Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008737.1 Hibiscus syriacus cultivar Beakdansim tig00111812_pilon, whole genome shotgun sequence
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: 2791265
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:457041 original size:14 final size:14
Alignment explanation
Indices: 457022--457061 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
457012 ATAATTTTAA
457022 TAATATTATATTTT
1 TAATATTATATTTT
*
457036 TCATATTATATTTT
1 TAATATTATATTTT
*
457050 TAATATTTTATT
1 TAATATTATATT
457062 AGTATATACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TAATATTATATTTT
Found at i:457216 original size:24 final size:24
Alignment explanation
Indices: 457132--457216 Score: 70
Period size: 24 Copynumber: 3.6 Consensus size: 24
457122 AATAAATTAT
* * *
457132 TAATATTTATATATTTTATAAATA
1 TAATATTAATATAATTTATATATA
*
457156 TAATATT-AT-TAAATTAT-TA-A
1 TAATATTAATATAATTTATATATA
* *
457176 TAATGAGTAATATTAATTTATATATG
1 TAAT-ATTAATA-TAATTTATATATA
457202 TAATATTAATATAAT
1 TAATATTAATATAAT
457217 AATTTAGTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
20 5 0.10
21 3 0.06
22 8 0.17
23 2 0.04
24 18 0.38
25 8 0.17
26 4 0.08
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TAATATTAATATAATTTATATATA
Found at i:457569 original size:30 final size:30
Alignment explanation
Indices: 457509--457575 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
457499 CACAAAAAAA
*
457509 ATGTAATTAATTTTACCTAAAACAGCTTTC
1 ATGTAATTAATTTTACCTAAAACAACTTTC
* * * *
457539 ATGTAATTCATTTTACTTAAAATAATTTTC
1 ATGTAATTAATTTTACCTAAAACAACTTTC
*
457569 AGGTAAT
1 ATGTAAT
457576 CTTTTTTACA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.43
Consensus pattern (30 bp):
ATGTAATTAATTTTACCTAAAACAACTTTC
Found at i:459779 original size:24 final size:25
Alignment explanation
Indices: 459737--459792 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
459727 TTTTTTAATC
*
459737 TTATTAATTTAATTTAATATATAAAA
1 TTATTAA-TTAATTAAATATATAAAA
*
459763 TTATTAA-TAATTAAATATATAATA
1 TTATTAATTAATTAAATATATAAAA
459787 TTATTA
1 TTATTA
459793 TATATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 21 0.75
26 7 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTATTAATTAATTAAATATATAAAA
Found at i:470862 original size:99 final size:99
Alignment explanation
Indices: 470691--470882 Score: 375
Period size: 99 Copynumber: 1.9 Consensus size: 99
470681 AAACATGAAG
*
470691 AAACAATGTTAATATAATCAATTAATCAGGCTATAATTGTTTTAGCCTTTTTCTCCTAACATTTC
1 AAACAATGGTAATATAATCAATTAATCAGGCTATAATTGTTTTAGCCTTTTTCTCCTAACATTTC
470756 TGATAGTTTTGGCTTTCACTGTTACCACTGGACT
66 TGATAGTTTTGGCTTTCACTGTTACCACTGGACT
470790 AAACAATGGTAATATAATCAATTAATCAGGCTATAATTGTTTTAGCCTTTTTCTCCTAACATTTC
1 AAACAATGGTAATATAATCAATTAATCAGGCTATAATTGTTTTAGCCTTTTTCTCCTAACATTTC
470855 TGATAGTTTTGGCTTTCACTGTTACCAC
66 TGATAGTTTTGGCTTTCACTGTTACCAC
470883 CAGACTTAAC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 92 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (99 bp):
AAACAATGGTAATATAATCAATTAATCAGGCTATAATTGTTTTAGCCTTTTTCTCCTAACATTTC
TGATAGTTTTGGCTTTCACTGTTACCACTGGACT
Found at i:474176 original size:18 final size:19
Alignment explanation
Indices: 474141--474177 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
474131 TACGGAATGT
474141 AAGATTACCACTGAGAATAA
1 AAGATTACCAC-GAGAATAA
474161 AAGATTACCA-GAGAATA
1 AAGATTACCACGAGAATA
474178 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (19 bp):
AAGATTACCACGAGAATAA
Found at i:475249 original size:20 final size:18
Alignment explanation
Indices: 475205--475250 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
475195 CATATTGTAA
475205 AATAAAAAAACTAATAAT
1 AATAAAAAAACTAATAAT
*
475223 AGA-AAAAAAATTAAT-AT
1 A-ATAAAAAAACTAATAAT
*
475240 AATAATAAAAC
1 AATAAAAAAAC
475251 ACATAAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 5
0.74 0.10 0.16
Matches are distributed among these distances:
16 1 0.04
17 9 0.39
18 12 0.52
19 1 0.04
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (18 bp):
AATAAAAAAACTAATAAT
Found at i:477175 original size:33 final size:34
Alignment explanation
Indices: 477138--477219 Score: 132
Period size: 33 Copynumber: 2.4 Consensus size: 34
477128 CTCGAAGGTC
477138 TTTGTGTTTCAAGAGAAAC-ATTTTCAAAGG-TTT
1 TTTGTGTTTCAAGAGAAACGA-TTTCAAAGGTTTT
477171 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGG-TTTT
477206 TTTGTGTTTCAAGA
1 TTTGTGTTTCAAGA
477220 AAAAATGTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
33 28 0.61
34 1 0.02
35 17 0.37
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.44
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:477364 original size:36 final size:36
Alignment explanation
Indices: 477279--477699 Score: 410
Period size: 36 Copynumber: 12.1 Consensus size: 36
477269 AATGTTGGTA
* *
477279 TTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTG
*
477316 TTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
* *
477352 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTG
* ** * **
477389 TTCCAAAAGAAACTGTCTCAAGGGAGATGAAATTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
* ** * *
477425 TTTCAAGGAAAAC-G--T--ATTGA-A-AGATTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
* *
477454 TTTCAAGGGAAACTGTCTCATGAGAAACAAAATTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
* * *
477490 TTTCAAGGTAAATTGTCTCAAGGGAGACAAAATTT-
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
* * * *
477525 TTTCAAGGAAAACATAT-TC-----A-A-ATATTTTG
1 TTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATTTG
* * *
477554 TTTCGAGGTAAACCGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
*
477590 TTTCAAGGGAAACTGTATCAAGAGAGACAAAATTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
*
477626 TTTCAAGGGAAACTGTCTCAAGAAAGAC--AATTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
477660 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTG
477697 TTT
1 TTT
477700 TAAGTAAATT
Statistics
Matches: 315, Mismatches: 48, Indels: 42
0.78 0.12 0.10
Matches are distributed among these distances:
28 6 0.02
29 31 0.10
30 3 0.01
31 3 0.01
32 1 0.00
33 1 0.00
34 36 0.11
35 16 0.05
36 150 0.48
37 68 0.22
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:477572 original size:100 final size:101
Alignment explanation
Indices: 477348--477699 Score: 384
Period size: 100 Copynumber: 3.4 Consensus size: 101
477338 AGAGATAAAA
* * * * * **
477348 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGGGAAACCGTCTCAAGAGAAACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGGG
** * *
477413 AGATGAAATTTGTTTCAAGGAAAACGTATTGAAAGAT
65 AGACAAAATTTGTTTCAAGGAAAACATATTCAAAGAT
* * * *
477450 TTTGTTTCAAGGGAAACTGTCTCATGAGAAACAAAATTTGTTTCAAGGTAAATTGTCTCAAGGGA
1 TTTGTTTCAAGGGAAACCGTCTCAAGAGAAACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGA
*
477515 GACAAAATTT-TTTCAAGGAAAACATATTCAAATAT
66 GACAAAATTTGTTTCAAGGAAAACATATTCAAAGAT
* * * * *
477550 TTTGTTTCGAGGTAAACCGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTATCAAGAGA
1 TTTGTTTCAAGGGAAACCGTCTCAAGAGAAACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGA
* * *
477615 GACAAAATTTGTTTCAAGGGAAAC-TGTCTCAAGAAAGACAA
66 GACAAAATTTGTTTCAAGGAAAACATAT-TC---AAAG--AT
* *
477656 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
1 TTTGTTTCAAGGGAAACCGTCTCAAGAGAAACAAAA-TTTGTTT
477700 TAAGTAAATT
Statistics
Matches: 212, Mismatches: 30, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
100 90 0.42
101 45 0.21
102 33 0.16
104 3 0.01
106 34 0.16
107 7 0.03
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (101 bp):
TTTGTTTCAAGGGAAACCGTCTCAAGAGAAACAAAATTTGTTTCAAGGGAAACTGTCTCAAGGGA
GACAAAATTTGTTTCAAGGAAAACATATTCAAAGAT
Found at i:477681 original size:70 final size:72
Alignment explanation
Indices: 477550--477699 Score: 232
Period size: 70 Copynumber: 2.1 Consensus size: 72
477540 ATTCAAATAT
* * *
477550 TTTGTTTCGAGGTAAACCGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTATCAAGAGA
1 TTTGTTTCAAGGGAAACCGTCTCAAGAAAGAC-AAATTTGTTTCAAGGGAAACTGTATCAAGAGA
477615 GACAAAA-
65 GACAAAAC
* *
477622 TTTGTTTCAAGGGAAACTGTCTCAAGAAAGAC-AATTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TTTGTTTCAAGGGAAACCGTCTCAAGAAAGACAAATTTGTTTCAAGGGAAACTGTATCAAGAGAG
477686 ACAAAAC
66 ACAAAAC
477693 TTTGTTT
1 TTTGTTT
477700 TAAGTAAATT
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
70 37 0.51
71 7 0.10
72 28 0.39
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (72 bp):
TTTGTTTCAAGGGAAACCGTCTCAAGAAAGACAAATTTGTTTCAAGGGAAACTGTATCAAGAGAG
ACAAAAC
Found at i:478081 original size:61 final size:61
Alignment explanation
Indices: 477996--478163 Score: 212
Period size: 61 Copynumber: 2.8 Consensus size: 61
477986 CATCTCTTTC
* * * * *
477996 GAGTTCAATAT-ATTTCACTGTGAAGTTGAAATTGACTCTAAAAGTTGGAAAATTGTTTGTT
1 GAGTCCAATATCA-TTCGCTGTGAAGTTGAAATTGACTCTAAAAGCTGCAAAATTATTTGTT
** * * *
478057 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGTTATGAAAGCTGCAAAGTTATTTGTT
1 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTAAAAGCTGCAAAATTATTTGTT
* *
478118 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTCTAAAAGCT
1 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTAAAAGCT
478164 ACAAGAGATT
Statistics
Matches: 90, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
61 89 0.99
62 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (61 bp):
GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTAAAAGCTGCAAAATTATTTGTT
Found at i:479466 original size:14 final size:12
Alignment explanation
Indices: 479447--479520 Score: 58
Period size: 14 Copynumber: 5.4 Consensus size: 12
479437 TCTTCTTCAC
479447 TTTTTCTTTGTTT
1 TTTTTCTTT-TTT
479460 TTGTTTCTCTTTTT
1 TT-TTTCT-TTTTT
*
479474 TATTTTCTCTTTGCT
1 T-TTTTCT-TTT-TT
479489 TTTTTCTTCTTTT
