Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 102 of 210
Found at i:29750798 original size:55 final size:55
Alignment explanation
Indices: 29750709--29750819 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
29750699 TTATAAGTGC
*
29750709 CAAGACTATGATGTTGACCATGTAGGAGCATTTGAATTGCCACACACCATTCTTT
1 CAAGACTATGATATTGACCATGTAGGAGCATTTGAATTGCCACACACCATTCTTT
*
29750764 CAAGACTATGATATTGACCATGTAGGAGCTTTTGAATTGCCACACACCATTCTTT
1 CAAGACTATGATATTGACCATGTAGGAGCATTTGAATTGCCACACACCATTCTTT
29750819 C
1 C
29750820 TCTATTGAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (55 bp):
CAAGACTATGATATTGACCATGTAGGAGCATTTGAATTGCCACACACCATTCTTT
Found at i:29769709 original size:16 final size:16
Alignment explanation
Indices: 29769670--29769702 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29769660 CGTTTGGTTC
29769670 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
29769686 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
29769702 G
1 G
29769703 GCGTAATAGT
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:0.36, C:0.06, G:0.33, T:0.24
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:29770147 original size:14 final size:14
Alignment explanation
Indices: 29770130--29770157 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29770120 CTCACATTTC
29770130 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
29770144 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
29770158 GATTTCTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:29770148 original size:19 final size:18
Alignment explanation
Indices: 29770110--29770154 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
29770100 TACGGTACGC
29770110 TTCTTTTC-TTCTCACAT
1 TTCTTTTCTTTCTCACAT
29770127 TTCTTTTCTTTTCTC-CATT
1 TTCTTTTC-TTTCTCACA-T
29770146 TTCTTTTCT
1 TTCTTTTCT
29770155 CCAGATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTTTTCTTTCTCACAT
Found at i:29773557 original size:61 final size:61
Alignment explanation
Indices: 29773500--29773690 Score: 230
Period size: 61 Copynumber: 3.2 Consensus size: 61
29773490 ATTTTATAGT
29773500 ATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
* ** ** * * * * *
29773561 ATTATATATTATTATTAAATTATATTTA-ATAATAATTATGTTAA-ATT-A-TATTTTA-TAGT
1 ATTATATATTATGATTTTAGAAAATTCATATAAGAA-TAT-TTAATATTAAGAATTTTATTA-A
29773620 ATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
29773681 ATTATATATT
1 ATTATATATT
29773691 TTTATTAAAT
Statistics
Matches: 102, Mismatches: 20, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
58 6 0.06
59 33 0.32
60 14 0.14
61 43 0.42
62 6 0.06
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (61 bp):
ATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
Found at i:29773654 original size:120 final size:120
Alignment explanation
Indices: 29773441--29773725 Score: 561
Period size: 120 Copynumber: 2.4 Consensus size: 120
29773431 NNNNNNNNNN
29773441 ATTATATATTATTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATA
1 ATTATATATTATTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATA
29773506 TATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
66 TATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
29773561 ATTATATATTATTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATA
1 ATTATATATTATTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATA
29773626 TATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
66 TATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
*
29773681 ATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
1 ATTATATATTATTATTAAATTATATTTAATAATAATTATGTTAAA
29773726 ATATGATTAA
Statistics
Matches: 164, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 164 1.00
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.51
Consensus pattern (120 bp):
ATTATATATTATTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATA
TATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
Found at i:29774410 original size:15 final size:16
Alignment explanation
Indices: 29774364--29774428 Score: 57
Period size: 18 Copynumber: 4.2 Consensus size: 16
29774354 ATAATACTAT
29774364 AAAATATAATTTAA-A
1 AAAATATAATTTAATA
* *
29774379 ATAAT-T-A-TTATTA
1 AAAATATAATTTAATA
*
29774392 AAAATATAATTTAGTAA
1 AAAATATAATTTAAT-A
29774409 AAATATATAATTTAATA
1 AAA-ATATAATTTAATA
29774426 AAA
1 AAA
29774429 TTCTTAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
12 3 0.08
13 6 0.15
14 2 0.05
15 5 0.13
16 4 0.10
17 8 0.21
18 11 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAATATAATTTAATA
Found at i:29774416 original size:18 final size:17
Alignment explanation
Indices: 29774391--29774428 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
29774381 AATTATTATT
*
29774391 AAAAATATAATTTAGTA
1 AAAAATATAATTTAATA
29774408 AAAATATATAATTTAATA
1 AAAA-ATATAATTTAATA
29774426 AAA
1 AAA
29774429 TTCTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAAATATAATTTAATA
Found at i:29774440 original size:122 final size:121
Alignment explanation
Indices: 29774212--29775097 Score: 1412
Period size: 122 Copynumber: 7.3 Consensus size: 121
29774202 NNNNNNNNNN
* * **
29774212 TTTACTAAAATCATAATATATAACACTATAAAATATAATTTAAAATAATTATCAATCGCAAATAT
1 TTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTAT-TAT-TAAAATAT
*
29774277 AATTTAACAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
64 AATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
* *
29774335 TTTTCTAAAATCATAAAATATAATACTATAAAATATAATTTAAAATAATTATTATTAAAAATATA
1 TTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATT-AAAATATA
* *
29774400 ATTTAGTAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAA
65 ATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
* *
29774457 TTTACTAAAATCATAATATATAACACTATAAAATATAATTTAAAATAATAATTATTAAAAATATA
1 TTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATT-AAAATATA
*
29774522 ATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTAAATGAA
65 ATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
* ** *
29774579 TTTAATAAAATCATAATATATAACGCTATAAAATATAATTTAAAATAATAATTATTAAAAATATA
1 TTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATT-AAAATATA
29774644 ATTTAGA-AAAAATATATAATTTAATAAAATTCTTAATATTAAATATTC-T-TA-GAA
65 ATTTA-ATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
* *
29774698 TTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAATTAATTATT-TTTAAATATAA
1 TTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAAATATAA
*
29774762 TTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTGTATGAA
66 TTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
*
29774818 TTTACTAAAATCATAATATATAATACCATAAAATATAATTTAAAATAATTATTATT-AAATATAA
1 TTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAAATATAA
*
29774882 TTTATTAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
66 TTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
* ** *
29774938 TTTACTATAGCCATAATATATAATACTATAAAATATAATCTAAAATAATTATTATT-AAATATAA
1 TTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAAATATAA
*
29775002 TTTAATAAAAATATATAATTTAATAAAATTCTTAATGTTAAATATTCTTATATGAA
66 TTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
*
29775058 TTTACTAAAATCAT-ATATAT-ATACTGTAAAATATAATTTA
1 TTTACTAAAATCATAATATATAATACTATAAAATATAATTTA
29775098 TAATCTACTT
Statistics
Matches: 717, Mismatches: 39, Indels: 19
0.93 0.05 0.02
Matches are distributed among these distances:
116 1 0.00
117 53 0.07
118 21 0.03
119 59 0.08
120 241 0.34
121 3 0.00
122 289 0.40
123 50 0.07
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (121 bp):
TTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTAAAATATAA
TTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAA
Found at i:29774506 original size:15 final size:14
Alignment explanation
Indices: 29774486--29774551 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 14
29774476 ATAACACTAT
29774486 AAAATATAATTTAA
1 AAAATATAATTTAA
* *
29774500 AATA-ATAATTATTA
1 AAAATATAATT-TAA
29774514 AAAATATAATTTAATAA
1 AAAATATAA-TT--TAA
29774531 AAATATATAATTTAA
1 AAA-ATATAATTTAA
29774546 TAAAAT
1 -AAAAT
29774552 TCTTAATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 6 0.14
14 8 0.19
15 9 0.21
16 5 0.12
17 8 0.19
18 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATATAATTTAA
Found at i:29774517 original size:28 final size:28
Alignment explanation
Indices: 29774486--29774657 Score: 86
Period size: 28 Copynumber: 5.8 Consensus size: 28
29774476 ATAACACTAT
29774486 AAAATATAATTTAAAATAATAATTATTA
1 AAAATATAATTTAAAATAATAATTATTA
* *
29774514 AAAATATAATTTAATAAAAATATATAATTTA
1 AAAATATAATTTAA-AATAATA-ATTA-TTA
* *
29774545 ATAAA-AT--TCTTAATATTAA-ATATTCTTA
1 A-AAATATAAT-TTAA-AATAATA-ATTATTA
* *
29774573 AATGAATTTAA--TAAAATCATAATATATAACGCTA
1 AA--AATATAATTTAAAATAATAAT-TAT-----TA
29774607 TAAAATATAATTTAAAATAATAATTATTA
1 -AAAATATAATTTAAAATAATAATTATTA
*
29774636 AAAATATAATTTAGAAAAAATA
1 AAAATATAATTTA-AAATAATA
29774658 TATAATTTAA
Statistics
Matches: 110, Mismatches: 13, Indels: 41
0.67 0.08 0.25
Matches are distributed among these distances:
27 1 0.01
28 36 0.33
29 28 0.25
30 12 0.11
31 6 0.05
32 3 0.03
33 6 0.05
34 5 0.05
35 13 0.12
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (28 bp):
AAAATATAATTTAAAATAATAATTATTA
Found at i:29774519 original size:16 final size:16
Alignment explanation
Indices: 29774498--29774550 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
29774488 AATATAATTT
*
29774498 AAAATAATAATTATTA
1 AAAATAATAATTAATA
29774514 AAAAT-ATAATTTAATA
1 AAAATAATAA-TTAATA
29774530 AAAATATATAATTTAATA
1 AAAATA-ATAA-TTAATA
29774548 AAA
1 AAA
29774551 TTCTTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
15 4 0.12
16 15 0.45
18 14 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATAATAATTAATA
Found at i:29774563 original size:18 final size:18
Alignment explanation
Indices: 29774513--29774550 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
29774503 AATAATTATT
29774513 AAAA-ATATAATTTAATA
1 AAAATATATAATTTAATA
29774530 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
29774548 AAA
1 AAA
29774551 TTCTTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATATATAATTTAATA
Found at i:29774628 original size:15 final size:14
Alignment explanation
Indices: 29774608--29774673 Score: 53
Period size: 15 Copynumber: 4.4 Consensus size: 14
29774598 ATAACGCTAT
29774608 AAAATATAATTTAA
1 AAAATATAATTTAA
* *
29774622 AATA-ATAATTATTA
1 AAAATATAATT-TAA
29774636 AAAATATAATTTAGAAA
1 AAAATATAATTT---AA
29774653 AAATATATAATTTAA
