Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 103 of 335
Found at i:32450400 original size:24 final size:25
Alignment explanation
Indices: 32450352--32450400 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
32450342 TTTTATTCTT
* **
32450352 AAAAATTTAAAAATAACAATTTTAA
1 AAAAATTTAAAAATAAAAAAATTAA
32450377 AAAAATTT-AAAATAAAAAAATTAA
1 AAAAATTTAAAAATAAAAAAATTAA
32450401 TGGTTCATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAAATTTAAAAATAAAAAAATTAA
Found at i:32450562 original size:34 final size:35
Alignment explanation
Indices: 32450508--32450577 Score: 133
Period size: 34 Copynumber: 2.0 Consensus size: 35
32450498 TTATAAGTAA
32450508 AATAGTTTTTTTTTTAAAACCCACAAACAAGATTT
1 AATAGTTTTTTTTTTAAAACCCACAAACAAGATTT
32450543 AATAGTTTTTTTTTT-AAACCCACAAACAAGATTT
1 AATAGTTTTTTTTTTAAAACCCACAAACAAGATTT
32450577 A
1 A
32450578 CTTTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 20 0.57
35 15 0.43
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (35 bp):
AATAGTTTTTTTTTTAAAACCCACAAACAAGATTT
Found at i:32450587 original size:35 final size:34
Alignment explanation
Indices: 32450508--32450587 Score: 119
Period size: 34 Copynumber: 2.4 Consensus size: 34
32450498 TTATAAGTAA
32450508 AATAGTTTTTTTTTTAAAACCCACAAACAAGATTT
1 AATA-TTTTTTTTTTAAAACCCACAAACAAGATTT
32450543 AATAGTTTTTTTTTT-AAACCCACAAACAAGATTT
1 AATA-TTTTTTTTTTAAAACCCACAAACAAGATTT
*
32450577 ACT-TTTTTTTT
1 AATATTTTTTTT
32450588 AATTTATAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
32 8 0.18
34 21 0.48
35 15 0.34
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (34 bp):
AATATTTTTTTTTTAAAACCCACAAACAAGATTT
Found at i:32454665 original size:21 final size:20
Alignment explanation
Indices: 32454616--32454672 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
32454606 TAATGAAATA
32454616 ATGAT-AATGAGAATAAAACG
1 ATGATAAATGA-AATAAAACG
*
32454636 A-AATAAAATGAAATAAATACG
1 ATGAT-AAATGAAATAAA-ACG
32454657 ATGATAAATGAAATAA
1 ATGATAAATGAAATAA
32454673 CAAAACAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 2 0.06
20 7 0.23
21 20 0.65
22 2 0.06
ACGTcount: A:0.61, C:0.04, G:0.14, T:0.21
Consensus pattern (20 bp):
ATGATAAATGAAATAAAACG
Found at i:32455252 original size:3 final size:3
Alignment explanation
Indices: 32455241--32455483 Score: 75
Period size: 3 Copynumber: 78.7 Consensus size: 3
32455231 AAAAAAGAAG
* * * * * *
32455241 TAA TGA TAA TAA TAA TAA TAG GAG TAA TAA TAA TAA T-A TAA TGA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
32455288 TAAA CAA TAA TAA -AA GGAA CAA AAA TAA TAG TAA TAA TAA -AGA TATT
1 T-AA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TA-A TA-A
* ** *
32455335 TAA TAA TAG TAA TAA TAA CGA TGA T-A TAGA TAA TAA TATA TACA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TA-A TAA
* * * * * *
32455382 AAA TAA TAGT TAGA -AA TAA AAA TAA TGGAA GTAG TAA TAA CAA TAG
1 TAA TAA TA-A TA-A TAA TAA TAA TAA T--AA -TAA TAA TAA TAA TAA
* * * * * *
32455428 TAA TAG TAA TAA -AGA TAA CAG CAA GAA TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
32455473 TAA TAA TAA TA
1 TAA TAA TAA TA
32455484 TATTTAATTC
Statistics
Matches: 179, Mismatches: 45, Indels: 32
0.70 0.18 0.12
Matches are distributed among these distances:
2 9 0.05
3 147 0.82
4 20 0.11
5 2 0.01
6 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:32460049 original size:46 final size:46
Alignment explanation
Indices: 32459993--32460087 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
32459983 AAAAATTGAG
32459993 ATTAAATTATAAAGTTCAAGAGTTTAAAGCTAAAAACTACAATTTT
1 ATTAAATTATAAAGTTCAAGAGTTTAAAGCTAAAAACTACAATTTT
32460039 ATTAAATTATAAAGTTCAAGAGTTTAAAGCTAAAAACTACAATTTT
1 ATTAAATTATAAAGTTCAAGAGTTTAAAGCTAAAAACTACAATTTT
32460085 ATT
1 ATT
32460088 TTATTTTATC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.36
Consensus pattern (46 bp):
ATTAAATTATAAAGTTCAAGAGTTTAAAGCTAAAAACTACAATTTT
Found at i:32460435 original size:2 final size:2
Alignment explanation
Indices: 32460428--32460459 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32460418 TTACTTAATT
32460428 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
32460460 AAAGGTGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32461366 original size:17 final size:18
Alignment explanation
Indices: 32461338--32461373 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
32461328 AAATTTGAAA
32461338 TTTTTATGTTTTAAATTT
1 TTTTTATGTTTTAAATTT
*
32461356 TTTTTAT-TTTTGAATTT
1 TTTTTATGTTTTAAATTT
32461373 T
1 T
32461374 AAAGAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTTTATGTTTTAAATTT
Found at i:32461412 original size:14 final size:14
Alignment explanation
Indices: 32461393--32461420 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
32461383 TTTATTTTTT
32461393 TATTTTTTAAATAA
1 TATTTTTTAAATAA
32461407 TATTTTTTAAATAA
1 TATTTTTTAAATAA
32461421 GAAAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTTTTTAAATAA
Found at i:32461446 original size:20 final size:20
Alignment explanation
Indices: 32461385--32461446 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
32461375 AAGAGTTATT
*
32461385 TATTTTTTTATTTTTTAAATAA
1 TATTTTTTAATTTTTT-AA-AA
* ****
32461407 TATTTTTTAAATAAGAAAAA
1 TATTTTTTAATTTTTTAAAA
32461427 TATTTTTTAATTTTTTAAAA
1 TATTTTTTAATTTTTTAAAA
32461447 AAATACGATA
Statistics
Matches: 29, Mismatches: 11, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
20 17 0.59
21 2 0.07
22 10 0.34
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TATTTTTTAATTTTTTAAAA
Found at i:32463387 original size:20 final size:21
Alignment explanation
Indices: 32463359--32463397 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
32463349 GTGCATGGGT
*
32463359 GCAATTTC-AGCTTTACAACA
1 GCAAGTTCAAGCTTTACAACA
*
32463379 GCAAGTTCAATCTTTACAA
1 GCAAGTTCAAGCTTTACAA
32463398 GCTGAACTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (21 bp):
GCAAGTTCAAGCTTTACAACA
Found at i:32468645 original size:25 final size:25
Alignment explanation
Indices: 32468611--32468668 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
32468601 CTAAGAAAGT
* *
32468611 TTTATAGAGAG-CTCACCAAAAATCC
1 TTTACAGAGAGTCT-ACCAAAAAGCC
* *
32468636 TTTACAGAGAGTCTACCATAAAGGC
1 TTTACAGAGAGTCTACCAAAAAGCC
32468661 TTTACAGA
1 TTTACAGA
32468669 ATATTAGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 26 0.93
26 2 0.07
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.26
Consensus pattern (25 bp):
TTTACAGAGAGTCTACCAAAAAGCC
Found at i:32468683 original size:25 final size:25
Alignment explanation
Indices: 32468655--32468787 Score: 94
Period size: 25 Copynumber: 5.3 Consensus size: 25
32468645 AGTCTACCAT
*
32468655 AAAGGCTTTACAGAATATTAGTCAC
1 AAAGGCTTTACAGAATATTAGCCAC
* * *
32468680 AAAGGTTTTACAG-ATAGCTCA-CCAA
1 AAAGGCTTTACAGAATA--TTAGCCAC
* * *
32468705 AAAGGCTTTACAAAATATTCGCCAT
1 AAAGGCTTTACAGAATATTAGCCAC
* * * **
32468730 AAAGGCTTTATA-AAGAAGTCCCCAC
1 AAAGGCTTTACAGAA-TATTAGCCAC
32468755 AAAGGCTTTACAGAATATTCA-CCAC
1 AAAGGCTTTACAGAATATT-AGCCAC
32468780 AAAGGCTT
1 AAAGGCTT
32468788 GGTTTGGTTT
Statistics
Matches: 83, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
24 6 0.07
25 70 0.84
26 7 0.08
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (25 bp):
AAAGGCTTTACAGAATATTAGCCAC
Found at i:32468711 original size:50 final size:49
Alignment explanation
Indices: 32468636--32468787 Score: 164
Period size: 50 Copynumber: 3.0 Consensus size: 49
32468626 CCAAAAATCC
* *
32468636 TTTACAGAGAGTCTACCATAAAGGCTTTACAGAATATTAGTCACAAAGG-T
1 TTTACAGA-AGTC-ACCAAAAAGGCTTTACAGAATATTAGCCACAAAGGCT
* * *
32468686 TTTACAGATAGCTCACCAAAAAGGCTTTACAAAATATTCGCCATAAAGGCT
1 TTTACAGA-AG-TCACCAAAAAGGCTTTACAGAATATTAGCCACAAAGGCT
* * *
32468737 TTATAAAGAAGTCCCCACAAAGGCTTTACAGAATATTCA-CCACAAAGGCT
1 TT-TACAGAAGTCACCAAAAAGGCTTTACAGAATATT-AGCCACAAAGGCT
32468787 T
1 T
32468788 GGTTTGGTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
50 74 0.86
51 7 0.08
52 5 0.06
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (49 bp):
TTTACAGAAGTCACCAAAAAGGCTTTACAGAATATTAGCCACAAAGGCT
Found at i:32471251 original size:12 final size:13
Alignment explanation
Indices: 32471234--32471265 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
32471224 AAACCCTAAT
32471234 TTTTCTTTT-TTC
1 TTTTCTTTTCTTC
32471246 TTTTCTTTTCTTC
1 TTTTCTTTTCTTC
32471259 -TTTCTTT
1 TTTTCTTT
32471266 CGCCCTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 16 0.84
13 3 0.16
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTCTTTTCTTC
Found at i:32471350 original size:16 final size:16
Alignment explanation
Indices: 32471339--32471374 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
32471329 ATTATTTAAT
32471339 TAATATAATATTATAA
1 TAATATAATATTATAA
*
32471355 TAATATAATATAATAA
1 TAATATAATATTATAA
32471371 TAAT
1 TAAT
32471375 TTCTTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATAATATTATAA
Found at i:32471430 original size:23 final size:21
Alignment explanation
Indices: 32471397--32471439 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
32471387 AAGTAATTAT
