Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 17 of 56
Found at i:3177987 original size:2 final size:2
Alignment explanation
Indices: 3177980--3178019 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3177970 ATTTACACTA
*
3177980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3178020 GACTTTAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3180458 original size:2 final size:2
Alignment explanation
Indices: 3180451--3180482 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3180441 AGGGATGGTC
3180451 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
3180483 CCATAAAAGA
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:3180808 original size:16 final size:16
Alignment explanation
Indices: 3180787--3180818 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3180777 ATATTTGCTA
3180787 AACAACTTAAATAAAT
1 AACAACTTAAATAAAT
3180803 AACAACTTAAATAAAT
1 AACAACTTAAATAAAT
3180819 GGTTTAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (16 bp):
AACAACTTAAATAAAT
Found at i:3181410 original size:26 final size:26
Alignment explanation
Indices: 3181372--3181444 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
3181362 AAATTTAATT
* *
3181372 ATAAAATATATAAATATAAATTTTTA
1 ATAAAATAAATAAATATAAATTTTAA
3181398 ATAAAATAAATAATAATATAAA-TTTAA
1 ATAAAATAAAT-A-AATATAAATTTTAA
*
3181425 AT-AAATTAATAAAT-TAAATT
1 ATAAAATAAATAAATATAAATT
3181445 AAATTAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
23 4 0.10
24 4 0.10
25 1 0.02
26 17 0.41
27 7 0.17
28 8 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
ATAAAATAAATAAATATAAATTTTAA
Found at i:3181425 original size:23 final size:23
Alignment explanation
Indices: 3181401--3181448 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
3181391 ATTTTTAATA
3181401 AAATAAA-TAAT-AATATAAATTT
1 AAATAAATTAATAAAT-TAAATTT
3181423 AAATAAATTAATAAATTAAA-TT
1 AAATAAATTAATAAATTAAATTT
3181445 AAAT
1 AAAT
3181449 TAATATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 13 0.54
23 8 0.33
24 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATAAATTAATAAATTAAATTT
Found at i:3181436 original size:18 final size:18
Alignment explanation
Indices: 3181415--3181453 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3181405 AAATAATAAT
3181415 ATAAATTTAAA-TAAATTA
1 ATAAA-TTAAATTAAATTA
3181433 ATAAATTAAATTAAATTA
1 ATAAATTAAATTAAATTA
3181451 ATA
1 ATA
3181454 TTTATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATTAAATTAAATTA
Found at i:3181450 original size:10 final size:9
Alignment explanation
Indices: 3181397--3181451 Score: 53
Period size: 10 Copynumber: 6.1 Consensus size: 9
3181387 ATAAATTTTT
*
3181397 AATAAAATA
1 AATAAATTA
3181406 AAT-AA-TA
1 AATAAATTA
3181413 ATATAAATTTA
1 A-ATAAA-TTA
3181424 AATAAATT-
1 AATAAATTA
3181432 AATAAATTA
1 AATAAATTA
3181441 AATTAAATTA
1 AA-TAAATTA
3181451 A
1 A
3181452 TATTTATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
7 3 0.08
8 12 0.30
9 9 0.22
10 13 0.32
11 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
AATAAATTA
Found at i:3181656 original size:13 final size:12
Alignment explanation
Indices: 3181633--3181663 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
3181623 TGATTAAAAA
3181633 TAAAATAAATTT
1 TAAAATAAATTT
3181645 TAAAAGTAAATTT
1 TAAAA-TAAATTT
3181658 TAAAAT
1 TAAAAT
3181664 TAATATCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (12 bp):
TAAAATAAATTT
Found at i:3184344 original size:19 final size:19
Alignment explanation
Indices: 3184322--3184360 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3184312 AAAATGAAAT
3184322 ATATGT-TAAATTTTTATTA
1 ATATGTATAAATTTTT-TTA
*
3184341 ATATTTATAAATTTTTTTA
1 ATATGTATAAATTTTTTTA
3184360 A
1 A
3184361 AAAATTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATATGTATAAATTTTTTTA
Found at i:3184856 original size:2 final size:2
Alignment explanation
Indices: 3184849--3184873 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3184839 TCCCTTTCTT
3184849 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 T
3184874 GGAAGAGATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3186077 original size:2 final size:2
Alignment explanation
Indices: 3186072--3186120 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
3186062 TCTGAATGGA
*
3186072 AT AT AT GT 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
3186114 AT AT AT A
1 AT AT AT A
3186121 GCTTAGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3187174 original size:2 final size:2
Alignment explanation
Indices: 3187167--3187211 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
3187157 TTCAATAAAT
*
3187167 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG TG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3187209 AG A
1 AG A
3187212 TTGCTTCATC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
AG
Found at i:3187503 original size:17 final size:16
Alignment explanation
Indices: 3187481--3187523 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3187471 TTTGTTATTT
*
3187481 TTTATTTATTATTAATA
1 TTTATTTATTA-TAAAA
3187498 TTTATTTA-TATAAAA
1 TTTATTTATTATAAAA
*
3187513 TTTAATTATTA
1 TTTATTTATTA
3187524 ATTATGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 11 0.48
16 4 0.17
17 8 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTATTTATTATAAAA
Found at i:3188094 original size:13 final size:14
Alignment explanation
Indices: 3188068--3188100 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3188058 TTTTATTTTA
3188068 TTTT-TTCTTCCTT
1 TTTTATTCTTCCTT
3188081 TTTTATTCTT-CTT
1 TTTTATTCTTCCTT
3188094 TTTTATT
1 TTTTATT
3188101 AACTATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTATTCTTCCTT
Found at i:3188267 original size:31 final size:33
Alignment explanation
Indices: 3188212--3188278 Score: 120
Period size: 31 Copynumber: 2.1 Consensus size: 33
3188202 AAACATATAA
3188212 AATATAACTATTTAAATAATAAATTATATCAAT
1 AATATAACTATTTAAATAATAAATTATATCAAT
3188245 AATATAA-TATTTAAA-AATAAATTATATCAAT
1 AATATAACTATTTAAATAATAAATTATATCAAT
3188276 AAT
1 AAT
3188279 TTTAAAACCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 19 0.56
32 8 0.24
33 7 0.21
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (33 bp):
AATATAACTATTTAAATAATAAATTATATCAAT
Found at i:3189492 original size:28 final size:28
Alignment explanation
Indices: 3189452--3189509 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3189442 TTATAGCCCT
3189452 TTACTCCACTTGTTGGTCACATTGTTCA
1 TTACTCCACTTGTTGGTCACATTGTTCA
3189480 TTACTCCACTTGTTGGTCACATTGTTCA
1 TTACTCCACTTGTTGGTCACATTGTTCA
3189508 TT
1 TT
3189510 TCATTAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.17, C:0.24, G:0.14, T:0.45
Consensus pattern (28 bp):
TTACTCCACTTGTTGGTCACATTGTTCA
Found at i:3191949 original size:2 final size:2
Alignment explanation
Indices: 3191942--3191968 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3191932 TTGTTTGGTA
3191942 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 A
3191969 ATTTTGTTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3194296 original size:2 final size:2
Alignment explanation
Indices: 3194289--3194326 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3194279 GATAGTTGGA
3194289 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
3194327 TCTTACATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3201355 original size:12 final size:12
Alignment explanation
Indices: 3201333--3201381 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
3201323 TAATTTATGA
3201333 TAATAAAATTTAT
1 TAAT-AAATTTAT
3201346 TAATAAATTTAT
1 TAATAAATTTAT
*
3201358 TAATTAATTTAAT
1 TAATAAATTT-AT
3201371 GTAAT-AATTTA
1 -TAATAAATTTA
3201382 AAAATATACA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 18 0.55
