Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1283
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: 103400
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:1356 original size:17 final size:16
Alignment explanation
Indices: 1334--1374 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1324 TTGTGTTGTT
1334 AAATTTTTTTGAAAAAA
1 AAATTTTTTT-AAAAAA
*
1351 AAATTTTTTTAAATAA
1 AAATTTTTTTAAAAAA
*
1367 TAATTTTT
1 AAATTTTT
1375 AAAAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
AAATTTTTTTAAAAAA
Found at i:1958 original size:19 final size:19
Alignment explanation
Indices: 1931--1981 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1921 ACAAAAAAAT
*
1931 AAAAAAAAAAAC-CCCACAC
1 AAAAAAAAAAACACCCA-AA
*
1950 AAGAAAAAAAACACCCAAA
1 AAAAAAAAAAACACCCAAA
1969 AAAAAAAAAAACA
1 AAAAAAAAAAACA
1982 ATTTTAACGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.76, C:0.22, G:0.02, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAACACCCAAA
Found at i:8770 original size:27 final size:27
Alignment explanation
Indices: 8731--8813 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 27
8721 ATTAAAAATT
*
8731 AATCATCAATTTTGAAAAATAAAAAAG
1 AATCATCATTTTTGAAAAATAAAAAAG
*
8758 AA--ATACTATTTTT-AATAAATACAAAAG
1 AATCAT-C-ATTTTTGAA-AAATAAAAAAG
8785 AATCATCATTTTTGACAAATATAAAAAAG
1 AATCATCATTTTTGA-AAA-ATAAAAAAG
8814 TGATTTTGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 25 0.56
28 4 0.09
29 11 0.24
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.30
Consensus pattern (27 bp):
AATCATCATTTTTGAAAAATAAAAAAG
Found at i:10552 original size:30 final size:30
Alignment explanation
Indices: 10513--10595 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
10503 ATTAAATACG
* *
10513 AAATAATAAATTAATTAAAGTAAAATTAAA
1 AAATAATAAATAAATTAAAATAAAATTAAA
* *
10543 AAATTATAAATAAATTAAAATATAATTAAA
1 AAATAATAAATAAATTAAAATAAAATTAAA
* *
10573 AATATAA-AAATAAAATAATATAA
1 AA-ATAATAAATAAATTAAAATAA
10596 TATAAATATT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 41 0.93
31 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (30 bp):
AAATAATAAATAAATTAAAATAAAATTAAA
Found at i:11001 original size:16 final size:15
Alignment explanation
Indices: 10949--11004 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
10939 AATTTTAATA
*
10949 TATTCATATTATTTT
1 TATTTATATTATTTT
10964 TA-TTA-ATTATTTTGT
1 TATTTATATTA-TTT-T
*
10979 TAATTATATTATATTT
1 TATTTATATTAT-TTT
10995 TATTTATATT
1 TATTTATATT
11005 TTAATTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 4 0.12
14 5 0.15
15 5 0.15
16 14 0.41
17 6 0.18
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (15 bp):
TATTTATATTATTTT
Found at i:13340 original size:11 final size:11
Alignment explanation
Indices: 13324--13398 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
13314 AAATATTTAA
13324 ATATTTATATT
1 ATATTTATATT
* *
13335 ATATTTGTTTTTT
1 ATA-TT-TATATT
*
13348 ATATTTATAAT
1 ATATTTATATT
13359 ATATTT-TATAT
1 ATATTTATAT-T
* *
13370 AAATTTTAAATT
1 ATA-TTTATATT
*
13382 ATTTTTATATT
1 ATATTTATATT
13393 ATATTT
1 ATATTT
13399 GGGTTTGAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
10 2 0.04
11 27 0.57
12 9 0.19
13 9 0.19
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (11 bp):
ATATTTATATT
Found at i:16773 original size:20 final size:19
Alignment explanation
Indices: 16735--16777 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
16725 TTAGTTATAT
16735 ATTAAAGATAATATTATTA
1 ATTAAAGATAATATTATTA
* *
16754 ATTAAATATATATTTTATTA
1 ATTAAAGATA-ATATTATTA
16774 ATTA
1 ATTA
16778 TTAATTATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTAAAGATAATATTATTA
Found at i:16798 original size:27 final size:27
Alignment explanation
Indices: 16747--16802 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
16737 TAAAGATAAT
*
16747 ATTATTAATTAAATATATATTTTATTA
1 ATTATTAATTAAATATATATATTATTA
16774 ATTATTAATTATACATA-ATA-ATTATTA
1 ATTATTAATTA-A-ATATATATATTATTA
16801 AT
1 AT
16803 ATCAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 19 0.73
28 4 0.15
29 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTATTAATTAAATATATATATTATTA
Found at i:18759 original size:28 final size:30
Alignment explanation
Indices: 18714--18784 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 30
18704 ATAATTTATG
18714 TAAGTTTTTATATTTTTA-TTATAATTAAA
1 TAAGTTTTTATATTTTTATTTATAATTAAA
*
18743 TAAGTTTTTAT-TTTTTATTTATATTTAAA
1 TAAGTTTTTATATTTTTATTTATAATTAAA
*
18772 TAAATTTTTATAT
1 TAAGTTTTTATAT
18785 CAAATAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 6 0.16
29 31 0.82
30 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (30 bp):
TAAGTTTTTATATTTTTATTTATAATTAAA
Found at i:19158 original size:21 final size:21
Alignment explanation
Indices: 19134--19173 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19124 TATAAGGGCT
* *
19134 AAATGTGTATTTAATTTAATA
1 AAATATGTATTTAAGTTAATA
*
19155 AAATATTTATTTAAGTTAA
1 AAATATGTATTTAAGTTAA
19174 AGGAATGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (21 bp):