32471397 ATATATTTTACA-AGTGTATAC
1 ATATATTTTACACA-TGTATAC
32471418 ATATACTTATTACACATGTATA
1 ATATA-TT-TTACACATGTATA
32471440 TTATCATCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 11 0.58
24 1 0.05
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (21 bp):
ATATATTTTACACATGTATAC
Found at i:32473988 original size:16 final size:17
Alignment explanation
Indices: 32473947--32473988 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
32473937 TTATAATTTT
32473947 GTATATGTTAAATATAAA
1 GTATAT-TTAAATATAAA
32473965 GT-TAATTTAAA-ATAAA
1 GTAT-ATTTAAATATAAA
32473981 GTATATTT
1 GTATATTT
32473989 TTATTTTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 11 0.50
17 7 0.32
18 4 0.18
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (17 bp):
GTATATTTAAATATAAA
Found at i:32475145 original size:13 final size:13
Alignment explanation
Indices: 32475127--32475151 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32475117 GATAATAAAT
32475127 TATATATATATAA
1 TATATATATATAA
32475140 TATATATATATA
1 TATATATATATA
32475152 TATTTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATATAA
Found at i:32477261 original size:17 final size:17
Alignment explanation
Indices: 32477228--32477260 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
32477218 CCATTAGTCA
32477228 AAATGAAATAATATTTT
1 AAATGAAATAATATTTT
*
32477245 AAATGCAATAAT-TTTT
1 AAATGAAATAATATTTT
32477261 TTTTTTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (17 bp):
AAATGAAATAATATTTT
Found at i:32484703 original size:14 final size:14
Alignment explanation
Indices: 32484692--32484730 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
32484682 ATAATAAATT
32484692 ATATAAATTAAAAA
1 ATATAAATTAAAAA
*
32484706 ATATAAATTATGAAA
1 ATATAAATTA-AAAA
32484721 ATATGAAATT
1 ATAT-AAATT
32484731 TGTAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
15 7 0.32
16 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (14 bp):
ATATAAATTAAAAA
Found at i:32484737 original size:16 final size:15
Alignment explanation
Indices: 32484692--32484747 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
32484682 ATAATAAATT
*
32484692 ATATAAATTA-AAAA
1 ATATAAATTATGAAA
32484706 ATATAAATTATGAAA
1 ATATAAATTATGAAA
*
32484721 ATATGAAATT-TGTAA
1 ATAT-AAATTATGAAA
32484736 A-A-AAATTATGAA
1 ATATAAATTATGAA
32484748 TTTATATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
12 5 0.14
13 3 0.08
14 11 0.31
15 12 0.33
16 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (15 bp):
ATATAAATTATGAAA
Found at i:32485319 original size:18 final size:18
Alignment explanation
Indices: 32485298--32485333 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
32485288 ATTCAAGATG
32485298 TAATT-TTTATTAATTTTT
1 TAATTATTTA-TAATTTTT
32485316 TAATTATTTATAATTTTT
1 TAATTATTTATAATTTTT
32485334 GAAAGTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TAATTATTTATAATTTTT
Found at i:32487466 original size:21 final size:21
Alignment explanation
Indices: 32487366--32487503 Score: 136
Period size: 21 Copynumber: 6.6 Consensus size: 21
32487356 AAAGCTCGAA
32487366 AGCTAAACAGAAGCTCATAAG
1 AGCTAAACAGAAGCTCATAAG
* * *
32487387 AGCTGAACAAAAACTCATAAG
1 AGCTAAACAGAAGCTCATAAG
* *
32487408 AGCTGAACAGAAACTCATAAG
1 AGCTAAACAGAAGCTCATAAG
* * * *
32487429 AGTTGAACAGAAGCTCGTAGG
1 AGCTAAACAGAAGCTCATAAG
*
32487450 AGCTAAACAGAAGCTCGA-AAA
1 AGCTAAACAGAAGCTC-ATAAG
*
32487471 AACTAAACAGAAGCTCGA-AAG
1 AGCTAAACAGAAGCTC-ATAAG
*
32487492 AACTAAACAGAA
1 AGCTAAACAGAA
32487504 AGTAAAACAC
Statistics
Matches: 101, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
21 101 1.00
ACGTcount: A:0.49, C:0.18, G:0.20, T:0.13
Consensus pattern (21 bp):
AGCTAAACAGAAGCTCATAAG
Found at i:32491601 original size:3 final size:3
Alignment explanation
Indices: 32491593--32491646 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
32491583 AACCTTCACA
* * * *
32491593 TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TTT TAC TAT CTAA TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
32491638 TAT TAT TAT
1 TAT TAT TAT
32491647 ACTTATTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:32491750 original size:17 final size:16
Alignment explanation
Indices: 32491704--32491751 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
32491694 TTATTGTACG
32491704 TATATA-TATACTTTTA
1 TATATAGTATA-TTTTA
32491720 TATATAGTATTATTTTA
1 TATATAGTA-TATTTTA
*
32491737 TATATCATTATATTT
1 TATAT-AGTATATTT
32491752 ATTATTATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 6 0.21
17 17 0.61
18 5 0.18
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (16 bp):
TATATAGTATATTTTA
Found at i:32492370 original size:18 final size:17
Alignment explanation
Indices: 32492349--32492382 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
32492339 ATCGGATCCC
*
32492349 AAAAATTTTCGTGTTTTA
1 AAAAATTCTCGT-TTTTA
32492367 AAAAATTCTCGTTTTT
1 AAAAATTCTCGTTTTT
32492383 CAATCGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (17 bp):
AAAAATTCTCGTTTTTA
Found at i:32494925 original size:23 final size:23
Alignment explanation
Indices: 32494897--32494943 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
32494887 TGTGATGTAG
32494897 ATAAATAAAAAATAAATTGAATA
1 ATAAATAAAAAATAAATTGAATA
32494920 ATAAATAAAAAATAAATTGAATA
1 ATAAATAAAAAATAAATTGAATA
32494943 A
1 A
32494944 GCAAACTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (23 bp):
ATAAATAAAAAATAAATTGAATA
Found at i:32498131 original size:28 final size:24
Alignment explanation
Indices: 32498079--32498129 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
32498069 CAATAACTTT
*
32498079 TAAATTATTTTTTTATTTTAAAAA
1 TAAAATATTTTTTTATTTTAAAAA
32498103 TAAAATATTTATTTTATATCTTAAAAA
1 TAAAATATTT-TTTTAT-T-TTAAAAA
32498130 ATTAGAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 9 0.39
25 6 0.26
26 1 0.04
27 7 0.30
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TAAAATATTTTTTTATTTTAAAAA
Found at i:32508242 original size:6 final size:6
Alignment explanation
Indices: 32508231--32508271 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
32508221 TTTTTTTGAA
*
32508231 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG AAAGA
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGA
32508272 TTAATTTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:32508794 original size:16 final size:17
Alignment explanation
Indices: 32508775--32508818 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
32508765 GTTTTTATGG
32508775 TTTAGGGTTA-GATTTT
1 TTTAGGGTTATGATTTT
*
32508791 TTTAGGGTTTATGGTTTT
1 TTTAGGG-TTATGATTTT
32508809 TTTAAGGGTT
1 TTT-AGGGTT
32508819 TAATTAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.29
17 3 0.12
18 10 0.42
19 4 0.17
ACGTcount: A:0.16, C:0.00, G:0.27, T:0.57
Consensus pattern (17 bp):
TTTAGGGTTATGATTTT
Found at i:32508849 original size:26 final size:26
Alignment explanation
Indices: 32508818--32508885 Score: 136
Period size: 26 Copynumber: 2.6 Consensus size: 26
32508808 TTTTAAGGGT
32508818 TTAATTAATTAAATTAGGGTGTAAGA
1 TTAATTAATTAAATTAGGGTGTAAGA
32508844 TTAATTAATTAAATTAGGGTGTAAGA
1 TTAATTAATTAAATTAGGGTGTAAGA
32508870 TTAATTAATTAAATTA
1 TTAATTAATTAAATTA
32508886 AATATTAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (26 bp):
TTAATTAATTAAATTAGGGTGTAAGA
Found at i:32508908 original size:16 final size:17
Alignment explanation
Indices: 32508869--32508909 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
32508859 AGGGTGTAAG
32508869 ATTAATTAATTAAATTAA
1 ATTAATTAATTAAA-TAA
32508887 A-T-ATTAATTAAA-AA
1 ATTAATTAATTAAATAA
32508901 ATTAATTAA
1 ATTAATTAA
32508910 ATTCGGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.14
15 1 0.05
16 15 0.71
17 1 0.05
18 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAATTAATTAAATAA
Found at i:32509231 original size:126 final size:126
Alignment explanation
Indices: 32509038--32509377 Score: 403
Period size: 126 Copynumber: 2.7 Consensus size: 126
32509028 TATCTGGATA
* * * *
32509038 AGAAGAAGTTTCTGAAGAAATAGTATCCAAAACGCTTCAAGCAGGATGCACTGTCAACAAAATTA
1 AGAAGAAGTTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTA
* * * * * ** *
32509103 CTGAAAAATGTTTCCACATGGATGCTTTTTTTCTACAGTGGTATCTGAGAAAATAAATT-TG
66 CTGAAAAAAGCTCCCACATGGACGCTCTTTTGATACAGTGGTATCTGAAAAAAT-AATTGTG
* * * *
32509164 AGAAGATGTTTCTGAAAAAATAGTGTAAAAAACGCTTTAAGCAGGATGCACTGTCAGCAAAAATA
1 AGAAGAAGTTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTA
**
32509229 CTGAAAAAAGCTCCCATGTGGACGCTCTTTTGATACAGTGGTATCTGAAAAAATAATTGTG
66 CTGAAAAAAGCTCCCACATGGACGCTCTTTTGATACAGTGGTATCTGAAAAAATAATTGTG
* ** ** * * * *
32509290 AGATGACCTTTCTGAACTAATAGTGTCAAAAATGCTTCATGCAGTATGCACTTTCAGCAAAATTA
1 AGAAGAAGTTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTA
* *
32509355 CTGAGAAAAGCTCCCACGTGGAC
66 CTGAAAAAAGCTCCCACATGGAC
32509378 ACGTTCTTTT
Statistics
Matches: 181, Mismatches: 32, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
125 4 0.02
126 177 0.98
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.27
Consensus pattern (126 bp):
AGAAGAAGTTTCTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAATTA
CTGAAAAAAGCTCCCACATGGACGCTCTTTTGATACAGTGGTATCTGAAAAAATAATTGTG
Found at i:32510619 original size:42 final size:42
Alignment explanation
Indices: 32510572--32510657 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
32510562 ATTAAAATAC
32510572 TAAAAACAACTTTTATTTTATTACAAATATAAAAGAGTAAAT
1 TAAAAACAACTTTTATTTTATTACAAATATAAAAGAGTAAAT
32510614 TAAAAACAACTTTTATTTTATTACAAATATAAAAGAGTAAAT
1 TAAAAACAACTTTTATTTTATTACAAATATAAAAGAGTAAAT
32510656 TA
1 TA
32510658 TAATTAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (42 bp):
TAAAAACAACTTTTATTTTATTACAAATATAAAAGAGTAAAT
Found at i:32511108 original size:18 final size:18
Alignment explanation
Indices: 32511087--32511122 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
32511077 AAAAGGAAGC
*
32511087 ATATAAGGGTTAGGATAT
1 ATATAAGGGCTAGGATAT
32511105 ATATAAGGGCTAGGATAT
1 ATATAAGGGCTAGGATAT
32511123 GCACCTGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.28, T:0.31
Consensus pattern (18 bp):
ATATAAGGGCTAGGATAT
Found at i:32511749 original size:7 final size:7
Alignment explanation
Indices: 32511739--32511790 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
32511729 TTGTATACAT
32511739 AATACTA
1 AATACTA
32511746 AATACTA
1 AATACTA
32511753 AATACTA
1 AATACTA
32511760 AATACTA
1 AATACTA
*
32511767 AATATTA
1 AATACTA
32511774 AATACTA
1 AATACTA
*
32511781 AATACGA
1 AATACTA
32511788 AAT
1 AAT
32511791 GAGTATTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.29
Consensus pattern (7 bp):
AATACTA
Found at i:32512815 original size:49 final size:50
Alignment explanation
Indices: 32512705--32512815 Score: 147
Period size: 47 Copynumber: 2.3 Consensus size: 50
32512695 AAAAAATTAT
* **
32512705 AAAATTAAAATTAAAATTGCATAAATGAAAAAAAATATTAAATTGTATTGA
1 AAAATTAAAATTAAAATTACATAAAT-AAAAAAAATATTAAATACTATTGA
*
32512756 AAAATT--AATTAAAATTACATAAAT-TAAAAAATATTAAATACTATTGA
1 AAAATTAAAATTAAAATTACATAAATAAAAAAAATATTAAATACTATTGA
*
32512803 AATATTAAAATTA
1 AAAATTAAAATTA
32512816 TCACTTACCA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
47 25 0.47
49 22 0.42
51 6 0.11
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (50 bp):
AAAATTAAAATTAAAATTACATAAATAAAAAAAATATTAAATACTATTGA
Found at i:32512985 original size:22 final size:22
Alignment explanation
Indices: 32512960--32513004 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
32512950 CAAAGAGAGC
32512960 TTTGAGAA-AATTTGAGAGAATT
1 TTTG-GAAGAATTTGAGAGAATT
32512982 TTTGGAAGAATTTGAGAGAATT
1 TTTGGAAGAATTTGAGAGAATT
32513004 T
1 T
32513005 GGATAGGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (22 bp):
TTTGGAAGAATTTGAGAGAATT
Found at i:32516541 original size:25 final size:24
Alignment explanation
Indices: 32516513--32516666 Score: 94
Period size: 25 Copynumber: 6.1 Consensus size: 24
32516503 TTTCTCATAC
32516513 ATTATTTATTTTAAATTGTTTTATT
1 ATTATTTATTTTAAATT-TTTTATT
* * * *
32516538 ATTATTTACTTTAAGTTTTTCACAT
1 ATTATTTATTTTAAATTTTTTA-TT
* ** *
32516563 ATTATGTATTTTAAACTATTTCAAACT
1 ATTATTTATTTTAAA-T-TTT-TTATT
** * *
32516590 ATTATCCATTCTAAAATTTTTATAT
1 ATTATTTATTTTAAATTTTTTAT-T
* *
32516615 ATTATTTATTTTAAACTGTTATATGT
1 ATTATTTATTTTAAA-TTTTTTAT-T
*
32516641 ATTATTTATTTTGAATTTTTT-TT
1 ATTATTTATTTTAAATTTTTTATT
32516664 ATT
1 ATT
32516667 TTTTTATATG
Statistics
Matches: 96, Mismatches: 27, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
23 4 0.04
24 6 0.06
25 48 0.50
26 21 0.22
27 16 0.17
28 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (24 bp):
ATTATTTATTTTAAATTTTTTATT
Found at i:32516662 original size:52 final size:49
Alignment explanation
Indices: 32516484--32516662 Score: 124
Period size: 52 Copynumber: 3.4 Consensus size: 49
32516474 TGTTATTTAT
* *
32516484 TTATTTATTTTAAACCTTTTTTCTCATACATTATTTATTTTAAATTGTTTTATTA
1 TTATTTATTTT-AA--TTTTTT-T-ATATATTATTTATTTTAAACTG-TTTATTA
* * * * * * *
32516539 TTATTTACTTTAAGTTTTTCACATATTATGTATTTTAAACTATTTCAAACTA
1 TTATTTATTTTAATTTTTTTATATATTATTTATTTTAAACTGTTT---ATTA
** * **
32516591 TTATCCATTCTAAAATTTTTATATATTATTTATTTTAAACTGTTATATGTA
1 TTATTTATTTTAATTTTTTTATATATTATTTATTTTAAACTGTT-TAT-TA
32516642 TTATTTATTTTGAATTTTTTT
1 TTATTTATTTT-AATTTTTTT
32516663 TATTTTTTTA
Statistics
Matches: 93, Mismatches: 25, Indels: 15
0.70 0.19 0.11
Matches are distributed among these distances:
49 3 0.03
50 18 0.19
51 10 0.11
52 49 0.53
53 1 0.01
54 2 0.02
55 10 0.11
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (49 bp):
TTATTTATTTTAATTTTTTTATATATTATTTATTTTAAACTGTTTATTA
Found at i:32516664 original size:37 final size:37
Alignment explanation
Indices: 32516618--32516689 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
32516608 TTTATATATT
*
32516618 ATTTATTTTAAACTGTTATATGTATTATTTATTTTGA
1 ATTTATTTTAAACTGTTATATGTATCATTTATTTTGA
* *** *
32516655 ATTTTTTTTATTTTTTTATATGTATCATTTATTTT
1 ATTTATTTTAAACTGTTATATGTATCATTTATTTT
32516690 TAAACTGTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.67
Consensus pattern (37 bp):
ATTTATTTTAAACTGTTATATGTATCATTTATTTTGA
Found at i:32516692 original size:64 final size:62
Alignment explanation
Indices: 32516606--32516729 Score: 160
Period size: 64 Copynumber: 2.0 Consensus size: 62
32516596 CATTCTAAAA
* * * *
32516606 TTTTTATATATTATTTATTTTAAACTGTTATATGTATTATTTATTTTGAATTT-TTTTTATT
1 TTTTTATATATCATTTATTTTAAACTGTTATATATATTATCTATTTTAAATTTCTTTTTATT
* *
32516667 TTTTTATATGTATCATTTATTTTTAAACTGTTTTGTATATTATCTATTTTAAATTTCTTTTTA
1 TTTTTATA--TATCATTTA-TTTTAAACTGTTATATATATTATCTATTTTAAATTTCTTTTTA
32516730 GGGTCCGTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
61 8 0.15
63 8 0.15
64 31 0.58
65 6 0.11
ACGTcount: A:0.26, C:0.04, G:0.05, T:0.65
Consensus pattern (62 bp):
TTTTTATATATCATTTATTTTAAACTGTTATATATATTATCTATTTTAAATTTCTTTTTATT
Found at i:32517489 original size:19 final size:20
Alignment explanation
Indices: 32517465--32517511 Score: 87
Period size: 19 Copynumber: 2.4 Consensus size: 20
32517455 CATTCAAACA
32517465 CCAGAAAAGTAAATCA-TTT
1 CCAGAAAAGTAAATCATTTT
32517484 CCAGAAAAGTAAATCATTTT
1 CCAGAAAAGTAAATCATTTT
32517504 CCAGAAAA
1 CCAGAAAA
32517512 TATTTTACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (20 bp):
CCAGAAAAGTAAATCATTTT
Found at i:32517599 original size:26 final size:24
Alignment explanation
Indices: 32517538--32517681 Score: 159
Period size: 26 Copynumber: 5.7 Consensus size: 24
32517528 AAACGGAGCC
*
32517538 TTATATATTATTTATTTTAAACTT
1 TTATATATTATTTATTTTAAATTT
32517562 TT-TATA-TA-TTATTTTAAATTGT
1 TTATATATTATTTATTTTAAATT-T
32517584 CTTATATATTATTTATTTTAAATTTT
1 -TTATATATTATTTATTTTAAA-TTT
32517610 TTCATATATTATTTATTTTAAACTTT
1 TT-ATATATTATTTATTTTAAA-TTT
*
32517636 TATATATATTATTTACTTTAAATTGTTT
1 T-TATATATTATTTATTTTAAA---TTT
32517664 TTATATATTATTTTATTT
1 TTATATATTA-TTTATTT
32517682 CATTTTTCTT
Statistics
Matches: 104, Mismatches: 5, Indels: 18
0.82 0.04 0.14
Matches are distributed among these distances:
21 11 0.11
22 3 0.03
23 6 0.06
24 6 0.06
25 4 0.04
26 52 0.50
27 12 0.12
28 10 0.10
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (24 bp):
TTATATATTATTTATTTTAAATTT
Found at i:32517648 original size:52 final size:51
Alignment explanation
Indices: 32517537--32517681 Score: 176
Period size: 52 Copynumber: 2.8 Consensus size: 51
32517527 CAAACGGAGC
*
32517537 CTTATATATTATTTATTTTAAA-CTTTT-TATA-TA-TTATTTTAAATTGT
1 CTTATATATTATTTATTTTAAATTTTTTATATATTATTTATTTTAAATTGT
32517584 CTTATATATTATTTATTTTAAATTTTTTCATATATTATTTATTTTAAACTT-T
1 CTTATATATTATTTATTTTAAATTTTTT-ATATATTATTTATTTTAAA-TTGT
*
32517636 -TATATATATTATTTACTTTAAATTGTTTTTATATATTATTTTATTT
1 CT-TATATATTATTTATTTTAAA-T-TTTTTATATATTA-TTTATTT
32517682 CATTTTTCTT
Statistics
Matches: 86, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
47 22 0.26
48 4 0.05
50 4 0.05
51 3 0.03
52 30 0.35
53 11 0.13
54 12 0.14
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (51 bp):
CTTATATATTATTTATTTTAAATTTTTTATATATTATTTATTTTAAATTGT
Found at i:32521708 original size:14 final size:14
Alignment explanation
Indices: 32521689--32521717 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
32521679 TGTCCAAAAC
32521689 ACGCTTATTACTAT
1 ACGCTTATTACTAT
32521703 ACGCTTATTACTAT
1 ACGCTTATTACTAT
32521717 A
1 A
32521718 AGCCAAGGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (14 bp):
ACGCTTATTACTAT
Found at i:32522994 original size:18 final size:17
Alignment explanation
Indices: 32522970--32523029 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
32522960 CCAATATATT
32522970 TTATATTTTTTATATAA
1 TTATATTTTTTATATAA
*
32522987 TTAT-TATTCTTATA-AA
1 TTATAT-TTTTTATATAA
32523003 -TATATTTTTTATTATATA
1 TTATATTTTTTA-TATA-A
32523021 TTATATTTT
1 TTATATTTT
32523030 AAATTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
15 8 0.23
16 6 0.17
17 12 0.34
18 1 0.03
19 8 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATATTTTTTATATAA
Found at i:32523014 original size:15 final size:16
Alignment explanation
Indices: 32522971--32523029 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 16
32522961 CAATATATTT
