Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 16 of 26
Found at i:2619558 original size:2 final size:2
Alignment explanation
Indices: 2619551--2619576 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2619541 AAAGGGACAC
2619551 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2619577 GACCACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2620635 original size:4 final size:4
Alignment explanation
Indices: 2620626--2620654 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2620616 CTTCTTTAAG
2620626 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
2620655 GCCAAAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2621219 original size:2 final size:2
Alignment explanation
Indices: 2621212--2621254 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
2621202 CATTCGTTGG
* *
2621212 AT AT AT AT AT AA AT A- AT AT AT AT AT AT AT AT GT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2621252 AT A
1 AT A
2621255 GTAGTCAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2621238 original size:21 final size:21
Alignment explanation
Indices: 2621212--2621254 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2621202 CATTCGTTGG
2621212 ATATATATATAAATAATATAT
1 ATATATATATAAATAATATAT
**
2621233 ATATATATATGTATAATATAT
1 ATATATATATAAATAATATAT
2621254 A
1 A
2621255 GTAGTCAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATATATATAAATAATATAT
Found at i:2623061 original size:2 final size:2
Alignment explanation
Indices: 2623054--2623082 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2623044 CCTTTTGGCT
2623054 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
2623083 GGATGATGCT
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:2627599 original size:5 final size:5
Alignment explanation
Indices: 2627582--2627613 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
2627572 AAAATTTTAA
*
2627582 TAATT TAAAT TAATT TAATT TAATT TAATT TA
1 TAATT TAATT TAATT TAATT TAATT TAATT TA
2627614 TTATTTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
TAATT
Found at i:2627625 original size:20 final size:20
Alignment explanation
Indices: 2627577--2627649 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
2627567 AATTAAAAAT
*
2627577 TTTAATAATTTAAATTA--A
1 TTTAATAATTTAATTTATTA
2627595 TTTAATTTAATTTAATTTATTA
1 TTTAA--TAATTTAATTTATTA
** *
2627617 TTTAATAATAAAATTTTTTA
1 TTTAATAATTTAATTTATTA
2627637 TTT-A-AATTTAATT
1 TTTAATAATTTAATT
2627650 ATAAAAATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 12 0.27
19 1 0.02
20 26 0.58
22 6 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATAATTTAATTTATTA
Found at i:2633510 original size:12 final size:12
Alignment explanation
Indices: 2633485--2633517 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2633475 ATACTTAAAA
2633485 TGCTGCTG-TGG
1 TGCTGCTGCTGG
*
2633496 TGCTGGTGCTGG
1 TGCTGCTGCTGG
2633508 TGCTGCTGCT
1 TGCTGCTGCT
2633518 ACTGCTACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.00, C:0.21, G:0.42, T:0.36
Consensus pattern (12 bp):
TGCTGCTGCTGG
Found at i:2635233 original size:2 final size:2
Alignment explanation
Indices: 2635226--2635256 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2635216 GCCCCAATGA
2635226 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2635257 GAAACAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2636061 original size:2 final size:2
Alignment explanation
Indices: 2636056--2636094 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2636046 GCTGTGGAAA
2636056 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2636095 AACAGTTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2642275 original size:18 final size:20
Alignment explanation
Indices: 2642249--2642285 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
2642239 AATGTTATGA
2642249 AAAAACTAT-AA-AAATACC
1 AAAAACTATGAAGAAATACC
*
2642267 AAAATCTATGAAGAAATAC
1 AAAAACTATGAAGAAATAC
2642286 ATATAAGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 2 0.12
20 6 0.38
ACGTcount: A:0.62, C:0.14, G:0.05, T:0.19
Consensus pattern (20 bp):
AAAAACTATGAAGAAATACC
Found at i:2642465 original size:2 final size:2
Alignment explanation
Indices: 2642450--2642493 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2642440 CACCAGTTGC
* *
2642450 GT GT GT GA GC GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2642492 GT
1 GT
2642494 TTGTATGAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.02, C:0.02, G:0.50, T:0.45
Consensus pattern (2 bp):
GT
Found at i:2648719 original size:6 final size:6
Alignment explanation
Indices: 2648700--2648741 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
2648690 TTTTTGAAGC
* *
2648700 AAAGACA AAGGAA AAAGAA AAA-AA AAAGAA AAAGAA ATAGAA
1 AAAGA-A AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
2648742 TAGAAAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
5 5 0.16
6 22 0.71
7 4 0.13
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:2648773 original size:16 final size:15
Alignment explanation
Indices: 2648700--2648777 Score: 54
Period size: 15 Copynumber: 5.1 Consensus size: 15
2648690 TTTTTGAAGC
*
2648700 AAAGACAAAGGAAAA
1 AAAGAAAAAGGAAAA
*
2648715 AGAA-AAAAA-AAAGAA
1 A-AAGAAAAAGGAA-AA
* *
2648730 AAAGAAATA-GAATAG
1 AAAGAAAAAGGAA-AA
*
2648745 AAAGAAAAGGGAAAA
1 AAAGAAAAAGGAAAA
2648760 AAAGTAAAAAGGAAAA
1 AAAG-AAAAAGGAAAA
2648776 AA
1 AA
2648778 TAAATGAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
14 4 0.08
15 27 0.56
16 17 0.35
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.04
Consensus pattern (15 bp):
AAAGAAAAAGGAAAA
Found at i:2654029 original size:33 final size:34
Alignment explanation
Indices: 2653962--2654043 Score: 105
Period size: 33 Copynumber: 2.4 Consensus size: 34
2653952 ATAATCGAAT
* *
2653962 TTAAAATATTAATATTTATATAAATATTAATATA
1 TTAATATATTTATATTTATATAAATATTAATATA
* *
2653996 TTAATAT-TTTATATTGTATA-AAATTTTATTATA
1 TTAATATATTTATATT-TATATAAATATTAATATA
2654029 TTAATATATTTATAT
1 TTAATATATTTATAT
2654044 AATATTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 25 0.60
34 17 0.40
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (34 bp):
TTAATATATTTATATTTATATAAATATTAATATA
Found at i:2654054 original size:24 final size:24
Alignment explanation
Indices: 2654022--2654068 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2654012 TATAAAATTT
2654022 TATTATATTAATATATTTATATAA
1 TATTATATTAATATATTTATATAA
* * *
2654046 TATTTTATTATTTTATTTATATA
1 TATTATATTAATATATTTATATA
