Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold127
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: 4281254
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 25 of 26
Found at i:3921905 original size:90 final size:91
Alignment explanation
Indices: 3921396--3921955 Score: 620
Period size: 90 Copynumber: 6.2 Consensus size: 91
3921386 TCTTGCAGTC
* * *
3921396 TTTCTTTTTTCCTAT-AAAAAGAATCCGATTTTCAGATATAATTTAA-GCATTAGTCTAATCCTT
1 TTTCTTTTTT-CTATAAAAAAAAATCTGATTCTCAGATATAA-TTAATGCATTAGTCTAATCCTT
* *
3921459 GCAATCT-ACATTTACAATCAATC-A-G
64 GCAGTCTGACATTTACAATCAATCAACT
* * * ** *
3921484 TCT-TTTTTTCTATAAAAAAAATTC-GATTTTCAGATATAATTTGTGCATTAGTCTAATCCTTAC
1 TTTCTTTTTTCTATAAAAAAAAATCTGATTCTCAGATATAATTAATGCATTAGTCTAATCCTTGC
* *
3921547 AGTCTGACATTTATAATCAATCAGTCT
66 AGTCTGACATTTACAATCAATCA-ACT
* * * * * *
3921574 TTTTTTTTTTCCAGAAAAAAAAATATGATTCTCAGATATAATTCATGCGTTAGTCTAATCCTTGC
1 TTTCTTTTTTCTATAAAAAAAAATCTGATTCTCAGATATAATTAATGCATTAGTCTAATCCTTGC
* *
3921639 AGTCTAACATTTACAATCAGTCAAC-
66 AGTCTGACATTTACAATCAATCAACT
* * **
3921664 TTT-TTTTTTATA-AAAAAAAAATCTGATTCTCAGATACAATTAATGCATTAGTCTAATCCTTAT
1 TTTCTTTTTTCTATAAAAAAAAATCTGATTCTCAGATATAATTAATGCATTAGTCTAATCCTTGC
* * *
3921727 AATCTGACATTTATAATCAGTCAACT
66 AGTCTGACATTTACAATCAATCAACT
* * *
3921753 TTTCTTTTTTTTTTATAAAAAAGAATCTGATTCTCAGATATAATTAATGGATTAGTCTAATCCTT
1 TTTC--TTTTTTCTATAAAAAAAAATCTGATTCTCAGATATAATTAATGCATTAGTCTAATCCTT
* * *
3921818 GCAGTTTGATATTTACAATCAACCAACT
64 GCAGTCTGACATTTACAATCAATCAACT
** * * *
3921846 TTTCTTTTTTCTATAAAAAGGAAT-TAATTCTTAGATATAATTCATGCATTAGTCTAATCCTTGC
1 TTTCTTTTTTCTATAAAAAAAAATCTGATTCTCAGATATAATTAATGCATTAGTCTAATCCTTGC
* *
3921910 AGTCTAACATTTACAATCAATTAACT
66 AGTCTGACATTTACAATCAATCAACT
*
3921936 TTTCTTTTTTCCATAAAAAA
1 TTTCTTTTTTCTATAAAAAA
3921956 GTGACGATTT
Statistics
Matches: 399, Mismatches: 60, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
85 2 0.01
86 41 0.10
87 29 0.07
88 69 0.17
89 10 0.03
90 80 0.20
91 36 0.09
92 62 0.16
93 70 0.18
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.41
Consensus pattern (91 bp):
TTTCTTTTTTCTATAAAAAAAAATCTGATTCTCAGATATAATTAATGCATTAGTCTAATCCTTGC
AGTCTGACATTTACAATCAATCAACT
Found at i:3922215 original size:123 final size:126
Alignment explanation
Indices: 3922088--3922398 Score: 332
Period size: 123 Copynumber: 2.5 Consensus size: 126
3922078 TATTTTTAAT
* *
3922088 AAAATAATATTTAATTAACTTTAAAAAATTTATATTAATAAACTAAAATATTAATTATT-T-TTA
1 AAAATAATATTTAATTAAGTTT-AAAAATTTATATTAATAAATTAAAATATTAATTATTATGTTA
** * *
3922151 AAAATAAAAA-ACTTTAAA-TAAAAATAAAAAGG-GTTTATTATTATTATTTTTAAT-AAATTA
65 AAAATAAAAATA--AAAAATTAAAAATAAAAAGGTGTTTATTATTATAATTTTTAATAAAATAA
* *
3922211 AAAATAATATTTAATATAAGTTTAAAAAGTTATATTAA-CAATTAAAATAATTAATTACTTATGT
1 AAAATAATATTTAAT-TAAGTTTAAAAATTTATATTAATAAATTAAAAT-ATTAATTA-TTATGT
**** * * *
3922275 TTTTTATAAAAATAAAAAATTTAAAATAAAAAGGTTTTTTTTTTATTATAATTTTTAATAAAATA
63 TAAAAATAAAAATAAAAAATTAAAAATAAAAAGG--TGTTTATTATTATAATTTTTAATAAAATA
3922340 A
126 A
* * *
3922341 AAAATAAGAGTTAATTAAGTTT-AAAATTTACATTAATAAATTAAAATATTAATTATTA
1 AAAATAATATTTAATTAAGTTTAAAAATTTATATTAATAAATTAAAATATTAATTATTA
3922399 GGTTTTTTAA
Statistics
Matches: 156, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
122 8 0.05
123 37 0.24
124 8 0.05
125 4 0.03
126 22 0.14
127 4 0.03
128 20 0.13
129 35 0.22
130 18 0.12
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (126 bp):
AAAATAATATTTAATTAAGTTTAAAAATTTATATTAATAAATTAAAATATTAATTATTATGTTAA
AAATAAAAATAAAAAATTAAAAATAAAAAGGTGTTTATTATTATAATTTTTAATAAAATAA
Found at i:3922830 original size:24 final size:23
Alignment explanation
Indices: 3922765--3922853 Score: 76
Period size: 23 Copynumber: 3.9 Consensus size: 23
3922755 AATAATGATA
* *
3922765 AATTTTTTTAATTCT-TTAAATGT
1 AATTTTTTAAATT-TATTAAATAT
* *
3922788 TATTTTTTAAATTTGTT-AATAT
1 AATTTTTTAAATTTATTAAATAT
3922810 AAATTTTTTAAATTTAATTAAATAT
1 -AATTTTTTAAATTT-ATTAAATAT
* *
3922835 TATTTTTT-ATTTTATTAAA
1 AATTTTTTAAATTTATTAAA
3922854 AAATAATAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
22 11 0.20
23 30 0.55
24 9 0.16
25 5 0.09
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (23 bp):
AATTTTTTAAATTTATTAAATAT
Found at i:3923032 original size:113 final size:111
Alignment explanation
Indices: 3922792--3923084 Score: 368
Period size: 111 Copynumber: 2.6 Consensus size: 111
3922782 AAATGTTATT
*
3922792 TTTTAAATTTGTTAATATAAATTTTTTAAATTTAATTAAATATTATTTTTTATTTTATTAAAAAA
1 TTTT-AATTTGTTAATATAAATTTTTTAAACTTAATTAAATATTA-TTTTTATTTTATTAAAAAA
3922857 TAATAATAAAAAATATTTTTTATTTTTATAAAAACATATTAATTAATA
64 TAATAATAAAAAATATTTTTTATTTTTATAAAAACATATTAATTAATA
*
3922905 TTTTAATTTGTTAATGT-AATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAAATA
1 TTTTAATTTGTTAATATAAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAAATA
*** * *
3922969 ATAATAAACCCTTTTTAATTTAATTTTTTATTTTAAAA-A-A-TAATTAATA
66 ATAATAAAAAATATTT--TTT-A-TTTTTA--TAAAAACATATTAATTAATA
* *
3923018 TTTTAATTTATTAATATAAATTTTTTTAAAGTTAATTAAATATTA---TT-TTTTATTAAAAAAT
1 TTTTAATTTGTTAATATAAA-TTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAAAT
3923079 AATAAT
65 AATAAT
3923085 TAATACATTA
Statistics
Matches: 162, Mismatches: 10, Indels: 18
0.85 0.05 0.09
Matches are distributed among these distances:
110 33 0.20
111 45 0.28
112 17 0.10
113 29 0.18
114 9 0.06
115 24 0.15
116 5 0.03
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (111 bp):
TTTTAATTTGTTAATATAAATTTTTTAAACTTAATTAAATATTATTTTTATTTTATTAAAAAATA
ATAATAAAAAATATTTTTTATTTTTATAAAAACATATTAATTAATA
Found at i:3923106 original size:31 final size:31
Alignment explanation
Indices: 3923050--3923109 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
3923040 TTTTTAAAGT
* *
3923050 TAATTAAATATTATTTTTTATTAAAAAATAA
1 TAATTAAACATTATTATTTATTAAAAAATAA
3923081 TAATTAATACATTATTATTTA-TAAAAAAT
1 TAATTAA-ACATTATTATTTATTAAAAAAT
3923110 TTTAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (31 bp):
TAATTAAACATTATTATTTATTAAAAAATAA
Found at i:3923153 original size:27 final size:27
Alignment explanation
Indices: 3923097--3923153 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
3923087 ATACATTATT
* **
3923097 ATTTATAAAAAATTTTAAATTTAATTA
1 ATTTATAAAAAATTTGAAATTTAAAAA
*
3923124 ATTTATAAAAAATTATGCAA-TTAAAAA
1 ATTTATAAAAAATT-TGAAATTTAAAAA
3923151 ATT
1 ATT
3923154 ACTATTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 22 0.88
28 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
ATTTATAAAAAATTTGAAATTTAAAAA
Found at i:3923209 original size:15 final size:15
Alignment explanation
Indices: 3923189--3923236 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
3923179 CGTATTCATA
3923189 AAAAAATTTTATTTT
1 AAAAAATTTTATTTT
* *
3923204 AAAAAATATT-TTAT
1 AAAAAATTTTATTTT
3923218 AAAAAA-TTTATTTAT
1 AAAAAATTTTATTT-T
3923233 AAAA
1 AAAA
3923237 TAAAAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 11 0.41
15 14 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAAAATTTTATTTT
Found at i:3923213 original size:29 final size:29
Alignment explanation
Indices: 3923181--3923236 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
3923171 TTTTTCAACG
3923181 TATTCATA-AAAAAATTTTATTT-TAAAAAA
1 TATT-ATATAAAAAA-TTTATTTATAAAAAA
*
3923210 TATTTTATAAAAAATTTATTTATAAAA
1 TATTATATAAAAAATTTATTTATAAAA
3923237 TAAAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
TATTATATAAAAAATTTATTTATAAAAAA
Found at i:3923970 original size:20 final size:19
Alignment explanation
Indices: 3923928--3923977 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
3923918 ATATCTTCAT
*
3923928 ATTATAAATTAAAAAAATT
1 ATTATAAATTAAAAAAATA
3923947 ATTATATAATT-AAAAAATA
1 ATTATA-AATTAAAAAAATA
*
3923966 AAT-TAAATTAAA
1 ATTATAAATTAAA
3923978 TTTGATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 4 0.15
18 4 0.15
19 15 0.56
20 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTATAAATTAAAAAAATA
Found at i:3924695 original size:20 final size:20
Alignment explanation
Indices: 3924672--3924714 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3924662 TATTTTATTT
*
3924672 TATTATA-ATTATATTTAAAA
1 TATTATATATT-TATATAAAA
*
3924692 TATTTTATATTTATATAAAA
1 TATTATATATTTATATAAAA
3924712 TAT
1 TAT