13 11 0.33
14 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
TAATAAATTTAT
Found at i:3201497 original size:23 final size:24
Alignment explanation
Indices: 3201461--3201508 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
3201451 AAAATTGATG
3201461 ATATTTAAAGATAATAAAATTTTAT
1 ATATTTAAAGATAAT-AAATTTTAT
*
3201486 ATATTT-AA-ATAATAATTTTTAT
1 ATATTTAAAGATAATAAATTTTAT
3201508 A
1 A
3201509 AAATTTACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 9 0.41
23 5 0.23
24 2 0.09
25 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
ATATTTAAAGATAATAAATTTTAT
Found at i:3201514 original size:23 final size:23
Alignment explanation
Indices: 3201471--3201515 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3201461 ATATTTAAAG
*
3201471 ATAATAAAATTTTATATATTTAA
1 ATAATAAAATTTTATAAATTTAA
*
3201494 ATAAT-AATTTTTATAAAATTTA
1 ATAATAAAATTTTAT-AAATTTA
3201516 CTATTATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATAATAAAATTTTATAAATTTAA
Found at i:3201576 original size:42 final size:42
Alignment explanation
Indices: 3201530--3201613 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
3201520 TATCTTTTAT
3201530 CATTTATTATCATATTATAAATAATTTTTT-TATATTATATTA
1 CATTTATTATCATATTATAAATAATTTTTTATATA-TATATTA
* *
3201572 CATTTATTATTATATTATCAATAATTTTTTATATATATATTA
1 CATTTATTATCATATTATAAATAATTTTTTATATATATATTA
3201614 TAAATTATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 35 0.90
43 4 0.10
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (42 bp):
CATTTATTATCATATTATAAATAATTTTTTATATATATATTA
Found at i:3201587 original size:22 final size:22
Alignment explanation
Indices: 3201531--3201618 Score: 83
Period size: 22 Copynumber: 4.0 Consensus size: 22
3201521 ATCTTTTATC
*
3201531 ATTTATTATCATATTATAAATA
1 ATTTATTATTATATTATAAATA
*
3201553 ATTT-TT-TTATATTAT-ATTA
1 ATTTATTATTATATTATAAATA
*
3201572 CATTTATTATTATATTATCAATA
1 -ATTTATTATTATATTATAAATA
*
3201595 ATTTTTTATATATATATTATAAAT
1 A-TTTAT-TAT-TATATTATAAAT
3201619 TATAAATTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
19 3 0.06
20 12 0.22
21 4 0.07
22 14 0.26
23 7 0.13
24 3 0.06
25 11 0.20
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTATTATTATATTATAAATA
Found at i:3204691 original size:2 final size:2
Alignment explanation
Indices: 3204684--3204720 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3204674 CTAATAGCTC
3204684 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3204721 AGTGTTACCA
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3206806 original size:27 final size:27
Alignment explanation
Indices: 3206741--3206806 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
3206731 CAATTTTAAT
*
3206741 AAACAAAAAATAACTACCATTTTTGAC
1 AAACAAAAAAGAACTACCATTTTTGAC
* * *
3206768 AAATAGAAAAAGAACTACTATTTTTTAC
1 AAACA-AAAAAGAACTACCATTTTTGAC
*
3206796 AAACACAAAAG
1 AAACAAAAAAG
3206807 GTGACTTTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.24
Consensus pattern (27 bp):
AAACAAAAAAGAACTACCATTTTTGAC
Found at i:3211277 original size:27 final size:27
Alignment explanation
Indices: 3211247--3211318 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 27
3211237 AAAATTAGCC
*
3211247 ACCACTTTTGATAAACAAAAAAGAACT
1 ACCACTTTTGACAAACAAAAAAGAACT
* *
3211274 ACCATTTTTGACAAATAAAAAAAGAACT
1 ACCACTTTTGACAAA-CAAAAAAGAACT
*
3211302 ACCAGTTTTGACAAACA
1 ACCACTTTTGACAAACA
3211319 TAAAGAGTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 14 0.36
28 25 0.64
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (27 bp):
ACCACTTTTGACAAACAAAAAAGAACT
Found at i:3214161 original size:9 final size:9
Alignment explanation
Indices: 3214149--3214196 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
3214139 ATTTGATATT
3214149 AAATATAAA
1 AAATATAAA
3214158 AAATATATATA
1 AAATATA-A-A
3214169 AAATATAAA
1 AAATATAAA
*
3214178 ATATA-AAA
1 AAATATAAA
*
3214186 AAACATAAA
1 AAATATAAA
3214195 AA
1 AA
3214197 TAATAATAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 6 0.18
9 17 0.52
10 2 0.06
11 8 0.24
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATATAAA
Found at i:3214182 original size:7 final size:7
Alignment explanation
Indices: 3214144--3214185 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
3214134 GATTTATTTG
*
3214144 ATATTAA
1 ATATAAA
3214151 ATATAAA
1 ATATAAA
* *
3214158 AAAT-AT
1 ATATAAA
3214164 ATATAAA
1 ATATAAA
3214171 ATATAAA
1 ATATAAA
3214178 ATATAAA
1 ATATAAA
3214185 A
1 A
3214186 AAACATAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
6 4 0.14
7 25 0.86
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
ATATAAA
Found at i:3214199 original size:16 final size:17
Alignment explanation
Indices: 3214157--3214199 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3214147 TTAAATATAA
* *
3214157 AAAATATATATAAAATAT
1 AAAATATA-AAAAAACAT
3214175 AAAATATAAAAAAACAT
1 AAAATATAAAAAAACAT
3214192 AAAA-ATAA
1 AAAATATAA
3214200 TAATAAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 8 0.35
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAATATAAAAAAACAT
Found at i:3214550 original size:35 final size:34
Alignment explanation
Indices: 3214503--3214597 Score: 118
Period size: 35 Copynumber: 2.7 Consensus size: 34
3214493 TGTTTTCATG
3214503 CAATGAATAAGAAATAAAGCTGCTGCAAACGACAA
1 CAATGAA-AAGAAATAAAGCTGCTGCAAACGACAA
* * *
3214538 CAATGCAAAAGAAATAAAACTGTTGCAAACGATAA
1 CAATG-AAAAGAAATAAAGCTGCTGCAAACGACAA
* *
3214573 TAATGAAAAAGAAATAAAGTTGCTG
1 CAATG-AAAAGAAATAAAGCTGCTG
3214598 AGATGCAATG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 49 0.96
36 2 0.04
ACGTcount: A:0.53, C:0.13, G:0.17, T:0.18
Consensus pattern (34 bp):
CAATGAAAAGAAATAAAGCTGCTGCAAACGACAA
Found at i:3215420 original size:20 final size:20
Alignment explanation
Indices: 3215395--3215433 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3215385 ATATGAAGGT
**
3215395 ATGATGCTTGATTTTGTTGC
1 ATGATGCTAAATTTTGTTGC
3215415 ATGATGCTAAATTTTGTTG
1 ATGATGCTAAATTTTGTTG
3215434 AAATTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.49
Consensus pattern (20 bp):
ATGATGCTAAATTTTGTTGC
Found at i:3218376 original size:21 final size:22
Alignment explanation
Indices: 3218346--3218386 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3218336 TAAAAAAATA
*
3218346 TTTTATATTATATTTATATATT
1 TTTTATATTAAATTTATATATT
3218368 TTTTA-ATTAAATTTATATA
1 TTTTATATTAAATTTATATA
3218387 ATTTACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTATATTAAATTTATATATT
Found at i:3218734 original size:22 final size:22
Alignment explanation
Indices: 3218702--3218756 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
3218692 ATTATTTTTT
3218702 TAATTTATTATT-TTT-TAATACA
1 TAATTT-TTATTATTTATAA-ACA
*
3218724 TAATTATTTATTATTTATAAATA
1 TAATT-TTTATTATTTATAAACA
3218747 TAATTTTTAT
1 TAATTTTTAT
3218757 AATTGATAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 15 0.52
23 11 0.38
24 3 0.10
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TAATTTTTATTATTTATAAACA
Found at i:3219288 original size:23 final size:23
Alignment explanation
Indices: 3219244--3219290 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3219234 TTATTTTTTT
*
3219244 AATAAATAAAGTTATAATTTAAA
1 AATAAAAAAAGTTATAATTTAAA
*
3219267 AATAAAAAAATTTA-AATATTAAA
1 AATAAAAAAAGTTATAAT-TTAAA
3219290 A
1 A
3219291 TTTAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (23 bp):
AATAAAAAAAGTTATAATTTAAA
Found at i:3221883 original size:30 final size:30
Alignment explanation
Indices: 3221847--3221920 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 30
3221837 AGTGAATCGA
3221847 ATAATATTATTTAATTAAAATTTTTAA-AA-
1 ATAATATTATTTAATT-AAATTTTTAATAAG
* **
3221876 ATAA-A-TATAATAATTTTATTTTTAATAAG
