Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 44 of 318
Found at i:16459257 original size:18 final size:18
Alignment explanation
Indices: 16459234--16459292 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
16459224 ACAAGTGGTG
16459234 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
** *
16459252 GTGGAGTGGAGT-TGG-TG
1 GTGGAG-CAAGTGTGGCTA
16459269 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
16459287 GTGGAG
1 GTGGAG
16459293 TTGGTGGTGG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
16 3 0.09
17 10 0.31
18 16 0.50
19 3 0.09
ACGTcount: A:0.19, C:0.07, G:0.51, T:0.24
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:16459291 original size:30 final size:32
Alignment explanation
Indices: 16459229--16459302 Score: 107
Period size: 35 Copynumber: 2.3 Consensus size: 32
16459219 TAGGTACAAG
16459229 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGC-A-T-GAGTGGAGT
16459264 TGGTGGTGGAGCAAGTGTGGC-T-AGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCATGAGTGGAGT
16459294 TGGTGGTGG
1 TGGTGGTGG
16459303 CAAAGGCTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
30 17 0.44
32 1 0.03
35 21 0.54
ACGTcount: A:0.15, C:0.05, G:0.53, T:0.27
Consensus pattern (32 bp):
TGGTGGTGGAGCAAGTGTGGCATGAGTGGAGT
Found at i:16462186 original size:51 final size:51
Alignment explanation
Indices: 16462108--16462271 Score: 274
Period size: 51 Copynumber: 3.2 Consensus size: 51
16462098 ACTTCTGATC
* * *
16462108 AGTGACAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATTAGTGACA
1 AGTGATAAATGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
* *
16462159 AGTGATAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACA
1 AGTGATAAATGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
*
16462210 AGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGATAAATGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
16462261 AGTGATAAATG
1 AGTGATAAATG
16462272 TGATCAGTGT
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 104 1.00
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (51 bp):
AGTGATAAATGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGTGACA
Found at i:16464005 original size:47 final size:47
Alignment explanation
Indices: 16463940--16464062 Score: 149
Period size: 47 Copynumber: 2.6 Consensus size: 47
16463930 TACATAATGG
* * * * *
16463940 TGCCATAGCCCAGCTATGGTCTTACAC-GTAATCACATATCTCACTGA
1 TGCCATATCCCAGATATGGTCTTACACAGT-AGCACATATCACACCGA
* * *
16463987 TGTCATATCCCAGATATGGTCTTATACAGTAGCATATATCACACCGA
1 TGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACACCGA
*
16464034 TGCCATATCCCAGATATGGTCTTATACAG
1 TGCCATATCCCAGATATGGTCTTACACAG
16464063 AAATCACTTG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
47 64 0.97
48 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (47 bp):
TGCCATATCCCAGATATGGTCTTACACAGTAGCACATATCACACCGA
Found at i:16464078 original size:7 final size:7
Alignment explanation
Indices: 16464066--16464094 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
16464056 TATACAGAAA
16464066 TCACTTG
1 TCACTTG
16464073 TCACTTG
1 TCACTTG
16464080 TCACTTG
1 TCACTTG
16464087 TCACTTG
1 TCACTTG
16464094 T
1 T
16464095 AGCCAAAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (7 bp):
TCACTTG
Found at i:16464128 original size:31 final size:31
Alignment explanation
Indices: 16464093--16464270 Score: 257
Period size: 31 Copynumber: 5.7 Consensus size: 31
16464083 CTTGTCACTT
* *
16464093 GTAGCCAAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* ** *
16464124 GTAGCTGGTGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
16464155 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
16464186 GTAGCCGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
16464217 GTAGCTGAAACTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
16464248 GTAGCTGAAGTTACCACTTTTCA
1 GTAGCCGAAGCTACCACTTTTCA
16464271 GTTGTCATTT
Statistics
Matches: 133, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 133 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:16464352 original size:50 final size:50
Alignment explanation
Indices: 16464288--16464424 Score: 229
Period size: 50 Copynumber: 2.7 Consensus size: 50
16464278 TTTGCCATTG
16464288 ATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTA
1 ATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTA
* * * * *
16464338 ATCAAATAAGTGTAGCCGAAGTTATTACTTATCACTTTCATTTGTCCTTG
1 ATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTA
16464388 ATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTT
1 ATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTT
16464425 GTTTCCATGG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 79 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (50 bp):
ATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTA
Found at i:16468416 original size:34 final size:35
Alignment explanation
Indices: 16468364--16468430 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
16468354 CAAACACCAG
* *
16468364 AAAATATTTTTCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
16468399 AAAACATTTTCCA-TAAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
16468431 TATTTTAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 18 0.62
35 11 0.38
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:16468868 original size:40 final size:41
Alignment explanation
Indices: 16468824--16468904 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
16468814 TCTGACCCAG
*
16468824 CTTGGTTTGGCATT-AATTAGTTAGGCCCCATTCCTTGACT
1 CTTGGTATGGCATTAAATTAGTTAGGCCCCATTCCTTGACT
16468864 CTTGGTATGGCATTAAATTAGTTAGGCCCCATTCCTTGACT
1 CTTGGTATGGCATTAAATTAGTTAGGCCCCATTCCTTGACT
16468905 TTCTTCATCG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 13 0.33
41 26 0.67
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (41 bp):
CTTGGTATGGCATTAAATTAGTTAGGCCCCATTCCTTGACT
Found at i:16471547 original size:16 final size:16
Alignment explanation
Indices: 16471513--16471547 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
16471503 AAAATCAAAT
* *
16471513 AAAATTACATTATATA
1 AAAATTACATTAAAAA
16471529 AAAATTACATTAAAAA
1 AAAATTACATTAAAAA
16471545 AAA
1 AAA
16471548 TCACAAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTACATTAAAAA
Found at i:16471620 original size:65 final size:67
Alignment explanation
Indices: 16471544--16471673 Score: 153
Period size: 65 Copynumber: 2.0 Consensus size: 67
16471534 TACATTAAAA
*
16471544 AAAATCACAAAACACTAAACTAA-ACACTAA-C-AATCATAAATTACTAACAAAATAA-ATAATT
1 AAAATCACAAAACA-TAAA-TAATACA-TAACCTAATCATAAACTACTAACAAAATAACATAATT
16471605 TTAAG
63 TTAAG
* **
16471610 AAAA-CACAAAACATTAATAATTTATAACCTAATCATAAACTACTAACAAAATAACTATAATTTT
1 AAAATCACAAAACATAAATAATACATAACCTAATCATAAACTACTAACAAAATAAC-ATAATTTT
16471674 TTTTTAAGAA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
63 6 0.11
64 5 0.09
65 32 0.58
66 4 0.07
67 8 0.15
ACGTcount: A:0.57, C:0.16, G:0.01, T:0.26
Consensus pattern (67 bp):
AAAATCACAAAACATAAATAATACATAACCTAATCATAAACTACTAACAAAATAACATAATTTTA
AG
Found at i:16473111 original size:53 final size:53
Alignment explanation
Indices: 16473030--16473185 Score: 210
Period size: 53 Copynumber: 3.0 Consensus size: 53
16473020 GACGCAAAAT
* *
16473030 ATGTGATAAGTGTG-C-CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* *
16473082 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGTATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* * *
16473135 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTA
16473186 TGATATGTGA
Statistics
Matches: 93, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
51 4 0.04
52 11 0.12
53 78 0.84
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
Found at i:16474473 original size:60 final size:60
Alignment explanation
Indices: 16474389--16474507 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
16474379 AAAACTCACT
*
16474389 AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
* *
16474449 AAACACAATAATTTATAACGTAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
16474508 TAAAAAAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.34
