Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008311.1 Hibiscus syriacus cultivar Beakdansim tig00111002_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1790494
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:246500 original size:266 final size:266
Alignment explanation
Indices: 246026--246535 Score: 975
Period size: 266 Copynumber: 1.9 Consensus size: 266
246016 TAATCCTCAC
246026 TAAGTGTATACTTAGTATGTTATAATATTCATGCTTAGAAAAAGAAGATCGAATGATTAAGGAGC
1 TAAGTGTATACTTAGTATGTTATAATATTCATGCTTAGAAAAAGAAGATCGAATGATTAAGGAGC
246091 TTAGCTTGACATCACTCAACGATGACTACTTATTGGTATCAATAATGAGATCCTACTATTGTTTT
66 TTAGCTTGACATCACTCAACGATGACTACTTATTGGTATCAATAATGAGATCCTACTATTGTTTT
246156 GATTTTCTAGTTAGCATGTATACGTGTTTAGGTGTTAGTAATGTTCTTATATGGCTATATTTAAT
131 GATTTTCTAGTTAGCATGTATACGTGTTTAGGTGTTAGTAATGTTCTTATATGGCTATATTTAAT
* *
246221 TGGGTCAGAAATGTTATGATATGTCTATAATGTTTAAATGGTTTGTAGTGTGTTTAGGTGTTTAG
196 TGGGTCAGAAATGTTATGATATGTCTATAACGTTTAAATGGTTTATAGTGTGTTTAGGTGTTTAG
246286 CATGTA
261 CATGTA
*
246292 TAAGTGTATACTTAGTGTGTTATAATATTCATGCTTAGAAAAAGAAGATCGAATGATTAAGGAGC
1 TAAGTGTATACTTAGTATGTTATAATATTCATGCTTAGAAAAAGAAGATCGAATGATTAAGGAGC
*
246357 TTAGCTTGACATCACTCATCGATGACTACTTATTGGTATCAATAATGAGATCCTACTATTGTTTT
66 TTAGCTTGACATCACTCAACGATGACTACTTATTGGTATCAATAATGAGATCCTACTATTGTTTT
246422 GATTTTCTAGTTAGCATGTATACGTGTTTAGGTGTTAGTAATGTTCTTATATGGCTATATTTAAT
131 GATTTTCTAGTTAGCATGTATACGTGTTTAGGTGTTAGTAATGTTCTTATATGGCTATATTTAAT
*
246487 TGGGTTAGAAATGTTATGATATGTCTATAACGTTTAAATGGTTTATAGT
196 TGGGTCAGAAATGTTATGATATGTCTATAACGTTTAAATGGTTTATAGT
246536 AATTTATATG
Statistics
Matches: 239, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
266 239 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.41
Consensus pattern (266 bp):
TAAGTGTATACTTAGTATGTTATAATATTCATGCTTAGAAAAAGAAGATCGAATGATTAAGGAGC
TTAGCTTGACATCACTCAACGATGACTACTTATTGGTATCAATAATGAGATCCTACTATTGTTTT
GATTTTCTAGTTAGCATGTATACGTGTTTAGGTGTTAGTAATGTTCTTATATGGCTATATTTAAT
TGGGTCAGAAATGTTATGATATGTCTATAACGTTTAAATGGTTTATAGTGTGTTTAGGTGTTTAG
CATGTA
Found at i:246546 original size:19 final size:20
Alignment explanation
Indices: 246519--246562 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
246509 GTCTATAACG
246519 TTTAAAT-GGTTTA-TAGTAA
1 TTTAAATGGGTTTAGTA-TAA
*
246538 TTTATATGGGTTTAGTATAA
1 TTTAAATGGGTTTAGTATAA
246558 TTTAA
1 TTTAA
246563 CCAACAATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 6 0.29
20 13 0.62
21 2 0.10
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (20 bp):
TTTAAATGGGTTTAGTATAA
Found at i:250035 original size:32 final size:35
Alignment explanation
Indices: 249999--250084 Score: 106
Period size: 37 Copynumber: 2.5 Consensus size: 35
249989 GGTGATTATT
* *
249999 GGATCGGTTG-TTTTT-A-AGTTCAGATCAATATC
1 GGATCGGTTGATTTTTGATAGGTCAGATCAATACC
*
250031 GGATCGGTTGATTTTTGGATTAGGTCAGGTCAATACC
1 GGATCGGTTGATTTTT-GA-TAGGTCAGATCAATACC
250068 GGATCGGTTGATTTTTG
1 GGATCGGTTGATTTTTG
250085 GGTCGGGTCA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.22
33 5 0.11
35 1 0.02
36 1 0.02
37 29 0.63
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.40
Consensus pattern (35 bp):
GGATCGGTTGATTTTTGATAGGTCAGATCAATACC
Found at i:250094 original size:32 final size:34
Alignment explanation
Indices: 249999--250097 Score: 98
Period size: 37 Copynumber: 2.9 Consensus size: 34
249989 GGTGATTATT
* * * *
249999 GGATCGGTTG-TTTTT-AAGTTCAGATCAATATC
1 GGATCGGTTGATTTTTGGAGGTCAGGTCAATACC
250031 GGATCGGTTGATTTTTGGATTAGGTCAGGTCAATACC
1 GGATCGGTTGATTTTTGG---AGGTCAGGTCAATACC
*
250068 GGATCGGTTGATTTTT-G-GGTCGGGTCAATA
1 GGATCGGTTGATTTTTGGAGGTCAGGTCAATA
250098 TCATATCAGT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
32 22 0.39
33 5 0.09
36 1 0.02
37 29 0.51
ACGTcount: A:0.21, C:0.12, G:0.29, T:0.37
Consensus pattern (34 bp):
GGATCGGTTGATTTTTGGAGGTCAGGTCAATACC
Found at i:250094 original size:37 final size:37
Alignment explanation
Indices: 250018--250094 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
250008 GTTTTTAAGT
* *
250018 TCAGATCAATATCGGATCGGTTGATTTTTGGATTAGG
1 TCAGATCAATACCGGATCGGTTGATTTTTGGATCAGG
* * *
250055 TCAGGTCAATACCGGATCGGTTGATTTTTGGGTCGGG
1 TCAGATCAATACCGGATCGGTTGATTTTTGGATCAGG
250092 TCA
1 TCA
250095 ATATCATATC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.21, C:0.14, G:0.30, T:0.35
Consensus pattern (37 bp):
TCAGATCAATACCGGATCGGTTGATTTTTGGATCAGG
Found at i:250704 original size:23 final size:23
Alignment explanation
Indices: 250674--250719 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
250664 ACTTTTTATT
*
250674 ATTTTA-TTAATTTAATATTTTTA
1 ATTTTATTTAAATTAAT-TTTTTA
250697 ATTTTATTTAAATTAATTTTTTA
1 ATTTTATTTAAATTAATTTTTTA
250720 TTGAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTTATTTAAATTAATTTTTTA
Found at i:250797 original size:16 final size:16
Alignment explanation
Indices: 250778--250913 Score: 92
Period size: 16 Copynumber: 8.4 Consensus size: 16
250768 TTGGGTTGCT
*
250778 TTCGGGTCGGGTTAAA
1 TTCGGTTCGGGTTAAA
***
250794 TTCGGTTCGGGTTGCT
1 TTCGGTTCGGGTTAAA
*
250810 TTCGGATCGGGTTAAAA
1 TTCGGTTCGGGTT-AAA
* *
250827 TTCGGTTCTGGTTAAT
1 TTCGGTTCGGGTTAAA
* * **
250843 TTCGGTTTGGTTTACT
1 TTCGGTTCGGGTTAAA
* **
250859 TTCGGTTTGGGTTACT
1 TTCGGTTCGGGTTAAA
* **
250875 TTCGATTCGGGTTACT
1 TTCGGTTCGGGTTAAA
* *
250891 TTTGGTTCGGGTTAAT
1 TTCGGTTCGGGTTAAA
250907 TTCGGTT
1 TTCGGTT
250914 TCAGTTCGGG
Statistics
Matches: 97, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
16 86 0.89
17 11 0.11
ACGTcount: A:0.12, C:0.13, G:0.30, T:0.45
Consensus pattern (16 bp):
TTCGGTTCGGGTTAAA
Found at i:250806 original size:32 final size:32
Alignment explanation
Indices: 250770--250913 Score: 135
Period size: 32 Copynumber: 4.5 Consensus size: 32
250760 CAACCTGTTT
* *
250770 GGGTTGCTTTCGGGTCGGGTTAAATTCGGTTC
1 GGGTTACTTTCGGTTCGGGTTAAATTCGGTTC
* *
250802 GGGTTGCTTTCGGATCGGGTTAAAATTCGGTTC
1 GGGTTACTTTCGGTTCGGGTT-AAATTCGGTTC
* * * * ** *
250835 TGGTTAATTTCGGTTTGGTTTACTTTCGGTTT
1 GGGTTACTTTCGGTTCGGGTTAAATTCGGTTC
* ** *
250867 GGGTTACTTTCGATTCGGGTTACTTTTGGTTC
1 GGGTTACTTTCGGTTCGGGTTAAATTCGGTTC
*
250899 GGGTTAATTTCGGTT
1 GGGTTACTTTCGGTT
250914 TCAGTTCGGG
Statistics
Matches: 92, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
32 66 0.72
33 26 0.28
ACGTcount: A:0.11, C:0.13, G:0.31, T:0.44
Consensus pattern (32 bp):
GGGTTACTTTCGGTTCGGGTTAAATTCGGTTC
Found at i:250841 original size:49 final size:49
Alignment explanation
Indices: 250778--250872 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 49
250768 TTGGGTTGCT
*
250778 TTCGGGTCGGGTTAAATTCGGTTCGGGTTGCTTTCGGATCGGGTTAAAA
1 TTCGGGTCGGGTTAAATTCGGTTCGGGTTACTTTCGGATCGGGTTAAAA
* * * * * * *
250827 TTCGGTTCTGGTTAATTTCGGTTTGGTTTACTTTCGGTTTGGGTTA
1 TTCGGGTCGGGTTAAATTCGGTTCGGGTTACTTTCGGATCGGGTTA
250873 CTTTCGATTC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.13, C:0.13, G:0.32, T:0.43
Consensus pattern (49 bp):
TTCGGGTCGGGTTAAATTCGGTTCGGGTTACTTTCGGATCGGGTTAAAA
Found at i:254566 original size:20 final size:20
Alignment explanation
Indices: 254528--254572 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
254518 TCGTTGGTAC
* *
254528 CGATATTGGCCCTTCAGTAT
1 CGATATTGACCCATCAGTAT
*
254548 CGATATTGACCCATGAGTAT
1 CGATATTGACCCATCAGTAT
*
254568 TGATA
1 CGATA
254573 CCCACCTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (20 bp):
CGATATTGACCCATCAGTAT
Found at i:257148 original size:15 final size:15
Alignment explanation
Indices: 257108--257148 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
257098 CAGCCCATTA
257108 AGTTAACTCATGTTG
1 AGTTAACTCATGTTG
*
257123 AGTCAAACTCATGTTG
1 AGT-TAACTCATGTTG
257139 AGTTAACTCA
1 AGTTAACTCA
257149 GACCTGTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (15 bp):
AGTTAACTCATGTTG
Found at i:258833 original size:2 final size:2
Alignment explanation
Indices: 258826--258854 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
258816 CTTTATTTGT
258826 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
258855 GAACTACCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:263659 original size:64 final size:65
Alignment explanation
Indices: 263586--263722 Score: 215
Period size: 65 Copynumber: 2.1 Consensus size: 65
263576 CATACCTCAT
* *
263586 ATCGAATGCATTTTATGCACCGATGCACA-GCCATGCATCGATGCACT-CTGGATTTTATTGATA
1 ATCGAATGCATTTTATGCACCGATGCACATGCCATGCATCGATGCACTCCTGGATTCT-TTGAAA
263649 C
65 C
* *
263650 ATCGAATGCATTTTATGCACCGATGCACATGTCATGCATCGATGCACTCCTGGCTTCTTTGAAAC
1 ATCGAATGCATTTTATGCACCGATGCACATGCCATGCATCGATGCACTCCTGGATTCTTTGAAAC
263715 ATCGAATG
1 ATCGAATG
263723 TAATTAGTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
64 29 0.43
65 31 0.46
66 7 0.10
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (65 bp):
ATCGAATGCATTTTATGCACCGATGCACATGCCATGCATCGATGCACTCCTGGATTCTTTGAAAC
Found at i:263737 original size:65 final size:64
Alignment explanation
Indices: 263586--263742 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 64
263576 CATACCTCAT
* * *
263586 ATCGAATGCATTTTATGCACCGATGCACAGCCATGCATCGATGCACTCTGGATTTTATTGATAC
1 ATCGAATGCATATTATGCACCGATGCACAGCCATGCATCGATGCACTCTGGATTCTATTGAAAC
* * *
263650 ATCGAATGCATTTTATGCACCGATGCACATGTCATGCATCGATGCACTCCTGGCTTCT-TTGAAA
1 ATCGAATGCATATTATGCACCGATGCACA-GCCATGCATCGATGCACT-CTGGATTCTATTGAAA
263714 C
64 C
* *
263715 ATCGAATGTA-ATTAGTGTACCGATGCAC
1 ATCGAATGCATATTA-TGCACCGATGCAC
263743 TCCTAGTGTA
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
64 32 0.39
65 44 0.53
66 7 0.08
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (64 bp):
ATCGAATGCATATTATGCACCGATGCACAGCCATGCATCGATGCACTCTGGATTCTATTGAAAC
Found at i:265688 original size:21 final size:21
Alignment explanation
Indices: 265664--265705 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
265654 TATGAGAAAT
*
265664 TATTTTAAAA-TACAAAAATGA
1 TATTTCAAAATTA-AAAAATGA
265685 TATTTCAAAATTAAAAAATGA
1 TATTTCAAAATTAAAAAATGA
265706 AAATAATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
TATTTCAAAATTAAAAAATGA
Found at i:280388 original size:8 final size:8
Alignment explanation
Indices: 280375--280407 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
280365 CTGCCACTTG
280375 TCTCTCCC
1 TCTCTCCC
280383 TCTCTCCC
1 TCTCTCCC
280391 TCTCTCCC
1 TCTCTCCC
280399 TCTCTCCC
1 TCTCTCCC
280407 T
1 T