32522971 TATATTTTTTATATAA
1 TATATTTTTTATATAA
32522987 T-TATTATTCTTATA-AA
1 TATATT-TT-TTATATAA
32523003 TATATTTTTTATTATATA
1 TATATTTTTTA-TATA-A
32523021 TTATATTTT
1 -TATATTTT
32523030 AAATTTATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
15 7 0.19
16 10 0.28
17 10 0.28
18 1 0.03
19 8 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATTTTTTATATAA
Found at i:32523054 original size:26 final size:26
Alignment explanation
Indices: 32523006--32523055 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
32522996 TTATAAATAT
* * * *
32523006 ATTTTTTATTATATATTATATTTTAA
1 ATTTATTATTAAATATCACATTTTAA
32523032 ATTTATTATTAAATATCACATTTT
1 ATTTATTATTAAATATCACATTTT
32523056 TTTATATGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTATTATTAAATATCACATTTTAA
Found at i:32523330 original size:27 final size:27
Alignment explanation
Indices: 32523299--32523354 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
32523289 CATTCACGTG
32523299 TACATTAAATTATTGGATTTTATATTT
1 TACATTAAATTATTGGATTTTATATTT
32523326 TACATTAAATTATTGGATTTTATATTT
1 TACATTAAATTATTGGATTTTATATTT
32523353 TA
1 TA
32523355 TGTAGATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (27 bp):
TACATTAAATTATTGGATTTTATATTT
Found at i:32530038 original size:37 final size:37
Alignment explanation
Indices: 32529960--32530038 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
32529950 AGGTGAATCT
* * *
32529960 TTTTCCAAGCTAACAGTTAGAACATTTGTGTGGATCT
1 TTTTCCAAGCTAACAGTTAGAACATTTGAGTGCATCC
32529997 TTTTCCAAGCTAACAGTTAGAACATTTGAGT-CATTCC
1 TTTTCCAAGCTAACAGTTAGAACATTTGAGTGCA-TCC
32530034 TTTTC
1 TTTTC
32530039 TGATCATTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.03
37 37 0.97
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (37 bp):
TTTTCCAAGCTAACAGTTAGAACATTTGAGTGCATCC
Found at i:32535486 original size:3 final size:3
Alignment explanation
Indices: 32535478--32535554 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
32535468 TGCCAATTTA
32535478 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
32535526 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
32535555 AGGCAAAGAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:32535727 original size:29 final size:28
Alignment explanation
Indices: 32535670--32535731 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
32535660 GTAATTTGTA
* *
32535670 ATAAAATATATAAATAAATAATAATAAT
1 ATAAAATATATAAATAAATAAAAAGAAT
*
32535698 AGTAAAATATA-AAAGTACATAAAAAGAAT
1 A-TAAAATATATAAA-TAAATAAAAAGAAT
32535727 ATAAA
1 ATAAA
32535732 TAAATGAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.26
Consensus pattern (28 bp):
ATAAAATATATAAATAAATAAAAAGAAT
Found at i:32537287 original size:2 final size:2
Alignment explanation
Indices: 32537280--32537317 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
32537270 CTCAACTGTG
32537280 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
32537318 GCAATGGAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32541105 original size:37 final size:38
Alignment explanation
Indices: 32541053--32541211 Score: 161
Period size: 37 Copynumber: 4.3 Consensus size: 38
32541043 AGGCCTAGTC
32541053 AAGGCCAACCTTTAAAAAAGGTTGAGATAGA-CTCGTCT
1 AAGG-CAACCTTTAAAAAAGGTTGAGATAGACCTCGTCT
* *
32541091 AAGGCAACCTTTAAAAAAAGTT-AGGATAGACC-CCTCT
1 AAGGCAACCTTTAAAAAAGGTTGA-GATAGACCTCGTCT
* * * *
32541128 AAGACAA-CATT-AAAAAGGTCG-GCATAGACCTTGTCT
1 AAGGCAACCTTTAAAAAAGGTTGAG-ATAGACCTCGTCT
*
32541164 AAGGCAACCTTTAAAAAAGGTTGAGATAGAGC-CGTCT
1 AAGGCAACCTTTAAAAAAGGTTGAGATAGACCTCGTCT
**
32541201 AATACAACCTT
1 AAGGCAACCTT
32541212 AGTAGAAGAT
Statistics
Matches: 98, Mismatches: 15, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
34 1 0.01
35 14 0.14
36 13 0.13
37 49 0.50
38 20 0.20
39 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (38 bp):
AAGGCAACCTTTAAAAAAGGTTGAGATAGACCTCGTCT
Found at i:32542212 original size:36 final size:35
Alignment explanation
Indices: 32542134--32542222 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 35
32542124 CGTTTGTTTA
*
32542134 ATGTTCACGAACATGTTCATTTAACTTAATCGAAC
1 ATGTTCACGAACATGTTCATTGAACTTAATCGAAC
* * *
32542169 ATATTCACGAATATGTTCA-TGAACATATAATTGAAC
1 ATGTTCACGAACATGTTCATTGAAC-T-TAATCGAAC
32542205 ATGTTCACGAACAATGTT
1 ATGTTCACGAAC-ATGTT
32542223 AATAAATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 4 0.09
35 18 0.40
36 18 0.40
37 5 0.11
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (35 bp):
ATGTTCACGAACATGTTCATTGAACTTAATCGAAC
Found at i:32544041 original size:15 final size:16
Alignment explanation
Indices: 32544009--32544042 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
32543999 ATTGAAATAT
32544009 GTTATAATATAAATTAA
1 GTTATAATAT-AATTAA
32544026 GTTATAATAT-ATTAA
1 GTTATAATATAATTAA
32544041 GT
1 GT
32544043 GGGGGTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (16 bp):
GTTATAATATAATTAA
Found at i:32545192 original size:24 final size:24
Alignment explanation
Indices: 32545160--32545316 Score: 201
Period size: 24 Copynumber: 6.5 Consensus size: 24
32545150 GAAATGACAT
32545160 TGGCACTATGTGTGCGGATTTAAA
1 TGGCACTATGTGTGCGGATTTAAA
*
32545184 TGGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTAAA
* *
32545208 CGGCACTATGTGTGCAGATTTAAA
1 TGGCACTATGTGTGCGGATTTAAA
* *
32545232 TAGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCGGATTTAAA
* **
32545256 TGGCACTATGTGTGCAGATTTGGA
1 TGGCACTATGTGTGCGGATTTAAA
*
32545280 TGGCACTACGTGTGCGGA-TTAGCAA
1 TGGCACTATGTGTGCGGATTTA--AA
32545305 -GGCACTATGTGT
1 TGGCACTATGTGT
32545317 ACAGGTTAGA
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
23 2 0.02
24 112 0.97
25 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.31
Consensus pattern (24 bp):
TGGCACTATGTGTGCGGATTTAAA
Found at i:32545217 original size:48 final size:47
Alignment explanation
Indices: 32545161--32545339 Score: 234
Period size: 48 Copynumber: 3.8 Consensus size: 47
32545151 AAATGACATT
*
32545161 GGCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCGGATTTGAA
1 GGCACTATGTGTGCAGATTTAAATGGCACTATGTGTGCGGATTTGAA
*
32545208 CGGCACTATGTGTGCAGATTTAAATAGCACTATGTGTGCGGATTTGAA
1 -GGCACTATGTGTGCAGATTTAAATGGCACTATGTGTGCGGATTTGAA
** * *
32545256 TGGCACTATGTGTGCAGATTTGGATGGCACTACGTGTGCGGATTAGCAA
1 -GGCACTATGTGTGCAGATTTAAATGGCACTATGTGTGCGGATTTG-AA
* * * *
32545305 GGCACTATGTGTACAG-GTTAGATGGCAATATGTGT
1 GGCACTATGTGTGCAGATTTAAATGGCACTATGTGT
32545340 ATGAATTTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
47 15 0.13
48 100 0.85
49 2 0.02
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.31
Consensus pattern (47 bp):
GGCACTATGTGTGCAGATTTAAATGGCACTATGTGTGCGGATTTGAA
Found at i:32545285 original size:72 final size:72
Alignment explanation
Indices: 32545162--32545299 Score: 222
Period size: 72 Copynumber: 1.9 Consensus size: 72
32545152 AATGACATTG
* *
32545162 GCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCGGATTTGAACGGCACTATGTGTGCAGAT
1 GCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCAGATTTGAACGGCACTACGTGTGCAGAT
32545227 TTAAATA
66 TTAAATA
* * * *
32545234 GCACTATGTGTGCGGATTTGAATGGCACTATGTGTGCAGATTTGGATGGCACTACGTGTGCGGAT
1 GCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCAGATTTGAACGGCACTACGTGTGCAGAT
32545299 T
66 T
32545300 AGCAAGGCAC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.32
Consensus pattern (72 bp):
GCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCAGATTTGAACGGCACTACGTGTGCAGAT
TTAAATA
Found at i:32545325 original size:24 final size:23
Alignment explanation
Indices: 32545160--32545340 Score: 82
Period size: 24 Copynumber: 7.6 Consensus size: 23
32545150 GAAATGACAT
* *
32545160 TGGCACTATGTGTGC-GGATTTAAA
1 TGGCACTATGTGTACAGG--TTAGA
* *
32545184 TGGCACTATGTGTGC-GGATTTGAA
1 TGGCACTATGTGTACAGG-TTAG-A
* * * *
32545208 CGGCACTATGTGTGCAGATTTAAA
1 TGGCACTATGTGTACAG-GTTAGA
* * *
32545232 TAGCACTATGTGTGC-GGATTTGAA
1 TGGCACTATGTGTACAGG-TTAG-A
* * *
32545256 TGGCACTATGTGTGCAGATTTGGA
1 TGGCACTATGTGTACAG-GTTAGA
* *
32545280 TGGCACTACGTGTGC-GGATTAGCA
1 TGGCACTATGTGTACAGG-TTAG-A
*
32545304 AGGCACTATGTGTACAGGTTAGA
1 TGGCACTATGTGTACAGGTTAGA
*
32545327 TGGCAATATGTGTA
1 TGGCACTATGTGTA
32545341 TGAATTTCCT
Statistics
Matches: 124, Mismatches: 23, Indels: 21
0.74 0.14 0.12
Matches are distributed among these distances:
23 22 0.18
24 93 0.75
25 9 0.07
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.31
Consensus pattern (23 bp):
TGGCACTATGTGTACAGGTTAGA
Found at i:32551626 original size:15 final size:16
Alignment explanation
Indices: 32551594--32551627 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
32551584 ATTGAAATAT
32551594 GTTATAATATAAATTAA
1 GTTATAATAT-AATTAA
32551611 GTTATAATAT-ATTAA
1 GTTATAATATAATTAA
32551626 GT
1 GT
32551628 GGGGGTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (16 bp):
GTTATAATATAATTAA
Found at i:32552792 original size:24 final size:24
Alignment explanation
Indices: 32552760--32552916 Score: 208
Period size: 24 Copynumber: 6.5 Consensus size: 24
32552750 GAAATGACAT
* *
32552760 TGGCACTATGTGTGCGGATTTAAA