1 ATAATATTAT-TTAATTAAATTTTTAATAAG
3221905 ATAATATTATTTAATT
1 ATAATATTATTTAATT
3221921 TATTATTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
27 11 0.31
28 8 0.22
29 8 0.22
30 6 0.17
31 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (30 bp):
ATAATATTATTTAATTAAATTTTTAATAAG
Found at i:3221923 original size:29 final size:28
Alignment explanation
Indices: 3221846--3221931 Score: 79
Period size: 29 Copynumber: 3.0 Consensus size: 28
3221836 TAGTGAATCG
*
3221846 AATAATATTATTTAATTAAAATTTTTAA-A
1 AATAATATTATTTAATT--TATTTTTAATA
*
3221875 AATAA-A-TATAATAATTTTATTTTTAATA
1 AATAATATTAT-TTAA-TTTATTTTTAATA
*
3221903 AGATAATATTATTTAATTTATTATTAATA
1 A-ATAATATTATTTAATTTATTTTTAATA
3221932 TATAGATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
27 11 0.23
28 6 0.13
29 23 0.49
30 4 0.09
31 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (28 bp):
AATAATATTATTTAATTTATTTTTAATA
Found at i:3221934 original size:23 final size:22
Alignment explanation
Indices: 3221908--3221959 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
3221898 TAATAAGATA
*
3221908 ATATTATTTAATTTA-TTATTAAT
1 ATATTATTT-ATATACTT-TTAAT
*
3221931 ATATAGATTTATATACTTTTAAT
1 ATAT-TATTTATATACTTTTAAT
3221954 ATATTA
1 ATATTA
3221960 AATATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
22 1 0.04
23 17 0.71
24 6 0.25
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
ATATTATTTATATACTTTTAAT
Found at i:3222138 original size:30 final size:29
Alignment explanation
Indices: 3222069--3222138 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 29
3222059 ATTATATATA
* *
3222069 TTATAAAA-TTTAAAAAATTAAAGATCAT
1 TTATAAAATTTTAAAAAATAAAAAATCAT
* *
3222097 TAATAATAAATTTTAAAAAATAAAAAATTATT
1 TTAT-A-AAATTTTAAAAAATAAAAAATCA-T
3222129 TTATAAAATT
1 TTATAAAATT
3222139 ATGTCTGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
28 3 0.09
29 1 0.03
30 8 0.24
31 17 0.52
32 4 0.12
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (29 bp):
TTATAAAATTTTAAAAAATAAAAAATCAT
Found at i:3222203 original size:33 final size:33
Alignment explanation
Indices: 3222164--3222238 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
3222154 TGAGCATAGC
* * *
3222164 ATTTATTTATAATACTATCACATTAAAAATAAT
1 ATTTATTTATAATAATATCAAATTAAAAATAAA
* *
3222197 ATTTATTTTTAATAATATCAAATTTAAAATAAA
1 ATTTATTTATAATAATATCAAATTAAAAATAAA
3222230 ATTT-TTTAT
1 ATTTATTTAT
3222239 CATTTTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 4 0.11
33 32 0.89
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (33 bp):
ATTTATTTATAATAATATCAAATTAAAAATAAA
Found at i:3222621 original size:17 final size:17
Alignment explanation
Indices: 3222587--3222637 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
3222577 ATAATTAAAA
*
3222587 TATAATA-TAAAATATTT
1 TATAATATTAATAT-TTT
*
3222604 TATGATATTAATATTTT
1 TATAATATTAATATTTT
3222621 TATAATATTAATTATTT
1 TATAATATTAA-TATTT
3222638 ACATGTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 19 0.66
18 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TATAATATTAATATTTT
Found at i:3222712 original size:20 final size:21
Alignment explanation
Indices: 3222676--3222717 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
3222666 TATCATGATT
3222676 ATAATATAAAAATAATA-ATA
1 ATAATATAAAAATAATATATA
*
3222696 ATAATAT-AACATAAATATATA
1 ATAATATAAAAAT-AATATATA
3222717 A
1 A
3222718 ATTATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.21
20 11 0.58
21 4 0.21
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAATATAAAAATAATATATA
Found at i:3224597 original size:18 final size:18
Alignment explanation
Indices: 3224574--3224615 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
3224564 TATTTTTAAA
*
3224574 ATATAAATATATTAT-TTT
1 ATATAAATAT-TTATAATT
3224592 ATATAAATATTTATAATT
1 ATATAAATATTTATAATT
3224610 ATATAA
1 ATATAA
3224616 TTAAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATAAATATTTATAATT
Found at i:3224931 original size:7 final size:7
Alignment explanation
Indices: 3224886--3224942 Score: 55
Period size: 7 Copynumber: 8.3 Consensus size: 7
3224876 CTTATTGTAC
*
3224886 TATTACA
1 TATTATA
*
3224893 TAATATA
1 TATTATA
3224900 TA-TATA
1 TATTATA
3224906 TATATATA
1 TAT-TATA
3224914 TATTA-A
1 TATTATA
*
3224920 TTTTATA
1 TATTATA
*
3224927 TTTTATA
1 TATTATA
3224934 TATTATA
1 TATTATA
3224941 TA
1 TA
3224943 ATTTTCATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
6 11 0.26
7 25 0.58
8 7 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (7 bp):
TATTATA
Found at i:3227953 original size:17 final size:18
Alignment explanation
Indices: 3227931--3227971 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3227921 ATGATATTTG
3227931 TATTTAAT-ATTTTGATA
1 TATTTAATAATTTTGATA
**
3227948 TATTTAATAATTTTTTTA
1 TATTTAATAATTTTGATA
3227966 TATTTA
1 TATTTA
3227972 TTTTTACACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TATTTAATAATTTTGATA
Found at i:3228427 original size:3 final size:3
Alignment explanation
Indices: 3228421--3228466 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3228411 GTTGTTGTTG
3228421 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3228467 ATTCTAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3230972 original size:15 final size:16
Alignment explanation
Indices: 3230948--3230986 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
3230938 GCTTTTTGAA
*
3230948 TTTAAGTTTAAATT-T
1 TTTAAATTTAAATTAT
3230963 TTTAAATTTAAATTAT
1 TTTAAATTTAAATTAT
*
3230979 TTCAAATT
1 TTTAAATT
3230987 ATAATATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTAAATTTAAATTAT
Found at i:3232225 original size:3 final size:3
Alignment explanation
Indices: 3232219--3232255 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3232209 GATGATGATG
3232219 ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3232256 ATGCTATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3232243 original size:17 final size:17
Alignment explanation
Indices: 3232221--3232257 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
3232211 TGATGATGAT
3232221 TATTATTATTATTATTA
1 TATTATTATTATTATTA
3232238 TATTATTATTATTATTA
1 TATTATTATTATTATTA
3232255 TAT
1 TAT
3232258 GCTATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:3232448 original size:2 final size:2
Alignment explanation
Indices: 3232441--3232478 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3232431 AATTTTTAAT
3232441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3232479 CATGCATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3234193 original size:15 final size:15
Alignment explanation
Indices: 3234159--3234199 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3234149 TATTGTTGAT
3234159 ATTTATTAATAATATA
1 ATTTATT-ATAATATA
* *
3234175 ATTTATTATCATATC
1 ATTTATTATAATATA
3234190 ATTTATTATA
1 ATTTATTATA
3234200 TTTATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTATAATATA
Found at i:3234362 original size:15 final size:17
Alignment explanation
Indices: 3234327--3234362 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
3234317 TTGTGGCATA
*
3234327 TTTTTATATGTTTTTCT
1 TTTTTATATGCTTTTCT
3234344 TTTTTAT-TGCTTTTCT
1 TTTTTATATGCTTTTCT
3234360 TTT
1 TTT
3234363 GTTTATGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.08, C:0.08, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTTTATATGCTTTTCT
Found at i:3234797 original size:2 final size:2
Alignment explanation
Indices: 3234740--3234786 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3234730 AATACAGAAG
3234740 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
3234782 AT AT A
1 AT AT A
3234787 CACACATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3235617 original size:2 final size:2
Alignment explanation