280408 ACTGGTGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (8 bp):
TCTCTCCC
Found at i:285197 original size:33 final size:35
Alignment explanation
Indices: 285135--285201 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 35
285125 TGCATACACC
*
285135 TTGATTGATGTGCAGTAATCAGAAGGAAGTGTAGTTG
1 TTGATTGATGTGAAGTAATC--AAGGAAGTGTAGTTG
285172 TTGATTGATGTGAAGTAATC-A-GAAGTGTAG
1 TTGATTGATGTGAAGTAATCAAGGAAGTGTAG
285202 ATGTCTATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 9 0.31
34 1 0.03
37 19 0.66
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.33
Consensus pattern (35 bp):
TTGATTGATGTGAAGTAATCAAGGAAGTGTAGTTG
Found at i:288234 original size:19 final size:19
Alignment explanation
Indices: 288210--288267 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 19
288200 ATGACCAACA
* *
288210 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCC
288229 AAATCGCAACGCGATCTCC
1 AAATCGCAACGCGATCTCC
*
288248 CAATCGCAACGCGATCTCC
1 AAATCGCAACGCGATCTCC
288267 A
1 A
288268 TTATCGCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.31, C:0.34, G:0.16, T:0.19
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCC
Found at i:288338 original size:21 final size:21
Alignment explanation
Indices: 288310--288363 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
288300 GATTTTGACC
*
288310 ATCGCATTGCGATTTTCGA-A
1 ATCGCATTGCGATTTTAGATA
288330 ATCCGCATTGCGATTTTAGATA
1 AT-CGCATTGCGATTTTAGATA
*
288352 ATCGCAATGCGA
1 ATCGCATTGCGA
288364 ATATGTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 25 0.83
22 3 0.10
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (21 bp):
ATCGCATTGCGATTTTAGATA
Found at i:288397 original size:41 final size:41
Alignment explanation
Indices: 288352--288462 Score: 125
Period size: 41 Copynumber: 2.7 Consensus size: 41
288342 ATTTTAGATA
* *
288352 ATCGCAATGCGAATATGTA-AATCGCAACGCGATAACACTTG
1 ATCGCAACGCGAATATG-ACAATCGCAACGCGATAACACGTG
* * * *
288393 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACGTG
1 ATCGCAACGCGAATATGACAATCGCAACGCGATAACACGTG
* * *
288434 ATCGCAACGCGATTCTGACTATCGCAACG
1 ATCGCAACGCGAATATGACAATCGCAACG
288463 AGATTCTGAC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 1 0.02
41 62 0.98
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGAATATGACAATCGCAACGCGATAACACGTG
Found at i:288398 original size:21 final size:20
Alignment explanation
Indices: 288372--288446 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 20
288362 GAATATGTAA
288372 ATCGCAACGCGATAACACTTG
1 ATCGCAACGCGATAACAC-TG
*
288393 ATCGCAACGCGAT-TCTGACT-
1 ATCGCAACGCGATAAC--ACTG
*
288413 ATCGCAACGCGATAATACGTG
1 ATCGCAACGCGATAACAC-TG
288434 ATCGCAACGCGAT
1 ATCGCAACGCGAT
288447 TCTGACTATC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 2 0.04
20 15 0.33
21 27 0.59
22 2 0.04
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGATAACACTG
Found at i:288418 original size:20 final size:20
Alignment explanation
Indices: 288393--288479 Score: 122
Period size: 20 Copynumber: 4.3 Consensus size: 20
288383 ATAACACTTG
288393 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
288413 ATCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
288433 GATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
288454 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
288474 ATCGCA
1 ATCGCA
288480 TTGCGATAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
19 2 0.03
20 40 0.68
21 15 0.25
22 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:288499 original size:61 final size:61
Alignment explanation
Indices: 288393--288508 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 61
288383 ATAACACTTG
* ***
288393 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACT
1 ATCGCAACGAGATTCTGACTATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACT
** * *
288454 ATCGCAACGAGATTCTGACTATCGCATTGCGATAATATAAAATCGCAATGCGATT
1 ATCGCAACGAGATTCTGACTATCGCAACGCGATAATACAAAATCGCAACGCGATT
288509 TTCAAAGCGC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (61 bp):
ATCGCAACGAGATTCTGACTATCGCAACGCGATAATACAAAATCGCAACGCGATTCTGACT
Found at i:288662 original size:22 final size:22
Alignment explanation
Indices: 288637--288698 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
288627 TCTCTCACTC
*
288637 TCTCCGGCGACATCCGTCCCCA
1 TCTCCGGCGAAATCCGTCCCCA
* *
288659 TCTCCGGCAAAATCCATCCCCA
1 TCTCCGGCGAAATCCGTCCCCA
288681 TCTCCGGCGAAATCCGTC
1 TCTCCGGCGAAATCCGTC
288699 TATCTCCATC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.19, C:0.45, G:0.16, T:0.19
Consensus pattern (22 bp):
TCTCCGGCGAAATCCGTCCCCA
Found at i:289087 original size:33 final size:34
Alignment explanation
Indices: 289037--289119 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 34
289027 CGCAATGACA
*
289037 AAATTCGCGTTGTGATTATCTCGTTGCGATAG-C
1 AAATTCGCGTTGCGATTATCTCGTTGCGATAGTC
* *
289070 CATTTCGCGTTGCGATTATCTCGTTGCGATAGTC
1 AAATTCGCGTTGCGATTATCTCGTTGCGATAGTC
289104 AAATTCGCGTTGCGAT
1 AAATTCGCGTTGCGAT
289120 AATCATTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 29 0.66
34 15 0.34
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (34 bp):
AAATTCGCGTTGCGATTATCTCGTTGCGATAGTC
Found at i:289116 original size:20 final size:20
Alignment explanation
Indices: 289091--289139 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
289081 GCGATTATCT
*
289091 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCG
**
289111 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAATCAAATTCG
*
289131 TGTTGCGAT
1 CGTTGCGAT
289140 TTTTATTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAATCAAATTCG
Found at i:289147 original size:20 final size:20
Alignment explanation
Indices: 289124--289162 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
289114 TGCGATAATC
*
289124 ATTTTCGTGTTGCGATTTTT
1 ATTTTCATGTTGCGATTTTT
*
289144 ATTTTCATGTTGCGGTTTT
1 ATTTTCATGTTGCGATTTT
289163 AAGTTTCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.59
Consensus pattern (20 bp):
ATTTTCATGTTGCGATTTTT
Found at i:289169 original size:20 final size:20
Alignment explanation
Indices: 289126--289171 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
289116 CGATAATCAT
* * *
289126 TTTCGTGTTGCGATTTTTAT
1 TTTCATGTTGCGATTTTAAG
*
289146 TTTCATGTTGCGGTTTTAAG
1 TTTCATGTTGCGATTTTAAG
289166 TTTCAT
1 TTTCAT
289172 AAACTATTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.11, G:0.20, T:0.57
Consensus pattern (20 bp):
TTTCATGTTGCGATTTTAAG
Found at i:289899 original size:21 final size:22
Alignment explanation
Indices: 289875--289934 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
289865 CTCCTATCGT
289875 TCAAGAGGCCCCTATCATCC-C
1 TCAAGAGGCCCCTATCATCCAC
* ** *
289896 TCAAGAGTCCCCTCCCA-CCAT
1 TCAAGAGGCCCCTATCATCCAC
*
289917 TCAAGAGGCCCCTGTCAT
1 TCAAGAGGCCCCTATCAT
289935 TGTTGAAGAG
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.23, C:0.42, G:0.15, T:0.20
Consensus pattern (22 bp):
TCAAGAGGCCCCTATCATCCAC
Found at i:289944 original size:42 final size:42
Alignment explanation
Indices: 289874--289965 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
289864 TCTCCTATCG
*
289874 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCA
1 TTCAAGAGGCCCCTATCATCCCTCAAGAGGT-CCCTCCCAACA
* *** *
289916 TTCAAGAGGCCCCTGTCATTGTTGAAGAGGTCCCTCCCAACA
1 TTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCAACA
*
289958 TTCTAGAG
1 TTCAAGAG
289966 CCCGATTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCAACA
Found at i:291362 original size:30 final size:31
Alignment explanation
Indices: 291328--291394 Score: 127
Period size: 30 Copynumber: 2.2 Consensus size: 31
291318 ATAAGAGTTG
291328 ATTTGTTTAATTGATGTGTAAAT-AATTCTT
1 ATTTGTTTAATTGATGTGTAAATAAATTCTT
291358 ATTTGTTTAATTGATGTGTAAATAAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAAATTCTT
291389 ATTTGT
1 ATTTGT
291395 GCTTGTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 23 0.64
31 13 0.36
ACGTcount: A:0.30, C:0.03, G:0.13, T:0.54
Consensus pattern (31 bp):
ATTTGTTTAATTGATGTGTAAATAAATTCTT
Found at i:291481 original size:54 final size:55
Alignment explanation
Indices: 291366--291481 Score: 173
Period size: 54 Copynumber: 2.1 Consensus size: 55
291356 TTATTTGTTT
* *
291366 AATTGATGTGTAAATAAATTCTTATTTGTGCTTGTTTAATTGATTAAAAGTTTAT
1 AATTGATGTGTAAATAAATTCTTATTTGTGCTTGTTTAATTGATTAAAAGTGTAA
* *
291421 TATTGATGTGTAAAT-AATTCTTATTTGTGCTTGTTTAATTGATTGAAA-TGTAA
1 AATTGATGTGTAAATAAATTCTTATTTGTGCTTGTTTAATTGATTAAAAGTGTAA
291474 AAGTTGAT
1 AA-TTGAT
291482 TTGTTGATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
53 4 0.07
54 37 0.67
55 14 0.25
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.48
Consensus pattern (55 bp):
AATTGATGTGTAAATAAATTCTTATTTGTGCTTGTTTAATTGATTAAAAGTGTAA
Found at i:291571 original size:20 final size:20
Alignment explanation
Indices: 291544--291807 Score: 257
Period size: 20 Copynumber: 13.8 Consensus size: 20
291534 GTGATTTTCT
*
291544 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
291564 CATTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
291584 CGTTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
291603 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
291623 CATTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
291643 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
** *
291663 TATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
291677 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
291697 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
291717 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
291731 CGTTGCGATATTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
291751 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
291771 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
291791 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
291808 GAATGTGTAA
Statistics
Matches: 200, Mismatches: 31, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.09
16 2 0.01
18 2 0.01
19 20 0.10
20 157 0.79
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:291702 original size:54 final size:54
Alignment explanation
Indices: 291561--291779 Score: 269
Period size: 54 Copynumber: 4.0 Consensus size: 54
291551 ATAGTCAAAT
* *
291561 TCCCATTGCGATAATCAAATTCGCGTTGCGATAGTCA-TTTCGCGTTGCGATAGTCAAA