1 TGGCACTATGTGTGCAGATTTGAA
32552784 TGGCACTATGTGTGCAGATTTGAA
1 TGGCACTATGTGTGCAGATTTGAA
*
32552808 TGGCACTATGTGTGCAGATTTAAA
1 TGGCACTATGTGTGCAGATTTGAA
* *
32552832 TAGCACTATGTGTGCGGATTTGAA
1 TGGCACTATGTGTGCAGATTTGAA
*
32552856 TGGCACTATGTGTGCAGATTTGGA
1 TGGCACTATGTGTGCAGATTTGAA
* * *
32552880 TGGCACTACGTGTGCGGATTAGCAA
1 TGGCACTATGTGTGCAGATTTG-AA
*
32552905 -CGCACTATGTGT
1 TGGCACTATGTGT
32552917 ACGGGTTAGC
Statistics
Matches: 117, Mismatches: 15, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
24 116 0.99
25 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (24 bp):
TGGCACTATGTGTGCAGATTTGAA
Found at i:32552916 original size:72 final size:72
Alignment explanation
Indices: 32552762--32552899 Score: 240
Period size: 72 Copynumber: 1.9 Consensus size: 72
32552752 AATGACATTG
* *
32552762 GCACTATGTGTGCGGATTTAAATGGCACTATGTGTGCAGATTTGAATGGCACTATGTGTGCAGAT
1 GCACTATGTGTGCGGATTTGAATGGCACTATGTGTGCAGATTTGAATGGCACTACGTGTGCAGAT
32552827 TTAAATA
66 TTAAATA
* *
32552834 GCACTATGTGTGCGGATTTGAATGGCACTATGTGTGCAGATTTGGATGGCACTACGTGTGCGGAT
1 GCACTATGTGTGCGGATTTGAATGGCACTATGTGTGCAGATTTGAATGGCACTACGTGTGCAGAT
32552899 T
66 T
32552900 AGCAACGCAC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.33
Consensus pattern (72 bp):
GCACTATGTGTGCGGATTTGAATGGCACTATGTGTGCAGATTTGAATGGCACTACGTGTGCAGAT
TTAAATA
Found at i:32552925 original size:24 final size:24
Alignment explanation
Indices: 32552882--32552941 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
32552872 GATTTGGATG
* *
32552882 GCACTACGTGTGCGGATTAGCAAC
1 GCACTATGTGTACGGATTAGCAAC
* **
32552906 GCACTATGTGTACGGGTTAGCATG
1 GCACTATGTGTACGGATTAGCAAC
*
32552930 GCAATATGTGTA
1 GCACTATGTGTA
32552942 TGAATTTCCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (24 bp):
GCACTATGTGTACGGATTAGCAAC
Found at i:32552931 original size:48 final size:48
Alignment explanation
Indices: 32552783--32552932 Score: 133
Period size: 48 Copynumber: 3.1 Consensus size: 48
32552773 GCGGATTTAA
* * * * * *
32552783 ATGGCACTATGTGTGCAGATTTGAATGGCACTATGTGTGCAGATTTA-A
1 ATGGCACTACGTGTGCGGATTAGAATCGCACTATGTGTACAGA-TTAGC
* * * * * * *
32552831 ATAGCACTATGTGTGCGGATTTGAATGGCACTATGTGTGCAGATTTGG
1 ATGGCACTACGTGTGCGGATTAGAATCGCACTATGTGTACAGATTAGC
* *
32552879 ATGGCACTACGTGTGCGGATTAGCAA-CGCACTATGTGTACGGGTTAGC
1 ATGGCACTACGTGTGCGGATTAG-AATCGCACTATGTGTACAGATTAGC
32552927 ATGGCA
1 ATGGCA
32552933 ATATGTGTAT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
47 2 0.02
48 83 0.95
49 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (48 bp):
ATGGCACTACGTGTGCGGATTAGAATCGCACTATGTGTACAGATTAGC
Found at i:32552931 original size:72 final size:72
Alignment explanation
Indices: 32552762--32552940 Score: 220
Period size: 72 Copynumber: 2.5 Consensus size: 72
32552752 AATGACATTG
* *
32552762 GCACTATGTGTGCGGATTTA-AATGGCACTATGTGTGCAGATTTGAATGGCACTATGTGTGCAGA
1 GCACTATGTGTACGGA-TTAGAATGGCACTATGTGTGCAGATTTGAATGGCACTACGTGTGCAGA
32552826 TTTAAATA
65 TTTAAATA
* * * *
32552834 GCACTATGTGTGCGGATTTGAATGGCACTATGTGTGCAGATTTGGATGGCACTACGTGTGCGGA-
1 GCACTATGTGTACGGATTAGAATGGCACTATGTGTGCAGATTTGAATGGCACTACGTGTGCAGAT
*
32552898 TTAGCAA-C
66 TTA--AATA
* * *
32552906 GCACTATGTGTACGGGTTAGCATGGCAATATGTGT
1 GCACTATGTGTACGGATTAGAATGGCACTATGTGT
32552941 ATGAATTTCC
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
71 5 0.05
72 87 0.93
73 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.31
Consensus pattern (72 bp):
GCACTATGTGTACGGATTAGAATGGCACTATGTGTGCAGATTTGAATGGCACTACGTGTGCAGAT
TTAAATA
Found at i:32555506 original size:46 final size:46
Alignment explanation
Indices: 32555450--32555625 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
32555440 CTAGGATGCA
32555450 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
32555496 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
32555543 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
32555589 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
32555626 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:32555606 original size:93 final size:93
Alignment explanation
Indices: 32555447--32555617 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
32555437 TCACTAGGAT
* *
32555447 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
32555512 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
32555540 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
32555605 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
32555618 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:32558598 original size:15 final size:15
Alignment explanation
Indices: 32558578--32558646 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
32558568 GTATCTTGGG
32558578 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
32558593 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
32558608 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
32558623 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
32558638 TTTCTTTAT
1 TTTCTTTAT
32558647 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:32558647 original size:30 final size:30
Alignment explanation
Indices: 32558569--32558656 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
32558559 CATAGTATCG
* * * *
32558569 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
32558599 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
32558629 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
32558657 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:32561062 original size:46 final size:46
Alignment explanation
Indices: 32561007--32561187 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
32560997 TAGGATGGTT
32561007 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
32561053 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
32561099 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
32561146 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
32561188 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:32561168 original size:93 final size:93
Alignment explanation
Indices: 32561009--32561179 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
32560999 GGATGGTTGA
* *
32561009 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
32561074 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
32561102 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
32561167 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
32561180 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:32562904 original size:44 final size:43
Alignment explanation
Indices: 32562855--32563379 Score: 401
Period size: 44 Copynumber: 11.9 Consensus size: 43
32562845 GGAATTGTCG
* * *
32562855 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAATATTCGCAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTAT
* * *
32562899 CTTCAATCTGCTTCACTACAACTTCAGGGAGATAAGATTCTTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTAT
* * ** * *
32562943 CTACAATCTGCTTCACTGCATTTTCAAGGAGATAAGACTTGTAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAT
* * *
32562987 CTTCAACCTGCTCCACTGCAACTCCAGGGAGATAAGGTT-TAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAT
* * * *
32563029 AGCTTTAGTCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTAT
1 --CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG-TAT
* * * * *
32563076 CCTT-AATCTGCTCCACTGCATCTTTAGGGAGACAAGACTTATAG
1 -CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAT
* ** * *
32563120 CTTTAA-CATGCTTTACTGCAACTTCAGAGAGACAAGATTTGTTAT
1 CTTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGA-TTG-TAT
* * *
32563165 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAATACTTATAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAT
* * * ** *
32563209 CTTTAACCTGCTCTACTGCAACTTCAAAGAGACAAGATTGTTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTG-TAT
32563253 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGT-AT
* * ** * * * * **
32563298 -TGCAACCTGCTCCACTTTAACTTCAAGTACATAAGACTCGTGG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAT
* * * *
32563341 CTTTAATTTGCTCCAATACAACTTCAGGGAGATAAGATT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
32563380 CGCTACGATG
Statistics
Matches: 375, Mismatches: 92, Indels: 29
0.76 0.19 0.06
Matches are distributed among these distances:
42 2 0.01
43 9 0.02
44 286 0.76
45 71 0.19
46 4 0.01
47 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (43 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAT
Found at i:32563141 original size:133 final size:133
Alignment explanation
Indices: 32562899--32563199 Score: 340
Period size: 133 Copynumber: 2.3 Consensus size: 133
32562889 ATATTCGCAT
* * *
32562899 CTTCAATCTGCTTCACTACAACTTCAGGGAGATAAGATTCTTATCTACAATCTGCTTCACTGCAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTTATCTACAATCTGCTCCACTGCAT
* * * * * *
32562964 TTTCAAGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTCCAGGGAGATAAGGTTT-A
66 TTTCAAGGAGACAAGACTTATAACTTCAACATGCTCCACTGCAACTCCAGAGAGACAAGATTTGA
32563028 TAG
131 TAG
* * * * *
