Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, 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: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 107 of 131
Found at i:19085599 original size:36 final size:35
Alignment explanation
Indices: 19085552--19085621 Score: 113
Period size: 36 Copynumber: 2.0 Consensus size: 35
19085542 TTCATATTAT
19085552 ATTTATTTTTATATTTATATTTAATAAGTATTTAAA
1 ATTTATTTTTATATTTAT-TTTAATAAGTATTTAAA
* *
19085588 ATTTATTTTTATTTTTATTTTTATAAGTATTTAA
1 ATTTATTTTTATATTTATTTTAATAAGTATTTAA
19085622 TGGGTACGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 15 0.47
36 17 0.53
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (35 bp):
ATTTATTTTTATATTTATTTTAATAAGTATTTAAA
Found at i:19087649 original size:21 final size:20
Alignment explanation
Indices: 19087614--19087663 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
19087604 TGATTAGACT
*
19087614 TTTGC-AAAAGTATCAATCCA
1 TTTGCAAAAAGAATC-ATCCA
**
19087634 TTTGCAAAAAGAATCATTTA
1 TTTGCAAAAAGAATCATCCA
19087654 TTTGCAAAAA
1 TTTGCAAAAA
19087664 ATCTACTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (20 bp):
TTTGCAAAAAGAATCATCCA
Found at i:19088838 original size:21 final size:20
Alignment explanation
Indices: 19088804--19088843 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
19088794 AACATGTGGT
*
19088804 AAATAAATAAATACATAATG
1 AAATAAAAAAATACATAATG
19088824 AAATAAAAAAGATACATAAT
1 AAATAAAAAA-ATACATAAT
19088844 TTACGTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (20 bp):
AAATAAAAAAATACATAATG
Found at i:19089741 original size:2 final size:2
Alignment explanation
Indices: 19089734--19089765 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
19089724 GTCCAGCATA
*
19089734 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19089766 TGTGCTTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19097349 original size:22 final size:22
Alignment explanation
Indices: 19097324--19097366 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
19097314 TGTATATTTA
*
19097324 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
19097346 TATTTGTATCCCTAGAATTAA
1 TATTTGTATCCCTAGAATTAA
19097367 TGATTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:19101368 original size:22 final size:22
Alignment explanation
Indices: 19101343--19101386 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19101333 CTGTATATTT
*
19101343 ATATTTGTATATCTAAAATTAA
1 ATATTTGTATACCTAAAATTAA
*
19101365 ATATTTGTATCCCTAAAATTAA
1 ATATTTGTATACCTAAAATTAA
19101387 GTACAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (22 bp):
ATATTTGTATACCTAAAATTAA
Found at i:19101907 original size:25 final size:24
Alignment explanation
Indices: 19101870--19101916 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
19101860 TCCTCCTTTA
*
19101870 AAAGAATTCCAAAAAACCCAAGTC
1 AAAGAATGCCAAAAAACCCAAGTC
*
19101894 AAAGACATGCCAAAAATCCCAAG
1 AAAGA-ATGCCAAAAAACCCAAG
19101917 CCTCATAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.53, C:0.26, G:0.11, T:0.11
Consensus pattern (24 bp):
AAAGAATGCCAAAAAACCCAAGTC
Found at i:19110569 original size:22 final size:23
Alignment explanation
Indices: 19110511--19110571 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
19110501 TTATAAATAT
*
19110511 ATTAATTACTTTAATATATTAAAG