1 AAA-ATATAATTTAA
29774668 TAAAAT
1 -AAAAT
29774674 TCTTAATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
13 6 0.15
14 9 0.22
15 10 0.24
16 3 0.07
17 4 0.10
18 9 0.22
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
AAAATATAATTTAA
Found at i:29776557 original size:49 final size:49
Alignment explanation
Indices: 29776485--29776588 Score: 181
Period size: 49 Copynumber: 2.1 Consensus size: 49
29776475 AGAAAAAAAC
* * *
29776485 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
29776534 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
29776583 AAATTA
1 AAATTA
29776589 TAACACATGA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
Found at i:29781271 original size:15 final size:15
Alignment explanation
Indices: 29781253--29781315 Score: 69
Period size: 15 Copynumber: 4.4 Consensus size: 15
29781243 ATTTTTAACA
29781253 TTAAATTTTTATATT
1 TTAAATTTTTATATT
29781268 TTAAATTTTT-T-TT
1 TTAAATTTTTATATT
* * **
29781281 TGAGATTTTTA-ACA
1 TTAAATTTTTATATT
29781295 TTAAATTTTTATATT
1 TTAAATTTTTATATT
29781310 TTAAAT
1 TTAAAT
29781316 ATTTGTTGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
13 10 0.27
14 10 0.27
15 17 0.46
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (15 bp):
TTAAATTTTTATATT
Found at i:29781271 original size:21 final size:21
Alignment explanation
Indices: 29781245--29781313 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
29781235 TTTTTCAGAT
29781245 TTTTAACATTAAATTTTTATA
1 TTTTAACATTAAATTTTTATA
** *
29781266 TTTTAA-ATT-TTTTTTTGAGA
1 TTTTAACATTAAATTTTT-ATA
29781286 TTTTTAACATTAAATTTTTATA
1 -TTTTAACATTAAATTTTTATA
29781308 TTTTAA
1 TTTTAA
29781314 ATATTTGTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 5 0.13
20 5 0.13
21 18 0.47
22 5 0.13
23 5 0.13
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (21 bp):
TTTTAACATTAAATTTTTATA
Found at i:29781288 original size:42 final size:42
Alignment explanation
Indices: 29781233--29781315 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
29781223 CTAATTATAA
29781233 TTTTTTTCAGATTTTTAACATTAAATTTTTATATTTTAAATT
1 TTTTTTTCAGATTTTTAACATTAAATTTTTATATTTTAAATT
*
29781275 TTTTTTTGAGATTTTTAACATTAAATTTTTATATTTTAAAT
1 TTTTTTTCAGATTTTTAACATTAAATTTTTATATTTTAAAT
29781316 ATTTGTTGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (42 bp):
TTTTTTTCAGATTTTTAACATTAAATTTTTATATTTTAAATT
Found at i:29786775 original size:24 final size:22
Alignment explanation
Indices: 29786719--29786764 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
29786709 AATGAGTAAG
29786719 TCTATCAACATCATATATCTGT
1 TCTATCAACATCATATATCTGT
29786741 TCTATCAACATCATATATCTGT
1 TCTATCAACATCATATATCTGT
29786763 TC
1 TC
29786765 ATTCTTAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.24, G:0.04, T:0.41
Consensus pattern (22 bp):
TCTATCAACATCATATATCTGT
Found at i:29791760 original size:30 final size:30
Alignment explanation
Indices: 29791688--29791760 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
29791678 ATGTTTACAC
29791688 ATTCTATCAATTTGATCCTAAATATAAAAA
1 ATTCTATCAATTTGATCCTAAATATAAAAA
* * * *
29791718 ATTCAATAAATTTGA-CCTTAATATTTACAAA
1 ATTCTATCAATTTGATCC-TAA-ATATAAAAA
29791749 ATT-TATCAATTT
1 ATTCTATCAATTT
29791761 AGTACTAACT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 2 0.06
30 23 0.66
31 10 0.29
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (30 bp):
ATTCTATCAATTTGATCCTAAATATAAAAA
Found at i:29792457 original size:22 final size:21
Alignment explanation
Indices: 29792430--29792478 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
29792420 ATAGAAACCG
29792430 ATAGAATTGTTATTAC-TAGAAA
1 ATAGAATT-TTA-TACTTAGAAA
29792452 ATAGAA-TTTATACTTAGAAA
1 ATAGAATTTTATACTTAGAAA
29792472 ATA-AATT
1 ATAGAATT
29792479 CTCACTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 5 0.20
20 13 0.52
21 1 0.04
22 6 0.24
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (21 bp):
ATAGAATTTTATACTTAGAAA
Found at i:29799701 original size:19 final size:19
Alignment explanation
Indices: 29799685--29799723 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
29799675 AAGAGAGAAT
*
29799685 ATTGAAAGAGTGAGAGATG
1 ATTGAAAAAGTGAGAGATG
*
29799704 ATTGAAAAAGTGAGAAATG
1 ATTGAAAAAGTGAGAGATG
29799723 A
1 A
29799724 GCTCTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.31, T:0.21
Consensus pattern (19 bp):
ATTGAAAAAGTGAGAGATG
Found at i:29804572 original size:17 final size:18
Alignment explanation
Indices: 29804550--29804583 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
29804540 TTTTGGGCCT
29804550 TGTGGGCC-ACACGGGCG
1 TGTGGGCCTACACGGGCG
29804567 TGTGGGCCTACACGGGC
1 TGTGGGCCTACACGGGC
29804584 CGACAACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.12, C:0.29, G:0.44, T:0.15
Consensus pattern (18 bp):
TGTGGGCCTACACGGGCG
Found at i:29806300 original size:203 final size:203
Alignment explanation
Indices: 29805951--29806345 Score: 736
Period size: 203 Copynumber: 1.9 Consensus size: 203
29805941 TAGTTTGAGG
29805951 CCTATATAAGTGATGGCCGGCCACCCCTTGTATAAACTTCTCAAATATATTAAAAAGTTCAGATT
1 CCTATATAAGTGATGGCCGGCCACCCCTTGTATAAACTTCTCAAATATATTAAAAAGTTCAGATT
29806016 TGTTTAAGTACAGAATTCTCCTTGAGTTTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAG
66 TGTTTAAGTACAGAATTCTCCTTGAGTTTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAG
* *
29806081 TTGTTTTAACAATCTTTTGATTGTGGGAGTCATCTTCAGCCTTCTTCTTGCCATTGATATTCTTC
131 TCGTTTTAACAATCTTTTGATTGTGGGAGTCATCTTCAGCCTTATTCTTGCCATTGATATTCTTC
29806146 AGCCTTCT
196 AGCCTTCT
* * *
29806154 CCTATATAAGTGATGGCCGGCCACCCCTTGTTTAAACTTCTCAAATATATTAAAAATTTCATATT
1 CCTATATAAGTGATGGCCGGCCACCCCTTGTATAAACTTCTCAAATATATTAAAAAGTTCAGATT
*
29806219 TGTTTAAGTGCAGAATTCTCCTTGAGTTTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAG
66 TGTTTAAGTACAGAATTCTCCTTGAGTTTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAG
29806284 TCGTTTTAACAATCTTTTGATTGTGGGAGTCATCTTCAGCCTTATTCTTGCCATTGATATTC
131 TCGTTTTAACAATCTTTTGATTGTGGGAGTCATCTTCAGCCTTATTCTTGCCATTGATATTC
29806346 CTTTGGAGGG
Statistics
Matches: 186, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
203 186 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (203 bp):
CCTATATAAGTGATGGCCGGCCACCCCTTGTATAAACTTCTCAAATATATTAAAAAGTTCAGATT
TGTTTAAGTACAGAATTCTCCTTGAGTTTTTCTCCAAGAATTCTCTCTTGAGTTTTCTTTAGAAG
TCGTTTTAACAATCTTTTGATTGTGGGAGTCATCTTCAGCCTTATTCTTGCCATTGATATTCTTC
AGCCTTCT
Found at i:29808160 original size:18 final size:20
Alignment explanation
Indices: 29808139--29808188 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
29808129 AAAGAAAGAT
29808139 AGAAAAAGA-AATCAAAAA-
1 AGAAAAAGAGAATCAAAAAG
*
29808157 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATCAAAAAG
29808177 AGCAAAAAGAGA
1 AG-AAAAAGAGA
29808189 TTGAGAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
20 2 0.07
21 9 0.32
ACGTcount: A:0.72, C:0.04, G:0.20, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAGAATCAAAAAG
Found at i:29814157 original size:20 final size:20
Alignment explanation
Indices: 29814132--29814171 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29814122 AATATTTTCC
*
29814132 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
29814152 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
29814172 TCATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:29814177 original size:34 final size:34
Alignment explanation
Indices: 29814120--29814185 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
29814110 CAAACACCAG
*
29814120 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTAC-GAAAAGT
29814155 AAAACATTTTCCAG-AAATCATTTTACGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACGAAAA
29814186 ATATTTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.32
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:29815230 original size:34 final size:33
Alignment explanation
Indices: 29815171--29815250 Score: 101
Period size: 34 Copynumber: 2.5 Consensus size: 33
29815161 GCTCAATTTA
*
29815171 ATAACAGT-TCAGT-TCAGTTGAGCCTTAGCCC
1 ATAACAGTGACAGTATCAGTTGAGCCTTAGCCC
* *
29815202 ATAATAGTGACAGTATCAGTGTGGGCCTTAGCCC
1 ATAACAGTGACAGTATCAGT-TGAGCCTTAGCCC
*
29815236 ATTACAGTGACAGTA
1 ATAACAGTGACAGTA
29815251 ATAGTTCAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
31 7 0.17
32 4 0.10
33 5 0.12
34 25 0.61
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (33 bp):
ATAACAGTGACAGTATCAGTTGAGCCTTAGCCC
Found at i:29815562 original size:27 final size:27
Alignment explanation
Indices: 29815521--29815644 Score: 171
Period size: 27 Copynumber: 4.6 Consensus size: 27
29815511 ATAACATTAA
* *
29815521 GCAT-ACAATCATTTTATAACATAGGG
1 GCATAACAGTCATTTTATAACATAAGG
* *
29815547 GCATAATAGTCATTTTATAACATAGGG
1 GCATAACAGTCATTTTATAACATAAGG
29815574 GCATAACAGTCATTTTATAACATAAGG
1 GCATAACAGTCATTTTATAACATAAGG
*
29815601 GCATAACCA-TTATTTTATAACATAAGG
1 GCATAA-CAGTCATTTTATAACATAAGG
*
29815628 GCATAACCGTCATTTTA
1 GCATAACAGTCATTTTA
29815645 CCTATGTGGG
Statistics
Matches: 88, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 81 0.92
28 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (27 bp):
GCATAACAGTCATTTTATAACATAAGG
Found at i:29818407 original size:15 final size:15
Alignment explanation
Indices: 29818387--29818415 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
29818377 TTCATTCATA
29818387 CATTTAGATAATTTT
1 CATTTAGATAATTTT
29818402 CATTTAGATAATTT
1 CATTTAGATAATTT
29818416 AATTTAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (15 bp):
CATTTAGATAATTTT
Found at i:29821191 original size:13 final size:13
Alignment explanation
Indices: 29821173--29821203 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
29821163 TTATACTGAT
29821173 TTCTAAGTATAAA
1 TTCTAAGTATAAA
29821186 TTCTAAGTATAAA
1 TTCTAAGTATAAA
29821199 TTCTA
1 TTCTA
29821204 TTTTTTCGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (13 bp):
TTCTAAGTATAAA
Found at i:29822909 original size:34 final size:33
Alignment explanation
Indices: 29822871--29822975 Score: 83
Period size: 34 Copynumber: 3.2 Consensus size: 33
29822861 TAGATTTCAT
29822871 ATTTTAAAAATATATCTTAGTCAATTTTAGTCAA
1 ATTTTAAAAATATATCTTAGT-AATTTTAGTCAA
**** *
29822905 ATTTTAGGCTTATGAT-TTA-TATTTTTAGT-AA
1 ATTTTAAAAATAT-ATCTTAGTAATTTTAGTCAA
*
29822936 A-TTTAAAAATTTTATCTTAGTAAATTTTAGTCAA
1 ATTTTAAAAA-TATATCTTAGT-AATTTTAGTCAA
*
29822970 AGTTTA
1 ATTTTA
29822976 GATTGGAGTG
Statistics
Matches: 53, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
30 6 0.11
31 8 0.15
32 9 0.17
33 9 0.17
34 15 0.28
35 6 0.11