1 TCCCATTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT--T---A
* * * *
291619 TTCGCATTGCGATAGTTAAATTCGTGTTGCGATAGTCATTTTCGTATTGCGATTA
1 -TCCCATTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
*
291674 TCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
1 TCCCATTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
* * * * *
291728 TCCCGTTGCGATATTCAAATTCACGTTGCGATAGTCATATTCGCGTTGCGAT
1 TCCCATTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGAT
291780 AGTCATATTC
Statistics
Matches: 144, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
54 97 0.67
55 1 0.01
58 1 0.01
59 33 0.23
60 12 0.08
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (54 bp):
TCCCATTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATTGCGATTA
Found at i:291708 original size:74 final size:73
Alignment explanation
Indices: 291585--291804 Score: 239
Period size: 74 Copynumber: 3.0 Consensus size: 73
291575 TCAAATTCGC
* * * * * * *
291585 GTTGCGATAGTC-ATTTCGCGTTGCGATAGTCAAATTCGCATTGCGATAGTTAAATTCGTGTTGC
1 GTTGCGATATTCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGC
291649 GATAGTCA
66 GATAGTCA
* * * * * * *
291657 TTTTCG-TATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGCATT
1 GTTGCGATATT-CAAAT-TCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTT
*
291721 GCGATTA-TCCC
64 GCGA-TAGT-CA
*
291732 GTTGCGATATTCAAATTCACGTTGCGATAGTCATATTCGCGTTGCGATAGTCATATTCGCGTTGC
1 GTTGCGATATTCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGC
291797 GATAGTCA
66 GATAGTCA
291805 AATGAATGTG
Statistics
Matches: 121, Mismatches: 20, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
71 3 0.02
72 5 0.04
73 6 0.05
74 93 0.77
75 10 0.08
76 4 0.03
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (73 bp):
GTTGCGATATTCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATATTCGCGTTGC
GATAGTCA
Found at i:292005 original size:18 final size:18
Alignment explanation
Indices: 291982--292016 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
291972 AAGCCGGTTG
*
291982 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
292000 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
292017 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:294311 original size:24 final size:24
Alignment explanation
Indices: 294277--294330 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
294267 CTGAAACATC
294277 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
294301 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
294325 ATCAAA
1 ATCAAA
294331 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:295094 original size:20 final size:20
Alignment explanation
Indices: 295066--295172 Score: 124
Period size: 20 Copynumber: 5.3 Consensus size: 20
295056 AATTCAGTGA
* *
295066 TGCGTTAGTTAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
* *
295086 TGCGATAGTCATAATCTCGT
1 TGCGATAGTCAGAATCGCGT
*
295106 TGCGATAGTCAGAATCGCAT
1 TGCGATAGTCAGAATCGCGT
* * **
295126 TGTGATAGTCCGAATCATGT
1 TGCGATAGTCAGAATCGCGT
*
295146 TGCGATAGTCATAATCGCGT
1 TGCGATAGTCAGAATCGCGT
295166 TGCGATA
1 TGCGATA
295173 ACGTGTTATC
Statistics
Matches: 70, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:295209 original size:20 final size:20
Alignment explanation
Indices: 295181--295233 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
295171 TAACGTGTTA
*
295181 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
295201 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
295221 TCGCATTGCGATT
1 TCGCATTGCGATT
295234 ATCTAAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:295251 original size:21 final size:20
Alignment explanation
Indices: 295221--295274 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
295211 ATTTACATAT
* *
295221 TCGCATTGCGATTATCTAAAA
1 TCGCAATGCGATT-TCAAAAA
295242 TCGCAATGCGGATTTCAAAAA
1 TCGCAATGC-GATTTCAAAAA
*
295263 TCACAATGCGAT
1 TCGCAATGCGAT
295275 GGTCAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.10
21 22 0.76
22 4 0.14
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTTCAAAAA
Found at i:295280 original size:21 final size:21
Alignment explanation
Indices: 295238--295282 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
295228 GCGATTATCT
* *
295238 AAAATCGCAATGCGGATTTCA
1 AAAATCACAATGCGGATGTCA
295259 AAAATCACAATGC-GATGGTCA
1 AAAATCACAATGCGGAT-GTCA
295280 AAA
1 AAA
295283 TCGCGTTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (21 bp):
AAAATCACAATGCGGATGTCA
Found at i:295330 original size:20 final size:19
Alignment explanation
Indices: 295306--295352 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
295296 TGGAAACTGA
*
295306 ATTGCGATAATGGAGATCGC
1 ATTGCGAT-ATAGAGATCGC
* *
295326 GTTGCGATTTAGAGATCGC
1 ATTGCGATATAGAGATCGC
295345 ATTGCGAT
1 ATTGCGAT
295353 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
ATTGCGATATAGAGATCGC
Found at i:295342 original size:19 final size:19
Alignment explanation
Indices: 295318--295354 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
295308 TGCGATAATG
*
295318 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
295337 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
295355 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:295521 original size:2 final size:2
Alignment explanation
Indices: 295514--295540 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
295504 TTTCCTACTG
295514 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
295541 ATTCTTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:295694 original size:14 final size:14
Alignment explanation
Indices: 295675--295709 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
295665 TCAATCTCAT
295675 CCATCCATATTCAC
1 CCATCCATATTCAC
295689 CCATCCATATTCAC
1 CCATCCATATTCAC
295703 CCATCCA
1 CCATCCA
295710 ACAGTAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.46, G:0.00, T:0.26
Consensus pattern (14 bp):
CCATCCATATTCAC
Found at i:295871 original size:17 final size:17
Alignment explanation
Indices: 295849--295893 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
295839 CTAAAAGGGA
*
295849 AGGGGAGGAAGATTCTC
1 AGGGGAGAAAGATTCTC
295866 AGGGGAGAAAGATTCTC
1 AGGGGAGAAAGATTCTC
*
295883 AGGGAAGAAAG
1 AGGGGAGAAAG
295894 GAGGTAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.40, T:0.13
Consensus pattern (17 bp):
AGGGGAGAAAGATTCTC
Found at i:296027 original size:3 final size:3
Alignment explanation
Indices: 296006--296070 Score: 62
Period size: 3 Copynumber: 21.3 Consensus size: 3
295996 CTACAAAAAC
*
296006 ATT ATT AATT A-T ATAT ATT ATT ATC ATT ATT ATT ATT A-T ATT ACTT
1 ATT ATT -ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* *
296052 ATT ATT TTT ATT TTT ATT A
1 ATT ATT ATT ATT ATT ATT A
296071 AATTACATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 4 0.08
3 38 0.75
4 9 0.18
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:296041 original size:15 final size:15
Alignment explanation
Indices: 296021--296082 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
296011 TAATTATATA
296021 TATTATTATCATTA-T
1 TATTATTAT-ATTACT
296036 TATTATTATATTACT
1 TATTATTATATTACT
296051 TATTATT-T-TTA-T
1 TATTATTATATTACT
* * *
296063 TTTTATTAAATTACA
1 TATTATTATATTACT
296078 TATTA
1 TATTA
296083 CATTTTGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 7 0.18
13 3 0.08
14 8 0.21
15 21 0.54
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTATTATATTACT
Found at i:296053 original size:27 final size:27
Alignment explanation
Indices: 296006--296086 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
295996 CTACAAAAAC
296006 ATTATTAATTATATATA-TTATTATCATT
1 ATTATT-ATTATAT-TACTTATTATCATT
**
296034 ATTATTATTATATTACTTATTATTTTT
1 ATTATTATTATATTACTTATTATCATT
* * *
296061 ATTTTTATTAAATTACATATTA-CATT
1 ATTATTATTATATTACTTATTATCATT
296087 TTGTTACAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 35 0.78
28 6 0.13
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTATTATTATATTACTTATTATCATT
Found at i:297585 original size:30 final size:29
Alignment explanation
Indices: 297549--297654 Score: 122
Period size: 30 Copynumber: 3.6 Consensus size: 29
297539 TCTTTCTGGA
297549 TTAGTCCTTTAAATTTATGTTTTTGCTATT
1 TTAGTCCTTTAAATTTATGTTTTT-CTATT
* * *
297579 TTAGTCCTTAAAATTTCTATTTTTACTATT
1 TTAGTCCTTTAAATTTATGTTTTT-CTATT
* *
297609 TTAGTCCTTTAAGTTTATGTTATTTTTATT
1 TTAGTCCTTTAAATTTATGTT-TTTCTATT
* *
297639 TTGGTCCCTTAAATTT
1 TTAGTCCTTTAAATTT
297655 TCAAATATGC
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
30 60 0.95
31 3 0.05
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.58
Consensus pattern (29 bp):
TTAGTCCTTTAAATTTATGTTTTTCTATT
Found at i:300003 original size:6 final size:6
Alignment explanation
Indices: 299992--300038 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
299982 GATCAATTTT
*
299992 TTTGCA TTTGCA TTTGCA TCTTTGCA TTTTGCA TATGCA TTT-CA TTT
1 TTTGCA TTTGCA TTTGCA --TTTGCA -TTTGCA TTTGCA TTTGCA TTT
300039 TTTAAGCATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
5 5 0.14
6 19 0.53
7 6 0.17
8 6 0.17
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.53
Consensus pattern (6 bp):
TTTGCA
Found at i:300024 original size:21 final size:20
Alignment explanation
Indices: 299992--300031 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
299982 GATCAATTTT
*
299992 TTTGCATTTGCATTTGCATC
1 TTTGCATTTGCATATGCATC
300012 TTTGCATTTTGCATATGCAT
1 TTTGCA-TTTGCATATGCAT
300032 TTCATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.50
Consensus pattern (20 bp):
TTTGCATTTGCATATGCATC
Found at i:300672 original size:25 final size:26
Alignment explanation
Indices: 300639--300701 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
300629 TTCTGTCTAA
*
300639 AACCCCAAAATAAAATATTGATTC-T
1 AACCCCAAAATAAAATATCGATTCTT
300664 AACCCCAAAATAAAATATCGATTCTT
1 AACCCCAAAATAAAATATCGATTCTT
*
300690 TA-CCCAAAATAA
1 AACCCCAAAATAA
300702 TTCATGGTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 33 0.94
26 2 0.06
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.25
Consensus pattern (26 bp):
AACCCCAAAATAAAATATCGATTCTT
Found at i:302518 original size:32 final size:32
Alignment explanation
Indices: 302482--302564 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
302472 AAGAAATGAT
*