1 TTTTTCTT-TTTT
479502 TTTTCTCTTTTTT
1 TTTT-TCTTTTTT
479515 CTTTTT
1 -TTTTT
479521 GTTCTGATTG
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
13 13 0.25
14 34 0.65
15 5 0.10
ACGTcount: A:0.01, C:0.15, G:0.04, T:0.80
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:479481 original size:42 final size:40
Alignment explanation
Indices: 479434--479519 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
479424 GCCTTGTCTT
*
479434 TTTTCTTCTTCAC-TTTTTCTTTGTTTTTGTTTCTCTTTTTTA
1 TTTTC-TCTTCACTTTTTTC-TTCTTTTT-TTTCTCTTTTTTA
** *
479476 TTTTCTCTTTGCTTTTTTCTTCTTTTTTTTCTCTTTTTTC
1 TTTTCTCTTCACTTTTTTCTTCTTTTTTTTCTCTTTTTTA
479516 TTTT
1 TTTT
479520 TGTTCTGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 16 0.41
41 12 0.31
42 11 0.28
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.77
Consensus pattern (40 bp):
TTTTCTCTTCACTTTTTTCTTCTTTTTTTTCTCTTTTTTA
Found at i:479503 original size:30 final size:29
Alignment explanation
Indices: 479447--479523 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 29
479437 TCTTCTTCAC
479447 TTTTTCTTTGTTTTTGTTTCTCTTTTTTA
1 TTTTTCTTTGTTTTTGTTTCTCTTTTTTA
* *
479476 TTTTCTCTTTGCTTTTT-TCTTCTTTTTTTTC
1 TTTT-TCTTTG-TTTTTGT-TTCTCTTTTTTA
* *
479507 TCTTT-TTTCTTTTTGTT
1 TTTTTCTTTGTTTTTGTT
479524 CTGATTGGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
28 6 0.15
29 8 0.20
30 8 0.20
31 18 0.45
ACGTcount: A:0.01, C:0.14, G:0.05, T:0.79
Consensus pattern (29 bp):
TTTTTCTTTGTTTTTGTTTCTCTTTTTTA
Found at i:479518 original size:28 final size:28
Alignment explanation
Indices: 479430--479520 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
479420 ATGCGCCTTG
* *
479430 TCTTTTTTCTTCTTCACTTTTTCT-TTGTT
1 TCTTTTTTCTTCTT--TTTTTTCTCTTTTT
* * *
479459 T-TTGTTTC-TCTTTTTTATTTTCTCTTT
1 TCTTTTTTCTTCTTTTTT-TTCTCTTTTT
*
479486 GCTTTTTTCTTCTTTTTTTTCTCTTTTT
1 TCTTTTTTCTTCTTTTTTTTCTCTTTTT
479514 TCTTTTT
1 TCTTTTT
479521 GTTCTGATTG
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
25 3 0.06
26 3 0.06
27 7 0.15
28 26 0.54
29 9 0.19
ACGTcount: A:0.02, C:0.18, G:0.03, T:0.77
Consensus pattern (28 bp):
TCTTTTTTCTTCTTTTTTTTCTCTTTTT
Found at i:484496 original size:17 final size:17
Alignment explanation
Indices: 484471--484523 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
484461 CAGATTGTAA
484471 AATAAAAAAAAACTAAT
1 AATAAAAAAAAACTAAT
* *
484488 AATAGAAAAAAATTAAT
1 AATAAAAAAAAACTAAT
* *
484505 -ATAATAATAAAACAAAT
1 AATAA-AAAAAAACTAAT
484522 AA
1 AA
484524 AATGGATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 3 0.11
17 24 0.86
18 1 0.04
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (17 bp):
AATAAAAAAAAACTAAT
Found at i:489643 original size:18 final size:17
Alignment explanation
Indices: 489611--489655 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
489601 AAAAACCCTT
*
489611 AAATTTGATGCAATTAG
1 AAATTTAATGCAATTAG
*
489628 ATAATTTAATGTAATTAG
1 A-AATTTAATGCAATTAG
489646 AAAGTTTAAT
1 AAA-TTTAAT
489656 ATAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.44, C:0.02, G:0.13, T:0.40
Consensus pattern (17 bp):
AAATTTAATGCAATTAG
Found at i:492585 original size:23 final size:23
Alignment explanation
Indices: 492531--492574 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
492521 AAATTCTCGC
* *
492531 GGTCCTTCGGGATATTTCTACAT
1 GGTCCTTCGGGACATTTATACAT
492554 GGTCCTTCGGGACATTTATAC
1 GGTCCTTCGGGACATTTATAC
492575 GTGGCACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (23 bp):
GGTCCTTCGGGACATTTATACAT
Found at i:494840 original size:43 final size:43
Alignment explanation
Indices: 494767--494853 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
494757 ATTATACATG
* * * *
494767 TCATCACTCAATTATCTTCTCTTTTGTATTTTGGCCACTAAAT
1 TCATCACTCAACTATCTTCCCTCTTCTATTTTGGCCACTAAAT
* *
494810 TCATCACTCAACTATTTTCCCTCTTCTATTTTGGTCACTAAAT
1 TCATCACTCAACTATCTTCCCTCTTCTATTTTGGCCACTAAAT
494853 T
1 T
494854 TTAAATATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.23, C:0.25, G:0.06, T:0.46
Consensus pattern (43 bp):
TCATCACTCAACTATCTTCCCTCTTCTATTTTGGCCACTAAAT
Found at i:495317 original size:13 final size:13
Alignment explanation
Indices: 495299--495363 Score: 94
Period size: 13 Copynumber: 5.0 Consensus size: 13
495289 GTCATAAATC
495299 TATGACACGCATT
1 TATGACACGCATT
495312 TATGACACGCATT
1 TATGACACGCATT
*
495325 TATGACACACATT
1 TATGACACGCATT
* *
495338 TATGACGCTCATT
1 TATGACACGCATT
*
495351 TATGACGCGCATT
1 TATGACACGCATT
495364 GAGCGTCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (13 bp):
TATGACACGCATT
Found at i:495449 original size:85 final size:85
Alignment explanation
Indices: 495368--495548 Score: 308
Period size: 85 Copynumber: 2.1 Consensus size: 85
495358 CGCATTGAGC
* * *
495368 GTCATTGAATCCCCCGTCATAAATGAAGATGACACACATTTGTGTGTCATAAATTTATAACACGT
1 GTCATTGAAGCCCCAGTCATAAATGAAGATGACACACATTTGTGTGTCATAAATTTATAACACGC
495433 ATGTATGACTTACATTGTGT
66 ATGTATGACTTACATTGTGT
* * *
495453 GCCATTGAAGCCCCAGTCATAAATGAAGTTGACACACATTTGTGTGTCATAAATTTATGACACGC
1 GTCATTGAAGCCCCAGTCATAAATGAAGATGACACACATTTGTGTGTCATAAATTTATAACACGC
495518 ATGTATGACTTACATTGTGT
66 ATGTATGACTTACATTGTGT
495538 GTCATTGAAGC
1 GTCATTGAAGC
495549 ACATATCATT
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 89 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (85 bp):
GTCATTGAAGCCCCAGTCATAAATGAAGATGACACACATTTGTGTGTCATAAATTTATAACACGC
ATGTATGACTTACATTGTGT
Found at i:495571 original size:85 final size:84
Alignment explanation
Indices: 495384--495585 Score: 282
Period size: 85 Copynumber: 2.4 Consensus size: 84
495374 GAATCCCCCG
*
495384 TCATAAATGAAGATGACACACATTTGTGTGTCATAAATTTATAACACGTATGTATGACTTACATT
1 TCATAAA-GAAGATGACACACATTTGTGTGTCATAAATTTATAACACGCATGTATGACTTACATT
* *
495449 GTGTGCCATTGAAGCCCCAG
65 GTGTGCCATTGAAGCCACAA
* *
495469 TCATAAATGAAGTTGACACACATTTGTGTGTCATAAATTTATGACACGCATGTATGACTTACATT
1 TCATAAA-GAAGATGACACACATTTGTGTGTCATAAATTTATAACACGCATGTATGACTTACATT
*
495534 GTGTGTCATTGAAG-CACATA
65 GTGTGCCATTGAAGCCACA-A
*
495554 TCATTAAA-AACGATGACACACATTCGTGTGTC
1 TCA-TAAAGAA-GATGACACACATTTGTGTGTC
495586 GTGATTGTAT
Statistics
Matches: 106, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
84 5 0.05
85 97 0.92
86 4 0.04
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (84 bp):
TCATAAAGAAGATGACACACATTTGTGTGTCATAAATTTATAACACGCATGTATGACTTACATTG
TGTGCCATTGAAGCCACAA
Found at i:495614 original size:2 final size:2
Alignment explanation
Indices: 495607--495641 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
495597 TCGTAAATTT
*
495607 TA TA TA TA TA TA TA TA TA TG 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
495642 TGTAGATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:497284 original size:39 final size:39
Alignment explanation
Indices: 497241--497340 Score: 182
Period size: 39 Copynumber: 2.6 Consensus size: 39
497231 CCCTTCTCCT
*
497241 TTCTCCTTTCTCCTCTTCCTTTTTCCTTTGCGGTGTCCC
1 TTCTCCTTTCCCCTCTTCCTTTTTCCTTTGCGGTGTCCC
*
497280 TTCTCCTTTCCCCTCTTCTTTTTTCCTTTGCGGTGTCCC
1 TTCTCCTTTCCCCTCTTCCTTTTTCCTTTGCGGTGTCCC
497319 TTCTCCTTTCCCCTCTTCCTTT
1 TTCTCCTTTCCCCTCTTCCTTT
497341 ACTTTCTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.00, C:0.40, G:0.08, T:0.52
Consensus pattern (39 bp):
TTCTCCTTTCCCCTCTTCCTTTTTCCTTTGCGGTGTCCC
Found at i:497288 original size:19 final size:19
Alignment explanation
Indices: 497264--497327 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
497254 TCTTCCTTTT
497264 TCCTTTGCGGTGTCCCTTC
1 TCCTTTGCGGTGTCCCTTC
* ** * ** *
497283 TCCTTTCCCCTCTTCTTTTT
1 TCCTTTGCGGT-GTCCCTTC
497303 TCCTTTGCGGTGTCCCTTC
1 TCCTTTGCGGTGTCCCTTC
497322 TCCTTT
1 TCCTTT
497328 CCCCTCTTCC
Statistics
Matches: 30, Mismatches: 14, Indels: 2
0.65 0.30 0.04
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.00, C:0.38, G:0.12, T:0.50
Consensus pattern (19 bp):
TCCTTTGCGGTGTCCCTTC
Found at i:501634 original size:18 final size:18
Alignment explanation
Indices: 501608--501643 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
501598 TATGCTGCCT
501608 AAATAATATTAGAAGTTA
1 AAATAATATTAGAAGTTA
*
501626 AAATCATATTAGAAGTTA
1 AAATAATATTAGAAGTTA
501644 GGAAAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.11, T:0.33
Consensus pattern (18 bp):
AAATAATATTAGAAGTTA
Found at i:504581 original size:24 final size:24
Alignment explanation
Indices: 504537--504586 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
504527 ATAAAGAACC
504537 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAATATACCATTA
*
504561 AAAATAAAGTTCAAATA-ACCATTA
1 AAAATAAACTT-AAATATACCATTA
504585 AA
1 AA
504587 TCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAATATACCATTA
Found at i:514300 original size:16 final size:15
Alignment explanation
Indices: 514277--514312 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
514267 TGGTAAAAAC
514277 AATAAATGAAAAGAA
1 AATAAATGAAAAGAA
*
514292 AATAGAATGTAAAGAA
1 AATA-AATGAAAAGAA
514308 AATAA
1 AATAA
514313 TCCTCATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (15 bp):
AATAAATGAAAAGAA
Found at i:514831 original size:24 final size:24
Alignment explanation
Indices: 514787--514836 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
514777 ATAAAGAACC
*
514787 AAAATAAACTTAAATACACCATTA
1 AAAATAAACTTAAACACACCATTA
*
514811 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACACACCATTA
514835 AA
1 AA
514837 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATAAACTTAAACACACCATTA
Found at i:520978 original size:178 final size:180
Alignment explanation
Indices: 520675--521036 Score: 683
Period size: 178 Copynumber: 2.0 Consensus size: 180
520665 CTTATATGCG
520675 CTCTGCCAGAGCTCCCTTCAGCCACCACGAACCGCCTTAGCTCACTAGCTCTTTTCGGACACCTA
1 CTCTGCCAGAGCTCCCTTCAGCCACCACGAACCGCCTTAG--C-CTAGCTCTTTTCGGACACCTA
520740 GATTACCACTCCCTCGAGCTTCACCAATGGAGGAACACCACCAAGAGGATGGAGGGAAGAAAATG