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (33 bp):
ATTTTAAAAATATATCTTAGTAATTTTAGTCAA
Found at i:29823623 original size:17 final size:18
Alignment explanation
Indices: 29823587--29823624 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29823577 CCAGTTCGTA
*
29823587 TTTTCGAAAAAACCTTTG
1 TTTTCGAAAAAACCTATG
*
29823605 TTTTCGTAAAAACC-ATG
1 TTTTCGAAAAAACCTATG
29823622 TTT
1 TTT
29823625 CCAGTCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (18 bp):
TTTTCGAAAAAACCTATG
Found at i:29827678 original size:20 final size:19
Alignment explanation
Indices: 29827641--29827681 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
29827631 CATTTGGGAC
**
29827641 TATTTTTGTTTTGGACTTT
1 TATTTTTGTTTTAAACTTT
29827660 TATTTTCTGTTTTAAACTTT
1 TATTTT-TGTTTTAAACTTT
29827680 TA
1 TA
29827682 ATCACTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.66
Consensus pattern (19 bp):
TATTTTTGTTTTAAACTTT
Found at i:29831761 original size:39 final size:38
Alignment explanation
Indices: 29831706--29831784 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 38
29831696 ACTTTATAAA
*
29831706 AAAAATTAATATATTCA-ATTATTTATTTTCTTTTCTACT
1 AAAAATTAATAAATTCATATTATTT-TTTTCTTTT-TACT
*
29831745 AAAAATTATTAAATTCATATTATTTTTTTCTTTTTACT
1 AAAAATTAATAAATTCATATTATTTTTTTCTTTTTACT
29831783 AA
1 AA
29831785 TTTTAACTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
38 6 0.16
39 24 0.65
40 7 0.19
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (38 bp):
AAAAATTAATAAATTCATATTATTTTTTTCTTTTTACT
Found at i:29834123 original size:27 final size:27
Alignment explanation
Indices: 29834082--29834314 Score: 367
Period size: 27 Copynumber: 8.6 Consensus size: 27
29834072 CATTAAGCAC
*
29834082 ACAGTTATTTTATAACATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
* * * *
29834109 ATAGACATTTAATAACATAAGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
29834136 ACAGTCATTTTATAACATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
* *
29834163 ATAGTCATTTTATAACATAGGGGTATA
1 ACAGTCATTTTATAACATAGGGGCATA
29834190 ACAGTCATTTTATAACATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
*
29834217 ACCGTCATTTTATAACATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
*
29834244 ACCGTCATTTTATAACATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
29834271 ACAGTCATTTTATAACATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
* *
29834298 ACCGTTATTTTATAACA
1 ACAGTCATTTTATAACA
29834315 GGTTGGGGGT
Statistics
Matches: 189, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 189 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (27 bp):
ACAGTCATTTTATAACATAGGGGCATA
Found at i:29841761 original size:27 final size:27
Alignment explanation
Indices: 29841722--29841874 Score: 204
Period size: 27 Copynumber: 5.7 Consensus size: 27
29841712 ATAACATTAA
*
29841722 GCAT-ACAGTCATTATATAACATAGGG
1 GCATAACAGTCATTTTATAACATAGGG
*
29841748 GCATAATAGTCATTTTATAACATAGGG
1 GCATAACAGTCATTTTATAACATAGGG
*
29841775 CCATAACAGTCATTTTATAACATAGGG
1 GCATAACAGTCATTTTATAACATAGGG
**
29841802 GCATAACCA-TCATTTTATAACATA-AA
1 GCATAA-CAGTCATTTTATAACATAGGG
*
29841828 GCATAATAGTCATTTTATAACATAGGG
1 GCATAACAGTCATTTTATAACATAGGG
* *
29841855 GCATAACTGTTATTTTATAA
1 GCATAACAGTCATTTTATAA
29841875 TAGTTTGGTA
Statistics
Matches: 110, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
25 1 0.01
26 25 0.23
27 82 0.75
28 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (27 bp):
GCATAACAGTCATTTTATAACATAGGG
Found at i:29841794 original size:54 final size:54
Alignment explanation
Indices: 29841712--29841874 Score: 226
Period size: 53 Copynumber: 3.1 Consensus size: 54
29841702 ACAATCATAC
* *
29841712 ATAACATTAAGCAT-ACAGTCATTATATAACATAGGGGCATAA-TAGTCATTTT
1 ATAACATAAAGCATAACAGTCATTTTATAACATAGGGGCATAACTAGTCATTTT
** *
29841764 ATAACATAGGGCCATAACAGTCATTTTATAACATAGGGGCATAACCA-TCATTTT
1 ATAACATAAAG-CATAACAGTCATTTTATAACATAGGGGCATAACTAGTCATTTT
* *
29841818 ATAACATAAAGCATAATAGTCATTTTATAACATAGGGGCATAACT-GTTATTTT
1 ATAACATAAAGCATAACAGTCATTTTATAACATAGGGGCATAACTAGTCATTTT
29841871 ATAA
1 ATAA
29841875 TAGTTTGGTA
Statistics
Matches: 97, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
52 8 0.08
53 45 0.46
54 43 0.44
55 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (54 bp):
ATAACATAAAGCATAACAGTCATTTTATAACATAGGGGCATAACTAGTCATTTT
Found at i:29844055 original size:41 final size:41
Alignment explanation
Indices: 29843977--29844062 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 41
29843967 CAAAAGCCCG
* * *
29843977 AAGGCTGAATAGAAGCTCATGAGAGCTAAACGGAAACCCAT
1 AAGGCTGAATAGAAGCTCATAAGAACTAAACGAAAACCCAT
* * * * *
29844018 AAGGTTGAATGGAAGCTCATAAGAATTGAACGAAAACCGAT
1 AAGGCTGAATAGAAGCTCATAAGAACTAAACGAAAACCCAT
29844059 AAGG
1 AAGG
29844063 GTTAAACAGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.43, C:0.15, G:0.26, T:0.16
Consensus pattern (41 bp):
AAGGCTGAATAGAAGCTCATAAGAACTAAACGAAAACCCAT
Found at i:29844168 original size:42 final size:42
Alignment explanation
Indices: 29843989--29844178 Score: 136
Period size: 41 Copynumber: 4.6 Consensus size: 42
29843979 GGCTGAATAG
* * * * ***
29843989 AAGCTCATGAGAGCTAAACGGAAACCCATAAG-GTTGAATGG
1 AAGCTCGTGAGAGCTGAACAGAAACCCATAAGAGTTAAACAA
* * ** * * *
29844030 AAGCTCATAAGAATTGAAC-GAAAACCGATAAGGGTTAAACAG
1 AAGCTCGTGAGAGCTGAACAG-AAACCCATAAGAGTTAAACAA
* * *
29844072 AAG-TCGTGTGAGTTGAACAGAAACCCATAAGGGTTAAACAA
1 AAGCTCGTGAGAGCTGAACAGAAACCCATAAGAGTTAAACAA
* * * *
29844113 AAGCTCAAT-AGAGCTGAACGGAAACTCATATGAGTTAAACAA
1 AAGCTC-GTGAGAGCTGAACAGAAACCCATAAGAGTTAAACAA
*
29844155 AAGCTCGTGAGAGCTAAACAGAAA
1 AAGCTCGTGAGAGCTGAACAGAAA
29844179 GTAAACACAA
Statistics
Matches: 119, Mismatches: 24, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
40 1 0.01
41 59 0.50
42 58 0.49
43 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (42 bp):
AAGCTCGTGAGAGCTGAACAGAAACCCATAAGAGTTAAACAA
Found at i:29849627 original size:20 final size:20
Alignment explanation
Indices: 29849602--29849640 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
29849592 TGCAAACAAA
*
29849602 CAAACAGTATACAGAATAAT
1 CAAACAGTAAACAGAATAAT
29849622 CAAACAGTAAACAGAATAA
1 CAAACAGTAAACAGAATAA
29849641 ACTCAGTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.15, G:0.10, T:0.15
Consensus pattern (20 bp):
CAAACAGTAAACAGAATAAT
Found at i:29860224 original size:21 final size:19
Alignment explanation
Indices: 29860190--29860257 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 19
29860180 CCATAAGGCT
29860190 TAAACAAAAGCTCAATAGAGC
1 TAAACAAAA-CTC-ATAGAGC
*
29860211 TAAACGAAAACTCATATGAGT
1 TAAAC-AAAACTCATA-GAGC
*
29860232 TAAACAGAAGCTCATGAGAGC
1 TAAACA-AAACTCAT-AGAGC
29860253 TAAAC
1 TAAAC
29860258 GGAAAGTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 4 0.10
21 31 0.77
22 5 0.12
ACGTcount: A:0.49, C:0.18, G:0.16, T:0.18
Consensus pattern (19 bp):
TAAACAAAACTCATAGAGC
Found at i:29860252 original size:42 final size:41
Alignment explanation
Indices: 29860022--29860258 Score: 199
Period size: 42 Copynumber: 5.6 Consensus size: 41
29860012 GCTCGAAGGC
*
29860022 TAAACAAAAGCTCATAAGAGCT-AACCAGAAACCCATAAGGGT
1 TAAACAAAAGCTCAT-AGAGCTGAACGA-AAACCCATAAGGGT
* ** *
29860064 TGAACGGAAGCTCATAAGAACTGAA-GAAAAACCCATAAGGGT
1 TAAACAAAAGCTCAT-AGAGCTGAACG-AAAACCCATAAGGGT
* ** * * *
29860106 TAAACAGAAGCTTGTGTGAGTTGAACGGAAACCCATAAGGGT
1 TAAACAAAAGCTCAT-AGAGCTGAACGAAAACCCATAAGGGT
* * * *
29860148 TAAACAAAAGCTTAATAAAGCTGAACGGAAACCCATAAGGCT
1 TAAACAAAAGC-TCATAGAGCTGAACGAAAACCCATAAGGGT
* * * *
29860190 TAAACAAAAGCTCAATAGAGCTAAACGAAAACTCATATGAGT
1 TAAACAAAAGCTC-ATAGAGCTGAACGAAAACCCATAAGGGT
* *
29860232 TAAACAGAAGCTCATGAGAGCTAAACG
1 TAAACAAAAGCTCAT-AGAGCTGAACG
29860259 GAAAGTAAAC
Statistics
Matches: 159, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
41 3 0.02
42 150 0.94
43 6 0.04
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.17
Consensus pattern (41 bp):
TAAACAAAAGCTCATAGAGCTGAACGAAAACCCATAAGGGT
Found at i:29860259 original size:126 final size:126
Alignment explanation
Indices: 29860022--29860262 Score: 274
Period size: 126 Copynumber: 1.9 Consensus size: 126
29860012 GCTCGAAGGC
* * * ** *
29860022 TAAACAAAAGCTCATAAGAGCTAACCAGAAACCCATAAGGGTTGAACGGAAGCTCATAAGAACTG
1 TAAACAAAAGCTAATAAGAGCTAACCAGAAACCCATAAGGCTTAAACAAAAGCTCATAAGAACTA
* ** * * *
29860087 AAGAAAAACCCATAAGGGTTAAACAGAAGCTTGTGTGAGTTGAACGGAAACCCATAAGGGT
66 AAGAAAAACCCATAAGAGTTAAACAGAAGCTCATGAGAGCTAAACGGAAACCCATAAGGGT
* *
29860148 TAAACAAAAGCTTAATAA-AGCTGAA-CGGAAACCCATAAGGCTTAAACAAAAGCTCA-ATAGAG
1 TAAACAAAAGC-TAATAAGAGCT-AACCAGAAACCCATAAGGCTTAAACAAAAGCTCATA-AGAA
* *
29860210 CTAAACG-AAAACTCATATGAGTTAAACAGAAGCTCATGAGAGCTAAACGGAAA
63 CTAAA-GAAAAACCCATAAGAGTTAAACAGAAGCTCATGAGAGCTAAACGGAAA
29860263 GTAAACACAA
Statistics
Matches: 95, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
125 1 0.01
126 86 0.91
127 8 0.08
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (126 bp):
TAAACAAAAGCTAATAAGAGCTAACCAGAAACCCATAAGGCTTAAACAAAAGCTCATAAGAACTA
AAGAAAAACCCATAAGAGTTAAACAGAAGCTCATGAGAGCTAAACGGAAACCCATAAGGGT
Found at i:29864569 original size:18 final size:18
Alignment explanation
Indices: 29864543--29864580 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29864533 AAGTTTATTA
*
29864543 AGTTCAAATTTGATTTTT
1 AGTTCAAATTGGATTTTT
*
29864561 AGTTTAAATTGGATTTTT
1 AGTTCAAATTGGATTTTT
29864579 AG
1 AG
29864581 AATTATGTTT
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:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (18 bp):
AGTTCAAATTGGATTTTT
Found at i:29864615 original size:14 final size:15
Alignment explanation
Indices: 29864596--29864635 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
29864586 TGTTTCATAC
*
29864596 TTTTAGATTTTAA-G
1 TTTTAGATTTAAATG
*
29864610 TTTTAGATTTAAATT
1 TTTTAGATTTAAATG
29864625 TTTTAGATTTA
1 TTTTAGATTTA
29864636 GATTTTAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (15 bp):
TTTTAGATTTAAATG
Found at i:29864630 original size:15 final size:15
Alignment explanation
Indices: 29864596--29864641 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
29864586 TGTTTCATAC
* *
29864596 TTTTAGATTTTAA-G
1 TTTTAGATTTAAATT
29864610 TTTTAGATTTAAATT
1 TTTTAGATTTAAATT
*
29864625 TTTTAGATTTAGATT
1 TTTTAGATTTAAATT
29864640 TT
1 TT
29864642 AGGTAAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (15 bp):
TTTTAGATTTAAATT
Found at i:29874938 original size:42 final size:42
Alignment explanation
Indices: 29874879--29874963 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