Indices: 3235610--3235638 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3235600 GTTTAGTGTT
3235610 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3235639 GGCTTATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3236256 original size:2 final size:2
Alignment explanation
Indices: 3236249--3236283 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3236239 TTTGTCTAAT
3236249 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3236284 TGGATATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3236353 original size:3 final size:3
Alignment explanation
Indices: 3236345--3236382 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3236335 CTAGCAGACA
3236345 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3236383 GGTGCAGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3238591 original size:2 final size:2
Alignment explanation
Indices: 3238584--3238619 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3238574 GTAGATAATT
3238584 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3238620 AATAAGAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3242646 original size:17 final size:17
Alignment explanation
Indices: 3242624--3242662 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
3242614 ATTTACTCAA
3242624 AATTTAAAATATTTTTT
1 AATTTAAAATATTTTTT
3242641 AATTT--AATATTTTTT
1 AATTTAAAATATTTTTT
3242656 -ATTTAAA
1 AATTTAAA
3242663 TTAATCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 4 0.20
15 10 0.50
16 1 0.05
17 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTAAAATATTTTTT
Found at i:3242943 original size:22 final size:22
Alignment explanation
Indices: 3242885--3242943 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
3242875 TATTTTTATT
3242885 ATTTAAAC-TTAATTTAATATA
1 ATTTAAACATTAATTTAATATA
*
3242906 ATTTATAA-ATAAATTTAATATA
1 ATTTA-AACATTAATTTAATATA
* *
3242928 TTTTAAACATTTATTT
1 ATTTAAACATTAATTT
3242944 GAGAGACAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 7 0.23
22 24 0.77
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTAAACATTAATTTAATATA
Found at i:3243174 original size:2 final size:2
Alignment explanation
Indices: 3243167--3243192 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3243157 CCATTAAAGC
3243167 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
3243193 GCACACTGCT
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:3243467 original size:27 final size:26
Alignment explanation
Indices: 3243424--3243475 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
3243414 TAATTTAATT
*
3243424 AATAAAATATTATATTTAAAATTTTTA
1 AATAAAATATTAAATTT-AAATTTTTA
3243451 AATAATAAT-TTAAATTTAAATTTTT
1 AATAA-AATATTAAATTTAAATTTTT
3243476 CTAATTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 8 0.35
27 12 0.52
28 3 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AATAAAATATTAAATTTAAATTTTTA
Found at i:3243751 original size:22 final size:21
Alignment explanation
Indices: 3243726--3243808 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 21
3243716 TAATAAAATA
3243726 TAAATTTAAACTTAAACACATT
1 TAAATTTAAACTTAAA-ACATT
* *
3243748 TAAACTTAAA-TTAAAAGTTCATA
1 TAAATTTAAACTTAAAA---CATT
*
3243771 TAAATTTAAACTCAAATACATT
1 TAAATTTAAACTTAAA-ACATT
*
3243793 TAAATCTAAACTTAAA
1 TAAATTTAAACTTAAA
3243809 GTTCATCTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 5 0.10
22 26 0.53
23 12 0.24
24 4 0.08
25 1 0.02
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (21 bp):
TAAATTTAAACTTAAAACATT
Found at i:3243774 original size:45 final size:45
Alignment explanation
Indices: 3243723--3243820 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 45
3243713 ATTTAATAAA
*
3243723 ATATAAATTTAAACTTAAACACATTTAAA-CTTAAA-TTAAAAGTTC
1 ATATAAATTTAAACTCAAACACATTTAAATC-TAAACTT-AAAGTTC
*
3243768 ATATAAATTTAAACTCAAATACATTTAAATCTAAACTTAAAGTTC
1 ATATAAATTTAAACTCAAACACATTTAAATCTAAACTTAAAGTTC
*
3243813 ATCTAAAT
1 ATATAAAT
3243821 CGAAAAAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
45 45 0.94
46 3 0.06
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (45 bp):
ATATAAATTTAAACTCAAACACATTTAAATCTAAACTTAAAGTTC
Found at i:3244956 original size:34 final size:32
Alignment explanation
Indices: 3244894--3244957 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 32
3244884 TCGATATATT
*
3244894 TTAAAATATATATAATATAAATTATTAATTTA
1 TTAAAATATATATAATATAAAATATTAATTTA
*
3244926 TTAAAATTTATATAAATATAAAATATTTAATT
1 TTAAAATATATAT-AATATAAAATA-TTAATT
3244958 ATGATTATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.43
33 10 0.36
34 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
TTAAAATATATATAATATAAAATATTAATTTA
Found at i:3257039 original size:2 final size:2
Alignment explanation
Indices: 3257032--3257070 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3257022 TGTAGATGTA
3257032 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3257071 TTACATGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3261066 original size:22 final size:23
Alignment explanation
Indices: 3261025--3261083 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
3261015 GTTATTAAAA
3261025 TTTAATTAATTTTAAAATTAT-C
1 TTTAATTAATTTTAAAATTATAC
*
3261047 TTTAATTAA-TTTAAGTATTATAC
1 TTTAATTAATTTTAA-AATTATAC
*
3261070 TTTAAATTTATTTT
1 TTT-AATTAATTTT
3261084 TAATTCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 5 0.16
22 14 0.45
23 4 0.13
24 5 0.16
25 3 0.10
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTAATTAATTTTAAAATTATAC
Found at i:3262029 original size:20 final size:19
Alignment explanation
Indices: 3261988--3262040 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
3261978 TATATATCAC
*
3261988 TTAATTTTGAATATGTTAAA
1 TTAATTTT-AATTTGTTAAA
*
3262008 TTAATTTTAATTTTTTAGAA
1 TTAATTTTAATTTGTTA-AA
*
3262028 TTACATTTAAATT
1 TTA-ATTTTAATT
3262041 AAATTAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 7 0.25
20 13 0.46
21 8 0.29
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (19 bp):
TTAATTTTAATTTGTTAAA
Found at i:3263498 original size:13 final size:14
Alignment explanation
Indices: 3263482--3263514 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3263472 AAATATAACT
3263482 ATAAAATAA-AAAA
1 ATAAAATAATAAAA
3263495 ATAAAA-AATAAAA
1 ATAAAATAATAAAA
3263508 ATAAAAT
1 ATAAAAT
3263515 TTAATGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 16 0.89
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
ATAAAATAATAAAA
Found at i:3264033 original size:13 final size:13
Alignment explanation
Indices: 3263996--3264038 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
3263986 CATTTGTTTT
3263996 TTATATTATATATA
1 TTATATTATA-ATA
3264010 TT-T-TT-TAATA
1 TTATATTATAATA
3264020 TTATATTATAATA
1 TTATATTATAATA
3264033 TTATAT
1 TTATAT
3264039 ATATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 5 0.19
11 3 0.12
12 4 0.15
13 12 0.46
14 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATATTATAATA
Found at i:3266303 original size:23 final size:23
Alignment explanation
Indices: 3266273--3266316 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
3266263 TTTCAATTAC
3266273 TTTAAAATTTTACA-TTTAATAAT
1 TTTAAAATTTTA-ATTTTAATAAT
3266296 TTTAAAATTTTAATTTTAATA
1 TTTAAAATTTTAATTTTAATA
3266317 TTTATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTAAAATTTTAATTTTAATAAT
Found at i:3267138 original size:14 final size:16
Alignment explanation
Indices: 3267119--3267152 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3267109 AATATTACAT
3267119 AATATT-ATAT-TAAA
1 AATATTAATATATAAA
3267133 AATATTAATATATAAA
1 AATATTAATATATAAA
3267149 AATA
1 AATA
3267153 AAATATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 4 0.22
16 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATTAATATATAAA
Found at i:3267143 original size:15 final size:15
Alignment explanation
Indices: 3267109--3267152 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
3267099 AATAATTTCA
*
3267109 AATATTACATAATATT
1 AATATTA-AAAATATT
3267125 -ATATTAAAAATATT
1 AATATTAAAAATATT
3267139 AATATATAAAAATA
1 AATAT-TAAAAATA
3267153 AAATATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 7 0.28
15 10 0.40
16 8 0.32
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATTAAAAATATT
Found at i:3267157 original size:21 final size:20
Alignment explanation
Indices: 3267131--3267197 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
3267121 TATTATATTA
3267131 AAAATATTAATATATAAAAAT
1 AAAATA-TAATATATAAAAAT
*
3267152 AAAATATAATATATTAAAAT
1 AAAATATAATATATAAAAAT
** *
3267172 -TTATATAATA-ATTAAAAT
1 AAAATATAATATATAAAAAT
3267190 AAAA-ATAA
1 AAAATATAA
3267198 AAAATATAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 12 0.30
19 9 0.22
20 13 0.32
21 6 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATATAATATATAAAAAT
Found at i:3267195 original size:39 final size:37
Alignment explanation
Indices: 3267124--3267197 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
3267114 TACATAATAT
3267124 TATATTAAAAATATTAATATATAAAAATAAAATATAA
1 TATATTAAAAATATTAATATATAAAAATAAAATATAA
* *
3267161 TATATTAAAATTTATATAATA-ATTAAAATAAAA-ATAA
1 TATATTAAAA-ATAT-TAATATATAAAAATAAAATATAA
3267198 AAAATATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 14 0.42
38 14 0.42
39 5 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (37 bp):
TATATTAAAAATATTAATATATAAAAATAAAATATAA
Found at i:3267556 original size:13 final size:15
Alignment explanation
Indices: 3267528--3267559 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
3267518 ATGATTTAAA
3267528 TTAAATTAATTTATT
1 TTAAATTAATTTATT
3267543 TTAAATT-A-TTATT
1 TTAAATTAATTTATT
3267556 TTAA
1 TTAA
3267560 TAATAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 1 0.06
15 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAAATTAATTTATT
Found at i:3267596 original size:46 final size:46
Alignment explanation
Indices: 3267535--3267623 Score: 119
Period size: 48 Copynumber: 1.9 Consensus size: 46
3267525 AAATTAAATT
* *
3267535 AATTTATTTTAAATTA-TT-ATTTTAATAATAAAATATTTTTATTTA
1 AATTTATTATAAATTATTTAATATTAAT-ATAAAATATTTTTATTTA
3267580 AATTTAATTATAAATTATTTAAATATTAATATAAAATATTTTTA
1 AATTT-ATTATAAATTATTT-AATATTAATATAAAATATTTTTA
3267624 ATATTTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
45 5 0.13
46 10 0.26
47 2 0.05
48 14 0.37
49 7 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (46 bp):
AATTTATTATAAATTATTTAATATTAATATAAAATATTTTTATTTA
Found at i:3267616 original size:22 final size:22
Alignment explanation
Indices: 3267573--3267637 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 22
3267563 TAAAATATTT
3267573 TTATTTAAATTTAAT-TATAAA
1 TTATTTAAATTTAATATATAAA
3267594 TTATTTAAATATTAATATA-AAA
1 TTATTTAAAT-TTAATATATAAA
*
3267616 TATTTTTAATATTTTAATATAT
1 T-TATTTAA-A-TTTAATATAT
3267638 TTTAAATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
21 10 0.27
22 9 0.24
23 8 0.22
24 9 0.24
25 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATTTAAATTTAATATATAAA
Found at i:3267653 original size:19 final size:19
Alignment explanation
Indices: 3267610--3267664 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 19
3267600 AAATATTAAT
3267610 ATAAAATAT-TTTT-AATA
1 ATAAAATATATTTTAAATA
* **
3267627 TTTTAATATATTTTAAATA
1 ATAAAATATATTTTAAATA
*
3267646 ATAAAATAAAATTTTAAAT
1 ATAAAAT-ATATTTTAAAT
3267665 CGTAATAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
17 6 0.21
18 4 0.14
19 8 0.29
20 10 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAAAATATATTTTAAATA
Found at i:3268486 original size:40 final size:40
Alignment explanation
Indices: 3268401--3268500 Score: 102
Period size: 42 Copynumber: 2.5 Consensus size: 40
3268391 CTTAACAATG
*
3268401 TATTTATATAACATTTATATATTTTATATTTGATAATTCGTA
1 TATTTATAT-ATATTTATATATTTTATATTTGATAATTCG-A
*
3268443 TATTTATATCATATTTATATATTTTAT-TTAATTATAA-TC-A
1 TATTTATAT-ATATTTATATATTTTATATT--TGATAATTCGA
3268483 TATTTA-ATATATTT-TATA
1 TATTTATATATATTTATATA
3268501 AAATTATATA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
37 4 0.08
38 6 0.11
39 2 0.04
40 7 0.13
41 2 0.04
42 27 0.51
43 5 0.09
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (40 bp):
TATTTATATATATTTATATATTTTATATTTGATAATTCGA
Found at i:3268495 original size:30 final size:29
Alignment explanation
Indices: 3268446--3268508 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 29
3268436 ATTCGTATAT
**
3268446 TTAT-ATCATATTTATATATTTTATTTAA
1 TTATAATCATATTTATATATTTTATAAAA
3268474 TTATAATCATATTTAATATATTTTATAAAA
1 TTATAATCATATTT-ATATATTTTATAAAA
3268504 TTATA
1 TTATA
3268509 TAAATTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 4 0.13
29 9 0.29
30 18 0.58
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (29 bp):
TTATAATCATATTTATATATTTTATAAAA
Found at i:3269079 original size:23 final size:24
Alignment explanation
Indices: 3269048--3269095 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
3269038 GTATCCGTCC
3269048 CTCTATATATATATATATTCATCT
1 CTCTATATATATATATATTCATCT
3269072 CTCT-TATATATATATATTCATCT
1 CTCTATATATATATATATTCATCT
3269095 C
1 C
3269096 CCTTCCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (24 bp):
CTCTATATATATATATATTCATCT
Found at i:3270632 original size:4 final size:4
Alignment explanation
Indices: 3270623--3270661 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
3270613 TACAAAAAAC
* *
3270623 ACAT ACAT ACAG ACAT ACGT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
3270662 AATATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.26, G:0.05, T:0.21
Consensus pattern (4 bp):
ACAT
Found at i:3270670 original size:2 final size:2
Alignment explanation
Indices: 3270663--3270687 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3270653 ATACATACAA
3270663 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3270688 AGGAGACAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3270939 original size:58 final size:58
Alignment explanation
Indices: 3270871--3270987 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
3270861 AAAGTTAGAA
3270871 TGCTACAATTGATGATGGTCTTTCTAGAATTTGCCTGATTTACACATTGGAAACCTAC
1 TGCTACAATTGATGATGGTCTTTCTAGAATTTGCCTGATTTACACATTGGAAACCTAC
*
3270929 TGCTACAATTGATGATGGTCTTTCTAGAATTTGCCTGATTTACACGTTGGAAACCTAC
1 TGCTACAATTGATGATGGTCTTTCTAGAATTTGCCTGATTTACACATTGGAAACCTAC
3270987 T
1 T
3270988 TTTACACATG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (58 bp):
TGCTACAATTGATGATGGTCTTTCTAGAATTTGCCTGATTTACACATTGGAAACCTAC
Found at i:3272078 original size:17 final size:17
Alignment explanation
Indices: 3272056--3272091 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3272046 ACTCAAACAC
3272056 TATCATCCACAGAAAAG
1 TATCATCCACAGAAAAG
3272073 TATCATCCACAGAAAAG
1 TATCATCCACAGAAAAG
3272090 TA
1 TA
3272092 GAGGGGCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.22, G:0.11, T:0.19
Consensus pattern (17 bp):
TATCATCCACAGAAAAG
Found at i:3274130 original size:18 final size:19
Alignment explanation
Indices: 3274087--3274130 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
3274077 TATTAGCATA
*
3274087 AAATATAATATTAATTTATT
1 AAATA-AATATTAATTTAAT
*
3274107 ATATAAAT-TTAATTTAAT
1 AAATAAATATTAATTTAAT
3274125 AAATAA
1 AAATAA
3274131 TTAAATATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 14 0.67
19 3 0.14
20 4 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATAAATATTAATTTAAT
Found at i:3280408 original size:19 final size:20
Alignment explanation
Indices: 3280371--3280409 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
