Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold444
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: 554371
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
File 3 of 5
Found at i:253214 original size:16 final size:16
Alignment explanation
Indices: 253193--253228 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
253183 ATAAATTTTC
253193 GAGCCAACCCTAACTT
1 GAGCCAACCCTAACTT
253209 GAGCCAACCCTAACTT
1 GAGCCAACCCTAACTT
253225 GAGC
1 GAGC
253229 ATGAGAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.36, G:0.17, T:0.17
Consensus pattern (16 bp):
GAGCCAACCCTAACTT
Found at i:257149 original size:8 final size:8
Alignment explanation
Indices: 257126--257159 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
257116 CGTGAATGTA
257126 ATAAATTAT
1 ATAAA-TAT
257135 AATAAATAT
1 -ATAAATAT
257144 ATAAATAT
1 ATAAATAT
257152 ATAAATAT
1 ATAAATAT
257160 CAATAGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 3 0.12
10 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAAATAT
Found at i:260755 original size:2 final size:2
Alignment explanation
Indices: 260748--260782 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
260738 AATATAAGTG
* *
260748 TA TA TA TA CA TA CA 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
260783 GTATGCTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:262603 original size:27 final size:30
Alignment explanation
Indices: 262551--262609 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
262541 TTAATATTTT
262551 TTATTATTAATATTATATTTATAATAATTAA
1 TTATTATTAATATTATATTTATAATAA-TAA
262582 TTATTA-TAATA-TAT-TTTA-AATAATAA
1 TTATTATTAATATTATATTTATAATAATAA
262608 TT
1 TT
262610 TGATTCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 5 0.18
27 5 0.18
28 4 0.14
29 3 0.11
30 5 0.18
31 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TTATTATTAATATTATATTTATAATAATAA
Found at i:263075 original size:4 final size:4
Alignment explanation
Indices: 263066--263092 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
263056 ATGCACAAAA
263066 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
263093 GCATTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:263493 original size:21 final size:21
Alignment explanation
Indices: 263452--263497 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
263442 TAAATTTGGG
263452 AAATATTTATTTATAAGATTTT
1 AAATATTTATTTATAAGA-TTT
*
263474 AAAT-TTTTTTTATATA-ATTT
1 AAATATTTATTTATA-AGATTT
263494 AAAT
1 AAAT
263498 GCTTAGCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 7 0.32
21 10 0.45
22 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
AAATATTTATTTATAAGATTT
Found at i:264037 original size:18 final size:18
Alignment explanation
Indices: 264014--264050 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
264004 AATATAAATG
*
264014 ATATATTATTTTTATTTA
1 ATATATTATTTTTAATTA
264032 ATATATTATTTTTAATTA
1 ATATATTATTTTTAATTA
264050 A
1 A
264051 ATTTAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATATTATTTTTAATTA
Found at i:264106 original size:25 final size:26
Alignment explanation
Indices: 264059--264118 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
264049 AAATTTAAGA
**
264059 ATTATATTAA-TAATATTTTTTAAAT
1 ATTATATTAATTAATATTCATTAAAT
264084 ATTATATTAATTAATA-TCATTAAAT
1 ATTATATTAATTAATATTCATTAAAT
*
264109 ACTA-ATTAAT
1 ATTATATTAAT
264119 ATTTTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 20 0.65
26 5 0.16
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTATATTAATTAATATTCATTAAAT
Found at i:265045 original size:14 final size:14
Alignment explanation
Indices: 265002--265046 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
264992 TAATAAATAC
* *
265002 TAATTTTTTTAAAA
1 TAATTTATTAAAAA
* *
265016 TAATTTATGAATAA
1 TAATTTATTAAAAA
265030 TAATTTATTAAAAA
1 TAATTTATTAAAAA
265044 TAA
1 TAA
265047 AATTATTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (14 bp):
TAATTTATTAAAAA
Found at i:265473 original size:17 final size:18
Alignment explanation
Indices: 265428--265479 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 18
265418 TTATTATTTA
*
265428 AATAATATAATTTAATGT
1 AATAATATAATTTAATAT
* *
265446 AGTACTA-AATTTAA-AT
1 AATAATATAATTTAATAT
265462 AATAATATAATTTAATAT
1 AATAATATAATTTAATAT
265480 TTAAATTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 6 0.22
17 14 0.52
18 7 0.26
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (18 bp):
AATAATATAATTTAATAT
Found at i:265502 original size:24 final size:24
Alignment explanation
Indices: 265454--265512 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 24
265444 GTAGTACTAA
*
265454 ATTTAAATAATAATATAATTTAAT
1 ATTTAAATAATAATATAATTCAAT
265478 ATTTAAATTTAATAA-AT-ATTCAAT
1 ATTTAAA--TAATAATATAATTCAAT
*
265502 AAATTAAATAA
1 -ATTTAAATAA
265513 AATTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
23 3 0.10
24 13 0.43
25 8 0.27
26 6 0.20
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTTAAATAATAATATAATTCAAT
Found at i:265520 original size:16 final size:17
Alignment explanation
Indices: 265475--265530 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 17
265465 AATATAATTT
*
265475 AATATTTAAATTTAATA
1 AATATTTAAATTAAATA
265492 AATATTCAATAAATTAAATA
1 AATATT---TAAATTAAATA
*
265512 AA-ATTTAAA-TATATA
1 AATATTTAAATTAAATA
265527 AATA
1 AATA
265531 AATATGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
15 7 0.21
16 5 0.15
17 6 0.18
19 3 0.09
20 12 0.36
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
AATATTTAAATTAAATA
Found at i:265522 original size:20 final size:19
Alignment explanation
Indices: 265452--265532 Score: 51
Period size: 20 Copynumber: 4.1 Consensus size: 19
265442 ATGTAGTACT
265452 AAATTTAAAT-AAT-AATA
1 AAATTTAAATAAATAAATA
* *
265469 TAATTTAATATTTAAATTTAAT-
1 AAATTTAA-A--TAAA-TAAATA
*
265491 AAATATTCAATAAATTAAATA
1 AAAT-TTAAATAAA-TAAATA
*
265512 AAATTTAAATATATAAATA
1 AAATTTAAATAAATAAATA
265531 AA
1 AA
265533 TATGAAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
17 7 0.14
18 1 0.02
19 8 0.16
20 17 0.34
21 6 0.12
22 5 0.10
23 6 0.12
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATTTAAATAAATAAATA
Found at i:265543 original size:25 final size:24
Alignment explanation
Indices: 265500--265548 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
265490 TAAATATTCA
265500 ATAAATTAAATAAAATTTAAATAT
1 ATAAATTAAATAAAATTTAAATAT
265524 ATAAA-TAAATATGAAATTTAAATAT
1 ATAAATTAAATA--AAATTTAAATAT
265549 CTAATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.26
24 5 0.22
25 12 0.52
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
ATAAATTAAATAAAATTTAAATAT
Found at i:265558 original size:23 final size:24
Alignment explanation
Indices: 265500--265558 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 24
265490 TAAATATTCA
*
265500 ATAAATTAAATAAAATTTAAATAT
1 ATAAATTATATAAAATTTAAATAT
* *
265524 ATAAATAAATATGAAATTTAAATAT
1 ATAAAT-TATATAAAATTTAAATAT
*
265549 CT-AATTATAT
1 ATAAATTATAT
265559 TATTATTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 4 0.14
24 9 0.31
25 16 0.55
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
ATAAATTATATAAAATTTAAATAT
Found at i:269386 original size:2 final size:2
Alignment explanation
Indices: 269379--269434 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
269369 TTTATGATTG
269379 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
