATAA--ATATATA-ATAT-A-AATATAAAGTATATAAG
* *
578889 TATATTATATATATATATATAAAGTAT-AATTATA-AAG
1 TATA-TAAATATATA-ATATAAA-TATAAAGTATATAAG
*
578926 -ACTA-AAATATA-AGTATATAATATAAAGTATATAAAG
1 TA-TATAAATATATAATATA-AATATAAAGTATAT-AAG
*
578962 TATATACATATA-AAGTATAAGTATATATAAGCTATA-AAG
1 TATATAAATATATAA-TATAA--ATATA-AAG-TATATAAG
* * * *
579001 TATATATATATAGTTTTAGTATATAATATAAATTATAAAAG
1 TATATA-A-ATA--TATAATATA-AATATAAAGTATATAAG
*
579042 TATATACATATA-AAGTATAAGCATATAAAGTATA-AAG
1 TATATAAATATATAA-TATAA--ATATAAAGTATATAAG
* *
579079 TATAAGTATATATATGGATATAAAGTATAAAG--TATAAG
1 TAT-A-TAAATATAT-AATATAAA-TATAAAGTATATAAG
* **
579117 TATATATATATAT-ATATAAAGT-TTTAGTATATAA-
1 TATATAAATATATAATATAAA-TATAAAGTATATAAG
* *
579151 TATA-AAGTATTAAAATATATAATATAAAGTATATAAG
1 TATATAAATA-TATAATATA-AATATAAAGTATATAAG
* * *
579188 TACATATACATATA-AAGTATAAGTATATA-TATATAA-
1 T--ATATAAATATATAA-TATAAATATAAAGTATATAAG
* *
579224 -ACTATAAAGTATA-AGTATATATATAAAAGT-TATAAG
1 TA-TATAAA-TATATAATATAAATAT-AAAGTATATAAG
*
579260 TAT-TAAAGTATATACTATAAAGTAT-AAGT-TATAAG
1 TATATAAA-TATATAATATAAA-TATAAAGTATATAAG
*
579295 TAT-TAAATATA-AAGTATTAAAGTATACCA-TATA-AAG
1 TATATAAATATATAA-TA-TAAA-TATA-AAGTATATAAG
579331 TAT-TAAAGTATATAAATATAAATATTAAA-TATA-AAG
1 TATATAAA-TATAT-AATATAAATA-TAAAGTATATAAG
** *
579367 TATATATGTATATAAGTATATAATATAAAGTAT-TAAAC
1 TATATAAATATATAA-TATA-AATATAAAGTATAT-AAG
*
579405 TATAT-AATATA-AGTATACAATATAAAGTAT-TACAG
1 TATATAAATATATAATATA-AATATAAAGTATATA-AG
579440 TATATAAATATA
1 TATATAAATATA
579452 GAGTTATATA
Statistics
Matches: 668, Mismatches: 75, Indels: 211
0.70 0.08 0.22
Matches are distributed among these distances:
31 4 0.01
32 21 0.03
33 34 0.05
34 57 0.09
35 119 0.18
36 126 0.19
37 122 0.18
38 81 0.12
39 57 0.09
40 16 0.02
41 19 0.03
42 5 0.01
43 5 0.01
44 2 0.00
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.37
Consensus pattern (36 bp):
TATATAAATATATAATATAAATATAAAGTATATAAG
Found at i:579450 original size:58 final size:59
Alignment explanation
Indices: 578930--579451 Score: 213
Period size: 58 Copynumber: 8.7 Consensus size: 59
578920 ATAAAGACTA
*
578930 AAATATAAGTA-TATAATATAAAGTATATAAAGTATATACATATAAAGTA-TAAGTA-TATAT
1 AAATATAAGTATTA-AATATAAAGTAT-TAAAGTATATAAATATAAAGTATTAA--ACTATAT
* * * * * * *
578990 AAGCTATAAAGTA-TATATATATAGT-TT-TAGTATAT-AATATAAATTATAAAAGTATAT
1 AA-ATAT-AAGTATTAAATATAAAGTATTAAAGTATATAAATATAAAGTATTAAACTATAT
* * * * *
579047 ACATATAAAGTA-TAAGCATATAAAGTA-TAAAGTATA-AGTATATATATGGATATAAAGTATA-
1 AAATAT-AAGTATTAA--ATATAAAGTATTAAAGTATATA-AATATA-AAGTAT-TAAACTATAT
* * * *
579108 AAGTATAAGTA-TATATATATA-TATATAAAGTTTTAGTATATAATATAAAGTATTAAAATATAT
1 AAATATAAGTATTAAATATAAAGTAT-TAAAG---TA-TATA-AATATAAAGTATTAAACTATAT
* * *
579171 -AATATAAAGTATATAAGTACATATACA-TA-TAAAG--TATAAGTATATA-TATATAAACTATA
1 AAATAT-AAGTAT-T-A--A-ATATAAAGTATTAAAGTATATAAATATAAAGTAT-TAAACTATA
579230 -
59 T
* * * * *
579230 AAGTATAAGTA-TATATATAAA--AGTTATAAGTAT-TAAAGTATATACTA-TAAAGTATA-