2654069 TTTAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TATTATATTAATATATTTATATAA
Found at i:2654068 original size:32 final size:30
Alignment explanation
Indices: 2653973--2654072 Score: 91
Period size: 32 Copynumber: 3.2 Consensus size: 30
2653963 TAAAATATTA
*
2653973 ATATTTATATAAATATTAATATATTAATATTT-T
1 ATATTTATATAAAT-TTTAT-TATT--TATTTAT
*
2654006 ATATTGTATA-AAATTTTATTA--TATTAAT
1 ATATT-TATATAAATTTTATTATTTATTTAT
2654034 ATATTTATATAATATTTTATTATTTTATTTAT
1 ATATTTATATAA-ATTTTATTA-TTTATTTAT
2654066 ATATTTA
1 ATATTTA
2654073 AAAATTAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
27 8 0.14
28 8 0.14
29 9 0.16
31 2 0.04
32 17 0.30
33 9 0.16
34 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
ATATTTATATAAATTTTATTATTTATTTAT
Found at i:2654418 original size:17 final size:17
Alignment explanation
Indices: 2654392--2654427 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2654382 TAATAATAAT
*
2654392 TATAATATAAAAAAATA
1 TATAAAATAAAAAAATA
*
2654409 TATAAAATAAAAATATA
1 TATAAAATAAAAAAATA
2654426 TA
1 TA
2654428 AATCTCCATC
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):
TATAAAATAAAAAAATA
Found at i:2656385 original size:130 final size:131
Alignment explanation
Indices: 2656147--2656408 Score: 472
Period size: 130 Copynumber: 2.0 Consensus size: 131
2656137 AGCAGTCAAG
*
2656147 TAAATGGACATAATGGTGAACATTAAACAATGCGTTATTACAGATTTTGCAAGAAATGGCTAATT
1 TAAATGGACATAATGGTGAACATTAAACAATGCGTTATTACAAATTTTGCAAGAAATGGCTAATT
*
2656212 AGGACTACAATTACTAGAGAATTAGGTTCATCTTCCTTGAACTTACATTTAACTCTTTACAAAAT
66 AGGACTACAATTACCAGAGAATTAGGTTCATCTTCCTTGAACTTACATTTAACTCTTTACAAAAT
2656277 T
131 T
*
2656278 TAAA-GGACATAATGGTGAACATTAAACAATGTGTTATTACAAATTTTGCAAGAAATGGCTAATT
1 TAAATGGACATAATGGTGAACATTAAACAATGCGTTATTACAAATTTTGCAAGAAATGGCTAATT
* *
2656342 AGGACTACGATTACCAGAGAATTAGGTTCATCTTCTTTGAACTTACATTTAACTCTTTACAAAAT
66 AGGACTACAATTACCAGAGAATTAGGTTCATCTTCCTTGAACTTACATTTAACTCTTTACAAAAT
2656407 T
131 T
2656408 T
1 T
2656409 TGGAGGAGGA
Statistics
Matches: 126, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
130 122 0.97
131 4 0.03
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (131 bp):
TAAATGGACATAATGGTGAACATTAAACAATGCGTTATTACAAATTTTGCAAGAAATGGCTAATT
AGGACTACAATTACCAGAGAATTAGGTTCATCTTCCTTGAACTTACATTTAACTCTTTACAAAAT
T
Found at i:2658762 original size:4 final size:4
Alignment explanation
Indices: 2658755--2658785 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2658745 TATATGTGTA
*
2658755 TATG TATG TATG TATG TATG TATG CATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
2658786 TTTGGGCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:2659157 original size:27 final size:27
Alignment explanation
Indices: 2659119--2659172 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
2659109 TTATATAAAT
2659119 ATATAAGAAAATGGATACTCCTATCAC
1 ATATAAGAAAATGGATACTCCTATCAC
2659146 ATATAAGAAAATGGATACTCCTATCAC
1 ATATAAGAAAATGGATACTCCTATCAC
2659173 GGCTGAGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (27 bp):
ATATAAGAAAATGGATACTCCTATCAC
Found at i:2659583 original size:16 final size:16
Alignment explanation
Indices: 2659535--2659585 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
2659525 TTAATTAAAA
*
2659535 TTATAAATAATTTTAT
1 TTATAAATAATTATAT
* *
2659551 TTA-AAATTATTAAAT
1 TTATAAATAATTATAT
*
2659566 TTATATATAATTATAT
1 TTATAAATAATTATAT
2659582 TTAT
1 TTAT
2659586 TTAATCAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATAAATAATTATAT
Found at i:2659923 original size:2 final size:2
Alignment explanation
Indices: 2659916--2659944 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2659906 TTGGTTAATA
2659916 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2659945 TGGTTTTATT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2660418 original size:2 final size:2
Alignment explanation
Indices: 2660411--2660435 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2660401 AATTCGATAC
2660411 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
2660436 CACACATACA
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:2668231 original size:2 final size:2
Alignment explanation
Indices: 2668224--2668254 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2668214 AAACCTCTTC
2668224 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2668255 ACTCAAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2668731 original size:10 final size:10
Alignment explanation
Indices: 2668718--2668773 Score: 53
Period size: 11 Copynumber: 5.4 Consensus size: 10
2668708 AATTTTAATT
2668718 TATTTATTTA
1 TATTTATTTA
2668728 TATTTATATTA
1 TATTTAT-TTA
*
2668739 TATTATATTTT
1 TATT-TATTTA
2668750 TATTTACTTTCA
1 TATTTA-TTT-A
2668762 T-TTT-TTTA
1 TATTTATTTA
2668770 TATT
1 TATT
2668774 CGAAACAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
8 2 0.05
9 5 0.13
10 9 0.23
11 19 0.49
12 4 0.10
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.70
Consensus pattern (10 bp):
TATTTATTTA
Found at i:2668744 original size:16 final size:15
Alignment explanation
Indices: 2668711--2668753 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
2668701 AAAAAATAAT
2668711 TTTA-ATTTAT-TTA
1 TTTATATTTATATTA
2668724 TTTATATTTATATTA
1 TTTATATTTATATTA
*
2668739 TATTATATTTTTATT
1 T-TTATATTTATATT
2668754 TACTTTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 4 0.15
14 6 0.23
15 4 0.15
16 12 0.46
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTATATTTATATTA
Found at i:2669068 original size:18 final size:17
Alignment explanation
Indices: 2669042--2669122 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 17
2669032 TATTTAAAAT
*
2669042 ATTTTATATTCATATAAA
1 ATTTAATATT-ATATAAA
* *
2669060 ATTTAATA-TATTTATA
1 ATTTAATATTATATAAA
2669076 A-TTAATATTATATAAA
1 ATTTAATATTATATAAA
* *
2669092 TTTTAAAATACTTATATAAT
1 ATTT--AATA-TTATATAAA
2669112 ATTT-ATATTAT
1 ATTTAATATTAT
2669123 TTTTTACATT
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
15 6 0.12
16 16 0.32
17 6 0.12
18 7 0.14
19 4 0.08
20 11 0.22
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTAATATTATATAAA
Found at i:2669097 original size:32 final size:30
Alignment explanation
Indices: 2669033--2669119 Score: 83
Period size: 32 Copynumber: 2.9 Consensus size: 30
2669023 TTATAATCGT
2669033 ATTTAAAATA-TT-T-T-ATATTCATATAAA
1 ATTTAAAATACTTATATAATATT-ATATAAA
* *
2669060 ATTTAATATATTTATAATTAATATTATATAAA
1 ATTTAAAATACTTAT-A-TAATATTATATAAA
*
2669092 TTTTAAAATACTTATATAATATTTATAT