3924715 AAAAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTATATATTTATATAAAA
Found at i:3924705 original size:22 final size:20
Alignment explanation
Indices: 3924674--3924714 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
3924664 TTTTATTTTA
3924674 TTATAATTATATTTAAAATATT
1 TTATAATTATA--TAAAATATT
*
3924696 TTATATTTATATAAAATAT
1 TTATAATTATATAAAATAT
3924715 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATAATTATATAAAATATT
Found at i:3924750 original size:32 final size:32
Alignment explanation
Indices: 3924693--3924781 Score: 90
Period size: 32 Copynumber: 2.7 Consensus size: 32
3924683 TATTTAAAAT
* *
3924693 ATTTTATATTTATATAAAATATAAAAAATTAATA
1 ATTTTATA-TTATATAAATTTTAAAAAA-TAATA
* * *
3924727 ATTTT-TATTATATAAATTTTAAAATATGATT
1 ATTTTATATTATATAAATTTTAAAAAATAATA
*
3924758 ATTTTATATTATATTATATTTTAA
1 ATTTTATATTATA-TAAATTTTAA
3924782 CTTTTTTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
31 8 0.17
32 23 0.49
33 11 0.23
34 5 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (32 bp):
ATTTTATATTATATAAATTTTAAAAAATAATA
Found at i:3927850 original size:2 final size:2
Alignment explanation
Indices: 3927845--3927877 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3927835 GGTAACTGGT
3927845 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3927878 CAAGAAACTA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3927949 original size:2 final size:2
Alignment explanation
Indices: 3927942--3927970 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3927932 TAATGTGGCG
3927942 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3927971 GGAAGAAAAG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3928564 original size:15 final size:15
Alignment explanation
Indices: 3928544--3928580 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3928534 TAGGCCTCTG
3928544 ATATAAAGTTTACCT
1 ATATAAAGTTTACCT
3928559 ATATAAAGTTTACCT
1 ATATAAAGTTTACCT
*
3928574 ACATAAA
1 ATATAAA
3928581 AAATTACACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (15 bp):
ATATAAAGTTTACCT
Found at i:3930597 original size:14 final size:14
Alignment explanation
Indices: 3930565--3930610 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 14
3930555 TATTCCATAT
*
3930565 TTAAAAAT-TTTAA
1 TTAAAAATATTAAA
3930578 -TAAAAATATTAAA
1 TTAAAAATATTAAA
*
3930591 TTAAAAAAATTTAAA
1 TTAAAAATA-TTAAA
3930606 TTAAA
1 TTAAA
3930611 TTGAGATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 7 0.25
13 4 0.14
14 7 0.25
15 10 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAAAATATTAAA
Found at i:3930604 original size:15 final size:16
Alignment explanation
Indices: 3930574--3930610 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
3930564 TTTAAAAATT
3930574 TTAATAAAAATATTAAA
1 TTAA-AAAAATATTAAA
3930591 TTAAAAAAAT-TTAAA
1 TTAAAAAAATATTAAA
3930606 TTAAA
1 TTAAA
3930611 TTGAGATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.50
16 6 0.30
17 4 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAAAAAATATTAAA
Found at i:3931715 original size:20 final size:21
Alignment explanation
Indices: 3931683--3931733 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3931673 ATTTTTAACA
* *
3931683 AAAAAAATATTTAAATTT-TTT
1 AAAATAAT-TTTAAATTTCGTT
*
3931704 AAAATAATTTTATATTTCGTT
1 AAAATAATTTTAAATTTCGTT
3931725 AAAATAATT
1 AAAATAATT
3931734 ATTTAATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
AAAATAATTTTAAATTTCGTT
Found at i:3931914 original size:23 final size:24
Alignment explanation
Indices: 3931869--3931923 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 24
3931859 ATAATAAAAT
*
3931869 AATTATTATAATGATCTAAACTTA
1 AATTATTATAATGAGCTAAACTTA
*
3931893 AATTATTA-AATGAGCTAGACTTA
1 AATTATTATAATGAGCTAAACTTA
3931916 AATTATTA
1 AATTATTA
3931924 GAGGCTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (24 bp):
AATTATTATAATGAGCTAAACTTA
Found at i:3932308 original size:25 final size:23
Alignment explanation
Indices: 3932254--3932321 Score: 63
Period size: 25 Copynumber: 3.0 Consensus size: 23
3932244 TGTATTATTA
3932254 TTATATTTATATTTAAAATTTTG
1 TTATATTTATATTTAAAATTTTG
*
3932277 --ACA--TATATTTAATAATATTTG
1 TTATATTTATATTTAA-AAT-TTTG
3932298 TTATATTTATATTTACAAGATTTT
1 TTATATTTATATTTA-AA-ATTTT
3932322 TTTAAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
19 9 0.26
20 3 0.09
21 6 0.17
23 2 0.06
25 12 0.34
26 3 0.09
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (23 bp):
TTATATTTATATTTAAAATTTTG
Found at i:3933848 original size:39 final size:39
Alignment explanation
Indices: 3933805--3933882 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
3933795 TTGGTGCTAA
* * *
3933805 CAAATATTGATTTTAATATATATATATGATTAAATATAT
1 CAAATATTGATTTTAATATATAAATATAATTAAAAATAT
3933844 CAAATATTGATTTTAATATATAAATATAATTAAAAATAT
1 CAAATATTGATTTTAATATATAAATATAATTAAAAATAT
3933883 GTTTTTATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (39 bp):
CAAATATTGATTTTAATATATAAATATAATTAAAAATAT
Found at i:3934472 original size:13 final size:13
Alignment explanation
Indices: 3934439--3934469 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
3934429 ATCATTAAAA
3934439 AATAAATTTATTT
1 AATAAATTTATTT
3934452 AATAAATTT-TTT
1 AATAAATTTATTT
3934464 AATAAA
1 AATAAA
3934470 ATTAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATAAATTTATTT
Found at i:3935181 original size:11 final size:10
Alignment explanation
Indices: 3935159--3935188 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
3935149 TAAATATTTA
3935159 TATATTTAAT
1 TATATTTAAT
3935169 TATATTATAAT
1 TATATT-TAAT
3935180 TATATTTAA
1 TATATTTAA
3935189 AATATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATATTTAAT
Found at i:3935204 original size:22 final size:23
Alignment explanation
Indices: 3935152--3935207 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
3935142 TTTATATTAA
* *
3935152 ATATTTATATATTTAATTATATT
1 ATATTTATATATTAAAATATATT
* *
3935175 ATAATTATAT-TTAAAATATTTT
1 ATATTTATATATTAAAATATATT
3935197 ATATTTATATA
1 ATATTTATATA
3935208 AATTTATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATATTTATATATTAAAATATATT
Found at i:3935213 original size:16 final size:16
Alignment explanation
Indices: 3935194--3935244 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
3935184 TTTAAAATAT
3935194 TTTATATTTATATAAA
1 TTTATATTTATATAAA
*
3935210 TTTATATTTATTAAAAA
1 TTTATATTTA-TATAAA
3935227 TTTATA-TTATATAAA
1 TTTATATTTATATAAA
3935242 TTT
1 TTT
3935245 TAAAATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 8 0.25
16 13 0.41
17 11 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTATATTTATATAAA
Found at i:3935215 original size:38 final size:36
Alignment explanation
Indices: 3935143--3935244 Score: 110
Period size: 38 Copynumber: 2.9 Consensus size: 36
3935133 TTTATTATTT
*
3935143 TTATATT-AAATATTTATATATTTA-AT-TATATTATAA
1 TTATATTAAAATATTT-TATATTTATATAAAT-TTAT-A
3935179 TTATATTTAAAATATTTTATATTTATATAAATTTATA
1 TTATA-TTAAAATATTTTATATTTATATAAATTTATA
3935216 TT-TATTAAAA-A-TTTATA-TTATATAAATTT
1 TTATATTAAAATATTTTATATTTATATAAATTT
3935245 TAAAATTTCA
Statistics
Matches: 61, Mismatches: 1, Indels: 12
0.82 0.01 0.16
Matches are distributed among these distances:
32 12 0.20
33 6 0.10
34 1 0.02
35 6 0.10
36 7 0.11
37 13 0.21
38 14 0.23
39 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (36 bp):
TTATATTAAAATATTTTATATTTATATAAATTTATA
Found at i:3935227 original size:17 final size:16
Alignment explanation
Indices: 3935179--3935241 Score: 74
Period size: 16 Copynumber: 3.8 Consensus size: 16
3935169 TATATTATAA
*
3935179 TTATATTTA-AAATATT
1 TTATATTTATAAA-AAT
*
3935195 TTATATTTATATAAAT
1 TTATATTTATAAAAAT
3935211 TTATATTTATTAAAAAT
1 TTATATTTA-TAAAAAT
3935228 TTATATTATATAAA
1 TTATATT-TATAAA
3935242 TTTTAAAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
16 20 0.49
17 19 0.46
18 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATTTATAAAAAT
Found at i:3935237 original size:32 final size:31
Alignment explanation
Indices: 3935162--3935244 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 31
3935152 ATATTTATAT
3935162 ATTTA-ATTATATTATAA-TTATATTTAAAATA
1 ATTTATATTATA-TA-AATTTATATTTAAAATA
*
3935193 TTTTATATTTATATAAATTTATATTTATTAAA-A
