Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 4 of 320
Found at i:990235 original size:16 final size:17
Alignment explanation
Indices: 990204--990630 Score: 74
Period size: 21 Copynumber: 23.1 Consensus size: 17
990194 TTAATTAAAG
990204 TTTAAAATAAATTTAAT
1 TTTAAAATAAATTTAAT
*
990221 TTTAAAA-ATATTTAA-
1 TTTAAAATAAATTTAAT
*
990236 ---AACAATCAAAATTAAT
1 TTTAA-AAT-AAATTTAAT
**
990252 TAAAGAAATAAATAAATTAAAT
1 TTTA-AAATAAAT---TTA-AT
*
990274 TTTAAAATAAATTAATTAAAG
1 TTTAAAATAAA-T--TT-AAT
990295 TTTAAAATAAATTTAAT
1 TTTAAAATAAATTTAAT
*
990312 TTTAAAA-ATATTTAA-
1 TTTAAAATAAATTTAAT
* *
990327 ---AACAATCAAAATTAAA
1 TTTAA-AAT-AAATTTAAT
** * *
990343 TAAATAAATTAATTAAAT
1 TTTA-AAATAAATTTAAT
*
990361 TTTAAAATAAATTAATTAAAG
1 TTTAAAATAAA-T--TT-AAT
990382 TTTAAAATAAATTTAAT
1 TTTAAAATAAATTTAAT
*
990399 TTTAAAA-ATATTTAA-
1 TTTAAAATAAATTTAAT
*
990414 ---AACAATAAAAATTAAT
1 TTTAA-AAT-AAATTTAAT
* *
990430 TAATGAAATAAATTAATTAAAT
1 T-TTAAAATAAA-T--TT-AAT
990452 TTTAAAATAAATTTAAT
1 TTTAAAATAAATTTAAT
**
990469 TTTAAAAAATAAAATAAAAT
1 TTT--AAAAT-AAATTTAAT
*
990489 TTTAAAAATCAAAATTAAT
1 TTT-AAAAT-AAATTTAAT
*
990508 TAAAGTTGAAAATAAATGAATTAAAG
1 T----TT-AAAATAAAT---TT-AAT
990534 TTTAAAATAAATTTAAT
1 TTTAAAATAAATTTAAT
* *
990551 TTAAAAAATTTAATTTAAT
1 TT-TAAAA-TAAATTTAAT
* *
990570 TTAAAAATCAAAATTAATTAAAG
1 TTTAAAAT--AAA-T--TT-AAT
990593 TTTAAAATAAATTTAAT
1 TTTAAAATAAATTTAAT
990610 TTTAAAAAATAGAATTTAAT
1 TTT--AAAATA-AATTTAAT
990630 T
1 T
990631 AAAAAGAATA
Statistics
Matches: 306, Mismatches: 44, Indels: 117
0.66 0.09 0.25
Matches are distributed among these distances:
12 6 0.02
13 6 0.02
15 18 0.06
16 21 0.07
17 47 0.15
18 33 0.11
19 48 0.16
20 28 0.09
21 61 0.20
22 17 0.06
23 16 0.05
25 2 0.01
26 3 0.01
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
TTTAAAATAAATTTAAT
Found at i:990288 original size:91 final size:91
Alignment explanation
Indices: 990190--990469 Score: 487
Period size: 91 Copynumber: 3.1 Consensus size: 91
990180 ATTACAGAAG
990190 TAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATCAAAATTAATTAA
1 TAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATCAAAATTAATTAA
*
990255 AGAAATAAATAAATTAAATTTTAAAA
66 AGAAATAAATTAATTAAATTTTAAAA
990281 TAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATC--AA--AATTAA
1 TAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATCAAAATTAATTAA
*
990342 ATAAATAAATTAATTAAATTTTAAAA
66 AGAAATAAATTAATTAAATTTTAAAA
*
990368 TAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATAAAAATTAATTAA
1 TAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATCAAAATTAATTAA
*
990433 TGAAATAAATTAATTAAATTTTAAAA
66 AGAAATAAATTAATTAAATTTTAAAA
990459 TAAATTTAATT
1 TAAA-TTAATT
990470 TTAAAAAATA
Statistics
Matches: 179, Mismatches: 5, Indels: 9
0.93 0.03 0.05
Matches are distributed among these distances:
87 82 0.46
89 4 0.02
91 87 0.49
92 6 0.03
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (91 bp):
TAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATCAAAATTAATTAA
AGAAATAAATTAATTAAATTTTAAAA
Found at i:990363 original size:87 final size:87
Alignment explanation
Indices: 990190--990469 Score: 452
Period size: 87 Copynumber: 3.1 Consensus size: 87
990180 ATTACAGAAG
990190 TAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATCAAAATTAATTAA
1 TAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATC--AA--AATTAA
* *
990255 AGAAATAAATAAATTAAATTTTAAAA
62 ATAAATAAATTAATTAAATTTTAAAA
990281 TAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATCAAAATTAAATAA
1 TAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATCAAAATTAAATAA
990346 ATAAATTAATTAAATTTTAAAA
66 ATAAATTAATTAAATTTTAAAA
*
990368 TAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATAAAAATTAATTAA
1 TAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATCAAAATT-A--AA
990433 TGAAATAAATTAATTAAATTTTAAAA
63 T-AAATAAATTAATTAAATTTTAAAA
990459 TAAATTTAATT
1 TAAA-TTAATT
990470 TTAAAAAATA
Statistics
Matches: 181, Mismatches: 3, Indels: 9
0.94 0.02 0.05
Matches are distributed among these distances:
87 88 0.49
88 1 0.01
89 2 0.01
90 3 0.02
91 81 0.45
92 6 0.03
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (87 bp):
TAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATCAAAATTAAATAA
ATAAATTAATTAAATTTTAAAA
Found at i:990394 original size:21 final size:21
Alignment explanation
Indices: 990257--990551 Score: 130
Period size: 21 Copynumber: 13.6 Consensus size: 21
990247 TTAATTAAAG
* *
990257 AAATAAATAAATTAAATTTTA
1 AAATAAATTAATTAAAGTTTA
990278 AAATAAATTAATTAAAGTTTA
1 AAATAAATTAATTAAAGTTTA
*
990299 AAATAAATTTAATTTTAAAAATATTTA
1 AAATAAA-TTAA--TT--AAA-GTTTA
* *
990326 AAA-CAATCAAAATTAAA---T-
1 AAATAAAT--TAATTAAAGTTTA
*
990344 AAATAAATTAATTAAATTTTA
1 AAATAAATTAATTAAAGTTTA
990365 AAATAAATTAATTAAAGTTTA
1 AAATAAATTAATTAAAGTTTA
*
990386 AAATAAATTTAATTTTAAAAATATTTA
1 AAATAAA-TTAA--TT--AAA-GTTTA
* ** *
990413 AAACAATAAAAATT-AA-TTAATG
1 AAATAA-ATTAATTAAAGTT--TA
*
990435 AAATAAATTAATTAAATTTTA
1 AAATAAATTAATTAAAGTTTA
*
990456 AAATAAATTTAATT----TTAAA
1 AAATAAA-TTAATTAAAGTT-TA
* ** *
990475 AAATAAAATAA--AATTTTAA
1 AAATAAATTAATTAAAGTTTA
*
990494 AAATCAAAATTAATTAAAGTTGA
1 AAAT--AAATTAATTAAAGTTTA
*
990517 AAATAAATGAATTAAAGTTTA
1 AAATAAATTAATTAAAGTTTA
990538 AAATAAATTTAATT
1 AAATAAA-TTAATT
990552 TAAAAAATTT
Statistics
Matches: 213, Mismatches: 26, Indels: 69
0.69 0.08 0.22
Matches are distributed among these distances:
17 7 0.03
18 8 0.04
19 18 0.08
20 5 0.02
21 94 0.44
22 29 0.14
23 14 0.07
24 4 0.02
25 5 0.02
26 8 0.04
27 20 0.09
28 1 0.00
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATAAATTAATTAAAGTTTA
Found at i:990427 original size:70 final size:68
Alignment explanation
Indices: 990334--990619 Score: 238
Period size: 70 Copynumber: 4.1 Consensus size: 68
990324 TAAAACAATC
*
990334 AAAA-TTAAATAAATAAATTAATTAAATTTTAAAAT-AAATTAATTAAAGTTTAAAATAAATTTA
1 AAAATTTAAA-AAATAAA--AATT-AATTTAAAAATAAAATTAATTAAAGTTTAAAATAAATTTA
990397 ATTTTAA
62 ATTTTAA
*
990404 AAATATTTAAAACAATAAAAATTAA-TTAATGAAAT-AAATTAATTAAATTTTAAAATAAATTTA
1 AAA-ATTTAAAA-AATAAAAATTAATTTAA--AAATAAAATTAATTAAAGTTTAAAATAAATTTA
990467 ATTTTAA
62 ATTTTAA
*
990474 AAAA--T--AAAAT-AAAA-T--TTTAAAAATCAAAATTAATTAAAGTTGAAAATAAATGAATTA
1 AAAATTTAAAAAATAAAAATTAATTTAAAAAT-AAAATTAATTAAAGTTTAAAATAAAT---TT-
*
990531 AAGTTTAAA
61 AA-TTTTAA
*
990540 ATAAATTTAATTTAAAA-AATTTAATTTAATTTAAAAATCAAAATTAATTAAAGTTTAAAATAAA
1 A-AAATTTAA---AAAATAA---AAATTAATTTAAAAAT-AAAATTAATTAAAGTTTAAAATAAA
990604 TTTAATTTTAA
58 TTTAATTTTAA
990615 AAAAT
1 AAAAT
990620 AGAATTTAAT
Statistics
Matches: 180, Mismatches: 8, Indels: 52
0.75 0.03 0.22
Matches are distributed among these distances:
59 4 0.02
61 27 0.15
62 1 0.01
63 4 0.02
64 5 0.03
65 4 0.02
66 6 0.03
67 4 0.02
68 3 0.02
69 4 0.02
70 48 0.27
71 2 0.01
72 11 0.06
74 9 0.05
75 6 0.03
76 2 0.01
77 4 0.02
78 1 0.01
80 35 0.19
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (68 bp):
AAAATTTAAAAAATAAAAATTAATTTAAAAATAAAATTAATTAAAGTTTAAAATAAATTTAATTT
TAA
Found at i:990537 original size:152 final size:153
Alignment explanation
Indices: 990278--990617 Score: 422
Period size: 152 Copynumber: 2.3 Consensus size: 153
990268 TTAAATTTTA
990278 AAATAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTTAAAACAATCAAAATTAAA
1 AAATAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATA-TT-AAACAATCAAAATTAAA
* * *
990343 TAAATAAATTAATTAAATTTTAAAATAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAAT
64 TAAATAAATTAATTAAAGTTGAAAATAAATGAATTAAAGTTTAAAATAAATTTAA-TTTAAAAA-
990408 ATTTAAAACAATAAAAATTAATTAATG
127 ATTTAAAACAATAAAAATTAATTAATG
* *
990435 AAATAAATTAATTAAATTTTAAAATAAATTTAATTTTAAAAA-A-T-AA-AAT-AAAATTTTAA-
1 AAATAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTAAACAATCAAAA-TTAAAT
990494 AAATCAAAATTAATTAAAGTTGAAAATAAATGAATTAAAGTTTAAAATAAATTTAATTTAAAAAA
65 AAAT--AAATTAATTAAAGTTGAAAATAAATGAATTAAAGTTTAAAATAAATTTAATTTAAAAAA
** * *
990559 TTT-----AATTTAATTTAA-AAAT-
128 TTTAAAACAATAAAAATTAATTAATG
*
990578 -CA-AAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAA
1 AAATAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAA
990618 ATAGAATTTA
Statistics
Matches: 169, Mismatches: 11, Indels: 22
0.84 0.05 0.11
Matches are distributed among these distances:
141 37 0.22
142 1 0.01
144 3 0.02
145 9 0.05
150 12 0.07
151 15 0.09
152 49 0.29
154 1 0.01
156 1 0.01
157 41 0.24
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (153 bp):
AAATAAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAATATTAAACAATCAAAATTAAATA
AATAAATTAATTAAAGTTGAAAATAAATGAATTAAAGTTTAAAATAAATTTAATTTAAAAAATTT
AAAACAATAAAAATTAATTAATG
Found at i:990561 original size:14 final size:14
Alignment explanation
Indices: 990542--990568 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
990532 AGTTTAAAAT
990542 AAATTTAATTTAAA
1 AAATTTAATTTAAA
990556 AAATTTAATTTAA
1 AAATTTAATTTAA
990569 TTTAAAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTTAATTTAAA
Found at i:990603 original size:80 final size:82
Alignment explanation
Indices: 990403--990604 Score: 263
Period size: 80 Copynumber: 2.5 Consensus size: 82
990393 TTTAATTTTA
* * *
990403 AAAATATTTAAAACAATAAAAATTAATT-AA--TG-AAATAAATTAATTAAATTTTAAAATAAAT
1 AAAAT-TTT-AAA-AATCAAAATTAATTAAAGTTGAAAATAAATGAATTAAAGTTTAAAATAAAT
990464 TTAATTTTAAAAAATAAAAT
63 TTAATTTTAAAAAATAAAAT
990484 AAAATTTTAAAAATCAAAATTAATTAAAGTTGAAAATAAATGAATTAAAGTTTAAAATAAATTTA
1 AAAATTTTAAAAATCAAAATTAATTAAAGTTGAAAATAAATGAATTAAAGTTTAAAATAAATTTA
**
990549 A-TTTAAAAAATTTAAT
66 ATTTTAAAAAATAAAAT
** *
990565 TTAA-TTTAAAAATCAAAATTAATTAAAGTTTAAAATAAAT