1 ATTTAAAATACTTATATAATA-TTATAT
2669120 TATTTTTTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
27 9 0.18
28 2 0.04
29 1 0.02
30 5 0.10
31 7 0.14
32 20 0.41
33 5 0.10
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (30 bp):
ATTTAAAATACTTATATAATATTATATAAA
Found at i:2669117 original size:11 final size:11
Alignment explanation
Indices: 2669047--2669119 Score: 57
Period size: 11 Copynumber: 6.9 Consensus size: 11
2669037 AAAATATTTT
*
2669047 ATATTCATATA
1 ATATTTATATA
*
2669058 AAATTTA-AT-
1 ATATTTATATA
2669067 ATATTTATAATTA
1 ATATTTAT-A-TA
2669080 ATA-TTATATA
1 ATATTTATATA
*
2669090 A-ATTT-TAAA
1 ATATTTATATA
*
2669099 ATACTTATATA
1 ATATTTATATA
2669110 ATATTTATAT
1 ATATTTATAT
2669120 TATTTTTTAC
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
9 11 0.23
10 10 0.21
11 19 0.40
12 5 0.10
13 3 0.06
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (11 bp):
ATATTTATATA
Found at i:2672151 original size:2 final size:2
Alignment explanation
Indices: 2672144--2672181 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2672134 GGTCTTTGAA
2672144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2672182 GTTTTAGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2684499 original size:17 final size:17
Alignment explanation
Indices: 2684479--2684513 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2684469 AAATAATTAA
2684479 ATATATTAATATTAGAC
1 ATATATTAATATTAGAC
* *
2684496 ATATATTTATATTTGAC
1 ATATATTAATATTAGAC
2684513 A
1 A
2684514 CTCAATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (17 bp):
ATATATTAATATTAGAC
Found at i:2685669 original size:18 final size:19
Alignment explanation
Indices: 2685632--2685678 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
2685622 AATTTAAATC
2685632 AATATTTATAAAATAATAA
1 AATATTTATAAAATAATAA
2685651 AATATTT-TAAAA-AATTAA
1 AATATTTATAAAATAA-TAA
2685669 AATATTTATA
1 AATATTTATA
2685679 TTTATATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.08
18 15 0.58
19 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AATATTTATAAAATAATAA
Found at i:2687131 original size:2 final size:2
Alignment explanation
Indices: 2687120--2687152 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2687110 TTCACAATAG
2687120 TA TA -A 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
2687153 AAATTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2689767 original size:2 final size:2
Alignment explanation
Indices: 2689760--2689794 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2689750 CTAACAGTTT
2689760 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
2689795 TATTTTCTAT
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:2696572 original size:37 final size:35
Alignment explanation
Indices: 2696504--2696608 Score: 93
Period size: 36 Copynumber: 2.8 Consensus size: 35
2696494 TTTAATTCAT
*
2696504 ATAAATAATTTAAATTCATAAATTTAAATATAATAAATAAA
1 ATAAA-AAATTAAATT-A-AAATTT--ATATAATAAA-AAA
* * *
2696545 ATAAAAAATTAAATATGATATTTATATAATATAAAA
1 ATAAAAAATTAAAT-TAAAATTTATATAATAAAAAA
* *
2696581 ATATAAAATTATATTAAAATTTATATAA
1 ATAAAAAATTAAATTAAAATTTATATAA
2696609 ATATATAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
35 12 0.22
36 15 0.27
37 9 0.16
39 5 0.09
40 8 0.15
41 6 0.11
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (35 bp):
ATAAAAAATTAAATTAAAATTTATATAATAAAAAA
Found at i:2696611 original size:28 final size:26
Alignment explanation
Indices: 2696574--2696625 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
2696564 ATTTATATAA
2696574 TATAAAAATATAAAATTATATTAAAATT
1 TATAAAAATATAAAA-TAT-TTAAAATT
* *
2696602 TATATAAATATATAATATTTAAAA
1 TATAAAAATATAAAATATTTAAAA
2696626 ACAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 3 0.14
28 13 0.59
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TATAAAAATATAAAATATTTAAAATT
Found at i:2702755 original size:25 final size:24
Alignment explanation
Indices: 2702723--2702772 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
2702713 GTTTAGGAAA
* *
2702723 TTTTTTTACATTTAATAAAT-TACG
1 TTTTTTTA-ATTAAAAAAATGTACG
2702747 TTTTATTTAATTAAAAAAATGTACG
1 TTTT-TTTAATTAAAAAAATGTACG
2702772 T
1 T
2702773 ATTCAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (24 bp):
TTTTTTTAATTAAAAAAATGTACG
Found at i:2702996 original size:21 final size:21
Alignment explanation
Indices: 2702966--2703005 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2702956 ATGTAATAAA
2702966 TAATAATTATATAAT-TTTAAT
1 TAATAATTATA-AATATTTAAT
*
2702987 TAATATTTATAAATATTTA
1 TAATAATTATAAATATTTA
2703006 TTTTACTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATAATTATAAATATTTAAT
Found at i:2708871 original size:31 final size:31
Alignment explanation
Indices: 2708809--2708872 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
2708799 TTATTTAAAT
* *
2708809 TTAAATTTTAAAATATTAAAAATTAATATAA
1 TTAAATTTTAAAATATTAAAAATAAAAATAA
* *
2708840 TTAAATTATTTAAATATT-AATATAAAAATAA
1 TTAAATT-TTAAAATATTAAAAATAAAAATAA
2708871 TT
1 TT
2708873 TTTAATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 19 0.68
32 9 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TTAAATTTTAAAATATTAAAAATAAAAATAA
Found at i:2709412 original size:13 final size:13
Alignment explanation
Indices: 2709391--2709438 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
2709381 TATTAAAAAA
*
2709391 ATAATTATATAAT
1 ATAAATATATAAT
2709404 ATAAATATATAAT
1 ATAAATATATAAT
* *
2709417 ATTAAA-AAATAAA
1 A-TAAATATATAAT
2709430 ATAAATATA
1 ATAAATATA
2709439 ATATCAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 4 0.14
13 21 0.72
14 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAAATATATAAT
Found at i:2709422 original size:35 final size:37
Alignment explanation
Indices: 2709380--2709449 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
2709370 TAATATTTTT
* *
2709380 ATATTAAAAAA-ATAAT-TATATAATATAAATATATA
1 ATATTAAAAAATAAAATAAATATAATATAAATATATA
*
2709415 ATATTAAAAAATAAAATAAATATAATATCAATATA
1 ATATTAAAAAATAAAATAAATATAATATAAATATA
2709450 AAAATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 11 0.37
36 4 0.13
37 15 0.50
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (37 bp):
ATATTAAAAAATAAAATAAATATAATATAAATATATA
Found at i:2709475 original size:37 final size:37
Alignment explanation
Indices: 2709380--2709457 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
2709370 TAATATTTTT
* * *
2709380 ATATTAAAAAA-ATAAT-TATATAATATAAATATATA
1 ATATTAAAAAATAAAATAAATATAATATAAATATAAA
*