1 ATTTATA-TTATATAAATTTATATTTA--AAATA
3935226 ATTTATATTATATAAATTT
1 ATTTATATTATATAAATTT
3935245 TAAAATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
31 6 0.13
32 24 0.53
33 12 0.27
34 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
ATTTATATTATATAAATTTATATTTAAAATA
Found at i:3935439 original size:21 final size:21
Alignment explanation
Indices: 3935414--3935468 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
3935404 AGTTAATAAT
*
3935414 TTATTTTATAT-AAATTTTTA
1 TTATTTTATATCAAATATTTA
*
3935434 TATATTTT-TATCATATATTTA
1 T-TATTTTATATCAAATATTTA
3935455 TTATTTTATTATCA
1 TTATTTTA-TATCA
3935469 TATTTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 10 0.34
21 14 0.48
22 5 0.17
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
TTATTTTATATCAAATATTTA
Found at i:3935442 original size:11 final size:10
Alignment explanation
Indices: 3935415--3935491 Score: 57
Period size: 11 Copynumber: 7.1 Consensus size: 10
3935405 GTTAATAATT
3935415 TATTTTATATA
1 TATTTT-TATA
*
3935426 AATTTTTATA
1 TATTTTTATA
3935436 TATTTTTATCA
1 TATTTTTAT-A
*
3935447 TATATTTAT-
1 TATTTTTATA
3935456 TATTTTATTATCA
1 TA-TTT-TTAT-A
*
3935469 TATTTTAATTA
1 TATTTTTA-TA
3935480 TATTTTTCATA
1 TATTTTT-ATA
3935491 T
1 T
3935492 CATCTAATCT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
9 2 0.04
10 14 0.26
11 30 0.57
12 5 0.09
13 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (10 bp):
TATTTTTATA
Found at i:3937190 original size:22 final size:21
Alignment explanation
Indices: 3937165--3937207 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
3937155 TATTAAAAAA
*
3937165 ATTTAAAAATTAATTTTTATAT
1 ATTTAAAAATTAA-ATTTATAT
* *
3937187 ATTTTATAATTAAATTTATAT
1 ATTTAAAAATTAAATTTATAT
3937208 CAAAATAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTAAAAATTAAATTTATAT
Found at i:3937252 original size:16 final size:18
Alignment explanation
Indices: 3937222--3937262 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3937212 ATAATTTTTA
3937222 TTAAAT-AAATAAT-AAT
1 TTAAATAAAATAATAAAT
3937238 TTAAATAAAAT-ATAAAT
1 TTAAATAAAATAATAAAT
3937255 TTCAAATA
1 TT-AAATA
3937263 TCATACTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.36
17 9 0.41
18 5 0.23
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAAATAAAATAATAAAT
Found at i:3937596 original size:34 final size:33
Alignment explanation
Indices: 3937539--3937603 Score: 89
Period size: 32 Copynumber: 1.9 Consensus size: 33
3937529 AATTAAAATT
3937539 AAAATAATTATTTATTAATTTTT-AAATTTTAA
1 AAAATAATTATTTATTAATTTTTAAAATTTTAA
3937571 AAAATATATT-TTTATATAATATTTTAAAATTTT
1 AAAATA-ATTATTTAT-TAAT-TTTTAAAATTTT
3937604 TACATTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 11 0.38
33 7 0.24
34 4 0.14
35 7 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
AAAATAATTATTTATTAATTTTTAAAATTTTAA
Found at i:3937773 original size:6 final size:6
Alignment explanation
Indices: 3937764--3937813 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
3937754 TTAAATTTAA
* * *
3937764 TAAAAT TAAAAT TAAAAT TAAAAT T-AAAT CGAATAT TAAAAT TTAAAT
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT -TAAAAT TAAAAT TAAAAT
3937812 TA
1 TA
3937814 TTATTATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
5 4 0.11
6 29 0.81
7 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (6 bp):
TAAAAT
Found at i:3937787 original size:18 final size:17
Alignment explanation
Indices: 3937751--3937813 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
3937741 AATTTAAATC
*
3937751 AAATTAAATT-TAA-TA
1 AAATTAAATTAAAATTA
3937766 AAATTAAAATTAAAATTA
1 AAATT-AAATTAAAATTA
* *
3937784 AAATTAAATCGAATATTA
1 AAATTAAAT-TAAAATTA
3937802 AAATTTAAATTA
1 AAA-TTAAATTA
3937814 TTATTATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 5 0.13
16 5 0.13
17 6 0.15
18 17 0.44
19 6 0.15
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
AAATTAAATTAAAATTA
Found at i:3937818 original size:18 final size:18
Alignment explanation
Indices: 3937764--3937819 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
3937754 TTAAATTTAA
* *
3937764 TAAAATTAAAATTAAAAT
1 TAAAATTTAAATTAATAT
*
3937782 TAAAA-TTAAATCGAATAT
1 TAAAATTTAAAT-TAATAT
*
3937800 TAAAATTTAAATTATTAT
1 TAAAATTTAAATTAATAT
3937818 TA
1 TA
3937820 TTATTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 5 0.16
18 20 0.65
19 6 0.19
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
TAAAATTTAAATTAATAT
Found at i:3939113 original size:20 final size:18
Alignment explanation
Indices: 3939090--3939143 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 18
3939080 TTATTATTTA
3939090 ATAAATAAAAATATTTAAAT
1 ATAAATAAAAATA-TT-AAT
3939110 ATAATTATAAAAATATTAAT
1 ATAA--ATAAAAATATTAAT
*
3939130 ATTAATATAAAATA
1 ATAAATA-AAAATA
3939144 ACCTTTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 3 0.10
19 6 0.20
20 10 0.33
21 2 0.07
22 9 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAATAAAAATATTAAT
Found at i:3940190 original size:17 final size:18
Alignment explanation
Indices: 3940163--3940196 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3940153 TATATATTAA
*
3940163 AAATAATTTAATAAATTC
1 AAATAATTTAACAAATTC
3940181 AAAT-ATTTAACAAATT
1 AAATAATTTAACAAATT
3940197 TTGATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATAATTTAACAAATTC
Found at i:3941498 original size:26 final size:23
Alignment explanation
Indices: 3941444--3941487 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
3941434 GCATTCGTGA
3941444 TATATTAATATTATTTTTTATAT
1 TATATTAATATTATTTTTTATAT
3941467 TATATTAATATTATTTTTTAT
1 TATATTAATATTATTTTTTAT
3941488 TATATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TATATTAATATTATTTTTTATAT
Found at i:3943865 original size:35 final size:35
Alignment explanation
Indices: 3943800--3943870 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
3943790 TCAATAAAAT
*
3943800 AATATAATTTATTATGATATACTTAAAAAATTAAA
1 AATATAATATATTATGATATACTTAAAAAATTAAA
* * *
3943835 AATATAATATATT-TTATATAGTTTATAAAATTAAA
1 AATATAATATATTATGATATA-CTTAAAAAATTAAA
3943870 A
1 A
3943871 TTTTTTAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 6 0.19
35 25 0.81
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (35 bp):
AATATAATATATTATGATATACTTAAAAAATTAAA
Found at i:3946081 original size:2 final size:2
Alignment explanation
Indices: 3946074--3946099 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3946064 TAATAGAAGG
3946074 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
3946100 TACATTAAAC
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:3947692 original size:39 final size:37
Alignment explanation
Indices: 3947610--3947693 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 37
3947600 AAAAAATATG
* *
3947610 TTATTAATATATTATTTTTTAAAATTTAATAAATTTA
1 TTATTAATATATTATTTTTTAAAATATAATAAATTAA
3947647 TATATTAATTATAATT-TTTTTTAAAATAATAATTAAA-TAA
1 T-TATTAA-TAT-ATTATTTTTTAAAAT-ATAA-TAAATTAA
3947687 TTATTAA
1 TTATTAA
3947694 CTAATATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
37 1 0.03
38 6 0.15
39 20 0.50
40 9 0.22
41 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (37 bp):
TTATTAATATATTATTTTTTAAAATATAATAAATTAA
Found at i:3949643 original size:26 final size:25
Alignment explanation
Indices: 3949597--3949646 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
3949587 AGTACAAAAT
3949597 TTTGATTTTTTTTAAAAAATTTTTA
1 TTTGATTTTTTTTAAAAAATTTTTA
3949622 TTTGA-TTTTTTTAAAATTAATTTTT
1 TTTGATTTTTTTTAAAA--AATTTTT
3949647 TTATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.48
25 5 0.22
26 7 0.30
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (25 bp):
TTTGATTTTTTTTAAAAAATTTTTA
Found at i:3949654 original size:24 final size:22
Alignment explanation
Indices: 3949596--3949655 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 22
3949586 TAGTACAAAA
*
3949596 TTTTGATTTTTTTTAAAAAATT
1 TTTTTATTTTTTTTAAAAAATT
3949618 TTTATT-TGATTTTTTTAAAATTAATT
1 TTT-TTAT--TTTTTTTAAAA--AATT
3949644 TTTTTATTTTTT
1 TTTTTATTTTTT
3949656 ATTTTCATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
22 4 0.13
23 1 0.03
24 16 0.52
25 2 0.06
26 8 0.26
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (22 bp):
TTTTTATTTTTTTTAAAAAATT