AAATATGTATTTAAGTTAATA
Found at i:19564 original size:38 final size:39
Alignment explanation
Indices: 19522--19596 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
19512 TTATGATTGT
19522 ATAAA-CCCATTTAGATTTTTACATAGAAAAATCAATGC
1 ATAAACCCCATTTAGATTTTTACATAGAAAAATCAATGC
*
19560 ATAAACCCCATTTAGATTTTTACATTGAAAAATCAAT
1 ATAAACCCCATTTAGATTTTTACATAGAAAAATCAAT
19597 TTTTTTGGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
38 5 0.14
39 30 0.86
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (39 bp):
ATAAACCCCATTTAGATTTTTACATAGAAAAATCAATGC
Found at i:23690 original size:23 final size:22
Alignment explanation
Indices: 23609--23700 Score: 73
Period size: 23 Copynumber: 4.1 Consensus size: 22
23599 AGTTAATAAA
*
23609 AAATTAAA-AATATTTTGATAATT
1 AAATTAAATAATAATTT--TAATT
* * *
23632 AAATTTAAATAAAAATTTTTACT
1 AAA-TTAAATAATAATTTTAATT
*
23655 ATTATTAAATAATAATTTTAATT
1 A-AATTAAATAATAATTTTAATT
*
23678 AAATTAAAT--TAATTTAAATT
1 AAATTAAATAATAATTTTAATT
23698 AAA
1 AAA
23701 AAATTTATGT
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
20 13 0.23
22 7 0.12
23 24 0.43
24 6 0.11
25 6 0.11
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (22 bp):
AAATTAAATAATAATTTTAATT
Found at i:29114 original size:2 final size:2
Alignment explanation
Indices: 29107--29138 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29097 GGTTAAAGAA
29107 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29139 CTAAAGAACA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31312 original size:14 final size:15
Alignment explanation
Indices: 31282--31315 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
31272 TAATAGAAAG
31282 AATTAAAAATATTAA
1 AATTAAAAATATTAA
*
31297 AATTTAAAAT-TTAA
1 AATTAAAAATATTAA
31311 AATTA
1 AATTA
31316 TTTAATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTAAAAATATTAA
Found at i:32722 original size:19 final size:19
Alignment explanation
Indices: 32698--32734 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
32688 ATTTGATACT
32698 TATTTAATATTAAATTATA
1 TATTTAATATTAAATTATA
*
32717 TATTTAATATTAATTTAT
1 TATTTAATATTAAATTAT
32735 TTATAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTAATATTAAATTATA
Found at i:33245 original size:17 final size:17
Alignment explanation
Indices: 33223--33260 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
33213 TATAAAAAAA
33223 TTAAATTTCATGTA-ATT
1 TTAAATTTCAT-TATATT
*
33240 TTAAATTTTATTATATT
1 TTAAATTTCATTATATT
33257 TTAA
1 TTAA
33261 TTTTTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (17 bp):
TTAAATTTCATTATATT
Found at i:33535 original size:25 final size:25
Alignment explanation
Indices: 33501--33559 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
33491 TGATTCAAGG
*
33501 ACCATCCATGCCAAAAATTTCTATC
1 ACCATCCATGCCAAAAATTTCTAGC
33526 ACCATCCATGCCAAAAATTTCTAGC
1 ACCATCCATGCCAAAAATTTCTAGC
*
33551 ACCAACCAT
1 ACCATCCAT
33560 TTATTAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.37, C:0.34, G:0.05, T:0.24
Consensus pattern (25 bp):
ACCATCCATGCCAAAAATTTCTAGC
Found at i:37484 original size:45 final size:44
Alignment explanation
Indices: 37351--37506 Score: 156
Period size: 45 Copynumber: 3.5 Consensus size: 44
37341 TGTATGCATA
* ** *
37351 GTAACTTGGTTACTCGCTTATATACCCTAAGTATTTTGTTACGTG
1 GTAACTTGGTTACTCGCTTATATGCTTTAAG-ATTTTGTTGCGTG
* * * * *
37396 GTAACTTGGTTACTCCACCTTGTA-G-TTTCATGGTATTT-ATGCGTG
1 GTAACTTGGTTACT-C-GCTTATATGCTTT-AAGAT-TTTGTTGCGTG
37441 GTAACTTGGTTACTCGCTTATATGCTTTAAGAATTTTGTTGCGTG
1 GTAACTTGGTTACTCGCTTATATGCTTTAAG-ATTTTGTTGCGTG
37486 GTAACTTGGTTACTCGCTTAT
1 GTAACTTGGTTACTCGCTTAT
37507 CCATGTTTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
43 5 0.06
44 7 0.08
45 66 0.74
46 6 0.07
47 5 0.06
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.43
Consensus pattern (44 bp):
GTAACTTGGTTACTCGCTTATATGCTTTAAGATTTTGTTGCGTG
Found at i:37527 original size:90 final size:88
Alignment explanation
Indices: 37336--37558 Score: 243
Period size: 90 Copynumber: 2.5 Consensus size: 88
37326 TGTAGCTCCG
* * * ** *
37336 TAGCATGTATGCATAGTAACTTGGTTACTCGCTTATATACCCTAAGTATTTTGTTACGTGGTAAC
1 TAGCATGTATGCGTGGTAACTTGGTTACTCGCTTATATGCTTTAAGAATTTTGTTACGTGGTAAC
*
37401 TTGGTTACTCCACCTTGTAGTTTCA
66 TTGGTTACTCCACCATGTA-TTT-A
* * * *
37426 TGGTATTTATGCGTGGTAACTTGGTTACTCGCTTATATGCTTTAAGAATTTTGTTGCGTGGTAAC
1 TAGCATGTATGCGTGGTAACTTGGTTACTCGCTTATATGCTTTAAGAATTTTGTTACGTGGTAAC
37491 TTGGTTACTCGCTTATCCATGT-TTT-
66 TTGGTTACTC-C--A-CCATGTATTTA
* * *
37516 TAGCATGTATGCGTGGTAACTTTTGTTGCTCGCTTTTATGCTT
1 TAGCATGTATGCGTGGTAAC-TTGGTTACTCGCTTATATGCTT
37559 CTGTTTAAAA
Statistics
Matches: 111, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
90 82 0.74
91 20 0.18
92 3 0.03
93 1 0.01
94 5 0.05
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (88 bp):
TAGCATGTATGCGTGGTAACTTGGTTACTCGCTTATATGCTTTAAGAATTTTGTTACGTGGTAAC
TTGGTTACTCCACCATGTATTTA
Found at i:37529 original size:45 final size:44
Alignment explanation
Indices: 37341--37558 Score: 142