Consensus pattern (60 bp):
AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:16474735 original size:13 final size:13
Alignment explanation
Indices: 16474717--16474746 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
16474707 CTGACAACCT
16474717 ATTTCAATATTTA
1 ATTTCAATATTTA
*
16474730 ATTTCAGTATTTA
1 ATTTCAATATTTA
16474743 ATTT
1 ATTT
16474747 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (13 bp):
ATTTCAATATTTA
Found at i:16476685 original size:19 final size:18
Alignment explanation
Indices: 16476656--16476692 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
16476646 TTCATAATAA
16476656 TTATATATTATTATAGAT
1 TTATATATTATTATAGAT
16476674 TTATAGTATTATTATAGAT
1 TTATA-TATTATTATAGAT
16476693 AATTGAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
TTATATATTATTATAGAT
Found at i:16477092 original size:28 final size:29
Alignment explanation
Indices: 16477038--16477117 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
16477028 AAAAATAGTT
* *
16477038 ATTTAATTATTAACATATTTTTATTTTCATC
1 ATTTAA-TATTAAAAT-TTTTTATTTTAATC
*
16477069 A-TTCATATTAAAATTTTTTATTTTAATC
1 ATTTAATATTAAAATTTTTTATTTTAATC
*
16477097 ATTTAATATTATTAATTTTTT
1 ATTTAATATTA-AAATTTTTT
16477118 GGTTTTTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
28 14 0.33
29 16 0.38
30 11 0.26
31 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (29 bp):
ATTTAATATTAAAATTTTTTATTTTAATC
Found at i:16477409 original size:20 final size:20
Alignment explanation
Indices: 16477386--16477431 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
16477376 ATTCATTTAT
**
16477386 TAAAATAAAAATTTTATAAA
1 TAAAATAAAAATACTATAAA
*
16477406 TAAAATAATAATACTATAAA
1 TAAAATAAAAATACTATAAA
16477426 TAAAAT
1 TAAAAT
16477432 TGTTTAAGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAATAAAAATACTATAAA
Found at i:16480221 original size:29 final size:29
Alignment explanation
Indices: 16480179--16480236 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
16480169 TGCCCTTGGC
16480179 CCAGCACTCCAGCACACCCTTCGTCTCTG
1 CCAGCACTCCAGCACACCCTTCGTCTCTG
16480208 CCAGCACTCCAGCACACCCTTCGTCTCTG
1 CCAGCACTCCAGCACACCCTTCGTCTCTG
16480237 TACTTTCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.48, G:0.14, T:0.21
Consensus pattern (29 bp):
CCAGCACTCCAGCACACCCTTCGTCTCTG
Found at i:16480288 original size:23 final size:23
Alignment explanation
Indices: 16480262--16480305 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
16480252 AATCGTCACT
*
16480262 TCCTTTTTCTTT-TCTTTCTTTTC
1 TCCTTTTCCTTTGT-TTTCTTTTC
16480285 TCCTTTTCCTTTGTTTTCTTT
1 TCCTTTTCCTTTGTTTTCTTT
16480306 AGCTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (23 bp):
TCCTTTTCCTTTGTTTTCTTTTC
Found at i:16480301 original size:18 final size:17
Alignment explanation
Indices: 16480270--16480303 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
16480260 CTTCCTTTTT
16480270 CTTTTCTTTCTTTTCTC
1 CTTTTCTTTCTTTTCTC
*
16480287 CTTTTCCTTTGTTTTCT
1 CTTTT-CTTTCTTTTCT
16480304 TTAGCTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (17 bp):
CTTTTCTTTCTTTTCTC
Found at i:16489022 original size:38 final size:39
Alignment explanation
Indices: 16488938--16489072 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
16488928 ACCAATATGG
*
16488938 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
16488977 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
16489015 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
16489056 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
16489073 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:16490649 original size:5 final size:5
Alignment explanation
Indices: 16490639--16490666 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
16490629 TTTATATATA
16490639 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA
16490667 CTTAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:16497762 original size:16 final size:16
Alignment explanation
Indices: 16497741--16497772 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16497731 ACATCTTTGG
16497741 GGTCTCCTAAATTAGC
1 GGTCTCCTAAATTAGC
16497757 GGTCTCCTAAATTAGC
1 GGTCTCCTAAATTAGC
16497773 ATTCTTGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (16 bp):
GGTCTCCTAAATTAGC
Found at i:16509659 original size:25 final size:25
Alignment explanation
Indices: 16509601--16509659 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
16509591 TTGAATGAGG
* **
16509601 TATGATTTCAAATGGAATTGTGGTA
1 TATGATTTCAAATGAAATTACGGTA
* *
16509626 TGTGTTTTCAAATGAAATTACGGTA
1 TATGATTTCAAATGAAATTACGGTA
16509651 TATGATTTC
1 TATGATTTC
16509660 TTATCTATTG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (25 bp):
TATGATTTCAAATGAAATTACGGTA
Found at i:16514488 original size:17 final size:17
Alignment explanation
Indices: 16514466--16514499 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16514456 ATCCACTAAT
*
16514466 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
16514483 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
16514500 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:16519125 original size:17 final size:17
Alignment explanation
Indices: 16519103--16519136 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16519093 ATCCACTAAT
*
16519103 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
16519120 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
16519137 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:16527771 original size:3 final size:3
Alignment explanation
Indices: 16527763--16527792 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
16527753 ATTAATTAGG
16527763 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16527793 AAACTGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16528096 original size:21 final size:22
Alignment explanation
Indices: 16528052--16528101 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
16528042 AATAACTTCA
* *
16528052 TAAAATATAATTTAGATAATTT
1 TAAAATATAATTAAAATAATTT
*
16528074 TAAAATGTAATTAAAAT-ATTT
1 TAAAATATAATTAAAATAATTT
16528095 TAAAATA
1 TAAAATA
16528102 GTTAAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
TAAAATATAATTAAAATAATTT
Found at i:16528108 original size:19 final size:20
Alignment explanation
Indices: 16528070--16528108 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16528060 AATTTAGATA
16528070 ATTTTAAAATGTAATTAAAAT
1 ATTTTAAAA-GTAATTAAAAT
*
16528091 ATTTTAAAA-TAGTTAAAA
1 ATTTTAAAAGTAATTAAAA
16528109 AAAAGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
ATTTTAAAAGTAATTAAAAT
Found at i:16533895 original size:16 final size:16
Alignment explanation
Indices: 16533827--16533896 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 16
16533817 AATCAAATAA
16533827 AATTTT-AATTTTTAAT
1 AATTTTAAATTTTT-AT
*
16533843 AA-TTTATATTTTTAT
1 AATTTTAAATTTTTAT
**
16533858 AATTTTTAAATAATTA-
1 AA-TTTTAAATTTTTAT
16533874 AA--TTAAATTTTTAT
1 AATTTTAAATTTTTAT
16533888 AATTTTAAA
1 AATTTTAAA
16533897 ATAGTGAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
13 9 0.21
14 2 0.05
15 7 0.17
16 15 0.36
17 9 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTTAAATTTTTAT
Found at i:16533916 original size:30 final size:30
Alignment explanation
Indices: 16533847--16533916 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
16533837 TTTAATAATT
* * * *
16533847 TATATTTTTATAATTTTTAAATAATTAAAT
1 TATAATTTTATAATTTTAAAATAATGAAAA
*
16533877 TA-AATTTTTATAATTTTAAAATAGTGAAAA
1 TATAA-TTTTATAATTTTAAAATAATGAAAA
16533907 TATAATTTTA
1 TATAATTTTA
16533917 ATTTTACCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 1 0.03
30 30 0.91
31 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (30 bp):
TATAATTTTATAATTTTAAAATAATGAAAA
Found at i:16538332 original size:23 final size:22
Alignment explanation
Indices: 16538280--16538332 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
16538270 TCCACGTCTT
*
16538280 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
16538302 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
16538325 TTTCTTTT
1 TTTCTTTT
16538333 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:16541687 original size:69 final size:69