63 GATTACCACTCCCTCGAGCTTCACCAATGGAGGAACACCACCAAGAGGATGGAGGGAAGAAAATG
520805 ATGGAGAAGATAAAGAAATTCAAGTTGTC-GGTGTGAGTGTGCAACCAATTTT
128 ATGGAGAAGATAAAGAAATTCAAGTTGTCGGGTGTGAGTGTGCAACCAATTTT
520857 CTCTGCCAGAGCTCCCTTCAGCCACCACGAACCGCCTTAG-CTAGCTCTTTTCGGACACCTAGAT
1 CTCTGCCAGAGCTCCCTTCAGCCACCACGAACCGCCTTAGCCTAGCTCTTTTCGGACACCTAGAT
520921 TACCACTCCCTCGAGCTTCACCAATGGAGGAACACCACCAAGAGGATGGAGGGAAGAAAATGATG
66 TACCACTCCCTCGAGCTTCACCAATGGAGGAACACCACCAAGAGGATGGAGGGAAGAAAATGATG
520986 GAGAAGATAAAGAAATTCAAGTTGTCGGGTGTGAGTGTGCAACCAATTTT
131 GAGAAGATAAAGAAATTCAAGTTGTCGGGTGTGAGTGTGCAACCAATTTT
521036 C
1 C
521037 CTCTCTCATG
Statistics
Matches: 179, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
178 115 0.64
179 24 0.13
182 40 0.22
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (180 bp):
CTCTGCCAGAGCTCCCTTCAGCCACCACGAACCGCCTTAGCCTAGCTCTTTTCGGACACCTAGAT
TACCACTCCCTCGAGCTTCACCAATGGAGGAACACCACCAAGAGGATGGAGGGAAGAAAATGATG
GAGAAGATAAAGAAATTCAAGTTGTCGGGTGTGAGTGTGCAACCAATTTT
Found at i:526158 original size:17 final size:17
Alignment explanation
Indices: 526136--526190 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
526126 GTAATAAATG
526136 AAAGAAAATTGAATTCA
1 AAAGAAAATTGAATTCA
*
526153 AAAGAAAAGTACTGAA-T-G
1 AAAGAAAA-T--TGAATTCA
*
526171 AAAGAAAATTGAGTTCA
1 AAAGAAAATTGAATTCA
526188 AAA
1 AAA
526191 TAAATAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
15 3 0.10
16 1 0.03
17 12 0.40
18 9 0.30
19 1 0.03
20 4 0.13
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.20
Consensus pattern (17 bp):
AAAGAAAATTGAATTCA
Found at i:526163 original size:35 final size:35
Alignment explanation
Indices: 526124--526190 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
526114 GGATAAAATG
526124 AAGTAATAAATGAAAGAAAATTGAATTCAAAAGAA
1 AAGTAATAAATGAAAGAAAATTGAATTCAAAAGAA
* * *
526159 AAGTACTGAATGAAAGAAAATTGAGTTCAAAA
1 AAGTAATAAATGAAAGAAAATTGAATTCAAAA
526191 TAAATAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.58, C:0.04, G:0.16, T:0.21
Consensus pattern (35 bp):
AAGTAATAAATGAAAGAAAATTGAATTCAAAAGAA
Found at i:533996 original size:595 final size:598
Alignment explanation
Indices: 532832--534032 Score: 2363
Period size: 595 Copynumber: 2.0 Consensus size: 598
532822 CATTGAATTA
532832 ATCAAAAGAAGAAAAAAAAGAGACAAAAGTTAAATTATAATACTTTAAACAAAGCAGAAAAAAAG
1 ATCAAAAGAAGAAAAAAAAGAGACAAAAGTTAAATTATAATACTTTAAACAAAGCAGAAAAAAAG
532897 AAATATATACACATGCCGAGAAATAGAATTAACATAATGGAAAATTAAAATAAATAGAAAAAAAA
66 AAATATATACACATGCCGAGAAATAGAATTAACATAATGGAAAATTAAAATAAATAGAAAAAAAA
532962 AACAAATCACACATATTTAAAACACAAAGTAATAAAAAATAATGTAAAGAAAAAGTCAATTAAAT
131 AACAAATCACACATATTTAAAACACAAAGTAATAAAAAATAATGTAAAGAAAAAGTCAATTAAAT
533027 TAAAAATAAAAAAAAATCAATTGCAAAATTAAACAAAGATAAAAATTACTAAAATAAAAATAAAA
196 TAAAAATAAAAAAAAATCAATTGCAAAATTAAACAAAGATAAAAATTACTAAAATAAAAATAAAA
533092 GAGATAATAAAAAAGAAAAATAAAAGAATGATTATTATCGAATTAATGACTCATTAAGTGTGGTA
261 GAGATAAT-AAAAAGAAAAATAAAAGAATGATTATTATCGAATTAATGACTCATTAAGTGTGGTA
533157 GTCTTTTAAATATAATTAAATAAAACATGAAATAAATAAATAAATAACCAAATTGAAAAATAAAA
325 GTCTTTTAAATATAATTAAATAAAACATGAAATAAATAAATAAATAACCAAATTGAAAAATAAAA
533222 TATAGTGAGGGTGAATTGAAAAGAAAAATCGGAATTAAAATCGAATTTAAGGTGCAAAACATGTT
390 TATAGTGAGGGTGAATTGAAAAGAAAAATCGGAATTAAAATCGAATTTAAGGTGCAAAACATGTT
533287 TTAAAAAGAAATCAGGGACCAGTTCTATATTTAGCCCTTACCCGATCAAAGACACGCGGATCCTG
455 TTAAAAAGAAATCAGGGACCAGTTCTATATTTAGCCCTTACCCGATCAAAGACACGCGGATCCTG
533352 GGGTGAATACGGTCGGGTTTCGGGTAGGCTATAAAGCCCAGAAATCACAAACTAAATTCATTTTC
520 GGGTGAATACGGTCGGGTTTCGGGTAGGCTATAAAGCCCAGAAATCACAAACTAAATTCATTTTC
533417 ACCCCTCAAAATGG
585 ACCCCTCAAAATGG
533431 ATCAAAAGAAGAAAAAAAAGAGACAAAAGTTAAATTATAATACTTTAAACAAAGCAGAAAAAAAG
1 ATCAAAAGAAGAAAAAAAAGAGACAAAAGTTAAATTATAATACTTTAAACAAAGCAGAAAAAAAG
533496 AAATATATACACATGCCGAGAAATAGAATTAACATAATGGAAAATTAAAATAAATAGAAAAAAAA
66 AAATATATACACATGCCGAGAAATAGAATTAACATAATGGAAAATTAAAATAAATAGAAAAAAAA
533561 AACAAATCACACATATTTAAAACACAAAGTAATAAAAAATAATGTAAAGAAAAAGTCAATTAAAT
131 AACAAATCACACATATTTAAAACACAAAGTAATAAAAAATAATGTAAAGAAAAAGTCAATTAAAT
533626 TAAAAATAAAAAAAAATCAATTGCAAAATTAAACAAAGATAAAAATTACTAAAATAAAAATAAAA
196 TAAAAATAAAAAAAAATCAATTGCAAAATTAAACAAAGATAAAAATTACTAAAATAAAAATAAAA
533691 GAGATAAT-AAAA-AAAAA-AAAAGAATGATTATTATCGAATTAATGACTCATTAAGTGTGGTAG
261 GAGATAATAAAAAGAAAAATAAAAGAATGATTATTATCGAATTAATGACTCATTAAGTGTGGTAG
533753 TCTTTTAAATATAATTAAATAAAACATGAAATAAATAAATAAATAACCAAATTGAAAAATAAAAT
326 TCTTTTAAATATAATTAAATAAAACATGAAATAAATAAATAAATAACCAAATTGAAAAATAAAAT
533818 ATAGTGAGGGTGAATTGAAAAGAAAAATCGGAATTAAAATCGAATTTAAGGTGCAAAACATGTTT
391 ATAGTGAGGGTGAATTGAAAAGAAAAATCGGAATTAAAATCGAATTTAAGGTGCAAAACATGTTT
*
533883 TAAAAAGAAATCAGGGACTAGTTCTATATTTAGCCCTTACCCGATCAAAGACACGCGGATCCTGG
456 TAAAAAGAAATCAGGGACCAGTTCTATATTTAGCCCTTACCCGATCAAAGACACGCGGATCCTGG
533948 GGTGAATACGGTCGGGTTTCGGGTAGGCTATAAAGCCCAGAAATCACAAACTAAATTCATTTTCA
521 GGTGAATACGGTCGGGTTTCGGGTAGGCTATAAAGCCCAGAAATCACAAACTAAATTCATTTTCA
534013 CCCCTCAAAATGG
586 CCCCTCAAAATGG
534026 ATCAAAA
1 ATCAAAA
534033 CCCCCCTTAT
Statistics
Matches: 601, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
595 324 0.54
596 5 0.01
597 4 0.01
599 268 0.45
ACGTcount: A:0.53, C:0.11, G:0.13, T:0.23
Consensus pattern (598 bp):
ATCAAAAGAAGAAAAAAAAGAGACAAAAGTTAAATTATAATACTTTAAACAAAGCAGAAAAAAAG
AAATATATACACATGCCGAGAAATAGAATTAACATAATGGAAAATTAAAATAAATAGAAAAAAAA
AACAAATCACACATATTTAAAACACAAAGTAATAAAAAATAATGTAAAGAAAAAGTCAATTAAAT
TAAAAATAAAAAAAAATCAATTGCAAAATTAAACAAAGATAAAAATTACTAAAATAAAAATAAAA
GAGATAATAAAAAGAAAAATAAAAGAATGATTATTATCGAATTAATGACTCATTAAGTGTGGTAG
TCTTTTAAATATAATTAAATAAAACATGAAATAAATAAATAAATAACCAAATTGAAAAATAAAAT
ATAGTGAGGGTGAATTGAAAAGAAAAATCGGAATTAAAATCGAATTTAAGGTGCAAAACATGTTT
TAAAAAGAAATCAGGGACCAGTTCTATATTTAGCCCTTACCCGATCAAAGACACGCGGATCCTGG
GGTGAATACGGTCGGGTTTCGGGTAGGCTATAAAGCCCAGAAATCACAAACTAAATTCATTTTCA
CCCCTCAAAATGG
Found at i:535104 original size:11 final size:11
Alignment explanation
Indices: 535090--535191 Score: 51
Period size: 13 Copynumber: 8.4 Consensus size: 11
535080 TATATTATAT
535090 ATATTTTTAAA
1 ATATTTTTAAA
*
535101 ATATTTTCAAAA
1 ATATTTT-TAAA
* *
535113 ACTATATATTATAT
1 A-TAT-TTTTA-AA
535127 ATATGTTTTCAAA
1 ATAT-TTTT-AAA
535140 ATATTTTCATAAA
1 ATATTTT--TAAA
* * *
535153 CTATATATTATAT
1 ATAT-TTTTA-AA
*
535166 ATATTTTCAAA
1 ATATTTTTAAA
535177 ATATTTTTAAA
1 ATATTTTTAAA
535188 ATAT
1 ATAT
535192 ATATATTATA
Statistics
Matches: 67, Mismatches: 15, Indels: 18
0.67 0.15 0.18
Matches are distributed among these distances:
11 22 0.33
12 12 0.18
13 25 0.37
14 8 0.12
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (11 bp):
ATATTTTTAAA
Found at i:535107 original size:37 final size:39
Alignment explanation
Indices: 535028--535280 Score: 329
Period size: 39 Copynumber: 6.6 Consensus size: 39
535018 TTAAATTTGT
* * * * *
535028 TTTTAAAAAATTATATTTTATATATATATATTCAAAACA
1 TTTTAAAAAACTATATATTATATATATGTTTTCAAAATA
*
535067 TTTTCAAAAACTATATATTATATATAT-TTTT-AAAATA
1 TTTTAAAAAACTATATATTATATATATGTTTTCAAAATA
*
535104 TTTTCAAAAACTATATATTATATATATGTTTTCAAAATA
1 TTTTAAAAAACTATATATTATATATATGTTTTCAAAATA
* *
535143 TTTTCATAAACTATATATTATATATA--TTTTCAAAATA
1 TTTTAAAAAACTATATATTATATATATGTTTTCAAAATA
* **
535180 TTTTTAAAATA-TATATATTATATATATGTTTTCAAAACG
1 -TTTTAAAAAACTATATATTATATATATGTTTTCAAAATA
*
535219 TTTTAAAAAACTATTTATTATATATATGTTTTCAAAAT-
1 TTTTAAAAAACTATATATTATATATATGTTTTCAAAATA
535257 TTTATAAAAAACTATATATTATAT
1 TTT-TAAAAAACTATATATTATAT
535281 CTTATATATA
Statistics
Matches: 192, Mismatches: 15, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
37 58 0.30
38 26 0.14
39 108 0.56
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.48
Consensus pattern (39 bp):
TTTTAAAAAACTATATATTATATATATGTTTTCAAAATA
Found at i:535128 original size:76 final size:76
Alignment explanation
Indices: 535028--535289 Score: 330
Period size: 76 Copynumber: 3.4 Consensus size: 76
535018 TTAAATTTGT
* *
535028 TTTTAAAAAATTATATTTTATATATATATATTCAAAACATTTTCAAAAACTATATATTATATATA
1 TTTTAAAAAACTATATATTATATATATATATTCAAAACATTTTCAAAAACTATATATTATATATA
535093 TTTTTAAAATA
66 TTTTTAAAATA
* * * * *
535104 TTTTCAAAAACTATATATTATATATATGTTTTCAAAATATTTTCATAAACTATATATTATATATA
1 TTTTAAAAAACTATATATTATATATATATATTCAAAACATTTTCAAAAACTATATATTATATATA
*
535169 TTTTCAAAATA
66 TTTTTAAAATA
* * * * * *
535180 TTTTTAAAATA-TATATATTATATATATGTTTTCAAAACGTTTTAAAAAACTATTTATTATATAT
1 -TTTTAAAAAACTATATATTATATATATATATTCAAAACATTTTCAAAAACTATATATTATATAT
535244 ATGTTTTCAAAAT-
65 AT-TTTT-AAAATA
*
535257 TTTATAAAAAACTATATATTATATCTTATATAT
1 TTT-TAAAAAACTATATATTATAT-ATATATAT
535290 ATTAAATAAA
Statistics
Matches: 160, Mismatches: 20, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
76 121 0.76
77 17 0.11
78 17 0.11
79 5 0.03
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (76 bp):
TTTTAAAAAACTATATATTATATATATATATTCAAAACATTTTCAAAAACTATATATTATATATA
TTTTTAAAATA
Found at i:535510 original size:31 final size:31
Alignment explanation
Indices: 535465--535563 Score: 144
Period size: 31 Copynumber: 3.2 Consensus size: 31
535455 GTTAAAAATT
535465 TAGGTACTAAAATGAAACAAAAAGTAAACAC
1 TAGGTACTAAAATGAAACAAAAAGTAAACAC
* * *
535496 TATGTATTAAAATGAAACGAAAAGTAAACAC
1 TAGGTACTAAAATGAAACAAAAAGTAAACAC
* * *
535527 TAGGTACTAAAATGAAATAAAAAGTAAATAT
1 TAGGTACTAAAATGAAACAAAAAGTAAACAC
535558 TAGGTA
1 TAGGTA
535564 TGATTTTGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.56, C:0.08, G:0.14, T:0.22
Consensus pattern (31 bp):
TAGGTACTAAAATGAAACAAAAAGTAAACAC
Found at i:543705 original size:23 final size:23
Alignment explanation
Indices: 543679--543724 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
543669 AGCTAATAGT
543679 TGATATGGGTAAAATGACAAATA
1 TGATATGGGTAAAATGACAAATA
543702 TGATATGGGTAAAATGACAAATA
1 TGATATGGGTAAAATGACAAATA