2709415 ATATTAAAAAATAAAATAAATATAATATCAATATAAAA
1 ATATTAAAAAATAAAATAAATATAATATAAATAT-AAA
2709453 ATATT
1 ATATT
2709458 TTAAAATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 11 0.31
36 4 0.11
37 14 0.39
38 7 0.19
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (37 bp):
ATATTAAAAAATAAAATAAATATAATATAAATATAAA
Found at i:2709493 original size:20 final size:19
Alignment explanation
Indices: 2709446--2709495 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
2709436 ATAATATCAA
* *
2709446 TATAAAAATATTTTAAAAT
1 TATATAAATATATTAAAAT
2709465 TATAT-AATATATTAAAATT
1 TATATAAATATATTAAAA-T
*
2709484 TATTTAAATATA
1 TATATAAATATA
2709496 AAATATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 11 0.42
19 9 0.35
20 6 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATAAATATATTAAAAT
Found at i:2710831 original size:20 final size:20
Alignment explanation
Indices: 2710806--2710844 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2710796 TTTTTATGTT
* *
2710806 ATGCATTGCGAGTTCTTTTG
1 ATGCATTGCAAGTTATTTTG
2710826 ATGCATTGCAAGTTATTTT
1 ATGCATTGCAAGTTATTTT
2710845 TAGTGTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGCATTGCAAGTTATTTTG
Found at i:2714307 original size:2 final size:2
Alignment explanation
Indices: 2714300--2714352 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
2714290 ACTTCTGTTC
* *
2714300 TA TA TA TA CA TA TA CA 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
2714342 TA TA TA -A TA TA
1 TA TA TA TA TA TA
2714353 ATCTTTTATG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2718431 original size:14 final size:14
Alignment explanation
Indices: 2718414--2718447 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2718404 AAATTAAAAA
*
2718414 TATTTATTTAATTT
1 TATTTATTAAATTT
*
2718428 TATTTGTTAAATTT
1 TATTTATTAAATTT
2718442 TATTTA
1 TATTTA
2718448 GGTTTATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
TATTTATTAAATTT
Found at i:2718517 original size:14 final size:14
Alignment explanation
Indices: 2718500--2718541 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2718490 GTTAATTTAT
**
2718500 ATTATATTTTTGTA
1 ATTATATTTTTAAA
2718514 ATTA-ATTTTTAAA
1 ATTATATTTTTAAA
*
2718527 AATATATTTTTAAA
1 ATTATATTTTTAAA
2718541 A
1 A
2718542 ATTTAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
ATTATATTTTTAAA
Found at i:2718550 original size:15 final size:15
Alignment explanation
Indices: 2718515--2718567 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
2718505 ATTTTTGTAA
2718515 TTAATTTTTAAAAAT
1 TTAATTTTTAAAAAT
*
2718530 AT-ATTTTTAAAAAT
1 TTAATTTTTAAAAAT
**
2718544 TTAATTTTTATTAAT
1 TTAATTTTTAAAAAT
2718559 TTAATTTTT
1 TTAATTTTT
2718568 TAATAAGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 13 0.39
15 20 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAATTTTTAAAAAT
Found at i:2718567 original size:16 final size:15
Alignment explanation
Indices: 2718515--2718579 Score: 69
Period size: 15 Copynumber: 4.3 Consensus size: 15
2718505 ATTTTTGTAA
*
2718515 TTAATTTTTAAAAAT
1 TTAATTTTTAATAAT
* *
2718530 AT-ATTTTTAAAAAT
1 TTAATTTTTAATAAT
*
2718544 TTAATTTTTATTAAT
1 TTAATTTTTAATAAT
2718559 TTAATTTTTTAATAAGT
1 TTAA-TTTTTAATAA-T
2718576 TTAA
1 TTAA
2718580 AAATATAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
14 13 0.31
15 15 0.36
16 9 0.21
17 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAATTTTTAATAAT
Found at i:2718669 original size:7 final size:7
Alignment explanation
Indices: 2718658--2718687 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
2718648 GATAAAAATT
*
2718658 ATATAAT
1 ATATAAA
2718665 ATATAAA
1 ATATAAA
2718672 ATATAAA
1 ATATAAA
2718679 ATATAAA
1 ATATAAA
2718686 AT
1 AT
2718688 TAATATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
ATATAAA
Found at i:2718675 original size:14 final size:14
Alignment explanation
Indices: 2718658--2718695 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
2718648 GATAAAAATT
2718658 ATATAATATATAAA
1 ATATAATATATAAA
*
2718672 ATATAAAATATAAA
1 ATATAATATATAAA
2718686 AT-TAATATAT
1 ATATAATATAT
2718696 TATTTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATAATATATAAA
Found at i:2721340 original size:15 final size:15
Alignment explanation
Indices: 2721302--2721334 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2721292 CATGAAATGA
*
2721302 CCAAAGCCAATAGAG
1 CCAAAGCCAATACAG
2721317 CCAAAGCCAATACAG
1 CCAAAGCCAATACAG
2721332 CCA
1 CCA
2721335 TTGCCATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.33, G:0.15, T:0.06
Consensus pattern (15 bp):
CCAAAGCCAATACAG
Found at i:2721537 original size:15 final size:16
Alignment explanation
Indices: 2721500--2721537 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
2721490 ATTTAAAATT
2721500 TTTA-TTTAAGTTTAA
1 TTTATTTTAAGTTTAA
2721515 TTTATTTTAA-TTTAA
1 TTTATTTTAAGTTTAA
2721530 TTTATTTT
1 TTTATTTT
2721538 TTAAACTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTATTTTAAGTTTAA
Found at i:2721673 original size:15 final size:16
Alignment explanation
Indices: 2721638--2721674 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
2721628 TGAATCAAAT
2721638 TTTTTAAATTATTTGA
1 TTTTTAAATTATTTGA
2721654 TTTTTAAATATATTT-A
1 TTTTTAAAT-TATTTGA
2721670 TTTTT
1 TTTTT
2721675 GCTAAGTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTTAAATTATTTGA
Found at i:2721896 original size:17 final size:17
Alignment explanation
Indices: 2721868--2721916 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
2721858 TAAATAAAAA
2721868 AATATAATTTTTTATCTT
1 AATAT-ATTTTTTATCTT
* *
2721886 AATATATTTTTAATTTT
1 AATATATTTTTTATCTT
2721903 AAT-TA-TTTTTATCT
1 AATATATTTTTTATCT
2721917 AATTAACTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 7 0.26
16 2 0.07
17 13 0.48
18 5 0.19
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (17 bp):
AATATATTTTTTATCTT
Found at i:2721897 original size:16 final size:15
Alignment explanation
Indices: 2721876--2721921 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
2721866 AAAATATAAT
2721876 TTTTTATCTTAATATA
1 TTTTTATCTTAAT-TA
*
2721892 TTTTTAATTTTAATTA
1 TTTTT-ATCTTAATTA
2721908 TTTTTATC-TAATTA
1 TTTTTATCTTAATTA
2721922 ACTCATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.22
15 2 0.07
16 12 0.44
17 7 0.26
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTATCTTAATTA
Found at i:2724887 original size:15 final size:16
Alignment explanation
Indices: 2724851--2724887 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2724841 GATAATAAAT
2724851 TATAAATATCAAATTA