Found at i:3949812 original size:16 final size:16
Alignment explanation
Indices: 3949770--3949815 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3949760 TTTATATTTA
*
3949770 TTTAATATTTAAA-AT
1 TTTAAAATTTAAATAT
3949785 TTTAAAATTTTAAATA-
1 TTTAAAA-TTTAAATAT
3949801 TTTATAAATTTAAAT
1 TTTA-AAATTTAAAT
3949816 TTATATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 6 0.22
16 17 0.63
17 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAAATTTAAATAT
Found at i:3951038 original size:6 final size:6
Alignment explanation
Indices: 3951017--3951049 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
3951007 AATAAATAAT
3951017 AAATGA TAAA-GA AAATGA AAATGA AAATGA AAA
1 AAATGA -AAATGA AAATGA AAATGA AAATGA AAA
3951050 AAAGAATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 3 0.12
6 19 0.76
7 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAATGA
Found at i:3951132 original size:26 final size:26
Alignment explanation
Indices: 3951103--3951168 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
3951093 TAAGAGATTT
*
3951103 TTAATATT-TATAAATATTTAATTAAA
1 TTAATATTATATAAAT-TTAAATTAAA
3951129 TTAATAATTATATAAATTTAAATTAAA
1 TTAAT-ATTATATAAATTTAAATTAAA
*
3951156 -TAATATTAAATAA
1 TTAATATTATATAA
3951169 TTATTATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 8 0.22
26 9 0.25
27 12 0.33
28 7 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAATATTATATAAATTTAAATTAAA
Found at i:3951141 original size:22 final size:23
Alignment explanation
Indices: 3951124--3951166 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3951114 AAATATTTAA
3951124 TTAAATT-AATAATTATATAAAT
1 TTAAATTAAATAATTATATAAAT
3951146 TTAAATTAAATAA-TAT-TAAAT
1 TTAAATTAAATAATTATATAAAT
3951167 AATTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 10 0.50
23 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTAAATTAAATAATTATATAAAT
Found at i:3952082 original size:23 final size:21
Alignment explanation
Indices: 3952056--3952110 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
3952046 TAAATTTATG
*
3952056 AAAAATAATATAAATGCTATATA
1 AAAAATAATATAAAT-ATA-ATA
* *
3952079 AAAATTAATTTAAATATAATA
1 AAAAATAATATAAATATAATA
3952100 AAAAATGAATA
1 AAAAAT-AATA
3952111 AGACACAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 8 0.31
22 5 0.19
23 13 0.50
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAATAATATAAATATAATA
Found at i:3952338 original size:11 final size:11
Alignment explanation
Indices: 3952322--3952409 Score: 56
Period size: 11 Copynumber: 8.0 Consensus size: 11
3952312 CGTATAAAAA
3952322 ATAATATAAAT
1 ATAATATAAAT
*
3952333 ATAATATAAAA
1 ATAATATAAAT
3952344 ATAA-ATTAAAAT
1 ATAATA-T-AAAT
*
3952356 ATAATAAAAAT
1 ATAATATAAAT
*
3952367 A-AATATGACAT
1 ATAATAT-AAAT
* *
3952378 -GAATATAAAA
1 ATAATATAAAT
* *
3952388 ATAATTTATAT
1 ATAATATAAAT
*
3952399 ATTATATAAAT
1 ATAATATAAAT
3952410 TTATAATATT
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
10 7 0.12
11 42 0.74
12 7 0.12
13 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:3952344 original size:23 final size:24
Alignment explanation
Indices: 3952314--3952371 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
3952304 TCAATTTACG
3952314 TATAAAAAATAATAT-AAATATAA
1 TATAAAAAATAATATAAAATATAA
3952337 TAT-AAAAATAA-ATTAAAATATAA
1 TATAAAAAATAATA-TAAAATATAA
*
3952360 TAAAAATAAATA
1 TATAAA-AAATA
3952372 TGACATGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.03
22 9 0.30
23 13 0.43
24 2 0.07
25 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (24 bp):
TATAAAAAATAATATAAAATATAA
Found at i:3952362 original size:21 final size:23
Alignment explanation
Indices: 3952329--3952370 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
3952319 AAAATAATAT
3952329 AAATATAATATAAAAATAAATTA
1 AAATATAATATAAAAATAAATTA
3952352 AAATAT-A-ATAAAAATAAAT
1 AAATATAATATAAAAATAAAT
3952371 ATGACATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 1 0.05
23 6 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATATAATATAAAAATAAATTA
Found at i:3953170 original size:17 final size:18
Alignment explanation
Indices: 3953148--3953188 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3953138 ATACAAAATA
3953148 TAAATTTAATTT-T-TTTT
1 TAAATTT-ATTTATATTTT
3953165 TAAA-TTATTTATATTTT
1 TAAATTTATTTATATTTT
3953182 TAAATTT
1 TAAATTT
3953189 GAAATAAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.19
16 3 0.14
17 12 0.57
18 2 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TAAATTTATTTATATTTT
Found at i:3953537 original size:17 final size:18
Alignment explanation
Indices: 3953501--3953540 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
3953491 CTTTCTCTCG
3953501 CCCAAATCTGATATAATC
1 CCCAAATCTGATATAATC
3953519 CCCAAATCTGATA-AATC
1 CCCAAATCTGATATAATC
3953536 CCCAA
1 CCCAA
3953541 GTTTGATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.40, C:0.33, G:0.05, T:0.23
Consensus pattern (18 bp):
CCCAAATCTGATATAATC
Found at i:3953547 original size:17 final size:17
Alignment explanation
Indices: 3953501--3953565 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
3953491 CTTTCTCTCG
*
3953501 CCCAAATCTGATATAATC
1 CCCAAATTTGATA-AATC
*
3953519 CCCAAATCTGATAAATC
1 CCCAAATTTGATAAATC
* *
3953536 CCCAAGTTTGATGGAAT-
1 CCCAAATTTGAT-AAATC
3953553 CCCAAATTTGATA
1 CCCAAATTTGATA
3953566 GCCCTTCTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
17 25 0.61
18 16 0.39
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.28
Consensus pattern (17 bp):
CCCAAATTTGATAAATC
Found at i:3954009 original size:19 final size:19
Alignment explanation
Indices: 3953975--3954020 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3953965 CGATTTTAAC
3953975 TTATTTTTAATCGATAAAA
1 TTATTTTTAATCGATAAAA
* *
3953994 TTAATTTTT-ATTGATATAA
1 TT-ATTTTTAATCGATAAAA
3954013 TTATTTTT
1 TTATTTTT
3954021 GTTTTTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 6 0.25
19 12 0.50
20 6 0.25
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (19 bp):
TTATTTTTAATCGATAAAA
Found at i:3954733 original size:26 final size:27
Alignment explanation
Indices: 3954704--3954754 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
3954694 AATTTTATGT
*
3954704 TTTTA-TTTTTATTTTTTAAAAAATAA
1 TTTTATTTTTTAATTTTTAAAAAATAA
3954730 TTTTATTTTTTAATTTTTAAAAAAT
1 TTTTATTTTTTAATTTTTAAAAAAT
3954755 TTAAAATGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TTTTATTTTTTAATTTTTAAAAAATAA
Found at i:3954746 original size:34 final size:33
Alignment explanation
Indices: 3954685--3954748 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
3954675 CTCTTTTTAG
*
3954685 TTTACAAAAAATTTTATGTTTTTATTTTTATTT
1 TTTAAAAAAAATTTTATGTTTTTATTTTTATTT
3954718 TTTAAAAAATAATTTTAT-TTTTTAATTTTTA
1 TTTAAAAAA-AATTTTATGTTTTT-ATTTTTA
3954749 AAAAATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (33 bp):
TTTAAAAAAAATTTTATGTTTTTATTTTTATTT
Found at i:3955224 original size:24 final size:23
Alignment explanation
Indices: 3955174--3955224 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
3955164 ATATAAATTT
* **
3955174 TAAAATTATAAATATTTAATATC
1 TAAAATTATAAATATTAAATAAA
3955197 TAAAATTTATAAATATTAAATAAA
1 TAAAA-TTATAAATATTAAATAAA
3955221 TAAA
1 TAAA
3955225 TATAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAAATTATAAATATTAAATAAA
Found at i:3955225 original size:23 final size:23
Alignment explanation
Indices: 3955174--3955236 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
3955164 ATATAAATTT
* * **
3955174 TAAAATTATAAATATTTAATATC
1 TAAATTTATAAATATTAAATAAA
3955197 TAAAATTTATAAATATTAAATAAA
1 T-AAATTTATAAATATTAAATAAA
* *
3955221 TAAATATAAAAATATT
1 TAAATTTATAAATATT
3955237 TAGAAATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATTTATAAATATTAAATAAA
Found at i:3955407 original size:25 final size:26
Alignment explanation
Indices: 3955350--3955407 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
3955340 AAAAGTATTT
* *
3955350 GAAATTATTTTTATAAAAATTAAATAA
1 GAAA-TATTTTTAAAAAAATTAAACAA
3955377 GTAAATATTTTTAAAAAAATTAAACAA
1 G-AAATATTTTTAAAAAAATTAAACAA
3955404 -AAAT
1 GAAAT
3955408 CAAAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 4 0.14
27 21 0.75
28 3 0.11
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (26 bp):