29874869 ACAAATAAGG
29874879 TGCAACTAGGTTTAGAATTTTATGTTTAATTAGATTTAAGTT
1 TGCAACTAGGTTTAGAATTTTATGTTTAATTAGATTTAAGTT
29874921 TGCAACTAGGTTTAGAATTTTATGTTTAATTAGATTTAAGTT
1 TGCAACTAGGTTTAGAATTTTATGTTTAATTAGATTTAAGTT
29874963 T
1 T
29874964 TAAACTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.31, C:0.05, G:0.16, T:0.48
Consensus pattern (42 bp):
TGCAACTAGGTTTAGAATTTTATGTTTAATTAGATTTAAGTT
Found at i:29879200 original size:31 final size:32
Alignment explanation
Indices: 29879162--29879230 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
29879152 TTAGGTTTAC
*
29879162 TTATATT-ATTTT-TTTAAA-ATTAAATAAATAT
1 TTATATTAATTTTAATTAAATATTAAAT-AAT-T
*
29879193 TTATATTAATTTTAATTAAATATTTAATAATT
1 TTATATTAATTTTAATTAAATATTAAATAATT
29879225 TTATAT
1 TTATAT
29879231 ATAGTCACCT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 7 0.21
32 12 0.36
33 8 0.24
34 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TTATATTAATTTTAATTAAATATTAAATAATT
Found at i:29879207 original size:23 final size:21
Alignment explanation
Indices: 29879181--29879227 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
29879171 TTTTTTAAAA
29879181 TTAAATAAATATTTATATTAATT
1 TTAAATAAATATTTA-A-TAATT
*
29879204 TTAATTAAATATTTAATAATT
1 TTAAATAAATATTTAATAATT
29879225 TTA
1 TTA
29879228 TATATAGTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
22 1 0.04
23 14 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAATAAATATTTAATAATT
Found at i:29879435 original size:15 final size:14
Alignment explanation
Indices: 29879395--29879439 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
29879385 AGGTAAGTAG
*
29879395 ACTTAATCTTTTTCA
1 ACTTAAT-TTTTTAA
*
29879410 AGTTAATTTTTTAA
1 ACTTAATTTTTTAA
*
29879424 ACTTAATATTTTAA
1 ACTTAATTTTTTAA
29879438 AC
1 AC
29879440 CCTCACACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 20 0.77
15 6 0.23
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (14 bp):
ACTTAATTTTTTAA
Found at i:29880665 original size:5 final size:5
Alignment explanation
Indices: 29880657--29880689 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
29880647 TGCCTTTTGT
29880657 TTTTA TTTTA TTTTA -TTTA TTATTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA TTT
29880690 CTCTTTCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:29884665 original size:70 final size:70
Alignment explanation
Indices: 29884552--29884752 Score: 241
Period size: 70 Copynumber: 2.9 Consensus size: 70
29884542 TTCTTGGTGA
* ** * * * *
29884552 GCACAACTATCGTCAGTTATCCGACTAGCGTTGGACACAATAATTTGTTGACTCGTTCAACTAGT
1 GCACAACTATCATCAGTTATCAAACTAGCGCTGGGCACAATAATTTGTCGACTTGTTCAACTAGT
29884617 G-TCGG
66 GAT-GG
* **
29884622 GCACAACTATCAT-AGGTTATCAAACCAGCGCTGGGCACAATAATTTGTCGACTTGTTTGACTAG
1 GCACAACTATCATCA-GTTATCAAACTAGCGCTGGGCACAATAATTTGTCGACTTGTTCAACTAG
29884686 TGATGG
65 TGATGG
* *
29884692 GCACAACTATCATCAGTTATCTAACTAGCGCT-GG-AC-ACAATTTGTCGACTTGTTCAACTAG
1 GCACAACTATCATCAGTTATCAAACTAGCGCTGGGCACAATAATTTGTCGACTTGTTCAACTAG
29884753 CCCTAGACAC
Statistics
Matches: 113, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
67 22 0.19
68 2 0.02
69 3 0.03
70 84 0.74
71 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (70 bp):
GCACAACTATCATCAGTTATCAAACTAGCGCTGGGCACAATAATTTGTCGACTTGTTCAACTAGT
GATGG
Found at i:29889409 original size:10 final size:10
Alignment explanation
Indices: 29889394--29889440 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
29889384 TAAAATTTTG
29889394 AATTTTAATT
1 AATTTTAATT
29889404 AATTTTATAATT
1 AA-TTT-TAATT
*
29889416 AATTTTGATT
1 AATTTTAATT
*
29889426 AATTTTGATT
1 AATTTTAATT
29889436 -ATTTT
1 AATTTT
29889441 CGATATATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.15
10 16 0.47
11 6 0.18
12 7 0.21
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (10 bp):
AATTTTAATT
Found at i:29890260 original size:9 final size:9
Alignment explanation
Indices: 29890246--29890284 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
29890236 CCCGTTAGTG
*
29890246 AAATAAATC
1 AAATAAATA
29890255 AAATAAA-A
1 AAATAAATA
*
29890263 AAATGAATA
1 AAATAAATA
29890272 AAATAAATA
1 AAATAAATA
29890281 AAAT
1 AAAT
29890285 TAAAAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 6 0.23
9 20 0.77
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAATA
Found at i:29898352 original size:16 final size:16
Alignment explanation
Indices: 29898331--29898374 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
29898321 GCCAGACATG
29898331 AAGTAGAAGAAGAAAA
1 AAGTAGAAGAAGAAAA
* *
29898347 AAGTAGAGAAAAGACAA
1 AAGTAGA-AGAAGAAAA
29898364 AAG-AGAAGAAG
1 AAGTAGAAGAAG
29898375 GGCACGTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 10 0.42
17 10 0.42
ACGTcount: A:0.66, C:0.02, G:0.27, T:0.05
Consensus pattern (16 bp):
AAGTAGAAGAAGAAAA
Found at i:29898885 original size:11 final size:11
Alignment explanation
Indices: 29898871--29898901 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
29898861 CATAAATTTA
29898871 TATATTCTTGG
1 TATATTCTTGG
29898882 TATATTCTTGG
1 TATATTCTTGG
29898893 TATATTCTT
1 TATATTCTT
29898902 TGATATTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.10, G:0.13, T:0.58
Consensus pattern (11 bp):
TATATTCTTGG
Found at i:29903812 original size:132 final size:132
Alignment explanation
Indices: 29903571--29903815 Score: 400
Period size: 132 Copynumber: 1.9 Consensus size: 132
29903561 GTAAAGATAG
*
29903571 CAGATCTTATCTCCCTAAGAAGTAGTGGAGCAAATCAAAGACGGCAAATCTTATCTTTCCAAGAT
1 CAGATCTTATCTCCCTAAGAAGTAGTGGAGCAAATCAAAGACGACAAATCTTATCTTTCCAAGAT
* * *
29903636 AGTGAGAAGCAGATTTAAGCCACCAGGCCTTGTCTCCCTGAGCAGTAGCGAAGTAGGTTGAAGAC
66 AGTGAGAAACAGATTTAAGCCACCAGGCCTTATCTCCCTAAGCAGTAGCGAAGTAGGTTGAAGAC
29903701 AC
131 AC
* * *
29903703 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAGGACGACAAATCTTATCTTTCCAAGAT
1 CAGATCTTATCTCCCTAAGAAGTAGTGGAGCAAATCAAAGACGACAAATCTTATCTTTCCAAGAT
* * *
29903768 AGTGGGAAATAGATTTAAGCCACCGGGCCTTATCTCCCTAAGCAGTAG
66 AGTGAGAAACAGATTTAAGCCACCAGGCCTTATCTCCCTAAGCAGTAG
29903816 TGGAGCAGAT
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
132 103 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (132 bp):
CAGATCTTATCTCCCTAAGAAGTAGTGGAGCAAATCAAAGACGACAAATCTTATCTTTCCAAGAT
AGTGAGAAACAGATTTAAGCCACCAGGCCTTATCTCCCTAAGCAGTAGCGAAGTAGGTTGAAGAC
AC
Found at i:29903816 original size:88 final size:88
Alignment explanation
Indices: 29903708--29903900 Score: 314
Period size: 88 Copynumber: 2.2 Consensus size: 88
29903698 GACACCAGAT
*
29903708 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAGGACGACAAATCTTATCTTTCCAAGATAGTGG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGG
* *
29903773 GAAATAGATTTAAGCCACCGGGC
66 GAAACAGATTTAAGCCACCAGGC
**
29903796 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGG
*
29903861 GAAGCAGATTTAAGCCACCAGGC
66 GAAACAGATTTAAGCCACCAGGC
* *
29903884 CTTGTCTCCCTGAGCAG
1 CTTATCTCCCTAAGCAG
29903901 CAGCGGAGTA
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 97 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (88 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGTGG
GAAACAGATTTAAGCCACCAGGC
Found at i:29903844 original size:44 final size:44
Alignment explanation
Indices: 29903562--29904110 Score: 190
Period size: 44 Copynumber: 12.5 Consensus size: 44
29903552 AACAGATCAG
* * * *
29903562 TAAAGATAGCAGATCTTATCTCCCTAAGAAGTAGTGGAGCAAAT
1 TAAAGACAGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
* * *
29903606 CAAAGACGGCAAATCTTATCTTTCC-AAG-A-TAGTGAGAAGCAGAT
1 TAAAGACAGCAAATCTTATC-TCCCTAAGCAGTAGTG-G-AGCAGAT
* * * *** * * * * * *
29903650 TTAAGCCACCAGGCCTTGTCTCCCTGAGCAGTAGCGAAGTAGGT
1 TAAAGACAGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
* * *
29903694 TGAAGACACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
1 TAAAGACAGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
* * * **
29903738 CAAGGAC-GACAAATCTTATCTTTCC-AAG-A-TAGTGGGAAATAGAT
1 TAAAGACAG-CAAATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGAT
* * * ****
29903782 TTAAGCCACCGGGCCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
1 TAAAGACAGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
* * * *
29903826 CAAAGACGGTAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGAT
1 TAAAGACAGCAAATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGAT
* * * *** * * * * * *
29903870 TTAAGCCACCAGGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
1 TAAAGACAGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
* * * *
29903914 TGAAGATAGCAGATCTTATCTCCCTAAGAAGTAGTGGAGCAGAT
1 TAAAGACAGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
* ** * *
29903958 CAAAGATGGAAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGAT
1 TAAAGACAGCAAATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGAT
* * * * * * * * * *
29904002 TTAAGCCA-CTGAACCTTGTCTCCCTCAGCAGCAGCGGAGTAGGT
1 TAAAGACAGC-AAATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
* * * * *
29904046 TTAAGATAGCAGATCTTATCTCCTTAAGTAGTAGTGGAGCAGAT
1 TAAAGACAGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
* *
29904090 CAAAGACGGCAAATCTTATCT
1 TAAAGACAGCAAATCTTATCT
29904111 TTCCAGGATA
Statistics
Matches: 347, Mismatches: 130, Indels: 56
0.65 0.24 0.11
Matches are distributed among these distances:
42 17 0.05
43 23 0.07
44 272 0.78
45 23 0.07
46 12 0.03
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (44 bp):
TAAAGACAGCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
Found at i:29903869 original size:132 final size:132
Alignment explanation
Indices: 29903574--29903846 Score: 366
Period size: 132 Copynumber: 2.1 Consensus size: 132
29903564 AAGATAGCAG
* * *
29903574 ATCTTATCTCCCTAAGAAGTAGTGGAGCAAATCAAAGACGGCAAATCTTATCTTTCCAAGATAGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGT
* * * * * **
29903639 GAGAAGCAGATTTAAGCCACCAGGCCTTGTCTCCCTGAGCAGTAGCGAAGTAGGTTGAAGACACC
66 GAGAAACAGATTTAAGCCACCAGGCCTTATCTCCCTAAGCAGTAGCGAAGCAGATCAAAGACACC
*
29903704 AG
131 AA
*
29903706 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAGGACGACAAATCTTATCTTTCCAAGATAGT
1 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGT
* * * * * ***
29903771 GGGAAATAGATTTAAGCCACCGGGCCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGT
66 GAGAAACAGATTTAAGCCACCAGGCCTTATCTCCCTAAGCAGTAGCGAAGCAGATCAAAGACACC
29903836 AA
131 AA
29903838 ATCTTATCT
1 ATCTTATCT
29903847 TTCCAAGATA
Statistics
Matches: 121, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