3280361 AGAATTTCAA
* *
3280371 ATTTTACAATTTATTATTTT
1 ATTTTACAAATTATAATTTT
3280391 ATTTT-CAAATTATAATTTT
1 ATTTTACAAATTATAATTTT
3280410 TAGATTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTACAAATTATAATTTT
Found at i:3294696 original size:22 final size:22
Alignment explanation
Indices: 3294664--3294718 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
3294654 CTCAAATTTG
*
3294664 ATTTAATTATT-ATTTAATTAA
1 ATTTAATTATTAAATTAATTAA
*
3294685 ATTTAAATTATTAAATTACTTAA
1 ATTT-AATTATTAAATTAATTAA
3294708 ATTTAATTATT
1 ATTTAATTATT
3294719 TTAATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 4 0.13
22 14 0.47
23 12 0.40
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTAATTATTAAATTAATTAA
Found at i:3295728 original size:40 final size:40
Alignment explanation
Indices: 3295676--3295761 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
3295666 GATTTGTCTC
*
3295676 AAATAATATATAATAATTTTTATAATCGTTTAAACCTAAT
1 AAATAATATATAATAATTTTTATAATCATTTAAACCTAAT
*
3295716 AAATAATATATAATAATTTTTATAATCATTTAAATCTAAT
1 AAATAATATATAATAATTTTTATAATCATTTAAACCTAAT
*
3295756 ATATAA
1 AAATAA
3295762 GCTATATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (40 bp):
AAATAATATATAATAATTTTTATAATCATTTAAACCTAAT
Found at i:3296202 original size:18 final size:17
Alignment explanation
Indices: 3296160--3296203 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
3296150 AAACAACTGT
3296160 AAAA-AATAAAATTTAA
1 AAAACAATAAAATTTAA
*
3296176 AAAATAATAAAATTTAA
1 AAAACAATAAAATTTAA
3296193 AAATACAATAA
1 AAA-ACAATAA
3296204 TAATAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 4 0.16
17 15 0.60
18 6 0.24
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAAACAATAAAATTTAA
Found at i:3298164 original size:22 final size:22
Alignment explanation
Indices: 3298139--3298181 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3298129 GATAAATACT
3298139 GATAAATATCATTGATAATAAC
1 GATAAATATCATTGATAATAAC
*
3298161 GATAAATATTATTGATAATAA
1 GATAAATATCATTGATAATAA
3298182 ATATATGACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (22 bp):
GATAAATATCATTGATAATAAC
Found at i:3301553 original size:6 final size:5
Alignment explanation
Indices: 3301513--3301550 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
3301503 CCTTCGCTAA
* *
3301513 AAAAT AATA- AAAAT AAAAT GAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
3301551 ATACAAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
4 3 0.11
5 25 0.89
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:3302040 original size:21 final size:20
Alignment explanation
Indices: 3302006--3302045 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3301996 AAAATAATTT
3302006 TAAATAAAATATTTTAATAA
1 TAAATAAAATATTTTAATAA
*
3302026 TAAATTAATATATTTTAATA
1 TAAA-TAAAATATTTTAATA
3302046 TAATATAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATAAAATATTTTAATAA
Found at i:3303281 original size:25 final size:25
Alignment explanation
Indices: 3303226--3303276 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3303216 TTATCTAATA
* *
3303226 AAAAATAAATTTGATTTTAATTTTT
1 AAAATTAAATTTGATTTTAATGTTT
*
3303251 AAAATTAAATTTGATTGTTTATGTTT
1 AAAATTAAATTTGATT-TTAATGTTT
3303277 GAATTTGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (25 bp):
AAAATTAAATTTGATTTTAATGTTT
Found at i:3305647 original size:310 final size:309
Alignment explanation
Indices: 3304784--3305703 Score: 1696
Period size: 310 Copynumber: 3.0 Consensus size: 309
3304774 TTTTGACTAC
*
3304784 TCTGTCTCTTATAGACCATACTGATCATATAGTGAAATGGTATTC-TTTTTCTTTAAAAAAAAAA
1 TCTGTCTCTTATAGACCATACTGATCATATAGTGAAATGGTATTCTTTTTTTTTTAAAAAAAAAA
3304848 AAAAAATTATAATAGCTCAACACTTGTTACACTGATTCTTGGATGTGTATTATATCAGCTAGAAA
66 AAAAAATTATAATAGCTCAACACTTGTTACACTGATTCTTGGATGTGTATTATATCAGCTAGAAA
3304913 CTCTCACATTGGATCAGATGGTTAGAAAGTAC--T------AATTGTTTGTCCTCTTGCTTAGCA
131 CTCTCACATTGGATCAGATGGTTAGAAAGTACTATCAGGCCAATTGTTTGTCCTCTTGCTTAGCA
3304970 TTCTTTTGTGCTTTCTTTTCCTCTAGTGTTTGAGAAGCATCAATGACTGCAATTTTAAGATTGAT
196 TTCTTTTGTGCTTTCTTTTCCTCTAGTGTTTGAGAAGCATCAATGACTGCAATTTTAAGATTGAT
3305035 TTTTCAAGCATTTTCTCTTTCAGGTCTGCCGTATCGAGTTGAGTTGTCA
261 TTTTCAAGCATTTTCTCTTTCAGGTCTGCCGTATCGAGTTGAGTTGTCA
**
3305084 TCTGTCTCTTATAGACCATACTGATCATATAGTGAAATGGTATTCTTTTTTTTAAAAAAAAAAAA
1 TCTGTCTCTTATAGACCATACTGATCATATAGTGAAATGGTATTCTTTTTTTTTTAAAAAAAAAA
3305149 AAAAAATTATAATAGCTCAACACTTGTTACACTGATTCTTGGATGTGTATTATATCAGCTAGAAA
66 AAAAAATTATAATAGCTCAACACTTGTTACACTGATTCTTGGATGTGTATTATATCAGCTAGAAA
3305214 CTCTCACATTGGATCAGATGGTTAGAAAGTACTATCAGGCCAATTGTTTGTCCTCTTGCTTAGCA
131 CTCTCACATTGGATCAGATGGTTAGAAAGTACTATCAGGCCAATTGTTTGTCCTCTTGCTTAGCA
3305279 TTCTTTTGTGCTTTCTTTTCCTCTAGTGTTTGAGAAGCATCAATGACTGCAATTTTAAGATTGAT
196 TTCTTTTGTGCTTTCTTTTCCTCTAGTGTTTGAGAAGCATCAATGACTGCAATTTTAAGATTGAT
3305344 TTTTCAAGCATTTTCTCTTTCAGGTCTGCCGTATCGAGTTGAGTTGTCA
261 TTTTCAAGCATTTTCTCTTTCAGGTCTGCCGTATCGAGTTGAGTTGTCA
****
3305393 TCTGTCTCTTATAGACCATACTGATCATATAGTGAAATGGTATTCTTTTTTTTTTTTTTTAAAAA
1 TCTGTCTCTTATAGACCATACTGATCATATAGTGAAATGGTATTC-TTTTTTTTTTAAAAAAAAA
3305458 AAAAAAATTATAATAGCTCAACACTTGTTACACTGATTCTTGGATGTGTATTATATCAGCTAGAA
65 AAAAAAATTATAATAGCTCAACACTTGTTACACTGATTCTTGGATGTGTATTATATCAGCTAGAA
3305523 ACTCTCACATTGGATCAGATGGTTAGAAAGTACTATCAGGCCAATTGTTTGTCCTCTTGCTTAGC
130 ACTCTCACATTGGATCAGATGGTTAGAAAGTACTATCAGGCCAATTGTTTGTCCTCTTGCTTAGC
*
3305588 ATTCTTTTGTGCTTTCTTTTCCTCTAGTGTTTGAGAAGCATCAATGACTGTAATTTTAAGATTGA
195 ATTCTTTTGTGCTTTCTTTTCCTCTAGTGTTTGAGAAGCATCAATGACTGCAATTTTAAGATTGA
3305653 TTTTTCAAGCATTTTCTCTTTCAGGTCTGCCGTATCGAGTTGAGTTGTCA
260 TTTTTCAAGCATTTTCTCTTTCAGGTCTGCCGTATCGAGTTGAGTTGTCA
3305703 T
1 T
3305704 TGTTGGTGCC
Statistics
Matches: 600, Mismatches: 10, Indels: 10
0.97 0.02 0.02
Matches are distributed among these distances:
300 45 0.08
301 113 0.19
303 1 0.00
309 183 0.31
310 258 0.43
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (309 bp):
TCTGTCTCTTATAGACCATACTGATCATATAGTGAAATGGTATTCTTTTTTTTTTAAAAAAAAAA
AAAAAATTATAATAGCTCAACACTTGTTACACTGATTCTTGGATGTGTATTATATCAGCTAGAAA
CTCTCACATTGGATCAGATGGTTAGAAAGTACTATCAGGCCAATTGTTTGTCCTCTTGCTTAGCA
TTCTTTTGTGCTTTCTTTTCCTCTAGTGTTTGAGAAGCATCAATGACTGCAATTTTAAGATTGAT
TTTTCAAGCATTTTCTCTTTCAGGTCTGCCGTATCGAGTTGAGTTGTCA
Found at i:3306509 original size:2 final size:2
Alignment explanation
Indices: 3306504--3306529 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3306494 TTTTTTGGGG
3306504 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
3306530 ATTAATAGGT
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:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:3310730 original size:2 final size:2
Alignment explanation
Indices: 3310723--3310755 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3310713 AGCCGTAAAT
*
3310723 TC TC TC TC TC TC TC TC TG 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
3310756 AACTGGGTAT
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:0.00, C:0.45, G:0.03, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3311569 original size:3 final size:3
Alignment explanation
Indices: 3311561--3311602 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
3311551 CTTATCTCTT
3311561 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
3311603 TTCAGCTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3313073 original size:21 final size:21
Alignment explanation
Indices: 3313049--3313088 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3313039 AATAAAATTG
*
3313049 TTAATACTATTATTATATATT
1 TTAAAACTATTATTATATATT
* *
3313070 TTAAAATTATTTTTATATA
1 TTAAAACTATTATTATATA
3313089 AAATATTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAAAACTATTATTATATATT
Found at i:3314297 original size:2 final size:2
Alignment explanation
Indices: 3314290--3314328 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3314280 CCTTGCAAAC
3314290 AT 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 AT A
3314329 ACCAAATTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3315019 original size:22 final size:24
Alignment explanation
Indices: 3314993--3315039 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
3314983 AGTATTTTTT
3314993 ATTAATCAAATTT-AA-TATTTAA
1 ATTAATCAAATTTAAATTATTTAA
* *
3315015 ATTAATTATATTTAAATTATTTAA
1 ATTAATCAAATTTAAATTATTTAA
3315039 A
1 A
3315040 ATTTAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 2 0.10
24 8 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTAATCAAATTTAAATTATTTAA
Found at i:3315027 original size:15 final size:15
Alignment explanation
Indices: 3315007--3315060 Score: 81
Period size: 15 Copynumber: 3.5 Consensus size: 15
3314997 ATCAAATTTA
3315007 ATATTTAAATTAATT
1 ATATTTAAATTAATT
*
3315022 ATATTTAAATTATTT
1 ATATTTAAATTAATT
*
3315037 AAAATTTAAATTAATT
1 -ATATTTAAATTAATT
3315053 ATATTTAA
1 ATATTTAA
3315061 TATTTAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 21 0.62
16 13 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTTAAATTAATT
Found at i:3315037 original size:31 final size:29
Alignment explanation
Indices: 3315002--3315068 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 29
3314992 TATTAATCAA
*
3315002 ATTTAATATTTAAATTAATTATATTTAAATT
1 ATTTAAAATTTAAATTAATTATATTT-AA-T
3315033 ATTTAAAATTTAAATTAATTATATTTAAT
1 ATTTAAAATTTAAATTAATTATATTTAAT
3315062 ATTTAAA
1 ATTTAAA
3315069 TTAAAAAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 8 0.23
30 2 0.06
31 25 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
ATTTAAAATTTAAATTAATTATATTTAAT
Found at i:3315081 original size:22 final size:22
Alignment explanation
Indices: 3315033--3315081 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
3315023 TATTTAAATT
* *
3315033 ATTTAAAATTTAAATTAATTAT
1 ATTTAAAATTTAAATTAATAAA
*
3315055 ATTTAATATTTAAATTAA-AAA
1 ATTTAAAATTTAAATTAATAAA
3315076 AGTTTA
1 A-TTTA
3315082 GATCAATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTTAAAATTTAAATTAATAAA
Found at i:3316330 original size:27 final size:27
Alignment explanation
Indices: 3316273--3316324 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3316263 TAAATATTAT
*
3316273 TTTAAAATAAATTTTGTTATTTTTTCA
1 TTTAAAATAAATATTGTTATTTTTTCA
*
3316300 TTTAATATAAATATT-TT-TTTTTTCA
1 TTTAAAATAAATATTGTTATTTTTTCA
3316325 AATTTAGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 8 0.35
26 2 0.09
27 13 0.57
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTAAAATAAATATTGTTATTTTTTCA
Found at i:3317756 original size:106 final size:107
Alignment explanation
Indices: 3317636--3317848 Score: 311
Period size: 106 Copynumber: 2.0 Consensus size: 107
3317626 ATTTTGGTAA
* * * *
3317636 AAAAAATCTCCATATATTTGGAAAAAAATATAGAATATAAATTTTTTATTGAATTTGTTGCTACA
1 AAAAAATCTCCATATATTTAGAAAAAAATATACAATATAAATTTTTGATTGAATTTGTTACTACA
* *
3317701 AGTTAATAACACCTATTTAGC-AAAAAAAATTATATAAAATC
66 AGTTAATAACACCAATTCAGCTAAAAAAAATTATATAAAATC
* * * * *
3317742 AAAAAATCTTCATATATTTAGAAAAAAATCTACAATATAAATTTTTGATTGAGTTTGTTATTACG
1 AAAAAATCTCCATATATTTAGAAAAAAATATACAATATAAATTTTTGATTGAATTTGTTACTACA
*
3317807 AGTTAATAATACCAATTCAGCTAAAAAAAATTATATAAAATC
66 AGTTAATAACACCAATTCAGCTAAAAAAAATTATATAAAATC
3317849 TCAACTCAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
106 74 0.79
107 20 0.21
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.35
Consensus pattern (107 bp):
AAAAAATCTCCATATATTTAGAAAAAAATATACAATATAAATTTTTGATTGAATTTGTTACTACA
AGTTAATAACACCAATTCAGCTAAAAAAAATTATATAAAATC
Found at i:3318445 original size:2 final size:2
Alignment explanation
Indices: 3318438--3318476 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3318428 TGATAAACTA
3318438 AT 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 AT A
3318477 CTGTTAAGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3320125 original size:19 final size:19
Alignment explanation
Indices: 3320080--3320129 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
3320070 TAATTTTTAA
* *
3320080 TATATTAAATAATACATTTT
1 TATA-TAAATAATAAATTAT
3320100 TATATAAATAATAAATTAAT
1 TATATAAATAATAAATT-AT
3320120 TA-AT-AATAAT
1 TATATAAATAAT
3320130 TCGAGGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.22
19 14 0.52
20 7 0.26
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TATATAAATAATAAATTAT
Found at i:3320454 original size:29 final size:30
Alignment explanation
Indices: 3320385--3320456 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
3320375 CAATAAGCAC
*
3320385 TAACCAAAGA-TATATATATATATATATAAT
1 TAACCAATGATTA-ATATATATATATATAAT
3320415 TAACCAATGATTAATATATATATATA-AAT
1 TAACCAATGATTAATATATATATATATAAT
*
3320444 TAACTAATGATTA
1 TAACCAATGATTA
3320457 TATTTAAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
29 15 0.38
30 22 0.56
31 2 0.05
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (30 bp):
TAACCAATGATTAATATATATATATATAAT
Found at i:3320459 original size:28 final size:29
Alignment explanation
Indices: 3320385--3320459 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
3320375 CAATAAGCAC
*
3320385 TAACCAAAGATATATATATATATATATAAT
1 TAACCAATGAT-TATATATATATATATAAT
3320415 TAACCAATGATTA-ATATATATATATAAAT
1 TAACCAATGATTATATATATATATAT-AAT
*
3320444 TAACTAATGATTATAT
1 TAACCAATGATTATAT
3320460 TTAAACAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 12 0.29
29 17 0.41
30 12 0.29
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.39
Consensus pattern (29 bp):
TAACCAATGATTATATATATATATATAAT
Found at i:3321691 original size:7 final size:7
Alignment explanation
Indices: 3321676--3321734 Score: 66
Period size: 7 Copynumber: 8.4 Consensus size: 7
3321666 TATATATATA
*
3321676 TATATAT
1 TATAGAT
3321683 TATAGAT
1 TATAGAT
*
3321690 TATAAAT
1 TATAGAT
3321697 TATAGAT
1 TATAGAT
3321704 TATAGAT
1 TATAGAT
3321711 TATA-ATT
1 TATAGA-T
*
3321718 TATATAT
1 TATAGAT
*
3321725 TATAAAT
1 TATAGAT
3321732 TAT
1 TAT
3321735 TTTGAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
6 1 0.02
7 44 0.96
8 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (7 bp):
TATAGAT
Found at i:3321698 original size:14 final size:14
Alignment explanation
Indices: 3321676--3321734 Score: 75
Period size: 14 Copynumber: 4.2 Consensus size: 14
3321666 TATATATATA
3321676 TATATATTATAGAT
1 TATATATTATAGAT
*
3321690 TATAAATTATAGAT
1 TATATATTATAGAT
*
3321704 TATAGATTATA-ATT
1 TATATATTATAGA-T
*
3321718 TATATATTATAAAT
1 TATATATTATAGAT
3321732 TAT
1 TAT
3321735 TTTGAAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
13 1 0.03
14 38 0.95
15 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (14 bp):
TATATATTATAGAT
Found at i:3321705 original size:21 final size:21
Alignment explanation
Indices: 3321676--3321734 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
3321666 TATATATATA
3321676 TATATATTATAGATTATAAAT
1 TATATATTATAGATTATAAAT
* *
3321697 TATAGATTATAGATTATAATT
1 TATATATTATAGATTATAAAT
*
3321718 TATATATTATAAATTAT
1 TATATATTATAGATTAT
3321735 TTTGAAGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
TATATATTATAGATTATAAAT
Found at i:3324114 original size:29 final size:29
Alignment explanation
Indices: 3324082--3324139 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
3324072 AAATATTAGG
3324082 TTAAATAAAA-AAATATAAAATCCAAAGTT
1 TTAAATAAAATAAATATAAAA-CCAAAGTT
* *
3324111 TTAACTAAAATAAATATAATACCAAAGTT
1 TTAAATAAAATAAATATAAAACCAAAGTT
3324140 AAATGTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (29 bp):
TTAAATAAAATAAATATAAAACCAAAGTT
Found at i:3324823 original size:15 final size:15