1 AAAATTTTAAAAATCAAAATTAATTAAAGTTGAAAATAAAT
990605 TTAATTTTAA
Statistics
Matches: 109, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
78 13 0.12
79 5 0.05
80 38 0.35
81 22 0.20
82 31 0.28
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (82 bp):
AAAATTTTAAAAATCAAAATTAATTAAAGTTGAAAATAAATGAATTAAAGTTTAAAATAAATTTA
ATTTTAAAAAATAAAAT
Found at i:990640 original size:20 final size:19
Alignment explanation
Indices: 990537--990641 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 19
990527 ATTAAAGTTT
990537 AAAATAAATTTAATTTAAA
1 AAAATAAATTTAATTTAAA
* *
990556 AAATTTAATTTAATTT--A
1 AAAATAAATTTAATTTAAA
*
990573 AAAATCAAAATTAA-TTAAA
1 AAAAT-AAATTTAATTTAAA
*
990592 GTTTAAAATAAATTTAATTTTAA
1 ----AAAATAAATTTAATTTAAA
990615 AAAATAGAATTTAA-TTAAA
1 AAAATA-AATTTAATTTAAA
990634 AAGAATAA
1 AA-AATAA
990642 TTAAAGAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
17 7 0.10
18 6 0.09
19 28 0.41
20 11 0.16
22 7 0.10
23 9 0.13
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (19 bp):
AAAATAAATTTAATTTAAA
Found at i:990645 original size:59 final size:59
Alignment explanation
Indices: 990521--990635 Score: 187
Period size: 59 Copynumber: 1.9 Consensus size: 59
990511 AGTTGAAAAT
* **
990521 AAATGAATTAAAGTTTAAAATAAATTTAATTTAAAAAATTTAATTTAATTTAAAAATCA
1 AAATTAATTAAAGTTTAAAATAAATTTAATTTAAAAAATAGAATTTAATTTAAAAATCA
990580 AAATTAATTAAAGTTTAAAATAAATTTAATTTTAAAAAATAGAATTTAA-TTAAAAA
1 AAATTAATTAAAGTTTAAAATAAATTTAA-TTTAAAAAATAGAATTTAATTTAAAAA
990636 GAATAATTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
59 35 0.67
60 17 0.33
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (59 bp):
AAATTAATTAAAGTTTAAAATAAATTTAATTTAAAAAATAGAATTTAATTTAAAAATCA
Found at i:992222 original size:29 final size:28
Alignment explanation
Indices: 992183--992266 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 28
992173 TAAATGTGAT
992183 TTTGGGCCTAATGGGCCATATACAGGTGG
1 TTTGGGCCTAATGGGCCATATACAGGT-G
**
992212 TTTGGGCCTAATGGGCCATATGA-ATATG
1 TTTGGGCCTAATGGGCCATAT-ACAGGTG
* * *
992240 ATTGGGCTTAATGGGCCAGATACAGGT
1 TTTGGGCCTAATGGGCCATATACAGGT
992267 ATGTGAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.02
28 21 0.46
29 23 0.50
30 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (28 bp):
TTTGGGCCTAATGGGCCATATACAGGTG
Found at i:992253 original size:28 final size:28
Alignment explanation
Indices: 992142--992257 Score: 108
Period size: 28 Copynumber: 4.0 Consensus size: 28
992132 ATGAACATGA
* * *
992142 ATATGAATGTGACTGGACATAATGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
* *
992170 ATGTAAATGTGATTTTGGGCCTAATGGGCC
1 ATATGAATGTGA--TTGGGCCTAATGGGCC
* *
992200 ATAT-ACAGGTGGTTTGGGCCTAATGGGCC
1 ATATGA-ATGT-GATTGGGCCTAATGGGCC
* *
992229 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
992257 A
1 A
992258 GATACAGGTA
Statistics
Matches: 71, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
28 27 0.38
29 23 0.32
30 20 0.28
31 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATGGGCC
Found at i:992581 original size:27 final size:25
Alignment explanation
Indices: 992539--992592 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
992529 AAGCCGTAAT
* *
992539 TAAGGGGAAATTACCAAAATGCCCC
1 TAAGGGGAAATGACCAAAATACCCC
992564 TAAGGGCGAAAATGACCAAAATACCCC
1 TAAGGG-G-AAATGACCAAAATACCCC
992591 TA
1 TA
992593 GGTGTAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.24
26 1 0.04
27 18 0.72
ACGTcount: A:0.43, C:0.24, G:0.19, T:0.15
Consensus pattern (25 bp):
TAAGGGGAAATGACCAAAATACCCC
Found at i:993469 original size:26 final size:27
Alignment explanation
Indices: 993386--993474 Score: 81
Period size: 27 Copynumber: 3.1 Consensus size: 27
993376 TTTTCTTCAT
* *
993386 GTTTTTGAATAAGATAAAAAACTATGA
1 GTTTTTGAATAACATAAAAAATTATGA
* *
993413 GTTTCTAAATAACATAAAATCAAGTAATATG-
1 GTTTTTGAATAACATAAAA--AA-T--TATGA
*
993444 GTTTTTGAATAACATAAAGAATTATGA
1 GTTTTTGAATAACATAAAAAATTATGA
993471 GTTT
1 GTTT
993475 CGATTTTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
26 4 0.08
27 20 0.41
28 1 0.02
29 4 0.08
31 16 0.33
32 4 0.08
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (27 bp):
GTTTTTGAATAACATAAAAAATTATGA
Found at i:1002113 original size:20 final size:20
Alignment explanation
Indices: 1002085--1002124 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1002075 CTCTAATTAG
*
1002085 AATCTCTAAAAATCAGCTAT
1 AATCCCTAAAAATCAGCTAT
* *
1002105 AATCCCTAAAGATTAGCTAT
1 AATCCCTAAAAATCAGCTAT
1002125 TCAATGCTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (20 bp):
AATCCCTAAAAATCAGCTAT
Found at i:1008326 original size:26 final size:26
Alignment explanation
Indices: 1008297--1008400 Score: 165
Period size: 26 Copynumber: 4.0 Consensus size: 26
1008287 ATGCCCATCG
1008297 TGGAACATTTACCTAAACCATTATCA
1 TGGAACATTTACCTAAACCATTATCA
*
1008323 TGGAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAAACCATTATCA
* *
1008349 TGGAATATTTACCTAATCCATTATCA
1 TGGAACATTTACCTAAACCATTATCA
1008375 TGGAACATTTACCT-AACCTATTATCA
1 TGGAACATTTACCTAAACC-ATTATCA
1008401 ATTTGTACCA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
25 3 0.04
26 69 0.96
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.34
Consensus pattern (26 bp):
TGGAACATTTACCTAAACCATTATCA
Found at i:1013692 original size:28 final size:28
Alignment explanation
Indices: 1013630--1013685 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1013620 AGAAAAAGAA
1013630 TGAACATATTCCTAGTAAGTTTTGAGTT
1 TGAACATATTCCTAGTAAGTTTTGAGTT
1013658 TGAACATATTCCTAGTAAGTTTTGAGTT
1 TGAACATATTCCTAGTAAGTTTTGAGTT
1013686 GAAACATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.43
Consensus pattern (28 bp):
TGAACATATTCCTAGTAAGTTTTGAGTT
Found at i:1020645 original size:18 final size:18
Alignment explanation
Indices: 1020622--1020659 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1020612 CTCAGCATCC
1020622 AAACAAAACAAAACAATA
1 AAACAAAACAAAACAATA
* *
1020640 AAACAAAATAAAATAATA
1 AAACAAAACAAAACAATA
1020658 AA
1 AA
1020660 TAAATTACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (18 bp):
AAACAAAACAAAACAATA
Found at i:1023071 original size:12 final size:13
Alignment explanation
Indices: 1023053--1023077 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1023043 TAGCCATAAG
1023053 TTTTTTTGTATTC
1 TTTTTTTGTATTC
1023066 TTTTTTTGTATT
1 TTTTTTTGTATT
1023078 GGCCTAAGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.04, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTTTTTGTATTC
Found at i:1024273 original size:47 final size:47
Alignment explanation
Indices: 1024243--1024530 Score: 504
Period size: 47 Copynumber: 6.1 Consensus size: 47
1024233 CACTTCCACG
** * *
1024243 TTCATCACATTGGCCATTCTACCTTACCACATATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
1024290 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
1024337 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
*
1024384 TTCATCACATTGGCCATTCGGCCTCATCACATATTTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
*
1024431 TTCATCACATTGGCCATTCGGCCTCATCACATATTTGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
* *
1024478 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
1024525 TTCATC
1 TTCATC
1024531 TCATAGAATC
Statistics
Matches: 233, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 233 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.35
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACA
Found at i:1024311 original size:94 final size:94
Alignment explanation
Indices: 1024203--1024530 Score: 473
Period size: 94 Copynumber: 3.5 Consensus size: 94
1024193 ACACATTTCG
* ** * * * * **
1024203 CATTAGCCATTCGGCTTCGCCACATATATACACT-TCCACGTTCATCACATTGGCCATTCTACCT
1 CATTGGCCATTCGGCTTCATCACATATTTGCA-TGTTCACATTCATCACATTGGCCATTCGGCCT
* *
1024267 TACCACATATATGCATGTTCACATTCATCA
65 TATCACATATTTGCATGTTCACATTCATCA
1024297 CATTGGCCATTCGGCCTT-ATCACATATTTGCATGTTCACATTCATCACATTGGCCATTCGGCCT
1 CATTGGCCATTCGG-CTTCATCACATATTTGCATGTTCACATTCATCACATTGGCCATTCGGCCT
1024361 TATCACATATTTGCATGTTCACATTCATCA
65 TATCACATATTTGCATGTTCACATTCATCA
* *
1024391 CATTGGCCATTCGGCCTCATCACATATTTGCATGTTCACATTCATCACATTGGCCATTCGGCCTC
1 CATTGGCCATTCGGCTTCATCACATATTTGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1024456 ATCACATATTTGCATGTTCACATTCATCA
66 ATCACATATTTGCATGTTCACATTCATCA
* *
1024485 CATTGGCCATTCGGCCTT-ATCACACATATGCATGTTCACATTCATC
1 CATTGGCCATTCGG-CTTCATCACATATTTGCATGTTCACATTCATC
1024531 TCATAGAATC
Statistics
Matches: 214, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
93 3 0.01
94 206 0.96
95 5 0.02
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.34
Consensus pattern (94 bp):
CATTGGCCATTCGGCTTCATCACATATTTGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCACATATTTGCATGTTCACATTCATCA
Found at i:1024566 original size:94 final size:91
Alignment explanation
Indices: 1024278--1024566 Score: 303
Period size: 94 Copynumber: 3.1 Consensus size: 91
1024268 ACCACATATA
1024278 TGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACATTCATC
1 TGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACATTCATC
* * * ** *
1024343 ACATTG-GCCATTCGGCCTTATCACATATT
66 ACATAGATCCAATC-AACATAT-A-A-ATT
*
1024372 TGCATGTTCACATTCATCACATTGGCCATTCGGCCTCATCACATATTTGCATGTTCACATTCATC
1 TGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACATTCATC
* * * ** *
1024437 ACATTG-GCCATTCGGCCTCATCACATATT
66 ACATAGATCCAATCAACAT-AT-A-A-ATT
* *
1024466 TGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATC
1 TGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACATTCATC
* *
1024531 TCATAGAATCCTAAATCAAAATATAAATT