1 ATTAATTA-TTTATTATATTAAAG
19110535 ATT-ATCTATTTATTAT-TTAAA-
1 ATTAAT-TATTTATTATATTAAAG
19110556 ATTAATTATATTATTA
1 ATTAATTAT-TTATTA
19110572 ATGAATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
21 6 0.18
22 13 0.39
23 9 0.27
24 5 0.15
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (23 bp):
ATTAATTATTTATTATATTAAAG
Found at i:19110641 original size:20 final size:20
Alignment explanation
Indices: 19110586--19110648 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 20
19110576 ATATTAAATT
*
19110586 AATTAATAAATTAATTATTTAA
1 AATTAAAAAATT--TTATTTAA
19110608 ATATTATATTAAAATTTTATTTAA
1 A-ATTA-A--AAAATTTTATTTAA
*
19110632 AATTAAAAAATTATATT
1 AATTAAAAAATTTTATT
19110649 AACTTTAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
20 10 0.29
22 2 0.06
23 8 0.23
24 10 0.29
26 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTAAAAAATTTTATTTAA
Found at i:19111111 original size:17 final size:18
Alignment explanation
Indices: 19111085--19111123 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
19111075 CACTTTATTG
19111085 TTTTATATTTT-TA-ATA
1 TTTTATATTTTATACATA
19111101 TTTTAATATTTTATACATA
1 TTTT-ATATTTTATACATA
19111120 TTTT
1 TTTT
19111124 TTAAACATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 2 0.10
19 7 0.35
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTATATTTTATACATA
Found at i:19111149 original size:29 final size:30
Alignment explanation
Indices: 19111092--19111156 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
19111082 TTGTTTTATA
* *
19111092 TTTTT-AATATTTTAATATTTTATACATAT
1 TTTTTAAACATTTTAATATTTCATACATAT
19111121 TTTTTAAACATTTTAAT-TATTCATA-ATAT
1 TTTTTAAACATTTTAATAT-TTCATACATAT
19111150 TTTTTAA
1 TTTTTAA
19111157 TATCAAATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTTAAACATTTTAATATTTCATACATAT
Found at i:19111198 original size:14 final size:16
Alignment explanation
Indices: 19111173--19111204 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19111163 ATACTTAAAA
19111173 TTTTTAATCATA-TTT
1 TTTTTAATCATACTTT
19111188 TTTTTAA-CATACTTT
1 TTTTTAATCATACTTT
19111203 TT
1 TT
19111205 AAAAGCTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTAATCATACTTT
Found at i:19120292 original size:23 final size:23
Alignment explanation
Indices: 19120264--19120412 Score: 82
Period size: 23 Copynumber: 6.4 Consensus size: 23
19120254 TTTTTATTTG
19120264 GTATTATTT-TTATT-TTATGTATT
1 GTATTATTTATTATTATTAT-TA-T
19120287 GTATTATTTATTATTATTATTAT
1 GTATTATTTATTATTATTATTAT
*
19120310 GTATTAATATATATATCT-TTATTTAT
1 GTATT-ATTTAT-TAT-TATTA-TTAT
* * *
19120336 TTATTTATTTATT-TTGTTAATAT
1 GTA-TTATTTATTATTATTATTAT
* *
19120359 TTA-TATGTATT-TTATTTATATAAT
1 GTATTATTTATTATTA-TTAT-T-AT
19120383 -TATATATTTATTA-TATTATTAT
1 GTAT-TATTTATTATTATTATTAT
19120405 -TATTATTT
1 GTATTATTT
19120413 TTTTAAATAT
Statistics
Matches: 104, Mismatches: 8, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
21 14 0.13
22 8 0.08
23 26 0.25
24 22 0.21
25 20 0.19
26 12 0.12
27 2 0.02
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (23 bp):
GTATTATTTATTATTATTATTAT
Found at i:19120296 original size:16 final size:15
Alignment explanation
Indices: 19120268--19120412 Score: 65
Period size: 16 Copynumber: 9.8 Consensus size: 15
19120258 TATTTGGTAT
19120268 TATTT-TTATTTTATG
1 TATTTATTA-TTTATG