32563031 CTTTAGTCTGCTCTACTGCAACTTCAGAGAGATAAGATT-TGCTATCCT-TAATCTGCTCCACTG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCT--TAT-CTACAATCTGCTCCACTG
* * * ** *
32563094 CATCTTT-AGGGAGACAAGACTTATAGCTTTAACATGCTTTACTGCAACTTCAGAGAGACAAGAT
63 CAT-TTTCAAGGAGACAAGACTTATAACTTCAACATGCTCCACTGCAACTCCAGAGAGACAAGAT
* *
32563158 TTGTTAT
127 TTGATAG
32563165 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
32563200 TACTTATAGC
Statistics
Matches: 138, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
131 1 0.01
132 33 0.24
133 66 0.48
134 38 0.28
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (133 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTTATCTACAATCTGCTCCACTGCAT
TTTCAAGGAGACAAGACTTATAACTTCAACATGCTCCACTGCAACTCCAGAGAGACAAGATTTGA
TAG
Found at i:32563220 original size:133 final size:131
Alignment explanation
Indices: 32562897--32563289 Score: 335
Period size: 133 Copynumber: 3.0 Consensus size: 131
32562887 TAATATTCGC
* * * ** *
32562897 ATCTTCAATCTGCTTCACTACAACTTCAGGGAGATAAGATTCTTAT-CTACAATCTGCTTCACTG
1 ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGAT-A-ATACTTATACTTTAATCTGCTCCACTG
* * * * * *
32562961 CATTTTCAAGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTCCAGGGAGATAAGGTT
64 CATTTTCAAGGAGACAAGACTTATAACTTCAACATGCTCCACTGCAACTCCAGAGAGACAAGATT
32563026 TAT
129 TAT
* * * * * * * * *
32563029 AGCTTTAGTCTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCCTTAATCTGCTCCACTG
1 ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAATACTT-ATA-CTTTAATCTGCTCCACTG
* * * ** *
32563094 CATCTTT-AGGGAGACAAGACTTATAGCTTTAACATGCTTTACTGCAACTTCAGAGAGACAAGAT
64 CAT-TTTCAAGGAGACAAGACTTATAACTTCAACATGCTCCACTGCAACTCCAGAGAGACAAGAT
*
32563158 TTGTT
128 TT-AT
* *
32563163 ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAATACTTATAGCTTTAACCTGCTCTACTGC
1 ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAATACTTATA-CTTTAATCTGCTCCACTGC
** * * * * * *
32563228 AACTTCAAAGAGACAAGA-TTGTTATCTTCAATC-TGCTCCACTGCAACTTCAGGGAGATAAGA
65 ATTTTCAAGGAGACAAGACTT-ATAACTTCAA-CATGCTCCACTGCAACTCCAGAGAGACAAGA
32563290 CTTGTAATTG
Statistics
Matches: 202, Mismatches: 51, Indels: 15
0.75 0.19 0.06
Matches are distributed among these distances:
130 3 0.01
131 2 0.01
132 32 0.16
133 125 0.62
134 40 0.20
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (131 bp):
ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAATACTTATACTTTAATCTGCTCCACTGCA
TTTTCAAGGAGACAAGACTTATAACTTCAACATGCTCCACTGCAACTCCAGAGAGACAAGATTTA
T
Found at i:32563323 original size:88 final size:89
Alignment explanation
Indices: 32562897--32563292 Score: 471
Period size: 89 Copynumber: 4.5 Consensus size: 89
32562887 TAATATTCGC
* * ** *
32562897 ATCTTCAATCTGCTTCACTACAACTTCAGGGAGATAAGATTCTTAT--CTACAATCTGCT-TCAC
1 ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA--CTTATAGCTTTAACCTGCTCT-AC
** * * *
32562959 TGCATTTTCAAGGAGATAAGACTTG-T
63 TGCAACTTCAAAGAGACAAGATTTGTT
* * * ** **
32562985 AACTTCAACCTGCTCCACTGCAACTCCAGGGAGATAAGGTTTATAGCTTTAGTCTGCTCTACTGC
1 ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATAGCTTTAACCTGCTCTACTGC
* * *
32563050 AACTTCAGAGAGATAAGATTTGCT
66 AACTTCAAAGAGACAAGATTTGTT
* * * * *
32563074 ATCCTT-AATCTGCTCCACTGCATCTTTAGGGAGACAAGACTTATAGCTTTAACATGCTTTACTG
1 AT-CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATAGCTTTAACCTGCTCTACTG
*
32563138 CAACTTCAGAGAGACAAGATTTGTT
65 CAACTTCAAAGAGACAAGATTTGTT
*
32563163 ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAATACTTATAGCTTTAACCTGCTCTACTGC
1 ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATAGCTTTAACCTGCTCTACTGC
32563228 AACTTCAAAGAGACAAGA-TTGTT
66 AACTTCAAAGAGACAAGATTTGTT
32563251 ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT
1 ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT
32563293 GTAATTGCAA
Statistics
Matches: 265, Mismatches: 37, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
86 4 0.02
88 113 0.43
89 145 0.55
90 3 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (89 bp):
ATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATAGCTTTAACCTGCTCTACTGC
AACTTCAAAGAGACAAGATTTGTT
Found at i:32565338 original size:42 final size:43
Alignment explanation
Indices: 32565289--32565396 Score: 130
Period size: 43 Copynumber: 2.5 Consensus size: 43
32565279 TGAGATTACG
* *
32565289 TGTAAGACCATATCTGGGATATGA-AATCGATATGAGA-CTTCA
1 TGTAAGACCATATCTGGGATATGAGAATCGATACGAGATC-CCA
* * * * *
32565331 TGTAAGACCATAGCTGGGCTATTAGCATTGATACGAGATCCCA
1 TGTAAGACCATATCTGGGATATGAGAATCGATACGAGATCCCA
32565374 TGTAAGACCATATCTGGGATATG
1 TGTAAGACCATATCTGGGATATG
32565397 GTATTGGTAT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 21 0.39
43 32 0.59
44 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (43 bp):
TGTAAGACCATATCTGGGATATGAGAATCGATACGAGATCCCA
Found at i:32572202 original size:28 final size:28
Alignment explanation
Indices: 32572168--32572237 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
32572158 TCATTTACAA
*
32572168 ATCAATTCAATTTCACT-TTTCATCAAT-
1 ATCAATTCAATTTCAATATTT-ATCAATC
* * *
32572195 ATACAATTCTATATCAATATTTATCTATC
1 AT-CAATTCAATTTCAATATTTATCAATC
32572224 ATCAATTCAATTTC
1 ATCAATTCAATTTC
32572238 TTTATCAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
27 2 0.06
28 27 0.79
29 5 0.15
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44
Consensus pattern (28 bp):
ATCAATTCAATTTCAATATTTATCAATC
Found at i:32572649 original size:13 final size:14
Alignment explanation
Indices: 32572631--32572671 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
32572621 TTAGTTTGTC
32572631 ATATAA-AAATATT
1 ATATAATAAATATT
*
32572644 ATATAATAATTATTT
1 ATATAATAAATA-TT
32572659 ATATAATAAATAT
1 ATATAATAAATAT
32572672 ATTTTACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 6 0.25
14 5 0.21
15 13 0.54
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATAATAAATATT
Found at i:32572814 original size:3 final size:3
Alignment explanation
Indices: 32572806--32572831 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
32572796 AATTTATTTG
32572806 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
32572832 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:32576258 original size:18 final size:18
Alignment explanation
Indices: 32576237--32576276 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
32576227 TACTCTATAG
32576237 CAGTCAGTTATACAATAA
1 CAGTCAGTTATACAATAA
* * *
32576255 CAGTCATTTATTCAGTAA
1 CAGTCAGTTATACAATAA
32576273 CAGT
1 CAGT
32576277 AAATTATTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (18 bp):
CAGTCAGTTATACAATAA
Found at i:32577534 original size:19 final size:20
Alignment explanation
Indices: 32577505--32577544 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
32577495 TCGTTTCATA
32577505 TTCTGTTCTTTCTA-TTCTTT
1 TTCTGTTCTTT-TATTTCTTT
32577525 TTCT-TTCTTTTATTTCTTT
1 TTCTGTTCTTTTATTTCTTT
32577544 T
1 T
32577545 GTTTCTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 13 0.68
20 4 0.21
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (20 bp):
TTCTGTTCTTTTATTTCTTT
Found at i:32577544 original size:18 final size:19
Alignment explanation
Indices: 32577505--32577556 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
32577495 TCGTTTCATA
32577505 TTCTGTTCTTTCTA-TTCTTT
1 TTCT-TTCTTT-TATTTCTTT
32577525 TTCTTTCTTTTATTTC-TT
1 TTCTTTCTTTTATTTCTTT
*
32577543 TTGTTTC-TTTATTT
1 TTCTTTCTTTTATTT
32577557 ATATTACTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.23
18 10 0.33
19 9 0.30
20 4 0.13
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (19 bp):
TTCTTTCTTTTATTTCTTT
Found at i:32577597 original size:13 final size:13
Alignment explanation
Indices: 32577566--32577590 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32577556 TATATTACTT
32577566 TATAATATAATAA
1 TATAATATAATAA
32577579 TATAATATAATA
1 TATAATATAATA
32577591 CTTTAATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TATAATATAATAA
Found at i:32582742 original size:2 final size:2
Alignment explanation
Indices: 32582735--32582768 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
32582725 TTTCATTTCT
32582735 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
32582769 CACTAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32583038 original size:3 final size:3
Alignment explanation
Indices: 32583030--32583073 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
32583020 TCAATTTATT
32583030 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
32583074 TTATTATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:32583078 original size:3 final size:3
Alignment explanation
Indices: 32583072--32583127 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
32583062 ATAATAATAA
*
32583072 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
32583119 TAT TAT TAT
1 TAT TAT TAT
32583128 AACAATAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:32583319 original size:30 final size:32
Alignment explanation
Indices: 32583279--32583337 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
32583269 TTAATTTTAT
*
32583279 AATAATAAGTAA-TAAATATCTAT-TTACTTA