66 ACATAG-ATCC--AATCAACATATAAATT
*
1024560 TTCATGT
1 TGCATGT
1024567 ATTCACATCA
Statistics
Matches: 175, Mismatches: 15, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
93 3 0.02
94 162 0.93
95 1 0.01
96 3 0.02
97 2 0.01
98 4 0.02
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (91 bp):
TGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATTTGCATGTTCACATTCATC
ACATAGATCCAATCAACATATAAATT
Found at i:1034206 original size:3 final size:3
Alignment explanation
Indices: 1034198--1034225 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1034188 AGTTCGTTTA
1034198 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1034226 CTTATGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1037056 original size:15 final size:15
Alignment explanation
Indices: 1037036--1037103 Score: 59
Period size: 15 Copynumber: 4.4 Consensus size: 15
1037026 GGACTTATGA
1037036 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
1037051 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
1037068 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
*
1037085 ATA-TTAATATTAA-
1 ATATTTATTATTAAT
1037098 ATATTT
1 ATATTT
1037104 TCAATAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.25
15 12 0.27
16 1 0.02
17 7 0.16
18 1 0.02
19 9 0.20
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:1037153 original size:13 final size:14
Alignment explanation
Indices: 1037117--1037163 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
1037107 ATAATATGTG
*
1037117 AATAATATTATTTAA
1 AATATTATT-TTTAA
1037132 AATTATTATTTTTAA
1 AA-TATTATTTTTAA
*
1037147 AAT-TTATTGTTAA
1 AATATTATTTTTAA
1037160 AATA
1 AATA
1037164 AAATTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 12 0.43
14 1 0.04
15 9 0.32
16 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
AATATTATTTTTAA
Found at i:1037191 original size:20 final size:20
Alignment explanation
Indices: 1037166--1037227 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
1037156 TTAAAATAAA
1037166 ATTAAAATATTAAATAATTT
1 ATTAAAATATTAAATAATTT
*
1037186 ATTAAAATAATAAAT--TTT
1 ATTAAAATATTAAATAATTT
**
1037204 ATTTATTATATT-AATAATTT
1 A-TTAAAATATTAAATAATTT
1037224 ATTA
1 ATTA
1037228 TATCACTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
18 7 0.20
19 10 0.29
20 18 0.51
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTAAAATATTAAATAATTT
Found at i:1038019 original size:20 final size:19
Alignment explanation
Indices: 1037994--1038032 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1037984 CTTTTTCTTT
1037994 ATAATTTGTTGAATTTTTTA
1 ATAATTTGTTG-ATTTTTTA
1038014 ATAATTTGTTGATTTTTTA
1 ATAATTTGTTGATTTTTTA
1038033 TAAAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (19 bp):
ATAATTTGTTGATTTTTTA
Found at i:1050658 original size:23 final size:22
Alignment explanation
Indices: 1050615--1050663 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
1050605 ACGAGGTTTA
*
1050615 AATTGAATTAATCGATTAAATT
1 AATTAAATTAATCGATTAAATT
1050637 GAATTAAATTAATC-ATTAAAATT
1 -AATTAAATTAATCGATT-AAATT
1050660 AATT
1 AATT
1050664 TTGATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (22 bp):
AATTAAATTAATCGATTAAATT
Found at i:1051671 original size:12 final size:10
Alignment explanation
Indices: 1051640--1051743 Score: 66
Period size: 10 Copynumber: 9.5 Consensus size: 10
1051630 GTTTTAGAAA
1051640 TTTTTAAA-T
1 TTTTTAAATT
1051649 TTTTTAAATT
1 TTTTTAAATT
*
1051659 TTTTTACATAT
1 TTTTTAAAT-T
1051670 TTTTTAGAATT
1 TTTTTA-AATT
1051681 TTTATTATAATTT
1 TTT-TTA-AA-TT
1051694 TTTTTAAAATAT
1 TTTTT-AAAT-T
*
1051706 AAGTTTTATAATT
1 --TTTTTA-AATT
**
1051719 TTTAAAAATT
1 TTTTTAAATT
*
1051729 ATTTTAAATT
1 TTTTTAAATT
1051739 TTTTT
1 TTTTT
1051744 TGTAATTTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 19
0.71 0.11 0.18
Matches are distributed among these distances:
9 8 0.11
10 24 0.32
11 15 0.20
12 12 0.16
13 8 0.11
14 7 0.09
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:1051672 original size:11 final size:11
Alignment explanation
Indices: 1051647--1051701 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
1051637 AAATTTTTAA
1051647 ATTTTTTAAAT
1 ATTTTTTAAAT
*
1051658 -TTTTTTACAT
1 ATTTTTTAAAT
1051668 ATTTTTTAGAAT
1 ATTTTTTA-AAT
1051680 -TTTTATTATAAT
1 ATTTT-TTA-AAT
*
1051692 TTTTTTTAAA
1 ATTTTTTAAA
1051702 ATATAAGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 9 0.24
11 13 0.35
12 11 0.30
13 4 0.11
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
ATTTTTTAAAT
Found at i:1051724 original size:23 final size:20
Alignment explanation
Indices: 1051694--1051741 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 20
1051684 ATTATAATTT
1051694 TTTTTAAAATATAAGTTTTATAA
1 TTTTTAAAA-ATAA-TTTTA-AA
*
1051717 TTTTTAAAAATTATTTTAAA
1 TTTTTAAAAATAATTTTAAA
1051737 TTTTT
1 TTTTT
1051742 TTTGTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 5 0.21
22 3 0.12
23 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTTAAAAATAATTTTAAA
Found at i:1057726 original size:9 final size:9
Alignment explanation
Indices: 1057712--1057744 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
1057702 TTCTTATATT
1057712 TTTTTTTAC
1 TTTTTTTAC
1057721 TTTTTTTA-
1 TTTTTTTAC
1057729 TTTTTTTAC
1 TTTTTTTAC
1057738 TTTTTTT
1 TTTTTTT
1057745 CTTATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTAC
Found at i:1057734 original size:17 final size:17
Alignment explanation
Indices: 1057712--1057744 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1057702 TTCTTATATT
1057712 TTTTTTTACTTTTTTTA
1 TTTTTTTACTTTTTTTA
1057729 TTTTTTTACTTTTTTT
1 TTTTTTTACTTTTTTT
1057745 CTTATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTACTTTTTTTA
Found at i:1057838 original size:18 final size:17
Alignment explanation
Indices: 1057787--1057834 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
1057777 TTTTTTTAGT
*
1057787 TTTATATTATTTTCTTAA
1 TTTATATTATTAT-TTAA
* *
1057805 TTTATTTTGCTTATTTAA
1 TTTATATT-ATTATTTAA
1057823 TTTATATTATTA
1 TTTATATTATTA
1057835 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATATTATTATTTAA
Found at i:1057847 original size:22 final size:21
Alignment explanation
Indices: 1057821--1057909 Score: 67
Period size: 21 Copynumber: 4.1 Consensus size: 21
1057811 TTGCTTATTT
*
1057821 AATTTATATTATTAATTTTAAA
1 AATTTATAATATT-ATTTTAAA
*
1057843 AATTTGTAATA-TATATTTAAA
1 AATTTATAATATTAT-TTTAAA
* *
1057864 ATGTTTTATAATATT-TTTTTAA
1 A--ATTTATAATATTATTTTAAA
*
1057886 AATTT-TAATTATTATTTTTAA
1 AATTTATAA-TATTATTTTAAA
1057907 AAT
1 AAT
1057910 ATTTTTTAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
19 3 0.05
20 9 0.16
21 18 0.33
22 15 0.27
23 9 0.16
24 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AATTTATAATATTATTTTAAA
Found at i:1057891 original size:21 final size:21
Alignment explanation
Indices: 1057836--1057909 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
1057826 ATATTATTAA
* * *
1057836 TTTTAAAAATTTGTAATATAT
1 TTTTAAAATTTTATAATATTT
*
1057857 ATTTAAAATGTTTTATAATATTT
1 TTTTAAAA--TTTTATAATATTT
*
1057880 TTTTAAAATTTTA-ATTATTAT
1 TTTTAAAATTTTATAATATT-T
1057901 TTTTAAAAT
1 TTTTAAAAT
1057910 ATTTTTTAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.11
21 22 0.50
23 17 0.39
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTTAAAATTTTATAATATTT
Found at i:1058200 original size:18 final size:18
Alignment explanation
Indices: 1058177--1058223 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
1058167 GTGACTATTA
1058177 ATAAATTTAAATATAAAT
1 ATAAATTTAAATATAAAT
*
1058195 ATAAATTTTAA-A-AAAT
1 ATAAATTTAAATATAAAT
*
1058211 ATATA-TTAAATAT
1 ATAAATTTAAATAT
1058224 TATTTTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
15 4 0.17
16 9 0.38
17 1 0.04
18 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAATTTAAATATAAAT
Found at i:1058599 original size:23 final size:21
Alignment explanation
Indices: 1058573--1058622 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1058563 GTATTGTATA
1058573 TTTAAAATGTTTTATAATATT-TT
1 TTTAAAA--TTTTA-AATATTATT
*
1058596 TTTACAATTTTAAATATTATT
1 TTTAAAATTTTAAATATTATT
1058617 TTTAAA
1 TTTAAA
1058623 TTCTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 6 0.25
21 12 0.50
23 6 0.25
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTAAAATTTTAAATATTATT
Found at i:1058613 original size:20 final size:21
Alignment explanation
Indices: 1058582--1058624 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1058572 ATTTAAAATG
1058582 TTTTATAATATT-TTTTTACAA
1 TTTTATAATATTATTTTTA-AA
1058603 TTTTA-AATATTATTTTTAAA
1 TTTTATAATATTATTTTTAAA
1058623 TT
1 TT
1058625 CTTTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTATAATATTATTTTTAAA
Found at i:1058743 original size:18 final size:16
Alignment explanation
Indices: 1058720--1058756 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
1058710 GTGACTATTA
1058720 ATAAATTTAAATATAAAT
1 ATAAATTTAAA-A-AAAT
1058738 ATAAATTTAAAAAAAT
1 ATAAATTTAAAAAAAT
1058754 ATA
1 ATA
1058757 TATTGAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATTTAAAAAAAT
Found at i:1061778 original size:30 final size:30
Alignment explanation
Indices: 1061742--1061894 Score: 243
Period size: 30 Copynumber: 5.1 Consensus size: 30
1061732 GTCCCAGAGC
* *
1061742 AGTTCATATAACCCGGACATAGGTGGTTCG
1 AGTTCATATCACCCGGACATGGGTGGTTCG
1061772 AGTTCATATCACCCGGACATGGGTGGTTCG
1 AGTTCATATCACCCGGACATGGGTGGTTCG
1061802 AGTTCATATCACCCGGACATGGGTGGTTCG
1 AGTTCATATCACCCGGACATGGGTGGTTCG
* *
1061832 AGTTTATATCACCCGGACATGGGTGGTTCA
1 AGTTCATATCACCCGGACATGGGTGGTTCG
* * *
1061862 AGTTCATATCACCCGGATATAGGCGGTTCG
1 AGTTCATATCACCCGGACATGGGTGGTTCG
1061892 AGT