19120283 TATTGTATTATTTAT-
1 TATT-TATTATTTATG
19120298 TA-TTATTA-TTATG
1 TATTTATTATTTATG
* * *
19120311 TA-TTAATATATATA
1 TATTTATTATTTATG
* *
19120325 TCTTTATTTATTTATT
1 TATTTA-TTATTTATG
* *
19120341 TATTTATTTTGTTA-A
1 TATTTATTAT-TTATG
* *
19120356 TATTTA-TATGTATTT
1 TATTTATTATTTA-TG
* *
19120371 TATTTATATAATTATA
1 TATTTAT-TATTTATG
19120387 TATTTATTATATTAT-
1 TATTTATTAT-TTATG
19120402 TA-TTATTATTT
1 TATTTATTATTT
19120413 TTTTAAATAT
Statistics
Matches: 101, Mismatches: 17, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
12 4 0.04
13 16 0.16
14 14 0.14
15 28 0.28
16 32 0.32
17 7 0.07
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (15 bp):
TATTTATTATTTATG
Found at i:19120300 original size:3 final size:3
Alignment explanation
Indices: 19120265--19120466 Score: 54
Period size: 3 Copynumber: 66.3 Consensus size: 3
19120255 TTTTATTTGG
* *
19120265 TAT TAT TTT TAT T-T TAT GTAT T-G TAT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * *
19120310 GTAT TAA TA- TAT ATAT CT-T TATT TATT TATT TATT TAT T-T TGT TAA
1 -TAT TAT TAT TAT -TAT -TAT TA-T TA-T TA-T TA-T TAT TAT TAT TAT
*
19120356 TAT T-T ATAT GTAT T-T TAT T-T ATAT AAT TAT ATATT TAT TA- TAT
1 TAT TAT -TAT -TAT TAT TAT TAT -TAT TAT TAT -TA-T TAT TAT TAT
* * * * *
19120399 TAT TAT TAT TAT T-T TTT TA- AAT ATAT TTT TGAG T-T TA- TCT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT T-AT TAT TAT TAT TAT
19120442 T-T TATT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT T
19120467 TTTTAAATTA
Statistics
Matches: 152, Mismatches: 21, Indels: 52
0.68 0.09 0.23
Matches are distributed among these distances:
2 21 0.14
3 87 0.57
4 43 0.28
5 1 0.01
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:19120334 original size:4 final size:4
Alignment explanation
Indices: 19120327--19120399 Score: 51
Period size: 4 Copynumber: 17.5 Consensus size: 4
19120317 TATATATATC
*
19120327 TTTA TTTA TTTA TTTA TTTA TTT- TGTTA -ATA TTTA TATGTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA T-T-TA -TTTA
* * *
19120373 TTTA TATA ATTA TATA TTTA TTATA TT
1 TTTA TTTA TTTA TTTA TTTA TT-TA TT
19120400 ATTATTATTA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
3 3 0.06
4 40 0.74
5 7 0.13
6 3 0.06
7 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:19120398 original size:19 final size:19
Alignment explanation
Indices: 19120369--19120471 Score: 58
Period size: 19 Copynumber: 5.4 Consensus size: 19
19120359 TTATATGTAT
19120369 TTTATTTATATAATTATATA
1 TTTATTTATATAATTAT-TA
*
19120389 TTTATTATATTATTATTATTA
1 TTTATT-TA-TATAATTATTA
19120410 TTT-TTT-TA-AATATATT-
1 TTTATTTATATAAT-TATTA
* *
19120426 TTTGAGTTTATCTTATT-TTA
1 TTT-A-TTTATATAATTATTA
*
19120446 TTTA-TTATTATTATTATTA
1 TTTATTTA-TATAATTATTA
19120465 TTT-TTTA
1 TTTATTTA
19120472 AATTATCTGT
Statistics
Matches: 66, Mismatches: 5, Indels: 25
0.69 0.05 0.26
Matches are distributed among these distances:
16 5 0.08
17 9 0.14
18 6 0.09
19 16 0.24
20 13 0.20
21 9 0.14
22 8 0.12
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTATTTATATAATTATTA
Found at i:19120860 original size:25 final size:23
Alignment explanation
Indices: 19120825--19120873 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 23
19120815 GATCGAAAAT
*
19120825 AATTTTTTAGAAATTTTTGGCGAA
1 AATTTTTTAGAAATTTCTGG-GAA