543725 AGAGAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (23 bp):
TGATATGGGTAAAATGACAAATA
Found at i:545699 original size:21 final size:21
Alignment explanation
Indices: 545673--545837 Score: 152
Period size: 21 Copynumber: 7.7 Consensus size: 21
545663 GATTCTACGC
545673 GGTCCTTCGGGACATATATGT
1 GGTCCTTCGGGACATATATGT
* * * *
545694 GGTCCTTTGGAATATATATGC
1 GGTCCTTCGGGACATATATGT
*
545715 GGTCCTTCGGGACATATATTT
1 GGTCCTTCGGGACATATATGT
* * *
545736 GGTCCTTTGGAACATTTATGT
1 GGTCCTTCGGGACATATATGT
* * *
545757 GGTCCTACGGGACAACTCTACGT
1 GGTCCTTCGGGAC-A-TATATGT
* * *
545780 GGTCCTTCGGGACATTTCTTT
1 GGTCCTTCGGGACATATATGT
545801 ACGGTCCTTCGGGACA-ATATGT
1 --GGTCCTTCGGGACATATATGT
*
545823 GGTCCTTCGAGACAT
1 GGTCCTTCGGGACAT
545838 TCTATGTGAC
Statistics
Matches: 112, Mismatches: 27, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
20 13 0.12
21 63 0.56
22 5 0.04
23 31 0.28
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.34
Consensus pattern (21 bp):
GGTCCTTCGGGACATATATGT
Found at i:550842 original size:19 final size:19
Alignment explanation
Indices: 550818--550862 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
550808 GTTTGGTTTG
550818 GGGAATGTGAGATTCCCAT
1 GGGAATGTGAGATTCCCAT
550837 GGGAATGTGAGATTCCCAT
1 GGGAATGTGAGATTCCCAT
550856 GGGAATG
1 GGGAATG
550863 GAATCCACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.27, C:0.13, G:0.36, T:0.24
Consensus pattern (19 bp):
GGGAATGTGAGATTCCCAT
Found at i:551488 original size:2 final size:2
Alignment explanation
Indices: 551481--551526 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
551471 CTAAGGGTAA
551481 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
551523 -T AT A
1 AT AT A
551527 GTTTATTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:555201 original size:3 final size:3
Alignment explanation
Indices: 555195--555220 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
555185 TTATTATTAT
555195 TAG TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TAG TA
555221 TTAAAATTAT
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:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:556801 original size:24 final size:27
Alignment explanation
Indices: 556749--556803 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 27
556739 GATGATTTGT
556749 TTGTTTATATTTTAATCATATTTGCATG
1 TTGTTTATATTTTAAT-ATATTTGCATG
556777 TTGTTT-TATTTTAAT-T-TTTGCATG
1 TTGTTTATATTTTAATATATTTGCATG
556801 TTG
1 TTG
556804 CTTGGATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 11 0.41
25 1 0.04
27 9 0.33
28 6 0.22
ACGTcount: A:0.20, C:0.05, G:0.13, T:0.62
Consensus pattern (27 bp):
TTGTTTATATTTTAATATATTTGCATG
Found at i:556819 original size:24 final size:24
Alignment explanation
Indices: 556769--556820 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
556759 TTTAATCATA
** *
556769 TTTGCATGTTGTTTTATTTTAATT
1 TTTGCATGTTGTTGGATGTTAATT
556793 TTTGCATGTTGCTTGGATGTTAATT
1 TTTGCATGTTG-TTGGATGTTAATT
556818 TTT
1 TTT
556821 TTTCATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.15, C:0.06, G:0.17, T:0.62
Consensus pattern (24 bp):
TTTGCATGTTGTTGGATGTTAATT
Found at i:557492 original size:131 final size:131
Alignment explanation
Indices: 557253--557617 Score: 507
Period size: 131 Copynumber: 2.8 Consensus size: 131
557243 TCAATATTGA
* * * *
557253 AAATAGTAATATCTTTTCATTTCGGTTGGAGTAATTAATGAATGCTTTAAGGCATGAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
* * * * * *
557318 TCATTCTCGATT-GAAAACAATTAGATATTATCGTTTTCTCTCGATTCATTATTGATTTTTAAGA
66 TTATTCTCGATTGGAAATC-ATTAGATATTATCGTTTTCGCTCGAATCAATATTGAATTTTAAGA
557382 CG
130 CG
* * * * *
557384 GAATAGTGATATCTCTTCGTTTCGATTGAAGTGATAAATGATTGCTTTAAGGCATGAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
*
557449 TTATTCTCGATTGGAAATCATTAGATATTATCATTTTCGCTCGAATCAATATTGAATTTTAAGAC
66 TTATTCTCGATTGGAAATCATTAGATATTATCGTTTTCGCTCGAATCAATATTGAATTTTAAGAC
557514 G
131 G
* * * * *
557515 AAATAGTGATATCTCTTCATTTTGATTGGAGTAATAAATGACTACTTTAAAGCGTGAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
* *
557580 TTATTCTCGATTGGAAATAATTAGACATTATCGTTTTC
66 TTATTCTCGATTGGAAATCATTAGATATTATCGTTTTC
557618 TCTCTTAAAA
Statistics
Matches: 205, Mismatches: 28, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
131 200 0.98
132 5 0.02
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (131 bp):
AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
TTATTCTCGATTGGAAATCATTAGATATTATCGTTTTCGCTCGAATCAATATTGAATTTTAAGAC
G
Found at i:567689 original size:9 final size:8
Alignment explanation
Indices: 567656--567705 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
567646 ATAAAGAAAT
567656 AAAATGAA
1 AAAATGAA
567664 AAAATGAA
1 AAAATGAA
567672 AAAA-GAA
1 AAAATGAA
567679 AATGAAT-AA
1 AA--AATGAA
*
567688 AAAAAGAGA
1 AAAATGA-A
567697 AAAATGAA
1 AAAATGAA
567705 A
1 A
567706 GAGAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
7 7 0.20
8 15 0.43
9 13 0.37
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (8 bp):
AAAATGAA
Found at i:567691 original size:26 final size:25
Alignment explanation
Indices: 567648--567721 Score: 69
Period size: 26 Copynumber: 2.9 Consensus size: 25
567638 TACTTCGCAT
* * * *
567648 AAAGAAATAAAATGAAAAAATGAAA
1 AAAGAAAGAGAATAAAAAAAAGAAA
567673 AAAGAAA-ATGAATAAAAAAAGAGAAA
1 AAAGAAAGA-GAATAAAAAAA-AGAAA
*
567699 AATGAAAGAGAATAAATAAAAAG
1 AAAGAAAGAGAATAAA-AAAAAG
567722 GGATTCAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 1 0.02
25 16 0.39
26 19 0.46
27 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (25 bp):
AAAGAAAGAGAATAAAAAAAAGAAA
Found at i:569228 original size:133 final size:133
Alignment explanation
Indices: 568923--569391 Score: 634
Period size: 133 Copynumber: 3.5 Consensus size: 133
568913 GCAAATCGAA
* * * *
568923 CTCGATTCAATCTTCCCTGAGGAACAGTGGAATGAATCAATGTCTCCAGATCTGATTTTCCCTGA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAACGAATCAACGTCTCCAGATCTGATTTTACCTGA
* ** * * * * * * *
568988 AGAAGCAACGAAATAGATCCCGCTCTTTCCATATTTGATATTCCCTGAGTAGTAGTGGAACAAGT
66 AGAAACAGTGGAACAGATCCC-CTCTTTCCAGATTTAATCTTCCCTGAGTAGCAGTGAAACAAGT
569053 CTGC
130 CTGC
* * * * **
569057 CTTGATTTAATCTTCCCTGAAGAATATTGGAATAAATCAACGTCTCCAGATCTGATTTTACCTGA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAACGAATCAACGTCTCCAGATCTGATTTTACCTGA
* *
569122 AGAAACAGTGGAACAGATCCCCTCTTTCCAGATTTAATCTTCCTTGAGTAGCAGTGAAACAAATC
66 AGAAACAGTGGAACAGATCCCCTCTTTCCAGATTTAATCTTCCCTGAGTAGCAGTGAAACAAGTC
569187 TGC
131 TGC
* * *
569190 CACGATTCAATTTTCCCTGAAGAACAGTGGAACGAATCAACGTCTCCAGATCTGATTTTACCTAA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAACGAATCAACGTCTCCAGATCTGATTTTACCTGA
* * *
569255 AGAAATAGTGGAACAAATCCCCTCTTTCCAGATTTAATCTTCCCTGAGTAGCAGTGAAATAAGTC
66 AGAAACAGTGGAACAGATCCCCTCTTTCCAGATTTAATCTTCCCTGAGTAGCAGTGAAACAAGTC
569320 TGC
131 TGC
* * *
569323 CTCGATTCAATTTTCCCTGAAGAACAGTGGAACGAATCAACGTTTCCAGATCTGA-TCTACCCTG
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAACGAATCAACGTCTCCAGATCTGATTTTA-CCTG
569387 AAGAA
65 AAGAA
569392 GTAGTTGAGA
Statistics
Matches: 296, Mismatches: 38, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
132 3 0.01
133 220 0.74
134 73 0.25
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (133 bp):
CTCGATTCAATCTTCCCTGAAGAACAGTGGAACGAATCAACGTCTCCAGATCTGATTTTACCTGA
AGAAACAGTGGAACAGATCCCCTCTTTCCAGATTTAATCTTCCCTGAGTAGCAGTGAAACAAGTC
TGC
Found at i:569896 original size:36 final size:35
Alignment explanation
Indices: 569815--569899 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 35
569805 CAGTAGCCGT
569815 CGTCGCT-TACCAACCACAACAGTCCTACTACCAC
1 CGTCGCTCTACCAACCACAACAGTCCTACTACCAC
* *** * *
569849 CATTATTTCTACCAACCACAACAGTCCTGCTGCCAC
1 C-GTCGCTCTACCAACCACAACAGTCCTACTACCAC
569885 CGTCGCATCTACCAA
1 CGTCGC-TCTACCAA
569900 TCACCCATCA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
34 1 0.03
35 3 0.08
36 34 0.89
ACGTcount: A:0.28, C:0.41, G:0.09, T:0.21
Consensus pattern (35 bp):
CGTCGCTCTACCAACCACAACAGTCCTACTACCAC
Found at i:570844 original size:106 final size:108
Alignment explanation
Indices: 570613--570831 Score: 245
Period size: 106 Copynumber: 2.0 Consensus size: 108
570603 TTACAAAATG
* * * * *
570613 GTCACATGTAAGGACTGAATCTACTA-TTTACCTATTTTTATGCATGCTTTATAATTTTAGGGTT
1 GTCACCTGTAGGGATTGATTCTAC-AGTTTACCCATTTTTATGCAT-CTTTATAATTTTAGGGTT
* **
570677 ATTTATTGTTTAGTCCCCTTAGTTTAGTCGTATTTTTGTATTTTA
64 ATTTATTGTTTAGTCCCCTTAGTTTAGTCATATTTTTACATTTTA
570722 GTCACCTGTAGGGATTGATTCTACAGTTTACCCATTTTTATGCA--TTTAT-ATATTTAGGGTTA
1 GTCACCTGTAGGGATTGATTCTACAGTTTACCCATTTTTATGCATCTTTATAAT-TTTAGGGTTA
* *
570784 TTTACTT-TTTAGT-CCCTCTATGTTTAG-CATGTTTTTACATTTTG
65 TTTA-TTGTTTAGTCCCCT-TA-GTTTAGTCATATTTTTACATTTTA
570828 GTCA
1 GTCA
570832 TGTGTAGTGA
Statistics
Matches: 95, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
105 6 0.06
106 43 0.45
107 8 0.08
108 1 0.01
109 37 0.39
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (108 bp):
GTCACCTGTAGGGATTGATTCTACAGTTTACCCATTTTTATGCATCTTTATAATTTTAGGGTTAT
TTATTGTTTAGTCCCCTTAGTTTAGTCATATTTTTACATTTTA
Found at i:571942 original size:108 final size:108
Alignment explanation
Indices: 571748--571960 Score: 338
Period size: 108 Copynumber: 2.0 Consensus size: 108
571738 TTTCTCTCGT
* * * * *
571748 ATCATTATTGATTTTTAAGATAGAATAGTGATATATCTTCATTTTGATTGGAGTGATAAATGACT
1 ATCAATATTGAATTTTAAGAGAGAATAGTGATATATCTTCATTTCGATTGGAGTAATAAATGACT
*
571813 GCCTTAAGGCATGAGATGTCATTTATTCTCGATTGGAAATCGA
66 GCCTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATCGA
*
571856 ATCAATATTGAATTTTAAGACGA-AATAGTGATATATCTTCATTTCGATTGGAGTAATAAATGAT
1 ATCAATATTGAATTTTAAGA-GAGAATAGTGATATATCTTCATTTCGATTGGAGTAATAAATGAC
*
571920 TGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAAT
65 TGCCTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAAT
571961 AATTAGATAT