1 AGT
1061895 CCATTTGACC
Statistics
Matches: 114, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 114 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (30 bp):
AGTTCATATCACCCGGACATGGGTGGTTCG
Found at i:1064920 original size:31 final size:34
Alignment explanation
Indices: 1064861--1064932 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 34
1064851 GTTTTATAAT
1064861 ATATT-TTTTTATAAATATTAAAAATATATTTTCA
1 ATATTATTTTTATAAATATT-AAAATATATTTTCA
*
1064895 A-ATTATTTTT-TAAATATT-AAATATATTTTTA
1 ATATTATTTTTATAAATATTAAAATATATTTTCA
1064926 ATATTAT
1 ATATTAT
1064933 AAAACATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
31 13 0.37
32 5 0.14
33 11 0.31
34 6 0.17
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (34 bp):
ATATTATTTTTATAAATATTAAAATATATTTTCA
Found at i:1064941 original size:19 final size:19
Alignment explanation
Indices: 1064901--1064988 Score: 65
Period size: 19 Copynumber: 4.6 Consensus size: 19
1064891 TTCAAATTAT
*
1064901 TTTTTAAATATTA-AATATA
1 TTTTT-AATATTATAAAATA
*
1064920 TTTTTAATATTATAAAACA
1 TTTTTAATATTATAAAATA
**
1064939 TTTAAAATGATT-TAAAATA
1 TTTTTAAT-ATTATAAAATA
*
1064958 TTTTTTAATATT-TTAAATGA
1 -TTTTTAATATTATAAAAT-A
*
1064978 TTTTAAATATT
1 TTTTTAATATT
1064989 TTTTAAATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
18 7 0.12
19 39 0.70
20 10 0.18
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTTTAATATTATAAAATA
Found at i:1064989 original size:29 final size:28
Alignment explanation
Indices: 1064888--1065000 Score: 109
Period size: 29 Copynumber: 3.9 Consensus size: 28
1064878 TTAAAAATAT
* *
1064888 ATTTTCAAATTATTTTTTAAATATTAAATAT
1 ATTTT-AAA-TATTTTTTAAATTTTAAAT-G
* * ** *
1064919 ATTTTTAATATTATAAAACATTTAAAATG
1 ATTTTAAATATTTTTTAA-ATTTTAAATG
*
1064948 ATTTAAAATATTTTTTAATATTTTAAATG
1 ATTTTAAATATTTTTTAA-ATTTTAAATG
1064977 ATTTTAAATATTTTTTAAATTTTA
1 ATTTTAAATATTTTTTAAATTTTA
1065001 CATAGAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
28 6 0.09
29 46 0.70
30 9 0.14
31 5 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (28 bp):
ATTTTAAATATTTTTTAAATTTTAAATG
Found at i:1064991 original size:10 final size:9
Alignment explanation
Indices: 1064902--1064990 Score: 63
Period size: 10 Copynumber: 9.4 Consensus size: 9
1064892 TCAAATTATT
1064902 TTTTAAATA
1 TTTTAAATA
*
1064911 -TTAAATATA
1 TTTTAA-ATA
*
1064920 TTTTTAATA
1 TTTTAAATA
* *
1064929 TTATAAAACA
1 TT-TTAAATA
*
1064939 TTTAAAATGA
1 TTTTAAAT-A
*
1064949 TTTAAAATA
1 TTTTAAATA
*
1064958 TTTTTTAATA
1 -TTTTAAATA
1064968 TTTTAAATGA
1 TTTTAAAT-A
1064978 TTTTAAATA
1 TTTTAAATA
1064987 TTTT
1 TTTT
1064991 TTAAATTTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
8 4 0.06
9 26 0.41
10 34 0.53
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (9 bp):
TTTTAAATA
Found at i:1065874 original size:18 final size:18
Alignment explanation
Indices: 1065829--1065885 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
1065819 TTTTAAAATT
*
1065829 AATAATATAAATTAAATA
1 AATAATATAAATTAAAAA
* *
1065847 AGTAAAATAAATTAAAAA
1 AATAATATAAATTAAAAA
1065865 AATAATATAAAACTTAAAAA
1 AATAATAT-AAA-TTAAAAA
1065885 A
1 A
1065886 GAAAAAAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 21 0.66
19 3 0.09
20 8 0.25
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AATAATATAAATTAAAAA
Found at i:1065945 original size:18 final size:16
Alignment explanation
Indices: 1065837--1065954 Score: 76
Period size: 17 Copynumber: 6.7 Consensus size: 16
1065827 TTAATAATAT
*
1065837 AAATTAAATAAGTAAAA
1 AAATTAAAAAAG-AAAA
*
1065854 TAAATTAAAAAAATAATATA
1 -AAATT-AAAAAAGAA-A-A
1065874 AAACTTAAAAAAGAAAA
1 AAA-TTAAAAAAGAAAA
* *
1065891 AAATCTAAGAAAGAGACA
1 AAAT-TAAAAAAGA-AAA
1065909 AAATATAAAAAA-AATAA
1 AAAT-TAAAAAAGAA-AA
1065926 AAAGTTAAAAAAGTAAAA
1 AAA-TTAAAAAAG-AAAA
*
1065944 AAAGTAAAAAA
1 AAATTAAAAAA
1065955 ATATAATAAC
Statistics
Matches: 81, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
16 2 0.02
17 31 0.38
18 26 0.32
19 19 0.23
20 3 0.04
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.18
Consensus pattern (16 bp):
AAATTAAAAAAGAAAA
Found at i:1069268 original size:20 final size:19
Alignment explanation
Indices: 1069230--1069269 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1069220 AAACACACAA
*
1069230 AAACAAACAATAGACAAAC
1 AAACAAACAATACACAAAC
*
1069249 AAACAAAACAATACATAAAC
1 AAAC-AAACAATACACAAAC
1069269 A
1 A
1069270 TTGATGCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.70, C:0.20, G:0.03, T:0.07
Consensus pattern (19 bp):
AAACAAACAATACACAAAC
Found at i:1073530 original size:28 final size:28
Alignment explanation
Indices: 1073498--1073553 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1073488 CAAAAGTTGA
1073498 ACAACAGAAACACCATTAATGCCTACGG
1 ACAACAGAAACACCATTAATGCCTACGG
*
1073526 ACAACAGAAGCACCATTAATGCCTACGG
1 ACAACAGAAACACCATTAATGCCTACGG
1073554 TGCGACGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.29, G:0.16, T:0.14
Consensus pattern (28 bp):
ACAACAGAAACACCATTAATGCCTACGG
Found at i:1080712 original size:3 final size:3
Alignment explanation
Indices: 1080667--1080695 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1080657 GTAGTAACCC
1080667 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1080696 ATACAGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1092878 original size:13 final size:13
Alignment explanation
Indices: 1092860--1092884 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1092850 CAATTTTTTA
1092860 TTTTTAATTAATG
1 TTTTTAATTAATG
1092873 TTTTTAATTAAT
1 TTTTTAATTAAT
1092885 AAATATATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:1094714 original size:4 final size:4
Alignment explanation
Indices: 1094707--1094745 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
1094697 AAACAATGTA
* *
1094707 ATAC ATAC ATAC ATGC AAAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1094746 GCTACCATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.03, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:1100769 original size:26 final size:26
Alignment explanation
Indices: 1100739--1100794 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
1100729 TTAGAATCGA
1100739 AATCTTGAAATCTAATCAATTAGATC
1 AATCTTGAAATCTAATCAATTAGATC
1100765 AATCTTGAAATCTAATCAATTAGATC
1 AATCTTGAAATCTAATCAATTAGATC
1100791 AATC
1 AATC
1100795 CGGACAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (26 bp):
AATCTTGAAATCTAATCAATTAGATC
Found at i:1107722 original size:26 final size:26
Alignment explanation
Indices: 1107693--1107801 Score: 182
Period size: 26 Copynumber: 4.2 Consensus size: 26
1107683 TGGTACAAAT
*
1107693 TGATAATGGGCTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
1107719 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1107745 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
1107771 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
1107797 TGATA
1 TGATA
1107802 GGAATTTCAT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:1109047 original size:27 final size:26
Alignment explanation
Indices: 1109005--1109145 Score: 183
Period size: 27 Copynumber: 5.2 Consensus size: 26
1108995 AGGAAGCGTC
*
1109005 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
* *
1109032 CTGCTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
1109059 CTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
1109086 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
1109113 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACATTATCTG-AT
1109140 CTGGTG
1 CTGGTG
1109146 ACTTCATCAC
Statistics
Matches: 100, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
26 10 0.10
27 88 0.88
28 2 0.02
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:1109143 original size:54 final size:53
Alignment explanation
Indices: 1109005--1109145 Score: 228
Period size: 54 Copynumber: 2.6 Consensus size: 53
1108995 AGGAAGCGTC
*
1109005 CTGGTGGCTATGCCACAATTATCTGATCTGCTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAA-TATCTGATCTGGTGGCTCTGCCACATATATCTGTT
*
1109059 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-AATATCTGATCTGGTGGCTCTGCCACATATATCTGTT
*
1109113 CTGGTGGCTCTGCCACAATATCTGTATCTGGTG
1 CTGGTGGCTATGCCACAATATCTG-ATCTGGTG
1109146 ACTTCATCAC
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
53 7 0.09
54 73 0.90
55 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATATCTGATCTGGTGGCTCTGCCACATATATCTGTT
Found at i:1113733 original size:5 final size:5
Alignment explanation
Indices: 1113723--1113748 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1113713 CAAATTCAAG
1113723 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
1113749 AAGTTATCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:1114370 original size:26 final size:26
Alignment explanation
Indices: 1114336--1114387 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1114326 ATCTCTTTGT
1114336 TTTTAGTTTTAATAATCTAGTCCAAA
1 TTTTAGTTTTAATAATCTAGTCCAAA
1114362 TTTTAGTTTTAATAATCTAGTCCAAA
1 TTTTAGTTTTAATAATCTAGTCCAAA
1114388 ACTAAAGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.46
Consensus pattern (26 bp):
TTTTAGTTTTAATAATCTAGTCCAAA
Found at i:1117213 original size:22 final size:21
Alignment explanation
Indices: 1117195--1117236 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1117185 TCCTTTTTTG
*
1117195 ATTTTTTTATATATTTTTTTAA
1 ATTTTATTAT-TATTTTTTTAA
*
1117217 ATTTTATTATTATTTATTTA
1 ATTTTATTATTATTTTTTTA
1117237 CTTAAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTTATTATTATTTTTTTAA
Found at i:1117564 original size:118 final size:118
Alignment explanation