269421 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
269435 CCTATGTCAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:272386 original size:36 final size:35
Alignment explanation
Indices: 272313--272391 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 35
272303 AATTTATAAG
*
272313 TATTTATTTATAATTTAAAAATTTTAAATTAAAATT
1 TATTT-TTTATAATTTAAAAATATTAAATTAAAATT
* * *
272349 TATATTTTTATATATTTAAAAA-ATTATATTCATATT
1 TAT-TTTTTATA-ATTTAAAAATATTAAATTAAAATT
272385 TATTTTT
1 TATTTTT
272392 AAATACATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
35 4 0.11
36 22 0.59
37 11 0.30
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (35 bp):
TATTTTTTATAATTTAAAAATATTAAATTAAAATT
Found at i:272388 original size:24 final size:24
Alignment explanation
Indices: 272343--272389 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
272333 ATTTTAAATT
* **
272343 AAAATTTATATTTTTATATATTTA
1 AAAAATTATATTCATATATATTTA
*
272367 AAAAATTATATTCATATTTATTT
1 AAAAATTATATTCATATATATTT
272390 TTAAATACAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
AAAAATTATATTCATATATATTTA
Found at i:276944 original size:30 final size:30
Alignment explanation
Indices: 276910--276977 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
276900 TTAAAAAATT
276910 TATAAA-T-ATTAAATTTAAATTTAAAATTTA
1 TATAAATTAATTAAA-TTAAA-TTAAAATTTA
*
276940 TATAAATTAATTAAATTAAATTCAAATTTA
1 TATAAATTAATTAAATTAAATTAAAATTTA
*
276970 TATTAATT
1 TATAAATT
276978 TCACACATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 22 0.65
31 6 0.18
32 6 0.18
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (30 bp):
TATAAATTAATTAAATTAAATTAAAATTTA
Found at i:276948 original size:28 final size:26
Alignment explanation
Indices: 276904--276956 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
276894 TCATAATTAA
276904 AAAATTTATAAATATTAAATTTAAATTT
1 AAAATTTATAAATATT-AA-TTAAATTT
276932 AAAATTTATATAA-ATTAATTAAATT
1 AAAATTTATA-AATATTAATTAAATT
276957 AAATTCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 7 0.29
27 2 0.08
28 13 0.54
29 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AAAATTTATAAATATTAATTAAATTT
Found at i:277220 original size:16 final size:15
Alignment explanation
Indices: 277179--277226 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
277169 TTGATTCAGG
* *
277179 ATAATTTAATTAAAA
1 ATAATTTAAATAAAT
277194 ATAATTTAAATAAAT
1 ATAATTTAAATAAAT
*
277209 ATAATATTAAATAGAT
1 ATAAT-TTAAATAAAT
277225 AT
1 AT
277227 TATATATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
ATAATTTAAATAAAT
Found at i:278497 original size:24 final size:24
Alignment explanation
Indices: 278435--278508 Score: 60
Period size: 24 Copynumber: 2.9 Consensus size: 24
278425 TCAGCTTAAA
*
278435 TTATTATTTATTTAATTA-AATAATATT
1 TTATTA-TT-TTTAATTATAA-AA-AAT
*
278462 TTATTTAATTTTAATTATAAAAAAT
1 TTA-TTATTTTTAATTATAAAAAAT
* *
278487 TTATTATTTTTTATTTTAAAAA
1 TTATTATTTTTAATTATAAAAA
278509 TAGTGATTCG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
24 16 0.40
25 5 0.12
26 10 0.25
27 6 0.15
28 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TTATTATTTTTAATTATAAAAAAT
Found at i:278625 original size:25 final size:25
Alignment explanation
Indices: 278579--278626 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
278569 ATTATTTAAA
**
278579 AATATTAATATATTATTTTTAAAAT
1 AATATTAATATATTATAATTAAAAT
* *
278604 AATATTTATATTTTATAATTAAA
1 AATATTAATATATTATAATTAAA
278627 TTATAAATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
AATATTAATATATTATAATTAAAAT
Found at i:285003 original size:3 final size:3
Alignment explanation
Indices: 284995--285032 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
284985 ATTTATTTAT
284995 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
285033 TTGCTACACA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:287622 original size:13 final size:13
Alignment explanation
Indices: 287604--287629 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
287594 TATTTTAATT
287604 TTAATTTATTTAA
1 TTAATTTATTTAA
287617 TTAATTTATTTAA
1 TTAATTTATTTAA
287630 ATTTTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTAATTTATTTAA
Found at i:290766 original size:27 final size:27
Alignment explanation
Indices: 290721--290772 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
290711 CATAATTATA
* *
290721 TTTAAAATATTTTATATTTTTATTAAT
1 TTTAAAATATTATATATTTATATTAAT
290748 TTTAAAATATTA-ATAATTTATATTA
1 TTTAAAATATTATAT-ATTTATATTA
290773 TAAAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTAAAATATTATATATTTATATTAAT
Found at i:291188 original size:9 final size:9
Alignment explanation
Indices: 291174--291228 Score: 76
Period size: 9 Copynumber: 6.1 Consensus size: 9
291164 CTCATACAAT
*
291174 ATTTAATTA
1 ATTTATTTA
*
291183 ATTTAATTA
1 ATTTATTTA
291192 ATTT-TTTA
1 ATTTATTTA
291200 CATTTATTTA
1 -ATTTATTTA
291210 ATTTATTTA
1 ATTTATTTA
291219 ATTTATTTA
1 ATTTATTTA
291228 A
1 A
291229 ATTTTAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
8 3 0.07
9 36 0.84
10 4 0.09
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (9 bp):
ATTTATTTA
Found at i:291208 original size:22 final size:21
Alignment explanation
Indices: 291175--291217 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
291165 TCATACAATA
291175 TTTAATTAATTTAATTAATTT
1 TTTAATTAATTTAATTAATTT
* *
291196 TTTACATTTATTTAATTTATTT
1 TTTA-ATTAATTTAATTAATTT
291218 AATTTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTAATTAATTTAATTAATTT
Found at i:294257 original size:1 final size:1
Alignment explanation
Indices: 294253--294277 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
294243 ATGCAAGCCT
294253 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
294278 CCAAATTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:295704 original size:19 final size:19
Alignment explanation
Indices: 295658--295697 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
295648 TTCACGTTGT
295658 GTCTCTTTAGTTTCAATGA
1 GTCTCTTTAGTTTCAATGA
295677 GTCTCTTTAGTTTCAATGA
1 GTCTCTTTAGTTTCAATGA
295696 GT
1 GT
295698 GCTTTTAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.47
Consensus pattern (19 bp):
GTCTCTTTAGTTTCAATGA
Found at i:300590 original size:11 final size:11
Alignment explanation
Indices: 300576--300602 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
300566 TATATTAAAT
300576 AAATATAATAA
1 AAATATAATAA
300587 AAATATAATAA
1 AAATATAATAA
300598 AAATA
1 AAATA
300603 ATTAATATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATATAATAA
Found at i:300728 original size:40 final size:39
Alignment explanation
Indices: 300684--300763 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 39
300674 AAAATGTGAT
300684 ATATAATGTGCAATTAATACATTAT-TTTTAAAATTTTAAA
1 ATATAAT-TGCAATTAATACATTATATTTT-AAATTTTAAA
** *
300724 ATATAATTTTAATTAATACATTATATTTTGAATTTTAAA
1 ATATAATTGCAATTAATACATTATATTTTAAATTTTAAA
300763 A
1 A
300764 AAAAATAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 25 0.69
40 11 0.31
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (39 bp):
ATATAATTGCAATTAATACATTATATTTTAAATTTTAAA
Found at i:300761 original size:22 final size:21
Alignment explanation
Indices: 300697--300761 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 21
300687 TAATGTGCAA
300697 TTAATACATTAT-TTTTAAAATT
1 TTAATACATTATATTTT--AATT
300719 TTAA-A-A-TATAATTTTAA--
1 TTAATACATTAT-ATTTTAATT
300736 TTAATACATTATATTTTGAATT
1 TTAATACATTATATTTT-AATT