Period size: 45 Copynumber: 4.8 Consensus size: 44
37331 CTCCGTAGCA
* * * ** *
37341 TGTATGCATAGTAACTTGGTTACTCGCTTATATACCCTAAGTATTT
1 TGTATGCGTGGTAACTTGGTTACTCGCTTATATGCTTTAAG-A-AT
* * * * *
37387 TGT-TACGTGGTAACTTGGTTACTCCACCTTGTA-G-TTTCATGGTAT
1 TGTATGCGTGGTAACTTGGTTACT-C-GCTTATATGCTTT-A-AGAAT
37432 T-TATGCGTGGTAACTTGGTTACTCGCTTATATGCTTTAAGAATTT
1 TGTATGCGTGGTAACTTGGTTACTCGCTTATATGCTTTAAGAA--T
* * *
37477 TGT-TGCGTGGTAACTTGGTTACTCGCTTATCCATGTTTTTAGCA-
1 TGTATGCGTGGTAACTTGGTTACTCGCTTAT--ATGCTTTAAGAAT
* * *
37521 TGTATGCGTGGTAACTTTTGTTGCTCGCTTTTATGCTT
1 TGTATGCGTGGTAAC-TTGGTTACTCGCTTATATGCTT
37559 CTGTTTAAAA
Statistics
Matches: 135, Mismatches: 23, Indels: 30
0.72 0.12 0.16
Matches are distributed among these distances:
43 7 0.05
44 12 0.09
45 82 0.61
46 19 0.14
47 15 0.11
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.44
Consensus pattern (44 bp):
TGTATGCGTGGTAACTTGGTTACTCGCTTATATGCTTTAAGAAT
Found at i:45288 original size:22 final size:21
Alignment explanation
Indices: 45263--45309 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
45253 ATATCAAATT
45263 AAATCAAATCAAATTTATATAA
1 AAATCAAATCAAATTTA-ATAA
* *
45285 AAATTAAATTAAATTTAATAA
1 AAATCAAATCAAATTTAATAA
45306 AAAT
1 AAAT
45310 TAAAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATCAAATCAAATTTAATAA
Found at i:45291 original size:27 final size:26
Alignment explanation
Indices: 45258--45329 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 26
45248 TTTAAATATC
45258 AAATTAAATCAAATCAAATTTATATAA
1 AAATTAAAT-AAATCAAATTTATATAA
45285 AAATTAAAT---T-AAATTTA-ATAA
1 AAATTAAATAAATCAAATTTATATAA
45306 AAATTAAAATAAATCAAATATTAT
1 AAATT-AAATAAATCAAAT-TTAT
45330 GGTTTGAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
21 9 0.24
22 11 0.29
23 1 0.03
25 1 0.03
26 4 0.11
27 12 0.32
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (26 bp):
AAATTAAATAAATCAAATTTATATAA
Found at i:45315 original size:22 final size:22
Alignment explanation
Indices: 45263--45319 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
45253 ATATCAAATT
* *
45263 AAATCAAATCAAATTTATATAA
1 AAATTAAATTAAATTTATATAA
45285 AAATTAAATTAAATTTA-ATAA
1 AAATTAAATTAAATTTATATAA
*
45306 AAATTAAAATAAAT
1 AAATTAAATTAAAT
45320 CAAATATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATTAAATTAAATTTATATAA
Found at i:45325 original size:21 final size:21
Alignment explanation
Indices: 45281--45325 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
45271 TCAAATTTAT
* **
45281 ATAAAAATTAAATTAAATTTA
1 ATAAAAATTAAAATAAATCAA
45302 ATAAAAATTAAAATAAATCAA
1 ATAAAAATTAAAATAAATCAA
45323 ATA
1 ATA
45326 TTATGGTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAAAAATTAAAATAAATCAA
Found at i:45615 original size:50 final size:46
Alignment explanation
Indices: 45553--45661 Score: 130
Period size: 50 Copynumber: 2.3 Consensus size: 46
45543 ATTTAATATT
* *
45553 TAATAAT-TAAAAATATTTTTTATTTAAATTTAATTATTAAATATATAAA
1 TAATAATATAAAAATAATTTTAATTTAAATTT--TTATT-AAT-TATAAA
* *
45602 TATTAATATAAAAATAATTTTAATTTTAATTTTTATTAATTATAAA
1 TAATAATATAAAAATAATTTTAATTTAAATTTTTATTAATTATAAA
*
45648 TAATAAAATAAAAA
1 TAATAATATAAAAA
45662 ATATAACGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
46 18 0.34
47 3 0.06
48 5 0.09
49 6 0.11
50 21 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (46 bp):
TAATAATATAAAAATAATTTTAATTTAAATTTTTATTAATTATAAA
Found at i:45793 original size:40 final size:39
Alignment explanation
Indices: 45742--45831 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 39
45732 TTTGACTTAA
* * *
45742 TAAATAATTTTTAAATAAATAAAAAAT-ATATTTATCCAT
1 TAAATTATTTTTAAAAAAATAAAAAATAATATTTAT-AAT
** *
45781 TAATATTATTTTTAAAAAAATTTAAAATAATTTTTATAAT
1 TAA-ATTATTTTTAAAAAAATAAAAAATAATATTTATAAT
45821 TAAATTATTTT
1 TAAATTATTTT
45832 AATTAATTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
39 11 0.26
40 25 0.58
41 7 0.16
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (39 bp):
TAAATTATTTTTAAAAAAATAAAAAATAATATTTATAAT
Found at i:46369 original size:24 final size:24
Alignment explanation
Indices: 46342--46460 Score: 64
Period size: 24 Copynumber: 4.7 Consensus size: 24
46332 GATCATTTTT
46342 AATATTATATAATTATAAAA-AA-TA
1 AATATTATATAA-TA-AAAATAATTA
** *
46366 AATAAAATATGATAAAAATAATTA
1 AATATTATATAATAAAAATAATTA
46390 AATATTATATAAATAATTAAATATATTA
1 AATATTATAT-AATAA--AAATA-ATTA
* * *
46418 AA-ATTTAAATAATATAAATTATTA
1 AATA-TTATATAATAAAAATAATTA
*
46442 ATTTATTAATATATATAAA
1 A-ATATT-ATATA-ATAAA
46461 TATATAATAT
Statistics
Matches: 72, Mismatches: 12, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
22 4 0.06
23 4 0.06
24 24 0.33
25 10 0.14
26 5 0.07
27 14 0.19
28 11 0.15
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (24 bp):
AATATTATATAATAAAAATAATTA
Found at i:46401 original size:21 final size:20
Alignment explanation
Indices: 46355--46435 Score: 79
Period size: 19 Copynumber: 4.4 Consensus size: 20
46345 ATTATATAAT
*
46355 TATA-AAAAATAAATAAA-A
1 TATATAAAAATAATTAAATA