1 TATAAATATCAAATTA
2724867 -AGTAAATAT-AAATTA
1 TA-TAAATATCAAATTA
2724882 TATAAA
1 TATAAA
2724888 AAATTATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (16 bp):
TATAAATATCAAATTA
Found at i:2725221 original size:18 final size:18
Alignment explanation
Indices: 2725187--2725220 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2725177 ATTTGAAATT
2725187 ATTAAAAATTAAATTTTA
1 ATTAAAAATTAAATTTTA
*
2725205 ATT-AAAATTTAATTTT
1 ATTAAAAATTAAATTTT
2725221 TGTCATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAAAAATTAAATTTTA
Found at i:2727819 original size:2 final size:2
Alignment explanation
Indices: 2727812--2727843 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2727802 TGCAGAGTAC
2727812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2727844 TCTTTTTCAC
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):
AT
Found at i:2728848 original size:15 final size:15
Alignment explanation
Indices: 2728798--2728851 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
2728788 AATTTTAAAA
* *
2728798 TTTTTAATAAT-TAA
1 TTTTTAAAAATATAT
*
2728812 TTTTTAAAAATATGT
1 TTTTTAAAAATATAT
**
2728827 TAATTAAAAATATAT
1 TTTTTAAAAATATAT
2728842 TTTTTAAAAA
1 TTTTTAAAAA
2728852 ATAAATATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 10 0.32
15 21 0.68
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
TTTTTAAAAATATAT
Found at i:2729226 original size:10 final size:11
Alignment explanation
Indices: 2729199--2729232 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
2729189 AATCAAACAG
2729199 TAATATTTAATT
1 TAAT-TTTAATT
2729211 TAATTTTAATT
1 TAATTTTAATT
2729222 T-ATTTTAATT
1 TAATTTTAATT
2729232 T
1 T
2729233 TAATATTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 8 0.36
12 4 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TAATTTTAATT
Found at i:2729228 original size:16 final size:16
Alignment explanation
Indices: 2729203--2729236 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2729193 AAACAGTAAT
2729203 ATTTAATTTAATTTTA
1 ATTTAATTTAATTTTA
*
2729219 ATTTATTTTAATTTTA
1 ATTTAATTTAATTTTA
2729235 AT
1 AT
2729237 ATTGATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTAATTTAATTTTA
Found at i:2732624 original size:2 final size:2
Alignment explanation
Indices: 2732617--2732648 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2732607 TCGACGTTAG
2732617 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2732649 ACACACACAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2732653 original size:2 final size:2
Alignment explanation
Indices: 2732648--2732673 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2732638 CTCTCTCTCT
2732648 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
2732674 GAGGGACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2733214 original size:2 final size:2
Alignment explanation
Indices: 2733207--2733246 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2733197 TTGCAGTTTG
2733207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2733247 CTATCGCGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2733576 original size:14 final size:13
Alignment explanation
Indices: 2733557--2733586 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
2733547 GTTTAAAAAG
2733557 TTTTATATTTTATA
1 TTTTATA-TTTATA
2733571 TTTTATATTTATA
1 TTTTATATTTATA
2733584 TTT
1 TTT
2733587 AAATATGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTATATTTATA
Found at i:2733587 original size:6 final size:7
Alignment explanation
Indices: 2733557--2733586 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2733547 GTTTAAAAAG
2733557 TTTTATA
1 TTTTATA
2733564 TTTTATA
1 TTTTATA
2733571 TTTTATA
1 TTTTATA
2733578 -TTTATA
1 TTTTATA
2733584 TTT
1 TTT
2733587 AAATATGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTATA
Found at i:2733782 original size:14 final size:14
Alignment explanation
Indices: 2733765--2733795 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2733755 TTATATTCTG
*
2733765 AATATTATAATAAT
1 AATATAATAATAAT
2733779 AATATAATAATAAT
1 AATATAATAATAAT
2733793 AAT
1 AAT
2733796 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATATAATAATAAT
Found at i:2736842 original size:2 final size:2
Alignment explanation
Indices: 2736835--2736870 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2736825 GGCAGACTGG
2736835 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
2736871 CAAGTGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2738753 original size:22 final size:22
Alignment explanation
Indices: 2738728--2738781 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2738718 GATTATAATT
2738728 TAATATTTATATTATTATTTT-A
1 TAATATTTATATT-TTATTTTCA
* *
2738750 TAATTTTTA-ATTTTTTTTTCGA
1 TAATATTTATATTTTATTTTC-A
2738772 TAATATTTAT
1 TAATATTTAT
2738782 TATAATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 6 0.23
21 3 0.12
22 17 0.65
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TAATATTTATATTTTATTTTCA
Found at i:2741650 original size:21 final size:21
Alignment explanation
Indices: 2741624--2741665 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2741614 ATAATTTAAA
*
2741624 TTATTATTTAATAAAAA-ATAT
1 TTATTAATT-ATAAAAATATAT
2741645 TTATTAATTATAAAAATATAT
1 TTATTAATTATAAAAATATAT
2741666 AAATATTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTATTAATTATAAAAATATAT
Found at i:2741886 original size:71 final size:72
Alignment explanation
Indices: 2741807--2741947 Score: 187
Period size: 71 Copynumber: 2.0 Consensus size: 72
2741797 ACCACAAGGA
* *
2741807 TCTGAGATGAGCA-AAGTGGGAACCAAGCGAAAGTGGTCCTGGAGTTTAACTGGG-CAACTCAAG
1 TCTGAGATGAGCACAA-TGAGAACCAAGCGAAAGTGGTCCTGGAGTTTAACCGGGCCAACTCAAG
2741870 GTACCATT
65 GTACCATT
* * * * *
2741878 TCTGAGATGTGCACAATGAGAACCAAGGGAGAGTGGTCCTGGTGTTTAGCCGGGCTCAACTCAAG
1 TCTGAGATGAGCACAATGAGAACCAAGCGAAAGTGGTCCTGGAGTTTAACCGGGC-CAACTCAAG
2741943 GTACC
65 GTACC
2741948 TATGGCACTG
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
71 44 0.73
72 2 0.03
73 14 0.23
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.21
Consensus pattern (72 bp):
TCTGAGATGAGCACAATGAGAACCAAGCGAAAGTGGTCCTGGAGTTTAACCGGGCCAACTCAAGG
TACCATT
Found at i:2742922 original size:2 final size:2
Alignment explanation
Indices: 2742917--2742949 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2742907 TCAAAATTTC
2742917 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2742950 TTTAAGTACG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2743454 original size:2 final size:2