1 AAATATAAGTATTAAATATAAAGTA-TTA-AAGTATATAAA-TATAAAGTATTAAACTATAT
** ** *
579286 AGTTATAAGTATTAAATATAAAGTATTAAAGTATA-CCATATAAAGTATTAAAGTATAT
1 AAATATAAGTATTAAATATAAAGTATTAAAGTATATAAATATAAAGTATTAAACTATAT
*
579344 AAATATAAATATTAAATATAAAGTATATATGTATA-TAAGTATATAATATAAAGTATTAAACTAT
1 AAATATAAGTATTAAATATAAAGTAT-TA---A-AGT-A-TATA-AATATAAAGTATTAAACTAT
579408 AT
58 AT
*
579410 -AATATAAGTA-TACAATATAAAGTATTACAGTATATAAATATA
1 AAATATAAGTATTA-AATATAAAGTATTAAAGTATATAAATATA
579452 GAGTTATATA
Statistics
Matches: 357, Mismatches: 52, Indels: 108
0.69 0.10 0.21
Matches are distributed among these distances:
52 1 0.00
53 6 0.02
54 2 0.01
55 3 0.01
56 40 0.11
57 50 0.14
58 58 0.16
59 27 0.08
60 35 0.10
61 23 0.06
62 31 0.09
63 13 0.04
64 12 0.03
65 22 0.06
66 21 0.06
67 5 0.01
69 8 0.02
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.36
Consensus pattern (59 bp):
AAATATAAGTATTAAATATAAAGTATTAAAGTATATAAATATAAAGTATTAAACTATAT
Found at i:579463 original size:35 final size:34
Alignment explanation
Indices: 579257--579463 Score: 137
Period size: 35 Copynumber: 6.0 Consensus size: 34
579247 TAAAAGTTAT
* *
579257 AAGTATTAAAGTATAT-ACTATAAAGTATAAGT-TA
1 AAGTATTAAAGTATATAAATAT-AAGT-TAAATATA
* *
579291 TAAGTATTAAA-TATA-AAGTATTAAAGTATACCATATA
1 -AAGTATTAAAGTATATAAATA-T-AAGT-TA-AATATA
*
579328 AAGTATTAAAGTATATAAATATAAATATTAAATATA
1 AAGTATTAAAGTATATAAATAT-AA-GTTAAATATA
* *
579364 AAGTA-TATATGTATATAAGTAT-A--T-AATATA
1 AAGTATTA-AAGTATATAAATATAAGTTAAATATA
*
579394 AAGTATTAAACTATAT-AATATAAGTATACAATATA
1 AAGTATTAAAGTATATAAATATAAGT-TA-AATATA
* *
579429 AAGTATTACAGTATATAAATATAGAGTTATATATA
1 AAGTATTAAAGTATATAAATATA-AGTTAAATATA
579464 TTAAATTATA
Statistics
Matches: 141, Mismatches: 14, Indels: 34
0.75 0.07 0.18
Matches are distributed among these distances:
29 4 0.03
30 18 0.13
31 3 0.02
33 1 0.01
34 8 0.06
35 46 0.33
36 41 0.29
37 15 0.11
38 5 0.04
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (34 bp):
AAGTATTAAAGTATATAAATATAAGTTAAATATA
Found at i:579468 original size:65 final size:66
Alignment explanation
Indices: 579099--579453 Score: 202
Period size: 65 Copynumber: 5.5 Consensus size: 66
579089 TATATGGATA
* * * *
579099 TAAAGTATAAAG--TATAAGTATATATATATA-TATATAAAGT-TT-TAGTATAT-AATATAAAG
1 TAAA-TATAAAGTATATAAGTATATAAATATAGAATATAAAGTATTAAACTATATAAATATAAA-
579158 TAT
64 TAT
* * * *
579161 TAAAATATATAA-TATA-AAGTATATAAGTACATATACATATAAAGTA-T-AAGTATATATATAT
1 T-AAATATA-AAGTATATAAGTATATAA--ATATAGA-ATATAAAGTATTAAACTATATAAATAT
579222 AAACTA-
61 AAA-TAT
* * *
579228 TAAAGTAT-AAGTATAT-A-TATA-AAAGTTATA-AGTATTAAAGTA-TATACTATA-AAGTATA
1 TAAA-TATAAAGTATATAAGTATATAAA--TATAGAATA-TAAAGTATTAAACTATATAAATATA
*
579286 AGT-T
62 AATAT
* ** *
579290 ATAAGTATTAAA-TATA-AAGTAT-TAAAGTATACCATATAAAGTATTAAAGTATATAAATATAA
1 -TAAATA-TAAAGTATATAAGTATATAAA-TATAGAATATAAAGTATTAAACTATATAAATATAA
579352 ATAT
63 ATAT
* * * *
579356 TAAATATAAAGTATATATGTATATAAGTATATAATATAAAGTATTAAACTATAT-AATATAAGTA