Alignment explanation
Indices: 16541576--16541716 Score: 273
Period size: 69 Copynumber: 2.0 Consensus size: 69
16541566 GCAATTCTCA
*
16541576 AAAGTGCATGTCTGTCGTTGGTGAGAGGTTAACGGCATGTTAATATGCATATGATCCAATCTTGT
1 AAAGTGCATGTCTATCGTTGGTGAGAGGTTAACGGCATGTTAATATGCATATGATCCAATCTTGT
16541641 ATTG
66 ATTG
16541645 AAAGTGCATGTCTATCGTTGGTGAGAGGTTAACGGCATGTTAATATGCATATGATCCAATCTTGT
1 AAAGTGCATGTCTATCGTTGGTGAGAGGTTAACGGCATGTTAATATGCATATGATCCAATCTTGT
16541710 ATTG
66 ATTG
16541714 AAA
1 AAA
16541717 TTTCTACACA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (69 bp):
AAAGTGCATGTCTATCGTTGGTGAGAGGTTAACGGCATGTTAATATGCATATGATCCAATCTTGT
ATTG
Found at i:16543685 original size:3 final size:3
Alignment explanation
Indices: 16543672--16543709 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
16543662 ATAAAGTAAG
16543672 AAT AA- AAT AAT AAT AAT AAT AAT AAT AACT AATT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AA-T AAT A
16543710 TTGAGCGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
2 2 0.06
3 24 0.75
4 6 0.19
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16547758 original size:4 final size:4
Alignment explanation
Indices: 16547749--16547802 Score: 63
Period size: 4 Copynumber: 13.0 Consensus size: 4
16547739 AATCATTACT
* * *
16547749 TGTA TGTA TGTA TGGA TGTA TGTA TGGA TGTA TGTA TGTGAA TGTA CGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT--A TGTA TGTA
16547799 TGTA
1 TGTA
16547803 GTTTGAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
4 38 0.90
6 4 0.10
ACGTcount: A:0.26, C:0.02, G:0.30, T:0.43
Consensus pattern (4 bp):
TGTA
Found at i:16547769 original size:12 final size:12
Alignment explanation
Indices: 16547752--16547800 Score: 71
Period size: 12 Copynumber: 3.9 Consensus size: 12
16547742 CATTACTTGT
16547752 ATGTATGTATGG
1 ATGTATGTATGG
16547764 ATGTATGTATGG
1 ATGTATGTATGG
16547776 ATGTATGTATGTG
1 ATGTATGTATG-G
*
16547789 AATGTACGTATG
1 -ATGTATGTATG
16547801 TAGTTTGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
12 23 0.68
13 1 0.03
14 10 0.29
ACGTcount: A:0.27, C:0.02, G:0.31, T:0.41
Consensus pattern (12 bp):
ATGTATGTATGG
Found at i:16550627 original size:22 final size:23
Alignment explanation
Indices: 16550602--16550661 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
16550592 TGGACTGAAT
16550602 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
16550624 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
16550646 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
16550662 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:16550629 original size:4 final size:4
Alignment explanation
Indices: 16550611--16550644 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
16550601 TATAAAAATT
16550611 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
16550645 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:16552049 original size:23 final size:22
Alignment explanation
Indices: 16551998--16552049 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
16551988 CCTCGTCTTT
*
16551998 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
16552020 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
16552043 TTCTTTT
1 TTCTTTT
16552050 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:16552064 original size:18 final size:18
Alignment explanation
Indices: 16552043--16552081 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
16552033 TTTCTTCAAC
* *
16552043 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
16552061 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
16552079 TTC
1 TTC
16552082 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:16554433 original size:22 final size:23
Alignment explanation
Indices: 16554408--16554467 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
16554398 TGGACTGAAT
16554408 ATAAAAATTTAAACTAAAT-AAA
1 ATAAAAATTTAAACTAAATAAAA
*
16554430 ATAAATAA-ATAAA-TAAATAAAA
1 ATAAA-AATTTAAACTAAATAAAA
*
16554452 ATAAAACTTTACAACT
1 ATAAAAATTTA-AACT
16554468 TGGGCCACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
21 6 0.20
22 19 0.63
23 4 0.13
24 1 0.03
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAAAATTTAAACTAAATAAAA
Found at i:16554435 original size:4 final size:4
Alignment explanation
Indices: 16554417--16554450 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
16554407 TATAAAAATT
16554417 TAAA CTAAA TAAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA -TAAA T-AAA TAAA TAAA TAAA TAAA TAAA
16554451 AATAAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:16559352 original size:21 final size:21
Alignment explanation
Indices: 16559328--16559369 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
16559318 TAGAAATTAC
16559328 TAAA-AAAATTAATACATAAAA
1 TAAATAAAA-TAATACATAAAA
* *
16559349 TAAATACAATAATAGATAAAA
1 TAAATAAAATAATACATAAAA
16559370 CGAGATGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAATAAAATAATACATAAAA
Found at i:16561099 original size:50 final size:50
Alignment explanation
Indices: 16560980--16561228 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
16560970 GATAATAACA
* * * ** * *
16560980 TGCCAAAGCCACGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
16561031 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
16561081 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
16561131 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
16561186 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
16561229 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 22, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 32 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:16561154 original size:100 final size:104
Alignment explanation
Indices: 16560979--16561228 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
16560969 TGATAATAAC
* **
16560979 ATGCCAAAGCCACGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
16561044 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
16561081 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
16561144 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
16561186 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
16561229 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 35 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:16561344 original size:13 final size:13
Alignment explanation
Indices: 16561323--16561354 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16561313 GCTTGGATCA
*
16561323 TCATCAAATAAAT
1 TCATAAAATAAAT
16561336 TCATAAAATAAAT
1 TCATAAAATAAAT
16561349 TCATAA
1 TCATAA
16561355 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:16561600 original size:30 final size:30
Alignment explanation
Indices: 16561566--16561623 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
16561556 CCTCGACTCT
**
16561566 AACTTTTTTAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
16561596 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
16561624 AAGGCTCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:16564146 original size:41 final size:41
Alignment explanation
Indices: 16564100--16564200 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 41
16564090 TCGACCTCGA
*
16564100 GTCGATGAGACACTGGGTGTCACTAAATTT-CTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAG
* ** * *
16564140 ATTCGATGAGGTACT-GG-GT-ACCAACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAG
*
16564179 GCCGATGAGACACTGGGTGTCA
1 GTCGATGAGACACTGGGTGTCA
16564201 ACTATTACTT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
38 17 0.37
39 13 0.28
40 4 0.09
41 12 0.26
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.28
Consensus pattern (41 bp):
GTCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAG
Found at i:16564209 original size:39 final size:39
Alignment explanation
Indices: 16564102--16564236 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
16564092 GACCTCGAGT
* * *
16564102 CGATGAGACACTGGGTGTC-ACTAAATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAACT--ATTACTTCGGCTAG-TC
** ** *
16564143 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