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
108 95 0.99
109 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (108 bp):
ATCAATATTGAATTTTAAGAGAGAATAGTGATATATCTTCATTTCGATTGGAGTAATAAATGACT
GCCTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATCGA
Found at i:575687 original size:13 final size:13
Alignment explanation
Indices: 575669--575703 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
575659 AACTGCAAAA
*
575669 AAATAAAATATTT
1 AAATAAAATAATT
575682 AAATAAAATAATT
1 AAATAAAATAATT
575695 AAA-AAAATA
1 AAATAAAATA
575704 CAATAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:575701 original size:30 final size:30
Alignment explanation
Indices: 575665--575721 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
575655 TTATAACTGC
*
575665 AAAAAAATAAAATATTTAAATAAAATAATT
1 AAAAAAATAAAATAATTAAATAAAATAATT
*
575695 AAAAAAATACAATAATTAAATAAAATA
1 AAAAAAATAAAATAATTAAATAAAATA
575722 CTAACAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (30 bp):
AAAAAAATAAAATAATTAAATAAAATAATT
Found at i:575708 original size:17 final size:18
Alignment explanation
Indices: 575682--575722 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
575672 TAAAATATTT
*
575682 AAATAAAATAATTAAA-A
1 AAATACAATAATTAAATA
575699 AAATACAATAATTAAATA
1 AAATACAATAATTAAATA
575717 AAATAC
1 AAATAC
575723 TAACAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATACAATAATTAAATA
Found at i:575811 original size:16 final size:16
Alignment explanation
Indices: 575792--575846 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
575782 TCTAAATAAT
575792 AAAATAAAATACTAAC
1 AAAATAAAATACTAAC
*
575808 AAAATATTAAATA-TAAT
1 AAAATA--AAATACTAAC
575825 AAAATAAAATACTAAC
1 AAAATAAAATACTAAC
575841 AAAATA
1 AAAATA
575847 TTAAATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 5 0.15
16 15 0.44
17 9 0.26
18 5 0.15
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATAAAATACTAAC
Found at i:575826 original size:33 final size:33
Alignment explanation
Indices: 575787--575863 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
575777 AAATATCTAA
575787 ATAATAAAATAAAATACTAACAAAATATTAAAT
1 ATAATAAAATAAAATACTAACAAAATATTAAAT
575820 ATAATAAAATAAAATACTAACAAAATATTAAAT
1 ATAATAAAATAAAATACTAACAAAATATTAAAT
575853 ATAATAAAATA
1 ATAATAAAATA
575864 TACCTTATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (33 bp):
ATAATAAAATAAAATACTAACAAAATATTAAAT
Found at i:575847 original size:114 final size:109
Alignment explanation
Indices: 575632--575856 Score: 292
Period size: 114 Copynumber: 2.0 Consensus size: 109
575622 TTTTCATCCA
* * *
575632 AACGAAGCAGACAACTTTCTATTTTATAACTGCAAAAAAATAAAATATTTAAATAAAATAATTAA
1 AACGAAGCAGACAACTTTCTATTTTATAACTGCAAAAAAATAAAATAATAAAATAAAATAACTAA
* *
575697 AAAAATACAATAATTAAATAAAATACTAACAAAATATTAAATAT
66 AAAAATAAAATAATAAAATAAAATACTAACAAAATATTAAATAT
* ** *
575741 AACGTAGCAGACTGCTTTC-ATTTTATAACTGTAAAAAAATATCTAAATAATAAAATAAAAT-AC
1 AACGAAGCAGACAACTTTCTATTTTATAACTGCAAAAAAATA---AAATAATAAAATAAAATAAC
575804 TAACAAAATATTAAATATAATAAAATAAAATACTAACAAAATATTAAATAT
63 TAA-AAAA-A-TAAA-ATAATAAAATAAAATACTAACAAAATATTAAATAT
575855 AA
1 AA
575857 TAAAATATAC
Statistics
Matches: 100, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
108 21 0.21
109 16 0.16
110 4 0.04
111 19 0.19
112 1 0.01
113 3 0.03
114 36 0.36
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.29
Consensus pattern (109 bp):
AACGAAGCAGACAACTTTCTATTTTATAACTGCAAAAAAATAAAATAATAAAATAAAATAACTAA
AAAAATAAAATAATAAAATAAAATACTAACAAAATATTAAATAT
Found at i:576989 original size:13 final size:13
Alignment explanation
Indices: 576971--576997 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
576961 CATAGTTGAA
576971 CAGTCTTCATATG
1 CAGTCTTCATATG
576984 CAGTCTTCATATG
1 CAGTCTTCATATG
576997 C
1 C
576998 GCGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:585405 original size:174 final size:174
Alignment explanation
Indices: 585115--585462 Score: 696
Period size: 174 Copynumber: 2.0 Consensus size: 174
585105 TCCGACGGAT
585115 TTAAAAATATTTGTAAATTAAATATATATATAAATATTAATAATGTAAAATTTTTATATGGCGTA
1 TTAAAAATATTTGTAAATTAAATATATATATAAATATTAATAATGTAAAATTTTTATATGGCGTA
585180 TATATATATAAAATTATAGATTATACGAGATCAATAAAATAAGTAATGATATAAAAAAATTTAAA
66 TATATATATAAAATTATAGATTATACGAGATCAATAAAATAAGTAATGATATAAAAAAATTTAAA
585245 TTCAAAAGTGGAAACTTGCACATCCTGAAAACAAGCTACATCCA
131 TTCAAAAGTGGAAACTTGCACATCCTGAAAACAAGCTACATCCA
585289 TTAAAAATATTTGTAAATTAAATATATATATAAATATTAATAATGTAAAATTTTTATATGGCGTA
1 TTAAAAATATTTGTAAATTAAATATATATATAAATATTAATAATGTAAAATTTTTATATGGCGTA
585354 TATATATATAAAATTATAGATTATACGAGATCAATAAAATAAGTAATGATATAAAAAAATTTAAA
66 TATATATATAAAATTATAGATTATACGAGATCAATAAAATAAGTAATGATATAAAAAAATTTAAA
585419 TTCAAAAGTGGAAACTTGCACATCCTGAAAACAAGCTACATCCA
131 TTCAAAAGTGGAAACTTGCACATCCTGAAAACAAGCTACATCCA
585463 CTGGACTTGA
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 174 1.00
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.33
Consensus pattern (174 bp):
TTAAAAATATTTGTAAATTAAATATATATATAAATATTAATAATGTAAAATTTTTATATGGCGTA
TATATATATAAAATTATAGATTATACGAGATCAATAAAATAAGTAATGATATAAAAAAATTTAAA
TTCAAAAGTGGAAACTTGCACATCCTGAAAACAAGCTACATCCA
Found at i:585514 original size:19 final size:20
Alignment explanation
Indices: 585492--585537 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
585482 AATAATATTT
*
585492 TTTATTTTTTATAAATA-TA
1 TTTATTTTTTAAAAATAGTA
*
585511 TTTA-ATTTTAAAAATAGTA
1 TTTATTTTTTAAAAATAGTA
585530 TTT-TTTTT
1 TTTATTTTT
585538 CATATATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTATTTTTTAAAAATAGTA
Found at i:587112 original size:131 final size:130
Alignment explanation
Indices: 586948--587317 Score: 483
Period size: 131 Copynumber: 2.8 Consensus size: 130
586938 ATAATTTTAA
* *
586948 GAGAGCAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATAATCTCTCATGCCTTAAAAT
1 GAGAG-AAAACGATAATATCTAATTATTTCCAATCGAGAATAAATAATCTCTCATGCCTTAAAAC
* * *
587013 AGTCATTTATTACTATAATCGAAATGAAGAGATATTACTATTTCGTCTTAAAATTTAATATCGAT
65 AGTCATTTATTACT-TAATCGAAATGAAGAGATATTACTATTCCGTCTTAAAAATCAATATCGAT
587078 TC
129 TC
* * * *
587080 GAGTGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATTATCTGTCATACCTTAAAACA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATAATCTCTCATGCCTTAAAACA
* * * * *
587145 ATCATTTATTGCTTCAATCGAACTGAAGAGATATCA-TCATTCCGTCTTAAAAATCAATATTGAT
66 GTCATTTATTACTT-AATCGAAATGAAGAGATATTACT-ATTCCGTCTTAAAAATCAATATCGAT
587209 TC
129 TC
* ** * *
587211 GAGAGAAAACGGTAATATAGAATTATTTCCAATCGAGAATAAATGATCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATAATCTCTCATGCCTTAAAACA
* *
587276 GTCATTTATTACTCCAA-CTGAAATGAAAAGATATTACTATTC
66 GTCATTTATTACT-TAATC-GAAATGAAGAGATATTACTATTC
587318 TCAATATGGA
Statistics
Matches: 205, Mismatches: 28, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
130 3 0.01
131 197 0.96
132 5 0.02
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (130 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATAATCTCTCATGCCTTAAAACA
GTCATTTATTACTTAATCGAAATGAAGAGATATTACTATTCCGTCTTAAAAATCAATATCGATTC
Found at i:590511 original size:16 final size:16
Alignment explanation
Indices: 590487--590532 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
590477 AAATTAAATA
*
590487 TTAATATAATTATATTTT
1 TTAATA-AA-TATAATTT
590505 TTAATAAATATAATTT
1 TTAATAAATATAATTT
590521 TT-A-AAATATAAT
1 TTAATAAATATAAT
590533 ATAATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 9 0.33
17 2 0.07
18 6 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATAAATATAATTT
Found at i:590553 original size:15 final size:16
Alignment explanation
Indices: 590521--590559 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
590511 AATATAATTT
*
590521 TTAAAATATAATATAA
1 TTAAAATATAATAAAA
590537 TTAAAATA-AATAAAA
1 TTAAAATATAATAAAA
590552 TTAAAATA
1 TTAAAATA
590560 GAGAATGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAAATATAATAAAA
Found at i:598062 original size:22 final size:22
Alignment explanation
Indices: 598037--598119 Score: 159
Period size: 22 Copynumber: 3.8 Consensus size: 22
598027 CCCACCGTTA
598037 TATTTTTTAATAATAAAAATAT
1 TATTTTTTAATAATAAAAATAT
598059 TATTTTTTAATAATAAAAATAT
1 TATTTTTTAATAATAAAAATAT
598081 TATTTTTTAATAATAAAAATAT
1 TATTTTTTAATAATAAAAATAT
598103 TATTTTTTAATAA-AAAA
1 TATTTTTTAATAATAAAA
598120 GAAAAAACTT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 4 0.07
22 57 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTTTTAATAATAAAAATAT
Found at i:600174 original size:19 final size:18
Alignment explanation
Indices: 600142--600191 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
600132 TCAAACCATC
600142 AATTAAA-A-ATATAAAA
1 AATTAAATATATATAAAA
600158 ATATCTAAAT-TATATAAAA
1 A-AT-TAAATATATATAAAA
600177 AATTAAATATATATA
1 AATTAAATATATATA
600192 GAACTTAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 1 0.03
17 7 0.24
18 12 0.41
19 9 0.31
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
AATTAAATATATATAAAA
Found at i:602642 original size:14 final size:14
Alignment explanation
Indices: 602618--602696 Score: 87
Period size: 14 Copynumber: 5.9 Consensus size: 14
602608 TCTGTAATAT
*
602618 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
602632 -TTCCATTTATGTTC
1 GTT-CATTTATGTTC
602646 GTTCATTTA---T-
1 GTTCATTTATGTTC
602656 GTTCATTTATGTTC
1 GTTCATTTATGTTC
* *
602670 GTTCGTTTATGTGC
1 GTTCATTTATGTTC
602684 GTTCATTTATGTT
1 GTTCATTTATGTT
602697 TAGCCCAATC
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
10 9 0.17
11 1 0.02
13 3 0.06
14 39 0.72
15 2 0.04
ACGTcount: A:0.13, C:0.14, G:0.16, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:602645 original size:24 final size:24
Alignment explanation
Indices: 602615--602681 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
602605 CGTTCTGTAA
* *
602615 TATGTTCGTTTATGTTCT-TCCATT