1 TAAATATAAAGTATATAAGTATATAAATATAGAATATAAAGTATTAAACTATATAAATATAAATA
579420 -
66 T
579420 TACAATATAAAGTAT-TACAGTATATAAATATAGA
1 TA-AATATAAAGTATATA-AGTATATAAATATAGA
579454 GTTATATATA
Statistics
Matches: 229, Mismatches: 31, Indels: 63
0.71 0.10 0.20
Matches are distributed among these distances:
62 11 0.05
63 49 0.21
64 37 0.16
65 61 0.27
66 38 0.17
67 24 0.10
68 9 0.04
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (66 bp):
TAAATATAAAGTATATAAGTATATAAATATAGAATATAAAGTATTAAACTATATAAATATAAATA
T
Found at i:579639 original size:81 final size:82
Alignment explanation
Indices: 579448--579842 Score: 617
Period size: 81 Copynumber: 5.0 Consensus size: 82
579438 AGTATATAAA
*
579448 TATAGAGTTATATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTAA
1 TATATAGTTATATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTAA
579513 AGCCTAAATTAATACAT
66 AGCCTAAATTAATACAT
579530 TATATAGTTATATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAAT-AAAATTTAA
1 TATATAGTTATATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTAA
579594 AGCCTAAATTAATACAT
66 AGCCTAAATTAATACAT
* *
579611 TATATAGTTATATATATTAAAATT-TAAAATTCGTAGGATCACATTGAAAT-AAA-AAAAACTTA
1 TATATAGTTATATATATT-AAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTA
*
579673 AAGCCTAAATTAATATAT
65 AAGCCTAAATTAATACAT
*
579691 TATATAGTTATATATATTAAATTATAAAATTCATAGG-TCAAATTGAAATAAAATAAAAATTTAA
1 TATATAGTTATATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTAA
579755 AGCCTAAA-T--T--A-
66 AGCCTAAATTAATACAT
579766 -ATATA--T-TATATATTAAATTAT-AAATTCGTAGGATCAAATTGAAAT-AAATAAAAATTTAA
1 TATATAGTTATATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTAA
579825 AGCCTAAATTAATACAT
66 AGCCTAAATTAATACAT
579842 T
1 T
579843 TTTTGGACTA
Statistics
Matches: 292, Mismatches: 8, Indels: 31
0.88 0.02 0.09
Matches are distributed among these distances:
70 32 0.11
71 28 0.10
72 1 0.00
73 1 0.00
74 5 0.02
75 1 0.00
76 1 0.00
78 1 0.00
79 16 0.05
80 61 0.21
81 86 0.29
82 59 0.20
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.35
Consensus pattern (82 bp):
TATATAGTTATATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTAA
AGCCTAAATTAATACAT
Found at i:579715 original size:161 final size:161
Alignment explanation
Indices: 579448--579842 Score: 616
Period size: 161 Copynumber: 2.5 Consensus size: 161
579438 AGTATATAAA
*
579448 TATAGAGTTATATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTAA
1 TATATAGTTATATATATTAAATT-TAAAATTCGTAGGATCAAATTGAAAT-AAATAAAAATTTAA
*
579513 AGCCTAAATTAATACATTATATAGTTATATATATTAAATTATAAAATTCGTAGGATCAAATTGAA
64 AGCCTAAATTAATACATTATATAGTTATATATATTAAATTATAAAATTCATAGG-TCAAATTGAA
579578 ATAAAAT-AAAATTTAAAGCCTAAATTAATACAT
128 ATAAAATAAAAATTTAAAGCCTAAATTAATACAT
* *
579611 TATATAGTTATATATATTAAAATTTAAAATTCGTAGGATCACATTGAAATAAA-AAAAACTTAAA
1 TATATAGTTATATATATT-AAATTTAAAATTCGTAGGATCAAATTGAAATAAATAAAAATTTAAA
*
579675 GCCTAAATTAATATATTATATAGTTATATATATTAAATTATAAAATTCATAGGTCAAATTGAAAT