16564181 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
16564220 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
16564237 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 3 0.04
41 15 0.20
42 3 0.04
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:16569255 original size:20 final size:20
Alignment explanation
Indices: 16569226--16569265 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
16569216 ATTTAAGTAT
*
16569226 TAAAATATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
16569246 TAAAAGATATTTATTAATTA
1 TAAAAGATATTTATTAATTA
16569266 AATAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TAAAAGATATTTATTAATTA
Found at i:16569497 original size:12 final size:11
Alignment explanation
Indices: 16569480--16569519 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
16569470 GAAAAGTAGG
16569480 GAAAGAAAGAAA
1 GAAAGAAAG-AA
*
16569492 GAAAGAAAGGA
1 GAAAGAAAGAA
16569503 GAAAAGAAAGAA
1 G-AAAGAAAGAA
16569515 GAAAG
1 GAAAG
16569520 GGAAAATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.24
12 19 0.76
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (11 bp):
GAAAGAAAGAA
Found at i:16569510 original size:20 final size:18
Alignment explanation
Indices: 16569485--16569525 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
16569475 GTAGGGAAAG
16569485 AAAGAAAGAAAGAAAGGAGA
1 AAAGAAAG-AAGAAAGG-GA
16569505 AAAGAAAGAAGAAAGGGA
1 AAAGAAAGAAGAAAGGGA
16569523 AAA
1 AAA
16569526 TTGAAGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAGAAAGGGA
Found at i:16571418 original size:6 final size:6
Alignment explanation
Indices: 16571407--16571431 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
16571397 CTTGTTTTTC
16571407 TATAAT TATAAT TATAAT TATAAT T
1 TATAAT TATAAT TATAAT TATAAT T
16571432 GTTATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATAAT
Found at i:16591685 original size:37 final size:37
Alignment explanation
Indices: 16591635--16591708 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
16591625 AAAAAATTGA
16591635 AAGTTTCTATACATATATGCTGGAAGTATATGATGAT
1 AAGTTTCTATACATATATGCTGGAAGTATATGATGAT
*
16591672 AAGTTTCTATACATATGTGCTGGAAGTATATGATGAT
1 AAGTTTCTATACATATATGCTGGAAGTATATGATGAT
16591709 TTGGCATGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (37 bp):
AAGTTTCTATACATATATGCTGGAAGTATATGATGAT
Found at i:16596067 original size:23 final size:23
Alignment explanation
Indices: 16596029--16596075 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
16596019 AGGATTTATA
16596029 ATATTCTGGGTGTGTTTGGGCTGG
1 ATATTCTGGGTGTGTTTGGG-TGG
16596053 ATATTCT-GGTGTGTTTGGGTGG
1 ATATTCTGGGTGTGTTTGGGTGG
16596075 A
1 A
16596076 ATCCGCGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.17
23 12 0.52
24 7 0.30
ACGTcount: A:0.11, C:0.06, G:0.40, T:0.43
Consensus pattern (23 bp):
ATATTCTGGGTGTGTTTGGGTGG
Found at i:16597071 original size:41 final size:40
Alignment explanation
Indices: 16597023--16597101 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
16597013 CGTGTGAGAA
* *
16597023 TGAGATAGCTCTCGACTATATATGGCACTTAGTGTGCGATT
1 TGAGATAGCTCT-GACTATATACGACACTTAGTGTGCGATT
* * *
16597064 TGAGATAGCTGTGGCTATGTACGACACTTAGTGTGCGA
1 TGAGATAGCTCTGACTATATACGACACTTAGTGTGCGA
16597102 GATATAGAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
40 22 0.67
41 11 0.33
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (40 bp):
TGAGATAGCTCTGACTATATACGACACTTAGTGTGCGATT
Found at i:16597126 original size:28 final size:28
Alignment explanation
Indices: 16597086--16597162 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 28
16597076 GGCTATGTAC
16597086 GACACTTAGTGTGCGAGATATAGAGTAT
1 GACACTTAGTGTGCGAGATATAGAGTAT
* *
16597114 GACACTTAGTGTGCAAGATATCGAGTAT
1 GACACTTAGTGTGCGAGATATAGAGTAT
* *
16597142 GGCACTTAGTGTGCGAAATAT
1 GACACTTAGTGTGCGAGATAT
16597163 TTAGTATTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (28 bp):
GACACTTAGTGTGCGAGATATAGAGTAT
Found at i:16602361 original size:27 final size:27
Alignment explanation
Indices: 16602071--16602353 Score: 415
Period size: 27 Copynumber: 10.5 Consensus size: 27
16602061 ATTACCAAAG
* *
16602071 TACCCTCAATTTATAGAATTACCGTTC
1 TACCCTCGATTTATAGAATTACCGTTT
*
16602098 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTT
16602125 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
16602152 TACCCTCGATTTACAGAATTACAGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
16602179 TACCCTCGATTTATAGAATTATCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
16602206 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
16602233 TACCCTCGATTTATCA-AATTACTGTTT
1 TACCCTCGATTTAT-AGAATTACCGTTT
*
16602260 TACCCTTGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
16602287 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * *
16602314 TACCCTTGACTTACAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
16602341 TACCCTCAATTTA
1 TACCCTCGATTTA
16602354 CAAAATTATT
Statistics
Matches: 228, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 1 0.00
27 226 0.99
28 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCGTTT
Found at i:16602372 original size:81 final size:81
Alignment explanation
Indices: 16602044--16602405 Score: 413
Period size: 81 Copynumber: 4.5 Consensus size: 81
16602034 ATTACTGAAA
* * * *** * * *
16602044 TACCCTCAAATTATAAAATTACCAAAGTACCCTCAATTTATAGAATTACCGTTCTACCCTCGATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATT
16602109 TATAGAATTACC-ATTT
66 TATAGAATTACCGA-TT
* *
16602125 TACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTACAGAATTACAGTTTTACCCTCGATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATT
* *
16602190 TATAGAATTATCGTTT
66 TATAGAATTACCGATT
* * *
16602206 TACCCTCGATTTACAGAATTACCATTTTACCCTCGATTTATCA-AATTACTGTTTTACCCTTGAT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTA-CAGAATTACCGTTTTACCCTCGAT
*
16602270 TTATAGAATTACCGTTT
65 TTATAGAATTACCGATT
* * *
16602287 TACCCTCGATTTATAGAATTACCATTTTACCCTTGACTTACAGAATTACCGTTTTACCCTCAATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATT
* * ** **
16602352 TACAAAATTATTGAAA
66 TATAGAATTACCGATT
* * ***
16602368 TACCCTTGATTTATAAAATTACCAAAATACCCTCGATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATT
16602406 AGTAAAATTT
Statistics
Matches: 240, Mismatches: 38, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
80 2 0.01
81 236 0.98
82 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.38
Consensus pattern (81 bp):
TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATT
TATAGAATTACCGATT
Found at i:16602395 original size:27 final size:27
Alignment explanation
Indices: 16602260--16602643 Score: 275
Period size: 27 Copynumber: 14.2 Consensus size: 27
16602250 ATTACTGTTT
* ****
16602260 TACCCTTGATTTATAGAATTACCGTTT
1 TACCCTTGATTTATAAAATTACCAAAA
* * ***
16602287 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTTGATTTATAAAATTACCAAAA
* * * ****
16602314 TACCCTTGACTTACAGAATTACCGTTT
1 TACCCTTGATTTATAAAATTACCAAAA
** * ***
16602341 TACCCTCAATTTACAAAATTATTGAAA
1 TACCCTTGATTTATAAAATTACCAAAA
16602368 TACCCTTGATTTATAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * *
16602395 TACCCTCGA-TTAGTAAAATTTCTAAAA
1 TACCCTTGATTTA-TAAAATTACCAAAA
* * * * *
16602422 TGCCCCTGGTTTGTAAAATTACTAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * *
16602449 TACCCTTGGTTTATAAAATTGCCAGAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * *
16602476 TACCCCTGTTTTGTAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * * **
16602503 TACCCCTGATTTGTGAAATTACTTAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * *
16602530 TACCCTCGACTTGTAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* *
16602557 TACCATTGGTTTATAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* *
16602584 TACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTTGATTTATAAAATTACCAAAA
* * * *
16602611 TACCATTGATTTGTGAAATTACCGAAA
1 TACCCTTGATTTATAAAATTACCAAAA
16602638 TACCCT
1 TACCCT
16602644 CAGTTTGCAA
Statistics
Matches: 292, Mismatches: 63, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
26 3 0.01
27 287 0.98
28 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (27 bp):