300758 TTAA
1 TTAA
300762 AAAAAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
17 4 0.11
18 1 0.03
19 11 0.31
20 6 0.17
21 5 0.14
22 8 0.23
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (21 bp):
TTAATACATTATATTTTAATT
Found at i:302060 original size:22 final size:22
Alignment explanation
Indices: 302035--302087 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
302025 GAAATTATAT
*
302035 TATTAAAATATTTT-TATATTAA
1 TATTTAAATATTTTATA-ATTAA
*
302057 TATTTATATATTTTATAATTAA
1 TATTTAAATATTTTATAATTAA
302079 -ATTTAAATA
1 TATTTAAATA
302088 AAAATATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.30
22 17 0.63
23 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTAAATATTTTATAATTAA
Found at i:308052 original size:3 final size:3
Alignment explanation
Indices: 308044--308089 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
308034 TTTAAACTAG
*
308044 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
308090 AAAATATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:308544 original size:39 final size:36
Alignment explanation
Indices: 308479--308551 Score: 85
Period size: 39 Copynumber: 1.9 Consensus size: 36
308469 AAAAAAATTA
* *
308479 TTTTAAATTAATTTATTTAATCAATTATAATTTTTATT
1 TTTTAAATTAATTGATTAAATCAA-T-TAATTTTTATT
308517 TTTTAAATTTAATTGATTAAAAT-AATTAATTTTTA
1 TTTTAAA-TTAATTGATT-AAATCAATTAATTTTTA
308552 ATTAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 9 0.29
38 8 0.26
39 11 0.35
40 3 0.10
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (36 bp):
TTTTAAATTAATTGATTAAATCAATTAATTTTTATT
Found at i:308733 original size:15 final size:15
Alignment explanation
Indices: 308715--308764 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
308705 AGATTAAATT
308715 ATTTTAATTTATTAA
1 ATTTTAATTTATTAA
*
308730 ATTTTAA-TTATTTTA
1 ATTTTAATTTA-TTAA
*
308745 ATTTTAAATTAATTAA
1 ATTTT-AATTTATTAA
308761 ATTT
1 ATTT
308765 AATATATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 3 0.10
15 15 0.52
16 9 0.31
17 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTAATTTATTAA
Found at i:308758 original size:20 final size:20
Alignment explanation
Indices: 308698--308759 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 20
308688 ATGATTCAAG
*
308698 TTAA-TTTAGATTAAATTATT
1 TTAATTTTAAATT-AATTATT
308718 TTAATTTATTAAATTTTAATTATT
1 TTAA-TT-TTAAA--TTAATTATT
308742 TTAATTTTAAATTAATTA
1 TTAATTTTAAATTAATTA
308760 AATTTAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
20 11 0.31
22 6 0.17
23 6 0.17
24 11 0.31
25 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TTAATTTTAAATTAATTATT
Found at i:308764 original size:22 final size:23
Alignment explanation
Indices: 308739--308786 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
308729 AATTTTAATT
*
308739 ATTTTAAT-TTTAAATTAATTAA
1 ATTTTAATATATAAATTAATTAA
*
308761 A-TTTAATATATGAATTAATTAA
1 ATTTTAATATATAAATTAATTAA
308783 ATTT
1 ATTT
308787 AAGTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 6 0.27
22 14 0.64
23 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTTTAATATATAAATTAATTAA
Found at i:308806 original size:52 final size:53
Alignment explanation
Indices: 308720--308821 Score: 145
Period size: 52 Copynumber: 1.9 Consensus size: 53
308710 AAATTATTTT
* * * *
308720 AATTTATTAAATTTTAATTATTTTAATTTTAAATTAATTAAATTTAATATATG
1 AATTAATTAAATTTTAATTATTTTAAGTTCAAATTAATCAAATTTAATATATG
308773 AATTAATTAAA-TTTAAGTTA-TTTAAGTTCAAATTAATCAAATTTAATAT
1 AATTAATTAAATTTTAA-TTATTTTAAGTTCAAATTAATCAAATTTAATAT
308822 TAAAATTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
52 31 0.70
53 13 0.30
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (53 bp):
AATTAATTAAATTTTAATTATTTTAAGTTCAAATTAATCAAATTTAATATATG
Found at i:308840 original size:52 final size:52
Alignment explanation
Indices: 308720--308841 Score: 140
Period size: 52 Copynumber: 2.3 Consensus size: 52
308710 AAATTATTTT
* * * * *
308720 AATTTATTAAATTTTAATTATTTTAATTTTAAATTAATTAAATTTAATATATG
1 AATTAATTAAA-TTTAATTATTTTAAGTTCAAATTAATCAAATTTAATATATA
308773 AATTAATTAAATTTAAGTTA-TTTAAGTTCAAATTAATCAAATTTAATAT-TAA
1 AATTAATTAAATTTAA-TTATTTTAAGTTCAAATTAATCAAATTTAATATAT-A
* *
308825 AATTAATTGAGTTTAAT
1 AATTAATTAAATTTAAT
308842 CAATCGAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
51 2 0.03
52 45 0.75
53 13 0.22
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (52 bp):
AATTAATTAAATTTAATTATTTTAAGTTCAAATTAATCAAATTTAATATATA
Found at i:308874 original size:36 final size:36
Alignment explanation
Indices: 308807--308881 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 36
308797 AGTTCAAATT
* **
308807 AATCAAATTTAATATTAAAATTAATTGAGTTTAATC
1 AATCAAATTCAATATTAAAATTAATCAAGTTTAATC
* * * *
308843 AATCGAATTCAATATTTAAATTTATCAAGTTTTATC
1 AATCAAATTCAATATTAAAATTAATCAAGTTTAATC
308879 AAT
1 AAT
308882 ACGAGTTCTG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (36 bp):
AATCAAATTCAATATTAAAATTAATCAAGTTTAATC
Found at i:309055 original size:15 final size:14
Alignment explanation
Indices: 309035--309068 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
309025 TCAATCTCAC
309035 TAATTTAATTAATTT
1 TAATTTAATT-ATTT
*
309050 TAATTTGATTATTT
1 TAATTTAATTATTT
309064 TAATT
1 TAATT
309069 ATTTACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (14 bp):
TAATTTAATTATTT
Found at i:309914 original size:14 final size:15
Alignment explanation
Indices: 309896--309928 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
309886 TTATCAAAAC
309896 ATTTTT-ATTTATT-
1 ATTTTTAATTTATTA
309909 ATTTTTAATTTATTA
1 ATTTTTAATTTATTA
309924 ATTTT
1 ATTTT
309929 AGTTGCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 7 0.39
15 5 0.28
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTTTAATTTATTA
Found at i:310241 original size:32 final size:32
Alignment explanation
Indices: 310205--310268 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
310195 TCCAGTTCTA
310205 TCATCCAAGATGTAGTAATGGCCAAATTTTAT
1 TCATCCAAGATGTAGTAATGGCCAAATTTTAT
*
310237 TCATCCAAGATGTAGTAATGGTCAAATTTTAT
1 TCATCCAAGATGTAGTAATGGCCAAATTTTAT
310269 AATTATGTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (32 bp):
TCATCCAAGATGTAGTAATGGCCAAATTTTAT
Found at i:310354 original size:33 final size:34
Alignment explanation
Indices: 310306--310418 Score: 106
Period size: 33 Copynumber: 3.2 Consensus size: 34
310296 AATTATGTTA
310306 AATATATTTTATATTTATATAAATTTTAATATATT
1 AATATATTTT-TATTTATATAAATTTTAATATATT
* *
310341 AATA-ATTTTTATTTAGT-TAAAATTTAAAATATT
1 AATATATTTTTATTTA-TATAAATTTTAATATATT
* * *
310374 TATATATTTAATTATTTTATATTAATTTTTATAT-TAT
1 AATATATTT--TTA-TTTATATAAATTTTAATATAT-T
310411 AATATATT
1 AATATATT
310419 ATAATTATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
33 23 0.37
34 10 0.16
35 4 0.06
36 5 0.08
37 21 0.33
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.58
Consensus pattern (34 bp):
AATATATTTTTATTTATATAAATTTTAATATATT
Found at i:310406 original size:27 final size:28
Alignment explanation
Indices: 310371--310446 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 28
310361 AATTTAAAAT
* *
310371 ATTTATATATT-TAAT-TATTTTATATTA
1 ATTTTTATATTATAATATATTATA-ATTA
310398 ATTTTTATATTATAATATATTATAATTA
1 ATTTTTATATTATAATATATTATAATTA
*
310426 TTTTTTA-ATTATAA-A-ATTATA
1 ATTTTTATATTATAATATATTATA
310447 TAATATTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
25 6 0.14
26 1 0.02
27 17 0.39
28 14 0.32