46373 TATGATAAAAATAATTAAATA
1 TAT-ATAAAAATAATTAAATA
*
46394 T-TATATAAATAATTAAATA
1 TATATAAAAATAATTAAATA
46413 TAT-T-AAAAT--TTAAATA
1 TATATAAAAATAATTAAATA
46429 -ATATAAA
1 TATATAAA
46436 TTATTAATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 13
0.77 0.04 0.19
Matches are distributed among these distances:
15 2 0.04
16 8 0.15
17 2 0.04
18 7 0.13
19 19 0.35
20 14 0.26
21 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (20 bp):
TATATAAAAATAATTAAATA
Found at i:46463 original size:8 final size:8
Alignment explanation
Indices: 46395--46467 Score: 53
Period size: 8 Copynumber: 8.9 Consensus size: 8
46385 AATTAAATAT
46395 TATATAAA
1 TATATAAA
46403 TA-ATTAAA
1 TATA-TAAA
46411 TATATTAAA
1 TATA-TAAA
*
46420 -ATTTAAA
1 TATATAAA
46427 TAATATAAA
1 T-ATATAAA
*
46436 T-TATTAA
1 TATATAAA
*
46443 TTTATTAATA
1 TATA-TAA-A
46453 TATATAAA
1 TATATAAA
46461 TATATAA
1 TATATAA
46468 TATTTTAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
7 11 0.21
8 20 0.38
9 18 0.34
10 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
TATATAAA
Found at i:46496 original size:33 final size:32
Alignment explanation
Indices: 46395--46496 Score: 109
Period size: 33 Copynumber: 3.1 Consensus size: 32
46385 AATTAAATAT
* * * *
46395 TATATAAATAATTAAATATATTAAAATTTAAA
1 TATATAAATTATTAAATTTATTATAATATAAA
46427 TAATATAAATTATT-AATTTATTAATATATATAAA
1 T-ATATAAATTATTAAATTTATT-ATA-ATATAAA
46461 TATATAATATT-TTAAATTTAATTATAATATAAA
1 TATATAA-ATTATTAAATTT-ATTATAATATAAA
46494 TAT
1 TAT
46497 TTTCTACAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
32 8 0.13
33 31 0.52
34 18 0.30
35 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
TATATAAATTATTAAATTTATTATAATATAAA
Found at i:46747 original size:6 final size:6
Alignment explanation
Indices: 46736--46791 Score: 58
Period size: 6 Copynumber: 8.7 Consensus size: 6
46726 TTCACATGTT
* *
46736 AATTTA AATTTA AATTTAAA AATTTT AATTAATT AATTTA AATTTA AATTTA
1 AATTTA AATTTA AATTT--A AATTTA AATT--TA AATTTA AATTTA AATTTA
46788 AATT
1 AATT
46792 GATAAAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
6 32 0.73
8 12 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:46804 original size:34 final size:33
Alignment explanation
Indices: 46734--46806 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 33
46724 TGTTCACATG
* **
46734 TTAATTTAAATTTAAATTTAAAAATTTTAATTAA
1 TTAATTTAAATTTAAATTT-AAAATTTAAAAAAA
46768 TTAATTTAAATTTAAATTT-AAATTGATAAAAAAA
1 TTAATTTAAATTTAAATTTAAAATT--TAAAAAAA
46802 TTAAT
1 TTAAT
46807 AATTTAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 5 0.15
34 29 0.85
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (33 bp):
TTAATTTAAATTTAAATTTAAAATTTAAAAAAA
Found at i:46816 original size:14 final size:13
Alignment explanation
Indices: 46742--46814 Score: 60
Period size: 12 Copynumber: 5.6 Consensus size: 13
46732 TGTTAATTTA
*
46742 AATTTAAATTTAAA
1 AATTTAAA-TTAAT
*
46756 AATTTTAATTAATT
1 AATTTAAATTAA-T
*
46770 AATTTAAATTTA-
1 AATTTAAATTAAT
*
46782 AATTTAAATTGAT
1 AATTTAAATTAAT
**
46795 AA-AAAAATTAAT
1 AATTTAAATTAAT
46807 AATTTAAA
1 AATTTAAA
46815 ATCGATTGAT
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
12 20 0.43
13 9 0.20
14 17 0.37
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (13 bp):
AATTTAAATTAAT
Found at i:46827 original size:52 final size:52
Alignment explanation
Indices: 46771--46874 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 52
46761 TAATTAATTA
**
46771 ATTTAAATTTAAATTTAAATTG-A-TAAAAAAATTAATAATTTAAAATCGATTG
1 ATTTAAATTTAAAAATAAATTGAACTAAAAAAATTAA-AATTTAAAAT-GATTG
* *
46823 ATTTAAATTTAAAAATAACTTGAACGTAAAAAAATTTAAATTTAAAATGATT
1 ATTTAAATTTAAAAATAAATTGAAC-TAAAAAAATTAAAATTTAAAATGATT
46875 CGAATATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
52 19 0.42
53 5 0.11
54 10 0.22
55 11 0.24
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (52 bp):
ATTTAAATTTAAAAATAAATTGAACTAAAAAAATTAAAATTTAAAATGATTG
Found at i:46911 original size:16 final size:16
Alignment explanation
Indices: 46892--46923 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
46882 AAAATTATTC
46892 GACTCGAAATGACTTA
1 GACTCGAAATGACTTA
*
46908 GACTTGAAATGACTTA
1 GACTCGAAATGACTTA
46924 AATAATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (16 bp):
GACTCGAAATGACTTA
Found at i:46996 original size:20 final size:19
Alignment explanation
Indices: 46973--47033 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 19
46963 TATTTTATTT
46973 AAAAAATTATTAAGTTAATA
1 AAAAAATTATTAAGTT-ATA
*
46993 AAAATAATATTTATAAGTTATA
1 AAAA-AAT-TAT-TAAGTTATA
*
47015 AAATAAATTATTAATTTAT
1 AAA-AAATTATTAAGTTAT
47034 TTTATTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
20 11 0.32
21 5 0.15
22 11 0.32
23 7 0.21
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
AAAAAATTATTAAGTTATA
Found at i:48425 original size:35 final size:34
Alignment explanation
Indices: 48324--48426 Score: 107
Period size: 35 Copynumber: 3.0 Consensus size: 34
48314 AAATATGTAA
* * * *
