Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 13 of 31
Found at i:2944355 original size:23 final size:24
Alignment explanation
Indices: 2944312--2944361 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
2944302 TGATTCATTT
2944312 TATTATTTTTAAAAAATATTA-AA
1 TATTATTTTTAAAAAATATTATAA
**
2944335 TATTATTTTATAATTAA-ATTATAA
1 TATTATTTT-TAAAAAATATTATAA
2944359 TAT
1 TAT
2944362 AAAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TATTATTTTTAAAAAATATTATAA
Found at i:2944389 original size:30 final size:31
Alignment explanation
Indices: 2944326--2944389 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
2944316 ATTTTTAAAA
* *
2944326 AATATTAAATATTATTTTATAATTAAATTAT
1 AATATAAAATATTATTTTATAATTAAATAAT
*
2944357 AATATAAAATA-T-TTTTATTAGTTAAATAAT
1 AATATAAAATATTATTTTA-TAATTAAATAAT
2944387 AAT
1 AAT
2944390 TTTATTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 5 0.17
30 14 0.48
31 10 0.34
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
AATATAAAATATTATTTTATAATTAAATAAT
Found at i:2944402 original size:21 final size:20
Alignment explanation
Indices: 2944364--2944403 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2944354 TATAATATAA
* *
2944364 AATATTTTTATTAGTTAAAT
1 AATAATTTTATTAATTAAAT
2944384 AATAATTTTATTTAATTAAA
1 AATAATTTTA-TTAATTAAA
2944404 CTTAAATCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AATAATTTTATTAATTAAAT
Found at i:2945746 original size:2 final size:2
Alignment explanation
Indices: 2945739--2945764 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2945729 TTGTACTTTA
2945739 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
2945765 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2947024 original size:32 final size:33
Alignment explanation
Indices: 2946979--2947040 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
2946969 ATCACGATAA
**
2946979 AAATACATAAATATATTAAAATTTATATAATAT
1 AAATACATAAATATATTAAAAAATATATAATAT
*
2947012 AAATA-ATTAATATATTAAAAAATATATAA
1 AAATACATAAATATATTAAAAAATATATAA
2947041 AAATATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 21 0.81
33 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (33 bp):
AAATACATAAATATATTAAAAAATATATAATAT
Found at i:2947045 original size:29 final size:31
Alignment explanation
Indices: 2946975--2947059 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 31
2946965 GGTGATCACG
* *
2946975 ATAAAAATACATAAATATATTAAAATTTATATA
1 ATAAAAATA-ATTAATATATTAAAA-TAATATA
*
2947008 ATATAAATAATTAATATATTAAAA-AATAT-
1 ATAAAAATAATTAATATATTAAAATAATATA
*
2947037 ATAAAAAT-ATATAATATCTTAAA
1 ATAAAAATAAT-TAATATATTAAA
2947060 TTTTTATAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
28 2 0.04
29 18 0.39
30 4 0.09
32 14 0.30
33 8 0.17
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (31 bp):
ATAAAAATAATTAATATATTAAAATAATATA
Found at i:2952044 original size:17 final size:17
Alignment explanation
Indices: 2952013--2952061 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
2952003 TTGCAATTTT
*
2952013 CTCTTTCTTTTTTCTTGC
1 CTCTTTCTCTTTTCTT-C
*
2952031 CTTTTTC-CTTTTCTTC
1 CTCTTTCTCTTTTCTTC
2952047 CTCTTTCTCTTTTCT
1 CTCTTTCTCTTTTCT
2952062 CTCCCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 7 0.26
17 14 0.52
18 6 0.22
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (17 bp):
CTCTTTCTCTTTTCTTC
Found at i:2952345 original size:15 final size:15
Alignment explanation
Indices: 2952309--2952338 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2952299 AATTAAAAAA
*
2952309 TAAATATATTTATAT
1 TAAATATATATATAT
2952324 TAAATATATATATAT
1 TAAATATATATATAT
2952339 ATAATATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAATATATATATAT
Found at i:2952409 original size:13 final size:13
Alignment explanation
Indices: 2952391--2952417 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2952381 TCTTTCCCCT
2952391 TACTCTCTTAGTA
1 TACTCTCTTAGTA
2952404 TACTCTCTTAGTA
1 TACTCTCTTAGTA
2952417 T
1 T
2952418 TTAATTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (13 bp):
TACTCTCTTAGTA
Found at i:2952562 original size:2 final size:2
Alignment explanation
Indices: 2952555--2952587 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2952545 AAACCAGTCC
2952555 CT 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 CT C
2952588 ACACACACAC
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:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2954611 original size:9 final size:10
Alignment explanation
Indices: 2954591--2954632 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 10
2954581 ATGATTGAAT
*
2954591 TAAATAAATA
1 TAAATAATTA
2954601 TAAATAA-TA
1 TAAATAATTA
*
2954610 TAAAAAATTA
1 TAAATAATTA
2954620 TAAA-AATTA
1 TAAATAATTA
2954629 TAAA
1 TAAA
2954633 ACTAATTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 17 0.57
10 13 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TAAATAATTA
Found at i:2955012 original size:18 final size:18
Alignment explanation
Indices: 2954978--2955015 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2954968 TTCATTTTTA
*
2954978 AATTTTTTACATTAAATT
1 AATTTTTTACATGAAATT
2954996 AATTATTTTA-ATGAAATT
1 AATT-TTTTACATGAAATT
2955014 AA
1 AA
2955016 AAAAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTTTTTACATGAAATT
Found at i:2960836 original size:22 final size:23
Alignment explanation
Indices: 2960796--2960841 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
2960786 GAGATTTAAA
*
2960796 TTTTAAAATTATTAAATATTAATT
1 TTTTAAAATAATT-AATATTAATT
2960820 TTTTAAAATAATT-ATATTAATT
1 TTTTAAAATAATTAATATTAATT
2960842 AATTACGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
24 12 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTAAAATAATTAATATTAATT
Found at i:2962399 original size:2 final size:2
Alignment explanation
Indices: 2962392--2962428 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2962382 ACTAACCCTC
2962392 AT AT AT 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 AT AT AT A
2962429 GCAAGCCACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2968184 original size:17 final size:17
Alignment explanation
Indices: 2968127--2968184 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
2968117 GCTTTTATAG
* *
2968127 ATTTGGGTAATTTATGG
1 ATTTGGATAATTTATGA
*
2968144 ATTTGGAT-TTTTGA-GA
1 ATTTGGATAATTT-ATGA
*
2968160 AGTTGGATAATTTATGA
1 ATTTGGATAATTTATGA
2968177 ATTTGGAT
1 ATTTGGAT
2968185 TTTGAAGTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
16 12 0.38
17 20 0.62
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (17 bp):
ATTTGGATAATTTATGA
Found at i:2968301 original size:13 final size:13
Alignment explanation
Indices: 2968283--2968327 Score: 90
Period size: 13 Copynumber: 3.5 Consensus size: 13
2968273 AATAATGTTG
2968283 AATTTATTTTATT
1 AATTTATTTTATT
2968296 AATTTATTTTATT
1 AATTTATTTTATT
2968309 AATTTATTTTATT
1 AATTTATTTTATT
2968322 AATTTA
1 AATTTA
2968328 AATTTGATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
AATTTATTTTATT
Found at i:2968339 original size:26 final size:24
Alignment explanation
Indices: 2968280--2968343 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 24
2968270 TTGAATAATG
2968280 TTGA-ATTTATTTTATTAATTTAT
1 TTGATATTTATTTTATTAATTTAT
*
2968303 TTTATTAATTTATTTTATTAATTTAAAT
1 TTGA-T-ATTTATTTTATTAATTT--AT
2968331 TTGATATTTATTT
1 TTGATATTTATTT
2968344 AAATATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 3 0.09
26 25 0.74
27 1 0.03
28 5 0.15
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (24 bp):
TTGATATTTATTTTATTAATTTAT
Found at i:2968356 original size:17 final size:17