132 121 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (132 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGACAAATCTTATCTTTCCAAGATAGT
GAGAAACAGATTTAAGCCACCAGGCCTTATCTCCCTAAGCAGTAGCGAAGCAGATCAAAGACACC
AA
Found at i:29903958 original size:220 final size:220
Alignment explanation
Indices: 29903576--29904010 Score: 737
Period size: 220 Copynumber: 2.0 Consensus size: 220
29903566 GATAGCAGAT
29903576 CTTATCTCCCTAAGAAGTAGTGGAGCAAATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGA
1 CTTATCTCCCTAAGAAGTAGTGGAGCAAATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGA
*
29903641 GAAGCAGATTTAAGCCACCAGGCCTTGTCTCCCTGAGCAGTAGCGAAGTAGGTTGAAGACACCAG
66 GAAGCAGATTTAAGCCACCAGGCCTTGTCTCCCTGAGCAGCAGCGAAGTAGGTTGAAGACACCAG
* *
29903706 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAGGA-CGACAAATCTTATCTTTCCAAGATAG
131 ATCTTATCTCCCTAAGAAGTAGTGGAGCAGATCAAAGATCGA-AAATCTTATCTTTCCAAGATAG
*
29903770 TGGGAAATAGATTTAAGCCACCGGGC
195 TGGGAAACAGATTTAAGCCACCGGGC
* * * *
29903796 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGG
1 CTTATCTCCCTAAGAAGTAGTGGAGCAAATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGA
* * *
29903861 GAAGCAGATTTAAGCCACCAGGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATAGCAG
66 GAAGCAGATTTAAGCCACCAGGCCTTGTCTCCCTGAGCAGCAGCGAAGTAGGTTGAAGACACCAG
*
29903926 ATCTTATCTCCCTAAGAAGTAGTGGAGCAGATCAAAGATGGAAAATCTTATCTTTCCAAGATAGT
131 ATCTTATCTCCCTAAGAAGTAGTGGAGCAGATCAAAGATCGAAAATCTTATCTTTCCAAGATAGT
*
29903991 GGGAAGCAGATTTAAGCCAC
196 GGGAAACAGATTTAAGCCAC
29904011 TGAACCTTGT
Statistics
Matches: 201, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
220 199 0.99
221 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (220 bp):
CTTATCTCCCTAAGAAGTAGTGGAGCAAATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTGA
GAAGCAGATTTAAGCCACCAGGCCTTGTCTCCCTGAGCAGCAGCGAAGTAGGTTGAAGACACCAG
ATCTTATCTCCCTAAGAAGTAGTGGAGCAGATCAAAGATCGAAAATCTTATCTTTCCAAGATAGT
GGGAAACAGATTTAAGCCACCGGGC
Found at i:29904199 original size:132 final size:132
Alignment explanation
Indices: 29903796--29904181 Score: 639
Period size: 132 Copynumber: 2.9 Consensus size: 132
29903786 GCCACCGGGC
* *
29903796 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTAAATCTTATCTTTCCAAGATAGTGG
1 CTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAGACGGAAAATCTTATCTTTCCAAGATAGTGG
29903861 GAAGCAGATTTAAGCCACC-AGGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATAGCA
66 GAAGCAGATTTAAGCCACCGA-GCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATAGCA
29903925 GAT
130 GAT
* *
29903928 CTTATCTCCCTAAGAAGTAGTGGAGCAGATCAAAGATGGAAAATCTTATCTTTCCAAGATAGTGG
1 CTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAGACGGAAAATCTTATCTTTCCAAGATAGTGG
* * * *
29903993 GAAGCAGATTTAAGCCACTGAACCTTGTCTCCCTCAGCAGCAGCGGAGTAGGTTTAAGATAGCAG
66 GAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATAGCAG
29904058 AT
131 AT
* * *
29904060 CTTATCTCCTTAAGTAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTTCCAGGATAGTGG
1 CTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAGACGGAAAATCTTATCTTTCCAAGATAGTGG
* *
29904125 GAAGCAGATCTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAA
66 GAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAA
29904182 AATTACAGGT
Statistics
Matches: 235, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
132 234 1.00
133 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (132 bp):
CTTATCTCCCTAAGTAGTAGTGGAGCAGATCAAAGACGGAAAATCTTATCTTTCCAAGATAGTGG
GAAGCAGATTTAAGCCACCGAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATAGCAG
AT
Found at i:29904480 original size:9 final size:9
Alignment explanation
Indices: 29904466--29904504 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
29904456 CCCGTTAGTG
*
29904466 AAATAAATC
1 AAATAAATA
29904475 AAATAAAT-
1 AAATAAATA
*
29904483 AAATGAATA
1 AAATAAATA
29904492 AAATAAATA
1 AAATAAATA
29904501 AAAT
1 AAAT
29904505 TAAAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (9 bp):
AAATAAATA
Found at i:29913696 original size:25 final size:25
Alignment explanation
Indices: 29913651--29913701 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
29913641 TCTCTTCTCA
* *
29913651 TCTCTTCACTTCTCTCTCATTTTTC
1 TCTCTTCACTTCCCTCTCATTATTC
*
29913676 TCTCTTCATTTCCCT-TCCATTATTC
1 TCTCTTCACTTCCCTCT-CATTATTC
29913701 T
1 T
29913702 TCATTCCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.10, C:0.35, G:0.00, T:0.55
Consensus pattern (25 bp):
TCTCTTCACTTCCCTCTCATTATTC
Found at i:29923460 original size:18 final size:17
Alignment explanation
Indices: 29923433--29923475 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
29923423 TTATTTACAA
29923433 TTTGTATGTGCTTTTATT
1 TTTGTATGTG-TTTTATT
* *
29923451 TTTGTGTGTGTTTTCTT
1 TTTGTATGTGTTTTATT
29923468 TTT-TATGT
1 TTTGTATGT
29923476 AGGTCACCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 9 0.41
ACGTcount: A:0.07, C:0.05, G:0.19, T:0.70
Consensus pattern (17 bp):
TTTGTATGTGTTTTATT
Found at i:29925615 original size:9 final size:9
Alignment explanation
Indices: 29925601--29925626 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
29925591 AAACATACAA
29925601 ATTTAAATT
1 ATTTAAATT
29925610 ATTTAAATT
1 ATTTAAATT
29925619 ATTTAAAT
1 ATTTAAAT
29925627 AATCTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATTTAAATT
Found at i:29928696 original size:34 final size:35
Alignment explanation
Indices: 29928631--29928697 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
29928621 TAGTATTCAC
** *
29928631 AGTGCACAGTTTGGGCCTAAGCCTTTTTCAGTATT
1 AGTGCACAGTTTGGGCCTAAGCCCATCTCAGTATT
29928666 AGTG-ACAGTTTGGGCCTTAA-CCCATCTCAGTA
1 AGTGCACAGTTTGGGCC-TAAGCCCATCTCAGTA
29928698 CAGTATCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 21 0.75
35 7 0.25
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (35 bp):
AGTGCACAGTTTGGGCCTAAGCCCATCTCAGTATT
Found at i:29935629 original size:26 final size:26
Alignment explanation
Indices: 29935596--29935650 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
29935586 CCTACAGTAA
29935596 TTTCAGAATATCATAACATATATCAG
1 TTTCAGAATATCATAACATATATCAG
* *
29935622 TTTCAGAATATCATAGCATGTATCAG
1 TTTCAGAATATCATAACATATATCAG
29935648 TTT
1 TTT
29935651 TAAAACACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (26 bp):
TTTCAGAATATCATAACATATATCAG
Found at i:29943866 original size:62 final size:62
Alignment explanation
Indices: 29943776--29943926 Score: 194
Period size: 62 Copynumber: 2.4 Consensus size: 62
29943766 CATGGCCTAG
* * *
29943776 ACACACACCTGTGCCCCTAGCCCGTGTGACCAAAAATACAAATAGTGAGTTCCACGGCCTGA
1 ACACACACCTATGCCCCTAGCCCGTGTGACCAAAAATACAAATAGTAAGTTACACGGCCTGA
* * * *
29943838 ACACACGCCTATGTCCCTAGCTCGTGTGACCAAAAATACAAATAGTAAGTTACACGGCCTGG
1 ACACACACCTATGCCCCTAGCCCGTGTGACCAAAAATACAAATAGTAAGTTACACGGCCTGA
* * * * *
29943900 AGACACATCTGTTCGCCTAGCCCGTGT
1 ACACACACCTATGCCCCTAGCCCGTGT
29943927 ACCTCCAATT
Statistics
Matches: 74, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
62 74 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (62 bp):
ACACACACCTATGCCCCTAGCCCGTGTGACCAAAAATACAAATAGTAAGTTACACGGCCTGA
Found at i:29947579 original size:95 final size:95
Alignment explanation
Indices: 29947443--29947618 Score: 280
Period size: 95 Copynumber: 1.9 Consensus size: 95
29947433 ATACTTTCAT
* * *
29947443 CTCTAGTTGGATATTTAATTAGACATTGGAAACCCTTATGATCTTTTGAACTACACCAACAACAT
1 CTCTAGTTGAATATTTAATTAGACATTGGAAACCCTTATGATATTTTGAACTACACCAACAACAG
*
29947508 TGCACAAAAGGTGATATTTCAATCGTATTC
66 TGAACAAAAGGTGATATTTCAATCGTATTC
* * * *
29947538 CTCTATTTGAATATTTAATTGGACATTGGAAAGCCTTATGATATTTTGAACTACACCAATAACAG
1 CTCTAGTTGAATATTTAATTAGACATTGGAAACCCTTATGATATTTTGAACTACACCAACAACAG
29947603 TGAACAAAAGGTGATA
66 TGAACAAAAGGTGATA
29947619 GCTCAATTGT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 73 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (95 bp):
CTCTAGTTGAATATTTAATTAGACATTGGAAACCCTTATGATATTTTGAACTACACCAACAACAG
TGAACAAAAGGTGATATTTCAATCGTATTC
Found at i:29959008 original size:80 final size:80
Alignment explanation
Indices: 29958848--29959172 Score: 287
Period size: 80 Copynumber: 3.9 Consensus size: 80
29958838 ATTAAATCAA
* * * *
29958848 AATAAAATTTGTTAAATGGCGGGAATAAATCCCGAAATAGATTTTATTTAATTTTAATTTCTCGT
1 AATAAAATTCGTTGAATGGCAGGAATAAATCCCGAAACAGA---T-TTT-A-TTTAA-TTCTCG-
* * *
29958913 TTTGGCAACAAAATAAAAAATAG
58 TTTGGAAATAAAATAAAAAATGG
* * *
29958936 AATAAAA-TCTGGTGAATGGCAAGAATAAATCCCGAAACAGATTTTATTTAATTCTTGTTTGGAA
1 AATAAAATTC-GTTGAATGGCAGGAATAAATCCCGAAACAGATTTTATTTAATTCTCGTTTGGAA
*
29959000 ATCAAATAAAAAATGG
65 ATAAAATAAAAAATGG
* ** *
29959016 AATAAAGTTCGTTGAGCGGCAGGAATAAATCCTGAAACAGATTTTATTTAACTTTAATTCTCGTT
1 AATAAAATTCGTTGAATGGCAGGAATAAATCCCGAAACAGA---T-TTT-A-TTTAATTCTCGTT
29959081 TGGAAATAAAATAAAAAATGG
60 TGGAAATAAAATAAAAAATGG
* * * * **
29959102 AATAAAATTCGTTGAACT-G-AGGGAATAAATCCCGAAATAGATTTTATTCACTTTTAATTTGGA
1 AATAAAATTCGTTGAA-TGGCA-GGAATAAATCCCGAAACAGATTTTATTTAATTCTCGTTTGGA
29959165 AATAAAAT
64 AATAAAAT
29959173 CGAATAAAAT
Statistics
Matches: 198, Mismatches: 29, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
80 71 0.36
81 8 0.04
82 8 0.04
83 3 0.02
84 6 0.03
85 3 0.02
86 65 0.33
87 1 0.01
88 33 0.17
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (80 bp):
AATAAAATTCGTTGAATGGCAGGAATAAATCCCGAAACAGATTTTATTTAATTCTCGTTTGGAAA
TAAAATAAAAAATGG
Found at i:29959101 original size:86 final size:84
Alignment explanation
Indices: 29958869--29959314 Score: 344
Period size: 86 Copynumber: 5.4 Consensus size: 84
29958859 TTAAATGGCG
* * *
29958869 GGAATAAATCCCGAAATAGATTTTATTTAATTTTAATTTCTCGTTTTGGCAACAAAATAAAAAAT
1 GGAATAAATCCCGAAACAGATTTTATTTAA-TTTAA-TTCTCG-TTTGGAAATAAAATAAAAAAT
* * * *
29958934 AGAATAAAATCTGGTGAATGGCA
63 GGAATAAATTC-GTTGAACGGCA
* * *
29958957 AGAATAAATCCCGAAACAGA---T-TTT-ATTTAATTCTTGTTTGGAAATCAAATAAAAAATGGA
1 GGAATAAATCCCGAAACAGATTTTATTTAATTTAATTCTCGTTTGGAAATAAAATAAAAAATGGA
*
29959017 ATAAAGTTCGTTGAGCGGCA
66 ATAAA-TTCGTTGAACGGCA
*
29959037 GGAATAAATCCTGAAACAGATTTTATTTAACTTTAATTCTCGTTTGGAAATAAAATAAAAAATGG
1 GGAATAAATCCCGAAACAGATTTTATTTAA-TTTAATTCTCGTTTGGAAATAAAATAAAAAATGG
*
29959102 AATAAAATTCGTTGAACTG-A
65 AAT-AAATTCGTTGAACGGCA
* * * **
29959122 GGGAATAAATCCCGAAATAGATTTTATTCACTTTTAA------TTTGGAAATAAAAT--CGAAT-
1 -GGAATAAATCCCGAAACAGATTTTATTTA-ATTTAATTCTCGTTTGGAAATAAAATAAAAAATG
* **
29959178 --A-AAATAT-GTTAAACGATA
64 GAATAAAT-TCGTTGAACGGCA
** * * *
29959196 GGAATAAATTTCGAAACATATTTTATTTAATTTTAATAT-TCATTTAGAAATAAAA-AAATAAA-
1 GGAATAAATCCCGAAACAGATTTTATTTAA-TTTAAT-TCTCGTTTGGAAATAAAATAAA-AAAT
*