48324 ATATATATAATAAATAATAAAAAAAATTTAAATT
1 ATATTTATATTAAATAATAAAAATAATTAAAATT
* * *
48358 TTATTTATATTAAATGATAAAATATAAATAAAATT
1 ATATTTATATTAAATAATAAAA-ATAATTAAAATT
* *
48393 ATATTTATCTTAAATAATTAAAAATTATTAAAAT
1 ATATTTATATTAAATAA-TAAAAATAATTAAAAT
48427 GAATTGAAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
34 18 0.33
35 32 0.58
36 5 0.09
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (34 bp):
ATATTTATATTAAATAATAAAAATAATTAAAATT
Found at i:49597 original size:20 final size:21
Alignment explanation
Indices: 49567--49605 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
49557 AATTAATTTA
*
49567 TTTAAATAAAATTTTAAATAT
1 TTTAAATAAAATTTAAAATAT
49588 TTTAAA-AAAATTTAAAAT
1 TTTAAATAAAATTTAAAAT
49606 TAAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTAAATAAAATTTAAAATAT
Found at i:49614 original size:16 final size:16
Alignment explanation
Indices: 49589--49631 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
49579 TTTAAATATT
*
49589 TTAAAAAAATTTAAAA
1 TTAAATAAATTTAAAA
*
49605 TTAAATAAATATAAAA
1 TTAAATAAATTTAAAA
49621 -TATAATAAATT
1 TTA-AATAAATT
49632 ATTAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 2 0.09
16 21 0.91
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAATAAATTTAAAA
Found at i:50464 original size:64 final size:64
Alignment explanation
Indices: 50394--50516 Score: 180
Period size: 65 Copynumber: 1.9 Consensus size: 64
50384 ACTTTTTTTG
*
50394 TCTTTTTAACTTATTATTGTTTAAAC-AAT-ATGTTTTTTAAAAAACA-TTATTTTTTTCACCCA
1 TCTTTTTAACTTATTATT-TTTAAACAAATAAT-TTTTTTAAAAAA-ATTTATTTTCTTCACCCA
50456 CA
63 CA
50458 TCTTTTTAACTTATTATTTTTAAACAAAATAATTTTTTTAAAAAAATTTATTTTCTTCA
1 TCTTTTTAACTTATTATTTTTAAAC-AAATAATTTTTTTAAAAAAATTTATTTTCTTCA
50517 TCCATACGTG
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
63 7 0.13
64 19 0.35
65 26 0.48
66 2 0.04
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (64 bp):
TCTTTTTAACTTATTATTTTTAAACAAATAATTTTTTTAAAAAAATTTATTTTCTTCACCCACA
Found at i:50510 original size:18 final size:18
Alignment explanation
Indices: 50468--50511 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
50458 TCTTTTTAAC
50468 TTATTATTTTTAAACAAAA
1 TTATT-TTTTTAAACAAAA
*
50487 TAATTTTTTTAAA-AAAA
1 TTATTTTTTTAAACAAAA
50504 TTTATTTT
1 -TTATTTT
50512 CTTCATCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATTTTTTTAAACAAAA
Found at i:50764 original size:22 final size:23
Alignment explanation
Indices: 50722--50765 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
50712 CAATAATTTT
*
50722 TAATAAAATAATTTTAAAATAAC
1 TAATAAAATAATTTCAAAATAAC
*
50745 TAATAAAA-AATTTCACAATAA
1 TAATAAAATAATTTCAAAATAA
50766 TTTTCTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (23 bp):
TAATAAAATAATTTCAAAATAAC
Found at i:51382 original size:20 final size:20
Alignment explanation
Indices: 51344--51382 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
51334 ATTTTTATGC
* *
51344 AATATTTGAATCTGGTTATT
1 AATATTTGAATATGATTATT
51364 AATATTTGAATATGATTAT
1 AATATTTGAATATGATTAT
51383 AATTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.49
Consensus pattern (20 bp):
AATATTTGAATATGATTATT
Found at i:51672 original size:2 final size:2
Alignment explanation
Indices: 51665--51704 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
51655 GGATGAGTGG
51665 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
51705 AACTTAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54114 original size:19 final size:19
Alignment explanation
Indices: 54090--54128 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
54080 ATTGATGCAA
54090 TCTATGAGGGTAGCTGGAT
1 TCTATGAGGGTAGCTGGAT
54109 TCTATGAGGGTAGCTGGAT
1 TCTATGAGGGTAGCTGGAT
54128 T
1 T
54129 GGGGGTGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.36, T:0.33
Consensus pattern (19 bp):
TCTATGAGGGTAGCTGGAT
Found at i:54846 original size:14 final size:14
Alignment explanation
Indices: 54827--54857 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
54817 GTTGCTATTT
54827 AAATATGTTAAAAA
1 AAATATGTTAAAAA
54841 AAATATGTTAAAAA
1 AAATATGTTAAAAA
54855 AAA
1 AAA
54858 AAACCTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (14 bp):
AAATATGTTAAAAA
Found at i:56322 original size:13 final size:14
Alignment explanation
Indices: 56304--56336 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
56294 ATAAAAATAT
56304 TAAATTTAAA-AAA
1 TAAATTTAAACAAA
56317 TAAATTTAAACAAA
1 TAAATTTAAACAAA
*
56331 AAAATT
1 TAAATT
56337 AAGTTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAATTTAAACAAA
Found at i:64387 original size:63 final size:63
Alignment explanation
Indices: 64301--64440 Score: 151
Period size: 63 Copynumber: 2.2 Consensus size: 63
64291 AATCATAATC
* * * *
64301 TAAATCAAATTTATTTTCGATATA-AAGTAAAATTTTATTCTAT-CGATTGCGTT-AATTATAAT
1 TAAATC-AATTTACTTAC-ATATACAAGTAAAAATTT-TTC-ATCCGATTAC-TTCAATTATAAT
*
64363 TTT
61 ATT
* *
64366 TAAATTAATTTACTTACATATACATGTAAAAATTTTTCATCCGATTACTTCAATTATAATATT
1 TAAATCAATTTACTTACATATACAAGTAAAAATTTTTCATCCGATTACTTCAATTATAATATT