Alignment explanation
Indices: 2968313--2968420 Score: 64
Period size: 17 Copynumber: 6.4 Consensus size: 17
2968303 TTTATTAATT
*
2968313 TATTTTATTAATTTAAA
1 TATTTAATTAATTTAAA
* *
2968330 T-TTGATATTTATTTAAA
1 TATTTA-ATTAATTTAAA
*
2968347 TATTTAATTTTTATTT-AA
1 TATTTAA--TTAATTTAAA
* *
2968365 T-TTTATTTAA--AAAA
1 TATTTAATTAATTTAAA
*
2968379 TAATTTAATAAATTTAAA
1 T-ATTTAATTAATTTAAA
* *
2968397 TATTTAGTGAATTTAAA
1 TATTTAATTAATTTAAA
2968414 TATTTAA
1 TATTTAA
2968421 CAAATAATGA
Statistics
Matches: 69, Mismatches: 13, Indels: 18
0.69 0.13 0.18
Matches are distributed among these distances:
14 3 0.04
15 3 0.04
16 9 0.13
17 37 0.54
18 10 0.14
19 7 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TATTTAATTAATTTAAA
Found at i:2968361 original size:11 final size:10
Alignment explanation
Indices: 2968284--2968374 Score: 54
Period size: 9 Copynumber: 9.6 Consensus size: 10
2968274 ATAATGTTGA
2968284 ATTT-ATTTT
1 ATTTAATTTT
2968293 A-TTAA-TTT
1 ATTTAATTTT
* *
2968301 ATTTTA-TTA
1 ATTTAATTTT
2968310 ATTT-ATTTT
1 ATTTAATTTT
*
2968319 A-TTAATTTAA
1 ATTTAATTT-T
*
2968329 ATTTGATATTT
1 ATTTAAT-TTT
*
2968340 ATTTAA--AT
1 ATTTAATTTT
2968348 ATTTAATTTTT
1 ATTTAA-TTTT
2968359 ATTTAATTTT
1 ATTTAATTTT
2968369 ATTTAA
1 ATTTAA
2968375 AAAATAATTT
Statistics
Matches: 63, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
8 16 0.25
9 18 0.29
10 11 0.17
11 16 0.25
12 2 0.03
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (10 bp):
ATTTAATTTT
Found at i:2968486 original size:17 final size:16
Alignment explanation
Indices: 2968457--2968502 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
2968447 TAATATTTAG
2968457 ATAATATTTAAATATAA
1 ATAA-ATTTAAATATAA
*
2968474 ATAAATTTAAAATTTAA
1 ATAAATTT-AAATATAA
2968491 ATAAA-TTAAATA
1 ATAAATTTAAATA
2968503 AGGTCGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 4 0.15
16 6 0.23
17 16 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAAATTTAAATATAA
Found at i:2969022 original size:2 final size:2
Alignment explanation
Indices: 2969011--2969041 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2969001 TTTTAATGTC
2969011 AT AT -T 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
2969042 GAAGAAGGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2971141 original size:22 final size:23
Alignment explanation
Indices: 2971107--2971160 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
2971097 TTTTATTTTT
2971107 ATTTTTTAAA-TTTTTA-AAATA
1 ATTTTTTAAATTTTTTATAAATA
*
2971128 ATTTTTTAGTATTTTTTATTAAATA
1 ATTTTTTA-AATTTTTTA-TAAATA
2971153 ATTTTTTA
1 ATTTTTTA
2971161 TTTTTGAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 8 0.29
22 1 0.04
23 6 0.21
25 13 0.46
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
ATTTTTTAAATTTTTTATAAATA
Found at i:2971172 original size:22 final size:24
Alignment explanation
Indices: 2971107--2971172 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 24
2971097 TTTTATTTTT
*
2971107 ATTTTTTAAATTTTT-A--AAATA
1 ATTTTTTATATTTTTGAGTAAATA
* *
2971128 ATTTTTTAGTATTTTTTATTAAATA
1 ATTTTTTA-TATTTTTGAGTAAATA
2971153 A-TTTTT-TATTTTTGAGTAAA
1 ATTTTTTATATTTTTGAGTAAA
2971173 ATATAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 8 0.21
22 18 0.47
23 1 0.03
24 5 0.13
25 6 0.16
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.61
Consensus pattern (24 bp):
ATTTTTTATATTTTTGAGTAAATA
Found at i:2971216 original size:18 final size:19
Alignment explanation
Indices: 2971169--2971225 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
2971159 TATTTTTGAG
*
2971169 TAAAATA-TAAAATTATTT-
1 TAAAATATTTAAATT-TTTA
2971187 TAAAATATTTAAATTTTTA
1 TAAAATATTTAAATTTTTA
2971206 TAAAA-ATTTAAA-TTTTA
1 TAAAATATTTAAATTTTTA
2971223 TAA
1 TAA
2971226 TATTTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
17 8 0.22
18 17 0.47
19 11 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAAATATTTAAATTTTTA
Found at i:2971221 original size:17 final size:17
Alignment explanation
Indices: 2971183--2971225 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
2971173 ATATAAAATT
*
2971183 ATTTTA-AAATATTTAA
1 ATTTTATAAAAATTTAA
2971199 ATTTTTATAAAAATTTAA
1 A-TTTTATAAAAATTTAA
2971217 ATTTTATAA
1 ATTTTATAA
2971226 TATTTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 13 0.54
18 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTTATAAAAATTTAA
Found at i:2971232 original size:17 final size:16
Alignment explanation
Indices: 2971183--2971230 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
2971173 ATATAAAATT
*
2971183 ATTTTAAAATATTTAA
1 ATTTTATAATATTTAA
*
2971199 ATTTTTATAAAAATTTAA
1 A-TTTTAT-AATATTTAA
2971217 ATTTTATAATATTT
1 ATTTTATAATATTT
2971231 TATTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 7 0.26
17 11 0.41
18 9 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTTATAATATTTAA
Found at i:2972064 original size:22 final size:22
Alignment explanation
Indices: 2972036--2972088 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
2972026 TAAAAGATAA
2972036 AATTTTAAAAATTTATAA-TTTT
1 AATTTTAAAAA-TTATAATTTTT
*
2972058 AATTTTAATAATTATAATTTTT
1 AATTTTAAAAATTATAATTTTT
*
2972080 TATTTTAAA
1 AATTTTAAA
2972089 TTATGATTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTTAAAAATTATAATTTTT
Found at i:2974452 original size:3 final size:3
Alignment explanation
Indices: 2974444--2974478 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2974434 ACTTTTTCTT
2974444 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2974479 TTATCTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2975154 original size:2 final size:2
Alignment explanation
Indices: 2975147--2975194 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2975137 TTCAAACTTA
2975147 AT 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 AT
2975189 AT AT AT
1 AT AT AT
2975195 CTTCTAACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2976053 original size:22 final size:22
Alignment explanation
Indices: 2976028--2976072 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2976018 CGATTATATG
*
2976028 AATATGATATAAAAAAATAAAT
1 AATATAATATAAAAAAATAAAT
*
2976050 AATATAATATAAATAAATAAAT
1 AATATAATATAAAAAAATAAAT
2976072 A
1 A
2976073 TCACGAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AATATAATATAAAAAAATAAAT
Found at i:2976119 original size:32 final size:32
Alignment explanation
Indices: 2976051--2976127 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
2976041 AAAATAAATA
2976051 ATATAATATAAATAAATAAATATCACGAAATTT
1 ATATAATATAAATAAATAAATATCAC-AAATTT
* * *
2976084 ATATAATATAAATCATTAAAGTATTA-AAATTT
1 ATATAATATAAATAAATAAA-TATCACAAATTT
2976116 ATATAATATAAA
1 ATATAATATAAA
2976128 ATAATTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 18 0.45
33 18 0.45
34 4 0.10
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (32 bp):
ATATAATATAAATAAATAAATATCACAAATTT
Found at i:2976855 original size:24 final size:26
Alignment explanation
Indices: 2976816--2976866 Score: 88
Period size: 24 Copynumber: 2.0 Consensus size: 26
2976806 AAAAATTAAG
2976816 AAAAATAATTATAATATATAAAAATT
1 AAAAATAATTATAATATATAAAAATT
2976842 AAAAAT-A-TATAATATATAAAAATT
1 AAAAATAATTATAATATATAAAAATT
2976866 A
1 A
2976867 TCATACAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 18 0.72
25 1 0.04
26 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAAATAATTATAATATATAAAAATT
Found at i:2977952 original size:10 final size:10
Alignment explanation
Indices: 2977937--2977971 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
2977927 AAAATTTTCT