29 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTTTTATATTATAATATATTATAATTA
Found at i:310448 original size:27 final size:28
Alignment explanation
Indices: 310390--310459 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
310380 TTTAATTATT
* *
310390 TTAT-ATTAATTTTTATATTATAATATA
1 TTATAATTATTTTTTATATTATAAAATA
310417 TTATAATTATTTTTTA-ATTATAAAAT-
1 TTATAATTATTTTTTATATTATAAAATA
*
310443 TATATAA-TATTTATTAT
1 T-TATAATTATTTTTTAT
310460 CAAGTTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 9 0.24
27 18 0.49
28 10 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TTATAATTATTTTTTATATTATAAAATA
Found at i:310531 original size:26 final size:25
Alignment explanation
Indices: 310508--310555 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
310498 ATATTATATT
310508 ATTTT-ATATTTAAAATATTATATAA
1 ATTTTAATATTTAAAAT-TTATATAA
*
310533 ATTTTAATATTTTAAATTTATAT
1 ATTTTAATATTTAAAATTTATAT
310556 TATATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.52
26 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTTTAATATTTAAAATTTATATAA
Found at i:310563 original size:15 final size:16
Alignment explanation
Indices: 310521--310570 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
310511 TTATATTTAA
310521 AATATTATATAAATTTT
1 AATATTATATAAA-TTT
310538 AATATT-T-TAAATTT
1 AATATTATATAAATTT
310552 -ATATTATATAAATATT
1 AATATTATATAAAT-TT
310568 AAT
1 AAT
310571 TAAATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 5 0.17
14 4 0.14
15 9 0.31
16 3 0.10
17 8 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATTATATAAATTT
Found at i:311082 original size:2 final size:2
Alignment explanation
Indices: 311030--311063 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
311020 AGAATGTGTG
311030 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
311064 ATGTAAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:311091 original size:21 final size:21
Alignment explanation
Indices: 311051--311099 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
311041 ATATATATAT
311051 ATATATATATATAATGTAAACAA
1 ATAT-TATATATAATGTAAA-AA
* *
311074 A-ATTATATATATTTTAAAAA
1 ATATTATATATAATGTAAAAA
311094 ATATTA
1 ATATTA
311100 ATACTTGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.13
21 17 0.74
22 2 0.09
23 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
ATATTATATATAATGTAAAAA
Found at i:311212 original size:16 final size:16
Alignment explanation
Indices: 311191--311221 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
311181 ATAATTAAAG
*
311191 TTTTTATTTATAATTT
1 TTTTTAATTATAATTT
311207 TTTTTAATTATAATT
1 TTTTTAATTATAATT
311222 CAATCATTGT
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:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTAATTATAATTT
Found at i:311735 original size:16 final size:16
Alignment explanation
Indices: 311711--311762 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
311701 AAAATATTAT
* *
311711 AATTTGAAATAATTTA
1 AATTCGAAATAACTTA
311727 AATTCGAAATAACTTA
1 AATTCGAAATAACTTA
* * *
311743 AAGTCAAAATGAC-TA
1 AATTCGAAATAACTTA
311758 AATTC
1 AATTC
311763 TAATATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 6 0.20
16 24 0.80
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.33
Consensus pattern (16 bp):
AATTCGAAATAACTTA
Found at i:311850 original size:16 final size:16
Alignment explanation
Indices: 311837--311926 Score: 137
Period size: 16 Copynumber: 5.6 Consensus size: 16
311827 CGAAATAATA
311837 AAAATTTAAAATAATTT
1 AAAA-TTAAAATAATTT
*
311854 AAAATTAAAATAACTT
1 AAAATTAAAATAATTT
*
311870 AAATTTAAAATAATTT
1 AAAATTAAAATAATTT
311886 AAAATTAAAATAATTT
1 AAAATTAAAATAATTT
*
311902 AAATTTAAAATAA-TT
1 AAAATTAAAATAATTT
311917 AAAATTAAAA
1 AAAATTAAAA
311927 CTATACAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
15 11 0.16
16 52 0.78
17 4 0.06
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATTAAAATAATTT
Found at i:311874 original size:32 final size:32
Alignment explanation
Indices: 311838--311926 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
311828 GAAATAATAA
311838 AAATTTAAAATAATTTAAAATTAAAATAACTT
1 AAATTTAAAATAATTTAAAATTAAAATAACTT
*
311870 AAATTTAAAATAATTTAAAATTAAAATAATTT
1 AAATTTAAAATAATTTAAAATTAAAATAACTT
311902 AAATTTAAAATAA-TTAAAATTAAAA
1 AAATTTAAAATAATTTAAAATTAAAA
311927 CTATACAAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
31 12 0.21
32 44 0.79
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (32 bp):
AAATTTAAAATAATTTAAAATTAAAATAACTT
Found at i:311946 original size:32 final size:31
Alignment explanation
Indices: 311829--311942 Score: 133
Period size: 32 Copynumber: 3.6 Consensus size: 31
311819 CCCAAACTCG
*
311829 AAATAATAAAAATTTAAAATAATTTAAAATTA
1 AAAT-ATACAAATTTAAAATAATTTAAAATTA
311861 AAATA-ACTTAAATTTAAAATAATTTAAAATTA
1 AAATATAC--AAATTTAAAATAATTTAAAATTA
**
311893 AAATAATTTAAATTTAAAATAA-TTAAAATTA
1 AAAT-ATACAAATTTAAAATAATTTAAAATTA
*
311924 AAACTATACAAATCTAAAA
1 AAA-TATACAAATTTAAAA
311943 ATAACATAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
30 1 0.01
31 24 0.34
32 45 0.63
33 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (31 bp):
AAATATACAAATTTAAAATAATTTAAAATTA
Found at i:314905 original size:21 final size:22
Alignment explanation
Indices: 314879--314922 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
314869 TAATATTTAT
314879 AAAATTATTAAA-ATAAACATA
1 AAAATTATTAAACATAAACATA
* *
314900 AAAATTTTTAAACATAAATATA
1 AAAATTATTAAACATAAACATA
314922 A
1 A
314923 TATAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAATTATTAAACATAAACATA
Found at i:315269 original size:13 final size:13
Alignment explanation
Indices: 315236--315278 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
315226 TTTTTTAAAT
315236 TTTTTATA-TATA
1 TTTTTATATTATA
**
315248 TTTAAATATTATA
1 TTTTTATATTATA
315261 TTTTTATATT-TA
1 TTTTTATATTATA
315273 TTTTTA
1 TTTTTA
315279 AAAATTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 14 0.54
13 12 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTTATATTATA
Found at i:323588 original size:12 final size:12
Alignment explanation
Indices: 323559--323593 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
323549 ATAACATGAT
323559 AAAATAAT-TAA
1 AAAATAATATAA
323570 AAAATAATATAA
1 AAAATAATATAA
*
323582 AATATAATATAA
1 AAAATAATATAA
323594 TACAAAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:323899 original size:33 final size:33
Alignment explanation
Indices: 323857--323919 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
323847 AAAATATGGG
323857 AAAATATTTTAAATTTATGTGAGTTTTTTTAAA
1 AAAATATTTTAAATTTATGTGAGTTTTTTTAAA
323890 AAAATATTTTAAATTTATGTGAGTTTTTTT
1 AAAATATTTTAAATTTATGTGAGTTTTTTT
323920 TTAAGAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.54
Consensus pattern (33 bp):
AAAATATTTTAAATTTATGTGAGTTTTTTTAAA
Found at i:324105 original size:6 final size:6
Alignment explanation
Indices: 324094--324147 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
324084 TTTTTATTAT
* *
324094 AATATA AATATAA TAATTTA AATATA ATTA-A AATATA AATAT- AATATA
1 AATATA AATAT-A -AATATA AATATA AATATA AATATA AATATA AATATA
324142 AATATA
1 AATATA
324148 TAAATTTACT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 9 0.22
6 25 0.62
7 2 0.05
8 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
AATATA
Found at i:324105 original size:11 final size:11
Alignment explanation