64429 TAAATCAATTTA
1 TAAATCAATTTA
64441 ATTGCAATGT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
62 4 0.06
63 36 0.56
64 19 0.30
65 5 0.08
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (63 bp):
TAAATCAATTTACTTACATATACAAGTAAAAATTTTTCATCCGATTACTTCAATTATAATATT
Found at i:66520 original size:15 final size:15
Alignment explanation
Indices: 66469--66520 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
66459 TTTAAAAAAA
66469 TAAATCAAATATTATAT
1 TAAATCAAAT-TT-TAT
* *
66486 AAAATCAAA-TTGAT
1 TAAATCAAATTTTAT
66500 TCAAATCAAATTTTAT
1 T-AAATCAAATTTTAT
66516 TAAAT
1 TAAAT
66521 TATATTGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 2 0.07
15 14 0.48
16 5 0.17
17 8 0.28
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (15 bp):
TAAATCAAATTTTAT
Found at i:67049 original size:12 final size:13
Alignment explanation
Indices: 67027--67055 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
67017 CTTATATTCA
67027 AACACATGATAAT
1 AACACATGATAAT
67040 AACA-ATGATAAT
1 AACACATGATAAT
67052 AACA
1 AACA
67056 TTGGAGACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (13 bp):
AACACATGATAAT
Found at i:72954 original size:26 final size:27
Alignment explanation
Indices: 72925--72980 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
72915 TGTTAATAAA
* *
72925 AAATTTTAAA-AAATATTTTTATAATT
1 AAATTTTAAATAAAAATTTATATAATT
*
72951 AAA-TTTAAATAAAAATTTATATTATT
1 AAATTTTAAATAAAAATTTATATAATT
72977 AAAT
1 AAAT
72981 AAAAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATTTTAAATAAAAATTTATATAATT
Found at i:72986 original size:26 final size:26
Alignment explanation
Indices: 72934--72993 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
72924 AAAATTTTAA
* **
72934 AAAATATTTTTATAATTAAATTTAAAT
1 AAAA-ATTTATATAATTAAATAAAAAT
*
72961 AAAAATTTATATTATTAAATAAAAAT
1 AAAAATTTATATAATTAAATAAAAAT
*
72987 TAAAATT
1 AAAAATT
72994 AAATTAACTC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AAAAATTTATATAATTAAATAAAAAT
Found at i:72994 original size:20 final size:20
Alignment explanation
Indices: 72955--72994 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
72945 ATAATTAAAT
* *
72955 TTAAATAAAAATTTATATTA
1 TTAAATAAAAATTAAAATTA
72975 TTAAATAAAAATTAAAATTA
1 TTAAATAAAAATTAAAATTA
72995 AATTAACTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAAATAAAAATTAAAATTA
Found at i:73963 original size:2 final size:2
Alignment explanation
Indices: 73956--74002 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
73946 AGTCTTCCTT
73956 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
73998 TA TA T
1 TA TA T
74003 TGTAAAACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:78244 original size:25 final size:26
Alignment explanation
Indices: 78196--78246 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
78186 CGAATGGTAC
78196 TTTAATAATTTTAAATTTTAATTTAA
1 TTTAATAATTTTAAATTTTAATTTAA
78222 TTTAATAA-TTTAAATTATT-ATTTAA
1 TTTAATAATTTTAAATT-TTAATTTAA
78247 AAATATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTAATAATTTTAAATTTTAATTTAA
Found at i:78297 original size:21 final size:21
Alignment explanation
Indices: 78272--78311 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
78262 TTAAAAATAT
78272 TATTTT-TAATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
*
78293 TATTTTATTATTAAATTTA
1 TATTTTATAATTAAATTTA
78312 AGTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:79018 original size:13 final size:14
Alignment explanation
Indices: 78987--79027 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
78977 GAACAAATTT
78987 ATTTTATTAAA-AA
1 ATTTTATTAAATAA
*
79000 ATTTTATTAAATAG
1 ATTTTATTAAATAA
*
79014 A-TTTATTTAATAA
1 ATTTTATTAAATAA
79027 A
1 A
79028 AAATAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 22 0.92
14 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
ATTTTATTAAATAA
Found at i:79229 original size:20 final size:20
Alignment explanation
Indices: 79204--79249 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
79194 AATTTTACCT
*
79204 ATTAATATATATTTTATTAA
1 ATTAATATACATTTTATTAA
79224 ATTAATATACATTTTATTAA
1 ATTAATATACATTTTATTAA
79244 ATTAAT
1 ATTAAT
79250 TAATTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTAATATACATTTTATTAA
Found at i:79536 original size:14 final size:14
Alignment explanation
Indices: 79517--79548 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
79507 TATTATATTA
*
79517 AATATTTTAAAAAT
1 AATATTATAAAAAT
79531 AATATTATAAAAAT
1 AATATTATAAAAAT
79545 AATA
1 AATA
79549 AAAGAAAAAA
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATTATAAAAAT
Found at i:79814 original size:20 final size:19
Alignment explanation
Indices: 79791--79830 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
79781 AATTAATTTA
79791 AATTTAATAAATTTAAAATT
1 AATTTAAT-AATTTAAAATT
* *
79811 AATTTTATCATTTAAAATT
1 AATTTAATAATTTAAAATT
79830 A
1 A
79831 TTAAATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTTAATAATTTAAAATT
Found at i:79828 original size:26 final size:24
Alignment explanation