Indices: 1117358--1117570 Score: 354
Period size: 118 Copynumber: 1.8 Consensus size: 118
1117348 TTTTACCCAA
* *
1117358 CACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCTAAGCACCCTACCCCGGTTGCTCAG
1 CACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAG
* *
1117423 TCAGTCACGATTTGAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACTTGT
66 TCAGTCACGATCTAAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACTTGT
*
1117476 CACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTTAG
1 CACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAG
***
1117541 TCAGTCACGATCTAAGTTGTACTCATAACC
66 TCAGTCACGATCTAAGCCATACTCATAACC
1117571 ATGGAAAACA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
118 87 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (118 bp):
CACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAG
TCAGTCACGATCTAAGCCATACTCATAACCTCGGCTAGCGGAGTTTTACTTGT
Found at i:1118377 original size:43 final size:42
Alignment explanation
Indices: 1118330--1118422 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 42
1118320 TGAAAAGGGG
* * * *
1118330 TGTTTGGCTGCAG-GTTTTGGGGATTCTAAGGCTGGAATAGGAC
1 TGTTTGGCTGCAGAGATAT-GGCATTCT-AGGCTGGAATAGAAC
*
1118373 TGTTTGGCTGCAGAGATATGGCATTCTGGGCTGGAATAGAAC
1 TGTTTGGCTGCAGAGATATGGCATTCTAGGCTGGAATAGAAC
1118415 TGTTTGGC
1 TGTTTGGC
1118423 AGCATGGATA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
42 21 0.48
43 20 0.45
44 3 0.07
ACGTcount: A:0.19, C:0.13, G:0.35, T:0.32
Consensus pattern (42 bp):
TGTTTGGCTGCAGAGATATGGCATTCTAGGCTGGAATAGAAC
Found at i:1118553 original size:16 final size:15
Alignment explanation
Indices: 1118528--1118584 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 15
1118518 AATATTTAAC
1118528 TAAAATAAAATAAAAA
1 TAAAA-AAAATAAAAA
1118544 TAAAAGAAAATAATAAA
1 TAAAA-AAAATAA-AAA
* *
1118561 TAATAAAAAGAAAAA
1 TAAAAAAAATAAAAA
*
1118576 GAAAAAAAA
1 TAAAAAAAA
1118585 GATTGGGTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 10 0.29
16 18 0.51
17 7 0.20
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (15 bp):
TAAAAAAAATAAAAA
Found at i:1118553 original size:21 final size:21
Alignment explanation
Indices: 1118536--1118574 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1118526 ACTAAAATAA
1118536 AATAAA-AAT-AAAAGAAAAT
1 AATAAATAATAAAAAGAAAAT
1118555 AATAAATAATAAAAAGAAAA
1 AATAAATAATAAAAAGAAAA
1118575 AGAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (21 bp):
AATAAATAATAAAAAGAAAAT
Found at i:1124357 original size:16 final size:16
Alignment explanation
Indices: 1124336--1124368 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1124326 GCCTCCGGTT
1124336 GTCTCATTCCGCCTTG
1 GTCTCATTCCGCCTTG
1124352 GTCTCATTCCGCCTTG
1 GTCTCATTCCGCCTTG
1124368 G
1 G
1124369 GCTTAATCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.36, G:0.21, T:0.36
Consensus pattern (16 bp):
GTCTCATTCCGCCTTG
Found at i:1129999 original size:35 final size:35
Alignment explanation
Indices: 1129959--1130032 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
1129949 TTAAAACATG
*
1129959 TAAGAATTTAATGAGAGTTTCTTTTAATACAAATT
1 TAAGAATTTAATGAGAATTTCTTTTAATACAAATT
1129994 TAAGAATTTAATGAGAATTTCTTTTAATACAAATT
1 TAAGAATTTAATGAGAATTTCTTTTAATACAAATT
1130029 TAAG
1 TAAG
1130033 GGTCAAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (35 bp):
TAAGAATTTAATGAGAATTTCTTTTAATACAAATT
Found at i:1139858 original size:43 final size:42
Alignment explanation
Indices: 1139810--1139942 Score: 171
Period size: 43 Copynumber: 3.1 Consensus size: 42
1139800 CCGGCATTAC
*
1139810 GCCTGCTAGGCAAGAAGGCCCGAATACATATCACCAGCACGAA
1 GCCTGCTAGGCAAGAAGGCCCGAATACA-ATCACCAGCACTAA
* *
1139853 GCCTGCTAGGCATGAAGGCCCGAATACACATCACCGGCACTAA
1 GCCTGCTAGGCAAGAAGGCCCGAATACA-ATCACCAGCACTAA
* * *
1139896 GCCTACTAGGCACA-AAGGCCCGAATATAAT-ACCAGCACTAG
1 GCCTGCTAGGCA-AGAAGGCCCGAATACAATCACCAGCACTAA
1139937 GCCTGC
1 GCCTGC
1139943 GGGATTTATC
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
41 14 0.18
42 2 0.03
43 63 0.80
ACGTcount: A:0.32, C:0.32, G:0.23, T:0.14
Consensus pattern (42 bp):
GCCTGCTAGGCAAGAAGGCCCGAATACAATCACCAGCACTAA
Found at i:1157666 original size:18 final size:18
Alignment explanation
Indices: 1157643--1157699 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
1157633 TGATTCTTTT
1157643 AAAATAAAAATAAATTAA
1 AAAATAAAAATAAATTAA
* *
1157661 AAAATATAAGTAAATTAA
1 AAAATAAAAATAAATTAA
* *
1157679 ATTATTAAAAATCAAATTAA
1 A-AAATAAAAAT-AAATTAA
1157699 A
1 A
1157700 TTATATTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 17 0.55
19 6 0.19
20 8 0.26
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
AAAATAAAAATAAATTAA
Found at i:1161409 original size:20 final size:19
Alignment explanation
Indices: 1161384--1161437 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
1161374 TTGTACGAGT
1161384 TTGCACTTCGGTGCCTCTG
1 TTGCACTTCGGTGCCTCTG
*
1161403 ATTGCACATT-TGTGCCTCTG
1 -TTGCAC-TTCGGTGCCTCTG
*
1161423 TCTACACTTCGGTGC
1 T-TGCACTTCGGTGC
1161438 TTTTGTTACG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 3 0.11
20 23 0.82
21 2 0.07
ACGTcount: A:0.11, C:0.30, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGCACTTCGGTGCCTCTG
Found at i:1163242 original size:30 final size:31
Alignment explanation
Indices: 1163199--1163261 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
1163189 GAATGGCTTG
* *
1163199 GATATGCCTAGATGTTGATAATGTGTTTTGT
1 GATATGCCAAGATGTTAATAATGTGTTTTGT
1163230 GATAT-CCAAGATGTTAATAATGTGTTTTGT
1 GATATGCCAAGATGTTAATAATGTGTTTTGT
1163260 GA
1 GA
1163262 CATATTGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.43
Consensus pattern (31 bp):
GATATGCCAAGATGTTAATAATGTGTTTTGT
Found at i:1170394 original size:17 final size:17
Alignment explanation
Indices: 1170372--1170409 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1170362 ATGTGTATAA
*
1170372 TTATATCAAATCAATTT
1 TTATATCAAATCAATAT
*
1170389 TTATATTAAATCAATAT
1 TTATATCAAATCAATAT
1170406 TTAT
1 TTAT
1170410 GTATAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATATCAAATCAATAT
Found at i:1173253 original size:31 final size:31
Alignment explanation
Indices: 1173210--1173324 Score: 187
Period size: 31 Copynumber: 3.7 Consensus size: 31
1173200 TTAGTCTTGA
*
1173210 CATAT-ACTGGGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1173240 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* *
1173271 CATATCATTGGGCTGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
1173302 CATATCACTGGGCTGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
1173325 ACTGTAAACG
Statistics
Matches: 80, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 5 0.06
31 75 0.94
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:1173395 original size:42 final size:42
Alignment explanation
Indices: 1173348--1173481 Score: 241
Period size: 42 Copynumber: 3.2 Consensus size: 42
1173338 TGGCCCTTAG
* *
1173348 GCCCATTTCAATATCACGTGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
*
1173390 GCCCATTTCAATATCACATCTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1173432 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1173474 GCCCATTT
1 GCCCATTT
1173482 GGGGAGACTA
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:1173693 original size:26 final size:26
Alignment explanation
Indices: 1173629--1173699 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 26
1173619 CTCTTTTAAT
1173629 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTCTGATA
* *
1173654 AACTAGGGCAAAGCCCTTTTC-GGTA
1 AACTGGGGCAAAGCCCTTTTCTGATA
*
1173679 AACTGGGGAAGAAGCCCTTTT
1 AACTGGGGCA-AAGCCCTTTT
1173700 GGCACTTCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 26 0.65
26 14 0.35
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (26 bp):
AACTGGGGCAAAGCCCTTTTCTGATA
Found at i:1174626 original size:26 final size:27
Alignment explanation
Indices: 1174581--1174674 Score: 111
Period size: 27 Copynumber: 3.5 Consensus size: 27
1174571 TCCTACAAGA
* *
1174581 GTATTTTGGTAATTTTACAAATTGAG-G
1 GTATTTCGGTAATTTTACAAACT-AGTG
* *
1174608 GTA-TTCGGTGATTTCACAAACTAGTG
1 GTATTTCGGTAATTTTACAAACTAGTG
*
1174634 GTATTTCGGTAATTTTACAAACTAGGG
1 GTATTTCGGTAATTTTACAAACTAGTG
*
1174661 GTATTTTGGTAATT
1 GTATTTCGGTAATT
1174675 CTATCCTACA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
25 2 0.04
26 19 0.33
27 36 0.63
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (27 bp):
GTATTTCGGTAATTTTACAAACTAGTG
Found at i:1174740 original size:27 final size:27
Alignment explanation
Indices: 1174706--1174849 Score: 191
Period size: 27 Copynumber: 5.3 Consensus size: 27
1174696 GTAATTTCAC
* *
1174706 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
*
1174733 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTCTGTA
* *
1174760 AATCGAGGGTAAAACGGCAATTCTGTA
1 AATCGAGGGTAAAATGGTAATTCTGTA
* *
1174787 AATTGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTGTA
**
1174814 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAATGGTAATTCTGTA
1174841 AATCGAGGG
1 AATCGAGGG
1174850 CATTTCAGTA
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
26 1 0.01
27 103 0.98
28 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTCTGTA
Found at i:1178271 original size:22 final size:22
Alignment explanation
Indices: 1178243--1178319 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
1178233 AAGTGTGTAT
1178243 ATGTGATAAGGCCGAATGGCTA
1 ATGTGATAAGGCCGAATGGCTA
* * *
1178265 ATGTGATGAATG-TGAAAGTGCATA
1 ATGTGAT-AAGGCCGAATG-GC-TA
* *
1178289 CATGAGATAAGGCCGAATGGTTA
1 -ATGTGATAAGGCCGAATGGCTA
1178312 ATGTGATA
1 ATGTGATA
1178320 TATGTGTAAG
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