Indices: 324091--324147 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 11
324081 ACTTTTTTAT
324091 TATAATATAAA
1 TATAATATAAA
**
324102 TATAATA-ATT
1 TATAATATAAA
*
324112 TA-AATATAAT
1 TATAATATAAA
*
324122 TAAAATATAAA
1 TATAATATAAA
324133 TATAATATAAA
1 TATAATATAAA
324144 TATA
1 TATA
324148 TAAATTTACT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
9 4 0.10
10 7 0.18
11 28 0.72
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TATAATATAAA
Found at i:324115 original size:14 final size:14
Alignment explanation
Indices: 324092--324147 Score: 62
Period size: 14 Copynumber: 4.0 Consensus size: 14
324082 CTTTTTTATT
324092 ATAATATAAATATA
1 ATAATATAAATATA
*
324106 ATAATTTAAATATA
1 ATAATATAAATATA
*
324120 ATTAAAATATAA-AT-
1 A-TAATATA-AATATA
324134 ATAATATAAATATA
1 ATAATATAAATATA
324148 TAAATTTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 2 0.06
13 8 0.24
14 15 0.44
15 7 0.21
16 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATATAAATATA
Found at i:324361 original size:20 final size:21
Alignment explanation
Indices: 324324--324384 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 21
324314 AAGCTGACGA
* *
324324 ATTAAATATTATACAATTATATT
1 ATTAAA-AATATA-AATTATAAT
*
324347 ATATAAAAA-AT-AATTAAAAT
1 AT-TAAAAATATAAATTATAAT
324367 ATTAAAAATATAAATTAT
1 ATTAAAAATATAAATTAT
324385 TGAGTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
19 6 0.19
20 11 0.35
21 5 0.16
22 2 0.06
23 3 0.10
24 4 0.13
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTAAAAATATAAATTATAAT
Found at i:324787 original size:20 final size:20
Alignment explanation
Indices: 324762--324805 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
324752 ATAAAATTTA
* *
324762 ATTTTTTAAATATATAAA-AT
1 ATTTTTAAAAAAT-TAAATAT
324782 ATTTTTAAAAAATTAAATAT
1 ATTTTTAAAAAATTAAATAT
324802 ATTT
1 ATTT
324806 ATATATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTTAAAAAATTAAATAT
Found at i:324788 original size:19 final size:19
Alignment explanation
Indices: 324764--324813 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
324754 AAAATTTAAT
324764 TTTTTAAATATATAAAATA
1 TTTTTAAATATATAAAATA
* *
324783 TTTTTAAA-AAATTAAATA
1 TTTTTAAATATATAAAATA
* *
324801 TATTTATATATAT
1 TTTTTAAATATAT
324814 TTATATTTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTTAAATATATAAAATA
Found at i:324799 original size:18 final size:18
Alignment explanation
Indices: 324754--324806 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
324744 ATACGAATAT
*
324754 AAAATTTAAT-TTTTTAA
1 AAAATTAAATATTTTTAA
* *
324771 ATATATAAAATATTTTTAA
1 A-AAATTAAATATTTTTAA
*
324790 AAAATTAAATATATTTA
1 AAAATTAAATATTTTTA
324807 TATATATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 1 0.04
18 19 0.68
19 8 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATTAAATATTTTTAA
Found at i:325878 original size:2 final size:2
Alignment explanation
Indices: 325873--325898 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
325863 ATAATTATTC
325873 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
325899 TTCCTAACTT
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:326119 original size:21 final size:21
Alignment explanation
Indices: 326093--326136 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
326083 AGATATTCGA
326093 TATTTATAATA-AATTTTTTAT
1 TATTTA-AATATAATTTTTTAT
*
326114 TATTTAATTATAATTTTTTAT
1 TATTTAAATATAATTTTTTAT
326135 TA
1 TA
326137 AAAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTAAATATAATTTTTTAT
Found at i:328478 original size:3 final size:3
Alignment explanation
Indices: 328470--328495 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
328460 ATAGGTTGAG
328470 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
328496 GCAGATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:328705 original size:6 final size:6
Alignment explanation
Indices: 328696--328726 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
328686 TCATGGCAGC
*
328696 GGCAAT GGCAAT GGCAAT GGCAAT GGGAAT G
1 GGCAAT GGCAAT GGCAAT GGCAAT GGCAAT G
328727 AAAACCCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.32, C:0.13, G:0.39, T:0.16
Consensus pattern (6 bp):
GGCAAT
Found at i:328711 original size:18 final size:18
Alignment explanation
Indices: 328688--328726 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
328678 GATGATGTTC
*
328688 ATGGCAGCGGCAATGGCA
1 ATGGCAACGGCAATGGCA
* *
328706 ATGGCAATGGCAATGGGA
1 ATGGCAACGGCAATGGCA
328724 ATG
1 ATG
328727 AAAACCCAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.15, G:0.38, T:0.15
Consensus pattern (18 bp):
ATGGCAACGGCAATGGCA
Found at i:330037 original size:24 final size:24
Alignment explanation
Indices: 330001--330089 Score: 58
Period size: 24 Copynumber: 3.5 Consensus size: 24
329991 TCATATATTT
* *
330001 ATTTTATTTTATTTTATTATATAA
1 ATTTTAATATATTTTATTATATAA
330025 ATTTTAATATATTTATATATTTATATTATA
1 ATTTTAATATA-TT-T-TA-TTATA-TA-A
* *
330055 A-TTTAAT-TATTTTTTTAT-TAT
1 ATTTTAATATATTTTATTATATAA
330076 ATTTATAATATATT
1 ATTT-TAATATATT
330090 CAAAATTATT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
21 1 0.02
22 4 0.08
23 4 0.08
24 17 0.33
25 3 0.06
26 2 0.04
27 4 0.08
28 7 0.13
29 8 0.15
30 2 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
ATTTTAATATATTTTATTATATAA
Found at i:330081 original size:28 final size:28
Alignment explanation
Indices: 330007--330084 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 28
329997 ATTTATTTTA
330007 TTTTATTTTATTATATAAATTTTAATATATTT
1 TTTTA-TTTATT-TAT-AA-TTTAATATATTT
* *
330039 ATATATTTATATTATAATTTAAT-TATTT
1 TTTTATTTAT-TTATAATTTAATATATTT
330067 TTTTATTATATTTATAAT
1 TTTTATT-TATTTATAAT
330085 ATATTCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 17 0.43
29 9 0.22
30 2 0.05
31 8 0.20
32 4 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTTATTTATTTATAATTTAATATATTT
Found at i:330087 original size:11 final size:11
Alignment explanation
Indices: 329994--330089 Score: 60
Period size: 11 Copynumber: 9.0 Consensus size: 11
329984 ACGTAATTCA
329994 TATATT-TATT
1 TATATTATATT
*
330004 T-TATTTTATT
1 TATATTATATT
*
330014 T-TATTATATA
1 TATATTATATT
* *
330024 AATTTTAATATAT
1 TATATT-ATAT-T
330037 T-TA-TATATT
1 TATATTATATT
330046 TATATTATAATT
1 TATATTAT-ATT
*
330058 TA-ATTATTTT
1 TATATTATATT
*
330068 TTTATTATATT
1 TATATTATATT
*
330079 TATAATATATT
1 TATATTATATT
330090 CAAAATTATT
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
9 6 0.09
10 22 0.33
11 28 0.42
12 10 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATATTATATT
Found at i:330189 original size:11 final size:10
Alignment explanation
Indices: 330171--330208 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
330161 AAAATTATAA
330171 TTTATATATT
1 TTTATATATT
*
330181 TTTAT-TATA
1 TTTATATATT
330190 TTTATATATT
1 TTTATATATT
*
330200 TTAATATAT
1 TTTATATAT
330209 CATAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTATATATT
Found at i:330194 original size:19 final size:20
Alignment explanation
Indices: 330164--330201 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
330154 AAATAAAAAA
330164 ATTATAATTTATATATTTTT
1 ATTATAATTTATATATTTTT
330184 ATTAT-ATTTATATATTTT
1 ATTATAATTTATATATTTT
330202 AATATATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTATAATTTATATATTTTT
Found at i:330235 original size:29 final size:28
Alignment explanation
Indices: 330167--330235 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