Alignment explanation
Indices: 2743447--2743490 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2743437 TAATCATGTC
2743447 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
2743489 TA
1 TA
2743491 ATGCTCCTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2743731 original size:27 final size:27
Alignment explanation
Indices: 2743701--2743756 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
2743691 TGATCATAAA
* *
2743701 ATATTAGATTGTAAAATCGACATTTGG
1 ATATTAAATTATAAAATCGACATTTGG
*
2743728 ATATTAAATTATAGAATCGACATTTGG
1 ATATTAAATTATAAAATCGACATTTGG
2743755 AT
1 AT
2743757 CGAATATAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (27 bp):
ATATTAAATTATAAAATCGACATTTGG
Found at i:2744115 original size:3 final size:3
Alignment explanation
Indices: 2744107--2744139 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2744097 GACAAAGATA
2744107 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2744140 GTAAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2744381 original size:2 final size:2
Alignment explanation
Indices: 2744374--2744434 Score: 63
Period size: 2 Copynumber: 30.5 Consensus size: 2
2744364 ATGAATTAAC
* *
2744374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AC A- AC AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
*
2744415 AT GT AT AT ACT AT AT AT AT A
1 AT AT AT AT A-T AT AT AT AT A
2744435 GTACAACATT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
1 2 0.04
2 45 0.88
3 4 0.08
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2744451 original size:30 final size:29
Alignment explanation
Indices: 2744389--2744452 Score: 101
Period size: 30 Copynumber: 2.2 Consensus size: 29
2744379 TATATATATA
*
2744389 TATATATATATATATAGTACAACATTATG
1 TATATATATATATATAGTACAACATTAGG
*
2744418 TATATACTATATATATAGTACAACATTCGG
1 TATATA-TATATATATAGTACAACATTAGG
2744448 TATAT
1 TATAT
2744453 GCTAATTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (29 bp):
TATATATATATATATAGTACAACATTAGG
Found at i:2747495 original size:25 final size:25
Alignment explanation
Indices: 2747461--2747517 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
2747451 TGTTGAACCT
*
2747461 AAAATGTATGACAGCAACCACAATC
1 AAAATCTATGACAGCAACCACAATC
2747486 AAAATCTATGACAGCAACCACAATC
1 AAAATCTATGACAGCAACCACAATC
2747511 AAAATCT
1 AAAATCT
2747518 CATAACACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.49, C:0.25, G:0.09, T:0.18
Consensus pattern (25 bp):
AAAATCTATGACAGCAACCACAATC
Found at i:2748837 original size:27 final size:28
Alignment explanation
Indices: 2748807--2748860 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 28
2748797 ATTTAAAAAT
*
2748807 TAATAAAAGATAAA-AATATATATTTTA
1 TAATAAAAGATAAATAAAATATATTTTA
* **
2748834 TAATTAAATTTAAATAAAATATATTTT
1 TAATAAAAGATAAATAAAATATATTTT
2748861 TATTATTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (28 bp):
TAATAAAAGATAAATAAAATATATTTTA
Found at i:2766045 original size:10 final size:10
Alignment explanation
Indices: 2766030--2766059 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2766020 ATAAATTATT
2766030 AATATATAAA
1 AATATATAAA
2766040 AATATATAAA
1 AATATATAAA
*
2766050 AATATTTAAA
1 AATATATAAA
2766060 TAAAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AATATATAAA
Found at i:2766375 original size:18 final size:19
Alignment explanation
Indices: 2766346--2766393 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
2766336 ACAAGTAAGT
2766346 TAAAATAAAAAATTTATGAAA
1 TAAAAT-AAAAATTTAT-AAA
2766367 -AAAATAAAAATTTA-AAA
1 TAAAATAAAAATTTATAAA
2766384 TAAAATAAAA
1 TAAAATAAAA
2766394 GTTATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.12
18 9 0.35
19 9 0.35
20 5 0.19
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (19 bp):
TAAAATAAAAATTTATAAA
Found at i:2766590 original size:28 final size:28
Alignment explanation
Indices: 2766535--2766618 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 28
2766525 ATTTATTATG
* *
2766535 AATAAGTTCAAATAAAAA-TTTATGAAA
1 AATAAGTTAAAATAAAAATTTTATAAAA
2766562 AATAAGTTAAAATAAAAATTTTATAAAA
1 AATAAGTTAAAATAAAAATTTTATAAAA
* * *
2766590 AATAAGTTGAAATATAAATCTTATAAAA
1 AATAAGTTAAAATAAAAATTTTATAAAA
2766618 A
1 A
2766619 TTAATAACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 17 0.33
28 34 0.67
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (28 bp):
AATAAGTTAAAATAAAAATTTTATAAAA
Found at i:2769097 original size:19 final size:18
Alignment explanation
Indices: 2769073--2769120 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
2769063 TATGTAAATA
2769073 TAAATAAAATATAAATTAT
1 TAAATAAAATATAAATT-T
*
2769092 TAAATAAATTA-AAATTT
1 TAAATAAAATATAAATTT
*
2769109 TAAATATAATAT
1 TAAATAAAATAT
2769121 TAAAAGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 5 0.20
19 10 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATAAAATATAAATTT
Found at i:2769104 original size:17 final size:18
Alignment explanation
Indices: 2769073--2769125 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
2769063 TATGTAAATA
2769073 TAAATAAA-ATATAAATTAT
1 TAAATAAATATA-AAATT-T
2769092 TAAATAAAT-TAAAATTT
1 TAAATAAATATAAAATTT
2769109 TAAATATAATATTAAAA
1 TAAATA-AATA-TAAAA
2769126 GATATTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.23
18 8 0.27
19 10 0.33
20 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATAAATATAAAATTT
Found at i:2770122 original size:17 final size:18
Alignment explanation
Indices: 2770102--2770144 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
2770092 ATTATATTAA
2770102 TATTTTTAATT-AAAAAG
1 TATTTTTAATTAAAAAAG
*
2770119 TATTTTTTATTAAAAAAAG
1 TATTTTTAATT-AAAAAAG
2770138 TATTTTT
1 TATTTTT
2770145 GTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.43
19 13 0.57
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
TATTTTTAATTAAAAAAG
Found at i:2770397 original size:16 final size:15
Alignment explanation
Indices: 2770376--2770426 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
2770366 AAATATATAA
*
2770376 AATATTTTATTATATT
1 AATATTTAATT-TATT
2770392 AATATTTAATTTATT
1 AATATTTAATTTATT
*
2770407 ATTAATTTAAATTT-TT
1 AAT-ATTT-AATTTATT
2770423 AATA
1 AATA
2770427 AATTTTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 7 0.23
16 18 0.60
17 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
AATATTTAATTTATT
Found at i:2770434 original size:13 final size:13
Alignment explanation
Indices: 2770418--2770446 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2770408 TTAATTTAAA