302482 GAATGATGGGGAATCTTTGGAGATTCAAAATC
1 GAATGATGGGGAATCTTTGGAGATTCAAAATA
* * *
302514 GAATGTTGGCGAATCTTTGGAGATTCAACATA
1 GAATGATGGGGAATCTTTGGAGATTCAAAATA
*
302546 GAAT-ATTGGGGCATCTTTG
1 GAATGA-TGGGGAATCTTTG
302565 AGGATTTAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.31
Consensus pattern (32 bp):
GAATGATGGGGAATCTTTGGAGATTCAAAATA
Found at i:302819 original size:36 final size:36
Alignment explanation
Indices: 302679--302824 Score: 138
Period size: 36 Copynumber: 4.0 Consensus size: 36
302669 ACGAAGGGTC
302679 GTCTCACTTGAGACAAGTTTTCTTAAAAACAAA-TTT
1 GTCTCACTTGAGAC-AGTTTTCTTAAAAACAAACTTT
* * * ** *
302715 TTTTCTCTTGAGACAGTTTT-TGCTAAAAATGAATTTT
1 GTCTCACTTGAGACAGTTTTCT--TAAAAACAAACTTT
* *
302752 GTCTCACTTGAGACA-ATTTCTTTCAAAACAAACTTT
1 GTCTCACTTGAGACAGTTTTC-TTAAAAACAAACTTT
*
302788 GTCTCACTTGAGACAGTCTTTCTT-AAGACAAACTTT
1 GTCTCACTTGAGACAGT-TTTCTTAAAAACAAACTTT
302824 G
1 G
302825 AAATTGTTTC
Statistics
Matches: 88, Mismatches: 15, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
34 1 0.01
35 6 0.07
36 59 0.67
37 17 0.19
38 5 0.06
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (36 bp):
GTCTCACTTGAGACAGTTTTCTTAAAAACAAACTTT
Found at i:302986 original size:129 final size:130
Alignment explanation
Indices: 302839--303089 Score: 351
Period size: 129 Copynumber: 1.9 Consensus size: 130
302829 TGTTTCTCTT
* * * *
302839 GAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTCTAAAGAAAAATCTTTGAGTCTGTTTTTTT
1 GAAACAAAATTTTATCTCTCTTGAGACAGTTTCTTCTAAAGAAAAATCTTTGAGTATGTTTATTT
*
302904 AGAAACAAAATTT-TGTCTCATGAGACAGTTTCTTTTGAAGAAAAATCTCTGAGTCTGTTTTTTG
66 AGAAACAAAATTTGTCTCTCATGAGACAGTTTCTTTTGAAGAAAAATCTCTGAGTCTGTTTTTTG
* * * * *
302968 GAAACAAAATTTTATCTCTTTTGAGACAGTTTCTTTTGAGGAAAATTCTTTGAGTATGTTTATTT
1 GAAACAAAATTTTATCTCTCTTGAGACAGTTTCTTCTAAAGAAAAATCTTTGAGTATGTTTATTT
* ** * * *
303033 GGGGACAAAATTTGTCTCTCTTGAGACAGTTTCTTTTGAAGGAAAATCTTTGAGTCT
66 AGAAACAAAATTTGTCTCTCATGAGACAGTTTCTTTTGAAGAAAAATCTCTGAGTCT
303090 ATTTCTCTTA
Statistics
Matches: 105, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
129 66 0.63
130 39 0.37
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (130 bp):
GAAACAAAATTTTATCTCTCTTGAGACAGTTTCTTCTAAAGAAAAATCTTTGAGTATGTTTATTT
AGAAACAAAATTTGTCTCTCATGAGACAGTTTCTTTTGAAGAAAAATCTCTGAGTCTGTTTTTTG
Found at i:303005 original size:65 final size:65
Alignment explanation
Indices: 302777--303089 Score: 338
Period size: 65 Copynumber: 4.9 Consensus size: 65
302767 ATTTCTTTCA
* * * * *
302777 AAAC-AAACTTTGTCTCACTTGAGACAG--TCTTTCTTAAGACAAA-CTTTGAAAT-TGTTTCTC
1 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTT-TGAAGAAAAATCTTTG-AGTCTGTTT-T-
302837 TT-G
62 TTGG
* * * *
302840 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTTCTAAAGAAAAATCTTTGAGTCTGTTTTTTTA
1 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAAGAAAAATCTTTGAGTCTG-TTTTTTG
302905 G
65 G
* *
302906 AAACAAAATTTTG--TCTCATGAGACAGTTTCTTTTGAAGAAAAATCTCTGAGTCTGTTTTTTGG
1 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAAGAAAAATCTTTGAGTCTGTTTTTTGG
* * * * *
302969 AAACAAAATTTTATCTCTTTTGAGACAGTTTCTTTTGAGGAAAATTCTTTGAGTATGTTTATTTG
1 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAAGAAAAATCTTTGAGTCTGTTT-TTTG
303034 G
65 G
** *
303035 GGACAAAA-TTTGTCTCTCTTGAGACAGTTTCTTTTGAAGGAAAATCTTTGAGTCT
1 AAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAAGAAAAATCTTTGAGTCT
303090 ATTTCTCTTA
Statistics
Matches: 212, Mismatches: 28, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
63 23 0.11
64 58 0.27
65 92 0.43
66 36 0.17
67 3 0.01
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (65 bp):
AAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAAGAAAAATCTTTGAGTCTGTTTTTTGG
Found at i:303279 original size:40 final size:39
Alignment explanation
Indices: 303224--303375 Score: 166
Period size: 40 Copynumber: 3.8 Consensus size: 39
303214 TGGTCTGTCG
* * *
303224 TCCTCATCGCGTAGGAGCCATATCATCCTCCGACCAGACC
1 TCCTCATCACGTAGGAGCCGTGTCATCC-CCGACCAGACC
*
303264 TCCTCATCACGTAGGAGCTGTGTCA-CCCCTAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCC--G---ACCAGACC
*
303306 ATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACC
1 -TCCTCATCACGTAGGAGCCGTGTCATCC-CCGACCAGACC
303347 TCCTCATCACGTAGGAGCCGTGTCA-CCCC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCC
303376 TAGATAACCA
Statistics
Matches: 96, Mismatches: 7, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
38 4 0.04
39 4 0.04
40 51 0.53
41 2 0.02
42 2 0.02
43 29 0.30
44 2 0.02
45 2 0.02
ACGTcount: A:0.23, C:0.39, G:0.18, T:0.20
Consensus pattern (39 bp):
TCCTCATCACGTAGGAGCCGTGTCATCCCCGACCAGACC
Found at i:303311 original size:43 final size:43
Alignment explanation
Indices: 303256--303412 Score: 191
Period size: 43 Copynumber: 3.7 Consensus size: 43
303246 TCATCCTCCG
*
303256 ACCAGACCTCCTCATCACGTAGGAGCTGTGTCACCCCTAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATA
*
303299 ACCAG-CCATCCTCATCACGTAGGAACCGTGTCATCCACC--G---
1 ACCAGACC-TCCTCATCACGTAGGAGCCGTGTCA-CC-CCTAGATA
303339 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATA
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATA
* * * *
303382 ACCAGTCGTCCTCATCATGTAGGAACCGTGT
1 ACCAGACCTCCTCATCACGTAGGAGCCGTGT
303413 TATCACCCTC
Statistics
Matches: 98, Mismatches: 7, Indels: 18
0.80 0.06 0.15
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 30 0.31
41 2 0.02
42 2 0.02
43 56 0.57
44 2 0.02
45 2 0.02
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.20
Consensus pattern (43 bp):
ACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATA
Found at i:303363 original size:83 final size:83
Alignment explanation
Indices: 303224--303412 Score: 297
Period size: 83 Copynumber: 2.3 Consensus size: 83
303214 TGGTCTGTCG
* * * * * *
303224 TCCTCATCGCGTAGGAGCCATATCATCCTCCGACCAGACCTCCTCATCACGTAGGAGCTGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCA
303289 CCCCTAGATAACCAGCCA
66 CCCCTAGATAACCAGCCA
303307 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCA
* *
303372 CCCCTAGATAACCAGTCG
66 CCCCTAGATAACCAGCCA
*
303390 TCCTCATCATGTAGGAACCGTGT
1 TCCTCATCACGTAGGAACCGTGT
303413 TATCACCCTC
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 97 1.00
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (83 bp):
TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCA
CCCCTAGATAACCAGCCA
Found at i:303682 original size:3 final size:3
Alignment explanation
Indices: 303665--303743 Score: 88
Period size: 3 Copynumber: 25.3 Consensus size: 3
303655 TCTAAAAAAC
*
303665 ATT ATT AATT A-T ATT ATT ATAT ATT ATT ATC ATT ATT ATT ATT ATT
1 ATT ATT -ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
* *
303711 ATAT ATT ACTT ATT ATT ATT TTT ATT TTT ATT A
1 AT-T ATT A-TT ATT ATT ATT ATT ATT ATT ATT A
303744 AATTACATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
2 2 0.03
3 51 0.78
4 12 0.18
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:303682 original size:12 final size:12
Alignment explanation
Indices: 303665--303730 Score: 59
Period size: 10 Copynumber: 5.5 Consensus size: 12
303655 TCTAAAAAAC
303665 ATTATTAATTAT
1 ATTATTAATTAT
303677 ATTATT-A-TAT
1 ATTATTAATTAT
303687 ATTATTATCATTATT
1 ATTATTA--ATTA-T
303702 ATTATT-ATTAT
1 ATTATTAATTAT
*
303713 A-TATTACTTATT
1 ATTATTAATTA-T
303725 ATTATT
1 ATTATT
303731 TTTATTTTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 15
0.74 0.02 0.25
Matches are distributed among these distances:
10 13 0.29
11 6 0.13
12 12 0.27
13 5 0.11
14 2 0.04
15 7 0.16
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTATTAATTAT
Found at i:305300 original size:30 final size:30
Alignment explanation
Indices: 305241--305342 Score: 120
Period size: 30 Copynumber: 3.5 Consensus size: 30
305231 TTTATGGTCC
**
305241 AGTCCTTTAAATTTCTATTTTTTTTTATTTT
1 AGTCCTTTAAATTTCTA-TTTTTACTATTTT
*
305272 AGTCCTCTAAATTTCTATTTTTACTATTTT
1 AGTCCTTTAAATTTCTATTTTTACTATTTT
*
305302 AGTCCTTTAAGTTTCT-TTTTT--TATTTT
1 AGTCCTTTAAATTTCTATTTTTACTATTTT
* *
305329 GGTCCCTTAAATTT
1 AGTCCTTTAAATTT
305343 TCAAATATGT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
27 17 0.27
29 5 0.08
30 25 0.40
31 16 0.25
ACGTcount: A:0.20, C:0.14, G:0.06, T:0.61
Consensus pattern (30 bp):
AGTCCTTTAAATTTCTATTTTTACTATTTT
Found at i:306523 original size:58 final size:58
Alignment explanation
Indices: 306461--306616 Score: 285
Period size: 58 Copynumber: 2.7 Consensus size: 58
306451 TCGTTAACAA
306461 CCATTACTAGAGTGATAAAATGTTGATATAACGCATTAAACTGAATGATCATTAACGG
1 CCATTACTAGAGTGATAAAATGTTGATATAACGCATTAAACTGAATGATCATTAACGG
* *
306519 CCATTACTAGAGTGATAAAATGTTGATATAAAGCATTAAATTGAATGATCATTAACGG
1 CCATTACTAGAGTGATAAAATGTTGATATAACGCATTAAACTGAATGATCATTAACGG
*
306577 CCATTACTAGAGTGATAAAATGTTGATATAACACATTAAA
1 CCATTACTAGAGTGATAAAATGTTGATATAACGCATTAAA
306617 TCGACCGATC
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 94 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (58 bp):
CCATTACTAGAGTGATAAAATGTTGATATAACGCATTAAACTGAATGATCATTAACGG
Found at i:308450 original size:12 final size:12
Alignment explanation
Indices: 308435--308472 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
308425 GTTATTTAAA
308435 CGGGTATTGGGC
1 CGGGTATTGGGC
*
308447 CGGGTATTGGGT
1 CGGGTATTGGGC
308459 CGGGTATTGGGC
1 CGGGTATTGGGC
308471 CG
1 CG
308473 AGAATCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.16, G:0.50, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:308462 original size:24 final size:24
Alignment explanation
Indices: 308435--308489 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
308425 GTTATTTAAA
* * *
308435 CGGGTATTGGGCCGGGTATTGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
308459 CGGGTATTGGGCCGAGAATCGGGT
1 CGGGTATTGGGCCGAGAATCGGGT
308483 CGGGTAT
1 CGGGTAT
308490 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (24 bp):
CGGGTATTGGGCCGAGAATCGGGT
Found at i:322068 original size:95 final size:94
Alignment explanation
Indices: 321873--322061 Score: 267
Period size: 95 Copynumber: 2.0 Consensus size: 94
321863 AGGTAGAATT
**
321873 GATACCATGATAAGGGGTATCGATACCAAGCAACATCGAATCTATTTGGTATCGATACCGGAAAG
1 GATACCATGATAAGGGGTATCGATACCAAGCAACATCGAATCTATTTGGTATCGATACAAGAAAG
* * *
321938 GGGTATCTGTACCATAGTATGGTAGTATC
66 GGGTATCGGTACCATAGTATAGAAGTATC