29959258 -GAATAAAATTTGTTGAACGGCA
63 GGAAT-AAATTCGTTGAACGGCA
* *
29959280 GGAATAAATCTCAAAACAGATTTTATTTAATTTAA
1 GGAATAAATCCCGAAACAGATTTTATTTAATTTAA
29959315 AATTTTATTT
Statistics
Matches: 290, Mismatches: 41, Indels: 59
0.74 0.11 0.15
Matches are distributed among these distances:
73 39 0.13
74 2 0.01
75 1 0.00
78 3 0.01
79 12 0.04
80 65 0.22
81 9 0.03
82 6 0.02
83 8 0.03
84 45 0.16
85 3 0.01
86 76 0.26
87 3 0.01
88 18 0.06
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (84 bp):
GGAATAAATCCCGAAACAGATTTTATTTAATTTAATTCTCGTTTGGAAATAAAATAAAAAATGGA
ATAAATTCGTTGAACGGCA
Found at i:29959133 original size:166 final size:158
Alignment explanation
Indices: 29958848--29959312 Score: 419
Period size: 159 Copynumber: 2.9 Consensus size: 158
29958838 ATTAAATCAA
* * * * * *
29958848 AATAAAATTTGTTAAATGGCGGGAATAAATCCCGAAATAGATTTTATTTAATTTTAATTTCTCGT
1 AATAAAATATGTTAAACGACAGGAATAAATCCTGAAACAGATTTTATTTAATTTTAA-TTCTCG-
* * * *
29958913 TTTGGCAACAAAATAAAAAATAGAATAAAA-TCTGGTGAA-TG-GCAAGAATAAATCCCGAAACA
64 TTTGGAAATAAAATAAAAAAT-GAATAAAATTC-GTTGAACTGAG--GGAATAAATCCCGAAACA
* *
29958975 GATTTTATTTAATTCTT-GTTTGGAAATCAAATAAAAAATGG
125 GATTTTATTTAATT-TTAATTTGG-----AAAT--AAAATCG
* * * * *
29959016 AATAAAGT-TCGTTGAGCGGCAGGAATAAATCCTGAAACAGATTTTATTTAACTTTAATTCTCGT
1 AATAAAATAT-GTTAAACGACAGGAATAAATCCTGAAACAGATTTTATTTAATTTTAATTCTCGT
*
29959080 TTGGAAATAAAATAAAAAATGGAATAAAATTCGTTGAACTGAGGGAATAAATCCCGAAATAGATT
65 TTGGAAATAAAATAAAAAAT-GAATAAAATTCGTTGAACTGAGGGAATAAATCCCGAAACAGATT
* *
29959145 TTATTCACTTTTAATTTGGAAATAAAATCG
129 TTATTTAATTTTAATTTGGAAATAAAATCG
* * * *
29959175 AATAAAATATGTTAAACGATAGGAATAAAT-TTCGAAACATATTTTATTTAATTTTAATAT-TCA
1 AATAAAATATGTTAAACGACAGGAATAAATCCT-GAAACAGATTTTATTTAATTTTAAT-TCTCG
* * * * *
29959238 TTTAGAAATAAAA-AAATAAA-GAATAAAATTTGTTGAACGGCA-GGAATAAATCTCAAAACAGA
64 TTTGGAAATAAAATAAA-AAATGAATAAAATTCGTTGAACTG-AGGGAATAAATCCCGAAACAGA
29959300 TTTTATTTAATTT
127 TTTTATTTAATTT
29959313 AAAATTTTAT
Statistics
Matches: 252, Mismatches: 35, Indels: 31
0.79 0.11 0.10
Matches are distributed among these distances:
157 46 0.18
158 5 0.02
159 69 0.27
160 2 0.01
161 4 0.02
165 2 0.01
166 65 0.26
167 11 0.04
168 48 0.19
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (158 bp):
AATAAAATATGTTAAACGACAGGAATAAATCCTGAAACAGATTTTATTTAATTTTAATTCTCGTT
TGGAAATAAAATAAAAAATGAATAAAATTCGTTGAACTGAGGGAATAAATCCCGAAACAGATTTT
ATTTAATTTTAATTTGGAAATAAAATCG
Found at i:29960005 original size:30 final size:31
Alignment explanation
Indices: 29959966--29960029 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
29959956 TCCATATTTA
* *
29959966 TGGAGAGTCAAAGATATGGGTATC-AAATAT
1 TGGAAAGTCAAAGATATAGGTATCGAAATAT
*
29959996 TGGAAAGTCAAAGATATAGGTATCGAGATAT
1 TGGAAAGTCAAAGATATAGGTATCGAAATAT
29960027 TGG
1 TGG
29960030 TATAAGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.27
Consensus pattern (31 bp):
TGGAAAGTCAAAGATATAGGTATCGAAATAT
Found at i:29964729 original size:25 final size:25
Alignment explanation
Indices: 29964695--29964745 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
29964685 ATATTTATGG
29964695 AAAGTCAAAGATATGAGTATCAAAT
1 AAAGTCAAAGATATGAGTATCAAAT
*
29964720 AAAGTCAAAGATATGGGTATCAAAT
1 AAAGTCAAAGATATGAGTATCAAAT
29964745 A
1 A
29964746 TTGGAAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.18, T:0.24
Consensus pattern (25 bp):
AAAGTCAAAGATATGAGTATCAAAT
Found at i:29964756 original size:30 final size:30
Alignment explanation
Indices: 29964692--29964780 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
29964682 TCCATATTTA
*
29964692 TGGAAAGTCAAAGATATGAGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
29964719 T--AAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
29964747 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
29964778 TGG
1 TGG
29964781 TATAAGAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
25 20 0.37
26 2 0.04
27 2 0.04
28 1 0.02
30 21 0.39
31 8 0.15
ACGTcount: A:0.43, C:0.07, G:0.25, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:29969851 original size:18 final size:18
Alignment explanation
Indices: 29969813--29969848 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29969803 TTATTATTTT
*
29969813 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
29969831 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
29969849 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:29969963 original size:9 final size:9
Alignment explanation
Indices: 29969949--29969981 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
29969939 TAATATTTTA
29969949 TTTTAATAT
1 TTTTAATAT
29969958 TTTTAATAT
1 TTTTAATAT
29969967 TTTTAATAT
1 TTTTAATAT
29969976 TTTTAA
1 TTTTAA
29969982 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTAATAT
Found at i:29970773 original size:24 final size:24
Alignment explanation
Indices: 29970744--29970798 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
29970734 TAGCTAATCC
29970744 ACCCTAATCTAAAGATAATTACAA
1 ACCCTAATCTAAAGATAATTACAA
29970768 ACCCTAATCTAAAGATAATTACAA
1 ACCCTAATCTAAAGATAATTACAA
29970792 ACCCTAA
1 ACCCTAA
29970799 AGCGAGTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.24
Consensus pattern (24 bp):
ACCCTAATCTAAAGATAATTACAA
Found at i:29973572 original size:10 final size:10
Alignment explanation
Indices: 29973553--29973594 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
29973543 GCCTATTAGA
29973553 TAAT-TTTTT
1 TAATATTTTT
29973562 TAATATTTTT
1 TAATATTTTT
*
29973572 TTATATTTTTT
1 TAATA-TTTTT
29973583 TAATAATTTTT
1 TAAT-ATTTTT
29973594 T
1 T
29973595 TAAAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 4 0.14
10 9 0.32
11 14 0.50
12 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TAATATTTTT
Found at i:29973573 original size:12 final size:11
Alignment explanation
Indices: 29973555--29973597 Score: 70
Period size: 10 Copynumber: 3.9 Consensus size: 11
29973545 CTATTAGATA
29973555 ATTTTTTTAAT
1 ATTTTTTTAAT
29973566 ATTTTTTT-AT
1 ATTTTTTTAAT
29973576 ATTTTTTTAAT
1 ATTTTTTTAAT
29973587 AATTTTTTTAA
1 -ATTTTTTTAA
29973598 AAAAATACGG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.33
11 10 0.33
12 10 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTTTTAAT
Found at i:29973579 original size:21 final size:22
Alignment explanation
Indices: 29973555--29973596 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
29973545 CTATTAGATA
29973555 ATTTTTTTAAT-ATTTTTTTAT
1 ATTTTTTTAATAATTTTTTTAT
29973576 ATTTTTTTAATAATTTTTTTA
1 ATTTTTTTAATAATTTTTTTA
29973597 AAAAAATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
ATTTTTTTAATAATTTTTTTAT
Found at i:29973688 original size:27 final size:27
Alignment explanation
Indices: 29973658--29973719 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
29973648 CCTATCAGGT
29973658 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
29973685 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
29973712 AGGCGCCA
1 AGGCGCCA
29973720 TTACTAGACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.34, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:29973858 original size:21 final size:20
Alignment explanation
Indices: 29973822--29973866 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 20
29973812 AATAAACACC
29973822 AAAAAATTTTTAAAAATAAA
1 AAAAAATTTTTAAAAATAAA
29973842 AAAAAAGTATTTTAAAAATAAA
1 AAAAAA-T-TTTTAAAAATAAA
29973864 AAA
1 AAA
29973867 TAAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 6 0.26
21 1 0.04
22 16 0.70
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAAAATTTTTAAAAATAAA
Found at i:29974050 original size:19 final size:19
Alignment explanation
Indices: 29974028--29974065 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
29974018 AATTTAATTT
*
29974028 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
29974047 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
29974066 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:29974235 original size:27 final size:27
Alignment explanation
Indices: 29974164--29974228 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
29974154 TACCGACATT
* *
29974164 CAATATTCATACAAAATTATAATATTA
1 CAATATTCATACAAAATTACAAAATTA
29974191 CAATATTCATACAAAATTACAAAATTA
1 CAATATTCATACAAAATTACAAAATTA
29974218 CAATATTCATA
1 CAATATTCATA
29974229 TTAAATTGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (27 bp):
CAATATTCATACAAAATTACAAAATTA
Found at i:29974542 original size:19 final size:19
Alignment explanation
Indices: 29974520--29974557 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
29974510 TATAAATTTA
*
29974520 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
29974539 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
29974558 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:29974815 original size:27 final size:28
Alignment explanation
Indices: 29974777--29974853 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
29974767 CCAGCCCGGC
*
29974777 CCATTGGCGCCTCTCAGAAT-GGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
*
29974804 CCATTGGCGCCTCCCAG-GTAGGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
29974831 CCATTGGCGCCTCCCAG-ATAGGC
1 CCATTGGCGCCTCCCAGAATAGGC
29974854 GCCAATACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (28 bp):
CCATTGGCGCCTCCCAGAATAGGCACCA
Found at i:29982354 original size:21 final size:22
Alignment explanation
Indices: 29982311--29982361 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
29982301 GAGCCGTGCT
29982311 CATGTGAGATAGGCCACAAGAC
1 CATGTGAGATAGGCCACAAGAC
* * *
29982333 CATGTG-GATGGGTCACACGAC
1 CATGTGAGATAGGCCACAAGAC
*
29982354 CGTGTGAG
1 CATGTGAG
29982362 CAAACCGTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.22, G:0.33, T:0.18
Consensus pattern (22 bp):
CATGTGAGATAGGCCACAAGAC
Found at i:29983145 original size:14 final size:15
Alignment explanation
Indices: 29983126--29983155 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29983116 TGTATTTTTC
29983126 TTTTC-TTTTTCTTT
1 TTTTCTTTTTTCTTT
29983140 TTTTCTTTTTTCTTT
1 TTTTCTTTTTTCTTT
29983155 T
1 T
29983156 CGGTTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTCTTTTTTCTTT
Found at i:29983265 original size:17 final size:18
Alignment explanation
Indices: 29983243--29983291 Score: 73
Period size: 17 Copynumber: 2.7 Consensus size: 18
29983233 CAAAAAAATG
29983243 TGTTCTTTTTTCTA-TTT
1 TGTTCTTTTTTCTATTTT
29983260 TGTTCTTTTTTCTATTTT
1 TGTTCTTTTTTCTATTTT
*
29983278 TTTTCTTTTCTTCT
1 TGTTCTTTT-TTCT
29983292 CTGTTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 14 0.48