2770418 TTTTTAAT-AAAT
1 TTTTTAATAAAAT
2770430 TTTTTAATAAAAT
1 TTTTTAATAAAAT
2770443 TTTT
1 TTTT
2770447 ATCATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTAATAAAAT
Found at i:2770435 original size:12 final size:11
Alignment explanation
Indices: 2770414--2770447 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
2770404 ATTATTAATT
2770414 TAAATTTTTAA
1 TAAATTTTTAA
2770425 TAAATTTTTTAA
1 TAAA-TTTTTAA
2770437 TAAAATTTTTA
1 T-AAATTTTTA
2770448 TCATTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 14 0.67
13 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TAAATTTTTAA
Found at i:2773512 original size:2 final size:2
Alignment explanation
Indices: 2773505--2773541 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2773495 GCAATATGTA
* *
2773505 TG TG TG TG TC TT TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2773542 AGATATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.03, G:0.43, T:0.54
Consensus pattern (2 bp):
TG
Found at i:2790717 original size:2 final size:2
Alignment explanation
Indices: 2790710--2790737 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2790700 TCAGAAATTC
2790710 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2790738 TGCTTGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2792116 original size:62 final size:63
Alignment explanation
Indices: 2792030--2792158 Score: 192
Period size: 62 Copynumber: 2.1 Consensus size: 63
2792020 AAATTTCGCT
*
2792030 AAATCTTTGGATTCTGATTTATTATAATTAGGTTTAGAGAG-TTTTTATTTATTT-ATTAAACC
1 AAATCTTTGGATTCTGATTCATTATAATTAGGTTTAGAGAGATTTTT-TTTATTTAATTAAACC
* *
2792092 AAATGTTTGGATGT-TGATTCATTATAATTAGGTTTAGAGAGATTTTTTTTATTTAATTGAACC
1 AAATCTTTGGAT-TCTGATTCATTATAATTAGGTTTAGAGAGATTTTTTTTATTTAATTAAACC
2792155 AAAT
1 AAAT
2792159 ATTCAGATGT
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
62 44 0.72
63 17 0.28
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.48
Consensus pattern (63 bp):
AAATCTTTGGATTCTGATTCATTATAATTAGGTTTAGAGAGATTTTTTTTATTTAATTAAACC
Found at i:2792956 original size:51 final size:51
Alignment explanation
Indices: 2792901--2793003 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
2792891 GGCTTATAAA
2792901 TGATTCATAATGAGCAAATAATTCAAAAATAACTGATAAGTTATTTATTTT
1 TGATTCATAATGAGCAAATAATTCAAAAATAACTGATAAGTTATTTATTTT
2792952 TGATTCATAATGAGCAAATAATTCAAAAATAACTGATAAGTTATTTATTTT
1 TGATTCATAATGAGCAAATAATTCAAAAATAACTGATAAGTTATTTATTTT
2793003 T
1 T
2793004 ATTTTTCATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.40
Consensus pattern (51 bp):
TGATTCATAATGAGCAAATAATTCAAAAATAACTGATAAGTTATTTATTTT
Found at i:2793590 original size:2 final size:2
Alignment explanation
Indices: 2793583--2793607 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2793573 TGTAATGAAA
2793583 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
2793608 GCTCGAAAAA
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:2793668 original size:2 final size:2
Alignment explanation
Indices: 2793661--2793699 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2793651 TACTTCCTTT
2793661 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2793700 CCCAAAAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2793844 original size:15 final size:14
Alignment explanation
Indices: 2793809--2793836 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2793799 AATTATAAAA
2793809 AATATAAAAATATT
1 AATATAAAAATATT
2793823 AATATAAAAATATT
1 AATATAAAAATATT
2793837 TTTTATAATA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATAAAAATATT
Found at i:2793847 original size:20 final size:19
Alignment explanation
Indices: 2793822--2793865 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2793812 ATAAAAATAT
2793822 TAATATAAAAATATTTTTTA
1 TAATATAAAAATA-TTTTTA
***
2793842 TAATATTTTAATATTTTTA
1 TAATATAAAAATATTTTTA
2793861 TAATA
1 TAATA
2793866 ATTTTAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATATAAAAATATTTTTA
Found at i:2793860 original size:19 final size:21
Alignment explanation
Indices: 2793831--2793873 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
2793821 TTAATATAAA
2793831 AATATTTTTTATAAT-ATTTT
1 AATATTTTTTATAATAATTTT
2793851 AATA-TTTTTATAATAATTTT
1 AATATTTTTTATAATAATTTT
2793871 AAT
1 AAT
2793874 TTACAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AATATTTTTTATAATAATTTT
Found at i:2794192 original size:2 final size:2
Alignment explanation
Indices: 2794185--2794218 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2794175 TTCCAAGATC
*
2794185 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2794219 TTTTTTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2795530 original size:27 final size:29
Alignment explanation
Indices: 2795472--2795534 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 29
2795462 CAATTTAAAA
* *
2795472 AATATAAAAATTAAATTTTTTAATTTTTT
1 AATATAAAAATTAAATTTTTTAACTTTAT
*
2795501 AATATTAAAATT-AATTTTTT-ACTTTAT
1 AATATAAAAATTAAATTTTTTAACTTTAT
2795528 AATATAA
1 AATATAA
2795535 TATAAGGACC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 11 0.37
28 8 0.27
29 11 0.37
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
AATATAAAAATTAAATTTTTTAACTTTAT
Found at i:2795708 original size:2 final size:2
Alignment explanation
Indices: 2795701--2795728 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2795691 TAACAACTTC
2795701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2795729 GCAATATTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2799469 original size:2 final size:2
Alignment explanation
Indices: 2799445--2799494 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
2799435 GCCATTTATG
* * *
2799445 TA TA AA TA TA TA CA TA TA CA 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
2799487 TA TA TA TA
1 TA TA TA TA
2799495 AGAATAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2800069 original size:17 final size:16
Alignment explanation
Indices: 2800047--2800101 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
2800037 TAAATTAAAA
2800047 TTTTAAAAAGTTTTATT
1 TTTTAAAAA-TTTTATT
2800064 TTTTAATAAATTTT-TT
1 TTTTAA-AAATTTTATT
* *
2800080 TATCAAAAATCTTTATT
1 TTTTAAAAAT-TTTATT
2800097 TTTTA
1 TTTTA
2800102 GCCTTAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 4 0.13
16 9 0.29
17 15 0.48
18 3 0.10
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTAAAAATTTTATT
Found at i:2800213 original size:19 final size:20
Alignment explanation
Indices: 2800172--2800215 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2800162 TAGAAATAAA