19120849 AATTTTTCTAGAAATTTCTGGGAA
1 AATTTTT-TAGAAATTTCTGGGAA
19120873 A
1 A
19120874 TTTCCAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (23 bp):
AATTTTTTAGAAATTTCTGGGAA
Found at i:19121481 original size:6 final size:6
Alignment explanation
Indices: 19121458--19121551 Score: 51
Period size: 6 Copynumber: 16.8 Consensus size: 6
19121448 TATTTAATAT
* * * * *
19121458 TTTTTA TCTTTA -TCTTA TTTTTA TTTTT- GTTTTA CTTTT- GTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * *
19121503 CTTTTT- TTATT- TTTTTA TTTTT- TTTTCA CTTTTA -TTTT- TTTTTA
1 -TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
19121547 TTTTT
1 TTTTT
19121552 TTAAAAATAA
Statistics
Matches: 67, Mismatches: 13, Indels: 16
0.70 0.14 0.17
Matches are distributed among these distances:
5 31 0.46
6 32 0.48
7 4 0.06
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:19121490 original size:11 final size:10
Alignment explanation
Indices: 19121475--19121553 Score: 63
Period size: 10 Copynumber: 7.3 Consensus size: 10
19121465 CTTTATCTTA
19121475 TTTTTATTTT
1 TTTTTATTTT
19121485 TGTTTTACTTTT
1 T-TTTTA-TTTT
*
19121497 GTTTTACTTTT
1 TTTTTA-TTTT
19121508 TTTATT-TTTT
1 TTT-TTATTTT
19121518 TATTTT-TTTT
1 T-TTTTATTTT
19121528 TCACTTTTATTTT
1 T---TTTTATTTT
19121541 TTTTTATTTT
1 TTTTTATTTT
19121551 TTT
1 TTT
19121554 AAAAATAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
10 25 0.42
11 19 0.32
12 10 0.17
13 5 0.08
ACGTcount: A:0.10, C:0.05, G:0.03, T:0.82
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:19121502 original size:39 final size:38
Alignment explanation
Indices: 19121459--19121540 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 38
19121449 ATTTAATATT
*
19121459 TTTTATCTTTATCTTA-TTTTTATTTTTGTTTT-ACTTTTG
1 TTTTA-CTTT-TCTTATTTTTTATTTTT-TTTTCACTTTTA
*
19121498 TTTTACTTTTTTTATTTTTTTATTTTTTTTTCACTTTTA
1 TTTTACTTTTCTTA-TTTTTTATTTTTTTTTCACTTTTA
19121537 TTTT
1 TTTT
19121541 TTTTTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
37 4 0.11
38 8 0.21
39 26 0.68
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.78
Consensus pattern (38 bp):
TTTTACTTTTCTTATTTTTTATTTTTTTTTCACTTTTA
Found at i:19121507 original size:28 final size:27
Alignment explanation
Indices: 19121476--19121550 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 27
19121466 TTTATCTTAT
19121476 TTTTATTTTTGTTTTACTTTTGTTTT-AC
1 TTTTATTTTT-TTTTA-TTTTGTTTTCAC
* *
19121504 TTTTTTTATTTTTTTATTTTTTTTTCAC
1 TTTTATT-TTTTTTTATTTTGTTTTCAC
19121532 TTTTATTTTTTTTTATTTT
1 TTTTATTTTTTTTTATTTT
19121551 TTTAAAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 20 0.48
28 19 0.45
29 3 0.07
ACGTcount: A:0.11, C:0.05, G:0.03, T:0.81
Consensus pattern (27 bp):
TTTTATTTTTTTTTATTTTGTTTTCAC
Found at i:19121552 original size:17 final size:17
Alignment explanation
Indices: 19121455--19121552 Score: 76
Period size: 17 Copynumber: 5.5 Consensus size: 17
19121445 ATTTATTTAA
* *
19121455 TATTTTTTATCTTTATCT
1 TATTTTTTAT-TTTTTTT
19121473 TA-TTTTTATTTTTGTTT
1 TATTTTTTATTTTT-TTT
19121490 TACTTTTGTT-TTACTTTTTT
1 TA-TTTT-TTATT--TTTTTT
19121510 TATTTTTTTATTTTTTTT
1 TA-TTTTTTATTTTTTTT
*
19121528 TCA-CTTTTATTTTTTTT
1 T-ATTTTTTATTTTTTTT
19121545 TATTTTTT
1 TATTTTTT
19121553 TAAAAATAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
16 4 0.06
17 29 0.44
18 9 0.14