18 11 0.38
19 4 0.14
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.78
Consensus pattern (18 bp):
TGTTCTTTTTTCTATTTT
Found at i:29984055 original size:25 final size:25
Alignment explanation
Indices: 29984025--29984100 Score: 118
Period size: 25 Copynumber: 3.0 Consensus size: 25
29984015 TTATTTTTGC
29984025 AATTTTATTTAT-TTATTTATTTTAA
1 AATTTT-TTTATATTATTTATTTTAA
*
29984050 ACTTTTTTTATATTATTTATTTTAA
1 AATTTTTTTATATTATTTATTTTAA
29984075 AATTTTTTTATTATTATTTATTTTAA
1 AATTTTTTTA-TATTATTTATTTTAA
29984101 GTTTTTCACA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
24 5 0.11
25 27 0.57
26 15 0.32
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (25 bp):
AATTTTTTTATATTATTTATTTTAA
Found at i:29984114 original size:25 final size:24
Alignment explanation
Indices: 29984037--29984176 Score: 81
Period size: 26 Copynumber: 5.6 Consensus size: 24
29984027 TTTTATTTAT
*
29984037 TTATTTATTTTAAACTTTTTTTATA
1 TTATTTATTTTAAAC-TTTTTAATA
* *
29984062 TTATTTATTTTAAAATTTTTTTATTA
1 TTATTTATTTT-AAA-CTTTTTAATA
*
29984088 TTATTTATTTT-AAGTTTTTCACATA
1 TTATTTATTTTAAACTTTTT-A-ATA
** *
29984113 TTATGCATTTTAAACTATATTAAACTA
1 TTATTTATTTTAAACT-T-TTTAA-TA
***
29984140 TTATCCGTTTTAAA---TTTACATA
1 TTATTTATTTTAAACTTTTTA-ATA
29984162 TTATTTATTTTAAAC
1 TTATTTATTTTAAAC
29984177 CATAGATATT
Statistics
Matches: 90, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
22 16 0.18
23 6 0.07
24 3 0.03
25 22 0.24
26 25 0.28
27 16 0.18
28 2 0.02
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (24 bp):
TTATTTATTTTAAACTTTTTAATA
Found at i:29984114 original size:51 final size:53
Alignment explanation
Indices: 29984027--29984126 Score: 125
Period size: 51 Copynumber: 1.9 Consensus size: 53
29984017 ATTTTTGCAA
** **
29984027 TTTTATTTATTTATTTATTTTAAACTTTTTTTATATTATTTATTTTAAAATTT
1 TTTTATTTATTTATTTATTTTAAACTTTTTACATATTATGCATTTTAAAATTT
*
29984080 TTTTA-TTA-TTATTTATTTT-AAGTTTTTCACATATTATGCATTTTAAA
1 TTTTATTTATTTATTTATTTTAAACTTTTT-ACATATTATGCATTTTAAA
29984127 CTATATTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 7 0.17
51 26 0.63
52 3 0.07
53 5 0.12
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (53 bp):
TTTTATTTATTTATTTATTTTAAACTTTTTACATATTATGCATTTTAAAATTT
Found at i:29984288 original size:28 final size:25
Alignment explanation
Indices: 29984251--29984323 Score: 83
Period size: 28 Copynumber: 2.8 Consensus size: 25
29984241 TTTTTAAAGA
*
29984251 AAACTGTTTTTTATATTATTCATTTG
1 AAACT-TTTTATATATTATTCATTTG
* *
29984277 AAATTTCTTTTTACATATTATTCATTTT
1 AAA---CTTTTTATATATTATTCATTTG
29984305 AAACTTTTTATATATTATT
1 AAACTTTTTATATATTATT
29984324 TTAAAATTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 15 0.38
26 3 0.08
28 20 0.50
29 2 0.05
ACGTcount: A:0.30, C:0.08, G:0.03, T:0.59
Consensus pattern (25 bp):
AAACTTTTTATATATTATTCATTTG
Found at i:29984381 original size:23 final size:23
Alignment explanation
Indices: 29984349--29984396 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
29984339 TGGTTATTTA
* * *
29984349 TTTTAATTTGCTTTGTATGTTAT
1 TTTTAATTTGCATTGCATATTAT
*
29984372 TTTTATTTTGCATTGCATATTAT
1 TTTTAATTTGCATTGCATATTAT
29984395 TT
1 TT
29984397 ACTTTGAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.19, C:0.06, G:0.10, T:0.65
Consensus pattern (23 bp):
TTTTAATTTGCATTGCATATTAT
Found at i:29984402 original size:21 final size:20
Alignment explanation
Indices: 29984369--29984408 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
29984359 CTTTGTATGT
* *
29984369 TATTTTTATTTTGCATTGCA
1 TATTTTTACTTTGAATTGCA
29984389 TATTATTTACTTTGAATTGC
1 TATT-TTTACTTTGAATTGC
29984409 TTTCTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.57
Consensus pattern (20 bp):
TATTTTTACTTTGAATTGCA
Found at i:29994206 original size:36 final size:36
Alignment explanation
Indices: 29994159--29994229 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
29994149 TATTATAAAA
* *
29994159 ACTGTCACATGGCATGAATAACATACCCACATATTT
1 ACTGTCACATGGCATAAATAACACACCCACATATTT
* *
29994195 ACTGTCACATGGCATAAATAGCACACCCTCATATT
1 ACTGTCACATGGCATAAATAACACACCCACATATT
29994230 CATTTTCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.27
Consensus pattern (36 bp):
ACTGTCACATGGCATAAATAACACACCCACATATTT
Found at i:29994239 original size:36 final size:36
Alignment explanation
Indices: 29994159--29994240 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 36
29994149 TATTATAAAA
* * *
29994159 ACTGTCACATGGCATGAATAACATACCCACATATTT
1 ACTGTCACATGGCATAAATAACACACCCACATATTC
* *
29994195 ACTGTCACATGGCATAAATAGCACACCCTCATATTC
1 ACTGTCACATGGCATAAATAACACACCCACATATTC
* *
29994231 ATTTTCACAT
1 ACTGTCACAT
29994241 CAATCATCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (36 bp):
ACTGTCACATGGCATAAATAACACACCCACATATTC
Found at i:29996375 original size:43 final size:43
Alignment explanation
Indices: 29996327--29996551 Score: 362
Period size: 43 Copynumber: 5.3 Consensus size: 43
29996317 TTATAGAAAT
* * *
29996327 AAACGCCGCTATAAAGCAGGACCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* *
29996370 AAACGCCGCTATAGACCAGGACCTTTAGCGGTGCTTTTCCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* * *
29996413 AAACGCCGCTATAGATTAGGACCTTTAGCGGTGCATTTCCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
29996456 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
*
29996499 AAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTTT-CCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
29996541 AAACGCCGCTA
1 AAACGCCGCTA
29996552 AAAACATATC
Statistics
Matches: 171, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
42 15 0.09
43 156 0.91
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
Found at i:30000280 original size:20 final size:20
Alignment explanation
Indices: 30000257--30000298 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
30000247 AATTGCAGTA
30000257 ACAATGAAAAACCCCCAAAT
1 ACAATGAAAAACCCCCAAAT
30000277 ACAATGAAAAACCCCCAAAT
1 ACAATGAAAAACCCCCAAAT
30000297 AC
1 AC
30000299 CAAATTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.31, G:0.05, T:0.10
Consensus pattern (20 bp):
ACAATGAAAAACCCCCAAAT
Found at i:30000790 original size:146 final size:145
Alignment explanation
Indices: 30000579--30000924 Score: 449
Period size: 146 Copynumber: 2.3 Consensus size: 145
30000569 ATGGCGCCTG
* *
30000579 TTTTTTTAAAGTCAAATTATTTTTTTGTGGCGTTTTTGATAAAAACGCCGCTATAGCTGATCTTT
1 TTTTTTTAAAGT-AAAAT-TTTTTTTGTGGCGTTTTT-ATAAAAACGCCGCTATAGCTGAACTTT
* *** * * *
30000644 TGCAGTGTTTTTGTTACAAACGCCGCAAAAAATTATTTCATTTAAAATAAAACGACACTGTTTTG
63 TGCAGCGTTTTCCATAAAAACGCAGCAAAAAATTATTTCATTCAAAATAAAACGACACTGTTTTG
* *
30000709 CTATGCTAAAAGGGCGCTA
128 CTAT-ATAAAAGGGAGCTA
* *
30000728 TTTTTTTAAAGTAAAATTTTTTTTGTGGCGTTTTTATAAAAACGCCGCTATTGCTTAACTTTTGC
1 TTTTTTTAAAGTAAAATTTTTTTTGTGGCGTTTTTATAAAAACGCCGCTATAGCTGAACTTTTGC
* * ** *
30000793 GGCGTTTTCCATAAAAACGCAGCAAAAAATTATTTTATTCGGAATAAAATGACACTGTTTTGCTA
66 AGCGTTTTCCATAAAAACGCAGCAAAAAATTATTTCATTCAAAATAAAACGACACTGTTTTGCTA
*
30000858 TATAAAATGGAGCTA
131 TATAAAAGGGAGCTA
* *
30000873 TTTTTTTAAAGTAAAATTATTTTTCGTGGCGTTTTTTATAAAAATGCCGCTA
1 TTTTTTTAAAGTAAAATT-TTTTTTGTGGCG-TTTTTATAAAAACGCCGCTA
30000925 AAAAATTATT
Statistics
Matches: 174, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
145 29 0.17
146 92 0.53
147 37 0.21
148 4 0.02
149 12 0.07
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (145 bp):
TTTTTTTAAAGTAAAATTTTTTTTGTGGCGTTTTTATAAAAACGCCGCTATAGCTGAACTTTTGC
AGCGTTTTCCATAAAAACGCAGCAAAAAATTATTTCATTCAAAATAAAACGACACTGTTTTGCTA
TATAAAAGGGAGCTA
Found at i:30001943 original size:96 final size:94
Alignment explanation
Indices: 30001831--30002071 Score: 326
Period size: 96 Copynumber: 2.7 Consensus size: 94
30001821 AATCCCAAAC
*
30001831 CCCTAACCACTAACCCCTAAATCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATT
1 CCCTAACCCCTAACCCCTAAA-CTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAA-T
*
30001896 CTAAATCCTAAACCCTAACCCAAGCCTAAAT
64 CTAAATCCTAAACCCTAACCCAACCCTAAAT
30001927 CCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACAC----TAAT-T-AATC
1 CCCTAACCCCTAACCCCTAAAC-TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATC
*
30001986 TAAATCCTAAACCCTAACCCGACCCTAAAT
65 TAAATCCTAAACCCTAACCCAACCCTAAAT
* *
30002016 CCCTAACCCCTAA-----ACA-TTATTTAATATATAAATTAAAACACACTAATTAATCTAAA
1 CCCTAACCCCTAACCCCTAAACTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAA
30002072 CCCTAACCTG
Statistics
Matches: 133, Mismatches: 5, Indels: 22
0.83 0.03 0.14
Matches are distributed among these distances:
82 26 0.20
84 2 0.02
86 4 0.03
87 1 0.01
88 2 0.02
89 43 0.32
90 2 0.02
91 1 0.01
92 4 0.03
95 1 0.01
96 47 0.35
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (94 bp):
CCCTAACCCCTAACCCCTAAACTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCT
AAATCCTAAACCCTAACCCAACCCTAAAT
Found at i:30001988 original size:89 final size:88
Alignment explanation
Indices: 30001831--30002077 Score: 319
Period size: 82 Copynumber: 2.8 Consensus size: 88
30001821 AATCCCAAAC
*
30001831 CCCTAACCACTAACCCCTAAATC-TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAAT
1 CCCTAACCCCTAACCCCTAAA-CATTATTTAATATATAAATTAAAAAACAC----TAAT-T-AA-
*
30001895 TCTAAATCCTAAACCCTAACCCAAGCCTAAA
58 TCTAAATCCTAAACCCTAACCCAACCCTAAA
30001926 TCCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAAT
1 -CCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAAT
*
30001991 CCTAAACCCTAACCCGACCCTAAA
65 CCTAAACCCTAACCCAACCCTAAA
* *
30002015 ---T---CCCTAACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACC
1 CCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATC
30002074 CTAA
66 CTAA
30002078 CCTGACACCG
Statistics
Matches: 145, Mismatches: 5, Indels: 16
0.87 0.03 0.10
Matches are distributed among these distances:
82 60 0.41
85 1 0.01
89 29 0.20
90 2 0.01
91 1 0.01
92 4 0.03
95 1 0.01
96 47 0.32
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.28
Consensus pattern (88 bp):
CCCTAACCCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATC
CTAAACCCTAACCCAACCCTAAA
Found at i:30002651 original size:41 final size:41
Alignment explanation
Indices: 30002606--30002689 Score: 143
Period size: 41 Copynumber: 2.0 Consensus size: 41
30002596 AAATGTTTTT
*
30002606 GCGGCGC-TTTTCTAAAAATGCCGCTAAAGATCTGAGCATCA
1 GCGGCGCATTTTC-AAAAACGCCGCTAAAGATCTGAGCATCA
30002647 GCGGCGCATTTTCAAAAACGCCGCTAAAGATCTGAGCATCA
1 GCGGCGCATTTTCAAAAACGCCGCTAAAGATCTGAGCATCA
30002688 GC
1 GC
30002690 ATATTTACAC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 36 0.88