GAAATATTTTTAAAAAAATTAAACAA
Found at i:3962941 original size:13 final size:13
Alignment explanation
Indices: 3962923--3962948 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3962913 CAATTTTTTG
3962923 TGTATCGATACAT
1 TGTATCGATACAT
3962936 TGTATCGATACAT
1 TGTATCGATACAT
3962949 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3963033 original size:20 final size:20
Alignment explanation
Indices: 3963008--3963080 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3962998 CAACTTTTTT
3963008 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
3963028 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
3963049 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
3963069 ATGTATCGATAC
1 ATGTATCGATAC
3963081 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:3963046 original size:41 final size:41
Alignment explanation
Indices: 3962987--3963080 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3962977 CTGCCAAGAA
*
3962987 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
3963028 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
3963069 ATGTATCGATAC
1 ATGTATCGATAC
3963081 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:3963062 original size:21 final size:21
Alignment explanation
Indices: 3962987--3963062 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
3962977 CTGCCAAGAA
* *
3962987 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
3963008 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
3963028 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
3963049 ATGTATCGATACAT
1 ATGTATCGATACAT
3963063 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:3965544 original size:13 final size:13
Alignment explanation
Indices: 3965526--3965564 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3965516 ATAATCACCT
*
3965526 TGTATCGATACAG
1 TGTATCGATACAA
3965539 TGTATCGATACAA
1 TGTATCGATACAA
3965552 TGTATCGATACAA
1 TGTATCGATACAA
3965565 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3965575 original size:20 final size:20
Alignment explanation
Indices: 3965550--3965628 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
3965540 GTATCGATAC
3965550 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
3965570 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
3965595 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
3965615 CATGTATCGATACA
1 AATGTATCGATACA
3965629 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:3967662 original size:15 final size:15
Alignment explanation
Indices: 3967642--3967672 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3967632 ATTTCGTTTG
*
3967642 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3967657 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3967672 G
1 G
3967673 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3971753 original size:13 final size:13
Alignment explanation
Indices: 3971735--3971760 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3971725 CAATTTTTTG
3971735 TGTATCGATACAT
1 TGTATCGATACAT
3971748 TGTATCGATACAT
1 TGTATCGATACAT
3971761 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3971845 original size:20 final size:20
Alignment explanation
Indices: 3971820--3971892 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3971810 CAACTTTTTT
3971820 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
3971840 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
3971861 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
3971881 ATGTATCGATAC
1 ATGTATCGATAC
3971893 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:3971858 original size:41 final size:41
Alignment explanation
Indices: 3971799--3971892 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3971789 CTGCCAAGAA
*
3971799 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
3971840 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
3971881 ATGTATCGATAC
1 ATGTATCGATAC
3971893 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:3971874 original size:21 final size:21
Alignment explanation
Indices: 3971799--3971874 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
3971789 CTGCCAAGAA
* *
3971799 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
3971820 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
3971840 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
3971861 ATGTATCGATACAT
1 ATGTATCGATACAT
3971875 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:3983421 original size:23 final size:23
Alignment explanation
Indices: 3983391--3983434 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
3983381 CTAAAGTTTA
3983391 TTTGAGCTAGGTGCATAAGCTAC
1 TTTGAGCTAGGTGCATAAGCTAC
3983414 TTTGAGCTAGGTGCATAAGCT
1 TTTGAGCTAGGTGCATAAGCT
3983435 GCATGGAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (23 bp):
TTTGAGCTAGGTGCATAAGCTAC
Found at i:3988580 original size:21 final size:21
Alignment explanation
Indices: 3988554--3988632 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
3988544 AAACATAATA
3988554 TTGTATCAATACAATATGGCC
1 TTGTATCAATACAATATGGCC
** * *
3988575 TTGTATTGATATAATA-GGCA
1 TTGTATCAATACAATATGGCC
* *
3988595 TTGTATTAATATAATATGG-C
1 TTGTATCAATACAATATGGCC
*
3988615 TTAGTATCGATACAATAT
1 TT-GTATCAATACAATAT
3988633 ATTTTACAAG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 20 0.43
21 27 0.57
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.39
Consensus pattern (21 bp):
TTGTATCAATACAATATGGCC
Found at i:3988611 original size:41 final size:41
Alignment explanation
Indices: 3988553--3988631 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
3988543 AAAACATAAT
* *
3988553 ATTGTATCAATACAATATGGCCTT-GTATTGATATAATAGGC
1 ATTGTATCAATACAATATGG-CTTAGTATCGATACAATAGGC
* *
3988594 ATTGTATTAATATAATATGGCTTAGTATCGATACAATA
1 ATTGTATCAATACAATATGGCTTAGTATCGATACAATA
3988632 TATTTTACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 3 0.09
41 30 0.91
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (41 bp):
ATTGTATCAATACAATATGGCTTAGTATCGATACAATAGGC
Found at i:3989267 original size:31 final size:29
Alignment explanation
Indices: 3989212--3989272 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 29
3989202 CTATAATTAA
* *
3989212 TATAGTAATATATAAACATATTTTATATT
1 TATAGTAATATATAAAAATATTTTAAATT
3989241 TATA-TAATATATAAAAATGAATTTTTAAATT
1 TATAGTAATATATAAAAAT--A-TTTTAAATT
3989272 T
1 T
3989273 TTTCATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 13 0.48
29 4 0.15
30 1 0.04
31 9 0.33
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (29 bp):
TATAGTAATATATAAAAATATTTTAAATT
Found at i:3998097 original size:36 final size:36
Alignment explanation
Indices: 3998026--3998098 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
3998016 ATTAAGGATT
** *
3998026 TCCTAATATTCTGATTATGATTACAAGATTGTAATC
1 TCCTAATATTCTGATTACAATTACAAGATTATAATC
*
3998062 TCCTAATATTTTGATTACAATTAC-AGAATTATAATC
1 TCCTAATATTCTGATTACAATTACAAG-ATTATAATC
3998098 T
1 T
3998099 TCATAATTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 2 0.06
36 30 0.94
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (36 bp):
TCCTAATATTCTGATTACAATTACAAGATTATAATC
Found at i:3999877 original size:20 final size:20
Alignment explanation
Indices: 3999852--3999913 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
3999842 TAAATTAATT
3999852 TTATAATTATTTAATA-TATA
1 TTATAA-TATTTAATATTATA
* *
3999872 TTATAAAATATAATATTATA
1 TTATAATATTTAATATTATA
*
3999892 TTATAA-ATATTAAAATTATA
1 TTATAATAT-TTAATATTATA
3999912 TT
1 TT
3999914 TTAAAAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.25
20 27 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATAATATTTAATATTATA
Found at i:3999918 original size:20 final size:19
Alignment explanation
Indices: 3999868--3999924 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
3999858 TTATTTAATA
*
3999868 TATATTATAAAATATAATAT
1 TATATTATAAAAT-TAAAAT
3999888 TATATTATAAATATTAAAAT
1 TATATTATAAA-ATTAAAAT
*
3999908 TATATTTTAAAAATTAA
1 TATATTAT-AAAATTAA
3999925 TAAAAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 28 0.85
21 5 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATTATAAAATTAAAAT
Found at i:4003628 original size:2 final size:2
Alignment explanation