Indices: 79763--79829 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 24
79753 ATAGCTAATC
*
79763 TTTTATTATTTAAAATTTAATTAA
1 TTTTATAATTTAAAATTTAATTAA
79787 -TTTA-AATTTAATAAATTTAAAATTAA
1 TTTTATAATTT-A-AAATTT--AATTAA
*
79813 TTTTATCATTTAAAATT
1 TTTTATAATTTAAAATT
79830 ATTAAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
22 4 0.11
23 5 0.14
24 6 0.17
26 11 0.31
27 5 0.14
28 4 0.11
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTATAATTTAAAATTTAATTAA
Found at i:79838 original size:15 final size:16
Alignment explanation
Indices: 79770--79841 Score: 69
Period size: 15 Copynumber: 4.4 Consensus size: 16
79760 ATCTTTTATT
79770 ATTTAAAATTTAATT-A
1 ATTTAAAA-TTAATTAA
*
79786 ATTTAAATTTAA-TAA
1 ATTTAAAATTAATTAA
*
79801 ATTTAAAATTAATTTTATC
1 ATTTAAAATTAA--TTA-A
79820 ATTTAAAATT-ATTAA
1 ATTTAAAATTAATTAA
79835 ATTTAAA
1 ATTTAAA
79842 CGAGTAAAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
14 1 0.02
15 23 0.49
16 10 0.21
18 3 0.06
19 10 0.21
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTAAAATTAATTAA
Found at i:81847 original size:32 final size:35
Alignment explanation
Indices: 81804--81892 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 35
81794 AGATTTATTT
81804 TTTATT-TTTAAATTATTTTTATTTAAT-TT-A-A
1 TTTATTATTTAAATTATTTTTATTTAATATTAATA
** **
81835 TTTATTATTTAAATTAAATAAATTTAATATTAATA
1 TTTATTATTTAAATTATTTTTATTTAATATTAATA
81870 TTTATTAAATTTAAATTATTTTT
1 TTTATT--ATTTAAATTATTTTT
81893 TAATAAATCG
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
31 6 0.14
32 17 0.39
33 2 0.05
34 1 0.02
35 7 0.16
37 11 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (35 bp):
TTTATTATTTAAATTATTTTTATTTAATATTAATA
Found at i:81851 original size:22 final size:22
Alignment explanation
Indices: 81811--81882 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
81801 TTTTTTATTT
*
81811 TTAAA-TTATT-TTT-ATTTAA
1 TTAAATTTATTATTTAAATTAA
*
81830 TTTAATTTATTATTTAAATTAA
1 TTAAATTTATTATTTAAATTAA
* * *
81852 ATAAATTTAATA-TTAATATTTA
1 TTAAATTTATTATTTAA-ATTAA
81874 TTAAATTTA
1 TTAAATTTA
81883 AATTATTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 4 0.10
20 5 0.12
21 7 0.17
22 26 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTAAATTTATTATTTAAATTAA
Found at i:81899 original size:21 final size:22
Alignment explanation
Indices: 81823--81900 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
81813 AAATTATTTT
* *
81823 TATTTAATTTAATTTATTATTTAA
1 TATTTAA-TAAATTTAATA-TTAA
*
81847 -ATTAAATAAATTTAATATTAA
1 TATTTAATAAATTTAATATTAA
* *
81868 TATTTATTAAATTTAA-ATTAT
1 TATTTAATAAATTTAATATTAA
*
81889 TTTTTAATAAAT
1 TATTTAATAAAT
81901 CGATTAATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
21 18 0.40
22 22 0.49
23 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTAATAAATTTAATATTAA
Found at i:82869 original size:33 final size:33
Alignment explanation
Indices: 82832--82897 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
82822 CATTATTTAT
82832 TTAATAAAAAAAAT-TTATTAA-ATTTTTTAAATA
1 TTAATAAAAAAAATATT-TTAATA-TTTTTAAATA
* *
82865 TTAATTAAAATAATATTTTAATATTTTTAAATA
1 TTAATAAAAAAAATATTTTAATATTTTTAAATA
82898 ATAAAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
TTAATAAAAAAAATATTTTAATATTTTTAAATA
Found at i:82911 original size:19 final size:19
Alignment explanation
Indices: 82887--82927 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
82877 ATATTTTAAT
*
82887 ATTTTTAAATAATAAAATA
1 ATTTTTAAACAATAAAATA
*
82906 ATTTTTAAACAGTAAAATA
1 ATTTTTAAACAATAAAATA
82925 ATT
1 ATT
82928 AATTAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
ATTTTTAAACAATAAAATA
Found at i:82975 original size:22 final size:22
Alignment explanation
Indices: 82942--82983 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
82932 AATTTTTATT
82942 TAAATTTAATTATAAAAATACA
1 TAAATTTAATTATAAAAATACA
82964 TAAATATT-ATTATAAAAATA
1 TAAAT-TTAATTATAAAAATA
82984 TTTTTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATACA
Found at i:85075 original size:20 final size:21
Alignment explanation
Indices: 85026--85076 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
85016 AAAATTTATA
*
85026 AATATTAATAAAAATAAATTT
1 AATATTAAAAAAAATAAATTT
85047 AATATTTAAAAAATAATAAA-TT
1 AATA-TTAAAAAA-AATAAATTT
85069 AA-ATTAAA
1 AATATTAAA
85077 TTTTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.19
21 5 0.19
22 11 0.41
23 6 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AATATTAAAAAAAATAAATTT
Found at i:85081 original size:27 final size:26
Alignment explanation
Indices: 85032--85082 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
85022 TATAAATATT
*
85032 AATAAAAATAAATTTAATATTTAAAA
1 AATAAAAATAAATTAAATATTTAAAA
85058 AATAATAAATTAAATTAAAT-TTTAA
1 AATAA-AAA-TAAATTAAATATTTAA
85083 TTTTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 5 0.23
27 8 0.36
28 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAAAAATAAATTAAATATTTAAAA
Found at i:85191 original size:2 final size:2
Alignment explanation