***
2800172 AAAAAATCATATTTGTTTAT
1 AAAAAATCATATTTCAATAT
2800192 AAAAAATCATATTTCAAT-T
1 AAAAAATCATATTTCAATAT
2800211 AAAAA
1 AAAAA
2800216 GTAATTTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAAATCATATTTCAATAT
Found at i:2808515 original size:20 final size:20
Alignment explanation
Indices: 2808474--2808527 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
2808464 AGCCAATATT
** *
2808474 ATATATTTTTT-ATTTTTTA
1 ATATATTTTTTAATAATTAA
2808493 ATATATTTTTTAATAATTAA
1 ATATATTTTTTAATAATTAA
2808513 ATATA-TTTTTAATAA
1 ATATATTTTTTAATAA
2808528 GTTTTTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 21 0.68
20 10 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATATTTTTTAATAATTAA
Found at i:2808644 original size:17 final size:18
Alignment explanation
Indices: 2808622--2808658 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
2808612 AAATTATAAC
2808622 TATTATTTTA-AAAAATA
1 TATTATTTTATAAAAATA
2808639 TATTATTTTATAAAAATA
1 TATTATTTTATAAAAATA
2808657 TA
1 TA
2808659 AAATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTATTTTATAAAAATA
Found at i:2808664 original size:18 final size:17
Alignment explanation
Indices: 2808626--2808665 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
2808616 TATAACTATT
**
2808626 ATTTTAAAAAATATATT
1 ATTTTAAAAAATATAAA
2808643 ATTTTATAAAAATATAAA
1 ATTTTA-AAAAATATAAA
2808661 ATTTT
1 ATTTT
2808666 TAATTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTTAAAAAATATAAA
Found at i:2808751 original size:19 final size:18
Alignment explanation
Indices: 2808727--2808772 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
2808717 AGATCGATCA
2808727 TTTTTAATTAAATTTTATT
1 TTTTTAATTAAA-TTTATT
2808746 TTTTT-ATCTAAATTTATT
1 TTTTTAAT-TAAATTTATT
*
2808764 TTTTAAATT
1 TTTTTAATT
2808773 TAATATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTAATTAAATTTATT
Found at i:2809007 original size:16 final size:15
Alignment explanation
Indices: 2808977--2809050 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 15
2808967 AATATTAAAG
2808977 ATATATATAAGTAAATAA
1 ATATATAT-A-TAAA-AA
*
2808995 ATATATATATAAAAT
1 ATATATATATAAAAA
*
2809010 ATA-AAATATAAAAA
1 ATATATATATAAAAA
* *
2809024 ATATA-ATATATATAT
1 ATATATATATA-AAAA
2809039 ATATATATATAA
1 ATATATATATAA
2809051 CAGTCAAACT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
14 17 0.35
15 13 0.27
16 9 0.19
17 1 0.02
18 8 0.17
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (15 bp):
ATATATATATAAAAA
Found at i:2811456 original size:19 final size:19
Alignment explanation
Indices: 2811415--2811456 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2811405 ATTATTTTAT
*
2811415 TAAATTATTGATAAAAATT
1 TAAATTATTGATAAAAATA
*
2811434 TAAA-TATTGAATAATAATA
1 TAAATTATTG-ATAAAAATA
2811453 TAAA
1 TAAA
2811457 ACAGTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
TAAATTATTGATAAAAATA
Found at i:2812328 original size:13 final size:13
Alignment explanation
Indices: 2812310--2812334 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2812300 AATAGAAGGG
2812310 AAAGGAAGGGAGT
1 AAAGGAAGGGAGT
2812323 AAAGGAAGGGAG
1 AAAGGAAGGGAG
2812335 CTTAGGCTCG
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:0.48, C:0.00, G:0.48, T:0.04
Consensus pattern (13 bp):
AAAGGAAGGGAGT
Found at i:2814178 original size:3 final size:3
Alignment explanation
Indices: 2814170--2814197 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2814160 TTGTTTAGGT
2814170 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
2814198 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:2820804 original size:6 final size:7
Alignment explanation
Indices: 2820779--2820803 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2820769 GAAATTTATT
2820779 AAAAATA
1 AAAAATA
2820786 AAAAATA
1 AAAAATA
2820793 AAAAATA
1 AAAAATA
2820800 AAAA
1 AAAA
2820804 TCATGTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2821446 original size:23 final size:23
Alignment explanation
Indices: 2821420--2821467 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2821410 AAAATATTTT
* * * *
2821420 TAAATATTTTTATATTTTAAATA
1 TAAATATATATATAATTAAAATA
2821443 TAAATATATATATAATTAAAATA
1 TAAATATATATATAATTAAAATA
2821466 TA
1 TA
2821468 TATTGTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAATATATATATAATTAAAATA
Found at i:2824709 original size:23 final size:23
Alignment explanation
Indices: 2824665--2824709 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2824655 TAATTACAGA
* *
2824665 TTATCTGCAACATTACATTTTTG
1 TTATCTGCAAAATCACATTTTTG
2824688 TTATCT-CAAAATCACATATTTT
1 TTATCTGCAAAATCACAT-TTTT
2824710 AAAGAGACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.31, C:0.18, G:0.04, T:0.47
Consensus pattern (23 bp):
TTATCTGCAAAATCACATTTTTG
Found at i:2825009 original size:2 final size:2
Alignment explanation
Indices: 2825002--2825037 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2824992 AATAATAGGA
2825002 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2825038 TTTTCTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2831736 original size:4 final size:4
Alignment explanation
Indices: 2831729--2831754 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2831719 TATCTATCTA
2831729 TCTT TCTT TCTT TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TC
2831755 GTTTACAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:2832103 original size:24 final size:24
Alignment explanation
Indices: 2832075--2832138 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
2832065 GTGTTATATT
2832075 AATATAATAAA-A-AATTTTATAATA
1 AATATAATAAATATAA--TTATAATA
**
2832099 AATATTTTAAATATAATTATAATA
1 AATATAATAAATATAATTATAATA
2832123 AATATAA-ATAATATAA
1 AATATAATA-AATATAA
2832139 AAAAATAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 1 0.03
24 29 0.88
25 1 0.03
26 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATATAATAAATATAATTATAATA
Found at i:2832138 original size:15 final size:15
Alignment explanation
Indices: 2832096--2832152 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
2832086 AAATTTTATA
* *
2832096 ATAAATATTTTAAAT
1 ATAAATAATATAAAT
*
2832111 AT-AATTATAATAAAT
1 ATAAATAAT-ATAAAT
2832126 ATAAATAATATAAA-
1 ATAAATAATATAAAT
2832140 A-AAATAATA-AAAT
1 ATAAATAATATAAAT
2832153 TTATATAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 3 0.09
13 8 0.23
14 5 0.14
15 14 0.40
16 5 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAAATAATATAAAT
Done.