Indices: 4003621--4003653 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4003611 CTTTATGGAA
4003621 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4003654 TATGTGTATT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4005614 original size:179 final size:183
Alignment explanation
Indices: 4005280--4005639 Score: 629
Period size: 179 Copynumber: 2.0 Consensus size: 183
4005270 CCATTTACTC
* *
4005280 AATAGCAGAGATTTCTGGTCCCTCTTCCTTTCCGTTGGGGAAAAATCCATTTCCCTTTTCTTTGT
1 AATAGCAGACATTTCTGGTCCCTCTTCCTTTCCATTGGGGAAAAATCCATTTCCCTTTTCTTTGT
4005345 AGGGTCTGGTATCCAGTTACCACTGAATTCTTTGGTAGCTATGTTCGCTTCTGTGCTAATGCCTC
66 AGGGTCTGGTATCCAGTTACCACTGAATTCTTTGGTAGCTATGTTCGCTTCTGTGCTAATGCCTC
*
4005410 TCCGAACTATATTTATGTCAGAGAAAGTGTTTAGGCGTGTTAGAATTTTTTAA
131 TCCCAACTATATTTATGTCAGAGAAAGTGTTTAGGCGTGTTAGAATTTTTTAA
*
4005463 AATAGCGGACATTTCTGGT-CC-C-T-CTTTCCATTGGGGAAAAATCCATTTCCCTTTTCTTTGT
1 AATAGCAGACATTTCTGGTCCCTCTTCCTTTCCATTGGGGAAAAATCCATTTCCCTTTTCTTTGT
* * *
4005524 GGGGTGTGGTATCCAGTTACCACTGAATTCTTTGGTGGCTATGTTCGCTTCTGTGCTAATGCCTC
66 AGGGTCTGGTATCCAGTTACCACTGAATTCTTTGGTAGCTATGTTCGCTTCTGTGCTAATGCCTC
4005589 TCCCAACTATATTTATGTCAGAGAAAGTGTTTAGGCGTGTTAGAATTTTTT
131 TCCCAACTATATTTATGTCAGAGAAAGTGTTTAGGCGTGTTAGAATTTTTT
4005640 TAGCTCCAAC
Statistics
Matches: 170, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
179 149 0.88
180 1 0.01
181 1 0.01
182 2 0.01
183 17 0.10
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (183 bp):
AATAGCAGACATTTCTGGTCCCTCTTCCTTTCCATTGGGGAAAAATCCATTTCCCTTTTCTTTGT
AGGGTCTGGTATCCAGTTACCACTGAATTCTTTGGTAGCTATGTTCGCTTCTGTGCTAATGCCTC
TCCCAACTATATTTATGTCAGAGAAAGTGTTTAGGCGTGTTAGAATTTTTTAA
Found at i:4005965 original size:2 final size:2
Alignment explanation
Indices: 4005958--4005983 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4005948 CTTGTGAGTT
4005958 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
4005984 CACAAATAAA
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):
TA
Found at i:4006586 original size:15 final size:17
Alignment explanation
Indices: 4006561--4006592 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4006551 ATCCCCCTAT
4006561 GAAGTATGAA-GGAACC
1 GAAGTATGAAGGGAACC
4006577 GAAG-ATGAAGGGAACC
1 GAAGTATGAAGGGAACC
4006593 AACCTGGCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.44, C:0.12, G:0.34, T:0.09
Consensus pattern (17 bp):
GAAGTATGAAGGGAACC
Found at i:4008097 original size:14 final size:13
Alignment explanation
Indices: 4008068--4008133 Score: 64
Period size: 13 Copynumber: 4.9 Consensus size: 13
4008058 ATAAATTTTT
*
4008068 ATTTAATAAAATA
1 ATTTATTAAAATA
4008081 ATTTATTAAATATA
1 ATTTATTAAA-ATA
4008095 ATTT-TTAAAA-A
1 ATTTATTAAAATA
4008106 ATTATAATTAATAATA
1 ATT-T-ATTAA-AATA
*
4008122 ATTAATTAAAAT
1 ATTTATTAAAAT
4008134 CTATAAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
11 4 0.09
12 2 0.04
13 17 0.38
14 16 0.36
15 2 0.04
16 4 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTATTAAAATA
Found at i:4008126 original size:24 final size:26
Alignment explanation
Indices: 4008070--4008155 Score: 65
Period size: 26 Copynumber: 3.3 Consensus size: 26
4008060 AAATTTTTAT
*
4008070 TTAA-TAAAATAATTTATTAAAT-ATAA
1 TTAATTAAAA-AATCTA-TAAATAATAA
* *
4008096 TT-TTTAAAAAAT-TATAATTAATAA
1 TTAATTAAAAAATCTATAAATAATAA
*
4008120 -TAATTAATTAAAATCTATAAATATTAA
1 TTAATTAA--AAAATCTATAAATAATAA
4008147 TTAATTAAA
1 TTAATTAAA
4008156 CCTATTTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
23 5 0.10
24 10 0.21
25 3 0.06
26 13 0.27
27 10 0.21
28 7 0.15
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (26 bp):
TTAATTAAAAAATCTATAAATAATAA
Found at i:4008166 original size:24 final size:24
Alignment explanation
Indices: 4008112--4008167 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
4008102 AAAAATTATA
* *
4008112 ATTAATAATAATTAATTAAAATCT
1 ATTAATATTAATTAATTAAAACCT
*
4008136 ATAAATATTAATTAATT-AAACCT
1 ATTAATATTAATTAATTAAAACCT
4008159 ATTTAATAT
1 A-TTAATAT
4008168 ATGTTATATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTAATATTAATTAATTAAAACCT
Found at i:4008260 original size:3 final size:3
Alignment explanation
Indices: 4008252--4008283 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4008242 TTATGCTACA
4008252 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4008284 AAAAACGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4011314 original size:2 final size:2
Alignment explanation
Indices: 4011297--4011330 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
4011287 TTATGCATAC
* *
4011297 AT AT AC AT AC 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
4011331 GAGAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4013268 original size:28 final size:27
Alignment explanation
Indices: 4013213--4013278 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
4013203 GCCACCCATT
4013213 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
4013240 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
*
4013268 TATTTGTCAAA
1 TGTTTGTCAAA
4013279 TATGAAGACT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.58
28 14 0.39
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:4017837 original size:28 final size:27
Alignment explanation
Indices: 4017782--4017847 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
4017772 GCCACCCATT
4017782 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
4017809 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
*
4017837 TATTTGTCAAA
1 TGTTTGTCAAA
4017848 TATGAAGGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.58
28 14 0.39
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:4017870 original size:24 final size:24
Alignment explanation
Indices: 4017839--4017899 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
4017829 TTCCTTTGTA
4017839 TTTGTC-AAATATGAAGGCTTGTTG
1 TTTGTCAAAAT-TGAAGGCTTGTTG
**
4017863 TTTGTCAAAATTGGTGGCTTGTTG
1 TTTGTCAAAATTGAAGGCTTGTTG
4017887 TTTGTCAAAATTG
1 TTTGTCAAAATTG
4017900 GTGGCTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 30 0.88
25 4 0.12
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.44
Consensus pattern (24 bp):
TTTGTCAAAATTGAAGGCTTGTTG
Found at i:4017900 original size:24 final size:24
Alignment explanation
Indices: 4017854--4017905 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
4017844 CAAATATGAA
4017854 GGCTTGTTGTTTGTCAAAATTGGT
1 GGCTTGTTGTTTGTCAAAATTGGT
4017878 GGCTTGTTGTTTGTCAAAATTGGT
1 GGCTTGTTGTTTGTCAAAATTGGT
4017902 GGCT
1 GGCT
4017906 AATTTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.15, C:0.10, G:0.31, T:0.44
Consensus pattern (24 bp):
GGCTTGTTGTTTGTCAAAATTGGT
Found at i:4024753 original size:16 final size:16
Alignment explanation
Indices: 4024714--4024800 Score: 52
Period size: 16 Copynumber: 5.4 Consensus size: 16
4024704 CTTGTTCGAA
* *
4024714 CTTATTCGGGTTCAGG
1 CTTATTCGAGTTCGGG
4024730 CTCT-TTCGAGTTCGGG
1 CT-TATTCGAGTTCGGG
* *
4024746 CTTATTCG-GATTTGGA
1 CTTATTCGAG-TTCGGG
* * *
4024762 TTTTTTCGAGTTTGGG
1 CTTATTCGAGTTCGGG
* * *
4024778 CTTATTTGGGTTCAGG
1 CTTATTCGAGTTCGGG
4024794 CTTATTC
1 CTTATTC
4024801 AGGTTTAGGT
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
15 2 0.04
16 49 0.92
17 2 0.04
ACGTcount: A:0.11, C:0.16, G:0.28, T:0.45
Consensus pattern (16 bp):
CTTATTCGAGTTCGGG
Found at i:4025190 original size:11 final size:10
Alignment explanation
Indices: 4025162--4025204 Score: 61
Period size: 11 Copynumber: 4.2 Consensus size: 10
4025152 AAACAGAATT
4025162 AATATTTAAA
1 AATATTTAAA
4025172 AA-ATTTAAA
1 AATATTTAAA
4025181 ATATATTTAATA
1 A-ATATTTAA-A
4025193 AATATTTAAA
1 AATATTTAAA
4025203 AA
1 AA
4025205 CCCATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.27
10 6 0.20
11 14 0.47
12 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATATTTAAA
Found at i:4025730 original size:16 final size:15
Alignment explanation
Indices: 4025702--4025732 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
4025692 TATGTTAACT
4025702 TTATATTCTATTCTA
1 TTATATTCTATTCTA
4025717 TTATATTACTATTCTA
1 TTATATT-CTATTCTA
4025733 AGTGTAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATTCTATTCTA
Found at i:4026261 original size:16 final size:16
Alignment explanation