TACCCTTGATTTATAAAATTACCAAAA
Found at i:16602399 original size:54 final size:54
Alignment explanation
Indices: 16602341--16602754 Score: 261
Period size: 54 Copynumber: 7.6 Consensus size: 54
16602331 ATTACCGTTT
* * * * *
16602341 TACCCTCAATTTACAAAATTATTGAAATACCCTTGATTTATAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAA
* * * *
16602395 TACCCTCGA-TTAGTAAAATT-TCTAAAATGCCCCTGGTTTGTAAAATTACTAAAA
1 TACCCTCGATTTA-TAAAATTATC-GAAATACCCCTGATTTGTAAAATTACCAAAA
* * * * *
16602449 TACCCTTGGTTTATAAAATT-GCCAGAATACCCCTGTTTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTATCGA-AATACCCCTGATTTGTAAAATTACCAAAA
* * * *
16602503 TACCC-CTGATTTGTGAAATTA-CTTAAATA-CCCTCGACTTGTAAAATTACCAAAA
1 TACCCTC-GATTTATAAAATTATC-GAAATACCCCT-GATTTGTAAAATTACCAAAA
* * * * * * *
16602557 TACCATTGGTTTATAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAA
* * * * * * * **
16602611 TACCATTGATTTGTGAAATTACCGAAATA-CCCTCAGTTTGCAAAATTACTGAAA
1 TACCCTCGATTTATAAAATTATCGAAATACCCCTGA-TTTGTAAAATTACCAAAA
* * * ** * ****
16602665 TACCCTCAACTTGTA-AAAATTA-CCAAAGTACCCCCGATTTACAGAATTACCGTTT
1 TACCCTCGA-TT-TATAAAATTATCGAAA-TACCCCTGATTTGTAAAATTACCAAAA
* *
16602720 TACCCTCGATTTACAAAATTATTGAAATACCCCTG
1 TACCCTCGATTTATAAAATTATCGAAATACCCCTG
16602755 TAGGGTAGAA
Statistics
Matches: 282, Mismatches: 60, Indels: 36
0.75 0.16 0.10
Matches are distributed among these distances:
53 14 0.05
54 222 0.79
55 41 0.15
56 5 0.02
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (54 bp):
TACCCTCGATTTATAAAATTATCGAAATACCCCTGATTTGTAAAATTACCAAAA
Found at i:16602440 original size:81 final size:81
Alignment explanation
Indices: 16602355--16602669 Score: 339
Period size: 81 Copynumber: 3.9 Consensus size: 81
16602345 CTCAATTTAC
* * * * *
16602355 AAAATTATTGAAATACCCTTGATTTATAAAATTACCAAAATACCCTCGATTAGTAAAATTTCTAA
1 AAAATTACTAAAATACCCTTGATTTATAAAATTACCAAAATACCCTCGTTTAGTAAAATTACCAA
*
16602420 AATGCCCCTGGTTTGT
66 AATACCCCTGGTTTGT
* * * *
16602436 AAAATTACTAAAATACCCTTGGTTTATAAAATTGCCAGAATACCC-CTGTTTTGTAAAATTACCA
1 AAAATTACTAAAATACCCTTGATTTATAAAATTACCAAAATACCCTC-GTTTAGTAAAATTACCA
*
16602500 AAATACCCCTGATTTGT
65 AAATACCCCTGGTTTGT
* * * * * * *
16602517 GAAATTACTTAAATACCCTCGACTTGTAAAATTACCAAAATACCATTGGTTTA-TAAAATTACCA
1 AAAATTACTAAAATACCCTTGATTTATAAAATTACCAAAATACC-CTCGTTTAGTAAAATTACCA
*
16602581 AAATACCCTTGGTTTGT
65 AAATACCCCTGGTTTGT
* * * * * * **
16602598 AAAATTACCAAAATACCATTGATTTGTGAAATTACCGAAATACCCTCAGTTT-GCAAAATTACTG
1 AAAATTACTAAAATACCCTTGATTTATAAAATTACCAAAATACCCTC-GTTTAGTAAAATTACCA
16602662 AAATACCC
65 AAATACCC
16602670 TCAACTTGTA
Statistics
Matches: 192, Mismatches: 37, Indels: 10
0.80 0.15 0.04
Matches are distributed among these distances:
80 2 0.01
81 186 0.97
82 4 0.02
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (81 bp):
AAAATTACTAAAATACCCTTGATTTATAAAATTACCAAAATACCCTCGTTTAGTAAAATTACCAA
AATACCCCTGGTTTGT
Found at i:16602650 original size:27 final size:28
Alignment explanation
Indices: 16602365--16602697 Score: 249
Period size: 27 Copynumber: 12.3 Consensus size: 28
16602355 AAAATTATTG
* *
16602365 AAATACCCT-TGATTTATAAAATTACCA
1 AAATACCCTCAGATTTGTAAAATTACCA
* * *
16602392 AAATACCCTC-GATTAGTAAAATTTCTA
1 AAATACCCTCAGATTTGTAAAATTACCA
* * * *
16602419 AAATGCCC-CTGGTTTGTAAAATTACTA
1 AAATACCCTCAGATTTGTAAAATTACCA
* * * *
16602446 AAATACCCT-TGGTTTATAAAATTGCCA
1 AAATACCCTCAGATTTGTAAAATTACCA
* * *
16602473 GAATACCC-CTGTTTTGTAAAATTACCA
1 AAATACCCTCAGATTTGTAAAATTACCA
* * **
16602500 AAATACCC-CTGATTTGTGAAATTACTT
1 AAATACCCTCAGATTTGTAAAATTACCA
*
16602527 AAATACCCTC-GACTTGTAAAATTACCA
1 AAATACCCTCAGATTTGTAAAATTACCA
* * * *
16602554 AAATACCAT-TGGTTTATAAAATTACCA
1 AAATACCCTCAGATTTGTAAAATTACCA
* *
16602581 AAATACCCT-TGGTTTGTAAAATTACCA
1 AAATACCCTCAGATTTGTAAAATTACCA
* * * *
16602608 AAATACCAT-TGATTTGTGAAATTACCG
1 AAATACCCTCAGATTTGTAAAATTACCA
* **
16602635 AAATACCCTCAG-TTTGCAAAATTACTG
1 AAATACCCTCAGATTTGTAAAATTACCA
*
16602662 AAATACCCTCA-ACTTGTAAAAATTACCA
1 AAATACCCTCAGATTTGT-AAAATTACCA
*
16602690 AAGTACCC
1 AAATACCC
16602698 CCGATTTACA
Statistics
Matches: 252, Mismatches: 45, Indels: 17
0.80 0.14 0.05
Matches are distributed among these distances:
26 1 0.00
27 234 0.93
28 17 0.07
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.32
Consensus pattern (28 bp):
AAATACCCTCAGATTTGTAAAATTACCA
Found at i:16602750 original size:27 final size:28
Alignment explanation
Indices: 16602518--16602751 Score: 110
Period size: 27 Copynumber: 8.6 Consensus size: 28
16602508 CTGATTTGTG
**
16602518 AAATTACTTAAATACCCTCGACTTGT--A
1 AAATTACCGAAATACCCTCGACTT-TACA
* * * * *
16602545 AAATTACCAAAATACCATTG-GTTTATA
1 AAATTACCGAAATACCCTCGACTTTACA
* * * **
16602572 AAATTACCAAAATACCCTTG-GTTTGTA
1 AAATTACCGAAATACCCTCGACTTTACA
* * * ***
16602599 AAATTACCAAAATACCATTGA-TTTGTG
1 AAATTACCGAAATACCCTCGACTTTACA
* *
16602626 AAATTACCGAAATACCCTC-AGTTTGCA
1 AAATTACCGAAATACCCTCGACTTTACA
* *
16602653 AAATTACTGAAATACCCTCAACTTGTA-A
1 AAATTACCGAAATACCCTCGACTT-TACA
*
16602681 AAATTACC-AAAGTACCCCCGA-TTTACA
1 AAATTACCGAAA-TACCCTCGACTTTACA
* ***
16602708 GAATTACCGTTTTACCCTCGA-TTTACA
1 AAATTACCGAAATACCCTCGACTTTACA
**
16602735 AAATTATTGAAATACCC
1 AAATTACCGAAATACCC
16602752 CTGTAGGGTA
Statistics
Matches: 167, Mismatches: 31, Indels: 18
0.77 0.14 0.08
Matches are distributed among these distances:
25 1 0.01
26 5 0.03
27 142 0.85
28 18 0.11
29 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (28 bp):
AAATTACCGAAATACCCTCGACTTTACA
Found at i:16602766 original size:27 final size:27
Alignment explanation
Indices: 16602736--16602902 Score: 219
Period size: 27 Copynumber: 6.2 Consensus size: 27
16602726 CGATTTACAA
*
16602736 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* *
16602763 AATTACCGAAATACCCCTATAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
*
16602790 AATTATTGAAATACCCCTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
*
16602817 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* *
16602844 AATTCTCGAAATACCCTTGTAGGGTAG
1 AATTATCGAAATACCCCTGTAGGGTAG
* * * *
16602871 AATTA-CTGAGATACCCTTGTGGGGTAA
1 AATTATC-GAAATACCCCTGTAGGGTAG
16602898 AATTA
1 AATTA
16602903 CCATTTTGCC
Statistics
Matches: 126, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
26 1 0.01
27 125 0.99
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.29
Consensus pattern (27 bp):
AATTATCGAAATACCCCTGTAGGGTAG
Found at i:16602896 original size:81 final size:81
Alignment explanation
Indices: 16602734--16602902 Score: 241
Period size: 81 Copynumber: 2.1 Consensus size: 81
16602724 CTCGATTTAC
* *
16602734 AAAATTATTGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTATTGA
1 AAAATTATCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTACTGA
16602799 AATACCCCTGTAGGGT
66 AATACCCCTGTAGGGT
* * * *
16602815 AGAATTATCGAAATACCCTTGTAGGGTAGAATT-CTCGAAATACCCTTGTAGGGTAGAATTACTG
1 AAAATTATCGAAATACCCCTGTAGGGTAGAATTAC-CGAAATACCCCTATAGGGTAGAATTACTG
* * *
16602879 AGATACCCTTGTGGGGT
65 AAATACCCCTGTAGGGT
16602896 AAAATTA
1 AAAATTA
16602903 CCATTTTGCC
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 1 0.01
81 76 0.99
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (81 bp):
AAAATTATCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTATAGGGTAGAATTACTGA
AATACCCCTGTAGGGT
Found at i:16603179 original size:24 final size:25
Alignment explanation
Indices: 16603109--16603202 Score: 145
Period size: 25 Copynumber: 3.8 Consensus size: 25
16603099 AGGAAGTGCT
* *
16603109 AAAAGGGCTTTGCCCCAGTTTACTG
1 AAAAGAGCTTTGCCCCAGTTTACCG
16603134 AAAAGAGCTTTGCCCCAGTTTACCG
1 AAAAGAGCTTTGCCCCAGTTTACCG
*
16603159 AAAAGAGCTTTG-CCCAGTTTACCA
1 AAAAGAGCTTTGCCCCAGTTTACCG
*
16603183 AAAAGGGCTTTGCCCCAGTT
1 AAAAGAGCTTTGCCCCAGTT
16603203 ATTAAAAGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
24 22 0.34
25 42 0.66
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (25 bp):
AAAAGAGCTTTGCCCCAGTTTACCG
Found at i:16603458 original size:31 final size:30
Alignment explanation
Indices: 16603423--16603504 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 30
16603413 CGTTTACAGT
*
16603423 AAAGGCTTCAGCCCAGTGATATGATT-TACG
1 AAAGGCTTCAGCCCAGT-ATATGATTAAACG