22 18 0.44
23 7 0.17
24 6 0.15
25 10 0.24
ACGTcount: A:0.35, C:0.09, G:0.30, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCTA
Found at i:1178277 original size:47 final size:47
Alignment explanation
Indices: 1178208--1178352 Score: 188
Period size: 47 Copynumber: 3.1 Consensus size: 47
1178198 AGCTTAAGAT
*
1178208 CGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGC
1 CGAATGGCTAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGC
** * *
1178255 CGAATGGCTAATGTGATGAATGTGAAAGTGCATACATGAGATAAGGC
1 CGAATGGCTAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGC
* * *
1178302 CGAATGGTTAATGTGAT-ATATGTGTAA--GTGAATATGTGATAAGGC
1 CGAATGGCTAATGTGATGA-ATGTGAAAGTGTGTATATGTGATAAGGC
1178347 CGAATG
1 CGAATG
1178353 ACCAATTGTG
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
45 19 0.22
46 1 0.01
47 65 0.76
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
CGAATGGCTAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGC
Found at i:1178488 original size:39 final size:40
Alignment explanation
Indices: 1178434--1178518 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
1178424 AAATGAATTG
* * * *
1178434 TGCTGAGATTGTATCCGGG-TTAGAGACCCGCTGGCTTCA
1 TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
*
1178473 TGCTGGGATTGTATCCGGGTTTAAAGTCCCGCAGGCTTAA
1 TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
1178513 TGCTGG
1 TGCTGG
1178519 TGAATTAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 18 0.45
40 22 0.55
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (40 bp):
TGCTGGGATTGTATCCGGGTTTAAAGACCCGCAGGCTTAA
Found at i:1181747 original size:31 final size:31
Alignment explanation
Indices: 1181704--1181787 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
1181694 TTAGTCTTGA
1181704 CATAT-ACTGGGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
*
1181734 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
1181765 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
1181788 ACTGTAAACG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 5 0.10
31 47 0.90
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTCCATAAAT
Found at i:1181858 original size:42 final size:42
Alignment explanation
Indices: 1181811--1181944 Score: 250
Period size: 42 Copynumber: 3.2 Consensus size: 42
1181801 TGGCCCTTAG
*
1181811 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1181853 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
*
1181895 GCCCATTTCAATATCATATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1181937 GCCCATTT
1 GCCCATTT
1181945 GGGGAGACTA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:1182120 original size:25 final size:25
Alignment explanation
Indices: 1182092--1182161 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
1182082 CTCTTTTAAT
1182092 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTC-GATA
1182117 AACTGGGGCAAAGCCCTTTTCGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
1182142 AACTGGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
1182162 GGCACTTCCT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
25 39 0.91
26 4 0.09
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:1183001 original size:27 final size:27
Alignment explanation
Indices: 1182971--1183035 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
1182961 GGGCATATTC
1182971 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
1182998 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
1183025 GTCTTTTTACC
1 GTCATTTTACC
1183036 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:1183100 original size:54 final size:54
Alignment explanation
Indices: 1183042--1183225 Score: 149
Period size: 54 Copynumber: 3.4 Consensus size: 54
1183032 TACCTATTAG
* ** * * * *
1183042 GGGTATTTTAGTCATTTCATCCTACAAG-GTTATTTTGGTAATTTTACAAATTGA
1 GGGTATTTTAGTAATTTCA-CAAACAAGTGGTATTTCGGTAATTTTACAAACTAA
** *
1183096 GGGTATTTCGGTAATTTCACAAACCAGTGGTATTTCGGTAATTTTACAAACTAA
1 GGGTATTTTAGTAATTTCACAAACAAGTGGTATTTCGGTAATTTTACAAACTAA
* * * * * ** *
1183150 GGGTATTTTGGTAATTTTACAAACTAG-GAGTATTTTGGTAATTCTATCCTAC-AG
1 GGGTATTTTAGTAATTTCACAAACAAGTG-GTATTTCGGTAATTTTA-CAAACTAA
*
1183204 GGGTATTTTAGTATTTTCACAA
1 GGGTATTTTAGTAATTTCACAA
1183226 TCGAGGGTAA
Statistics
Matches: 106, Mismatches: 21, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
53 6 0.06
54 97 0.92
55 3 0.03
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (54 bp):
GGGTATTTTAGTAATTTCACAAACAAGTGGTATTTCGGTAATTTTACAAACTAA
Found at i:1183102 original size:27 final size:26
Alignment explanation
Indices: 1183072--1183192 Score: 161
Period size: 27 Copynumber: 4.5 Consensus size: 26
1183062 CCTACAAGGT
*
1183072 TATTTTGGTAATTTTACAAATTGAGGG
1 TATTTTGGTAATTTTACAAACT-AGGG
* * *
1183099 TATTTCGGTAATTTCACAAACCAGTGG
1 TATTTTGGTAATTTTACAAACTAG-GG
*
1183126 TATTTCGGTAATTTTACAAACTAAGGG
1 TATTTTGGTAATTTTACAAACT-AGGG
1183153 TATTTTGGTAATTTTACAAACTAGGAG
1 TATTTTGGTAATTTTACAAACTAGG-G
1183180 TATTTTGGTAATT
1 TATTTTGGTAATT
1183193 CTATCCTACA
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
26 5 0.06
27 77 0.92
28 2 0.02
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (26 bp):
TATTTTGGTAATTTTACAAACTAGGG
Found at i:1183209 original size:27 final size:27
Alignment explanation
Indices: 1183072--1183212 Score: 126
Period size: 27 Copynumber: 5.2 Consensus size: 27
1183062 CCTACAAGGT
* *
1183072 TATTTTGGTAATTTTACAAA-TTGAGGG
1 TATTTTGGTAATTCTACAAACTAG-GGG
* * *
1183099 TATTTCGGTAATT-TCACAAACCAGTGG
1 TATTTTGGTAATTCT-ACAAACTAGGGG
* * *
1183126 TATTTCGGTAATTTTACAAACTAAGGG
1 TATTTTGGTAATTCTACAAACTAGGGG
* *
1183153 TATTTTGGTAATTTTACAAACTAGGAG
1 TATTTTGGTAATTCTACAAACTAGGGG
**
1183180 TATTTTGGTAATTCTATCCTAC-AGGGG
1 TATTTTGGTAATTCTA-CAAACTAGGGG
1183207 TATTTT
1 TATTTT
1183213 AGTATTTTCA
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
26 1 0.01
27 90 0.94
28 5 0.05
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (27 bp):
TATTTTGGTAATTCTACAAACTAGGGG
Found at i:1183361 original size:27 final size:27
Alignment explanation
Indices: 1183224--1183367 Score: 191
Period size: 27 Copynumber: 5.3 Consensus size: 27
1183214 GTATTTTCAC
* *
1183224 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTATA
*
1183251 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTTTATA
* *
1183278 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
*
1183305 AATCGATGGTAAAATGGTAATTTTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
* *
1183332 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAATGGTAATTTTATA
*
1183359 AATCAAGGG
1 AATCGAGGG
1183368 CATTTTAGTA
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
26 1 0.01
27 102 0.98
28 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTTTATA
Found at i:1194884 original size:31 final size:31
Alignment explanation
Indices: 1194844--1194927 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
1194834 TTAGTCTTGA
1194844 CATAT-ACTGGGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
*
1194874 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
1194905 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
1194928 ACTGTAAACG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 5 0.10
31 47 0.90
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTCCATAAAT
Found at i:1194998 original size:42 final size:42
Alignment explanation
Indices: 1194951--1195084 Score: 250
Period size: 42 Copynumber: 3.2 Consensus size: 42
1194941 TGGCCCTTAG
*
1194951 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1194993 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
*
1195035 GCCCATTTCAATATCATATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1195077 GCCCATTT
1 GCCCATTT
1195085 GGGGAGACTA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 90 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:1195260 original size:25 final size:25
Alignment explanation
Indices: 1195232--1195301 Score: 115
Period size: 25 Copynumber: 2.8 Consensus size: 25
1195222 CTCTTTTAAT
1195232 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTGGGGCAAAGCCCTTTTC-GATA
1195257 AACTGGGGCAAAGCCCTTTTCGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
1195282 AACTGGGGCAGAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
1195302 GGCACTTCCT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
25 39 0.91
26 4 0.09
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:1196141 original size:27 final size:27
Alignment explanation
Indices: 1196111--1196175 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
1196101 GGGCATATTC
1196111 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * *
1196138 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
1196165 GTCTTTTTACC
1 GTCATTTTACC
1196176 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:1196242 original size:27 final size:26
Alignment explanation
Indices: 1196212--1196331 Score: 152
Period size: 27 Copynumber: 4.5 Consensus size: 26
1196202 CCTACAAGGT
*
1196212 TATTTTGGTAATTTTACAAATTGAGGG
1 TATTTTGGTAATTTTACAAACT-AGGG
* * *
1196239 TATTTCGGTAATTTCACAAACCAGTGG
1 TATTTTGGTAATTTTACAAACTAG-GG
*
1196266 TATTTCGGTAATTTTACAAACTAAGGG
1 TATTTTGGTAATTTTACAAACT-AGGG
1196293 TA-TTTGGTAATTTTACAAACTAGGAG
1 TATTTTGGTAATTTTACAAACTAGG-G
1196319 TATTTTGGTAATT
1 TATTTTGGTAATT
1196332 CTATCCTACA
Statistics
Matches: 82, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
25 3 0.04
26 23 0.28
27 54 0.66
28 2 0.02
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (26 bp):
TATTTTGGTAATTTTACAAACTAGGG
Found at i:1196329 original size:53 final size:54