1 AATAAAAAGTAATTAAATATCTATGTTACTTA
*
32583309 AATAAAAAGTAATTAAATATTTATGTTAC
1 AATAAAAAGTAATTAAATATCTATGTTAC
32583338 AATTGTATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.44
31 10 0.40
32 4 0.16
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (32 bp):
AATAAAAAGTAATTAAATATCTATGTTACTTA
Found at i:32591074 original size:20 final size:20
Alignment explanation
Indices: 32591042--32591095 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
32591032 ACATGACATG
*
32591042 AGAATATAA-AAAATAATAAA
1 AGAA-ATAATAAAATAACAAA
32591062 AGAAATAATAAAATAACAAA
1 AGAAATAATAAAATAACAAA
32591082 A-ATAATATATAAAA
1 AGA-AATA-ATAAAA
32591096 AAATTAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.17
20 19 0.63
21 6 0.20
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (20 bp):
AGAAATAATAAAATAACAAA
Found at i:32591074 original size:21 final size:21
Alignment explanation
Indices: 32591050--32591131 Score: 53
Period size: 22 Copynumber: 3.9 Consensus size: 21
32591040 TGAGAATATA
32591050 AAAAATAATAAAAGAAATAAT
1 AAAAATAATAAAAGAAATAAT
*
32591071 -AAAATAACAAAA-ATAATATAT
1 AAAAATAATAAAAGA-AATA-AT
* *
32591092 AAAAA-AATTAAAATAAAATGAT
1 AAAAATAA-TAAAA-GAAATAAT
** *
32591114 AGCAATAATAATAGAAAT
1 AAAAATAATAAAAGAAAT
32591132 GCACAAATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
19 1 0.02
20 15 0.32
21 8 0.17
22 17 0.36
23 5 0.11
24 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (21 bp):
AAAAATAATAAAAGAAATAAT
Found at i:32592738 original size:18 final size:19
Alignment explanation
Indices: 32592705--32592741 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
32592695 ACTTAAATTG
32592705 TTTAATTTTAATTTTATTT
1 TTTAATTTTAATTTTATTT
*
32592724 TTTAA-TTTGATTTTATTT
1 TTTAATTTTAATTTTATTT
32592742 ATTTGGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (19 bp):
TTTAATTTTAATTTTATTT
Found at i:32594323 original size:8 final size:8
Alignment explanation
Indices: 32594312--32594358 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
32594302 TCCTTTAAAC
32594312 AAATATAA
1 AAATATAA
32594320 AAATATAA
1 AAATATAA
*
32594328 AATTAT-A
1 AAATATAA
32594335 AAATATTAA
1 AAATA-TAA
*
32594344 AATTATAA
1 AAATATAA
*
32594352 AATTATA
1 AAATATA
32594359 TTTTTATCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 5 0.15
8 24 0.71
9 5 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAATATAA
Found at i:32594336 original size:16 final size:16
Alignment explanation
Indices: 32594315--32594358 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
32594305 TTTAAACAAA
32594315 TATAAAAATATAAAAT
1 TATAAAAATATAAAAT
32594331 TAT-AAAATATTAAAAT
1 TATAAAAATA-TAAAAT
*
32594347 TATAAAATTATA
1 TATAAAAATATA
32594359 TTTTTATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 6 0.24
16 14 0.56
17 5 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TATAAAAATATAAAAT
Found at i:32594350 original size:24 final size:23
Alignment explanation
Indices: 32594312--32594358 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
32594302 TCCTTTAAAC
32594312 AAATATAAAAATATAAAATTATA
1 AAATATAAAAATATAAAATTATA
*
32594335 AAATATTAAAATTATAAAATTATA
1 AAATA-TAAAAATATAAAATTATA
32594359 TTTTTATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATATAAAAATATAAAATTATA
Found at i:32597286 original size:130 final size:130
Alignment explanation
Indices: 32597037--32597275 Score: 320
Period size: 130 Copynumber: 1.8 Consensus size: 130
32597027 TAAAATACAT
* * * * *
32597037 GTGAAATTCCAAGGAGATATTCGATTATTTTGGACAAATGAAAAAGCGCAGCCCAGTACAATGGG
1 GTGAAATTCCAAGGAGATATCCAATTATTTCGGACAAATGAAAAAGCGCAACCCAGCACAATGGG
*
32597102 GCTCGATTCTCAAATCGCCAAACATCGAACATCGCCTTCATTTTGAAGGATTTTAGAAAATGTGA
66 GCACGATTCTCAAATCGCCAAACATCGAACATCGCCTTCATTTTGAAGGATTTTAGAAAATGTGA
* * * **
32597167 GTGAAATTCCGAAGG-GATCTCCAATTGTTTCGGACCAATGAAAAAGCGCAACCCAGCACGGTAG
1 GTGAAATTCC-AAGGAGATATCCAATTATTTCGGACAAATGAAAAAGCGCAACCCAGCACAAT-G
* * *
32597231 GGG-ACGATTCTCAAATCGCCAAACATTGAACATCGTCTTCGTTTT
64 GGGCACGATTCTCAAATCGCCAAACATCGAACATCGCCTTCATTTT
32597276 TAAGTGTTTT
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
130 85 0.91
131 8 0.09
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (130 bp):
GTGAAATTCCAAGGAGATATCCAATTATTTCGGACAAATGAAAAAGCGCAACCCAGCACAATGGG
GCACGATTCTCAAATCGCCAAACATCGAACATCGCCTTCATTTTGAAGGATTTTAGAAAATGTGA
Found at i:32597479 original size:131 final size:131
Alignment explanation
Indices: 32597316--32597677 Score: 343
Period size: 131 Copynumber: 2.8 Consensus size: 131
32597306 AAAGAAATGT
* ** * ** * * *
32597316 TCGATCATTTTGAGCAAACGA-GAAATCACAACCCATCTTGATAGGGCATGA-TTCTCGAATT-G
1 TCGATTATTTTGAGCAAAC-ACGAAATTGCAACCCAACACGATAGGGCACGATTTCGCGAATTAC
* * ** *
32597378 TCAAATGCCGAATATTGCCTTCGTTTTAAATAAATTTTAGGAGATATGAATGAAATCTTGAAGGG
65 T-AAATACCGAATATCGCCTTCGTTTTAAA-AAATTTTAAAAGACATGAATGAAATCTTGAAGGG
32597443 ATAC
128 ATAC
*
32597447 TCGATTATTTTGAGCAAACACGAAATTGCAACCCAACACGTTAGGGCACGATTTCGCGAATTACT
1 TCGATTATTTTGAGCAAACACGAAATTGCAACCCAACACGATAGGGCACGATTTCGCGAATTACT
** * * ** * * *
32597512 AAATATTGAATCTCGTCTTCGTTTTGGAGAATTTTAAAAGACATGAATGAAATTTTGAAGTGATA
66 AAATACCGAATATCGCCTTCGTTTTAAAAAATTTTAAAAGACATGAATGAAATCTTGAAGGGATA
*
32597577 T
131 C
* * * * * *
32597578 TTGATTATTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCC
1 TCGATTATTTTGAGCAAACACGAAATTGCAACCCAACACGATAGGGCACGATTTCGCGAATTACT
* * * * * *
32597643 AAACATCGAATCTCGTCTTCGTTTTGAAGAATTTT
66 AAATACCGAATATCGCCTTCGTTTTAAAAAATTTT
32597678 TTGAATAAAT
Statistics
Matches: 195, Mismatches: 33, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
130 1 0.01
131 164 0.84
132 29 0.15
133 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (131 bp):
TCGATTATTTTGAGCAAACACGAAATTGCAACCCAACACGATAGGGCACGATTTCGCGAATTACT
AAATACCGAATATCGCCTTCGTTTTAAAAAATTTTAAAAGACATGAATGAAATCTTGAAGGGATA
C
Found at i:32598672 original size:2 final size:2
Alignment explanation
Indices: 32598665--32598711 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
32598655 CAATACAAAG
32598665 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
32598707 TA TA T
1 TA TA T
32598712 TAATGTTTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32600757 original size:87 final size:87
Alignment explanation
Indices: 32600611--32600791 Score: 281
Period size: 87 Copynumber: 2.1 Consensus size: 87
32600601 CCCACAGCAG
* * * * *
32600611 CTTCAGGGAGACATGATCTTAAATTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTG
1 CTTCAGGGAAACAGGATCTAAAATTTCAACCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTG
* *
32600676 GCTTAAATCTGATTCACTGCAA
66 ACTTAAATCGGATTCACTGCAA
*
32600698 CTTCAGGGAAACAGGATCTAAAATTTCAACCTACTCCATTACAACTTTAGGGAGCTAGGTTAGTG
1 CTTCAGGGAAACAGGATCTAAAATTTCAACCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTG
*
32600763 ACTTAAATCGGCTTCACTGCAA
66 ACTTAAATCGGATTCACTGCAA
32600785 CTTCAGG
1 CTTCAGG
32600792 AAGCCGAGAT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (87 bp):
CTTCAGGGAAACAGGATCTAAAATTTCAACCTACTCCACTACAACTTTAGGGAGCTAGGTTAGTG
ACTTAAATCGGATTCACTGCAA
Found at i:32600887 original size:44 final size:44
Alignment explanation
Indices: 32600808--32601112 Score: 384
Period size: 44 Copynumber: 7.0 Consensus size: 44
32600798 AGATTCGTCG
* * *
32600808 TCTTCGATCTG-CGCTCTGTCAACACAGAGATGCCAAATCTGCTA
1 TCTTCGATCTGTC-CTCTGCCAATACAGAGACGCCAAATCTGCTA
* *
32600852 TCTTCGATCTGTCCTCTGACAATACAGGGACGCCAAATCTGCTA
1 TCTTCGATCTGTCCTCTGCCAATACAGAGACGCCAAATCTGCTA
* *
32600896 TCTTCGATTTGCTCTTC-GCCAATACAGAGACGCCAAATCTGCTA
1 TCTTCGATCTG-TCCTCTGCCAATACAGAGACGCCAAATCTGCTA
* * * *
32600940 TCTTCAATCTGCCCTCTGACAATACAGAGACGACAAATCTGCTA
1 TCTTCGATCTGTCCTCTGCCAATACAGAGACGCCAAATCTGCTA
* * *
32600984 TCTTTGATCTGTTCTCTGCCAATACAGAGACGCAAAATCTGCTA
1 TCTTCGATCTGTCCTCTGCCAATACAGAGACGCCAAATCTGCTA
* *
32601028 TCTTCGATCTG-CTCTCCGCCAATACAGAGACACCAAATCTGCTA
1 TCTTCGATCTGTC-CTCTGCCAATACAGAGACGCCAAATCTGCTA
* * *
32601072 TCTTCGATCTGT-TTCTGCCAATACAGAAATGCCAAATCTGC
1 TCTTCGATCTGTCCTCTGCCAATACAGAGACGCCAAATCTGC
32601113 AGGATTCGCC
Statistics
Matches: 225, Mismatches: 31, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
43 27 0.12
44 193 0.86
45 5 0.02
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (44 bp):
TCTTCGATCTGTCCTCTGCCAATACAGAGACGCCAAATCTGCTA
Found at i:32601048 original size:132 final size:132
Alignment explanation
Indices: 32600808--32601082 Score: 424
Period size: 132 Copynumber: 2.1 Consensus size: 132
32600798 AGATTCGTCG
* * * *
32600808 TCTTCGATCTGCGCTCTGTCAACACAGAGATGCCAAATCTGCTATCTTCGATCTGTCCTCTGACA
1 TCTTCGATCTGCCCTCTGACAACACAGAGACGACAAATCTGCTATCTTCGATCTGTCCTCTGACA
* * * * *
32600873 ATACAGGGACGCCAAATCTGCTATCTTCGATTTGCTCTTCGCCAATACAGAGACGCCAAATCTGC
66 ATACAGAGACGCAAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACACCAAATCTGC
32600938 TA
131 TA
* * * * *
32600940 TCTTCAATCTGCCCTCTGACAATACAGAGACGACAAATCTGCTATCTTTGATCTGTTCTCTGCCA
1 TCTTCGATCTGCCCTCTGACAACACAGAGACGACAAATCTGCTATCTTCGATCTGTCCTCTGACA
32601005 ATACAGAGACGCAAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACACCAAATCTGC
66 ATACAGAGACGCAAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACACCAAATCTGC
32601070 TA
131 TA
32601072 TCTTCGATCTG
1 TCTTCGATCTG
32601083 TTTCTGCCAA
Statistics
Matches: 128, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 128 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.28
Consensus pattern (132 bp):
TCTTCGATCTGCCCTCTGACAACACAGAGACGACAAATCTGCTATCTTCGATCTGTCCTCTGACA
ATACAGAGACGCAAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACACCAAATCTGC
TA
Found at i:32603191 original size:46 final size:46
Alignment explanation
Indices: 32603141--32603313 Score: 212
Period size: 46 Copynumber: 3.7 Consensus size: 46
32603131 TGGTTGAGCA
32603141 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
32603187 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
32603232 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
32603280 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
32603314 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 8, Indels: 20
0.80 0.06 0.15
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 59 0.54
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:32603297 original size:93 final size:93
Alignment explanation
Indices: 32603138--32603308 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
32603128 GGATGGTTGA
*
32603138 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
32603203 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
32603231 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
32603295 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
32603309 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:32610806 original size:46 final size:46
Alignment explanation
Indices: 32610705--32610829 Score: 209
Period size: 46 Copynumber: 2.7 Consensus size: 46
32610695 TGGTTGAGCA
*
32610705 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
32610750 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
32610796 -CCTAAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTA
32610830 GGGGCGGGTT
Statistics
Matches: 76, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
45 35 0.46
46 41 0.54
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:32626777 original size:20 final size:19
Alignment explanation
Indices: 32626736--32626773 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
32626726 CTCACCTACC
32626736 TAAAAAACCAAATTACCCA
1 TAAAAAACCAAATTACCCA
*
32626755 TAAATAAACCCAA-TACCCA
1 TAAA-AAACCAAATTACCCA
32626774 ATAAGCCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.16
Consensus pattern (19 bp):
TAAAAAACCAAATTACCCA
Found at i:32629270 original size:19 final size:19
Alignment explanation
Indices: 32629246--32629285 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
32629236 AAAAAAAATG
32629246 TTTGCTTGTACATAAATAA
1 TTTGCTTGTACATAAATAA
*
32629265 TTTGCTTGTGCATAAATAA
1 TTTGCTTGTACATAAATAA
32629284 TT
1 TT
32629286 AAATAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (19 bp):
TTTGCTTGTACATAAATAA
Found at i:32630067 original size:12 final size:11
Alignment explanation
Indices: 32630044--32630088 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 11
32630034 TAGAAAAATC
32630044 TTATTTTATTT
1 TTATTTTATTT
32630055 TTATTTCTATTTT
1 TTATTT-TA-TTT
32630068 TTGATTTTATTT
1 TT-ATTTTATTT
*
32630080 TGATTTTAT
1 TTATTTTAT
32630089 ATTAAATTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 13 0.43
12 6 0.20
13 7 0.23
14 4 0.13
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (11 bp):
TTATTTTATTT
Found at i:32632085 original size:48 final size:48
Alignment explanation
Indices: 32632030--32632131 Score: 159
Period size: 48 Copynumber: 2.1 Consensus size: 48
32632020 TTTTAAGGGG
* * *
32632030 ATCACATATTGATGTCAATGCCATGTCCCAGATATGGTCTTACATGGT
1 ATCACATATCGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGT
* *
32632078 ATCACATATCGATGCCAATGTCATGTTCCAGACATGGTCTTACATGGT
1 ATCACATATCGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGT
32632126 ATCACA
1 ATCACA
32632132 ATGCCATAGC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (48 bp):
ATCACATATCGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGT
Found at i:32632152 original size:37 final size:38
Alignment explanation
Indices: 32632111--32632197 Score: 124
Period size: 37 Copynumber: 2.3 Consensus size: 38
32632101 TGTTCCAGAC
*
32632111 ATGGTCTTACATGGT-ATCACAATGCCATAGCTCAGCT
1 ATGGTCTTACATGGTCATCACAATGCCATAGCACAGCT
* *
32632148 ATGGTCTTACAT-GTCATTACGATGCCATAGCACAGCT
1 ATGGTCTTACATGGTCATCACAATGCCATAGCACAGCT
*
32632185 ATGGTCATACATG
1 ATGGTCTTACATG
32632198 TACTTGCATA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 2 0.05
37 42 0.95
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (38 bp):
ATGGTCTTACATGGTCATCACAATGCCATAGCACAGCT
Found at i:32634481 original size:28 final size:28
Alignment explanation
Indices: 32634450--32634506 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
32634440 CATTAAATCT
32634450 CATGATTACCAATTATTCATTCATAGTG
1 CATGATTACCAATTATTCATTCATAGTG
*
32634478 CATGATTACCAGTTATTCATTCATAGTG
1 CATGATTACCAATTATTCATTCATAGTG
32634506 C
1 C
32634507 TTACTCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (28 bp):
CATGATTACCAATTATTCATTCATAGTG
Found at i:32640502 original size:2 final size:2
Alignment explanation
Indices: 32640495--32640523 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
32640485 TATGCCATGA
32640495 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32640524 AACTGTGCTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32645125 original size:30 final size:31
Alignment explanation
Indices: 32645067--32645126 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
32645057 TTGAAATAAA
**
32645067 GAACAAGCTGAAAGAAAGCTCAGTTGAGCTC
1 GAACAAGCTGAAAGAAAGCTCAAATGAGCTC
* *
32645098 GAACGAGCTGAAA-CAAGCTCAAATGAGCT
1 GAACAAGCTGAAAGAAAGCTCAAATGAGCT
32645127 GAGTTGAGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (31 bp):
GAACAAGCTGAAAGAAAGCTCAAATGAGCTC
Found at i:32649587 original size:3 final size:3
Alignment explanation
Indices: 32649572--32649607 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
32649562 AAGAGGACAT
* *
32649572 TGA TGA CGA TGA TGA TGA TGG TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
32649608 ATACGATGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.36, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:32658956 original size:2 final size:2
Alignment explanation
Indices: 32658949--32658983 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
32658939 CATAGGTTTG
32658949 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32658984 CTGTTTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32659445 original size:11 final size:12
Alignment explanation
Indices: 32659410--32659452 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
32659400 AATAATTTTT
*
32659410 ATAAATTTTAAA
1 ATAAATTATAAA
32659422 CATAAATTATAAA
1 -ATAAATTATAAA
*
32659435 ATAAATATAAAAA
1 ATAAAT-TATAAA
32659448 ATAAA
1 ATAAA
32659453 AGAAAAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 6 0.22
13 21 0.78
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
ATAAATTATAAA
Found at i:32660480 original size:20 final size:22
Alignment explanation
Indices: 32660442--32660484 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
32660432 TATCATTTCA
32660442 TATAATAAATAACTTAAAATAT
1 TATAATAAATAACTTAAAATAT
32660464 TATAA-AAATAA-TTAAAATAT
1 TATAATAAATAACTTAAAATAT
32660484 T
1 T
32660485 TACAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 6 0.29
22 5 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TATAATAAATAACTTAAAATAT
Found at i:32660491 original size:20 final size:21
Alignment explanation
Indices: 32660442--32660492 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
32660432 TATCATTTCA
32660442 TATAATAAATAACTTAAAATAT
1 TATAA-AAATAACTTAAAATAT
32660464 TATAAAAATAA-TTAAAATAT
1 TATAAAAATAACTTAAAATAT
32660484 T-TACAAAAT
1 TATA-AAAAT
32660493 TACAATCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.07
20 15 0.54
21 6 0.21
22 5 0.18
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (21 bp):
TATAAAAATAACTTAAAATAT
Found at i:32660491 original size:21 final size:21
Alignment explanation
Indices: 32660448--32660491 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
32660438 TTCATATAAT
*
32660448 AAATAACTTAAAATATTATAA
1 AAATAACTTAAAATATTACAA
32660469 AAATAA-TTAAAATATTTACAA
1 AAATAACTTAAAATA-TTACAA
32660490 AA
1 AA
32660492 TTACAATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATAACTTAAAATATTACAA
Found at i:32664362 original size:14 final size:15
Alignment explanation
Indices: 32664326--32664367 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
32664316 ACAGAGAAGT
*
32664326 ATTTCTTTATCAATT
1 ATTTCTTTATCAATA
*
32664341 CTTT-TTTAT-AATA
1 ATTTCTTTATCAATA
32664354 ATTTCTTTATCAAT
1 ATTTCTTTATCAAT
32664368 TTGTTGATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
13 6 0.27
14 10 0.45
15 6 0.27
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTCTTTATCAATA
Done.