* * **
16603453 AAAAGGCTTCGGCCTAGTA-ACCATTAAACG
1 -AAAGGCTTCAGCCCAGTATATGATTAAACG
16603483 AAAGGCTTCAGCCCAGTATATG
1 AAAGGCTTCAGCCCAGTATATG
16603505 TCGAGACCGA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
29 20 0.50
30 5 0.12
31 15 0.38
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.23
Consensus pattern (30 bp):
AAAGGCTTCAGCCCAGTATATGATTAAACG
Found at i:16607118 original size:23 final size:23
Alignment explanation
Indices: 16607058--16607122 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
16607048 CTTGATTAGT
16607058 ATACGACACAT-AAGTGCCTGAA
1 ATACGACACATGAAGTGCCTGAA
* *
16607080 AT--GACACACGAGGTGCCTGAA
1 ATACGACACATGAAGTGCCTGAA
*
16607101 ATACGACACATGATGTGCCTGA
1 ATACGACACATGAAGTGCCTGA
16607123 TCGACAAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 6 0.17
21 12 0.33
22 2 0.06
23 16 0.44
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (23 bp):
ATACGACACATGAAGTGCCTGAA
Found at i:16607336 original size:16 final size:17
Alignment explanation
Indices: 16607310--16607343 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
16607300 TTCAATACAT
16607310 ATTCATCATTCAACTCA
1 ATTCATCATTCAACTCA
*
16607327 ATTC-TCATTCAATTCA
1 ATTCATCATTCAACTCA
16607343 A
1 A
16607344 CAGTAACACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTCATCATTCAACTCA
Found at i:16610711 original size:17 final size:16
Alignment explanation
Indices: 16610682--16610715 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
16610672 GTCCTCCCTC
16610682 ATTTATCACTTGAGCA
1 ATTTATCACTTGAGCA
*
16610698 ATTTAATCATTTGAGCA
1 ATTT-ATCACTTGAGCA
16610715 A
1 A
16610716 ATTTTGCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (16 bp):
ATTTATCACTTGAGCA
Found at i:16614473 original size:6 final size:6
Alignment explanation
Indices: 16614454--16614496 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
16614444 GAAGCAGGGG
* * *
16614454 AGAAAA AGAGAA AGAAAA AGGAAA AGAAAA ATAAAA GAGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA -AGAAAA
16614497 CTCAGGATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:16615662 original size:18 final size:18
Alignment explanation
Indices: 16615639--16615679 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
16615629 AGGAAAAAAA
16615639 AGAAATT-GAATTATGAAT
1 AGAAATTGGAATTATG-AT
*
16615657 AGAAATTGGAATTGTGAT
1 AGAAATTGGAATTATGAT
16615675 AGAAA
1 AGAAA
16615680 GAGAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (18 bp):
AGAAATTGGAATTATGAT
Found at i:16616188 original size:20 final size:20
Alignment explanation
Indices: 16616165--16616202 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16616155 GTTATTAAGT
16616165 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
16616185 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
16616203 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:16616425 original size:16 final size:19
Alignment explanation
Indices: 16616386--16616425 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 19
16616376 GGACTTAATT
16616386 ATTATATTATACTATGTAA
1 ATTATATTATACTATGTAA
*
16616405 GTTATATTA-A-T-TGTAA
1 ATTATATTATACTATGTAA
16616421 ATTAT
1 ATTAT
16616426 TTGTAAGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
16 9 0.47
17 1 0.05
18 1 0.05
19 8 0.42
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (19 bp):
ATTATATTATACTATGTAA
Found at i:16617264 original size:29 final size:29
Alignment explanation
Indices: 16617227--16617283 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
16617217 CACCTTGACA
* *
16617227 CGAATTCTCAATGAACAAGTTCTTCACCG
1 CGAACTCTCAACGAACAAGTTCTTCACCG
16617256 CGAACTCTCAACGAACAAGTTCTTCACC
1 CGAACTCTCAACGAACAAGTTCTTCACC
16617284 TCTTCTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.25
Consensus pattern (29 bp):
CGAACTCTCAACGAACAAGTTCTTCACCG
Found at i:16618639 original size:4 final size:4
Alignment explanation
Indices: 16618630--16618664 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
16618620 GAGCAAATGT
16618630 GAAA GAAA G-AA GAAA GAAA GAAA GAAA GAAA -AAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
16618665 GGAAATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:16625485 original size:13 final size:14
Alignment explanation
Indices: 16625438--16625488 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
16625428 ACTGTTTCCG
16625438 TGAA-ATTTATTCA
1 TGAATATTTATTCA
16625451 TGAATATTTATTCA
1 TGAATATTTATTCA
16625465 TGAATATTTATT-A
1 TGAATATTTATTCA
16625478 -GAAATATTTAT
1 TG-AATATTTAT
16625489 GAATTATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 1 0.03
13 14 0.39
14 21 0.58
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (14 bp):
TGAATATTTATTCA
Found at i:16635192 original size:17 final size:18
Alignment explanation
Indices: 16635161--16635195 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
16635151 AATTTAATTA
*
16635161 TTTTATCTAATAAATATC
1 TTTTATCTAAAAAATATC
16635179 TTTTA-CTAAAAAATATC
1 TTTTATCTAAAAAATATC
16635196 ACAAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTATCTAAAAAATATC
Found at i:16635693 original size:41 final size:41
Alignment explanation
Indices: 16635643--16635725 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
16635633 ACTTAATAAT
*
16635643 GATTACACTTTTACAATTTAGTCCCCATATTATAGTTAACC
1 GATTACACTTTTACAATTTAGTCCCCATACTATAGTTAACC
*
16635684 GATTGCACTTTTACAATTTAGTCCCCATACTATAGTTAACC
1 GATTACACTTTTACAATTTAGTCCCCATACTATAGTTAACC
16635725 G
1 G
16635726 CTTTCTCGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (41 bp):
GATTACACTTTTACAATTTAGTCCCCATACTATAGTTAACC
Found at i:16664209 original size:2 final size:2
Alignment explanation
Indices: 16664202--16664236 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16664192 CAGATGAGGC
16664202 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
16664237 ATAGAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16665058 original size:13 final size:13
Alignment explanation
Indices: 16665040--16665066 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16665030 AAGAAAGTAT
16665040 TGAAACATGTTTC
1 TGAAACATGTTTC
16665053 TGAAACATGTTTC
1 TGAAACATGTTTC
16665066 T
1 T
16665067 ATTACTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGAAACATGTTTC
Found at i:16671134 original size:13 final size:14
Alignment explanation
Indices: 16671116--16671144 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
16671106 TCTTCTAATA
16671116 ATTTAATTAT-TAT
1 ATTTAATTATATAT
16671129 ATTTAATTATATAT
1 ATTTAATTATATAT
16671143 AT
1 AT
16671145 AAATCATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTAATTATATAT
Found at i:16672579 original size:5 final size:5
Alignment explanation
Indices: 16672569--16672593 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
16672559 TTTAATCAAA
16672569 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
16672594 GGCCTCTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:16675418 original size:19 final size:19
Alignment explanation
Indices: 16675394--16675431 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16675384 CTTTGAACTG
16675394 AAAGAAAACTTGAAACTTT
1 AAAGAAAACTTGAAACTTT
*
16675413 AAAGAAAACTTGAACCTTT
1 AAAGAAAACTTGAAACTTT
16675432 CCTCGAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (19 bp):
AAAGAAAACTTGAAACTTT
Found at i:16677585 original size:31 final size:31
Alignment explanation
Indices: 16677550--16677626 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
16677540 ATGTATAATT
* * * *
16677550 TTTTGGACAAGTTTAAGTATCAATTAGATAC
1 TTTTGGACAAGTTCAAGTACCAACTAAATAC
16677581 TTTTGGACAAGTTCAAGTACCAACTAAATAC
1 TTTTGGACAAGTTCAAGTACCAACTAAATAC
16677612 TTTTGGACAAGTTCA
1 TTTTGGACAAGTTCA
16677627 TAGGGCAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (31 bp):
TTTTGGACAAGTTCAAGTACCAACTAAATAC
Found at i:16679201 original size:3 final size:3
Alignment explanation
Indices: 16679193--16679238 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
16679183 GGTTTAGAAT
16679193 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16679239 CAAAACTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16688938 original size:45 final size:45