2977937 ATATATATAA
1 ATATATATAA
*
2977947 ATATATATAT
1 ATATATATAA
*
2977957 ATATATATGA
1 ATATATATAA
2977967 ATATA
1 ATATA
2977972 AAATACATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (10 bp):
ATATATATAA
Found at i:2981445 original size:2 final size:2
Alignment explanation
Indices: 2981438--2981469 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2981428 CATAACTTGA
2981438 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
2981470 TTCTGATTTC
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:2981854 original size:15 final size:15
Alignment explanation
Indices: 2981816--2981854 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2981806 TTCTCCAAGG
2981816 ATTCTTTAAATCTGT
1 ATTCTTTAAATCTGT
* * *
2981831 TTTCATTAAATTTGT
1 ATTCTTTAAATCTGT
2981846 ATTCTTTAA
1 ATTCTTTAA
2981855 TCTTCCTTTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.05, T:0.56
Consensus pattern (15 bp):
ATTCTTTAAATCTGT
Found at i:2990644 original size:19 final size:19
Alignment explanation
Indices: 2990617--2990739 Score: 53
Period size: 19 Copynumber: 6.6 Consensus size: 19
2990607 TCATAGTCTC
*
2990617 ATATAAATATATATATATT
1 ATATTAATATATATATATT
* *
2990636 ATATTAATATTTTTATA-T
1 ATATTAATATATATATATT
* * *
2990654 AAATTTAA-ATGT-TA-AAT
1 ATA-TTAATATATATATATT
* *
2990671 ATTATTAAAATATATAAATT
1 A-TATTAATATATATATATT
* *
2990691 AT-TTATTAT-TATACTCTT
1 ATATTAATATATATA-TATT
*
2990709 ATTATTAAAATATATATTATT
1 A-TATTAATATATATA-TATT
2990730 -TATTAATATA
1 ATATTAATATA
2990740 CTCTTACTTC
Statistics
Matches: 77, Mismatches: 17, Indels: 20
0.68 0.15 0.18
Matches are distributed among these distances:
16 1 0.01
17 12 0.16
18 18 0.23
19 31 0.40
20 8 0.10
21 7 0.09
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (19 bp):
ATATTAATATATATATATT
Found at i:2990729 original size:36 final size:37
Alignment explanation
Indices: 2990670--2990745 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 37
2990660 AAATGTTAAA
*
2990670 TATTATTAAAATATATAAATTATTTATTATTATACTCT
1 TATTATTAAAATATAT-AATTATTTATTAATATACTCT
2990708 TATTATTAAAATATAT-ATTATTTATTAATATACTCT
1 TATTATTAAAATATATAATTATTTATTAATATACTCT
2990744 TA
1 TA
2990746 CTTCAATATT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 21 0.57
38 16 0.43
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (37 bp):
TATTATTAAAATATATAATTATTTATTAATATACTCT
Found at i:2990739 original size:17 final size:17
Alignment explanation
Indices: 2990682--2990739 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
2990672 TTATTAAAAT
*
2990682 ATATAAATTATTTATTA
1 ATATATATTATTTATTA
* *
2990699 TTATACTCTTA-TTATTAAA
1 ATATA-TATTATTTATT--A
2990718 ATATATATTATTTATTA
1 ATATATATTATTTATTA
2990735 ATATA
1 ATATA
2990740 CTCTTACTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
17 15 0.47
18 7 0.22
19 10 0.31
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATATTATTTATTA
Found at i:2991162 original size:15 final size:15
Alignment explanation
Indices: 2991144--2991181 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2991134 GATATAAAAT
2991144 ATTTATCATTTTA-AA
1 ATTTAT-ATTTTATAA
2991159 ATTTATATTTTATAA
1 ATTTATATTTTATAA
*
2991174 ATATATAT
1 ATTTATAT
2991182 GTGATGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTATATTTTATAA
Found at i:2993491 original size:20 final size:20
Alignment explanation
Indices: 2993453--2993491 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2993443 TAATAATATA
*
2993453 TTAAATTAAATTATTTAAAT
1 TTAAATTAAATTATATAAAT
2993473 TTAAATATAAA-TATATAAA
1 TTAAAT-TAAATTATATAAA
2993492 AAATAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAATTAAATTATATAAAT
Found at i:2993577 original size:18 final size:17
Alignment explanation
Indices: 2993544--2993595 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2993534 AAATATTTAA
2993544 AAAATTATTAATTTTTT
1 AAAATTATTAATTTTTT
* *
2993561 AAAATTATTTATCTTTT
1 AAAATTATTAATTTTTT
*
2993578 -AAATATATTAATATTTT
1 AAAAT-TATTAATTTTTT
2993595 A
1 A
2993596 TTTATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 4 0.14
17 25 0.86
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
AAAATTATTAATTTTTT
Found at i:2993705 original size:36 final size:35
Alignment explanation
Indices: 2993647--2993715 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
2993637 CCTTATCAAG
**
2993647 TTAAATTTTTTTAAAATTTAATAA-AAATAATATA
1 TTAAATTTTTTTAAAAAATAATAATAAATAATATA
2993681 TTAAATATATTTTTAAAAAATAATAATTAAATAAT
1 TTAAAT-T-TTTTTAAAAAATAATAA-TAAATAAT
2993716 TTTAATCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 6 0.21
35 1 0.03
36 15 0.52
38 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (35 bp):
TTAAATTTTTTTAAAAAATAATAATAAATAATATA
Found at i:2993727 original size:24 final size:27
Alignment explanation
Indices: 2993669--2993718 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2993659 AAAATTTAAT
2993669 AAAAATAATATATTAAATATATTTTTA
1 AAAAATAATATATTAAATATATTTTTA
2993696 AAAAATAATA-ATTAAATA-ATTTT
1 AAAAATAATATATTAAATATATTTT
2993719 AATCAATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 5 0.22
26 8 0.35
27 10 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AAAAATAATATATTAAATATATTTTTA
Found at i:2998862 original size:5 final size:5
Alignment explanation
Indices: 2998852--2998882 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
2998842 CACTCCATAC
2998852 CAATA CAATA CAATA CAATA CAATA CAATA C
1 CAATA CAATA CAATA CAATA CAATA CAATA C
2998883 TTTTTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (5 bp):
CAATA
Found at i:3000063 original size:22 final size:22
Alignment explanation
Indices: 3000038--3000110 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
3000028 TAATATATTT
3000038 TTATAATAAATTTAAAATATAA
1 TTATAATAAATTTAAAATATAA
** ** *
3000060 TTATTTTTTATTAAATAAATAATAA
1 TTATAATAAATT-TA-AAAT-ATAA
3000085 TTTATAATAAATTT-AAATATAA
1 -TTATAATAAATTTAAAATATAA
3000107 TTAT
1 TTAT
3000111 TTGTATTAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 9
0.66 0.18 0.16
Matches are distributed among these distances:
21 4 0.11
22 12 0.32
23 5 0.14
24 4 0.11
25 4 0.11
26 8 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTATAATAAATTTAAAATATAA
Found at i:3000130 original size:46 final size:47
Alignment explanation
Indices: 3000037--3000147 Score: 172
Period size: 46 Copynumber: 2.4 Consensus size: 47
3000027 ATAATATATT
*
3000037 TTTATAATAAATTTAAAATATAATTATTTTTTATTAAATAAATAATAA
1 TTTATAATAAATTT-AAATATAATTATTTTGTATTAAATAAATAATAA
3000085 TTTATAATAAATTTAAATATAATTA-TTTGTATTAAATAAATAATAA
1 TTTATAATAAATTTAAATATAATTATTTTGTATTAAATAAATAATAA
**
3000131 TTT-TAATTTATTTAAAT
1 TTTATAATAAATTTAAAT
3000148 TATTTTAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
45 12 0.20
46 23 0.38
47 11 0.18
48 14 0.23
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (47 bp):
TTTATAATAAATTTAAATATAATTATTTTGTATTAAATAAATAATAA
Found at i:3005355 original size:23 final size:23
Alignment explanation
Indices: 3005299--3005360 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
3005289 TTTATCATAT
*
3005299 ATTTAAATA-TAAATATAAAAAT
1 ATTTAAATATTAAATATAAAAAA
* *
3005321 A-TTATATTTTAAATATAAAAAA
1 ATTTAAATATTAAATATAAAAAA
*
3005343 ATTTAAAAATTAAATATA
1 ATTTAAATATTAAATATA
3005361 TTTAAATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 5 0.16
22 14 0.44
23 13 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATTTAAATATTAAATATAAAAAA
Found at i:3010611 original size:26 final size:27
Alignment explanation
Indices: 3010582--3010633 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