330157 TAAAAAAATT
** * *
330167 ATAATTTATATATTTTTATTATATTTAT
1 ATAATTTATATATCATAATTATATTTAA
*
330195 ATATTTTAATATATCATAATTATATTTTAA
1 ATAATTT-ATATATCATAATTATA-TTTAA
330225 ATAATTTATAT
1 ATAATTTATAT
330236 TTATATTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 6 0.18
29 17 0.52
30 10 0.30
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (28 bp):
ATAATTTATATATCATAATTATATTTAA
Found at i:330243 original size:27 final size:27
Alignment explanation
Indices: 330175--330286 Score: 79
Period size: 27 Copynumber: 4.1 Consensus size: 27
330165 TTATAATTTA
* * *
330175 TATATTTTTATTATA-TTTATATATTT
1 TATATTTATATTATATTTTAAATAATT
*
330201 TAATATATCATAATTATATTTTAAATAATT
1 T-ATAT-TTAT-ATTATATTTTAAATAATT
*
330231 TATATTTATATTA-ATTTTGATATAA-T
1 TATATTTATATTATATTTT-AAATAATT
* *
330257 AATAAATTATATTATATTTTATAA-AATT
1 TAT-ATTTATATTATATTTTA-AATAATT
330285 TA
1 TA
330287 AAAATATATT
Statistics
Matches: 67, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
26 9 0.13
27 25 0.37
28 13 0.19
29 10 0.15
30 10 0.15
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (27 bp):
TATATTTATATTATATTTTAAATAATT
Found at i:330245 original size:16 final size:16
Alignment explanation
Indices: 330185--330269 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
330175 TATATTTTTA
*
330185 TTATATTTAT-ATATT
1 TTATATTTATAATAAT
* *
330200 TTA-ATATATCATAA-
1 TTATATTTATAATAAT
330214 TTATATTT-TAAATAAT
1 TTATATTTAT-AATAAT
*
330230 TTATATTTATATTAAT
1 TTATATTTATAATAAT
* *
330246 TT-TGATATAATAATAAA
1 TTAT-AT-TTATAATAAT
330263 TTATATT
1 TTATATT
330270 ATATTTTATA
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
14 9 0.17
15 14 0.26
16 18 0.33
17 12 0.22
18 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (16 bp):
TTATATTTATAATAAT
Found at i:330294 original size:27 final size:27
Alignment explanation
Indices: 330213--330301 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 27
330203 ATATATCATA
* **
330213 ATTATATTTTA-AATAATTTATATTTAT
1 ATTATATTTTATAA-AATTTAAAAATAT
*
330240 ATTA-ATTTTGATATAA--TAATAAATTAT
1 ATTATATTTT-ATAAAATTTAA-AAA-TAT
330267 ATTATATTTTATAAAATTTAAAAATAT
1 ATTATATTTTATAAAATTTAAAAATAT
330294 ATT-TATTT
1 ATTATATTT
330302 ATATTATATT
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
25 2 0.04
26 11 0.22
27 25 0.50
28 9 0.18
29 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
ATTATATTTTATAAAATTTAAAAATAT
Found at i:330318 original size:32 final size:31
Alignment explanation
Indices: 330233--330319 Score: 77
Period size: 32 Copynumber: 2.7 Consensus size: 31
330223 AAATAATTTA
* * *
330233 TATTTATATTA-ATTTTGATATAATAATAAAT
1 TATTTATATTATATTAT-ATTTAAAAATAAAT
* * * *
330264 TATATTATATTTTATAAAATTTAAAAATATATT
1 TAT-TTATATTATATTATATTTAAAAATA-AAT
330297 TATTTATATTATATTATATTTAA
1 TATTTATATTATATTATATTTAA
330320 TATTGTGGTG
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
31 3 0.07
32 33 0.77
33 7 0.16
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
TATTTATATTATATTATATTTAAAAATAAAT
Found at i:330687 original size:46 final size:48
Alignment explanation
Indices: 330629--330737 Score: 154
Period size: 46 Copynumber: 2.3 Consensus size: 48
330619 TTAAAAAATT
330629 ATTTTTATTTAAATAATATTTTAAATCAAATC-AAA-TT-AAA-TTAAAA
1 ATTTTTATTTAAATAATATTTTAAAT-AAA-CAAAATTTGAAACTTAAAA
330675 ATTTTTATTTAAATAATATTTTAAATAAACAAAATTTGAAACTTAAAA
1 ATTTTTATTTAAATAATATTTTAAATAAACAAAATTTGAAACTTAAAA
* *
330723 ACTTTTACTTAAATA
1 ATTTTTATTTAAATA
330738 CAACCTAATC
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
44 1 0.02
45 6 0.11
46 28 0.49
47 3 0.05
48 19 0.33
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.43
Consensus pattern (48 bp):
ATTTTTATTTAAATAATATTTTAAATAAACAAAATTTGAAACTTAAAA
Found at i:330861 original size:18 final size:20
Alignment explanation
Indices: 330838--330885 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
330828 ATTTAAATTG
330838 AATTATTTTAAAATT-TTA-
1 AATTATTTTAAAATTGTTAT
*
330856 AATTATTTTTAAATTGTTAT
1 AATTATTTTAAAATTGTTAT
330876 AATTTATTTT
1 AA-TTATTTT
330886 TATATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 14 0.54
19 3 0.12
20 2 0.08
21 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
AATTATTTTAAAATTGTTAT
Found at i:331098 original size:11 final size:10
Alignment explanation
Indices: 331063--331095 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
331053 TTATTTTAAA
331063 TTAAATTATT
1 TTAAATTATT
331073 TTAAA--ATT
1 TTAAATTATT
331081 TTAAATTATT
1 TTAAATTATT
331091 TTAAA
1 TTAAA
331096 ATTTTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TTAAATTATT
Found at i:331108 original size:17 final size:18
Alignment explanation
Indices: 331063--331100 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
331053 TTATTTTAAA
331063 TTAAATTATTTTAAAATT
1 TTAAATTATTTTAAAATT
331081 TTAAATTATTTTAAAATT
1 TTAAATTATTTTAAAATT
331099 TT
1 TT
331101 TATTATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAAATTATTTTAAAATT
Found at i:331111 original size:228 final size:227
Alignment explanation
Indices: 330709--331166 Score: 801
Period size: 228 Copynumber: 2.0 Consensus size: 227
330699 ATAAACAAAA
*
330709 TTTGAAACTTAAAAACTTTTACTTAAATACAACCTAATCCAAAACCAAGACAAGCATACTATGAA
1 TTTGAAACTTAAAAACTTTTACTTAAATACAACCTAATCCAAAACCAAGACAAGCATACCATGAA
*
330774 GGTCGGTGAGCTGATAATTAGACTTTGTCATCCAGTAAAATCTGAGTCATGTTAATTTAAATTGA
66 GGTCGGTGAGCTGATAATTAGACTTTGTCATCCAGTAAAATCTGAGTCATGTTAATTTAAATTAA
*
330839 ATTATTTTAAAATTTTAAATTATTTTTAAATTGTTATAATTTATTTTTATATTATATTAAGTTAA
131 ATTATTTTAAAATTTTAAATTATTTTAAAATTGTTATAATTTA-TTTTATATTATATTAAGTTAA
330904 AATTAATTTAATTTAATAATTTAATTAATTATT
195 AATTAATTTAATTTAATAATTTAATTAATTATT
*
330937 TTTGAAACTTAAAAACTTTTACTTAAATACAACCTAATCCAAAGCCAAGACAAGTC-TACCATGA
1 TTTGAAACTTAAAAACTTTTACTTAAATACAACCTAATCCAAAACCAAGACAAG-CATACCATGA
*** *
331001 AGGTCGGTGAGCTGATAATTAGACTTTGTCATGGGGTAAAATCTGAGTCATGTTATTTTAAATTA
65 AGGTCGGTGAGCTGATAATTAGACTTTGTCATCCAGTAAAATCTGAGTCATGTTAATTTAAATTA
* *
331066 AATTATTTTAAAATTTTAAATTATTTTAAAATTTTTATTATTTATTTTATATTATATTAAGTTAA
130 AATTATTTTAAAATTTTAAATTATTTTAAAATTGTTATAATTTATTTTATATTATATTAAGTTAA
331131 AATTAATTTAATTTAATAATTTAATTAATTATT
195 AATTAATTTAATTTAATAATTTAATTAATTATT
331164 TTT
1 TTT
331167 AAATCAATTA
Statistics
Matches: 219, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
227 57 0.26
228 161 0.74
229 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (227 bp):
TTTGAAACTTAAAAACTTTTACTTAAATACAACCTAATCCAAAACCAAGACAAGCATACCATGAA
GGTCGGTGAGCTGATAATTAGACTTTGTCATCCAGTAAAATCTGAGTCATGTTAATTTAAATTAA
ATTATTTTAAAATTTTAAATTATTTTAAAATTGTTATAATTTATTTTATATTATATTAAGTTAAA
ATTAATTTAATTTAATAATTTAATTAATTATT
Found at i:331167 original size:22 final size:22
Alignment explanation
Indices: 331142--331212 Score: 56
Period size: 22 Copynumber: 3.1 Consensus size: 22
331132 ATTAATTTAA
331142 TTTAATAATTTAATTAATTATT
1 TTTAATAATTTAATTAATTATT
*
331164 TTTAAATCAATTATATTTAA-TA-T
1 TTT-AAT-AATT-TAATTAATTATT
* *
331187 TTAAATATATTAAATTTAATTATT
1 TTTAATA-ATTTAA-TTAATTATT
331211 TT
1 TT
331213 AAATTTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
21 2 0.05
22 13 0.34
23 8 0.21
24 9 0.24
25 6 0.16
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTAATAATTTAATTAATTATT
Found at i:331205 original size:37 final size:38
Alignment explanation
Indices: 331118--331205 Score: 92
Period size: 37 Copynumber: 2.4 Consensus size: 38
331108 TATTTTATAT