321967 GATACCATGATAA-GGGTATCGATACC-AGACAACATCGAA-CTTAATTTTGGTATCGATACAAG
1 GATACCATGATAAGGGGTATCGATACCAAG-CAACATCGAATC-T-A-TTTGGTATCGATACAAG
*
322029 AATGGGGTATCGGTACCATAGTATAGAAGTATC
62 AAAGGGGTATCGGTACCATAGTATAGAAGTATC
322062 AGTACCAGGG
Statistics
Matches: 85, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
92 3 0.04
93 24 0.28
94 14 0.16
95 44 0.52
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (94 bp):
GATACCATGATAAGGGGTATCGATACCAAGCAACATCGAATCTATTTGGTATCGATACAAGAAAG
GGGTATCGGTACCATAGTATAGAAGTATC
Found at i:322081 original size:95 final size:93
Alignment explanation
Indices: 321873--322086 Score: 238
Period size: 95 Copynumber: 2.3 Consensus size: 93
321863 AGGTAGAATT
* * **
321873 GATACCATGATAAGGGGTATCGATACCAAGCAACATCGAATCTATTTGGTATCGATACCGGAAAG
1 GATACCAGGATAA-GAGTATCGATACCAAGCAACATCGAATCTATTTGGTATCGATACAAGAAAG
* * *
321938 GGGTATCTGTACCATAGTATGGTAGTATC
65 GGGTATCGGTACCATAGTATAGAAGTATC
* *
321967 GATACCATGATAAGGGTATCGATACC-AGACAACATCGAA-CTTAATTTTGGTATCGATACAAGA
1 GATACCAGGATAAGAGTATCGATACCAAG-CAACATCGAATC-T-A-TTTGGTATCGATACAAGA
*
322030 ATGGGGTATCGGTACCATAGTATAGAAGTATC
62 AAGGGGTATCGGTACCATAGTATAGAAGTATC
*
322062 -AGTACCAGGGT-AGTAGTATCGATAC
1 GA-TACCAGGATAAG-AGTATCGATAC
322087 TATGTAGGCA
Statistics
Matches: 105, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
92 3 0.03
93 24 0.23
94 17 0.16
95 61 0.58
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (93 bp):
GATACCAGGATAAGAGTATCGATACCAAGCAACATCGAATCTATTTGGTATCGATACAAGAAAGG
GGTATCGGTACCATAGTATAGAAGTATC
Found at i:322495 original size:55 final size:55
Alignment explanation
Indices: 322402--322827 Score: 538
Period size: 55 Copynumber: 7.7 Consensus size: 55
322392 CTTCGTATGT
** *
322402 ATATTCACGGAATTCATCATGAGTTGATGAATCACCGTACATGCACCTTGTGTGC
1 ATATTCATAGAATTCATCATGAGTTGATGAATCACCGTACAAGCACCTTGTGTGC
* * * *
322457 AAATCCACAGAATTCATCATGAGTTGATGAATCACCGTACAAGCACTTTGTGTGC
1 ATATTCATAGAATTCATCATGAGTTGATGAATCACCGTACAAGCACCTTGTGTGC
* ** * * * *
322512 ATATTAACGGAATTCATCATGATTTGATGAATCACTGTATATGCACCTTGTGTGC
1 ATATTCATAGAATTCATCATGAGTTGATGAATCACCGTACAAGCACCTTGTGTGC
* * *
322567 AAATCCAT-GAAATTCATCATGAGTTAATGAATCACCGTAC-AG-ACACTTCGTGTGC
1 ATATTCATAG-AATTCATCATGAGTTGATGAATCACCGTACAAGCAC-CTT-GTGTGC
*
322622 ATATTCATAGAATTCATCATGAGTTGATGAATCACCGTACATGCA-CTTCGTGTGC
1 ATATTCATAGAATTCATCATGAGTTGATGAATCACCGTACAAGCACCTT-GTGTGC
*
322677 ATATTCATAGAATTCATCATGAGTTGATGAATCACTGTACAAGCACCTTGTGTGC
1 ATATTCATAGAATTCATCATGAGTTGATGAATCACCGTACAAGCACCTTGTGTGC
* * * * * *
322732 AAATCCATGGAATCCATCATGAGTTGATGAATCACCGTACAAGCA-ATTCATGTGC
1 ATATTCATAGAATTCATCATGAGTTGATGAATCACCGTACAAGCACCTT-GTGTGC
*
322787 ATATTCATGGAATTCATCATGAGTTGATGAATCACCGTACA
1 ATATTCATAGAATTCATCATGAGTTGATGAATCACCGTACA
322828 GACGCTATAT
Statistics
Matches: 324, Mismatches: 39, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
53 2 0.01
54 7 0.02
55 309 0.95
56 5 0.02
57 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (55 bp):
ATATTCATAGAATTCATCATGAGTTGATGAATCACCGTACAAGCACCTTGTGTGC
Found at i:322692 original size:165 final size:165
Alignment explanation
Indices: 322412--322827 Score: 631
Period size: 165 Copynumber: 2.5 Consensus size: 165
322402 ATATTCACGG
* * *
322412 AATTCATCATGAGTTGATGAATCACCGTACATG-CACCTT-GTGTGCAAATCCACAGAATTCATC
1 AATTCATCATGAGTTGATGAATCACCGTACA-GACA-CTTCGTGTGCATATTCATAGAATTCATC
* * *
322475 ATGAGTTGATGAATCACCGTACAAGCACTTTGTGTGCATATTAACGGAATTCATCATGATTTGAT
64 ATGAGTTGATGAATCACCGTACAAGCACTTCGTGTGCATATTAACAGAATTCATCATGAGTTGAT
* *
322540 GAATCACTGTATATGCACCTTGTGTGCAAATCCATGA
129 GAATCACTGTACAAGCACCTTGTGTGCAAATCCATGA
*
322577 AATTCATCATGAGTTAATGAATCACCGTACAGACACTTCGTGTGCATATTCATAGAATTCATCAT
1 AATTCATCATGAGTTGATGAATCACCGTACAGACACTTCGTGTGCATATTCATAGAATTCATCAT
* * *
322642 GAGTTGATGAATCACCGTACATGCACTTCGTGTGCATATTCATAGAATTCATCATGAGTTGATGA
66 GAGTTGATGAATCACCGTACAAGCACTTCGTGTGCATATTAACAGAATTCATCATGAGTTGATGA
*
322707 ATCACTGTACAAGCACCTTGTGTGCAAATCCATGG
131 ATCACTGTACAAGCACCTTGTGTGCAAATCCATGA
* * * *
322742 AATCCATCATGAGTTGATGAATCACCGTACA-AGCAATTCATGTGCATATTCATGGAATTCATCA
1 AATTCATCATGAGTTGATGAATCACCGTACAGA-CACTTCGTGTGCATATTCATAGAATTCATCA
322806 TGAGTTGATGAATCACCGTACA
65 TGAGTTGATGAATCACCGTACA
322828 GACGCTATAT
Statistics
Matches: 230, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
164 5 0.02
165 225 0.98
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (165 bp):
AATTCATCATGAGTTGATGAATCACCGTACAGACACTTCGTGTGCATATTCATAGAATTCATCAT
GAGTTGATGAATCACCGTACAAGCACTTCGTGTGCATATTAACAGAATTCATCATGAGTTGATGA
ATCACTGTACAAGCACCTTGTGTGCAAATCCATGA
Found at i:329270 original size:55 final size:55
Alignment explanation
Indices: 329210--329836 Score: 661
Period size: 55 Copynumber: 11.4 Consensus size: 55
329200 GCATATTAAC
* *
329210 GAAATTCATCATGATTTGATGAATCACCGTATAGGCACCTT-GTGTGCAAATCCAT
1 GAAATTCATCATGAGTTGATGAATCACCGTACAGGCA-CTTCGTGTGCAAATCCAT
* * * * *
329265 GAAATTCATCATGAGTTAATGTATTACTGTACAGGCACTTCGTGTGCATATTCACA-
1 GAAATTCATCATGAGTTGATGAATCACCGTACAGGCACTTCGTGTGCA-AATC-CAT
* * * * * *
329321 G-AATTCATCATGAGTTGATGAATCACCTTACAAGCACTTCATATGCATATTCAT
1 GAAATTCATCATGAGTTGATGAATCACCGTACAGGCACTTCGTGTGCAAATCCAT
* * *
329375 GGAATTCATCATGAGTTGATGAATCACCGTATAGGTACCTT-GTGTGCAAATCCAT
1 GAAATTCATCATGAGTTGATGAATCACCGTACAGGCA-CTTCGTGTGCAAATCCAT
* * *
329430 GAAATTCATCATGAGTTAATGAATCACCGTACAGGCACTTCGTGTGCATATTCAT
1 GAAATTCATCATGAGTTGATGAATCACCGTACAGGCACTTCGTGTGCAAATCCAT
* * * * * *
329485 -AGAATTCATCATGAGTTGATTAATCATCGTACAAGCACTTCGTATGCATATACAT
1 GA-AATTCATCATGAGTTGATGAATCACCGTACAGGCACTTCGTGTGCAAATCCAT
* * * * *
329540 GGAATTCATCATGAGTTGATGAATCACTGTACAAGCACTTCGTGTGCATATTAACA-
1 GAAATTCATCATGAGTTGATGAATCACCGTACAGGCACTTCGTGTGCA-AAT-CCAT
*
329596 G-AATTCATCATGAGTTGATGAATCACCGTATAGGCACCTT-GTGTGCAAATCCAT
1 GAAATTCATCATGAGTTGATGAATCACCGTACAGGCA-CTTCGTGTGCAAATCCAT
* * *
329650 GAAATTCATCATGAGTTAATGAATCACCGTACAGTCACTTCGTGTGCATATTCACA-
1 GAAATTCATCATGAGTTGATGAATCACCGTACAGGCACTTCGTGTGCA-AATC-CAT
* *
329706 G-AATTCATCTTGAGTTGATGAATCACCGTACAAGCACCTT-GTGTGCAAATCCAT
1 GAAATTCATCATGAGTTGATGAATCACCGTACAGGCA-CTTCGTGTGCAAATCCAT
* * * ** *
329760 GGAATTCATCATGAGTTGATGAATCACCGTACATGCACTAT-ATGTGC-AGCCCAC
1 GAAATTCATCATGAGTTGATGAATCACCGTACAGGCACT-TCGTGTGCAAATCCAT
*
329814 G-AATTCATCACGAGTTGATGAAT
1 GAAATTCATCATGAGTTGATGAAT
329837 TCCCATATAG
Statistics
Matches: 485, Mismatches: 66, Indels: 44
0.82 0.11 0.07
Matches are distributed among these distances:
53 27 0.06
54 26 0.05
55 406 0.84
56 19 0.04
57 7 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (55 bp):
GAAATTCATCATGAGTTGATGAATCACCGTACAGGCACTTCGTGTGCAAATCCAT
Found at i:329385 original size:165 final size:163
Alignment explanation
Indices: 329212--329836 Score: 794
Period size: 165 Copynumber: 3.8 Consensus size: 163
329202 ATATTAACGA
* * *
329212 AATTCATCATGATTTGATGAATCACCGTATAGGCACCTTGTGTGCAAATCCATGAAATTCATCAT
1 AATTCATCATGAGTTGATGAATCACCGTACAAGCACCTTGTGTGCAAATCCATGAAATTCATCAT
* * *
329277 GAGTTAATGTATTACTGTACAGGCACTTCGTGTGCATATTCACAGAATTCATCATGAGTTGATGA
66 GAGTTAATGAATCACCGTACAGGCACTT-GTGTGCA-ATTCACAGAATTCATCATGAGTTGATGA
* *
329342 ATCACCTTACAAGCACTTCATATGCATATTCATGG
129 ATCACCGTACAAGCACTTCGTATGCATATTCATGG
* * *
329377 AATTCATCATGAGTTGATGAATCACCGTATAGGTACCTTGTGTGCAAATCCATGAAATTCATCAT
1 AATTCATCATGAGTTGATGAATCACCGTACAAGCACCTTGTGTGCAAATCCATGAAATTCATCAT
* *
329442 GAGTTAATGAATCACCGTACAGGCACTTCGTGTGCATATTCATAGAATTCATCATGAGTTGATTA
66 GAGTTAATGAATCACCGTACAGGCACTT-GTGTGCA-ATTCACAGAATTCATCATGAGTTGATGA
* *
329507 ATCATCGTACAAGCACTTCGTATGCATATACATGG
129 ATCACCGTACAAGCACTTCGTATGCATATTCATGG
* * *
329542 AATTCATCATGAGTTGATGAATCACTGTACAAGCA-CTTCGTGTGCATATTAACA-G-AATTCAT
1 AATTCATCATGAGTTGATGAATCACCGTACAAGCACCTT-GTGTGCA-AAT-CCATGAAATTCAT
* * * *
329604 CATGAGTTGATGAATCACCGTATAGGCACCTTGTGTGCAAATC-CATGAAATTCATCATGAGTTA
63 CATGAGTTAATGAATCACCGTACAGGCA-CTTGTGTGCAATTCACA-G-AATTCATCATGAGTTG
* **
329668 ATGAATCACCGTAC-AGTCACTTCGTGTGCATATTCACAG
125 ATGAATCACCGTACAAG-CACTTCGTATGCATATTCATGG
* *
329707 AATTCATCTTGAGTTGATGAATCACCGTACAAGCACCTTGTGTGCAAATCCATGGAATTCATCAT
1 AATTCATCATGAGTTGATGAATCACCGTACAAGCACCTTGTGTGCAAATCCATGAAATTCATCAT
* * * *** *
329772 GAGTTGATGAATCACCGTACATGCACTATATGTGCAGCCCAC-GAATTCATCACGAGTTGATGAA
66 GAGTTAATGAATCACCGTACAGGCACT-TGTGTGCAATTCACAGAATTCATCATGAGTTGATGAA
329836 T
130 T
329837 TCCCATATAG
Statistics
Matches: 408, Mismatches: 40, Indels: 26
0.86 0.08 0.05
Matches are distributed among these distances:
163 23 0.06
164 15 0.04
165 358 0.88
166 10 0.02
167 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (163 bp):
AATTCATCATGAGTTGATGAATCACCGTACAAGCACCTTGTGTGCAAATCCATGAAATTCATCAT
GAGTTAATGAATCACCGTACAGGCACTTGTGTGCAATTCACAGAATTCATCATGAGTTGATGAAT
CACCGTACAAGCACTTCGTATGCATATTCATGG
Found at i:329806 original size:110 final size:110
Alignment explanation
Indices: 329212--329836 Score: 746
Period size: 110 Copynumber: 5.7 Consensus size: 110
329202 ATATTAACGA
* * * *
329212 AATTCATCATGATTTGATGAATCACCGTATAGGCACCTT-GTGTGCA-AATC-CATGAAATTCAT
1 AATTCATCATGAGTTGATGAATCACCGTACAAGCA-CTTCGTGTGCATATTCACA-G-AATTCAT
* * * * * * **
329274 CATGAGTTAATGTATTACTGTACAGGCA-CTTCGTGTGCATATTCACAG
63 CATGAGTTGATGAATCACCGTACAGGCACCTT-GTGTGCAAATCCATGG
* * * **
329322 AATTCATCATGAGTTGATGAATCACCTTACAAGCACTTCATATGCATATTCATGGAATTCATCAT
1 AATTCATCATGAGTTGATGAATCACCGTACAAGCACTTCGTGTGCATATTCACAGAATTCATCAT
* * *
329387 GAGTTGATGAATCACCGTATAGGTACCTTGTGTGCAAATCCATGA
66 GAGTTGATGAATCACCGTACAGGCACCTTGTGTGCAAATCCATGG
* * *
329432 AATTCATCATGAGTTAATGAATCACCGTACAGGCACTTCGTGTGCATATTCATAGAATTCATCAT
1 AATTCATCATGAGTTGATGAATCACCGTACAAGCACTTCGTGTGCATATTCACAGAATTCATCAT
* * * * * *
329497 GAGTTGATTAATCATCGTACAAGCA-CTTCGTATGCATATACATGG
66 GAGTTGATGAATCACCGTACAGGCACCTT-GTGTGCAAATCCATGG
* *
329542 AATTCATCATGAGTTGATGAATCACTGTACAAGCACTTCGTGTGCATATTAACAGAATTCATCAT
1 AATTCATCATGAGTTGATGAATCACCGTACAAGCACTTCGTGTGCATATTCACAGAATTCATCAT
* *
329607 GAGTTGATGAATCACCGTATAGGCACCTTGTGTGCAAATCCATGA
66 GAGTTGATGAATCACCGTACAGGCACCTTGTGTGCAAATCCATGG
* *
329652 AATTCATCATGAGTTAATGAATCACCGTAC-AGTCACTTCGTGTGCATATTCACAGAATTCATCT
1 AATTCATCATGAGTTGATGAATCACCGTACAAG-CACTTCGTGTGCATATTCACAGAATTCATCA
*
329716 TGAGTTGATGAATCACCGTACAAGCACCTTGTGTGCAAATCCATGG
65 TGAGTTGATGAATCACCGTACAGGCACCTTGTGTGCAAATCCATGG
* * ***
329762 AATTCATCATGAGTTGATGAATCACCGTACATGCACTAT-ATGTGCA-GCCCAC-GAATTCATCA