3010572 TTTAATTATA
*
3010582 AATATTAATATAAATTA-AAAAAATTT
1 AATATTAATATAAATAATAAAAAATTT
* *
3010608 AATATTATTTTAAATAATAAAAAATT
1 AATATTAATATAAATAATAAAAAATT
3010634 AAAATTTGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
AATATTAATATAAATAATAAAAAATTT
Found at i:3011058 original size:210 final size:209
Alignment explanation
Indices: 3010628--3011016 Score: 645
Period size: 210 Copynumber: 1.9 Consensus size: 209
3010618 TAAATAATAA
* *
3010628 AAAATTAAAATTTGGTTAAATTTATAAAACGCTTTTAATGACGTCATTTGCAATTTAAATAAGGT
1 AAAATTTAAATTTGGTTAAATTTATAAAACCCTTTTAATGACGTCATTTGCAATTTAAATAAGGT
3010693 AAAGGGAAACAGGGTCAGCCAAGCCTAGCCCACTAAGGTAAAAAGTTGGTTTGGGAGGAAGCCGA
66 AAAGGGAAACAGGGTCAGCCAAGCCTAGCCCACTAAGGTAAAAAGTTGGTTTGGGAGGAAGCCGA
* ****
3010758 ACCTCCAGGCCTGGCTCAATATTAGGTGGAACGCGACCAACCAATCAGATTAAAAATTTTTAATA
131 ACCTCCAGGCCTGGCTCAATATTAGGTGGAACGAGACCAACCAATCAGATTAAAAATGGGCAATA
** *
3010823 TTATTTTAAATAAT
196 TTAGGTTAAAGAAT
3010837 AAAAAATTTAAATTTGGTTAAATTTATAAAACCCTTTTAATGACGTCATTTGCAATTTAAATAAG
1 --AAAATTTAAATTTGGTTAAATTTATAAAACCCTTTTAATGACGTCATTTGCAATTTAAATAAG
* *
3010902 GTTAAGGGAAACA-GGTCGGCCAAGCCTAGCCCACTAAGGTAAAAAGTTGGTTTGGGAGGAAGCC
64 GTAAAGGGAAACAGGGTCAGCCAAGCCTAGCCCACTAAGGTAAAAAGTTGGTTTGGGAGGAAGCC
3010966 GAACCTCCAGGCCTGGCTCAATATTAGGTGGAACGAGACCAACCAATCAGA
129 GAACCTCCAGGCCTGGCTCAATATTAGGTGGAACGAGACCAACCAATCAGA
3011017 GCCCGTTAAA
Statistics
Matches: 173, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
210 100 0.58
211 73 0.42
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.26
Consensus pattern (209 bp):
AAAATTTAAATTTGGTTAAATTTATAAAACCCTTTTAATGACGTCATTTGCAATTTAAATAAGGT
AAAGGGAAACAGGGTCAGCCAAGCCTAGCCCACTAAGGTAAAAAGTTGGTTTGGGAGGAAGCCGA
ACCTCCAGGCCTGGCTCAATATTAGGTGGAACGAGACCAACCAATCAGATTAAAAATGGGCAATA
TTAGGTTAAAGAAT
Found at i:3011963 original size:20 final size:20
Alignment explanation
Indices: 3011938--3011976 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
3011928 TTAAAATAAT
3011938 TTAAA-TTTTATTATTTTTAG
1 TTAAATTTTTA-TATTTTTAG
3011958 TTAAATTTTTATATTTTTA
1 TTAAATTTTTATATTTTTA
3011977 TTATATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TTAAATTTTTATATTTTTAG
Found at i:3011976 original size:29 final size:28
Alignment explanation
Indices: 3011937--3012002 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
3011927 GTTAAAATAA
* * **
3011937 TTTAAATTTTATTATTTTTAGTTAAATT
1 TTTAATTTTTATTATATTTAAATAAATT
3011965 TTTATATTTTTATTATATTTAAATAAATT
1 TTTA-ATTTTTATTATATTTAAATAAATT
3011994 TTTAATTTT
1 TTTAATTTT
3012003 AATGTGCACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 9 0.27
29 24 0.73
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (28 bp):
TTTAATTTTTATTATATTTAAATAAATT
Found at i:3018799 original size:17 final size:18
Alignment explanation
Indices: 3018773--3018828 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
3018763 TTTTTTTTTA
3018773 ATAA-TTAAA-TATAAAT
1 ATAATTTAAATTATAAAT
3018789 ATAATTTAAATTATTAAAT
1 ATAATTTAAATTA-TAAAT
* *
3018808 A-AATTAAAATTTTAAAT
1 ATAATTTAAATTATAAAT
3018825 ATAA
1 ATAA
3018829 ATATAATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 4 0.12
17 11 0.32
18 13 0.38
19 6 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATTTAAATTATAAAT
Found at i:3023355 original size:29 final size:28
Alignment explanation
Indices: 3023310--3023415 Score: 85
Period size: 29 Copynumber: 3.7 Consensus size: 28
3023300 ATGGCTTTAT
*
3023310 AATTATATAAAAATATATAAAATAATTAA
1 AATTA-ATATAAATATATAAAATAATTAA
*
3023339 AATATAATATAAATATA-AAAATTTATTAA
1 AAT-TAATATAAATATATAAAA-TAATTAA
*
3023368 AATTTATAT-AATA-A-AAATATTTAAATTAA
1 AATTAATATAAATATATAAA-A--T-AATTAA
*
3023397 AATTAATATAAACATATAA
1 AATTAATATAAATATATAA
3023416 CACTTTAATT
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
26 4 0.06
27 5 0.08
28 11 0.17
29 35 0.56
30 5 0.08
31 1 0.02
32 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (28 bp):
AATTAATATAAATATATAAAATAATTAA
Found at i:3023934 original size:17 final size:17
Alignment explanation
Indices: 3023908--3023940 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3023898 TATTTTTATA
3023908 TATAAAATAAAATAAAT
1 TATAAAATAAAATAAAT
*
3023925 TATAACATAAAATAAA
1 TATAAAATAAAATAAA
3023941 AATAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
TATAAAATAAAATAAAT
Found at i:3024517 original size:21 final size:22
Alignment explanation
Indices: 3024470--3024537 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 22
3024460 AAGCTCACAG
* * *
3024470 TTTAAATTATTAAATAAGTTAAA
1 TTTAAATAATTTAATAA-TTTAA
* *
3024493 TTTACATATTTTAAT-ATTTAA
1 TTTAAATAATTTAATAATTTAA
*
3024514 TTTAAATAATTTATTAATTTAA
1 TTTAAATAATTTAATAATTTAA
3024536 TT
1 TT
3024538 AATTTTTTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
21 16 0.44
22 9 0.25
23 11 0.31
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (22 bp):
TTTAAATAATTTAATAATTTAA
Found at i:3024523 original size:9 final size:9
Alignment explanation
Indices: 3024510--3024542 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3024500 ATTTTAATAT
3024510 TTAATTTAA
1 TTAATTTAA
*
3024519 ATAATTT-A
1 TTAATTTAA
3024527 TTAATTTAA
1 TTAATTTAA
3024536 TTAATTT
1 TTAATTT
3024543 TTTATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTAATTTAA
Found at i:3024532 original size:17 final size:17
Alignment explanation
Indices: 3024510--3024542 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3024500 ATTTTAATAT
3024510 TTAATTTAAATAATTTA
1 TTAATTTAAATAATTTA
*
3024527 TTAATTTAATTAATTT
1 TTAATTTAAATAATTT
3024543 TTTATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAATTTAAATAATTTA
Found at i:3024745 original size:16 final size:16
Alignment explanation
Indices: 3024724--3024756 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3024714 TCAAACTTCT
3024724 TACCATTTCAATTCAA
1 TACCATTTCAATTCAA
*
3024740 TACCATTTGAATTCAA
1 TACCATTTCAATTCAA
3024756 T
1 T
3024757 TTATTTGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (16 bp):
TACCATTTCAATTCAA
Found at i:3029104 original size:19 final size:19
Alignment explanation
Indices: 3029080--3029119 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3029070 ATTAAATATT
*
3029080 ATATAATATAAAAATATAA
1 ATATAAAATAAAAATATAA
* *
3029099 ATATAAAATTAATATATAA
1 ATATAAAATAAAAATATAA
3029118 AT
1 AT
3029120 TATCAAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATAAAATAAAAATATAA
Found at i:3029113 original size:35 final size:35
Alignment explanation
Indices: 3029035--3029115 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
3029025 TCGAGACAAC
* * * *
3029035 ATTAAATTTTATATAATATAAAAGTAACGATAATA
1 ATTAAATATTATATAATATAAAAATAACAATAAAA
3029070 ATTAAATATTATATAATATAAAAATATA-AATATAAA
1 ATTAAATATTATATAATATAAAAATA-ACAATA-AAA
3029106 ATTAATATAT
1 ATTAA-ATAT
3029116 AAATTATCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 27 0.69
36 8 0.21
37 4 0.10
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (35 bp):
ATTAAATATTATATAATATAAAAATAACAATAAAA
Found at i:3029133 original size:19 final size:19
Alignment explanation
Indices: 3029093--3029165 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
3029083 TAATATAAAA
3029093 ATATAAATATAAAATTAAT
1 ATATAAATATAAAATTAAT
* *
3029112 ATATAAATTATCAAATT-TT
1 ATATAAA-TATAAAATTAAT
3029131 ATAT-AATATAAATTATTAATT
1 ATATAAATATAAA--ATTAA-T
* *
3029152 TTAAAAATATAAAA
1 ATATAAATATAAAA
3029166 ATAAAAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
17 5 0.12
18 2 0.05
19 15 0.36
20 9 0.21
21 3 0.07
22 8 0.19
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATAAATATAAAATTAAT
Found at i:3029161 original size:27 final size:27
Alignment explanation
Indices: 3029131--3029199 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
3029121 ATCAAATTTT
3029131 ATATAATATAAATTATTAATTTTAAAA
1 ATATAATATAAATTATTAATTTTAAAA
* * * *
3029158 ATATAAAAATAAA-AAATAATTTTATAA
1 ATAT-AATATAAATTATTAATTTTAAAA
*
3029185 ATTTAAT-TAAATTAT
1 ATATAATATAAATTAT
3029200 AATATAAATA
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
25 4 0.12
26 3 0.09
27 18 0.56
28 7 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
ATATAATATAAATTATTAATTTTAAAA
Found at i:3030430 original size:23 final size:26
Alignment explanation
Indices: 3030381--3030434 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
3030371 ATTATACGTG
* *
3030381 ATTAATAAATTAAATGATAATATTTT
1 ATTAATAAATAAAATGAAAATATTTT
3030407 ATTAA-AAATAAAAT-AAAATATTTAT
1 ATTAATAAATAAAATGAAAATATTT-T
3030432 ATT
1 ATT
3030435 TAATTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.32
25 12 0.48
26 5 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTAATAAATAAAATGAAAATATTTT
Found at i:3030910 original size:22 final size:22
Alignment explanation
Indices: 3030883--3030924 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3030873 ATTAAGTATT
3030883 TATTTAAATATAAAT-ATAAATA
1 TATTTAAATA-AAATAATAAATA
*
3030905 TATTTAGATAAAATAATAAA
1 TATTTAAATAAAATAATAAA
3030925 ATTAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TATTTAAATAAAATAATAAATA
Found at i:3035757 original size:71 final size:71
Alignment explanation
Indices: 3035641--3035789 Score: 289
Period size: 71 Copynumber: 2.1 Consensus size: 71
3035631 GTCAGCTAGT
3035641 TCTCCTTCCATAGACTTTCCTAATTTATAATTTGGCTCAATAGCATGTCTAATGGTCTACAACCA
1 TCTCCTTCCATAGACTTTCCTAATTTATAATTTGGCTCAATAGCATGTCTAATGGTCTACAACCA
3035706 AGTTCA
66 AGTTCA
3035712 TCTCCTTCCATAGACTTTCCTAATTTATAATTTGGCTCAATAGCATGTCTAATGGTCTACAACCA
1 TCTCCTTCCATAGACTTTCCTAATTTATAATTTGGCTCAATAGCATGTCTAATGGTCTACAACCA
*
3035777 AGTTTA
66 AGTTCA
3035783 TCTCCTT
1 TCTCCTT
3035790 TAACAGATCA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 77 1.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (71 bp):
TCTCCTTCCATAGACTTTCCTAATTTATAATTTGGCTCAATAGCATGTCTAATGGTCTACAACCA
AGTTCA
Found at i:3036912 original size:42 final size:41
Alignment explanation
Indices: 3036860--3036957 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 41
3036850 GATAGTTTAG
* *
3036860 AAGGTTTAGAGGTGAGTTTTACAAGGGGCTCAAAAGGTTCAA
1 AAGGCTTAGAGGTGAGTTCTACAAGGGGCTCAAAAGGTTC-A
* **
3036902 AAGGCTTAGAGGTGAGTTCTACAAGGGGTTCAAGGGGTTCA
1 AAGGCTTAGAGGTGAGTTCTACAAGGGGCTCAAAAGGTTCA
*
3036943 AAGGGTTCAGAGGTG
1 AAGGCTT-AGAGGTG
3036958 GGTACTACCA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 7 0.14
42 42 0.86
ACGTcount: A:0.30, C:0.10, G:0.36, T:0.24
Consensus pattern (41 bp):
AAGGCTTAGAGGTGAGTTCTACAAGGGGCTCAAAAGGTTCA
Found at i:3043336 original size:42 final size:42
Alignment explanation
Indices: 3043289--3043372 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
3043279 ATTCAAATTA
* *
3043289 TACCTTCTTATATAATTCCA-AGTTTTCTTGACGAATTAGGTT
1 TACCTTCTTATAGAATTCCACA-TTTTCTTGACGAATGAGGTT
* *
3043331 TACCTTCTTATAGAGTTCCACATTTTCTTGATGAATGAGGTT
1 TACCTTCTTATAGAATTCCACATTTTCTTGACGAATGAGGTT
3043373 CCCCTACAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 36 0.97
43 1 0.03
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (42 bp):
TACCTTCTTATAGAATTCCACATTTTCTTGACGAATGAGGTT
Found at i:3047450 original size:2 final size:2
Alignment explanation
Indices: 3047443--3047467 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3047433 GCTGTTGTTA
3047443 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 T
3047468 TTAGAATCTT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3048360 original size:24 final size:25
Alignment explanation
Indices: 3048332--3048378 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
3048322 CAAAACTACA
*
3048332 TTTTAGA-AGTCAAATTTTCTTAAT
1 TTTTAGACAGTCAAACTTTCTTAAT
* *
3048356 TTTTATACATTCAAACTTTCTTA
1 TTTTAGACAGTCAAACTTTCTTA
3048379 GAAAATTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.32, C:0.13, G:0.04, T:0.51
Consensus pattern (25 bp):
TTTTAGACAGTCAAACTTTCTTAAT
Found at i:3048981 original size:21 final size:21
Alignment explanation
Indices: 3048926--3048981 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
3048916 ATCATTTTGT
* *
3048926 TAAAAAAAAATGATATTTATG
1 TAAAAAAGAATGATATTTATA
* *
3048947 T-AAAAAGTATTGATCTTTATA
1 TAAAAAAG-AATGATATTTATA
*
3048968 TAAAAAAGAGTGAT
1 TAAAAAAGAATGAT
3048982 GCACTTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 5 0.18
21 17 0.61
22 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.34
Consensus pattern (21 bp):
TAAAAAAGAATGATATTTATA
Found at i:3053316 original size:19 final size:18
Alignment explanation
Indices: 3053254--3053322 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 18
3053244 TTTTTTACAA
*
3053254 TAATTTTTTATTATTTTAT
1 TAATTTTTT-TTAATTTAT
* * * *
3053273 TTATTTTTTTAAATCTAG
1 TAATTTTTTTTAATTTAT
3053291 TATATTTATTTTTAATTTAT
1 TA-ATTT-TTTTTAATTTAT
3053311 TAATTTATTTTT
1 TAATTT-TTTTT
3053323 GACTTGAATA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 6 0.15
19 22 0.56
20 11 0.28
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (18 bp):
TAATTTTTTTTAATTTAT
Found at i:3053546 original size:21 final size:21
Alignment explanation
Indices: 3053512--3053551 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3053502 TGATTTAATC
*
3053512 TTATAATACTTAATCTTACCG
1 TTATAATACTTAATATTACCG
3053533 TTATAATAAC-TAATATTAC
1 TTATAAT-ACTTAATATTAC
3053552 TAACATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (21 bp):
TTATAATACTTAATATTACCG
Found at i:3053804 original size:131 final size:138
Alignment explanation
Indices: 3053663--3053933 Score: 421
Period size: 143 Copynumber: 2.0 Consensus size: 138
3053653 TGAATTTTCA
3053663 TCCATAAACCAAATTTTGGATTTGAGTTC-AA-TTTTTT-T-TTTT-TA-TTA-CACTAAAAGAA
1 TCCATAAACCAAATTTTGGATTTGAGTTCAAATTTTTTTATATTTTATATTTATCACTAAAAGAA
* *
3053721 ATCTAAATAAGATTAAACCTTAATTCAAAGGGTTCTTGTAAAGGTAGAAAAGAAGAAGGAGGTCA
66 ATCTAAATAAGATTAAACCTTAATTCAAAGGGTTCTTGTAAAGGGAGAAAAGAAGAAGAAGGTCA
3053786 CATTATTT
131 CATTATTT
3053794 TCCATAAACCAAATTTTGGATTTGAGTTCAAATTTTTTTTATATTTTATATTTTTATTGCACTAA
1 TCCATAAACCAAATTTTGGATTTGAGTTCAAA-TTTTTTTATATTTTATA--TTTA-T-CACTAA
*
3053859 AAGAAATCTAAATAAGATTAAACCTTAGTTCAAAGGGTTCTTGTAAAGGGAGAAAAGAAGAAGAA
61 AAGAAATCTAAATAAGATTAAACCTTAATTCAAAGGGTTCTTGTAAAGGGAGAAAAGAAGAAGAA
3053924 GGTCACATTA
126 GGTCACATTA
3053934 ATTGTCGCAC
Statistics
Matches: 125, Mismatches: 3, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
131 29 0.23
132 2 0.02
134 6 0.05
135 1 0.01
136 4 0.03
137 2 0.02
140 3 0.02
143 78 0.62
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (138 bp):
TCCATAAACCAAATTTTGGATTTGAGTTCAAATTTTTTTATATTTTATATTTATCACTAAAAGAA
ATCTAAATAAGATTAAACCTTAATTCAAAGGGTTCTTGTAAAGGGAGAAAAGAAGAAGAAGGTCA
CATTATTT
Found at i:3059759 original size:2 final size:2
Alignment explanation
Indices: 3059752--3059792 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
3059742 TGATATGTTC
* *
3059752 AT AT AT AT AT AT AT AC AT AT AC 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 AT AT AT AT AT A
3059793 AAATAGTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3061608 original size:2 final size:2
Alignment explanation
Indices: 3061601--3061636 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3061591 AAGAAAGGAA
3061601 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
3061637 GTGTGTGTGT