* * * *
331118 TATATTAAGTTAAAATTAATTTAATTTAATAATTTAAT
1 TATATTAAATTTAAATCAATTTAATTTAATAATTTAAA
**
331156 TA-ATTATTTTTAAATCAA-TTATATTTAAT-ATTTAAA
1 TATATTAAATTTAAATCAATTTA-ATTTAATAATTTAAA
331192 TATATTAAATTTAA
1 TATATTAAATTTAA
331206 TTATTTTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
36 11 0.27
37 28 0.68
38 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (38 bp):
TATATTAAATTTAAATCAATTTAATTTAATAATTTAAA
Found at i:334252 original size:20 final size:20
Alignment explanation
Indices: 334223--334322 Score: 60
Period size: 22 Copynumber: 4.7 Consensus size: 20
334213 TTAATTTAAA
*
334223 TTTATTTTATATTATATATT
1 TTTATATTATATTATATATT
*
334243 TTTATATTATATTTAAAATATT
1 TTTATATTATA-TT-ATATATT
* * *
334265 TTATATTTATATAAATTATAAAATA
1 TT-TA--TAT-TATATTAT-ATATT
*
334290 TTGATAATTATATT-TATA-T
1 TTTAT-ATTATATTATATATT
334309 TTTATATTATATTA
1 TTTATATTATATTA
334323 ATGTGATTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 19
0.67 0.12 0.21
Matches are distributed among these distances:
18 8 0.13
19 4 0.07
20 12 0.20
21 3 0.05
22 14 0.23
23 4 0.07
24 2 0.03
25 10 0.17
26 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (20 bp):
TTTATATTATATTATATATT
Found at i:334273 original size:27 final size:26
Alignment explanation
Indices: 334243--334310 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 26
334233 ATTATATATT
*
334243 TTTATATTATATTTAAAATATTTTATA
1 TTTATATTATATTTAAAATA-TTGATA
*
334270 TTTATA-TAAATTATAAAATATTGATA
1 TTTATATTATATT-TAAAATATTGATA
*
334296 ATTATATTTATATTT
1 TTTATA-TTATATTT
334311 TATATTATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 15 0.44
27 14 0.41
28 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
TTTATATTATATTTAAAATATTGATA
Found at i:334277 original size:29 final size:29
Alignment explanation
Indices: 334231--334310 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
334221 AATTTATTTT
* *
334231 ATATTATATATTTTTATATTATATTTAAA
1 ATATTTTATATTTATATATTATATTTAAA
334260 ATATTTTATATTTATATA--A-ATTATAAA
1 ATATTTTATATTTATATATTATATT-TAAA
* *
334287 ATA-TTGATAATTATAT-TTATATTT
1 ATATTTTATATTTATATATTATATTT
334311 TATATTATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
26 14 0.33
27 10 0.23
28 3 0.07
29 16 0.37
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (29 bp):
ATATTTTATATTTATATATTATATTTAAA
Found at i:335339 original size:2 final size:2
Alignment explanation
Indices: 335332--335363 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
335322 TTAAAGAATC
335332 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
335364 TAAATTTTTA
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:336848 original size:16 final size:15
Alignment explanation
Indices: 336807--336848 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
336797 AATTATTTTA
*
336807 TAAATAATAATAAAT
1 TAAATAATTATAAAT
*
336822 TAAAAAATTATAAAT
1 TAAATAATTATAAAT
336837 TAAATTAATTAT
1 TAAA-TAATTAT
336849 TTTTTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAATAATTATAAAT
Found at i:336873 original size:15 final size:15
Alignment explanation
Indices: 336855--336892 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
336845 TTATTTTTTA
336855 ATTTTTTAAATATAT
1 ATTTTTTAAATATAT
*
336870 ATTTTTAAAATATAT
1 ATTTTTTAAATATAT
*
336885 ATTATTTA
1 ATTTTTTA
336893 TAAAATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTTTAAATATAT
Found at i:336905 original size:18 final size:18
Alignment explanation
Indices: 336864--336898 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
336854 AATTTTTTAA
*
336864 ATATA-TATTTTTAAAAT
1 ATATATTATTTATAAAAT
336881 ATATATTATTTATAAAAT
1 ATATATTATTTATAAAAT
336899 TTTTATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATATTATTTATAAAAT
Found at i:337384 original size:10 final size:10
Alignment explanation
Indices: 337361--337401 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
337351 AATTTGCTAA
*
337361 TATATTAAATT
1 TATA-TAAAAT
337372 TATATAAAAT
1 TATATAAAAT
337382 TATA-AAAA-
1 TATATAAAAT
337390 TATATAAAAT
1 TATATAAAAT
337400 TA
1 TA
337402 ATTTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
8 4 0.15
9 8 0.30
10 11 0.41
11 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
TATATAAAAT
Found at i:337917 original size:6 final size:6
Alignment explanation
Indices: 337906--337941 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
337896 TAAAATATAA
337906 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
337942 TAAAATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATAT
Found at i:337965 original size:8 final size:7
Alignment explanation
Indices: 337888--337969 Score: 61
Period size: 6 Copynumber: 12.0 Consensus size: 7
337878 TAACTTTTTA
337888 TAAATAAT
1 TAAAT-AT
337896 TAAA-AT
1 TAAATAT
*
337902 ATAAAAAT
1 -TAAATAT
337910 ATAAATA-
1 -TAAATAT
337917 TAAATA-
1 TAAATAT
337923 TAAATA-
1 TAAATAT
337929 TAAATA-
1 TAAATAT
337935 TAAATAT
1 TAAATAT
337942 TAAA-AT
1 TAAATAT
337948 TAAA-ATT
1 TAAATA-T
337955 TAAATTAT
1 TAAA-TAT
337963 TAAATAT
1 TAAATAT
337970 AATTTTTTAA
Statistics
Matches: 67, Mismatches: 1, Indels: 13
0.83 0.01 0.16
Matches are distributed among these distances:
6 33 0.49
7 16 0.24
8 17 0.25
9 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
TAAATAT
Found at i:338668 original size:21 final size:22
Alignment explanation
Indices: 338642--338682 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
338632 AATTTCAAGG
338642 GATAATGT-TTAA-TATTTTAGA
1 GATAAT-TATTAATTATTTTAGA
338663 GATAATTATTAATTATTTTA
1 GATAATTATTAATTATTTTA
338683 AATTTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 10 0.56
22 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (22 bp):
GATAATTATTAATTATTTTAGA
Found at i:340610 original size:14 final size:14
Alignment explanation
Indices: 340593--340624 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
340583 ATTAAATTAT
*
340593 TTAAATTTATTTAG
1 TTAAATTTATTTAC
340607 TTAAATTTATTTAC
1 TTAAATTTATTTAC
340621 TTAA
1 TTAA
340625 TAAAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
TTAAATTTATTTAC
Found at i:341749 original size:13 final size:13
Alignment explanation
Indices: 341713--341757 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
341703 TTATATAAAT
* *
341713 ATATAATATTTTA
1 ATATAAAATTATA
*
341726 A-ATATAATTATA
1 ATATAAAATTATA
341738 ATATAAAATTATA
1 ATATAAAATTATA
341751 ATATAAA
1 ATATAAA
341758 TAAATATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATATAAAATTATA
Found at i:342538 original size:24 final size:24
Alignment explanation
Indices: 342519--342565 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
342509 ATTAAGATTG
*
342519 ACCTTAATCTATTTTCTAAGTTCA
1 ACCTTAATCTACTTTCTAAGTTCA
342543 ACCTTAATCTACTTTCTAAGTTC
1 ACCTTAATCTACTTTCTAAGTTC
342566 TAACTTGCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (24 bp):
ACCTTAATCTACTTTCTAAGTTCA
Found at i:343923 original size:3 final size:3
Alignment explanation
Indices: 343915--343960 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
343905 TTATATGCAA
343915 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
343961 GTAGTAGTAG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:344438 original size:22 final size:21
Alignment explanation
Indices: 344413--344474 Score: 83
Period size: 20 Copynumber: 3.0 Consensus size: 21
344403 ATATGTTAAG
*
344413 TTTTATATATAAATATTAAATA
1 TTTTAAATATAAATA-TAAATA
*