1 AATTCATCATGAGTTGATGAATCACCGTACAAGCACT-TCGTGTGCATATTCACAGAATTCATCA
*
329824 CGAGTTGATGAAT
65 TGAGTTGATGAAT
329837 TCCCATATAG
Statistics
Matches: 443, Mismatches: 63, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
108 21 0.05
109 11 0.02
110 399 0.90
111 12 0.03
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (110 bp):
AATTCATCATGAGTTGATGAATCACCGTACAAGCACTTCGTGTGCATATTCACAGAATTCATCAT
GAGTTGATGAATCACCGTACAGGCACCTTGTGTGCAAATCCATGG
Found at i:330507 original size:54 final size:54
Alignment explanation
Indices: 330411--330513 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 54
330401 AAATACAGTT
* * *
330411 GTTCATCAACATATGATGAATTCCGTGGGCTGTACACTTAGTGCCTATACGGCC
1 GTTCATCAACATATGATGAATTCCGTGAGCTGCACACATAGTGCCTATACGGCC
* * * *
330465 GTTCATCAATATATGATGAATTTCGTGAGTTGCAGACATAGTGCCTATA
1 GTTCATCAACATATGATGAATTCCGTGAGCTGCACACATAGTGCCTATA
330514 GTACACTTAG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (54 bp):
GTTCATCAACATATGATGAATTCCGTGAGCTGCACACATAGTGCCTATACGGCC
Found at i:331006 original size:95 final size:91
Alignment explanation
Indices: 330900--331077 Score: 239
Period size: 95 Copynumber: 1.9 Consensus size: 91
330890 CTCTCTTTTA
* * *
330900 GTATCGATACCATTTCAACATTCCAGAATCCATGGTATTGATACCTTTCTCTTAGTATCGATACT
1 GTATCGATACCATTTCAACATTCCAGAATCAATGGTATCGATACCTTTCTCATAGTATCGATAC-
330965 CATACACTATAGTACCGATACTCCATTATG
65 C-TACA-T-TAGTACCGATACTCCATTATG
* ** **
330995 GTATCGTTACCATTTCTGCATTCTGGAATCAATGGTATCGATACCTTTCTCATAGTATCGATACC
1 GTATCGATACCATTTCAACATTCCAGAATCAATGGTATCGATACCTTTCTCATAGTATCGATACC
*
331060 TACATTAGTATCGATACT
66 TACATTAGTACCGATACT
331078 AATTGTTTCA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
91 12 0.16
92 1 0.01
93 4 0.05
94 1 0.01
95 56 0.76
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (91 bp):
GTATCGATACCATTTCAACATTCCAGAATCAATGGTATCGATACCTTTCTCATAGTATCGATACC
TACATTAGTACCGATACTCCATTATG
Found at i:337161 original size:54 final size:54
Alignment explanation
Indices: 337111--337539 Score: 456
Period size: 54 Copynumber: 8.1 Consensus size: 54
337101 TGTAGTGCGA
* * * *
337111 ATACGGTTGTTCATCAACATATGAGGAATTCCGTAGGTTGCACACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCCT
* * * * *
337165 CTATGGTCATTCATCAACATATAATGAA-T-T-TGGGTTGCACACATAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCCT
* * * * * *
337216 ATATGGTCGTTCATTATCACATGATGAATTCAGTGGGTTGCACACTTAGTGTCT
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCCT
* * * * * *
337270 ATATGATCGTTCATCATCATATAATGAATT-TGTGGGTTGCACACATAGT--AT
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCCT
* *
337321 ATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTTGTACACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCCT
*** * * * *
337375 ATACAACCGTTCATCATCATATGATGAATTATGTGGGTTGCACACATAGTTCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCCT
* * *
337429 ATACGGTCGTTCATCAATATATGATAAATTCTGTGGGTTGTACACTTAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCCT
* * * * * **
337483 ATATGGTCATTCATCAACATATGATAAATTCCGTGAGTTGCACACACAGTGCCT
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCCT
337537 ATA
1 ATA
337540 GTACACTTAG
Statistics
Matches: 311, Mismatches: 58, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
51 68 0.22
52 18 0.06
53 18 0.06
54 207 0.67
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (54 bp):
ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCCT
Found at i:337465 original size:108 final size:107
Alignment explanation
Indices: 337111--337539 Score: 515
Period size: 105 Copynumber: 4.0 Consensus size: 107
337101 TGTAGTGCGA
* * * * * *
337111 ATACGGTTGTTCATCAACATATGAGGAATTCCGTAGGTTGCACACTTAGTGCCTCTATGGTCATT
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCCTATATGATCATT
337176 CATCAACATATAATGAA-TT-TGGGTTGCACACATAGTGCCT
66 CATCAACATATAATGAATTTGTGGGTTGCACACATAGTGCCT
* * * * * * *
337216 ATATGGTCGTTCATTATCACATGATGAATTCAGTGGGTTGCACACTTAGTGTCTATATGATCGTT
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCCTATATGATCATT
* *
337281 CATCATCATATAATGAATTTGTGGGTTGCACACATAGT--AT
66 CATCAACATATAATGAATTTGTGGGTTGCACACATAGTGCCT
* * ** * *
337321 ATACGGTCGTTCATCAACATATGATGAATTTTGTGGGTTGTACACTTAGTGCCTATACAACCGTT
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCCTATATGATCATT
* * *
337386 CATCATCATATGATGAATTATGTGGGTTGCACACATAGTTCCT
66 CATCAACATATAATGAATT-TGTGGGTTGCACACATAGTGCCT
* * * *
337429 ATACGGTCGTTCATCAATATATGATAAATTCTGTGGGTTGTACACTTAGTGCCTATATGGTCATT
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCCTATATGATCATT
* * * * *
337494 CATCAACATATGATAAATTCCGTGAGTTGCACACACAGTGCCT
66 CATCAACATATAATGAATT-TGTGGGTTGCACACATAGTGCCT
337537 ATA
1 ATA
337540 GTACACTTAG
Statistics
Matches: 277, Mismatches: 42, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
105 142 0.51
106 21 0.08
107 17 0.06
108 97 0.35
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (107 bp):
ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGCCTATATGATCATT
CATCAACATATAATGAATTTGTGGGTTGCACACATAGTGCCT
Found at i:346186 original size:56 final size:55
Alignment explanation
Indices: 346095--346240 Score: 220
Period size: 56 Copynumber: 2.6 Consensus size: 55
346085 ATGGTGATTA
* * *
346095 CCGTATGGGCACCTTGTGTGCAAAAACTAATAAATTCATAATGAGTTTATGAATTT
1 CCGTAT-GGCACTTTATGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTT
346151 CCGTATGAGCACTTTATGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTT
1 CCGTATG-GCACTTTATGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTT
* *
346207 TCGTATGGACACTTTATGTGAAAAAACTAAGAAA
1 CCGTATGG-CACTTTATGTGCAAAAACTAAGAAA
346241 GTATAAGAAT
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
55 2 0.02
56 81 0.98
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (55 bp):
CCGTATGGCACTTTATGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTT
Found at i:354020 original size:56 final size:56
Alignment explanation
Indices: 353931--354134 Score: 327
Period size: 56 Copynumber: 3.6 Consensus size: 56
353921 ATGGTGATTA
* *
353931 CCGTATGGGCACCTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTT
1 CCGTATGGGCACTTTATGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTT
**
353987 CTTTATGGGCACTTTATGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTT
1 CCGTATGGGCACTTTATGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTT
* *
354043 CCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAACGAGTTTATGAATTT
1 CCGTATGGGCACTTTATGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTT
* * *
354099 CCGTATGGACACTTTATGTGTAAAAACTAGGAAATT
1 CCGTATGGGCACTTTATGTGCAAAAACTAAGAAATT
354135 ATATGAATTT
Statistics
Matches: 136, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 136 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (56 bp):
CCGTATGGGCACTTTATGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATTT
Found at i:359203 original size:2 final size:2
Alignment explanation
Indices: 359196--359228 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
359186 TAAATTTACT
359196 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
359229 GTTTTCTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:360893 original size:12 final size:12
Alignment explanation
Indices: 360876--360900 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
360866 ATTTCAACAT
360876 ATAATTTCGATA
1 ATAATTTCGATA
360888 ATAATTTCGATA
1 ATAATTTCGATA
360900 A
1 A
360901 GACTCTATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATAATTTCGATA
Found at i:361619 original size:16 final size:16
Alignment explanation
Indices: 361594--361624 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
361584 AATATAAAAA
*
361594 ATTTTTAAAAAAATCT
1 ATTTTAAAAAAAATCT
361610 ATTTTAAAAAAAATC
1 ATTTTAAAAAAAATC
361625 ATCCCAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTTTAAAAAAAATCT
Found at i:361685 original size:21 final size:21
Alignment explanation
Indices: 361645--361684 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
361635 ATAAAAATAT
361645 AAAATTTGTTTATATATTTTA
1 AAAATTTGTTTATATATTTTA
361666 AAAATATT-TTTATA-ATTTT
1 AAAAT-TTGTTTATATATTTT
361685 TTAAGTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 11 0.61
22 2 0.11
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
AAAATTTGTTTATATATTTTA
Found at i:362239 original size:19 final size:19
Alignment explanation
Indices: 362215--362257 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
362205 CTTAATTGTG
*
362215 AAATTTAAAATTTAAACTA
1 AAATTTAAAAATTAAACTA
* *
362234 AAATTTAAAAATTCAATTA
1 AAATTTAAAAATTAAACTA
362253 AAATT
1 AAATT
362258 AATTACCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATTTAAAAATTAAACTA
Found at i:362359 original size:21 final size:19
Alignment explanation
Indices: 362319--362362 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
362309 TGCAAAAAAA
*
362319 AAAAAATATGTAAAAGAAT
1 AAAAAATATATAAAAGAAT
*
362338 AAAAAATGATATAATAATAAT
1 AAAAAAT-ATATAA-AAGAAT
362359 AAAA
1 AAAA
362363 TAAATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (19 bp):
AAAAAATATATAAAAGAAT
Found at i:362419 original size:17 final size:17
Alignment explanation
Indices: 362399--362446 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
362389 GTAGAAGGAA
362399 AAATAATAAAAATAAAG
1 AAATAATAAAAATAAAG
* *
362416 AAATAATAATAATAATG
1 AAATAATAAAAATAAAG
362433 AAATAA-AAAAATAA
1 AAATAATAAAAATAA
362447 TAAAGGGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (17 bp):
AAATAATAAAAATAAAG
Found at i:362444 original size:25 final size:23
Alignment explanation
Indices: 362400--362449 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 23
362390 TAGAAGGAAA
*
362400 AATAATAAAAATAAAGAAATAAT
1 AATAATAAAAATAAAAAAATAAT
362423 AATAATAATGAAATAAAAAAATAAT
1 AATAATAA--AAATAAAAAAATAAT
362448 AA
1 AA
362450 AGGGTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 8 0.33
25 16 0.67
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (23 bp):
AATAATAAAAATAAAAAAATAAT
Found at i:363012 original size:37 final size:37
Alignment explanation
Indices: 362971--363046 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
362961 GAACTGCTCG
* * *
362971 TCTCACCCTCAAGACCTTAAATCCAAACCCCAAAACA
1 TCTCACACTCAAAACCCTAAATCCAAACCCCAAAACA
*
363008 TCTCACACTCAAAACCCTAAATCTAAACCCCAAAACA