Alignment explanation
Indices: 1196212--1196331 Score: 172
Period size: 53 Copynumber: 2.2 Consensus size: 54
1196202 CCTACAAGGT
* *
1196212 TATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGG
1 TATTTTGGTAATTTTACAAACTAAGGGTATTTCGGTAATTTCACAAACCAGTGG
* * *
1196266 TATTTCGGTAATTTTACAAACTAAGGGTATTT-GGTAATTTTACAAACTAG-GAG
1 TATTTTGGTAATTTTACAAACTAAGGGTATTTCGGTAATTTCACAAACCAGTG-G
1196319 TATTTTGGTAATT
1 TATTTTGGTAATT
1196332 CTATCCTACA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
52 1 0.02
53 29 0.49
54 29 0.49
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (54 bp):
TATTTTGGTAATTTTACAAACTAAGGGTATTTCGGTAATTTCACAAACCAGTGG
Found at i:1196500 original size:27 final size:27
Alignment explanation
Indices: 1196363--1196506 Score: 191
Period size: 27 Copynumber: 5.3 Consensus size: 27
1196353 GTATTTTCAC
* *
1196363 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTATA
*
1196390 AA-CTGAGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTTTATA
* *
1196417 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
*
1196444 AATCGATGGTAAAATGGTAATTTTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
* *
1196471 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAATGGTAATTTTATA
*
1196498 AATCAAGGG
1 AATCGAGGG
1196507 CATTTTAGTA
Statistics
Matches: 104, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
26 1 0.01
27 102 0.98
28 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTTTATA
Found at i:1208738 original size:18 final size:18
Alignment explanation
Indices: 1208715--1208750 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1208705 TTGAATAGCA
1208715 AAATTTAATAAAAAAATT
1 AAATTTAATAAAAAAATT
*
1208733 AAATTTAATAACAAAATT
1 AAATTTAATAAAAAAATT
1208751 CAATCAAATA
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:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTTAATAAAAAAATT
Found at i:1208748 original size:31 final size:33
Alignment explanation
Indices: 1208702--1208768 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 33
1208692 TTTAAAATAA
* * *
1208702 AAATTGAATAGCAAAATTTAAT-AAA-AAAATT
1 AAATTGAATAACAAAATTCAATCAAATAAAAGT
*
1208733 AAATTTAATAACAAAATTCAATCAAATAAAAGT
1 AAATTGAATAACAAAATTCAATCAAATAAAAGT
1208766 AAA
1 AAA
1208769 GCCACAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 19 0.63
32 3 0.10
33 8 0.27
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (33 bp):
AAATTGAATAACAAAATTCAATCAAATAAAAGT
Found at i:1212644 original size:22 final size:20
Alignment explanation
Indices: 1212596--1212635 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1212586 ATTAATGTCC
*
1212596 TTTCATTGATTCCTCCTAAA
1 TTTCATTGATTCATCCTAAA
* *
1212616 TTACATTGATTTATCCTAAA
1 TTTCATTGATTCATCCTAAA
1212636 AATTTCATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTCATTGATTCATCCTAAA
Found at i:1213579 original size:31 final size:31
Alignment explanation
Indices: 1213539--1213602 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1213529 AAATTTTTAA
* *
1213539 AATTTAAAAAGTA-TAAGAGCTAAAATTGATC
1 AATTCAAAAAGTACAAAGA-CTAAAATTGATC
*
1213570 AATTCAAAAAGTACAAAGATTAAAATTGATC
1 AATTCAAAAAGTACAAAGACTAAAATTGATC
1213601 AA
1 AA
1213603 ATTAAAGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.27
Consensus pattern (31 bp):
AATTCAAAAAGTACAAAGACTAAAATTGATC
Found at i:1218293 original size:17 final size:18
Alignment explanation
Indices: 1218251--1218304 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
1218241 TGGGCTGGTA
* *
1218251 AATGGGTTTAAGTGGGTCT
1 AATGGGTTTAAG-GGTTTT
*
1218270 GATGGG-TTAAGGGTTTT
1 AATGGGTTTAAGGGTTTT
*
1218287 AATGGGTTTAGGGGTTTT
1 AATGGGTTTAAGGGTTTT
1218305 GTTATTTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 9 0.31
18 15 0.52
19 5 0.17
ACGTcount: A:0.19, C:0.02, G:0.39, T:0.41
Consensus pattern (18 bp):
AATGGGTTTAAGGGTTTT
Found at i:1225047 original size:25 final size:25
Alignment explanation
Indices: 1225018--1225069 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1225008 TAAATGTGAA
1225018 ATTAGATTTTAATCCAAAGCTAAAT
1 ATTAGATTTTAATCCAAAGCTAAAT
1225043 ATTAGATTTTAATCCAAAGCTAAAT
1 ATTAGATTTTAATCCAAAGCTAAAT
1225068 AT
1 AT
1225070 CAGAAGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (25 bp):
ATTAGATTTTAATCCAAAGCTAAAT
Found at i:1227698 original size:29 final size:30
Alignment explanation
Indices: 1227633--1227713 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
1227623 AATACAAAAA
* *
1227633 CTATACATGAACTTTGATATAATGTGCAATAT
1 CTATACATAAACTTTGAT-T-TTGTGCAATAT
1227665 C-ATACATAAACTTTGATTTTGTGCAAT-T
1 CTATACATAAACTTTGATTTTGTGCAATAT
*
1227693 CTATACATTAAATTTTGATTT
1 CTATACA-TAAACTTTGATTT
1227714 GATTTAGTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.05
29 13 0.30
30 13 0.30
31 15 0.34
32 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (30 bp):
CTATACATAAACTTTGATTTTGTGCAATAT
Found at i:1234169 original size:3 final size:3
Alignment explanation
Indices: 1234161--1234226 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
1234151 AATATAAGCC
1234161 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1234209 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
1234227 AAACTTGGTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1242064 original size:11 final size:11
Alignment explanation
Indices: 1242050--1242090 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1242040 TATTTTCTCC
1242050 CTATTTTGCTA
1 CTATTTTGCTA
*
1242061 CTATTTTACTA
1 CTATTTTGCTA
* *
1242072 TTATGTTGCTA
1 CTATTTTGCTA
1242083 CTATTTTG
1 CTATTTTG
1242091 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:1242189 original size:30 final size:30
Alignment explanation
Indices: 1242131--1242191 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1242121 ATTTTATTGT
* *
1242131 TAATTTTTTTATTATTTTAAAGATATTTGC
1 TAATTTTATTATTATTTTAAAGACATTTGC
* *
1242161 TAATTTTATTATTATTTTAGAGGCATTTGC
1 TAATTTTATTATTATTTTAAAGACATTTGC
1242191 T
1 T
1242192 TGTTAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.57
Consensus pattern (30 bp):
TAATTTTATTATTATTTTAAAGACATTTGC
Found at i:1244270 original size:4 final size:4
Alignment explanation
Indices: 1244261--1244288 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1244251 TTAAACTAAG
1244261 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1244289 AATAAAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:1254318 original size:210 final size:211
Alignment explanation
Indices: 1253786--1254393 Score: 1031
Period size: 210 Copynumber: 2.9 Consensus size: 211
1253776 ATTTTTTTTG
*
1253786 CGCATGTATCACATTACAAAAACAAAATTTTAAATAGTTATACTTAATAAAACATGTATCTCATT
1 CGCATGTATCACATTACAAAAACAAAATTTTAAATACTTATACTTAATAAAACATGTATCTCATT
*
1253851 ACAATAATAGTTATTTTCCAAATAACATATTGTTTTATAATTTTATTTCTTATTTAATATTTTAA
66 ACAATAATTGTTATTTTCCAAATAACATATTGTTTTATAATTTTATTTCTTATTTAATATTTTAA
* * *
1253916 TTTAATTTTAATAATGCATATTTTATCTAGATGAAGTATGTATTAGCAGATTCAGTAATATGATT
131 TTTAATTTTAATAATGCATACTTTATC-CGATGAAGTATGTATTAGCAGATTCACTAATATG--T
1253981 ATATATATATATATATTTA
193 ATATATATATATATATTTA
* * *
1254000 TGCATGTATCACATTACAAAAACAAAATTTTAAATATTTATACCTAATAAAACATGTATCTCATT
1 CGCATGTATCACATTACAAAAACAAAATTTTAAATACTTATACTTAATAAAACATGTATCTCATT
* * *
1254065 ATAATAATTGTTATTTCCCAAATAACATATTGTTTTGTAATTTTATTTCTTATTTAATATTTTAA
66 ACAATAATTGTTATTTTCCAAATAACATATTGTTTTATAATTTTATTTCTTATTTAATATTTTAA
* *
1254130 TTTAATTTTAATAATGCATACTTTATCCGTATGAAGTACGCATTAGCAGATTCACTAATATG-AT
131 TTTAATTTTAATAATGCATACTTTATCCG-ATGAAGTATGTATTAGCAGATTCACTAATATGTAT
1254194 -TATATATATATATTTA
195 ATATATATATATATTTA
1254210 CGCATGTATCACATTACAAAAACAAAATTTTAAATACTTATACTTAATAAAACATGTATCTCATT
1 CGCATGTATCACATTACAAAAACAAAATTTTAAATACTTATACTTAATAAAACATGTATCTCATT
1254275 ACAATAATTGTTATTTTCCAAATAACATATTGTTTTATAATTTTATTTCTTATTTAATATTTTAA
66 ACAATAATTGTTATTTTCCAAATAACATATTGTTTTATAATTTTATTTCTTATTTAATATTTTAA
*
1254340 TTTAATTTTAATAATGCATACTTTATCCGGATGAAGTATGTATTAGCATATTCA
131 TTTAATTTTAATAATGCATACTTTATCC-GATGAAGTATGTATTAGCAGATTCA
1254394 ATATTTAATT
Statistics
Matches: 371, Mismatches: 21, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
210 189 0.51
211 3 0.01
213 1 0.00
214 178 0.48
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.44
Consensus pattern (211 bp):
CGCATGTATCACATTACAAAAACAAAATTTTAAATACTTATACTTAATAAAACATGTATCTCATT
ACAATAATTGTTATTTTCCAAATAACATATTGTTTTATAATTTTATTTCTTATTTAATATTTTAA
TTTAATTTTAATAATGCATACTTTATCCGATGAAGTATGTATTAGCAGATTCACTAATATGTATA
TATATATATATATTTA
Found at i:1254425 original size:16 final size:16
Alignment explanation
Indices: 1254404--1254437 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1254394 ATATTTAATT
1254404 TAATTTTAAGAATGCA
1 TAATTTTAAGAATGCA
*
1254420 TAATTTTAATAATGCA
1 TAATTTTAAGAATGCA
1254436 TA
1 TA
1254438 CAAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (16 bp):
TAATTTTAAGAATGCA
Found at i:1254523 original size:55 final size:54
Alignment explanation
Indices: 1254447--1254657 Score: 205
Period size: 55 Copynumber: 3.8 Consensus size: 54
1254437 ACAAAAAAAA
*
1254447 TTTAATACTGGTGCCAGCCATTGACAGGCCAGCACCAAAAAAATTTCAAATTTTT
1 TTTAATACTGGTGCCGGCCATTGACAGGCCAGCACCAAAAAAATTTC-AATTTTT
* *
1254502 TTTAATATTGGTGCCGGCCATTGACAGGCCAGCACCCAAAAAATTT---TTTTT
1 TTTAATACTGGTGCCGGCCATTGACAGGCCAGCACCAAAAAAATTTCAATTTTT
** * * *
1254553 TGAAAACTCGTATTTTGGTGTCGGCCATTGACAGGCCAGCA-CAAAAAAAATTCAACTTTTTT
1 T-TTAA----TA--CTGGTGCCGGCCATTGACAGGCCAGCACCAAAAAAATTTCAA--TTTTT
* **
1254615 TTTAATACTGGTGCCGGCCATTGATAGGCCAAAACCAAAAAAA
1 TTTAATACTGGTGCCGGCCATTGACAGGCCAGCACCAAAAAAA
1254658 ATAATTTTTT
Statistics
Matches: 128, Mismatches: 15, Indels: 25