344435 TTTTAAATATAATTAT-AATA
1 TTTTAAATATAAATATAAATA
344455 TTTTAAATAT-AATATAAATA
1 TTTTAAATATAAATATAAATA
344475 AATAAATTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 4 0.11
20 18 0.50
21 1 0.03
22 13 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTTAAATATAAATATAAATA
Found at i:344451 original size:32 final size:31
Alignment explanation
Indices: 344362--344444 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 31
344352 AAATATTATT
344362 AATATTTAAATATTTTAAA-ATTTATATAATA
1 AATA-TTAAATATTTTAAATATTTATATAATA
* * *
344393 AAAATTATTAATATGTTAAGT-TTTATAT-ATA
1 AATATTA--AATATTTTAAATATTTATATAATA
344424 AATATTAAATATTTTAAATAT
1 AATATTAAATATTTTAAATAT
344445 AATTATAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
29 10 0.24
30 4 0.10
31 12 0.29
32 16 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
AATATTAAATATTTTAAATATTTATATAATA
Found at i:344799 original size:5 final size:5
Alignment explanation
Indices: 344782--344816 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
344772 TTTTCCCAGA
*
344782 TTTTC TTTCC TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
344817 CTAGGTAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:347195 original size:8 final size:8
Alignment explanation
Indices: 347184--347227 Score: 70
Period size: 8 Copynumber: 5.2 Consensus size: 8
347174 TATTATATTT
347184 TATATTAA
1 TATATTAA
347192 TATATTAA
1 TATATTAA
347200 TATATTAATA
1 TATATT-A-A
347210 TATATTAA
1 TATATTAA
347218 TATATTAA
1 TATATTAA
347226 TA
1 TA
347228 CACATATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 25 0.74
9 2 0.06
10 7 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TATATTAA
Found at i:347204 original size:10 final size:10
Alignment explanation
Indices: 347191--347222 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
347181 TTTTATATTA
347191 ATATATT-A-
1 ATATATTAAT
347199 ATATATTAAT
1 ATATATTAAT
347209 ATATATTAAT
1 ATATATTAAT
347219 ATAT
1 ATAT
347223 TAATACACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 7 0.32
9 1 0.05
10 14 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATATTAAT
Found at i:347214 original size:18 final size:18
Alignment explanation
Indices: 347191--347227 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
347181 TTTTATATTA
347191 ATATATTAATATATTAAT
1 ATATATTAATATATTAAT
347209 ATATATTAATATATTAAT
1 ATATATTAATATATTAAT
347227 A
1 A
347228 CACATATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATATTAATATATTAAT
Found at i:347299 original size:22 final size:22
Alignment explanation
Indices: 347277--347343 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
347267 AATTATTAAT
347277 ATATTTT--ATATAAATATAAA
1 ATATTTTAAATATAAATATAAA
* *
347297 ATATTTTAAATATAATTATAAT
1 ATATTTTAAATATAAATATAAA
* *
347319 ATA-ATAAAATATAAA-ATAAA
1 ATATTTTAAATATAAATATAAA
347339 TATAT
1 -ATAT
347344 GAATTTTCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 11 0.30
21 12 0.32
22 14 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATTTTAAATATAAATATAAA
Found at i:348957 original size:28 final size:24
Alignment explanation
Indices: 348898--348946 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
348888 TTAACTATAC
*
348898 TTATAAAT-ATTTATTAATTTTTT
1 TTATAAATAATATATTAATTTTTT
*
348921 TTATAAATAATATATTAATATTTT
1 TTATAAATAATATATTAATTTTTT
348945 TT
1 TT
348947 CTATGTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTATAAATAATATATTAATTTTTT
Found at i:349370 original size:26 final size:27
Alignment explanation
Indices: 349319--349376 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
349309 TTATTTTATA
* **
349319 ATAAAAATATTTTATTTAAATTTAATT
1 ATAAAAATATTTTATATAAAAATAATT
349346 ATAAAAATA-TTTATATAAAAATAATT
1 ATAAAAATATTTTATATAAAAATAATT
*
349372 TTAAA
1 ATAAA
349377 TTTTTACTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
ATAAAAATATTTTATATAAAAATAATT
Found at i:349372 original size:15 final size:14
Alignment explanation
Indices: 349313--349368 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
349303 AAAATATTAT
349313 TTTATAATAAAAATA
1 TTTAT-ATAAAAATA
**
349328 TTT-TATTTAAAT-
1 TTTATATAAAAATA
*
349340 TTAATTATAAAAATA
1 TTTA-TATAAAAATA
349355 TTTATATAAAAATA
1 TTTATATAAAAATA
349369 ATTTTAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
12 2 0.06
13 6 0.19
14 18 0.56
15 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTTATATAAAAATA
Found at i:349382 original size:24 final size:27
Alignment explanation
Indices: 349350--349399 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 27
349340 TTAATTATAA
349350 AAATATTTA-T-ATAAA-AATAATTTT
1 AAATATTTACTAATAAACAATAATTTT
*
349374 AAATTTTTACTAATAAACAATAATTT
1 AAATATTTACTAATAAACAATAATTT
349400 AGGATTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 1 0.05
26 5 0.23
27 8 0.36
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (27 bp):
AAATATTTACTAATAAACAATAATTTT
Found at i:352594 original size:21 final size:21
Alignment explanation
Indices: 352549--352627 Score: 53
Period size: 21 Copynumber: 3.9 Consensus size: 21
352539 AGAGAAAGAG
*
352549 ATTTTAAATGT-TTAAAT-TT
1 ATTTTAAATTTATTAAATATT
352568 GAATTTTAAATTTATTAAATATT
1 --ATTTTAAATTTATTAAATATT
*
352591 ATTTT--TTTTA-TAAATATT
1 ATTTTAAATTTATTAAATATT
* *
352609 -TATATAAATTAATTAAATA
1 AT-TTTAAATTTATTAAATA
352628 AATTTTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
17 1 0.02
18 10 0.21
19 4 0.09
20 3 0.06
21 21 0.45
22 6 0.13
23 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (21 bp):
ATTTTAAATTTATTAAATATT
Found at i:352769 original size:29 final size:30
Alignment explanation
Indices: 352733--352803 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 30
352723 TTAATGACAA
*
352733 TTTA-TATATTCAT-ATTATTTTT-ATATAT
1 TTTATTATATT-ATAATTATTTTTAAAATAT
352761 TTTATTATATTATAATTATTTTTAAAATAT
1 TTTATTATATTATAATTATTTTTAAAATAT
*
352791 TTTA-TATTTTATA
1 TTTATTATATTATA
352804 TTAATAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
28 6 0.16
29 23 0.61
30 9 0.24
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTATTATATTATAATTATTTTTAAAATAT
Found at i:352809 original size:20 final size:20
Alignment explanation
Indices: 352733--352903 Score: 78
Period size: 20 Copynumber: 8.8 Consensus size: 20
352723 TTAATGACAA
*
352733 TTTATATATTCATATT-AT-T
1 TTTATAT-TTTATATTAATAT
352752 TTTATATATTT-TATT-ATAT
1 TTTATAT-TTTATATTAATAT
* *
352771 TATAATTATTTT-TA-AAATAT
1 T-TTA-TATTTTATATTAATAT
*
352791 TTTATATTTTATATTAATAA
1 TTTATATTTTATATTAATAT
352811 TTTATA--TTATA-TAA-AT
1 TTTATATTTTATATTAATAT
* *
352827 TGATATATTTATATATTTATATT
1 T-TTATATTT-TATATTAATA-T
* * * *
352850 TTTATATTATATTTTATTTT
1 TTTATATTTTATATTAATAT
* *
352870 TTTATATTATATAATAATA-
1 TTTATATTTTATATTAATAT
*
352889 -TTATATTTAATATTA
1 TTTATATTTTATATTA
352904 TTAACTTACC
Statistics
Matches: 117, Mismatches: 22, Indels: 27
0.70 0.13 0.16
Matches are distributed among these distances:
16 2 0.02
17 7 0.06
18 29 0.25
19 17 0.15
20 42 0.36
21 11 0.09
22 7 0.06
23 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (20 bp):
TTTATATTTTATATTAATAT
Found at i:353979 original size:13 final size:13
Alignment explanation
Indices: 353963--353996 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
353953 TTAATTTTAA
*
353963 ATATTTATATTTG
1 ATATATATATTTG
353976 ATATATATATTTG
1 ATATATATATTTG
353989 ATATATAT
1 ATATATAT
353997 TTAAATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATATATATTTG
Done.