42 5 0.12
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (41 bp):
GCGGCGCATTTTCAAAAACGCCGCTAAAGATCTGAGCATCA
Found at i:30010321 original size:115 final size:117
Alignment explanation
Indices: 30010154--30010385 Score: 317
Period size: 115 Copynumber: 2.0 Consensus size: 117
30010144 GTTTTATAAG
* * *
30010154 TTTCTTAACATAAATTAGTAATGGTTTGTGGGTAGATGAGTGGTTAAACAACCATGGTA-ACAT-
1 TTTCTTAACATAAACTAGCAATGGTTTGTGGGTAGATGAGCGGTTAAACAACCATGG-AGACATG
* * *
30010217 GGAGACCCAGGTTTGACTTCTTCTAGGAATAGTAAG-TTTAATTTTTTCCCTA
65 GGAGACCCAAGTTTGACTACTTCTAGGAATAGCAAGTTTTAATTTTTTCCCTA
* * *
30010269 TTTCTTGACATAAACTAGCAATGGTTTGTGGGTAGATGAGCGGTTAAACAACCTTGGAGACTTGG
1 TTTCTTAACATAAACTAGCAATGGTTTGTGGGTAGATGAGCGGTTAAACAACCATGGAGACATGG
* * * *
30010334 GGGACCCAAGTTTGACTACTTTTAGGAATAGCAGGTTTTATTTTTTTCCCTA
66 GAGACCCAAGTTTGACTACTTCTAGGAATAGCAAGTTTTAATTTTTTCCCTA
30010386 CCAGATTTTG
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
114 1 0.01
115 55 0.54
116 30 0.30
117 15 0.15
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (117 bp):
TTTCTTAACATAAACTAGCAATGGTTTGTGGGTAGATGAGCGGTTAAACAACCATGGAGACATGG
GAGACCCAAGTTTGACTACTTCTAGGAATAGCAAGTTTTAATTTTTTCCCTA
Found at i:30020331 original size:27 final size:27
Alignment explanation
Indices: 30020307--30020430 Score: 108
Period size: 27 Copynumber: 4.6 Consensus size: 27
30020297 CTGCCTCGAC
* *
30020307 GGACTATCCCGTTTTTAATGTCTCGTT
1 GGACTATCCCATGTTTAATGTCTCGTT
* *
30020334 AGACTATCTCATGTTTAATGTCTCGTT
1 GGACTATCCCATGTTTAATGTCTCGTT
*
30020361 GGACTAT-CCATGTTTAATGTC-CCTT
1 GGACTATCCCATGTTTAATGTCTCGTT
* *** *
30020386 CAGACTATCTTGTGTTTAATGTCTCATT
1 -GGACTATCCCATGTTTAATGTCTCGTT
* * *
30020414 GGGCTATCTCGTGTTTA
1 GGACTATCCCATGTTTA
30020431 TTTTCTCGAC
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
25 3 0.04
26 19 0.24
27 54 0.68
28 3 0.04
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.44
Consensus pattern (27 bp):
GGACTATCCCATGTTTAATGTCTCGTT
Found at i:30020392 original size:53 final size:54
Alignment explanation
Indices: 30020320--30020430 Score: 145
Period size: 53 Copynumber: 2.1 Consensus size: 54
30020310 CTATCCCGTT
* *
30020320 TTTAATGTCTCGTTAGACTATCTCATGTTTAATGTCTCGTTGGACTATC-CATG
1 TTTAATGTCTCCTTAGACTATCTCATGTTTAATGTCTCATTGGACTATCTCATG
** * *
30020373 TTTAATGTC-CCTTCAGACTATCTTGTGTTTAATGTCTCATTGGGCTATCTCGTG
1 TTTAATGTCTCCTT-AGACTATCTCATGTTTAATGTCTCATTGGACTATCTCATG
30020427 TTTA
1 TTTA
30020431 TTTTCTCGAC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
52 3 0.06
53 40 0.80
54 7 0.14
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (54 bp):
TTTAATGTCTCCTTAGACTATCTCATGTTTAATGTCTCATTGGACTATCTCATG
Found at i:30022541 original size:22 final size:21
Alignment explanation
Indices: 30022515--30022558 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
30022505 CAAACTTACT
*
30022515 AGAGTATGCCATAAGGGCCAAC
1 AGAGTATGCCATAAAGG-CAAC
30022537 AGAGTATGCCATAAAGGCAAC
1 AGAGTATGCCATAAAGGCAAC
30022558 A
1 A
30022559 AACCGAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (21 bp):
AGAGTATGCCATAAAGGCAAC
Found at i:30025474 original size:42 final size:43
Alignment explanation
Indices: 30025409--30025494 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 43
30025399 TTATGTTTTG
* * *
30025409 GAACCACATGGGTAGAGGACACGGGCATGTGTCCAGGCCGTGT
1 GAACCACATAGGCAGAGGACACGGGCATGTGTCAAGGCCGTGT
*
30025452 GAACCACATAGGCA-AGGACACGGGCGTGTGTCAAGGCCGTGT
1 GAACCACATAGGCAGAGGACACGGGCATGTGTCAAGGCCGTGT
30025494 G
1 G
30025495 GCATATAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 27 0.69
43 12 0.31
ACGTcount: A:0.24, C:0.23, G:0.37, T:0.15
Consensus pattern (43 bp):
GAACCACATAGGCAGAGGACACGGGCATGTGTCAAGGCCGTGT
Found at i:30038080 original size:23 final size:22
Alignment explanation
Indices: 30038030--30038080 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
30038020 AGCTTTGCAG
30038030 AAAAG-ACTGCATTACATTCCC
1 AAAAGCACTGCATTACATTCCC
30038051 AAGAAGCACTGCATTACATTCCCC
1 AA-AAGCACTGCATTACATT-CCC
30038075 AAAAGC
1 AAAAGC
30038081 CAAGCAGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 2 0.07
22 3 0.11
23 17 0.63
24 5 0.19
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (22 bp):
AAAAGCACTGCATTACATTCCC
Found at i:30039350 original size:11 final size:11
Alignment explanation
Indices: 30039334--30039368 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
30039324 ACTTTTAGTC
30039334 TCGCTACAGTA
1 TCGCTACAGTA
30039345 TCGCTACAGTA
1 TCGCTACAGTA
*
30039356 TCGCTACAATA
1 TCGCTACAGTA
30039367 TC
1 TC
30039369 TAATCTCACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (11 bp):
TCGCTACAGTA
Found at i:30039925 original size:17 final size:17
Alignment explanation
Indices: 30039905--30039937 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
30039895 TTGAGTCAGG
30039905 ATTGAATTTTAAATTTC
1 ATTGAATTTTAAATTTC
30039922 ATTGAATTTTAAATTT
1 ATTGAATTTTAAATTT
30039938 TGAAATGTAT
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:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTGAATTTTAAATTTC
Found at i:30043424 original size:342 final size:342
Alignment explanation
Indices: 30042791--30043476 Score: 1070
Period size: 342 Copynumber: 2.0 Consensus size: 342
30042781 TGGAAGCTAA
30042791 TGGTTTTGGTGATTCAAATAGAGATGCATGCTTTGAAGAAAAAGGTGGCTGGAGAAGCACACACT
1 TGGTTTTGGTGATTCAAATAGAGATGCATGCTTTGAAGAAAAAGGTGGCTGGAGAAGCACACACT
* *
30042856 ACCACTCAGACAATGCAGATCAGGCAGTTGGACATCATTTCAGCAGATTTAATAATATACGATCC
66 ACCACTCACACAATGCAGATCAGACAGTTGGACATCATTTCAGCAGATTTAATAATATACGATCC
* * *
30042921 CAAGTGAGTCAACAAAATGAAAATATTGTTGTGAAAAGAGATAATGCTAGTGGAGGAAACAATAG
131 CAAGTGAGTCAACAAAATGAAAATATAGTTGTGAAAAGAGATAATGCTAGTGGAGAAAACAACAG
* * ** *
30042986 GACCACATGTGATGGTCCGGAAAGTCATGATGCAACTGAAAAAGCTGGTGTGATTGTCTCAAAAT
196 GACCACATGTGATGGTCCAGAAAATCATGATGCAACTGAAAAAGCTCCTATGATTGTCTCAAAAT
*
30043051 TCAACCAAAGAAGTGAACCTTCTAGTGCAAAAAACATACTGCCTAAAAGGCAAACAAAACATGTA
261 TCAACCAAAGAAGTGAACCTTCTAGTGCAAAAAACATACTGCCTAAAAGGCAAACAAAACATGCA
*
30043116 TTGAACTCAAGAAATAG
326 TTAAACTCAAGAAATAG
* *
30043133 TGGTTTTGGTGATTCAAATAGAGATGCATGCTTTGAAGGAAAAGGTGGCTGGAGAAGCACACATT
1 TGGTTTTGGTGATTCAAATAGAGATGCATGCTTTGAAGAAAAAGGTGGCTGGAGAAGCACACACT
** * * * *
30043198 ACTGCTCACATAATGCAGATCAGACAGTTGGACATCATTTTAGCAGATTTAATAATGTACGATGC
66 ACCACTCACACAATGCAGATCAGACAGTTGGACATCATTTCAGCAGATTTAATAATATACGATCC
* *
30043263 GAAGTGAGTCAACAAAATGAAAATATAGTTGTGAAAAGAGATAATGCTAGTGGAGAAAAGAACAG
131 CAAGTGAGTCAACAAAATGAAAATATAGTTGTGAAAAGAGATAATGCTAGTGGAGAAAACAACAG
***
30043328 GACTGTATGTGATGGTCCAGAAAATCATGATGCAACT-AAAACAGCTCCTATGATTGTCTCAAAA
196 GACCACATGTGATGGTCCAGAAAATCATGATGCAACTGAAAA-AGCTCCTATGATTGTCTCAAAA
* * * * *
30043392 TTCAACTACATAAGTGAACCTTCTCA-TGCAAAAAACATGCTGCCTAAAAGGCAAACACAACATG
260 TTCAACCAAAGAAGTGAACCTTCT-AGTGCAAAAAACATACTGCCTAAAAGGCAAACAAAACATG
30043456 CATTAAACTCAAGAAATAG
324 CATTAAACTCAAGAAATAG
30043475 TG
1 TG
30043477 ATGAAAGTGC
Statistics
Matches: 312, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
341 4 0.01
342 307 0.98
343 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (342 bp):
TGGTTTTGGTGATTCAAATAGAGATGCATGCTTTGAAGAAAAAGGTGGCTGGAGAAGCACACACT
ACCACTCACACAATGCAGATCAGACAGTTGGACATCATTTCAGCAGATTTAATAATATACGATCC
CAAGTGAGTCAACAAAATGAAAATATAGTTGTGAAAAGAGATAATGCTAGTGGAGAAAACAACAG
GACCACATGTGATGGTCCAGAAAATCATGATGCAACTGAAAAAGCTCCTATGATTGTCTCAAAAT
TCAACCAAAGAAGTGAACCTTCTAGTGCAAAAAACATACTGCCTAAAAGGCAAACAAAACATGCA
TTAAACTCAAGAAATAG
Found at i:30049653 original size:16 final size:17
Alignment explanation
Indices: 30049632--30049665 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
30049622 ATCACTTGTA
30049632 ACAACT-TTCTAATATT
1 ACAACTCTTCTAATATT
*
30049648 ACAACTCTTCTATTATT
1 ACAACTCTTCTAATATT
30049665 A
1 A
30049666 TTTTTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (17 bp):
ACAACTCTTCTAATATT
Found at i:30052728 original size:69 final size:69
Alignment explanation
Indices: 30052641--30052807 Score: 167
Period size: 69 Copynumber: 2.4 Consensus size: 69
30052631 GCCTCGGTGG
* * * * * ** *
30052641 ACTCTAATGGTTGGCATAGCCGAGCTAT-AAACTTATACCTTATAATCCCTGTGTTTACTGTC-C
1 ACTCTATTAGTTGCCATAGACGAGCTATGAAA-TTACACCTTATAATCCCCATGTTTACTATCTC
30052704 TGACAA
65 -GACAA
** ** *
30052710 ACTCTATTAGTTGCCATAGTTGAGCTATGGTATTACATCTTATAATCCCCATGTTTACTATCTCG
1 ACTCTATTAGTTGCCATAGACGAGCTATGAAATTACACCTTATAATCCCCATGTTTACTATCTCG
30052775 ACAA
66 ACAA
* *
30052779 AATCTATTAGTTTCCATAGACGAGCTATG
1 ACTCTATTAGTTGCCATAGACGAGCTATG
30052808 GTGTTACATT
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
69 78 0.98
70 2 0.03
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (69 bp):
ACTCTATTAGTTGCCATAGACGAGCTATGAAATTACACCTTATAATCCCCATGTTTACTATCTCG
ACAA
Found at i:30052808 original size:69 final size:69
Alignment explanation
Indices: 30052679--30052816 Score: 188
Period size: 69 Copynumber: 2.0 Consensus size: 69
30052669 AAACTTATAC
** * * **
30052679 CTTATAATCCCTGTGTTTACTGTCCTGACAAACTCTATTAGTTGCCATAGTTGAGCTATGGTATT
1 CTTATAATCCCCATGTTTACTATCCTGACAAAATCTATTAGTTGCCATAGACGAGCTATGGTATT
30052744 ACAT
66 ACAT
* *
30052748 CTTATAATCCCCATGTTTACTAT-CTCGACAAAATCTATTAGTTTCCATAGACGAGCTATGGTGT
1 CTTATAATCCCCATGTTTACTATCCT-GACAAAATCTATTAGTTGCCATAGACGAGCTATGGTAT
30052812 TACAT
65 TACAT
30052817 TATATACATC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 2 0.03
69 58 0.97
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (69 bp):
CTTATAATCCCCATGTTTACTATCCTGACAAAATCTATTAGTTGCCATAGACGAGCTATGGTATT
ACAT
Found at i:30063082 original size:30 final size:30
Alignment explanation
Indices: 30063048--30063110 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
30063038 TTCATCACCA
30063048 ACTAGCCAATTATTAATTGAGCAACTATTG
1 ACTAGCCAATTATTAATTGAGCAACTATTG
30063078 ACTAGCCAATTATTAATTGAGCAACTATTG
1 ACTAGCCAATTATTAATTGAGCAACTATTG
30063108 ACT
1 ACT
30063111 TACATATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (30 bp):
ACTAGCCAATTATTAATTGAGCAACTATTG
Found at i:30063091 original size:15 final size:15
Alignment explanation
Indices: 30063047--30063093 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
30063037 CTTCATCACC
30063047 AACTAGCCAATTATT
1 AACTAGCCAATTATT
* *
30063062 AATTGAG-CAACTATT
1 AACT-AGCCAATTATT
*
30063077 GACTAGCCAATTATT
1 AACTAGCCAATTATT
30063092 AA
1 AA
30063094 TTGAGCAACT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 2 0.08
15 20 0.83
16 2 0.08
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (15 bp):
AACTAGCCAATTATT
Done.