Indices: 4026231--4026283 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
4026221 GTTTAGGTTC
*
4026231 TTTCGGGTTTGGGCTT
1 TTTCGGGTTCGGGCTT
*
4026247 TTTCGGGTTCAGGCTAT
1 TTTCGGGTTCGGGCT-T
* *
4026264 CTT-GGGTTCGGGCTA
1 TTTCGGGTTCGGGCTT
4026279 TTTCG
1 TTTCG
4026284 AGTTAGGGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 2 0.07
16 24 0.83
17 3 0.10
ACGTcount: A:0.06, C:0.17, G:0.34, T:0.43
Consensus pattern (16 bp):
TTTCGGGTTCGGGCTT
Found at i:4030743 original size:58 final size:58
Alignment explanation
Indices: 4030657--4030807 Score: 178
Period size: 58 Copynumber: 2.6 Consensus size: 58
4030647 CCCAGTCATA
* * *
4030657 GAAAATGACTTAAATGACATCAAAATTCATAAAATTGCATCAAAG-TCTCTAAGTTATG
1 GAAAATGACCTAAATGACATCAAAATTCATAAAATTACATCAAAGTTCT-TAAGTGATG
* ** *
4030715 GAAAATGACCTAATTGATGTCAACATTCATAAAATTACATCAAAGTTCTTAAGTGATG
1 GAAAATGACCTAAATGACATCAAAATTCATAAAATTACATCAAAGTTCTTAAGTGATG
* * * **
4030773 AAAAATAACCTAAATGGCATCAGCATTCATAAAAT
1 GAAAATGACCTAAATGACATCAAAATTCATAAAAT
4030808 AACAGAAATC
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
58 75 0.96
59 3 0.04
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (58 bp):
GAAAATGACCTAAATGACATCAAAATTCATAAAATTACATCAAAGTTCTTAAGTGATG
Found at i:4030878 original size:48 final size:47
Alignment explanation
Indices: 4030813--4030909 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 47
4030803 AAAATAACAG
* * *
4030813 AAATCCTTAAGCTATGAAAAATGACTAAAATGATATAAAAATGCATGA
1 AAATCCTCAAGCCATGAAAAATGACTAAAATGACATAAAAAT-CATGA
* *
4030861 AAATCCTCAAGCCATGAAAAATGTCTAAAATGACATAAAAGTCATGA
1 AAATCCTCAAGCCATGAAAAATGACTAAAATGACATAAAAATCATGA
4030908 AA
1 AA
4030910 GATGACATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
47 7 0.16
48 37 0.84
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.23
Consensus pattern (47 bp):
AAATCCTCAAGCCATGAAAAATGACTAAAATGACATAAAAATCATGA
Found at i:4030931 original size:21 final size:21
Alignment explanation
Indices: 4030877--4030931 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
4030867 TCAAGCCATG
4030877 AAAAATGTC-TAAA-ATGACAT
1 AAAAATG-CATAAAGATGACAT
*
4030897 AAAAGT-CATGAAAGATGACAT
1 AAAAATGCAT-AAAGATGACAT
4030918 AAAAATGCATAAAG
1 AAAAATGCATAAAG
4030932 GTTGTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 8 0.28
21 16 0.55
22 3 0.10
ACGTcount: A:0.56, C:0.09, G:0.15, T:0.20
Consensus pattern (21 bp):
AAAAATGCATAAAGATGACAT
Found at i:4031601 original size:15 final size:15
Alignment explanation
Indices: 4031572--4031602 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
4031562 AAAGCCATAG
4031572 TTTTCCTTTCTTTTT
1 TTTTCCTTTCTTTTT
4031587 TTTTCGCTTTCTTTTT
1 TTTTC-CTTTCTTTTT
4031603 GCTTTATGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTCCTTTCTTTTT
Found at i:4034137 original size:524 final size:522
Alignment explanation
Indices: 4033057--4034096 Score: 1480
Period size: 524 Copynumber: 2.0 Consensus size: 522
4033047 TTGAAGCATG
** ** * * *
4033057 AGAAGATACTGCACCATGCTTATGCTAATTCCAGATATTTTGTGAAAGAATTAAATTATACTAAT
1 AGAAGATACTGCAAAATGAGTATGATTATTCCAGATATTTGGTGAAAGAATTAAATTATACTAAT
* ** * *
4033122 AGGTTGCATAGTAAAAAGGTTTCAAATAGGTTATTTTAACTTTTAAATATTTAGGTTGTCATGCT
66 AGGTTGCATAATAAAAAGGTTTCAAATAGGTTACCTTAACTCTTAAATATTTAGGTTGTCATGAT
* * * *
4033187 AAATTGTTAGATCTCGCTCATGCTTTATATTTATCATAAATTTCTTTTTCCTTTCTGACGTTGGA
131 AAATTGTTAGATCCCGCTCATCCTCTATATTTATCATAAATTTCTTTTTCCTTTCTCACGTTGGA
4033252 CTAAATTGCTAGAATGAATAGTATATATGACTTAACCTTGAATGGCCATTATGAAATGACAAAAA
196 CTAAATTGCTAGAATGAATAGTATATATGACTTAACCTTGAATGGCCATTATGAAATGACAAAAA
** **
4033317 GGTAGTTGTTAATCTATTTTGACTAAGTGAAATTGATCACCTACCGGAGTTTATCTTTTAAGAGT
261 GGTAGTTGTTAATCTATTTTGACTAAGTGAAATTGATCACCTACCAAAGTTTATCTTCAAAGAGT
* *
4033382 TAAACCTTCAAAACAAACTCCGAAGTCTGCTTAAAATCCAAATTGTCATATAAAAAGGGTTTAAG
326 TAAACCTTCAAAACAAACTCCAAAGTCTGCTTAAAATCCAAATTGTCATATAAAAAGCGTTTAAG
* * *
4033447 AGTCAATTACGAAAAAAGTGAAACGTATTCCCTTCATGATGTTTGTACTTTGATACCTGTTAATT
391 AGTCAATTACGAAAAAAGTGAAACGTACTCCCTTCATGATGGTTGTACTTTGATACCTATTAATT
4033512 ACATGTTATCCTAATTCTCGATTTAAATTAATTTAACTTTTCAATATTTAATTTTAATAGGTACC
456 ACATGTTATCCTAATTCTCGATTTAAATTAATTTAACTTTTCAATATTTAATTTTAAT--GTACC
4033577 AATT
519 AATT
*** ** *
4033581 AGAAGATACTGCGGCATGCTTATGCTTATTCCAGATATTTGGTGAAAGAATTAAATTATACTAAT
1 AGAAGATACTGCAAAATGAGTATGATTATTCCAGATATTTGGTGAAAGAATTAAATTATACTAAT
* *
4033646 AGGTTGC-TCAAT-ATAAGGTTTCAAATAGGTTACCTTAACTCTTCAATATTTAGGTTGTCATGA
66 AGGTTGCAT-AATAAAAAGGTTTCAAATAGGTTACCTTAACTCTTAAATATTTAGGTTGTCATGA
4033709 TAAATTGTTAGATCCCGCTCATCCTCTATATTTATCATAAATTTCTTTTTCCTTTCTCACGTTAG
130 TAAATTGTTAGATCCCGCTCATCCTCTATATTTATCATAAATTTCTTTTTCCTTTCTCACGTT-G
* * *
4033774 GACTAAATTGCTAGAATGAATCGTATATCTGACTTAACCTTGAATGGCTATTATGAAATGACCAA
194 GACTAAATTGCTAGAATGAATAGTATATATGACTTAACCTTGAATGGCCATTATGAAATGA-CAA
* * * *
4033839 AAA-GTAGTTGTTAATTTATTTTGACT-AGATGAAATTGGTCACCTATCAAAGTTTGTCTATCAA
258 AAAGGTAGTTGTTAATCTATTTTGACTAAG-TGAAATTGATCACCTACCAAAGTTTATCT-TCAA
* *
4033902 AG-GTTACAAAACCTTCAAAATAAACTCTAAAGTCTGCTTAAAATCCAAATAT-TCATATAAAAA
321 AGAGTT---AAACCTTCAAAACAAACTCCAAAGTCTGCTTAAAATCCAAAT-TGTCATATAAAAA
* * *** * * *
4033965 GCGTTTAGGAGTCAGTTACGTGCAAAGTGAGACGTACTCCCTTCATGATGGTTGTATTTTGGTAC
382 GCGTTTAAGAGTCAATTACGAAAAAAGTGAAACGTACTCCCTTCATGATGGTTGTACTTTGATAC
*
4034030 CTATTAATTACGTGTTATCCTAATTCTCGATTTAAATTAATTTAACTTTTCAATATTTAATTTTA
447 CTATTAATTACATGTTATCCTAATTCTCGATTTAAATTAATTTAACTTTTCAATATTTAATTTTA
4034095 AT
512 AT
4034097 TCCCACATTT
Statistics
Matches: 465, Mismatches: 42, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
523 107 0.23
524 178 0.38
525 10 0.02
527 169 0.36
528 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.38
Consensus pattern (522 bp):
AGAAGATACTGCAAAATGAGTATGATTATTCCAGATATTTGGTGAAAGAATTAAATTATACTAAT
AGGTTGCATAATAAAAAGGTTTCAAATAGGTTACCTTAACTCTTAAATATTTAGGTTGTCATGAT
AAATTGTTAGATCCCGCTCATCCTCTATATTTATCATAAATTTCTTTTTCCTTTCTCACGTTGGA
CTAAATTGCTAGAATGAATAGTATATATGACTTAACCTTGAATGGCCATTATGAAATGACAAAAA
GGTAGTTGTTAATCTATTTTGACTAAGTGAAATTGATCACCTACCAAAGTTTATCTTCAAAGAGT
TAAACCTTCAAAACAAACTCCAAAGTCTGCTTAAAATCCAAATTGTCATATAAAAAGCGTTTAAG
AGTCAATTACGAAAAAAGTGAAACGTACTCCCTTCATGATGGTTGTACTTTGATACCTATTAATT
ACATGTTATCCTAATTCTCGATTTAAATTAATTTAACTTTTCAATATTTAATTTTAATGTACCAA
TT
Found at i:4034699 original size:78 final size:78
Alignment explanation
Indices: 4034493--4034944 Score: 343
Period size: 78 Copynumber: 5.8 Consensus size: 78
4034483 AGAAAATTGA
* * * * * ** * *
4034493 TTTTCATGTAATATTACATAAATACCCTTAATGGATATTTTTTGACATGAAAGTTCTCACCTAAT
1 TTTTCATGTAATATTACCTAAATACTCTTAATAGACATGTTTCAACATGAAAGTTCTCACATGAT
* * * * *
4034558 CCTAAGGTCTCAA
66 CTTAAAGACTTAG
* * * * * * *
4034571 TTTTTATGTCATATTACCTAAATAAC-CCTAATAGATATAATTT-AATATAAAAGTTCAT-ACAT
1 TTTTCATGTAATATTACCTAAAT-ACTCTTAATAGACAT-GTTTCAACATGAAAGTTC-TCACAT
* *
4034633 GATCTTAAAGATTTGG
63 GATCTTAAAGACTTAG
* * * * * * * * *
4034649 CTTTCTTGTAATATTTCCTAAACAATCTTAATAAACATGTTTCAACATAAAAGTTCTCTCATTAT
1 TTTTCATGTAATATTACCTAAATACTCTTAATAGACATGTTTCAACATGAAAGTTCTCACATGAT
* *
4034714 CCTAAGGACTTAG
66 CTTAAAGACTTAG
* * * * * * * *
4034727 TTTTCTTGTAATATTGCCTAAATACTTTTAATGGACATGTTTTAACATGAAGGTTCCCATATGAT
1 TTTTCATGTAATATTACCTAAATACTCTTAATAGACATGTTTCAACATGAAAGTTCTCACATGAT
* * *
4034792 CTTAAAAACTCAA
66 CTTAAAGACTTAG
* * * ** *
4034805 TTTTCATGTAATATTACCTAAATACCCTTAATAGACATGTTTCGACATGAAAGTTTTGGCACGAT
1 TTTTCATGTAATATTACCTAAATACTCTTAATAGACATGTTTCAACATGAAAGTTCTCACATGAT
* * *
4034870 CTTAAGGAGTTGG
66 CTTAAAGACTTAG
* * *
4034883 TTTTCATGAAATATTACCTAAATACTCTTAACAGACATATTTCAACATGAAAGTTCTCACAT
1 TTTTCATGTAATATTACCTAAATACTCTTAATAGACATGTTTCAACATGAAAGTTCTCACAT
4034945 AACCTTAGAG
Statistics
Matches: 284, Mismatches: 84, Indels: 12
0.75 0.22 0.03
Matches are distributed among these distances:
77 5 0.02
78 273 0.96
79 6 0.02
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (78 bp):
TTTTCATGTAATATTACCTAAATACTCTTAATAGACATGTTTCAACATGAAAGTTCTCACATGAT
CTTAAAGACTTAG
Found at i:4035280 original size:29 final size:29
Alignment explanation
Indices: 4035195--4035280 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 29
4035185 AAATAACTGG
* * * *
4035195 ACCCTAAAATGAATGAAAATTGTAAAATG
1 ACCCTAAAATGCATGAAAATAGCAAAATA