0.76 0.09 0.15
Matches are distributed among these distances:
51 6 0.05
52 2 0.02
55 65 0.51
56 10 0.08
57 11 0.09
58 26 0.20
61 2 0.02
62 6 0.05
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (54 bp):
TTTAATACTGGTGCCGGCCATTGACAGGCCAGCACCAAAAAAATTTCAATTTTT
Found at i:1254666 original size:113 final size:113
Alignment explanation
Indices: 1254463--1254666 Score: 302
Period size: 113 Copynumber: 1.8 Consensus size: 113
1254453 ACTGGTGCCA
* *
1254463 GCCATTGACAGGCCAGCACCAAAAAAATTTCAAATTTTTTTTAATATTGGTGCCGGCCATTGACA
1 GCCATTGACAGGCCAGCACCAAAAAAAATTCAAATTTTTTTTAATACTGGTGCCGGCCATTGACA
** * * **
1254528 GGCCAGCACCCAAAAAATTTTTTTTTGAAAACTCGTATTTTGGTGTCG
66 GGCCAAAACCAAAAAAAATAATTTTTGAAAACTCGTATTTTGGTGTCG
* *
1254576 GCCATTGACAGGCCAGCA-CAAAAAAAATTCAACTTTTTTTTTAATACTGGTGCCGGCCATTGAT
1 GCCATTGACAGGCCAGCACCAAAAAAAATTCAA-ATTTTTTTTAATACTGGTGCCGGCCATTGAC
1254640 AGGCCAAAACCAAAAAAAATAATTTTT
65 AGGCCAAAACCAAAAAAAATAATTTTT
1254667 TAAAGCCTGA
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
112 13 0.16
113 67 0.84
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (113 bp):
GCCATTGACAGGCCAGCACCAAAAAAAATTCAAATTTTTTTTAATACTGGTGCCGGCCATTGACA
GGCCAAAACCAAAAAAAATAATTTTTGAAAACTCGTATTTTGGTGTCG
Found at i:1256099 original size:19 final size:18
Alignment explanation
Indices: 1256054--1256101 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
1256044 TTTCTCAACA
1256054 AAAAATTTTAAAAAAATC
1 AAAAATTTTAAAAAAATC
*
1256072 -AAAATATTTATAAAAATTCC
1 AAAAAT-TTTA-AAAAAAT-C
1256092 AAAAATTTTA
1 AAAAATTTTA
1256102 TATGTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.20
18 4 0.16
19 6 0.24
20 5 0.20
21 5 0.20
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAATTTTAAAAAAATC
Found at i:1256101 original size:20 final size:19
Alignment explanation
Indices: 1256054--1256103 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1256044 TTTCTCAACA
1256054 AAAAATTTTA-AAAAAATC
1 AAAAATTTTATAAAAAATC
*
1256072 -AAAATATTTATAAAAATTCC
1 AAAAAT-TTTATAAAAAAT-C
1256092 AAAAATTTTATA
1 AAAAATTTTATA
1256104 TGTTTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.19
18 4 0.15
19 6 0.22
20 7 0.26
21 5 0.19
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTTTATAAAAAATC
Found at i:1256163 original size:9 final size:9
Alignment explanation
Indices: 1256054--1256171 Score: 67
Period size: 9 Copynumber: 12.7 Consensus size: 9
1256044 TTTCTCAACA
1256054 AAAAATTTT
1 AAAAATTTT
** *
1256063 AAAAAAATC
1 AAAAATTTT
1256072 AAAATATTTAT
1 AAAA-ATTT-T
**
1256083 AAAAATTCC
1 AAAAATTTT
1256092 AAAAATTTT
1 AAAAATTTT
* **
1256101 ATATGTTTT
1 AAAAATTTT
*
1256110 AAAATTTTT
1 AAAAATTTT
*
1256119 AAAAATTCT
1 AAAAATTTT
*
1256128 AAAGAATATAT
1 AAA-AAT-TTT
**
1256139 AAAGAAAGTT
1 AAA-AATTTT
1256149 -AAAATTTT
1 AAAAATTTT
1256157 AAAAATTTT
1 AAAAATTTT
1256166 AAAAAT
1 AAAAAT
1256172 AATAATTTTA
Statistics
Matches: 80, Mismatches: 24, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
8 4 0.05
9 55 0.69
10 9 0.11
11 12 0.15
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (9 bp):
AAAAATTTT
Found at i:1259462 original size:29 final size:29
Alignment explanation
Indices: 1259416--1259477 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
1259406 TTTCAACTTT
*
1259416 TTTTATTTTATTTCAATAAATCATTATAC
1 TTTTATTATATTTCAATAAATCATTATAC
*
1259445 TTTTATTATA-TTCAAATAAATTATTATAC
1 TTTTATTATATTTC-AATAAATCATTATAC
1259474 TTTT
1 TTTT
1259478 GAATCCCAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 3 0.10
29 27 0.90
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTTATTATATTTCAATAAATCATTATAC
Found at i:1261356 original size:26 final size:24
Alignment explanation
Indices: 1261301--1261502 Score: 104
Period size: 26 Copynumber: 8.0 Consensus size: 24
1261291 ATATTAAATG
*
1261301 ATTTTAAATTGTTTTATTCTATTT
1 ATTTTAAATTGTTTTATACTATTT
*
1261325 ATTTTAAATTGCTTTCTATAGTATTT
1 ATTTTAAATTG-TTT-TATACTATTT
*
1261351 ATTTTAAACATGTTTTTCTATA-TATTATT
1 ATTTT-AA-AT-TGTTT-TATACTA-T-TT
* * * *
1261380 CATTTAAAATTGTCTTAAATTATTT
1 -ATTTTAAATTGTTTTATACTATTT
* * *
1261405 AGTTTAAATCGTTTTGTATATTATTT
1 ATTTTAAATTG-TTT-TATACTATTT
* * * * *
1261431 GTTTTAAGTT-TCTCTACACATCGTTT
1 ATTTTAAATTGT-TTTATAC-T-ATTT
1261457 ATTTTAAATTGTTTTATACTATTT
1 ATTTTAAATTGTTTTATACTATTT
* *
1261481 ACTTCAAATTGTTTTATA-TATT
1 ATTTTAAATTGTTTTATACTATT
1261503 ATTCCATTTC
Statistics
Matches: 136, Mismatches: 27, Indels: 31
0.70 0.14 0.16
Matches are distributed among these distances:
23 4 0.03
24 42 0.31
25 10 0.07
26 48 0.35
27 10 0.07
28 13 0.10
29 5 0.04
30 4 0.03
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.57
Consensus pattern (24 bp):
ATTTTAAATTGTTTTATACTATTT
Found at i:1261495 original size:76 final size:79
Alignment explanation
Indices: 1261301--1261505 Score: 200
Period size: 76 Copynumber: 2.6 Consensus size: 79
1261291 ATATTAAATG
* * * * *
1261301 ATTTTAAATTGTTTTATTCTATTTATTTTAAATTGCTTTCTATAGTATTTATTTTAAACATGTTT
1 ATTTTAAATTGTTTTATACTATTTACTTTAAATTGTTTTATATATTATTTATTTT-AACATGTTT
* * * *
1261366 TTCTATATATTATTC
65 CTCTACACATCATTC
* * * * * * * *
1261381 ATTTAAAATTGTCTTAAATTATTTAGTTTAAATCGTTTTGTATATTATTTGTTTT-A-A-GTTTC
1 ATTTTAAATTGTTTTATACTATTTACTTTAAATTGTTTTATATATTATTTATTTTAACATGTTTC
* *
1261443 TCTACACATCGTTT
66 TCTACACATCATTC
*
1261457 ATTTTAAATTGTTTTATACTATTTACTTCAAATTGTTTTATATATTATT
1 ATTTTAAATTGTTTTATACTATTTACTTTAAATTGTTTTATATATTATT
1261506 CCATTTCATT
Statistics
Matches: 100, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
76 54 0.54
77 1 0.01
78 1 0.01
80 44 0.44
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (79 bp):
ATTTTAAATTGTTTTATACTATTTACTTTAAATTGTTTTATATATTATTTATTTTAACATGTTTC
TCTACACATCATTC
Found at i:1268287 original size:21 final size:21
Alignment explanation
Indices: 1268243--1268287 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1268233 GGTGATTTAA
*
1268243 TTTAATAATTTAAATAATTTT
1 TTTAATAATTTAAATAATTAT
*
1268264 TTTAATTAATTT-AATGATTAT
1 TTTAA-TAATTTAAATAATTAT
1268285 TTT
1 TTT
1268288 TTAACTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTAATAATTTAAATAATTAT
Found at i:1274174 original size:3 final size:3
Alignment explanation
Indices: 1274160--1274210 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
1274150 AATAGAATAG
* * * *
1274160 TTA TTG TTA TTA TTA TTA TTG TTG TTG TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1274208 TTA
1 TTA
1274211 ATAAAAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1274504 original size:17 final size:16
Alignment explanation
Indices: 1274482--1274513 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1274472 GACTCAGTTA
1274482 TAATTAATTGAAACTAG
1 TAATTAATT-AAACTAG
1274499 TAATTAATTAAACTA
1 TAATTAATTAAACTA
1274514 ATTGAAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (16 bp):
TAATTAATTAAACTAG
Found at i:1283382 original size:39 final size:39
Alignment explanation
Indices: 1283296--1283431 Score: 127
Period size: 39 Copynumber: 3.5 Consensus size: 39
1283286 ACTTGAAACC
* *
1283296 AATTACCAGCAC-AAGCCTGCGGGAATTTAAACCCGG-TAT
1 AATT-CCAGCACGAAGCCTGCGGGACTTT-AGCCCGGATAT
* * *
1283335 AATACCAGCTCGAAGCCTGCGGGACTTTAGCCCGGACAT
1 AATTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATAT
* * * *
1283374 ATTTCCAGCACGTAGCCTGC-GGACCTTAAGTCCGGATAT
1 AATTCCAGCACGAAGCCTGCGGGA-CTTTAGCCCGGATAT
1283413 AATTCCAGCAC-ATAGCCTG
1 AATTCCAGCACGA-AGCCTG
1283432 TGGACCCTAA
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
38 15 0.19
39 64 0.81
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (39 bp):
AATTCCAGCACGAAGCCTGCGGGACTTTAGCCCGGATAT
Found at i:1283437 original size:39 final size:39
Alignment explanation
Indices: 1283366--1283452 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
1283356 GGACTTTAGC
* * * *
1283366 CCGGACATATTTCCAGCACGTAGCCTGCGGACCTTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
*
1283405 CCGGATATAATTCCAGCACATAGCCTGTGGACCCTAAGT
1 CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
1283444 CCGGATATA
1 CCGGATATA
1283453 CATCACTGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (39 bp):
CCGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGT
Found at i:1284971 original size:132 final size:132
Alignment explanation
Indices: 1284730--1285067 Score: 448
Period size: 132 Copynumber: 2.6 Consensus size: 132
1284720 CATATTCATT
* * *
1284730 TAAAAATTCTTTAAAACGGAGACGATATTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
1 TAAAAATCCTTTAAAACGAAGGCGATATTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
* *
1284795 GTTGGGTTGCAATTTCGCGTTTGCTCAAAATAATCGAATATCCCTCCAAAAT-TTCGTTCATGTC
66 GCTGGGTTGCAATTTCGCATTTGCTCAAAATAATCGAATATCCCTCCAAAATCTT-GTTCATGTC
1284859 TTC
130 TTC
* *
1284862 TAAAAATCCTTTAAAACGAAGGCGATGTTTGACATTTGGCAATTCGCGGAATCGTGCCCTAACGT
1 TAAAAATCCTTTAAAACGAAGGCGATATTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
* * * ** *
1284927 GCTGGGTTGCAATTTCTCATTTGCTCAAAGTAATCGAATGTCCCTTTAGAATCTTGTTCATGTCT
66 GCTGGGTTGCAATTTCGCATTTGCTCAAAATAATCGAATATCCCTCCAAAATCTTGTTCATGTCT
1284992 TC
131 TC
* ** * * * * *
1284994 TAAAAA-CTCTTTAAAACAAAGGAAATACTTGATGTTTGGAAATTTG-GGAATCGTGCCCTATCG
1 TAAAAATC-CTTTAAAACGAAGGCGATATTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACG
1285057 TGCTGGGTTGC
65 TGCTGGGTTGC
1285068 GATTCTCCTA
Statistics
Matches: 181, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
131 28 0.15
132 151 0.83
133 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (132 bp):
TAAAAATCCTTTAAAACGAAGGCGATATTTGATATTTGGCAATTCGCGGAATCGTGCCCTAACGT
GCTGGGTTGCAATTTCGCATTTGCTCAAAATAATCGAATATCCCTCCAAAATCTTGTTCATGTCT
TC
Done.