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):
AT
Found at i:3063951 original size:2 final size:2
Alignment explanation
Indices: 3063944--3063983 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3063934 TATTATGTGG
3063944 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
3063984 GATAATGTCT
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:3066410 original size:28 final size:28
Alignment explanation
Indices: 3066379--3066439 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
3066369 AAAATTGATT
*
3066379 TTTATAT-TAATATTGTTATTAAATTAAA
1 TTTATATAAAATATTGTTATT-AATTAAA
* * *
3066407 TTTAAATAAAATATTTTTATTTATTAAA
1 TTTATATAAAATATTGTTATTAATTAAA
3066435 TTTAT
1 TTTAT
3066440 CTTATCCCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTATATAAAATATTGTTATTAATTAAA
Found at i:3070283 original size:2 final size:2
Alignment explanation
Indices: 3070278--3070311 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3070268 TATCCCCCCT
3070278 TC 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 TC
3070312 CTTCCTGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3072895 original size:17 final size:18
Alignment explanation
Indices: 3072863--3072902 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3072853 TTTAAATATT
3072863 TTATTATATAATTTGATA
1 TTATTATATAATTTGATA
* *
3072881 TTATTAT-TTATTTGATT
1 TTATTATATAATTTGATA
3072898 TTATT
1 TTATT
3072903 CTTATCCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
TTATTATATAATTTGATA
Found at i:3081178 original size:2 final size:2
Alignment explanation
Indices: 3081171--3081202 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3081161 GTATTTGTTC
*
3081171 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3081203 TTGTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3089099 original size:29 final size:30
Alignment explanation
Indices: 3089062--3089124 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
3089052 AGGCTTATGA
*
3089062 TTTA-TATATTCAT-ATCATATTT-ATATAT
1 TTTATTATA-TCATAATCATATTTAAAATAT
*
3089090 TTTATTATATCATAATTATATTTAAAATAT
1 TTTATTATATCATAATCATATTTAAAATAT
3089120 TTTAT
1 TTTAT
3089125 ATTTATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 8 0.27
29 12 0.40
30 10 0.33
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (30 bp):
TTTATTATATCATAATCATATTTAAAATAT
Found at i:3089124 original size:16 final size:16
Alignment explanation
Indices: 3089105--3089152 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 16
3089095 TATATCATAA
3089105 TTATATTTAAAATATT
1 TTATATTTAAAATATT
3089121 TTATATTTATATAA-ATT
1 TTATATTTA-A-AATATT
3089138 TTCATATATTAAAAT
1 TT-ATAT-TTAAAAT
3089153 TTATATTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 9 0.33
17 8 0.30
18 7 0.26
19 3 0.11
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATTTAAAATATT
Found at i:3089196 original size:11 final size:11
Alignment explanation
Indices: 3089180--3089204 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3089170 TAGACATTTA
3089180 TATATTAATAT
1 TATATTAATAT
3089191 TATATTAATAT
1 TATATTAATAT
3089202 TAT
1 TAT
3089205 TTTTTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATTAATAT
Found at i:3093271 original size:22 final size:22
Alignment explanation
Indices: 3093222--3093291 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 22
3093212 CATTATGCCA
* * *
3093222 TATATATAAAT-ATATATATAT
1 TATATAAAAATAATAAAAATAT
*
3093243 TA-A-AAAAATAATTAAAATAT
1 TATATAAAAATAATAAAAATAT
3093263 TATATAAAAATAATAAAAATA-
1 TATATAAAAATAATAAAAATAT
3093284 TAT-TAAAA
1 TATATAAAA
3093292 TTTTATATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
19 5 0.12
20 15 0.37
21 6 0.15
22 15 0.37
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TATATAAAAATAATAAAAATAT
Found at i:3093272 original size:25 final size:27
Alignment explanation
Indices: 3093228--3093286 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
3093218 GCCATATATA
*
3093228 TAAATATATATATATTAAAAAAATAAT
1 TAAATATATATATATAAAAAAAATAAT
*
3093255 TAAA-ATAT-TATATAAAAATAATAA-
1 TAAATATATATATATAAAAAAAATAAT
3093279 -AAATATAT
1 TAAATATAT
3093287 TAAAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 3 0.10
24 4 0.14
25 14 0.48
26 4 0.14
27 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAATATATATATATAAAAAAAATAAT
Found at i:3093289 original size:32 final size:31
Alignment explanation
Indices: 3093246--3093336 Score: 105
Period size: 32 Copynumber: 2.9 Consensus size: 31
3093236 TATATATTAA
3093246 AAAAATA-ATTAAAATATTATATAAA-AATAAT
1 AAAAATATATTAAAAT-TTATATAAATAA-AAT
*
3093277 AAAAATATATTAAAATTTTATATAATATAAATT
1 AAAAATATATTAAAA-TTTATATAA-ATAAAAT
**
3093310 ATTAATATATTAAAATTTATATAAATA
1 AAAAATATATTAAAATTTATATAAATA
3093337 TATTATTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
31 10 0.19
32 24 0.45
33 17 0.32
34 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAAATATATTAAAATTTATATAAATAAAAT
Found at i:3093303 original size:20 final size:19
Alignment explanation
Indices: 3093280--3093341 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
3093270 AAATAATAAA
3093280 AATATATTAAAATTT-TAT
1 AATATATTAAAATTTATAT
3093298 -ATA-A-TATAAA-TTAT-T
1 AATATATTA-AAATTTATAT
3093313 AATATATTAAAATTTATAT
1 AATATATTAAAATTTATAT
3093332 AAATATATTA
1 -AATATATTA
3093342 TTTTAAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
15 5 0.14
16 8 0.22
17 7 0.19
18 6 0.17
19 1 0.03
20 9 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATATTAAAATTTATAT
Found at i:3093317 original size:18 final size:16
Alignment explanation
Indices: 3093280--3093327 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
3093270 AAATAATAAA
*
3093280 AATATATTAAAATTTT
1 AATATAATAAAATTTT
3093296 -ATATAATATAAATTATT
1 AATATAATA-AAATT-TT
*
3093313 AATATATTAAAATTT
1 AATATAATAAAATTT
3093328 ATATAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 7 0.26
16 6 0.22
17 7 0.26
18 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATAATAAAATTTT
Found at i:3093329 original size:18 final size:17
Alignment explanation
Indices: 3093280--3093341 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 17
3093270 AAATAATAAA
3093280 AATATATTAAAATT-TT
1 AATATATTAAAATTATT
*
3093296 -ATATAATATAAATTATT
1 AATATATTA-AAATTATT
3093313 AATATATTAAAATTTATAT
1 AATATATTAAAA-TTAT-T
3093332 AAATATATTA
1 -AATATATTA
3093342 TTTTAAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 7 0.18
16 5 0.13
17 5 0.13
18 11 0.29
19 1 0.03
20 9 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATATTAAAATTATT
Found at i:3093382 original size:20 final size:20
Alignment explanation
Indices: 3093248--3093384 Score: 57
Period size: 20 Copynumber: 6.5 Consensus size: 20
3093238 TATATTAAAA
*
3093248 AAATA-ATTAAAATATTATAT
1 AAATATATTAAAA-AATATAT
* *
3093268 AAAAATAAT-AAAAATATATT
1 AAATATATTAAAAAATATA-T
*
3093288 AAAATTTTATATAATATAAAT-TAT
1 -AAA-TATAT-TAA-A-AAATATAT
* **
3093312 TAATATATTAAAATTTATAT
1 AAATATATTAAAAAATATAT
**
3093332 AAATATATTATTTTAAATATA-
1 AAATATATTA--AAAAATATAT
*
3093353 ATTATAATATTAAAAAATATAT
1 A-AAT-ATATTAAAAAATATAT
3093375 AAATATATTA
1 AAATATATTA
3093385 TGAACAAACA
Statistics
Matches: 84, Mismatches: 19, Indels: 28
0.64 0.15 0.21
Matches are distributed among these distances:
19 7 0.08
20 27 0.32
21 18 0.21
22 14 0.17
23 9 0.11
24 2 0.02
25 3 0.04
26 4 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATATATTAAAAAATATAT
Found at i:3093399 original size:43 final size:42
Alignment explanation
Indices: 3093310--3093406 Score: 99
Period size: 43 Copynumber: 2.3 Consensus size: 42
3093300 AATATAAATT