Indices: 85184--85219 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
85174 TCTAGCTAAA
85184 AT AT AT AT A- AT AT -T 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
85220 TGAACTACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85341 original size:23 final size:24
Alignment explanation
Indices: 85304--85350 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
85294 AAAATGTAAA
*
85304 TTTAATATATTATT-ATAATATATT
1 TTTAATATATAATTAAT-ATATATT
85328 TTTAA-ATATAATTAATATATATT
1 TTTAATATATAATTAATATATATT
85351 ATATTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTAATATATAATTAATATATATT
Found at i:85602 original size:16 final size:17
Alignment explanation
Indices: 85555--85623 Score: 51
Period size: 17 Copynumber: 4.3 Consensus size: 17
85545 TTTTAATTTT
85555 TTATTAAA--AATTATA
1 TTATTAAATTAATTATA
*
85570 TTATTAAATTAAATATA
1 TTATTAAATTAATTATA
**
85587 TT-TTTTATTAATTATA
1 TTATTAAATTAATTATA
85603 -TA-TAATATTTAATT-TA
1 TTATTAA-A-TTAATTATA
85619 TTATT
1 TTATT
85624 TAAAACAATC
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
15 10 0.24
16 14 0.34
17 16 0.39
18 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATTAAATTAATTATA
Found at i:85613 original size:20 final size:21
Alignment explanation
Indices: 85557--85613 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
85547 TTAATTTTTT
* *
85557 ATTAAAAATTATA-TTATTAA
1 ATTAAATATAATATTTATTAA
* *
85577 ATTAAATATATTTTTTATT-A
1 ATTAAATATAATATTTATTAA
*
85597 ATTATATATAATATTTA
1 ATTAAATATAATATTTA
85614 ATTTATTATT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTAAATATAATATTTATTAA
Found at i:96358 original size:18 final size:19
Alignment explanation
Indices: 96313--96369 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
96303 AAAATTTGAG
96313 TAAAAGTTTAAA-TT-A-T
1 TAAAAGTTTAAACTTAATT
*
96329 AAAAAGTTTAAACTTAATT
1 TAAAAGTTTAAACTTAATT
*
96348 TAAAA-TTTAAAGTTAATT
1 TAAAAGTTTAAACTTAATT
96366 TAAA
1 TAAA
96370 CTAATTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.31
17 2 0.06
18 17 0.49
19 5 0.14
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (19 bp):
TAAAAGTTTAAACTTAATT
Found at i:96450 original size:13 final size:13
Alignment explanation
Indices: 96415--96450 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
96405 TAAAAATCAA
96415 ATTTATTAAACTC
1 ATTTATTAAACTC
96428 ATTTGATTAAACTC
1 ATTT-ATTAAACTC
*
96442 ATTTCTTAA
1 ATTTATTAA
96451 TAAAATAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (13 bp):
ATTTATTAAACTC
Found at i:99871 original size:12 final size:12
Alignment explanation
Indices: 99854--99884 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
99844 TTAATAAAAA
99854 ATTAATTTTTAT
1 ATTAATTTTTAT
99866 ATTAATTTTTAT
1 ATTAATTTTTAT
99878 -TTAATTT
1 ATTAATTT
99885 AAATTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTAATTTTTAT
Found at i:100072 original size:19 final size:21
Alignment explanation
Indices: 100048--100096 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
100038 TCATTCAAAA
100048 ATATTAAAAATT-TA-TTTTT
1 ATATTAAAAATTATATTTTTT
* *
100067 ATATTAATATTTATATTTTTT
1 ATATTAAAAATTATATTTTTT
100088 ATAATTAAA
1 AT-ATTAAA
100097 TTTAATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 10 0.42
20 2 0.08
21 7 0.29
22 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTAAAAATTATATTTTTT
Found at i:100088 original size:21 final size:22
Alignment explanation
Indices: 100061--100111 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
100051 TTAAAAATTT
100061 ATTTTTAT-ATTAATATTT-ATA
1 ATTTTTATAATTAA-ATTTAATA
*
100082 TTTTTTATAATTAAATTTAATA
1 ATTTTTATAATTAAATTTAATA
100104 ATTTTTAT
1 ATTTTTAT
100112 TTTATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTTATAATTAAATTTAATA
Found at i:101708 original size:26 final size:25
Alignment explanation
Indices: 101674--101723 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
101664 AGAAGAAAAA
* *
101674 AAATTTAAATATATTTTTAAAAATTT
1 AAATATAAATAT-TTTTAAAAAATTT
101700 AAATATAAATATTTTTAAAAAATT
1 AAATATAAATATTTTTAAAAAATT
101724 ATATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATATAAATATTTTTAAAAAATTT
Found at i:101743 original size:16 final size:16
Alignment explanation
Indices: 101697--101743 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
101687 TTTTTAAAAA
*
101697 TTTAAAT-ATAAATATT
1 TTTAAATAATTAATA-T
*
101713 TTTAAAAAATT-ATAT
1 TTTAAATAATTAATAT
101728 TTTAAATAATTAATAT
1 TTTAAATAATTAATAT
101744 CATATGTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 11 0.42
16 13 0.50
17 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTAAATAATTAATAT
Found at i:102404 original size:25 final size:25
Alignment explanation
Indices: 102370--102417 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
102360 AATATTGATC
102370 AACATCATATATTAATTAAAAAATA
1 AACATCATATATTAATTAAAAAATA
102395 AACATCATATATTAATTAAAAAA
1 AACATCATATATTAATTAAAAAA
102418 AAGATTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.31
Consensus pattern (25 bp):
AACATCATATATTAATTAAAAAATA
Done.