1 TCTCACACTCAAAACCCTAAATCCAAACCCCAAAACA
363045 TC
1 TC
363047 AAAATCAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.42, C:0.39, G:0.01, T:0.17
Consensus pattern (37 bp):
TCTCACACTCAAAACCCTAAATCCAAACCCCAAAACA
Found at i:363041 original size:21 final size:21
Alignment explanation
Indices: 363017--363060 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
363007 ATCTCACACT
*
363017 CAAAAC-CCTAAATCTAAACCC
1 CAAAACACCAAAATC-AAACCC
*
363038 CAAAACATCAAAATCAAACCC
1 CAAAACACCAAAATCAAACCC
363059 CA
1 CA
363061 TCGACGTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.52, C:0.36, G:0.00, T:0.11
Consensus pattern (21 bp):
CAAAACACCAAAATCAAACCC
Found at i:363778 original size:36 final size:37
Alignment explanation
Indices: 363719--363795 Score: 113
Period size: 36 Copynumber: 2.1 Consensus size: 37
363709 GTTATATATA
363719 AAAAATATTTCCATAAACTATATACTATATATATTTTC
1 AAAAATATTTCCATAAACTATATACTATATAT-TTTTC
* *
363757 AAAAATATTT-TA-AAACTATATATTATATATTTTTC
1 AAAAATATTTCCATAAACTATATACTATATATTTTTC
363792 AAAA
1 AAAA
363796 TGTTTTCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 9 0.24
36 17 0.46
37 1 0.03
38 10 0.27
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (37 bp):
AAAAATATTTCCATAAACTATATACTATATATTTTTC
Found at i:363873 original size:38 final size:37
Alignment explanation
Indices: 363798--363916 Score: 136
Period size: 38 Copynumber: 3.2 Consensus size: 37
363788 TTTCAAAATG
** *
363798 TTTTCAAAATGTTTTA-AAACTATATATTATATATATA
1 TTTTCAAAATCATTTACAAACTCTATA-TATATATATA
363835 TTTTCAAGAATCATTTACAAACTCTATATATATATATA
1 TTTTCAA-AATCATTTACAAACTCTATATATATATATA
* * *
363873 TATTCAAAATCATTTTCAAA-GCTATATA-ATATATA
1 TTTTCAAAATCATTTACAAACTCTATATATATATATA
*
363908 TTTTTAAAA
1 TTTTCAAAA
363917 ATCAATTTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
35 14 0.19
36 7 0.10
37 19 0.26
38 23 0.32
39 9 0.12
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTTCAAAATCATTTACAAACTCTATATATATATATA
Found at i:363905 original size:37 final size:36
Alignment explanation
Indices: 363798--363961 Score: 140
Period size: 37 Copynumber: 4.5 Consensus size: 36
363788 TTTCAAAATG
* *
363798 TTTTCAAAAT-GTTTTAAAACTATATATTATATATATA
1 TTTTCAAAATCATTTTCAAACTATATA--ATATATATA
* *
363835 TTTTCAAGAATCATTTACAAACTCTATATATATATATA
1 TTTTCAA-AATCATTTTCAAACTATATA-ATATATATA
*
363873 TATTCAAAATCATTTTCAAAGCTATATAATATATAT-
1 TTTTCAAAATCATTTTCAAA-CTATATAATATATATA
* * *
363909 TTTTAAAAATCAATTTTTAAAC-AGTAT-AT-TATATG
1 TTTTCAAAATC-ATTTTCAAACTA-TATAATATATATA
*
363944 TTTTAAAAATTCATTTTC
1 TTTTCAAAA-TCATTTTC
363962 TAAAAAATTA
Statistics
Matches: 109, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
34 5 0.05
35 17 0.16
36 15 0.14
37 35 0.32
38 25 0.23
39 12 0.11
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (36 bp):
TTTTCAAAATCATTTTCAAACTATATAATATATATA
Found at i:364923 original size:85 final size:84
Alignment explanation
Indices: 364807--365276 Score: 634
Period size: 85 Copynumber: 5.5 Consensus size: 84
364797 CTCGACAGCT
* *
364807 TTTTGTTGACAGATAGTCCTTCTCGCCTTGAGTTATGCTGTAAATTTGACATGCCCTTGAGCTGA
1 TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCCTTGAGCTGA
* *
364872 ATGGAATCGAACTTGAAGG
66 ATGTAATCGAACTCGAAGG
* * * * *
364891 TATTTTTTGACAGATAACCCTTCTCACCTTGAGTTATGTTGCAAATTTGATATGCCCTTGAGCTG
1 T-TTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCCTTGAGCTG
*
364956 AATGTAATCGAACTCAAAGG
65 AATGTAATCGAACTCGAAGG
* *
364976 TCTTTGTTGACAGATAGCCCTTCTCACCTTGAGTTATGTTGTAAATTTGATATGCCCTTGAGCTG
1 T-TTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCCTTGAGCTG
*
365041 AATGTAATCGAACTCGAAAG
65 AATGTAATCGAACTCGAAGG
* * * *
365061 TCTTTGTTAACAGATAACCCTTCTCGCCTTGAGTTATGCTATAAATTTGATATGTCCTTGAGCTG
1 T-TTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCCTTGAGCTG
* *
365126 AATGTAATCAAACTCAAAGG
65 AATGTAATCGAACTCGAAGG
* * *
365146 TTTTGGTTGACAGATAGCCCTTCTTGCCTTGAGCTATGCTGTAAATTTGATATGTCCTTGAGCTG
1 TTTT-GTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCCTTGAGCTG
* *
365211 AGTGTAATCAAACTCGAAGG
65 AATGTAATCGAACTCGAAGG
* * * * *
365231 TTTTTGTAGGCAGATAGCCCTTTTCGCCTTGAGCTATGTTGTAAAT
1 -TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAAT
365277 AGTTCCTTTA
Statistics
Matches: 346, Mismatches: 37, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
84 4 0.01
85 338 0.98
86 4 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (84 bp):
TTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCCTTGAGCTGA
ATGTAATCGAACTCGAAGG
Found at i:371766 original size:13 final size:14
Alignment explanation
Indices: 371734--371763 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
371724 ATAAGCACTT
371734 AAAGAAGAAAACAA
1 AAAGAAGAAAACAA
*
371748 AAAGAAGAAAATAA
1 AAAGAAGAAAACAA
371762 AA
1 AA
371764 GAAAAGAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAGAAGAAAACAA
Found at i:375006 original size:22 final size:22
Alignment explanation
Indices: 374977--375036 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
374967 TAGATTGTAA
374977 AATAAAAAATAAATATGAAAAAG
1 AATAAAAAATAAATAT-AAAAAG
* * *
375000 AATAAAAAATTAATATAATAAT
1 AATAAAAAATAAATATAAAAAG
375022 AATAAAAAATAAATA
1 AATAAAAAATAAATA
375037 AAATTGAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 18 0.55
23 15 0.45
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (22 bp):
AATAAAAAATAAATATAAAAAG
Found at i:375067 original size:9 final size:9
Alignment explanation
Indices: 375053--375090 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
375043 AGTAAACAAC
375053 AAAATAATA
1 AAAATAATA
375062 AAAATAA-A
1 AAAATAATA
375070 TAAAATAATA
1 -AAAATAATA
*
375080 ATAATAATA
1 AAAATAATA
375089 AA
1 AA
375091 TGAAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 1 0.04
9 23 0.92
10 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATAATA
Found at i:375079 original size:21 final size:21
Alignment explanation
Indices: 375055--375098 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
375045 TAAACAACAA
375055 AATAATAAAAATAAATAAAAT
1 AATAATAAAAATAAATAAAAT
* *
375076 AATAATAATAATAAATGAAAT
1 AATAATAAAAATAAATAAAAT
375097 AA
1 AA
375099 AAAATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (21 bp):
AATAATAAAAATAAATAAAAT
Found at i:376743 original size:73 final size:70
Alignment explanation
Indices: 376334--376856 Score: 324
Period size: 73 Copynumber: 7.6 Consensus size: 70
376324 ATAAAAAATA
* * * *
376334 TTTTCATAAACTATATAATACATATATTTTC-AAAATGTTTTCAAAACTATATATTATATAGTTT
1 TTTTCAAAAACTATAT-ATA-TTATATTTTCAAAAATATTTTCAAAA-GATATA-TATATA-TTT
376398 TCAAAAAT-G
61 TCAAAAATCG
* * * *
376407 TTTT--AAAACTATATTTA-TATAGTTTC-AAAATGTTTTCAAAA-CTATATTATATAGTTTTC-
1 TTTTCAAAAACTATATATATTATATTTTCAAAAATATTTTCAAAAGATATA-TATATA-TTTTCA
376466 AAAAT--
64 AAAATCG
* * * *
376471 TTTT-TAAAA-TATATATA-TA-GTTTTCAAAAATGTTTT-AAAA-CTATATAT-TAGTTTTCAA
1 TTTTCAAAAACTATATATATTATATTTTCAAAAATATTTTCAAAAGATATATATATA-TTTTCAA
376529 AAAT-G
65 AAATCG
* * * *
376534 TTTT---AAA-TATATATA-TATGTTTTCAAAAATGTTTTCAAAACATATATTATATAAGTTTC-
1 TTTTCAAAAACTATATATATTATATTTTCAAAAATATTTTCAAAAGATATA-TATAT-ATTTTCA
376593 AAAAT-G
64 AAAATCG
* * * *
376599 ATTTC-AAAAC--TATATATTATAAGTTTT-TAAAATGTTTTCAAAA-AAATATTATATATTTTC
1 TTTTCAAAAACTATATATATTAT-A-TTTTCAAAAATATTTTCAAAAGATATA-TATATATTTTC
376659 -AAAAT-G
63 AAAAATCG
* ** *
376665 TTTTCAAAAACTATATATTATGTATATTTTCAAAAATAATTTGCAAACTATATATATATATATTC
1 TTTTCAAAAACTATATA-TAT-TATATTTTCAAAAAT-ATTTTCAAAAGATATATATATATTTTC
*
376730 AAAAATCA
63 AAAAATCG
* * * *
376738 TTTTC-AAAGCTATATAATATATATATTTTTAAAAATCGATTTTTAAAAGA-ATATTATATGTTT
1 TTTTCAAAAACTATAT-ATAT-TATATTTTCAAAAAT--ATTTTCAAAAGATATA-TATATATTT
376801 TCAAAAATCG
61 TCAAAAATCG
*
376811 TTTTCTAAAAAAT-TATATATTATATTTTTCAAAAATATTTTCAAAA
1 TTTTC-AAAAACTATATATATTATA-TTTTCAAAAATATTTTCAAAA
376857 TTATACTATA
Statistics
Matches: 381, Mismatches: 37, Indels: 66
0.79 0.08 0.14
Matches are distributed among these distances:
61 21 0.06
62 25 0.07
63 21 0.06
64 27 0.07
65 21 0.06
66 43 0.11
67 22 0.06
68 38 0.10
69 12 0.03
70 11 0.03
71 38 0.10
72 42 0.11
73 53 0.14
74 3 0.01
75 4 0.01
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (70 bp):
TTTTCAAAAACTATATATATTATATTTTCAAAAATATTTTCAAAAGATATATATATATTTTCAAA
AATCG
Found at i:376857 original size:34 final size:35
Alignment explanation
Indices: 376327--376861 Score: 466
Period size: 34 Copynumber: 15.6 Consensus size: 35
376317 ATTATATATA
* *
376327 AAAAATATTTTCATAAACTATATAATACATATATTTTC
1 AAAAATGTTTTCA-AAACTATAT-AT-TATATATTTTC
376365 -AAAATGTTTTCAAAACTATATATTATATAGTTTTC
1 AAAAATGTTTTCAAAACTATATATTATATA-TTTTC
*
376400 AAAAATGTTTT-AAAACTATAT-TTATATAGTTTC
1 AAAAATGTTTTCAAAACTATATATTATATATTTTC
376433 -AAAATGTTTTCAAAAC--TATATTATATAGTTTTC
1 AAAAATGTTTTCAAAACTATATATTATATA-TTTTC
* *
376466 -AAAAT-TTTTTAAAA-TATATA-TATA-GTTTTC
1 AAAAATGTTTTCAAAACTATATATTATATATTTTC
*
376496 AAAAATGTTTT-AAAACTATATA-T-TA-GTTTTC
1 AAAAATGTTTTCAAAACTATATATTATATATTTTC
*
376527 AAAAATGTTTT--AAA-TATATA-TATATGTTTTC
1 AAAAATGTTTTCAAAACTATATATTATATATTTTC
*
376558 AAAAATGTTTTCAAAAC-ATATATTATATAAGTTTC
1 AAAAATGTTTTCAAAACTATATATTATAT-ATTTTC
*
376593 -AAAATGATTTCAAAACTATATATTATA-AGTTTT-
1 AAAAATGTTTTCAAAACTATATATTATATA-TTTTC
* *
376626 TAAAATGTTTTCAAAA--AAATATTATATATTTTC
1 AAAAATGTTTTCAAAACTATATATTATATATTTTC
376659 -AAAATGTTTTCAAAAACTATATATTATGTATATTTTC
1 AAAAATGTTTTC-AAAACTATATATTA--TATATTTTC
* * *
376696 AAAAATAATTTGC-AAACTATATA-TATATATATTC
1 AAAAAT-GTTTTCAAAACTATATATTATATATTTTC
* * *
376730 AAAAATCATTTTCAAAGCTATATAATATATATATTTTT
1 AAAAAT-GTTTTCAAAACTATAT-AT-TATATATTTTC
* * *
376768 AAAAATCGATTTTTAAAA-GA-ATATTATATGTTTTC
1 AAAAAT-G-TTTTCAAAACTATATATTATATATTTTC
*
376803 AAAAATCGTTTTCTAAAAAATTATATATTATAT-TTTTC
1 AAAAAT-GTTTTC---AAAACTATATATTATATATTTTC
* *
376841 AAAAATATTTTCAAAATTATA
1 AAAAATGTTTTCAAAACTATA
376862 CTATATTAAT
Statistics
Matches: 428, Mismatches: 30, Indels: 82
0.79 0.06 0.15
Matches are distributed among these distances:
29 7 0.02
30 10 0.02
31 48 0.11
32 64 0.15
33 36 0.08
34 81 0.19
35 63 0.15
36 24 0.06
37 41 0.10
38 34 0.08
39 20 0.05
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (35 bp):
AAAAATGTTTTCAAAACTATATATTATATATTTTC
Found at i:376867 original size:39 final size:39
Alignment explanation
Indices: 376644--376856 Score: 124