** *** *
3093310 ATTAATATATTAAAATTTATATAAATATATTATTTTAAATATA
1 ATTAA-ATATTAAAAAATATATAAATATATTATAACAAACATA
3093353 ATTATAATATTAAAAAATATATAAATATATTATGAACAAACA-A
1 ATTA-AATATTAAAAAATATATAAATATATTAT-AACAAACATA
3093396 ATTAAAT-TTAA
1 ATTAAATATTAA
3093407 TTATTAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
41 4 0.09
42 3 0.07
43 34 0.74
44 5 0.11
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (42 bp):
ATTAAATATTAAAAAATATATAAATATATTATAACAAACATA
Found at i:3096973 original size:34 final size:34
Alignment explanation
Indices: 3096927--3097145 Score: 300
Period size: 34 Copynumber: 6.5 Consensus size: 34
3096917 GTAAAAACCA
*
3096927 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3096961 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
*
3096995 CCATTTAATCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
3097029 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3097063 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
3097097 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
3097130 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
3097146 TCTCCCACTT
Statistics
Matches: 169, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
33 18 0.11
34 147 0.87
35 4 0.02
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:3097069 original size:102 final size:101
Alignment explanation
Indices: 3096925--3097145 Score: 343
Period size: 102 Copynumber: 2.2 Consensus size: 101
3096915 TGGTAAAAAC
*
3096925 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAA
3096990 ATCACCCATTTAATCAACAATGGTAAACCACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACCACCAAAT
* * * * *
3097026 CACCCATTTAATCAATAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCA
** * *
3097091 AATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACCACCAAAT
3097128 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
3097146 TCTCCCACTT
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 17 0.16
102 91 0.84
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACCACCAAAT
Found at i:3098686 original size:34 final size:34
Alignment explanation
Indices: 3098640--3098822 Score: 244
Period size: 34 Copynumber: 5.4 Consensus size: 34
3098630 GTAAAAACCA
*
3098640 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3098674 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
3098708 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
3098742 CCATCTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
3098776 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
3098809 CCATTTAATCAACA
1 CCATTTAATCAACA
3098823 CCTTCAAAAT
Statistics
Matches: 131, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
33 16 0.12
34 111 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:3100819 original size:2 final size:2
Alignment explanation
Indices: 3100812--3100838 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3100802 TCTAGTTACT
3100812 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 T
3100839 CATTGTGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3105020 original size:25 final size:25
Alignment explanation
Indices: 3104986--3105039 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
3104976 CTCTTCCATT
*
3104986 TTTCAGTGAGTTTACATATATAAGC
1 TTTCAGTGAGTTTACATATACAAGC
3105011 TTTCAGTGAGTTTACATATACAAGC
1 TTTCAGTGAGTTTACATATACAAGC
3105036 TTTC
1 TTTC
3105040 TCTTATGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (25 bp):
TTTCAGTGAGTTTACATATACAAGC
Found at i:3116116 original size:16 final size:16
Alignment explanation
Indices: 3116095--3116125 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3116085 AAACATATAA
*
3116095 TAAAAATAATATTTTT
1 TAAAAAAAATATTTTT
3116111 TAAAAAAAATATTTT
1 TAAAAAAAATATTTT
3116126 AGAAACAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAAAAAATATTTTT
Found at i:3116502 original size:2 final size:2
Alignment explanation
Indices: 3116495--3116527 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3116485 GTGTAATCAA
*
3116495 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3116528 AGATGGACGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3118725 original size:16 final size:17
Alignment explanation
Indices: 3118684--3118718 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3118674 AACATAAAAA
*
3118684 TATATATATTTTTCATT
1 TATATTTATTTTTCATT
3118701 TATATTTATTTTT-ATT
1 TATATTTATTTTTCATT
3118717 TA
1 TA
3118719 AGTTTATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
TATATTTATTTTTCATT
Found at i:3120292 original size:2 final size:2
Alignment explanation
Indices: 3120285--3120313 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3120275 ACTTTAAATC
3120285 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 C
3120314 CGATCATCTT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3122481 original size:12 final size:13
Alignment explanation
Indices: 3122464--3122537 Score: 53
Period size: 13 Copynumber: 5.8 Consensus size: 13
3122454 GATGGGGGAC
3122464 AGGAAGAAAAG-A
1 AGGAAGAAAAGAA
*
3122476 AGGAAGGAAAGAA
1 AGGAAGAAAAGAA
* *
3122489 AGAAAGAAAAAAA
1 AGGAAGAAAAGAA
** *
3122502 AAAAAAAAAAGAA
1 AGGAAGAAAAGAA
*
3122515 AGAAAGGAAAAG-A
1 AGGAA-GAAAAGAA
*
3122528 AGAAAGAAAA
1 AGGAAGAAAA
3122538 AAATATTTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
12 15 0.29
13 31 0.61
14 5 0.10
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AGGAAGAAAAGAA
Found at i:3122512 original size:26 final size:29
Alignment explanation
Indices: 3122486--3122540 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
3122476 AGGAAGGAAA
3122486 GAAAGAAA-GAAAA-AA-AAAAAAAAAAA
1 GAAAGAAAGGAAAAGAAGAAAAAAAAAAA
*
3122512 GAAAGAAAGGAAAAGAAGAAAGAAAAAAA
1 GAAAGAAAGGAAAAGAAGAAAAAAAAAAA
3122541 TATTTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 5 0.20
28 2 0.08
29 10 0.40
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (29 bp):
GAAAGAAAGGAAAAGAAGAAAAAAAAAAA
Found at i:3122524 original size:5 final size:4
Alignment explanation
Indices: 3122471--3122536 Score: 57
Period size: 4 Copynumber: 16.8 Consensus size: 4
3122461 GACAGGAAGA
* * * *
3122471 AAAG AAGG AAGG AAAG AAAG AAAG AAA- AAA- AAAA AAAA AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
3122517 AAAGG AAA- AGAAG AAAG AAA
1 AAA-G AAAG A-AAG AAAG AAA
3122537 AAAATATTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
3 7 0.13
4 43 0.78
5 5 0.09
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:3123231 original size:17 final size:17
Alignment explanation
Indices: 3123209--3123241 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3123199 TTTGTAACCA
*
3123209 TGATAAATATGATGTGC
1 TGATAAATACGATGTGC
3123226 TGATAAATACGATGTG
1 TGATAAATACGATGTG
3123242 ATTGAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (17 bp):
TGATAAATACGATGTGC
Found at i:3127295 original size:34 final size:34
Alignment explanation
Indices: 3127249--3127467 Score: 300
Period size: 34 Copynumber: 6.5 Consensus size: 34
3127239 GTAAAAACCA
*
3127249 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3127283 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
*
3127317 CCATTTAATCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
3127351 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3127385 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
3127419 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
3127452 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
3127468 TCTCCCACTT
Statistics
Matches: 169, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