1 TATGTTCGTTCAT-TTATGTCCATT
*
602639 TATGTTCGTTCATTTATGTTCATT
1 TATGTTCGTTCATTTATGTCCATT
*
602663 TATGTTCGTTCGTTTATGT
1 TATGTTCGTTCATTTATGT
602682 GCGTTCATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 3 0.08
24 35 0.92
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.58
Consensus pattern (24 bp):
TATGTTCGTTCATTTATGTCCATT
Found at i:602658 original size:28 final size:26
Alignment explanation
Indices: 602618--602696 Score: 99
Period size: 28 Copynumber: 3.0 Consensus size: 26
602608 TCTGTAATAT
602618 GTTCGTTTATGTTCTTCCATTTATGTTC
1 GTTCGTTTATG-TCTT-CATTTATGTTC
*
602646 GTTCATTTATG--TTCATTTATGTTC
1 GTTCGTTTATGTCTTCATTTATGTTC
602670 GTTCGTTTATGTGCGTTCATTTATGTT
1 GTTCGTTTATGT-C-TTCATTTATGTT
602697 TAGCCCAATC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
24 21 0.47
25 2 0.04
28 22 0.49
ACGTcount: A:0.13, C:0.14, G:0.16, T:0.57
Consensus pattern (26 bp):
GTTCGTTTATGTCTTCATTTATGTTC
Found at i:602658 original size:38 final size:38
Alignment explanation
Indices: 602615--602696 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
602605 CGTTCTGTAA
* *
602615 TATGTTCGTTTATGTTC-TTCCATTTATGTTCGTTCATT
1 TATGTTCATTTATGTTCGTT-CATTTATGTGCGTTCATT
*
602653 TATGTTCATTTATGTTCGTTCGTTTATGTGCGTTCATT
1 TATGTTCATTTATGTTCGTTCATTTATGTGCGTTCATT
602691 TATGTT
1 TATGTT
602697 TAGCCCAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 38 0.95
39 2 0.05
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.57
Consensus pattern (38 bp):
TATGTTCATTTATGTTCGTTCATTTATGTGCGTTCATT
Found at i:603502 original size:24 final size:24
Alignment explanation
Indices: 603469--603515 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
603459 TTTATTAGTT
*
603469 TAATTTAATATATAAAATTATTAA
1 TAATTAAATATATAAAATTATTAA
* *
603493 TAATTAAATATGTAATATTATTA
1 TAATTAAATATATAAAATTATTA
603516 TATATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TAATTAAATATATAAAATTATTAA
Found at i:604577 original size:24 final size:24
Alignment explanation
Indices: 604527--604578 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
604517 TATACTAATA
* *
604527 AAATTATTATATAAATTAAAATGT
1 AAATTATTAAATAAATTAAAATCT
*
604551 AAATTATTAAATATATTAAGAA-CT
1 AAATTATTAAATAAATTAA-AATCT
604575 AAAT
1 AAAT
604579 ATGGTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATTATTAAATAAATTAAAATCT
Found at i:605171 original size:22 final size:22
Alignment explanation
Indices: 605146--605192 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
605136 TTCTCTCTAT
* * *
605146 TTTCTATGTTGGTTGGTTGTTG
1 TTTCTATATTGCTTGGTTGCTG
*
605168 TTTCTCTATTGCTTGGTTGCTG
1 TTTCTATATTGCTTGGTTGCTG
605190 TTT
1 TTT
605193 TCTTGCTCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.04, C:0.11, G:0.26, T:0.60
Consensus pattern (22 bp):
TTTCTATATTGCTTGGTTGCTG
Found at i:608141 original size:3 final size:3
Alignment explanation
Indices: 608133--608158 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
608123 CCAAGGTTTC
608133 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
608159 AATGTTAAGA
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:616703 original size:6 final size:6
Alignment explanation
Indices: 616692--616716 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
616682 GGAAAAACAT
616692 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
616717 TATACAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:617477 original size:19 final size:18
Alignment explanation
Indices: 617454--617498 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
617444 ATAATTCAAA
617454 ATAATATTAAATTACTAT
1 ATAATATTAAATTACTAT
*
617472 ACTAATA--AAATTATTAT
1 A-TAATATTAAATTACTAT
617489 ATAA-ATTAAA
1 ATAATATTAAA
617499 ATGTAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
15 1 0.04
16 3 0.13
17 13 0.57
18 1 0.04
19 5 0.22
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATATTAAATTACTAT
Found at i:617553 original size:2 final size:2
Alignment explanation
Indices: 617546--617571 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
617536 ATTTATCCTA
617546 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
617572 GCAGTAATGA
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:618128 original size:22 final size:22
Alignment explanation
Indices: 618088--618130 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
618078 TCTTCTTCTC
* *
618088 TATTTCTCTGTTGGATGGTTGT
1 TATTTCTCTATTGCATGGTTGT
*
618110 TATTTCTCTATTGCTTGGTTG
1 TATTTCTCTATTGCATGGTTG
618131 CTGTTTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.09, C:0.12, G:0.23, T:0.56
Consensus pattern (22 bp):
TATTTCTCTATTGCATGGTTGT
Found at i:620648 original size:170 final size:170
Alignment explanation
Indices: 620216--620697 Score: 441
Period size: 170 Copynumber: 2.8 Consensus size: 170
620206 TAGAAAATAG
* * * * * * * ** *
620216 ATGATGTTCCTATTCGAGCAACTATTTATGTCAATACCTCCTATGTCT-AATGGAATGGGGA-AT
1 ATGATGTTCCCATTTGGGGAACTATTCATGTCAAAACCTCCTATGCCTAAATGG-AT-AAGACAC
* * * * * *
620279 TATGACATGGCAGAGTTTCCCTACGAAAGGTGAAAGTGCTTCTTATGAGAAGAGCCTTCCCTTTT
64 TATGACATGACAGAGATTCCCTACAAAAGGTGAAAGCGCTTCATACGAGAAGAGCCTTCCCTTTT
* *
620344 TTGTCAGAGATTCTCTGCATTTTCAGTCAACTATATGCATAG
129 TTGTCAGAGATTCTCTGCATTTTCAGTCAACTATATGCACAA
* * * * * *
620386 ATGATTTTCTCATTTGGGGAACTATTCATGTCAACATCTCCTATGTCTAAATGGATGAGACACTA
1 ATGATGTTCCCATTTGGGGAACTATTCATGTCAAAACCTCCTATGCCTAAATGGATAAGACACTA
* * * * * * *
620451 TGACATGACATAAATTACTTACAAAAGGTGAAAGCGCTTCATGCGAGAATAGTCTTCCTCTTTTT
66 TGACATGACAGAGATTCCCTACAAAAGGTGAAAGCGCTTCATACGAGAAGAGCCTTCC-CTTTTT
* * *
620516 T-TTAGAGATTCTCTGTATTTTCAGTCAATTATATGCACAA
130 TGTCAGAGATTCTCTGCATTTTCAGTCAACTATATGCACAA
* * *
620556 ATGATGTTCCCATTTGGGTAACTATTCATGTCAAAACCTTCTATGCCT-GATGGGATAAGACACT
1 ATGATGTTCCCATTTGGGGAACTATTCATGTCAAAACCTCCTATGCCTAAAT-GGATAAGACACT
*** * * ** * * ** *
620620 ATGACATTTTAGAGATTCCCTGCAAAAGGTAAAAATGTTTCTTGTGAGAAGAACCTTCCCTTTTA
65 ATGACATGACAGAGATTCCCTACAAAAGGTGAAAGCGCTTCATACGAGAAGAGCCTTCCCTTTT-
*
620685 TTGTCAAAGATTC
129 TTGTCAGAGATTC
620698 CTTACAAAAG
Statistics
Matches: 249, Mismatches: 57, Indels: 11
0.79 0.18 0.03
Matches are distributed among these distances:
169 10 0.04
170 219 0.88
171 20 0.08
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (170 bp):
ATGATGTTCCCATTTGGGGAACTATTCATGTCAAAACCTCCTATGCCTAAATGGATAAGACACTA
TGACATGACAGAGATTCCCTACAAAAGGTGAAAGCGCTTCATACGAGAAGAGCCTTCCCTTTTTT
GTCAGAGATTCTCTGCATTTTCAGTCAACTATATGCACAA
Found at i:620725 original size:60 final size:60
Alignment explanation
Indices: 620632--620746 Score: 176
Period size: 60 Copynumber: 1.9 Consensus size: 60
620622 GACATTTTAG
*
620632 AGATTCCCTGCAAAAGGTAAAAATGTTTCTTGTGAGAAGAACCTTCCCTTTTATTGTCAA
1 AGATTCCCTACAAAAGGTAAAAATGTTTCTTGTGAGAAGAACCTTCCCTTTTATTGTCAA
* * * * *
620692 AGATTCCTTACAAAAGGTGAAAGTGTTTCTTGTGAGAAGAGCTTTCCCTTTTATT
1 AGATTCCCTACAAAAGGTAAAAATGTTTCTTGTGAGAAGAACCTTCCCTTTTATT
620747 ATTAGATATT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36
Consensus pattern (60 bp):
AGATTCCCTACAAAAGGTAAAAATGTTTCTTGTGAGAAGAACCTTCCCTTTTATTGTCAA
Found at i:621970 original size:15 final size:16
Alignment explanation
Indices: 621950--621982 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
621940 TATATAATAT
621950 AAAAATAAAA-TATAA
1 AAAAATAAAATTATAA
621965 AAAAATAAAATTATAA
1 AAAAATAAAATTATAA
621981 AA
1 AA
621983 TTACAACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATAAAATTATAA
Found at i:625087 original size:14 final size:14
Alignment explanation
Indices: 625068--625102 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
625058 AAATTACATG
625068 CTTACTCATTGAAC
1 CTTACTCATTGAAC
*
625082 CTTACTTATTGAAC
1 CTTACTCATTGAAC
*
625096 TTTACTC
1 CTTACTC
625103 TTTCTCCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (14 bp):
CTTACTCATTGAAC
Found at i:626846 original size:21 final size:20
Alignment explanation
Indices: 626820--626858 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
626810 CTTTAATTAG
626820 CTAAGG-AAGTGGGAGAAAGTT
1 CTAAGGCAA-TGGG-GAAAGTT
626841 CTAAGGCAATGGGGAAAG
1 CTAAGGCAATGGGGAAAG
626859 AAAAGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 10 0.59
22 2 0.12
ACGTcount: A:0.38, C:0.08, G:0.38, T:0.15
Consensus pattern (20 bp):
CTAAGGCAATGGGGAAAGTT
Found at i:629369 original size:22 final size:22
Alignment explanation
Indices: 629328--629381 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
629318 TATCAGTGTA
*
629328 AATGCACTTTTGATTCAGTGCG
1 AATGCACTTTAGATTCAGTGCG
*
629350 AATGCACTTTAGTATT-AGTGCT
1 AATGCACTTTAG-ATTCAGTGCG
*
629372 AAGGCACTTT
1 AATGCACTTT
629382 CGTTATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 25 0.89
23 3 0.11
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (22 bp):
AATGCACTTTAGATTCAGTGCG
Found at i:645696 original size:29 final size:30
Alignment explanation
Indices: 645634--645698 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
645624 CTAAGAAAAT
645634 AGACTTGACTCGAACTCAATTTTTTTTAAA
1 AGACTTGACTCGAACTCAATTTTTTTTAAA
645664 AGACTTGACTCGAACTCAA-TTTTTTTAAA
1 AGACTTGACTCGAACTCAATTTTTTTTAAA
645693 AGACTT
1 AGACTT
645699 AACCCAAGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 16 0.46
30 19 0.54
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (30 bp):
AGACTTGACTCGAACTCAATTTTTTTTAAA
Found at i:656975 original size:27 final size:27
Alignment explanation
Indices: 656937--656990 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
656927 GGAAGCAGAA
656937 AACACAATTGAGCATGTATTATTCTTC
1 AACACAATTGAGCATGTATTATTCTTC
656964 AACACAATTGAGCATGTATTATTCTTC
1 AACACAATTGAGCATGTATTATTCTTC
656991 TGCGCAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (27 bp):
AACACAATTGAGCATGTATTATTCTTC
Found at i:666018 original size:8 final size:8
Alignment explanation
Indices: 665978--666024 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