Period size: 38 Copynumber: 5.8 Consensus size: 39
376634 TTTCAAAAAA
* *
376644 ATATTATATATTTTC-AAAAT-GTTTTC--AAAAACTAT
1 ATATTATATGTTTTCAAAAATCATTTTCTAAAAAACTAT
* * *
376679 ATATTATGTATATTTTCAAAAATAATTTGC----AAACTAT
1 ATATTA--TATGTTTTCAAAAATCATTTTCTAAAAAACTAT
* * *
376716 ATA-TATATATATTCAAAAATCATTTTC---AAAGCTAT
1 ATATTATATGTTTTCAAAAATCATTTTCTAAAAAACTAT
* * *
376751 ATAATATATATATTTTTAAAAATCGATTTT-T--AAAA-GA-
1 AT-AT-TATATGTTTTCAAAAATC-ATTTTCTAAAAAACTAT
* *
376788 ATATTATATGTTTTCAAAAATCGTTTTCTAAAAAATTAT
1 ATATTATATGTTTTCAAAAATCATTTTCTAAAAAACTAT
376827 ATATTATAT-TTTTCAAAAAT-ATTTTC-AAAA
1 ATATTATATGTTTTCAAAAATCATTTTCTAAAA
376857 TTATACTATA
Statistics
Matches: 148, Mismatches: 15, Indels: 29
0.77 0.08 0.15
Matches are distributed among these distances:
34 23 0.16
35 31 0.21
36 9 0.06
37 30 0.20
38 34 0.23
39 21 0.14
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (39 bp):
ATATTATATGTTTTCAAAAATCATTTTCTAAAAAACTAT
Found at i:376877 original size:2 final size:2
Alignment explanation
Indices: 376858--376896 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
376848 TTTTCAAAAT
376858 TA TA CTA TA T- TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
376897 ATGAAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 30 0.88
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:378055 original size:3 final size:3
Alignment explanation
Indices: 378041--378091 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
378031 CCGAGCGATT
* * *
378041 TTA TTT TTA TTA TTA TTA TCT- TTA TTA TTA TCA TTTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA -TTA TTA TTA TTA
378087 TTA TT
1 TTA TT
378092 CATATAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 1 0.03
3 35 0.90
4 3 0.08
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:378106 original size:22 final size:19
Alignment explanation
Indices: 378038--378107 Score: 50
Period size: 21 Copynumber: 3.4 Consensus size: 19
378028 TGTCCGAGCG
* * *
378038 ATTTTATTTTTATTATTATT
1 ATTTTATTATTATCATTA-A
*
378058 ATCTTTATTATTATCATTTA
1 AT-TTTATTATTATCATTAA
*
378078 ATATTATTATTATTCATATAAA
1 ATTTTATTATTA-TCAT-T-AA
378100 ATTTTATT
1 ATTTTATT
378108 TATATTTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
19 9 0.23
20 8 0.21
21 14 0.36
22 8 0.21
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTATTATTATCATTAA
Found at i:381077 original size:13 final size:13
Alignment explanation
Indices: 381059--381083 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
381049 GAACAAGAAG
381059 AATAAAGAAAAAA
1 AATAAAGAAAAAA
381072 AATAAAGAAAAA
1 AATAAAGAAAAA
381084 TATATTGCCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (13 bp):
AATAAAGAAAAAA
Found at i:387889 original size:18 final size:18
Alignment explanation
Indices: 387866--387912 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
387856 GGGGAGTTTA
387866 TGATTCTATGTGAAAAAT
1 TGATTCTATGTGAAAAAT
387884 TGATTCTATGTGAAAAAT
1 TGATTCTATGTGAAAAAT
*
387902 TGATTATATGT
1 TGATTCTATGT
387913 TCAAATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.43
Consensus pattern (18 bp):
TGATTCTATGTGAAAAAT
Found at i:388066 original size:22 final size:23
Alignment explanation
Indices: 388041--388101 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
388031 TTAGTGCAGA
* *
388041 GGGAATCGATACCTCC-TTGAAG
1 GGGAACCGATACCCCCTTTGAAG
*
388063 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCCTTTGAAG
*
388086 GGGAACCGATTCCCCC
1 GGGAACCGATACCCCC
388102 CACAAGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 13 0.37
23 22 0.63
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (23 bp):
GGGAACCGATACCCCCTTTGAAG
Found at i:388087 original size:23 final size:23
Alignment explanation
Indices: 388057--388101 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
388047 CGATACCTCC
388057 TTGAAGGGGAACCGATTCCCCCT
1 TTGAAGGGGAACCGATTCCCCCT
388080 TTGAAGGGGAACCGATTCCCCC
1 TTGAAGGGGAACCGATTCCCCC
388102 CACAAGGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.20
Consensus pattern (23 bp):
TTGAAGGGGAACCGATTCCCCCT
Found at i:389994 original size:10 final size:10
Alignment explanation
Indices: 389979--390004 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
389969 GGGAGAAATG
389979 TTAAAGTGTT
1 TTAAAGTGTT
389989 TTAAAGTGTT
1 TTAAAGTGTT
389999 TTAAAG
1 TTAAAG
390005 GGGAGAAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (10 bp):
TTAAAGTGTT
Found at i:392510 original size:39 final size:39
Alignment explanation
Indices: 392460--392565 Score: 137
Period size: 39 Copynumber: 2.7 Consensus size: 39
392450 ATTAAAAAAT
*
392460 AATTTAAAATGTTAATGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
*
392499 AATTTAGAATGTT-ATGGTGGTAA-AATTTAAGAAATTAAG
1 AATTTAGAATGTTAAT-GT-GAAATAATTTAAGAAATTAAG
*
392538 AATTTTGAATGTTAGA-GTGAAATAATTT
1 AATTTAGAATGTTA-ATGTGAAATAATTT
392566 GAAATTTATC
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
38 5 0.09
39 49 0.84
40 3 0.05
41 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
Found at i:410490 original size:22 final size:22
Alignment explanation
Indices: 410424--410492 Score: 102
Period size: 22 Copynumber: 3.0 Consensus size: 22
410414 CATAACATGG
*
410424 TACATAGATGTTTCATACATCGTG
1 TACATAGATGTTTCATACATC--A
410448 TACATAGATGTTTCATACATCA
1 TACATAGATGTTTCATACATCA
*
410470 TACATAGATGTTTTATACATCA
1 TACATAGATGTTTCATACATCA
410492 T
1 T
410493 CTGGAAGACT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
22 22 0.51
24 21 0.49
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (22 bp):
TACATAGATGTTTCATACATCA
Found at i:416869 original size:29 final size:31
Alignment explanation
Indices: 416821--416879 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
416811 AGAAAAATTT
416821 GGGACCATTATGTAATTTTTG-AAAAGTTGG
1 GGGACCATTATGTAATTTTTGAAAAAGTTGG
416851 GGGACCATT-T-TAATATTTTGAAAAAGTTG
1 GGGACCATTATGTAAT-TTTTGAAAAAGTTG
416880 TGAATGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 4 0.15
29 6 0.22
30 17 0.63
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (31 bp):
GGGACCATTATGTAATTTTTGAAAAAGTTGG
Found at i:420514 original size:17 final size:17
Alignment explanation
Indices: 420480--420524 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
420470 CCCTTCCCTT
* *
420480 TCTTT-GAGAGAAATTC
1 TCTTTCGAGAAAAACTC
420496 TCTTTCGAGAAAAACTC
1 TCTTTCGAGAAAAACTC
*
420513 TCGTTCGAGAAA
1 TCTTTCGAGAAA
420525 TAAACACTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (17 bp):
TCTTTCGAGAAAAACTC
Found at i:429544 original size:23 final size:24
Alignment explanation
Indices: 429516--429561 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
429506 GTTTCATGTT
429516 ACATTGA-ATGTTATTAATTCATG
1 ACATTGATATGTTATTAATTCATG
*
429539 ACATTGATTTGTTATTAATTCAT
1 ACATTGATATGTTATTAATTCAT
429562 ATGTCATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.48
Consensus pattern (24 bp):
ACATTGATATGTTATTAATTCATG
Found at i:430169 original size:18 final size:18
Alignment explanation
Indices: 430146--430187 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
430136 ACAATCGCCG
430146 GCCGGCCGGGAAGAGGTC
1 GCCGGCCGGGAAGAGGTC
430164 GCCGGCCGGGAAGAGGTC
1 GCCGGCCGGGAAGAGGTC
*
430182 GTCGGC
1 GCCGGC
430188 GCGCCACACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.29, G:0.50, T:0.07
Consensus pattern (18 bp):
GCCGGCCGGGAAGAGGTC
Found at i:433507 original size:11 final size:12
Alignment explanation
Indices: 433491--433519 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
433481 CATGATATGA
433491 ATTTAAAAT-TT
1 ATTTAAAATGTT
433502 ATTTAAAATGTT
1 ATTTAAAATGTT
433514 ATTTAA
1 ATTTAA
433520 GCCTAGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (12 bp):
ATTTAAAATGTT
Found at i:434906 original size:23 final size:23
Alignment explanation
Indices: 434864--434907 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
434854 TTCGGGACAA
* *
434864 TCTATGTGGTCCTCCGGGATATT
1 TCTATGTAGTCCTCCAGGATATT
*
434887 TCTATGTAGTCCTTCAGGATA
1 TCTATGTAGTCCTCCAGGATA
434908 AATTCTACGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (23 bp):
TCTATGTAGTCCTCCAGGATATT
Found at i:434922 original size:24 final size:24
Alignment explanation
Indices: 434895--434940 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
434885 TTTCTATGTA
*
434895 GTCCTTCAGGATAAATTCTACGCG
1 GTCCTTCAGGACAAATTCTACGCG
**
434919 GTCCTTTGGGACAAATTCTACG
1 GTCCTTCAGGACAAATTCTACG
434941 TGACACTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (24 bp):
GTCCTTCAGGACAAATTCTACGCG
Found at i:441754 original size:22 final size:22
Alignment explanation
Indices: 441729--441787 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
441719 GTTCTACGCG
441729 GTCCTTCGGGACAATCTATGTA
1 GTCCTTCGGGACAATCTATGTA
** * *
441751 GTCCTTCATGACATTTCTATGTG
1 GTCCTTCGGGACA-ATCTATGTA
*
441774 GTCATTCGGGACAA
1 GTCCTTCGGGACAA
441788 ATTCTACGCG
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (22 bp):
GTCCTTCGGGACAATCTATGTA
Found at i:441786 original size:23 final size:23
Alignment explanation
Indices: 441728--441830 Score: 93
Period size: 24 Copynumber: 4.4 Consensus size: 23
441718 GGTTCTACGC
441728 GGTCCTTCGGGACAA-TCTATGT
1 GGTCCTTCGGGACAATTCTATGT
* ** *
441750 AGTCCTTCATGACATTTCTATGT
1 GGTCCTTCGGGACAATTCTATGT
* * *
441773 GGTCATTCGGGACAAATTCTACGC
1 GGTCCTTCGGGAC-AATTCTATGT
*
441797 GGTCCTTCGGGAAAAATTCTATGT
1 GGTCCTTCGGG-ACAATTCTATGT
441821 GG-CTCTTCGG
1 GGTC-CTTCGG
441831 TGTAATTTAT
Statistics
Matches: 62, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
22 11 0.18
23 17 0.27
24 33 0.53
25 1 0.02
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.33
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTATGT
Found at i:450190 original size:40 final size:40
Alignment explanation
Indices: 450146--450235 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 40
450136 CAATAAGCAG
*
450146 TATCGATACTGCT-ATGAGGGTATCGATACTACAAGAACAA
1 TATCGATACTGCTCATG-GGGTATCGATACTACAAGAAAAA
* * * *
450186 TATCGATAATGTTCATGTGGTATCGATACTATAAGAAAAA
1 TATCGATACTGCTCATGGGGTATCGATACTACAAGAAAAA
450226 TATCGATACT
1 TATCGATACT
450236 TCTTTCAAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 40 0.93
41 3 0.07
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (40 bp):
TATCGATACTGCTCATGGGGTATCGATACTACAAGAAAAA
Done.