* * * *
4035224 ACCCTAAATTACAT-AAAATAAACTAAATA
1 ACCCTAAAATGCATGAAAAT-AGCAAAATA
*
4035253 ACCCTAAAATGCATGGAAATAGCAAAAT
1 ACCCTAAAATGCATGAAAATAGCAAAAT
4035281 GGTCCTTAGA
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
28 5 0.12
29 33 0.79
30 4 0.10
ACGTcount: A:0.53, C:0.15, G:0.09, T:0.22
Consensus pattern (29 bp):
ACCCTAAAATGCATGAAAATAGCAAAATA
Found at i:4035280 original size:58 final size:59
Alignment explanation
Indices: 4035195--4035325 Score: 147
Period size: 59 Copynumber: 2.2 Consensus size: 59
4035185 AAATAACTGG
* * *
4035195 ACCCTAAAATGAATGAAAATTGTAAAAT-GACCCTAAATTACATAAAATAAACTAAATA
1 ACCCTAAAATGCATGAAAATAGCAAAATGGACCCTAAATTACATAAAATAAACTAAATA
* * * * * * *
4035253 ACCCTAAAATGCATGGAAATAGCAAAATGGTCCTTAGATTTCATAAAATTACCTAAATA
1 ACCCTAAAATGCATGAAAATAGCAAAATGGACCCTAAATTACATAAAATAAACTAAATA
* *
4035312 AGCTTAAAATGCAT
1 ACCCTAAAATGCAT
4035326 ATGGATTGCA
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
58 24 0.40
59 36 0.60
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (59 bp):
ACCCTAAAATGCATGAAAATAGCAAAATGGACCCTAAATTACATAAAATAAACTAAATA
Found at i:4035357 original size:59 final size:58
Alignment explanation
Indices: 4035235--4035359 Score: 130
Period size: 59 Copynumber: 2.1 Consensus size: 58
4035225 CCCTAAATTA
*
4035235 CATAAAATAAACTAAATAACCCTAAAATGCATGGAAATAGCAAAATGGTCCTTAGATTT
1 CATAAAATAAACTAAATAACCCTAAAATGCATGG-AATAGCAAAATGGTCCTTAGATTG
* * * * *
4035294 CATAAAATTACCTAAATAAGCTTAAAATGCATATGG-ATTGCAAAATGGTACC-TA-ATATG
1 CATAAAATAAACTAAATAACCCTAAAATGC--ATGGAATAGCAAAATGGT-CCTTAGAT-TG
4035353 CATAAAA
1 CATAAAA
4035360 ACATTGTGAG
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
58 2 0.04
59 48 0.86
60 2 0.04
61 4 0.07
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.26
Consensus pattern (58 bp):
CATAAAATAAACTAAATAACCCTAAAATGCATGGAATAGCAAAATGGTCCTTAGATTG
Found at i:4035521 original size:3 final size:3
Alignment explanation
Indices: 4035513--4035540 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4035503 CTTGGAGATG
4035513 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
4035541 ATTTTTATAA
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:4049383 original size:47 final size:47
Alignment explanation
Indices: 4049281--4049371 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 47
4049271 TTTTGTAAGG
* * *
4049281 ATAAAGTTATAAACCTTTCTCACAAACATCTTGTAACTTTTGCACAC
1 ATAAAGTTAAAAAACTTTCTCACAAACAACTTGTAACTTTTGCACAC
4049328 ATAAAGTTAAAAAAC-TTCTTCACAAACAACTTGTAACTTTTGCA
1 ATAAAGTTAAAAAACTTTC-TCACAAACAACTTGTAACTTTTGCA
4049372 TGAATAAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 3 0.08
47 37 0.93
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.33
Consensus pattern (47 bp):
ATAAAGTTAAAAAACTTTCTCACAAACAACTTGTAACTTTTGCACAC
Found at i:4050492 original size:21 final size:21
Alignment explanation
Indices: 4050466--4050507 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
4050456 TAAAATATAA
*
4050466 TATATATTATTTATTAAATAT
1 TATATATTATTTAATAAATAT
4050487 TATATATTATTTAATAAATAT
1 TATATATTATTTAATAAATAT
4050508 AATGTACAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATATTATTTAATAAATAT
Found at i:4051107 original size:20 final size:19
Alignment explanation
Indices: 4051082--4051130 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
4051072 GTTAAAATAT
4051082 ATATATAATATGAATTATAA
1 ATATATAATATGAA-TATAA
* **
4051102 ATATATCAAAATTTATATAA
1 ATATAT-AATATGAATATAA
4051122 ATATATAAT
1 ATATATAAT
4051131 GCATTAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.08
20 17 0.71
21 5 0.21
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
ATATATAATATGAATATAA
Found at i:4054982 original size:2 final size:2
Alignment explanation
Indices: 4054969--4055002 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
4054959 TTCAAATTTT
4054969 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
4055003 CTCTTTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4057842 original size:21 final size:19
Alignment explanation
Indices: 4057814--4057852 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
4057804 TTTAAAATTG
*
4057814 ATTCTGATTTATTTTTTAAA
1 ATTCTGA-TTATGTTTTAAA
4057834 ATTCTTGATTATGTTTTAA
1 ATTC-TGATTATGTTTTAA
4057853 CACCTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.59
Consensus pattern (19 bp):
ATTCTGATTATGTTTTAAA
Found at i:4058458 original size:16 final size:16
Alignment explanation
Indices: 4058437--4058472 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4058427 TTTAATTTTG
* *
4058437 ATTTGGTTATTATTAT
1 ATTTGGTGATTATTAA
4058453 ATTTGGTGATTATTAA
1 ATTTGGTGATTATTAA
4058469 ATTT
1 ATTT
4058473 ATATTTGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (16 bp):
ATTTGGTGATTATTAA
Found at i:4058502 original size:2 final size:2
Alignment explanation
Indices: 4058490--4058522 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4058480 TGTTTGGATT
*
4058490 TA TA AA 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
4058523 CATTGAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 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):
TA
Found at i:4066867 original size:16 final size:16
Alignment explanation
Indices: 4066813--4066867 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
4066803 TATCTTCTTT
* *
4066813 ATTTACTTTTTAATTA
1 ATTTAATTTTTAAATA
**
4066829 ATTTAATTTAAAAATA
1 ATTTAATTTTTAAATA
**
4066845 AAATAATTTTTAAATA
1 ATTTAATTTTTAAATA
4066861 ATTTAAT
1 ATTTAAT
4066868 CTCTTTATGA
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTTTTAAATA
Found at i:4067067 original size:15 final size:16
Alignment explanation
Indices: 4067047--4067081 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
4067037 TATGTATAAC
*
4067047 TTAATTAAAA-ATTCT
1 TTAATTAAAAGATTAT
4067062 TTAATTAAAAGATTAT
1 TTAATTAAAAGATTAT
4067078 TTAA
1 TTAA
4067082 AAATAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (16 bp):
TTAATTAAAAGATTAT
Found at i:4068179 original size:44 final size:47
Alignment explanation
Indices: 4068091--4068185 Score: 119
Period size: 47 Copynumber: 2.1 Consensus size: 47
4068081 AGGTATGACT
*
4068091 TTTTTGTCATTATTTTTTCTTTTTTTTTCTCTCTCCGTTTACTTTTC
1 TTTTTGTCATTATTTTTTCTTTTTTATTCTCTCTCCGTTTACTTTTC
*
4068138 TTTTT-TCATTTTTTTTATCTTTTTTATT-T-T-TCC-TTTCACTTTTC
1 TTTTTGTCATTATTTTT-TCTTTTTTATTCTCTCTCCGTTT-ACTTTTC
4068182 TTTT
1 TTTT
4068186 CCTTTTCTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
43 3 0.07
44 14 0.32
45 1 0.02
46 11 0.25
47 15 0.34
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (47 bp):
TTTTTGTCATTATTTTTTCTTTTTTATTCTCTCTCCGTTTACTTTTC
Found at i:4068914 original size:2 final size:2
Alignment explanation
Indices: 4068907--4068936 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
4068897 GATAATTTCT
4068907 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
4068937 TTTAGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4069899 original size:26 final size:27
Alignment explanation
Indices: 4069860--4069912 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
4069850 GTTAATGTAA
4069860 TATTTTTAAAAAATATAAT-TAATAAAT
1 TATTTTTAAAAAAT-TAATATAATAAAT
* *
4069887 TATTTTT-TAAAATTAATATATTAAAT
1 TATTTTTAAAAAATTAATATAATAAAT
4069913 ATAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 4 0.17
26 12 0.52
27 7 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TATTTTTAAAAAATTAATATAATAAAT
Found at i:4077280 original size:24 final size:24
Alignment explanation
Indices: 4077242--4077295 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
4077232 TATTTTTAAA
*
4077242 AATTATATTTATTATTT-TGATTTGT
1 AATT-TATTTATTATTTAT-ATTTAT
*
4077267 AATTTATTTTTTATTTATATTTAT
1 AATTTATTTATTATTTATATTTAT
4077291 AATTT
1 AATTT
4077296 TTAAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (24 bp):
AATTTATTTATTATTTATATTTAT
Found at i:4077561 original size:12 final size:13
Alignment explanation
Indices: 4077532--4077561 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
4077522 GAATACTTTG
4077532 AAAAATTAATTTC
1 AAAAATTAATTTC
4077545 AAAAATTAATTTC
1 AAAAATTAATTTC
4077558 AAAA
1 AAAA
4077562 GCATAAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAAATTAATTTC
Done.