665968 TCAAAGTTTT
665978 GGTCAACAG
1 GGTCAAC-G
665987 TGGTCAACG
1 -GGTCAACG
665996 TCGGTCAAC-
1 --GGTCAACG
666005 GGTCAACG
1 GGTCAACG
666013 GGTCAACG
1 GGTCAACG
666021 GGTC
1 GGTC
666025 GGGTTATGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 12 0.35
9 1 0.03
10 14 0.41
ACGTcount: A:0.23, C:0.26, G:0.34, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:666018 original size:15 final size:16
Alignment explanation
Indices: 665988--666021 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
665978 GGTCAACAGT
665988 GGTCAACGTCGGTCAAC
1 GGTCAACG-CGGTCAAC
666005 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
666020 GG
1 GG
666022 GTCGGGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:669785 original size:13 final size:13
Alignment explanation
Indices: 669767--669807 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
669757 CGGTCAACGA
669767 TCAACGGGTCGGG
1 TCAACGGGTCGGG
669780 TCAACGGGTCGGG
1 TCAACGGGTCGGG
**
669793 AAAACGGGTCGGG
1 TCAACGGGTCGGG
669806 TC
1 TC
669808 GGGTTATGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.44, T:0.15
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:671695 original size:24 final size:24
Alignment explanation
Indices: 671664--671712 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
671654 GGTCTTCATG
*
671664 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATATAC
671688 ATGATGTATAAAACATCTATATAC
1 ATGATGTATAAAACATCTATATAC
671712 A
1 A
671713 ATGTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATATAC
Found at i:672306 original size:30 final size:31
Alignment explanation
Indices: 672249--672318 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
672239 CAACCATTCA
* ** *
672249 CAACTTTTCCAAAATTATTGAATTGGTCCCC
1 CAACTTTTCAAAAATTATCAAAATGGTCCCC
672280 CAACTTTTCAAAAATTA-CAAAATGGTCCCC
1 CAACTTTTCAAAAATTATCAAAATGGTCCCC
* *
672310 AAATTTTTC
1 CAACTTTTC
672319 TAAGGCTTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (31 bp):
CAACTTTTCAAAAATTATCAAAATGGTCCCC
Found at i:674718 original size:2 final size:2
Alignment explanation
Indices: 674706--674768 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
674696 CTAGTCTACC
674706 AT AT A- 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
674747 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
674769 TTCTAAGAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:683655 original size:20 final size:22
Alignment explanation
Indices: 683625--683664 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
683615 AATTAGTTAA
683625 AAAATTAAA-GGTAAATTATTT
1 AAAATTAAAGGGTAAATTATTT
683646 AAAA-TAAAGGGTAAATTAT
1 AAAATTAAAGGGTAAATTAT
683665 ACCACTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (22 bp):
AAAATTAAAGGGTAAATTATTT
Found at i:685077 original size:23 final size:24
Alignment explanation
Indices: 685033--685077 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
685023 TTACCTTTTA
**
685033 TTTTAAATAATTTACTTTTTATTT
1 TTTTAAATAATTTACTAATTATTT
*
685057 TTTTAACTAATTTA-TAATTAT
1 TTTTAAATAATTTACTAATTAT
685078 ACGTTGAGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTAAATAATTTACTAATTATTT
Found at i:685400 original size:2 final size:2
Alignment explanation
Indices: 685393--685458 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
685383 ATGATAGAGA
685393 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
685435 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
685459 TAATTTCTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:685661 original size:17 final size:17
Alignment explanation
Indices: 685639--685671 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
685629 AATCTAAATT
*
685639 TAAAAATTAAAAATTAA
1 TAAAAATAAAAAATTAA
685656 TAAAAATAAAAAATTA
1 TAAAAATAAAAAATTA
685672 CATCAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAAATAAAAAATTAA
Found at i:689666 original size:42 final size:42
Alignment explanation
Indices: 689607--689701 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 42
689597 TCGGGTCATT
* * *
689607 TCGGGTTTTGATTTATTCGGCTCTATAGTAAGTTAGGTCGGG
1 TCGGGTTTCGATTTATTCGGCTCTATAGTAAGTCAAGTCGGG
* *
689649 TCGGGTTTCGGTTTATTCGGCTGTATAGTAAGTCAAGTCGGG
1 TCGGGTTTCGATTTATTCGGCTCTATAGTAAGTCAAGTCGGG
*
689691 TCGGGTATCGA
1 TCGGGTTTCGA
689702 GTCGAGTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.33, T:0.37
Consensus pattern (42 bp):
TCGGGTTTCGATTTATTCGGCTCTATAGTAAGTCAAGTCGGG
Found at i:689825 original size:19 final size:19
Alignment explanation
Indices: 689803--689842 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
689793 GGTTTAGGTT
689803 AACTTTGGATCTTTACGTC
1 AACTTTGGATCTTTACGTC
689822 AACTTTGGATCTTTACGTC
1 AACTTTGGATCTTTACGTC
689841 AA
1 AA
689843 TTCAAGTTGA
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:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (19 bp):
AACTTTGGATCTTTACGTC
Found at i:690457 original size:152 final size:152
Alignment explanation
Indices: 690288--690580 Score: 552
Period size: 152 Copynumber: 1.9 Consensus size: 152
690278 AAATATATAC
690288 CTTTATATTATAAAAATAAGTTATTTGTGTAGTATAAAAA-AAGTCAATTTTATATTAAATTTAA
1 CTTTATATTATAAAAATAAGTTATTTGTGTAGTATAAAAATAAGTCAATTTTATATTAAATTTAA
*
690352 CTAACTATATTTTTTTCATATACACAAGAATTAAAATAATTTGTAAATTAATTTAATAGATTTAG
66 ATAACTATA-TTTTTTCATATACACAAGAATTAAAATAATTTGTAAATTAATTTAATAGATTTAG
690417 AAAGTTATTTTATATATAGATAT
130 AAAGTTATTTTATATATAGATAT
690440 CTTTATATTATAAAAATAAGTTATTTGTGTAGTATAAAAATAAGTCAATTTTATATTAAATTTAA
1 CTTTATATTATAAAAATAAGTTATTTGTGTAGTATAAAAATAAGTCAATTTTATATTAAATTTAA
*
690505 ATAACTATATTTTTTCATATACACAAGAATTAAAATAATTTGTAAATTAATTTAATAGTTTTAGA
66 ATAACTATATTTTTTCATATACACAAGAATTAAAATAATTTGTAAATTAATTTAATAGATTTAGA
690570 AAGTTATTTTA
131 AAGTTATTTTA
690581 GTAGTTCCAA
Statistics
Matches: 138, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
152 106 0.77
153 32 0.23
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (152 bp):
CTTTATATTATAAAAATAAGTTATTTGTGTAGTATAAAAATAAGTCAATTTTATATTAAATTTAA
ATAACTATATTTTTTCATATACACAAGAATTAAAATAATTTGTAAATTAATTTAATAGATTTAGA
AAGTTATTTTATATATAGATAT
Found at i:693848 original size:18 final size:18
Alignment explanation
Indices: 693825--693860 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
693815 TTATTTCACA
693825 CTGACCGATTTATAGACG
1 CTGACCGATTTATAGACG
693843 CTGACCGATTTATAGACG
1 CTGACCGATTTATAGACG
693861 AAAAGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (18 bp):
CTGACCGATTTATAGACG
Found at i:693955 original size:14 final size:15
Alignment explanation
Indices: 693929--693957 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
693919 TTATAAATGA
693929 TTTTATACGAAATAT
1 TTTTATACGAAATAT
693944 TTTTATAC-AAATAT
1 TTTTATACGAAATAT
693958 ACATGTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (15 bp):
TTTTATACGAAATAT
Found at i:703229 original size:54 final size:54
Alignment explanation
Indices: 703147--703256 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
703137 GTTGAGAATG
703147 TCTCCCTCGTCTCTGCAGTATATATTCTAGAATAGTCGATCAATAGATCAGACA
1 TCTCCCTCGTCTCTGCAGTATATATTCTAGAATAGTCGATCAATAGATCAGACA
703201 TCTCCCTCGTCTCTGCAGTATATATTCTAGAATAGTCGATCAATAGATCAGACA
1 TCTCCCTCGTCTCTGCAGTATATATTCTAGAATAGTCGATCAATAGATCAGACA
703255 TC
1 TC
703257 AATGGTTATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.32
Consensus pattern (54 bp):
TCTCCCTCGTCTCTGCAGTATATATTCTAGAATAGTCGATCAATAGATCAGACA
Found at i:710136 original size:18 final size:18
Alignment explanation
Indices: 710110--710145 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
710100 ATGCGTGGAC
*
710110 ATGTGTATAATATATAGT
1 ATGTATATAATATATAGT
*
710128 ATGTATATAGTATATAGT
1 ATGTATATAATATATAGT
710146 TGGCATATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (18 bp):
ATGTATATAATATATAGT
Found at i:710311 original size:28 final size:28
Alignment explanation
Indices: 710257--710314 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
710247 TTGCATATCA
*
710257 TATAGTTTCATATCAAATAATTGTATAT
1 TATAGTTTCATATCAAATAATAGTATAT
* *
710285 TATA-TTTGATATTAAATAACTAGTATAT
1 TATAGTTTCATATCAAATAA-TAGTATAT
710313 TA
1 TA
710315 CATAGTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (28 bp):
TATAGTTTCATATCAAATAATAGTATAT
Found at i:710343 original size:18 final size:18
Alignment explanation
Indices: 710317--710353 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
710307 GTATATTACA
* *
710317 TAGTTTATATTATATAGT
1 TAGTATATACTATATAGT
710335 TAGTATATACTATATAGT
1 TAGTATATACTATATAGT
710353 T
1 T
710354 TGCATGTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
TAGTATATACTATATAGT
Found at i:711126 original size:7 final size:7
Alignment explanation
Indices: 711114--711231 Score: 51
Period size: 7 Copynumber: 17.9 Consensus size: 7
711104 TTGTAAACTA
711114 TATATAG
1 TATATAG
711121 TATATAG
1 TATATAG
711128 TATATA-
1 TATATAG
*
711134 AATATCA-
1 TATAT-AG
*
711141 AATATAG
1 TATATAG
711148 TATATAG
1 TATATAG
711155 T-T-TA-
1 TATATAG
711159 TATATA-
1 TATATAG
*
711165 AACTATAG
1 TA-TATAG
* *
711173 TTTTTA-
1 TATATAG
711179 TATATAG
1 TATATAG
711186 T-TGATATG
1 TAT-ATA-G
*
711194 TA-A-AC
1 TATATAG
711199 TATATAG
1 TATATAG
711206 TATATA-
1 TATATAG
*
711212 TATTTAG
1 TATATAG
*
711219 TATATAC
1 TATATAG
711226 TATATA
1 TATATA
711232 AATAGTTTAT
Statistics
Matches: 85, Mismatches: 13, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
4 1 0.01
5 5 0.06
6 21 0.25
7 56 0.66
8 2 0.02
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (7 bp):
TATATAG
Found at i:711212 original size:31 final size:31
Alignment explanation
Indices: 711143--711214 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
711133 AAATATCAAA
* *
711143 TATAGTATATAGTTTATATATAAACTATAGTT
1 TATA-TATATAGTTGATATATAAACTATAGTG
* *
711175 TTTATATATAGTTGATATGTAAACTATA-TAG
1 TATATATATAGTTGATATATAAACTATAGT-G