Alignment explanation
Indices: 3324790--3324861 Score: 60
Period size: 15 Copynumber: 5.0 Consensus size: 15
3324780 TTAATTTATT
*
3324790 TAAAATTT-AATATA
1 TAAAATTTAAATAAA
*
3324804 TAAAATTTATATAAA
1 TAAAATTTAAATAAA
*
3324819 TAAAATATAAAT-AA
1 TAAAATTTAAATAAA
* *
3324833 TTAGA-TTAAATAAA
1 TAAAATTTAAATAAA
* *
3324847 TAAAAATTATATAAA
1 TAAAATTTAAATAAA
3324862 ATTACAACCG
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
13 5 0.11
14 18 0.40
15 22 0.49
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (15 bp):
TAAAATTTAAATAAA
Found at i:3325124 original size:23 final size:23
Alignment explanation
Indices: 3325098--3325168 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
3325088 TGATTTGAAT
3325098 TATTAATAATATATAAATTTATA
1 TATTAATAATATATAAATTTATA
* * * *
3325121 TATTATTAATAAATTAATTTAAA
1 TATTAATAATATATAAATTTATA
*
3325144 TACTTAAATAATTATATATATTTAT
1 TA-TT-AATAA-TATATAAATTTAT
3325169 GTGTATATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
23 21 0.58
24 2 0.06
25 4 0.11
26 9 0.25
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTAATAATATATAAATTTATA
Found at i:3325125 original size:26 final size:26
Alignment explanation
Indices: 3325096--3325168 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 26
3325086 TATGATTTGA
3325096 ATTATTAATAATATATAAATTTATAT
1 ATTATTAATAATATATAAATTTATAT
*
3325122 ATTATTAATAA-AT-T-AATTTAAAT
1 ATTATTAATAATATATAAATTTATAT
*
3325145 ACTTA--AATAATTATATATATTTAT
1 A-TTATTAATAA-TATATAAATTTAT
3325169 GTGTATATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
22 5 0.13
23 9 0.23
24 6 0.15
25 3 0.08
26 16 0.41
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTATTAATAATATATAAATTTATAT
Found at i:3325452 original size:24 final size:23
Alignment explanation
Indices: 3325417--3325495 Score: 67
Period size: 24 Copynumber: 3.5 Consensus size: 23
3325407 TTAATTTTTT
3325417 AATTTACTTAAATTTAATATATAA
1 AATTTA-TTAAATTTAATATATAA
*
3325441 AATTTATATAAA--TAAAATAT-A
1 AATTTAT-TAAATTTAATATATAA
* * *
3325462 AA-TAATTAAATTAAATAAATAA
1 AATTTATTAAATTTAATATATAA
3325484 AATTTATATAAA
1 AATTTAT-TAAA
3325496 ATTACAAGCG
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 4 0.09
20 3 0.07
21 8 0.19
22 10 0.23
23 4 0.09
24 14 0.33
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (23 bp):
AATTTATTAAATTTAATATATAA
Found at i:3325456 original size:28 final size:28
Alignment explanation
Indices: 3325425--3325498 Score: 66
Period size: 28 Copynumber: 2.7 Consensus size: 28
3325415 TTAATTTACT
*
3325425 TAAATTTAATATATAAAATTTATATAAA
1 TAAATTTAATATATAAAATTTAAATAAA
* *
3325453 TAAAATATAA-ATAATTAAA-TTAAATAAA
1 T-AAATTTAATAT-ATAAAATTTAAATAAA
*
3325481 TAAAATT--TATATAAAATT
1 TAAATTTAATATATAAAATT
3325499 ACAAGCGTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
25 5 0.14
26 3 0.08
27 4 0.11
28 12 0.33
29 12 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
TAAATTTAATATATAAAATTTAAATAAA
Found at i:3325457 original size:15 final size:15
Alignment explanation
Indices: 3325426--3325495 Score: 74
Period size: 15 Copynumber: 4.9 Consensus size: 15
3325416 TAATTTACTT
*
3325426 AAATTT-AATATATA
1 AAATTTAAATAAATA
*
3325440 AAATTTATATAAATA
1 AAATTTAAATAAATA
* *
3325455 AAATATAAAT-AATT
1 AAATTTAAATAAATA
3325469 AAA-TTAAATAAATA
1 AAATTTAAATAAATA
*
3325483 AAATTTATATAAA
1 AAATTTAAATAAA
3325496 ATTACAAGCG
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
13 5 0.11
14 18 0.40
15 22 0.49
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTTAAATAAATA
Found at i:3325708 original size:634 final size:627
Alignment explanation
Indices: 3324457--3325707 Score: 1824
Period size: 634 Copynumber: 2.0 Consensus size: 627
3324447 TTAAAGAATG
* * *
3324457 TGATTTAATTTATTAATAATATATAAATTTATATATTATCAGTAAATAAATATAAATATTTTAAT
1 TGATTTAATTTATTAATAATATATAAATTTATATATTATCAATAAATAAATATAAATACTTAAAT
* * *
3324522 AATTGTATATATTTATATGTATATATATACACACGTGAAAATAAATTTATACTAAATTTATTTAA
66 AATTATATATATTTATATGTATATATAT--A-ACGTGAAAATAAATTTATACTAAAATTAATTAA
* *
3324587 TATATTTTTATAATTTTACATGATTGATATTTTAATAAATTAATTATCAAATTTGATAATATAAT
128 TATATTTTTATAATTTTAAATGATTAATATTTTAATAAATTAATTATCAAATTTGATAATATAAT
* * *
3324652 CACATTTATTATTTATATAAAATTTTAAATCGATTTAATATTTATATTTTATTTATTAAAAATAT
193 CACATTTATTATCTACATAAAATTTTAAATCGATTTAATATTTATATTTTATTTATAAAAAATAT
*
3324717 CATCTTTTTATATATATATATTTAAAGTAAAATTTTTTTATATTAAAAAAATAATCTAATTTTTT
258 CATC-TTTTATATATATATATTTAAAGTAAAATTTTTTTATATCAAAAAAATAATCTAATTTTTT
* *
3324782 AATTTATTTAAAATTTAATATATAAAATTTATATAAATAAAATATAAATAATTAGATTAAATAAA
322 AATTTACTTAAAATTTAATATATAAAATTTATATAAATAAAATATAAATAATTAAATTAAATAAA
*
3324847 TAAAAATTATATAAAATTACAACCGTGTAAAATATTTGGGACAAACAATCGGTGGCTAGGCGGCG
387 TAAAAATTATATAAAATTACAACCGTGTAAAATATTTGGGACAAAAAATCGGTGGCTAGGCGGCG
* *
3324912 GAAACGGGCATTCAGGGACATTTAAGAATTTATATATCTTTGCAGTCATACCTTTGAAGTTTTAA
452 GAAACCGGCATTCAGGGACATTTAAGAATTTATATATCTTTGCAGTCATACCTTTGAAGTTCTAA
* ** * ** *
3324977 TTGTTTGGTTAAATTCCAAAAAATTTTATTGATTTTCATTTCAAAATTATTAAAGTCTTGCCTAA
517 TTGATTGGTTAAATTCCAAAAAACGTAATTGATTGCCATTTCAAAATTATTAAAGTCCTGCCTAA
* *
3325042 CTTTGAATTTGGTGGTTAAAAGCATTAAAAAAATAATTAGTTCGTA
582 CTTTGAATTTGATGGTTAAAAGCATAAAAAAAATAATTAGTTCGTA
* * *
3325088 TGATTTGAA-TTATTAATAATATATAAATTTATATATTATTAATAAATTAATTTAAATACTTAAA
1 TGATTT-AATTTATTAATAATATATAAATTTATATATTATCAATAAATAAATATAAATACTTAAA
* * *
3325152 TAATTATATATATTTATGTGTATATATAT-ATGTGAAGATAAATTTTTATTGACATAAAATTAAT
65 TAATTATATATATTTATATGTATATATATAACGTGAAAATAAA--TTTA-T-AC-TAAAATTAAT
3325216 TAATTCTATATGTTTTTATAATTTTATAAATGATTAATATTTTAATAAATTAATTATCAAATTTG
125 TAA---TATA--TTTTTATAA-TTT-TAAATGATTAATATTTTAATAAATTAATTATCAAATTTG
* *
3325281 ATAATATAATCATATTTATTATCTACATAAAATTTTGAATCGATCTT-ATATTTATATTTTATTT
183 ATAATATAATCACATTTATTATCTACATAAAATTTTAAATCGAT-TTAATATTTATATTTTATTT
*
3325345 ATAAAAAATA-CTATC-TTT-T-TATATATATTTAAAGTTAAAA-TTTTTTATATCAAATAAATA
247 ATAAAAAATATC-ATCTTTTATATATATATATTTAAAG-TAAAATTTTTTTATATCAAAAAAATA
*
3325405 ATTTAATTTTTTAATTTACTT-AAATTTAATATATAAAATTTATATAAATAAAATATAAATAATT
310 ATCTAATTTTTTAATTTACTTAAAATTTAATATATAAAATTTATATAAATAAAATATAAATAATT
* *
3325469 AAATTAAATAAATAAAATTTATATAAAATTACAAGCGTGTAAAATATTTGGGACAAAAAATCGGT
375 AAATTAAATAAATAAAAATTATATAAAATTACAACCGTGTAAAATATTTGGGACAAAAAATCGGT
** *
3325534 GGCTAAGG-GGCGGAAACCGGCATTCAGGGACATTTAAGAATTTATATATCTTTGTGGTCCTACC
440 GGCT-AGGCGGCGGAAACCGGCATTCAGGGACATTTAAGAATTTATATATCTTTGCAGTCATACC
* *
3325598 TTTGAAGTTCTAATT-ATTGGTTAAATTCC-CATAACGTAATTGATTGCCATTTCAAAATTATTA
504 TTTGAAGTTCTAATTGATTGGTTAAATTCCAAAAAACGTAATTGATTGCCATTTCAAAATTATTA
*
3325661 AAGTCCTGCCTAACTTTGAATTTGATGGTTAAAGGCATAGAAAAAAA
569 AAGTCCTGCCTAACTTTGAATTTGATGGTTAAAAGCATA-AAAAAAA
3325708 AAAATAATGA
Statistics
Matches: 558, Mismatches: 44, Indels: 34
0.88 0.07 0.05
Matches are distributed among these distances:
627 11 0.02
629 4 0.01
630 1 0.00
631 84 0.15
632 75 0.13
633 20 0.04
634 174 0.31
635 59 0.11
636 6 0.01
637 12 0.02
638 4 0.01
639 106 0.19
640 2 0.00
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.43
Consensus pattern (627 bp):
TGATTTAATTTATTAATAATATATAAATTTATATATTATCAATAAATAAATATAAATACTTAAAT
AATTATATATATTTATATGTATATATATAACGTGAAAATAAATTTATACTAAAATTAATTAATAT
ATTTTTATAATTTTAAATGATTAATATTTTAATAAATTAATTATCAAATTTGATAATATAATCAC
ATTTATTATCTACATAAAATTTTAAATCGATTTAATATTTATATTTTATTTATAAAAAATATCAT
CTTTTATATATATATATTTAAAGTAAAATTTTTTTATATCAAAAAAATAATCTAATTTTTTAATT
TACTTAAAATTTAATATATAAAATTTATATAAATAAAATATAAATAATTAAATTAAATAAATAAA
AATTATATAAAATTACAACCGTGTAAAATATTTGGGACAAAAAATCGGTGGCTAGGCGGCGGAAA
CCGGCATTCAGGGACATTTAAGAATTTATATATCTTTGCAGTCATACCTTTGAAGTTCTAATTGA
TTGGTTAAATTCCAAAAAACGTAATTGATTGCCATTTCAAAATTATTAAAGTCCTGCCTAACTTT
GAATTTGATGGTTAAAAGCATAAAAAAAATAATTAGTTCGTA
Done.