65 GCCTAAATTAATACATTATATAGTTATATATATTAAATTATAAAATTCATAGGTCAAATTGAAAT
*
579740 AAAATAAAAATTTAAAGCCTAAATTAATATAT
130 AAAATAAAAATTTAAAGCCTAAATTAATACAT
579772 TATATA--T-TA-A-ATT--A--T-AAATTCGTAGGATCAAATTGAAATAAATAAAAATTTAAAG
1 TATATAGTTATATATATTAAATTTAAAATTCGTAGGATCAAATTGAAATAAATAAAAATTTAAAG
579827 CCTAAATTAATACATT
66 CCTAAATTAATACATT
579843 TTTTGGACTA
Statistics
Matches: 220, Mismatches: 9, Indels: 18
0.89 0.04 0.07
Matches are distributed among these distances:
150 26 0.12
151 27 0.12
153 1 0.00
156 3 0.01
157 1 0.00
158 2 0.01
159 1 0.00
160 17 0.08
161 92 0.42
162 3 0.01
163 42 0.19
164 5 0.02
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.35
Consensus pattern (161 bp):
TATATAGTTATATATATTAAATTTAAAATTCGTAGGATCAAATTGAAATAAATAAAAATTTAAAG
CCTAAATTAATACATTATATAGTTATATATATTAAATTATAAAATTCATAGGTCAAATTGAAATA
AAATAAAAATTTAAAGCCTAAATTAATACAT
Found at i:579830 original size:70 final size:71
Alignment explanation
Indices: 579701--579838 Score: 244
Period size: 70 Copynumber: 2.0 Consensus size: 71
579691 TATATAGTTA
579701 TATATATTAAATTATAAAATTCATAGGTCAAATTGAAATAAAATAAAAATTTAAAGCCTAAATTA
1 TATATATTAAATTATAAAATTCATAGGTCAAATTGAAATAAAATAAAAATTTAAAGCCTAAATTA
579766 ATATAT
66 ATATAT
*
579772 TATATATTAAATTAT-AAATTCGTAGGATCAAATTGAAAT-AAATAAAAATTTAAAGCCTAAATT
1 TATATATTAAATTATAAAATTCATAGG-TCAAATTGAAATAAAATAAAAATTTAAAGCCTAAATT
579835 AATA
65 AATA
579839 CATTTTTTGG
Statistics
Matches: 65, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
70 38 0.58
71 27 0.42
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.35
Consensus pattern (71 bp):
TATATATTAAATTATAAAATTCATAGGTCAAATTGAAATAAAATAAAAATTTAAAGCCTAAATTA
ATATAT
Found at i:581321 original size:16 final size:16
Alignment explanation
Indices: 581268--581313 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
581258 GTAATATAAA
581268 TCAGGTAAATGTCAAG
1 TCAGGTAAATGTCAAG
*
581284 TCAGATAAATGTCAAG
1 TCAGGTAAATGTCAAG
581300 TCAGGTAAATGTCA
1 TCAGGTAAATGTCA
581314 TATCAGGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (16 bp):
TCAGGTAAATGTCAAG
Found at i:586138 original size:59 final size:61
Alignment explanation
Indices: 586011--586178 Score: 220
Period size: 59 Copynumber: 2.8 Consensus size: 61
586001 TATAGGATAC
* *
586011 TACTTTCTTGAGT--CTTCTGACTATTAAAAGTTACAAAATGGTCCCTCAATGATATAAAAT
1 TACTTTGTTGAGTCACTTC-GACTATTAAAAGTTACAAAATGGTCCCTCGATGATATAAAAT
** *
586071 TACTTTGTTGAGTCAC-TCGACTATTAAAAGTTAC-AAATGGTCCCTCGATGATATGGAGT
1 TACTTTGTTGAGTCACTTCGACTATTAAAAGTTACAAAATGGTCCCTCGATGATATAAAAT
* * *
586130 TATTTTGTTGAGTCCCTTC-ACTATTAAAAGTTACAAAATGGTCACTCGA
1 TACTTTGTTGAGTCACTTCGACTATTAAAAGTTACAAAATGGTCCCTCGA
586179 CTATTCGTTA
Statistics
Matches: 96, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
59 50 0.52
60 43 0.45
61 2 0.02
62 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (61 bp):
TACTTTGTTGAGTCACTTCGACTATTAAAAGTTACAAAATGGTCCCTCGATGATATAAAAT
Done.