711206 TATATATAT
1 TATATATAT
711215 TTAGTATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 1 0.03
31 30 0.88
32 3 0.09
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (31 bp):
TATATATATAGTTGATATATAAACTATAGTG
Found at i:711369 original size:7 final size:7
Alignment explanation
Indices: 711354--711456 Score: 50
Period size: 6 Copynumber: 16.3 Consensus size: 7
711344 ATATCAACTG
711354 TAGTATA
1 TAGTATA
*
711361 TAGTTTA
1 TAGTATA
711368 TA-TATA
1 TAGTATA
* *
711374 AACTATA
1 TAGTATA
*
711381 GT-TTATA
1 -TAGTATA
711388 TAGT-T-
1 TAGTATA
711393 TA-TATA
1 TAGTATA
711399 TA-TATA
1 TAGTATA
711405 TA-TATA
1 TAGTATA
711411 TA-TATA
1 TAGTATA
711417 TA-TATA
1 TAGTATA
711423 TA-TATA
1 TAGTATA
711429 TA-TATA
1 TAGTATA
* *
711435 TAGTTTT
1 TAGTATA
711442 TA-TATA
1 TAGTATA
*
711448 TAGTTTA
1 TAGTATA
711455 TA
1 TA
711457 TACATAATAT
Statistics
Matches: 78, Mismatches: 11, Indels: 14
0.76 0.11 0.14
Matches are distributed among these distances:
4 1 0.01
5 3 0.04
6 48 0.62
7 26 0.33
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (7 bp):
TAGTATA
Found at i:711372 original size:25 final size:26
Alignment explanation
Indices: 711318--711447 Score: 105
Period size: 27 Copynumber: 5.2 Consensus size: 26
711308 ATTATATAAG
*
711318 TATAAACTATA-TTATATAGTATATAAA
1 TATAAACTATAGTTATATAGT-T-TATA
* *
711345 TATCAACTGTAG-TATATAGTTTATA
1 TATAAACTATAGTTATATAGTTTATA
711370 TATAAACTATAGTTTATATAGTTTATA
1 TATAAACTATAG-TTATATAGTTTATA
* *
711397 TATATA-TATA--TATATA-TATATA
1 TATAAACTATAGTTATATAGTTTATA
* *
711419 TATATA-TATA-TATATATAGTTTTTA
1 TATAAACTATAGT-TATATAGTTTATA
711444 TATA
1 TATA
711448 TAGTTTATAT
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
22 15 0.17
23 6 0.07
24 6 0.07
25 21 0.24
26 5 0.06
27 35 0.40
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (26 bp):
TATAAACTATAGTTATATAGTTTATA
Found at i:711673 original size:2 final size:2
Alignment explanation
Indices: 711393--711661 Score: 113
Period size: 2 Copynumber: 128.0 Consensus size: 2
711383 TTATATAGTT
711393 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
711435 TA GTT TT TA TA TA TA GTT TA TA TA CA TA -A TA TA TT TA TA TA TA
1 TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
711478 TCA -A CTC TA GTA AA TGG TA TA TA GTA TA TA AA TA TA AA CTA TA
1 T-A TA -TA TA -TA TA T-A TA TA TA -TA TA TA TA TA TA TA -TA TA
* * * *
711521 GTT TA TA TA GTT TA TA TA TA TA -A TA TA TA CTA TA TA AA TA GTT
1 -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA
* *
711564 TA TA TA GT- TCA TA TG TA AA CTA TA TA TA T- TA TA TA GTA TA TA
1 TA TA TA -TA T-A TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA
* * * *
711606 AA TA T- TA -A CTA -A GTA TA TA GTT TA TA TA TA AA CTA TA GTT TA
1 TA TA TA TA TA -TA TA -TA TA TA -TA TA TA TA TA TA -TA TA -TA TA
711648 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
711662 GTTTTTATAT
Statistics
Matches: 200, Mismatches: 38, Indels: 58
0.68 0.13 0.20
Matches are distributed among these distances:
1 8 0.04
2 168 0.84
3 24 0.12
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (2 bp):
TA
Found at i:711767 original size:15 final size:15
Alignment explanation
Indices: 711747--711780 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
711737 GTTAATTAAT
711747 GTATTCA-ACTATATA
1 GTATTCATAC-ATATA
711762 GTATTCATACATATA
1 GTATTCATACATATA
711777 GTAT
1 GTAT
711781 ATGCTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (15 bp):
GTATTCATACATATA
Found at i:711816 original size:15 final size:16
Alignment explanation
Indices: 711789--711825 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
711779 ATATGCTTTG
711789 AATT-TACATAGTATA
1 AATTATACATAGTATA
711804 AATTATACA-AGTATA
1 AATTATACATAGTATA
*
711819 AACTATA
1 AATTATA
711826 TTATATAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.35
Consensus pattern (16 bp):
AATTATACATAGTATA
Found at i:711898 original size:27 final size:27
Alignment explanation
Indices: 711819--711888 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
711809 TACAAGTATA
*
711819 AACTATATTATATAGTATATAAATATC
1 AACTATAATATATAGTATATAAATATC
* *
711846 AACTATAGTATGTAGTATATAAATATC
1 AACTATAATATATAGTATATAAATATC
711873 AACTATAATATATAGT
1 AACTATAATATATAGT
711889 TTTTATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (27 bp):
AACTATAATATATAGTATATAAATATC
Found at i:711940 original size:33 final size:32
Alignment explanation
Indices: 711892--711996 Score: 101
Period size: 33 Copynumber: 3.3 Consensus size: 32
711882 ATATAGTTTT
*
711892 TATATATATATATATACTAATGAACTTTATAA
1 TATATATATATATATACTAATGAACTATATAA
* *
711924 TATATAGTTTATATATACTAATGAACTATATAG
1 TATATA-TATATATATACTAATGAACTATATAA
* * *
711957 TTTAT-TA-ATATA-ATTATATAAACTATATAA
1 TATATATATATATATACTA-ATGAACTATATAA
711987 T-TCATATATA
1 TAT-ATATATA
711997 CACTATAAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
29 4 0.07
30 19 0.32
31 3 0.05
32 7 0.12
33 27 0.45
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (32 bp):
TATATATATATATATACTAATGAACTATATAA
Found at i:712011 original size:18 final size:20
Alignment explanation
Indices: 711971--712012 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
711961 TTAATATAAT
*
711971 TATATAAACTATATAATTCA
1 TATATAAACTATATAACTCA
*
711991 TATATACACTATA-AACT-A
1 TATATAAACTATATAACTCA
712009 TATA
1 TATA
712013 GTTTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 3 0.15
20 12 0.60
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (20 bp):
TATATAAACTATATAACTCA
Found at i:713000 original size:6 final size:6
Alignment explanation
Indices: 712991--713021 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
712981 GTCGTGGTCG
712991 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
713022 ACGTGTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:713170 original size:42 final size:42
Alignment explanation
Indices: 713111--713482 Score: 577
Period size: 42 Copynumber: 8.9 Consensus size: 42
713101 TGCGATTTTG
* *
713111 GACTATCGCAACGAACTTCGAATAAATCGCAACGTGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
713153 GACTATCGCAACGAACTTCGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
713195 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
713237 GACTATCGCAACGAATTTGGAATAAATCGCAACGTGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
713279 GACTATCACAATGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
713321 GACTATCGCAACGAACTTGGAATAAATTGCAAAGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
713363 GACTATCGCAACGAACTTGGAATAAATCGCAATGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
713405 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
713447 GACTATCACAACGAACTTCGACT--ATCGCAACGCGAA
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAA
713483 TTTGGAATAA
Statistics
Matches: 304, Mismatches: 26, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
40 13 0.04
42 291 0.96
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:713501 original size:42 final size:41
Alignment explanation
Indices: 713108--713538 Score: 420
Period size: 42 Copynumber: 10.3 Consensus size: 41
713098 CGTTGCGATT
* * *
713108 TTGGACTATCGCAACGAACTTCGAATAAATCGCAACGTGAAC
1 TTGGAATATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* * * *
713150 TTCGACTATCGCAACGAACTTCGAATAAATCGCAATGCGAAC
1 TTGGAATATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* *
713192 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGAATATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* * *
713234 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGTGAAC
1 TTGGAATATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* * * *
713276 TTCGACTATCACAATGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGAATATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* * * *
713318 TTCGACTATCGCAACGAACTTGGAATAAATTGCAAAGCGAAC
1 TTGGAATATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* * *
713360 TTCGACTATCGCAACGAACTTGGAATAAATCGCAATGCGAAC
1 TTGGAATATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* *
713402 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGAATATCGCAACGAACTTGGAAT-AATCGCAACGCGAAC
* * * * * *
713444 TTCGACTATCACAACGAACTTCGACT-ATCGCAACGCGAAT
1 TTGGAATATCGCAACGAACTTGGAATAATCGCAACGCGAAC
* *
713484 TTGGAATAAATCGCAACGCGAACTTGGACT-ATCGCAA--CGAAT
1 TTGGAAT--ATCGCAA--CGAACTTGGAATAATCGCAACGCGAAC
*
713526 TTGGAAAATCGCA
1 TTGGAATATCGCA
713539 TTGCGATAGT
Statistics
Matches: 352, Mismatches: 33, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
40 24 0.07
42 310 0.88
44 18 0.05
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (41 bp):
TTGGAATATCGCAACGAACTTGGAATAATCGCAACGCGAAC
Found at i:713515 original size:44 final size:40
Alignment explanation
Indices: 713458--713538 Score: 117
Period size: 44 Copynumber: 1.9 Consensus size: 40
713448 ACTATCACAA
713458 CGAACTTCGACTATCGCAACGCGAATTTGGAATAAATCGCAACG
1 CGAACTTCGACTATCGCAA--CGAATTTGG-A-AAATCGCAACG
*
713502 CGAACTTGGACTATCGCAACGAATTTGGAAAATCGCA
1 CGAACTTCGACTATCGCAACGAATTTGGAAAATCGCA
713539 TTGCGATAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
40 8 0.22
41 1 0.03
42 9 0.25
44 18 0.50
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (40 bp):
CGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAACG
Found at i:713719 original size:2 final size:2
Alignment explanation
Indices: 713712--713764 Score: 60
Period size: 2 Copynumber: 28.0 Consensus size: 2
713702 TATTTTCTCT
*
713712 TA TA TA TA TA T- TA TA T- TA -A TA TA TA CTT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
713752 TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA
713765 ATTGTTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
1 4 0.09
2 39 0.89
3 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.