33 18 0.11
34 147 0.87
35 4 0.02
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:3127391 original size:102 final size:101
Alignment explanation
Indices: 3127247--3127467 Score: 343
Period size: 102 Copynumber: 2.2 Consensus size: 101
3127237 TGGTAAAAAC
*
3127247 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAA
3127312 ATCACCCATTTAATCAACAATGGTAAACCACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACCACCAAAT
* * * * *
3127348 CACCCATTTAATCAATAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCA
** * *
3127413 AATTTCCCATTTAGTCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACCACCAAAT
3127450 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
3127468 TCTCCCACTT
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 17 0.16
102 91 0.84
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACCACCAAAT
Found at i:3129005 original size:34 final size:34
Alignment explanation
Indices: 3128959--3129141 Score: 244
Period size: 34 Copynumber: 5.4 Consensus size: 34
3128949 GTAAAAACCA
*
3128959 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3128993 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
3129027 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
3129061 CCATCTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
3129095 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
3129128 CCATTTAATCAACA
1 CCATTTAATCAACA
3129142 CCTTCAAAAT
Statistics
Matches: 131, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
33 16 0.12
34 111 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:3131142 original size:2 final size:2
Alignment explanation
Indices: 3131135--3131190 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
3131125 GTCTAGTACT
3131135 TA 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 TA TA
3131176 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
3131191 CATTGTGTGC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3135365 original size:25 final size:25
Alignment explanation
Indices: 3135331--3135384 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
3135321 CTCTTCCATT
*
3135331 TTTCAGTGAGTTTACATATATAAGC
1 TTTCAGTGAGTTTACATATACAAGC
3135356 TTTCAGTGAGTTTACATATACAAGC
1 TTTCAGTGAGTTTACATATACAAGC
3135381 TTTC
1 TTTC
3135385 TCTTATGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (25 bp):
TTTCAGTGAGTTTACATATACAAGC
Found at i:3149057 original size:16 final size:17
Alignment explanation
Indices: 3149016--3149054 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3149006 AACATAAAAA
*
3149016 TATATATATTTTTCATT
1 TATATTTATTTTTCATT
3149033 TATATTTATTTTT-ATT
1 TATATTTATTTTTCATT
3149049 TA-ATTT
1 TATATTT
3149055 TATCGAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 5 0.24
17 12 0.57
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
TATATTTATTTTTCATT
Found at i:3150630 original size:2 final size:2
Alignment explanation
Indices: 3150623--3150652 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3150613 ACACTTTAAA
3150623 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
3150653 CGATCATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3152825 original size:4 final size:4
Alignment explanation
Indices: 3152807--3152861 Score: 60
Period size: 4 Copynumber: 13.8 Consensus size: 4
3152797 GACAGGAAGA
* *
3152807 AAAG AAGG AAGG AAAG AAAG AAAG AAA- AAAG AAAG AAAGG AAA- AGAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA-G AAAG A-AAG
3152855 AAAG AAA
1 AAAG AAA
3152862 AAATATTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
3 4 0.09
4 36 0.80
5 5 0.11
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:3152839 original size:15 final size:15
Alignment explanation
Indices: 3152819--3152864 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
3152809 AGAAGGAAGG
3152819 AAAGAAAGAAAGAAA
1 AAAGAAAGAAAGAAA
*
3152834 AAAGAAAGAAAG-GA
1 AAAGAAAGAAAGAAA
3152848 AAAG-AAGAAAGAAA
1 AAAGAAAGAAAGAAA
3152862 AAA
1 AAA
3152865 TATTTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 7 0.25
14 9 0.32
15 12 0.43
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAGAAA
Found at i:3152849 original size:28 final size:27
Alignment explanation
Indices: 3152806--3152864 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 27
3152796 GGACAGGAAG
*
3152806 AAAAGAAGGAAGG-AAAGAAAGAAAGAA
1 AAAAGAAGAAAGGAAAAG-AAGAAAGAA
3152833 AAAAGAAAGAAAGGAAAAGAAGAAAGAA
1 AAAAG-AAGAAAGGAAAAGAAGAAAGAA
3152861 AAAA
1 AAAA
3152865 TATTTATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 5 0.17
28 20 0.69
29 4 0.14
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (27 bp):
AAAAGAAGAAAGGAAAAGAAGAAAGAA
Found at i:3153549 original size:17 final size:17
Alignment explanation
Indices: 3153527--3153559 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3153517 TTTGTAACCA
*
3153527 TGATAAATATGATGTGC
1 TGATAAATACGATGTGC
3153544 TGATAAATACGATGTG
1 TGATAAATACGATGTG
3153560 ATTGAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (17 bp):
TGATAAATACGATGTGC
Found at i:3161033 original size:15 final size:15
Alignment explanation
Indices: 3160997--3161034 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3160987 CACAGATCAA
*
3160997 GATGATCATGAGATT
1 GATGATGATGAGATT
*
3161012 GATGATGATGAGTTT
1 GATGATGATGAGATT
3161027 GATGATGA
1 GATGATGA
3161035 AGTGTTGGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.34
Consensus pattern (15 bp):
GATGATGATGAGATT
Found at i:3165582 original size:43 final size:43
Alignment explanation
Indices: 3165521--3165604 Score: 159
Period size: 43 Copynumber: 2.0 Consensus size: 43
3165511 TTGTGAGTAA
3165521 CTTCTCTAGTTGCTCCTATTGGATTGAATTTTTTTTTTTTTAC
1 CTTCTCTAGTTGCTCCTATTGGATTGAATTTTTTTTTTTTTAC
*
3165564 CTTCTCTAGTTGCTCCTATTGGATTGATTTTTTTTTTTTTT
1 CTTCTCTAGTTGCTCCTATTGGATTGAATTTTTTTTTTTTT
3165605 TGGCTTGCTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.12, C:0.15, G:0.12, T:0.61
Consensus pattern (43 bp):
CTTCTCTAGTTGCTCCTATTGGATTGAATTTTTTTTTTTTTAC
Found at i:3169395 original size:2 final size:2
Alignment explanation
Indices: 3169388--3169419 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3169378 TAGAATCTCA
3169388 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
3169420 TTATGCATAT
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:3179912 original size:91 final size:91
Alignment explanation
Indices: 3179770--3179938 Score: 234
Period size: 91 Copynumber: 1.9 Consensus size: 91
3179760 GTCAGGTCAA
* * *
3179770 CTCTCTCTCTTAATCCACATGCATGGATATGATTATGCAGACATGTCATAACATGTACATAGTTG
1 CTCTCTCTCTCAATCCACATGCATGGACATGATTATGCAGACAAGTCATAACATGTACATAGTTG
3179835 AATGTATACTATGAGGTCAACTCTCT
66 AATGTATACTATGAGGTCAACTCTCT
** *
3179861 CTCTCTCTCTCAATCTGCATGC-TAGGACATGATTATGCATG-CAAGTCATAACATGTTCATAGT
1 CTCTCTCTCTCAATCCACATGCAT-GGACATGATTATGCA-GACAAGTCATAACATGTACATAGT
* *
3179924 TTAATGTATATTATG
64 TGAATGTATACTATG
3179939 TACCATGCAC
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
90 1 0.01
91 66 0.97
92 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (91 bp):
CTCTCTCTCTCAATCCACATGCATGGACATGATTATGCAGACAAGTCATAACATGTACATAGTTG
AATGTATACTATGAGGTCAACTCTCT
Found at i:3183542 original size:24 final size:23
Alignment explanation
Indices: 3183508--3183553 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
3183498 TTTGAAATTT
*
3183508 TTAAAAGTTTAAACATTCATTTAG
1 TTAAAAATTTAAA-ATTCATTTAG
*
3183532 TTAAAAATTTAAAATTTATTTA
1 TTAAAAATTTAAAATTCATTTA
3183554 TGATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (23 bp):
TTAAAAATTTAAAATTCATTTAG
Done.