Alignment explanation
Indices: 16688889--16688977 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
16688879 TATAATTTAG
16688889 TTTTTCATGTATAAACGTTATTGTAGAAAAGTTTATTAGTCAAAT
1 TTTTTCATGTATAAACGTTATTGTAGAAAAGTTTATTAGTCAAAT
16688934 TTTTTCATGTATAAACGTTATTGTAGAAAAGTTTATTAGTCAAA
1 TTTTTCATGTATAAACGTTATTGTAGAAAAGTTTATTAGTCAAA
16688978 CTTGCTCCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (45 bp):
TTTTTCATGTATAAACGTTATTGTAGAAAAGTTTATTAGTCAAAT
Found at i:16691913 original size:25 final size:25
Alignment explanation
Indices: 16691879--16691930 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
16691869 CATATATGCC
16691879 ATTGCTAATTCCCTAATGGTCTCAG
1 ATTGCTAATTCCCTAATGGTCTCAG
16691904 ATTGCTAATTCCCTAATGGTCTCAG
1 ATTGCTAATTCCCTAATGGTCTCAG
16691929 AT
1 AT
16691931 ACTTTAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (25 bp):
ATTGCTAATTCCCTAATGGTCTCAG
Found at i:16698169 original size:5 final size:5
Alignment explanation
Indices: 16698154--16698183 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
16698144 ATCAAAATGT
16698154 AAAAGG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAA-G AAAAG AAAAG AAAAG AAAAG AAAA
16698184 ACAAACTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:16700072 original size:26 final size:27
Alignment explanation
Indices: 16700005--16700072 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
16699995 AACAACGATA
* *
16700005 AAAACTAAATCTAACTTTTTAAATCCG
1 AAAACTAAATCTAACTTTTCAAATACG
* *
16700032 AAAA-TAAAAAACTAA-TTTTCAAATATG
1 AAAACT--AAATCTAACTTTTCAAATACG
16700059 AAAACTAAATCTAA
1 AAAACTAAATCTAA
16700073 AACTCTTACT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
26 8 0.24
27 17 0.52
28 8 0.24
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.29
Consensus pattern (27 bp):
AAAACTAAATCTAACTTTTCAAATACG
Found at i:16706812 original size:61 final size:64
Alignment explanation
Indices: 16706683--16706812 Score: 164
Period size: 61 Copynumber: 2.1 Consensus size: 64
16706673 GAAAACAAAA
* *
16706683 TAAATTATTTAAGTTTATTTTTTACCTAATTAATATTTAGAAACTATTTATACTTAGATATTAC
1 TAAATTATTAAAGTTTATTTTTTACCAAATTAATATTTAGAAACTATTTATACTTAGATATTAC
* * *
16706747 --AATTATTAAATTTTA-TTTTTACCAAATTAATATTTAGATACTATTTCGTA-TTAG-T-TTAC
1 TAAATTATTAAAGTTTATTTTTTACCAAATTAATATTTAGAAACTATTT-ATACTTAGATATTAC
16706806 TAAATTA
1 TAAATTA
16706813 AACTAAATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
59 4 0.07
60 1 0.02
61 38 0.66
62 15 0.26
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.50
Consensus pattern (64 bp):
TAAATTATTAAAGTTTATTTTTTACCAAATTAATATTTAGAAACTATTTATACTTAGATATTAC
Found at i:16706846 original size:14 final size:12
Alignment explanation
Indices: 16706814--16706843 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16706804 ACTAAATTAA
16706814 ACTAAATATATC
1 ACTAAATATATC
16706826 ACTAAATATATC
1 ACTAAATATATC
*
16706838 ATTAAA
1 ACTAAA
16706844 AATTATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (12 bp):
ACTAAATATATC
Found at i:16709740 original size:20 final size:20
Alignment explanation
Indices: 16709717--16709782 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 20
16709707 AAAGAATAAC
16709717 ATTAATAATAAAAAAATCAA
1 ATTAATAATAAAAAAATCAA
*
16709737 ATTAAAATACAAAAAATAAAATCAA
1 ATT--AAT--AATAAA-AAAATCAA
16709762 ATTAA-AATAAAAAAAT-AA
1 ATTAATAATAAAAAAATCAA
16709780 ATT
1 ATT
16709783 CCACCATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
18 5 0.13
19 5 0.13
20 8 0.21
22 3 0.08
23 2 0.05
24 5 0.13
25 11 0.28
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (20 bp):
ATTAATAATAAAAAAATCAA
Found at i:16709763 original size:19 final size:19
Alignment explanation
Indices: 16709723--16709780 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
16709713 TAACATTAAT
*
16709723 AATAAAAAAATCAAATTAA
1 AATAAAAAAATCAAAATAA
16709742 AATACAAAAAAT-AAAATCAA
1 AATA-AAAAAATCAAAAT-AA
*
16709762 ATTAAAATAAA--AAAATAA
1 AATAAAA-AAATCAAAATAA
16709780 A
1 A
16709781 TTCCACCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 3 0.09
19 16 0.47
20 15 0.44
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (19 bp):
AATAAAAAAATCAAAATAA
Found at i:16709768 original size:18 final size:18
Alignment explanation
Indices: 16709705--16709756 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 18
16709695 TCTACTAGAC
16709705 AAAAAGAATAACATTAATAAT
1 AAAAA-AATAA-ATTAA-AAT
16709726 AAAAAAATCAAATTAAAAT
1 AAAAAAAT-AAATTAAAAT
16709745 ACAAAAAATAAA
1 A-AAAAAATAAA
16709757 ATCAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.24
20 15 0.52
21 7 0.24
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAAAAATAAATTAAAAT
Found at i:16709792 original size:25 final size:25
Alignment explanation
Indices: 16709729--16709780 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
16709719 TAATAATAAA
16709729 AAAATCAAATTAAAATACAAAAAAT
1 AAAATCAAATTAAAATACAAAAAAT
16709754 AAAATCAAATTAAAATA-AAAAAAT
1 AAAATCAAATTAAAATACAAAAAAT
16709778 AAA
1 AAA
16709781 TTCCACCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (25 bp):
AAAATCAAATTAAAATACAAAAAAT
Found at i:16711454 original size:17 final size:17
Alignment explanation
Indices: 16711432--16711465 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16711422 ATCCACTAAT
*
16711432 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
16711449 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
16711466 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:16716094 original size:17 final size:17
Alignment explanation
Indices: 16716072--16716105 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16716062 ATCCACTAAT
*
16716072 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
16716089 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
16716106 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:16724283 original size:22 final size:20
Alignment explanation
Indices: 16724257--16724298 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
16724247 GTTATAAGTT
16724257 TAAAAATTAAAATTAATTTAAA
1 TAAAAATT-AAATT-ATTTAAA
16724279 TAAAAATTAAATTATTTAAA
1 TAAAAATTAAATTATTTAAA
16724299 AATTAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 5 0.25
22 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATTAAATTATTTAAA
Found at i:16724284 original size:16 final size:16
Alignment explanation
Indices: 16724260--16724305 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
16724250 ATAAGTTTAA
*
16724260 AAATTAAAATTAATTT
1 AAATAAAAATTAATTT
*
16724276 AAATAAAAATTAAATT
1 AAATAAAAATTAATTT
**
16724292 ATTTAAAAATTAAT
1 AAATAAAAATTAAT
16724306 AAAATTAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATAAAAATTAATTT
Found at i:16724301 original size:22 final size:22
Alignment explanation
Indices: 16724256--16724316 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 22
16724246 TGTTATAAGT
16724256 TTAAAAATTAAAATTAATTTAAA
1 TTAAAAATT-AAATTAATTTAAA
16724279 -TAAAAATTAAATT-ATTTAAAAA
1 TTAAAAATTAAATTAATTT--AAA
16724301 TTAATAAAATTAAATT
1 TT-A-AAAATTAAATT
16724317 TCTTCAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
20 4 0.12
21 5 0.15
22 11 0.33
23 1 0.03
24 1 0.03
25 11 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAAAAATTAAATTAATTTAAA
Found at i:16724310 original size:20 final size:20
Alignment explanation
Indices: 16724257--16724312 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
16724247 GTTATAAGTT
16724257 TAAAAATTAAAATTAATTTAAA
1 TAAAAA-TAAAATT-ATTTAAA
*
16724279 TAAAAATTAAATTATTTAAA
1 TAAAAATAAAATTATTTAAA
*
16724299 -AATTAATAAAATTA
1 TAA-AAATAAAATTA
16724313 AATTTCTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 2 0.07
20 16 0.53
21 6 0.20
22 6 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATAAAATTATTTAAA
Found at i:16729447 original size:17 final size:18
Alignment explanation
Indices: 16729420--16729458 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
16729410 CATGCTAGTT
16729420 TTTTGAATTTTTATGAAA
1 TTTTGAATTTTTATGAAA
* *
16729438 TTTT-AATTTTTTTTAAA
1 TTTTGAATTTTTATGAAA
16729455 TTTT
1 TTTT
16729459 TAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTGAATTTTTATGAAA
Found at i:16730071 original size:31 final size:32
Alignment explanation
Indices: 16730012--16730076 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
16730002 TTATCAAAAA
16730012 AAATTATTTAAAAATAATTTATTATTAT-ATT
1 AAATTATTTAAAAATAATTTATTATTATAATT
*
16730043 AAATTATTTAATTAA-AATTTA-TAGTTATAATT
1 AAATTATTTAA-AAATAATTTATTA-TTATAATT
16730075 AA
1 AA
16730077 TATTTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 2 0.07
31 21 0.70
32 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (32 bp):
AAATTATTTAAAAATAATTTATTATTATAATT
Found at i:16741117 original size:19 final size:19
Alignment explanation
Indices: 16741083--16741144 Score: 90
Period size: 19 Copynumber: 3.2 Consensus size: 19
16741073 ATTACAAAAA
16741083 AAATAATTTTTAAAAATTCT
1 AAATAATTTTT-AAAATTCT
16741103 AAATAATTTTTAAAATTCT
1 AAATAATTTTTAAAATTCT
*
16741122 AAAT-ATTTATAAAAATTCT
1 AAATAATTT-TTAAAATTCT
16741141 AAAT
1 AAAT
16741145 TTTATATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
18 4 0.10
19 25 0.62
20 11 0.28
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATAATTTTTAAAATTCT
Found at i:16741144 original size:26 final size:25
Alignment explanation
Indices: 16741115--16741168 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
16741105 ATAATTTTTA
16741115 AAATTCTAAATATTTATAAAAATTCT
1 AAATTCTAAATATTTA-AAAAATTCT
* * *
16741141 AAATTTTATATTTTTAAAAAATTCT
1 AAATTCTAAATATTTAAAAAATTCT
16741166 AAA
1 AAA
16741169 AAATATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATTCTAAATATTTAAAAAATTCT
Found at i:16741175 original size:25 final size:26
Alignment explanation
Indices: 16741127--16741176 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
16741117 ATTCTAAATA
***
16741127 TTTATAAAAATTCTAAATTTTATATT
1 TTTATAAAAATTCTAAAAAATATATT
16741153 TTTA-AAAAATTCTAAAAAATATAT
1 TTTATAAAAATTCTAAAAAATATAT
16741177 AAAGAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTATAAAAATTCTAAAAAATATATT
Found at i:16755027 original size:11 final size:11
Alignment explanation
Indices: 16755011--16755035 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16755001 ATATCTAGAA
16755011 TTCTCTTCATT
1 TTCTCTTCATT
16755022 TTCTCTTCATT
1 TTCTCTTCATT
16755033 TTC
1 TTC
16755036 ATCATCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:16757349 original size:6 final size:6
Alignment explanation
Indices: 16757338--16757371 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
16757328 TGTAAGATAT
* *
16757338 TGTTAC TGTTAC TGTTAC CGTTAC TATTAC TGTT
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TGTT
16757372 TTTTTATTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.50
Consensus pattern (6 bp):
TGTTAC
Found at i:16757635 original size:18 final size:18
Alignment explanation
Indices: 16757582--16757742 Score: 74
Period size: 18 Copynumber: 8.5 Consensus size: 18
16757572 AAAGATCGAC
*
16757582 TGTTACTGAATAATTTAAT
1 TGTTACTGAATAA-TTGAT
* *
16757601 TGTTACTGTATATTTGAT
1 TGTTACTGAATAATTGAT
*
16757619 T-TCTACTGAATAATTGAC
1 TGT-TACTGAATAATTGAT
16757637 TGTTACTGGGTAACCGATCAATTGAT
1 TGTTACT--G--A---AT-AATTGAT
* *
16757663 TGATACTGAATAACTGAT
1 TGTTACTGAATAATTGAT
** *
16757681 TAATATTGAATAATTGAT
1 TGTTACTGAATAATTGAT
* * *
16757699 TGTTACCGAATAACTGAC
1 TGTTACTGAATAATTGAT
* * * *
16757717 TATTACTAAATAAATAAT
1 TGTTACTGAATAATTGAT
16757735 TGTT-CTGA
1 TGTTACTGA
16757743 TACGTTAATG
Statistics
Matches: 106, Mismatches: 26, Indels: 22
0.69 0.17 0.14
Matches are distributed among these distances:
17 4 0.04
18 70 0.66
19 14 0.13
20 1 0.01
22 2 0.02
24 1 0.01
25 2 0.02
26 12 0.11
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (18 bp):
TGTTACTGAATAATTGAT
Found at i:16757729 original size:36 final size:36
Alignment explanation
Indices: 16757656--16757738 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
16757646 GTAACCGATC
* * * * *
16757656 AATTGATTGATACTGAATAACTGATTAATATTGAAT
1 AATTGATTGTTACCGAATAACTGACTAATACTAAAT
*
16757692 AATTGATTGTTACCGAATAACTGACTATTACTAAAT
1 AATTGATTGTTACCGAATAACTGACTAATACTAAAT
* *
16757728 AAATAATTGTT
1 AATTGATTGTT
16757739 CTGATACGTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (36 bp):
AATTGATTGTTACCGAATAACTGACTAATACTAAAT
Found at i:16761611 original size:29 final size:30
Alignment explanation
Indices: 16761562--16761621 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
16761552 AGAATTGGAT
* *
16761562 AAAATTAAAATTTTATGTATAAAATTACAC
1 AAAATTAAAAGTTTATATATAAAATTACAC
*
16761592 AAAATT-AAAGTTTATATATACAATTACAC
1 AAAATTAAAAGTTTATATATAAAATTACAC
16761621 A
1 A
16761622 TTAAATCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTAAAAGTTTATATATAAAATTACAC
Found at i:16775409 original size:16 final size:16
Alignment explanation
Indices: 16775388--16775420 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
16775378 CTCTAAGGAG
16775388 CATACTTATATTTTGC
1 CATACTTATATTTTGC
16775404 CATACTTATATTTTGC
1 CATACTTATATTTTGC
16775420 C
1 C
16775421 TTTGCAATAT
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:0.24, C:0.21, G:0.06, T:0.48
Consensus pattern (16 bp):
CATACTTATATTTTGC
Found at i:16777107 original size:6 final size:6
Alignment explanation
Indices: 16777096--16777131 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
16777086 TCTTCACTCA
16777096 CCATAT CCATAT CCATAT CCATAT CCATAT CCATAT
1 CCATAT CCATAT CCATAT CCATAT CCATAT CCATAT
16777132 GCTGCTCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
CCATAT
Found at i:16783241 original size:107 final size:107
Alignment explanation
Indices: 16783050--16783269 Score: 422
Period size: 107 Copynumber: 2.1 Consensus size: 107
16783040 ATTTTTTTAG
*
16783050 GGTAGAACTCATTTGGGTTAATTTCAATGCACGATATTTTCTCAACCACAACCTACTAGGTTCTC
1 GGTATAACTCATTTGGGTTAATTTCAATGCACGATATTTTCTCAACCACAACCTACTAGGTTCTC
16783115 TGTGTCATGTTTTTTTTTGGTAATATGAAAATTGCTTACCAT
66 TGTGTCATGTTTTTTTTTGGTAATATGAAAATTGCTTACCAT
*
16783157 GGTATAACTCATTTGGGTTAATTTCAATGCACGATATTTTCTTAACCACAACCTACTAGGTTCTC
1 GGTATAACTCATTTGGGTTAATTTCAATGCACGATATTTTCTCAACCACAACCTACTAGGTTCTC
16783222 TGTGTCATGTTTTTTTTTGGTAATATGAAAATTGCTTACCAT
66 TGTGTCATGTTTTTTTTTGGTAATATGAAAATTGCTTACCAT
16783264 GGTATA
1 GGTATA
16783270 CAATATTTTT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 111 1.00
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (107 bp):
GGTATAACTCATTTGGGTTAATTTCAATGCACGATATTTTCTCAACCACAACCTACTAGGTTCTC
TGTGTCATGTTTTTTTTTGGTAATATGAAAATTGCTTACCAT
Found at i:16788184 original size:26 final size:26
Alignment explanation
Indices: 16788138--16788197 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
16788128 TGACTTAAAT
*
16788138 CTCAAACCTTAAACCTTAAAC-CTAA
1 CTCAAACCTCAAACCTTAAACTCTAA
*
16788163 GCTCAAACCTCAAA-TTTCAAACTCTAA
1 -CTCAAACCTCAAACCTT-AAACTCTAA
16788190 -TCAAACCT
1 CTCAAACCT
16788198 TGAACCCTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 10 0.33
26 16 0.53
27 4 0.13
ACGTcount: A:0.42, C:0.32, G:0.02, T:0.25
Consensus pattern (26 bp):
CTCAAACCTCAAACCTTAAACTCTAA
Found at i:16788962 original size:23 final size:22
Alignment explanation
Indices: 16788931--16788973 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
16788921 AAATTTAAAT
*
16788931 TTATCTATTTTTATTTTAAAAAA
1 TTATCTATTTAT-TTTTAAAAAA
*
16788954 TTATTTATTTATTTTTAAAA
1 TTATCTATTTATTTTTAAAA
16788974 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATCTATTTATTTTTAAAAAA
Found at i:16802942 original size:7 final size:8
Alignment explanation
Indices: 16802926--16802953 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
16802916 TAAATTTGGG
16802926 TTTTCTTT
1 TTTTCTTT
16802934 TTTTCTTT
1 TTTTCTTT
16802942 TTTTCTTT
1 TTTTCTTT
16802950 TTTT
1 TTTT
16802954 TTAGATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTCTTT
Found at i:16804812 original size:20 final size:21
Alignment explanation
Indices: 16804787--16804826 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16804777 ATTAAATTGT
* *
16804787 TAAATT-TATTTATATTTTTC
1 TAAATTCTATATAAATTTTTC
16804807 TAAATTCTATATAAATTTTT
1 TAAATTCTATATAAATTTTT
16804827 AAATAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TAAATTCTATATAAATTTTTC
Done.