19 8 0.12
20 13 0.20
21 3 0.05
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (17 bp):
TATTTTTTATTTTTTTT
Found at i:19121634 original size:60 final size:59
Alignment explanation
Indices: 19121561--19122191 Score: 647
Period size: 59 Copynumber: 10.7 Consensus size: 59
19121551 TTTAAAAATA
* *
19121561 AAAAAATATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCTTTGAAAATTAAAATTTCC
1 AAAAAA-ATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCTTT-AAAAATAAAATTTTC
* * *
19121622 AAAAAAATATTTTTAGGGAAAGGTTGAAAGTAGTC------C-TTAAAAA-AAATTTTTC
1 AAAAAAATATTTTTAGGAAAAAGTTGAAAGTA-TCAATTTTCTTTAAAAATAAAATTTTC
* * *
19121674 AAAAAAAGATTTTTGAGG-AAAAGTTGAAAGTATCAATTTTTTTTGAAAATCAAAATTTTC
1 AAAAAAATATTTTT-AGGAAAAAGTTGAAAGTATCAATTTTCTTTAAAAAT-AAAATTTTC
* * * *
19121734 -AAAAAATATCTTTAGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAAAAAAAAATTTTC
1 AAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAA-TTTTCTT--TAAAAATAAAATTTTC
* * * *
19121795 AAAAACAAAGGATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAAAATTTTC
1 -AAAA-AAA-TATTTTTAGGAAAAAGTTGAAAGTATCAATTTT-CTTTAAAA-ATAAAATTTTC
19121859 -AAAAAATATTTTTAGGGAAAAA-TTGAAAGTATCAATTTTCCTTTAAAAATAAAA-TTTC
1 AAAAAAATATTTTTA-GGAAAAAGTTGAAAGTATCAATTTT-CTTTAAAAATAAAATTTTC
* ** * *
19121917 AAAAAGAGGTTCTTAAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC
1 AAAAAAATATT-TTTAGGAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAAATTTTC
** * *
19121975 AAAAAAAGGGTTTTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAATTTTC
1 AAAAAAA-TATTTTT-AGGAAAAAGTTGAAAGTATCAATTTTCTTTAAAAAT-AAAATTTTC
*
19122036 AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTT-TCTTAAAAAT-AAATTTTC
1 AAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCT-TTAAAAATAAAATTTTC
* *
19122094 -AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTC-TTAAAAA-AATAAATTTC
1 AAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAA-AATTTTC
* *
19122151 AAAAAAATATTTTTTGGGGAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATA-TTTTTAGGAAAAAGTTGAAAGTATCAATTTT
19122192 TTCTACACAA
Statistics
Matches: 491, Mismatches: 42, Indels: 76
0.81 0.07 0.12
Matches are distributed among these distances:
51 2 0.00
52 33 0.07
53 7 0.01
54 2 0.00
55 1 0.00
56 8 0.02
57 46 0.09
58 54 0.11
59 130 0.26
60 106 0.22
61 42 0.09
62 7 0.01
63 7 0.01
64 18 0.04
65 28 0.06
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (59 bp):
AAAAAAATATTTTTAGGAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAAATTTTC
Found at i:19126141 original size:24 final size:25
Alignment explanation
Indices: 19126112--19126159 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
19126102 ATCAACAATA
**
19126112 GATGAAAAATGAAA-AAAAAAAGAT
1 GATGAAAAAAAAAAGAAAAAAAGAT
19126136 GATGAAAAAAAAAAGAAAAAAAGA
1 GATGAAAAAAAAAAGAAAAAAAGA
19126160 AAAAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (25 bp):
GATGAAAAAAAAAAGAAAAAAAGAT
Found at i:19126154 original size:22 final size:22
Alignment explanation
Indices: 19126112--19126186 Score: 61
Period size: 22 Copynumber: 3.5 Consensus size: 22
19126102 ATCAACAATA
*
19126112 GATGAAAAATGAAAAAAAAAAGAT
1 GATGAAAAA--AAAAAGAAAAGAT
19126136 GATGAAAAAAAAAAGAAAA-A-
1 GATGAAAAAAAAAAGAAAAGAT
*
19126156 -AAG-AAAAAAAAAG-AAAGAAT
1 GATGAAAAAAAAAAGAAAAG-AT
19126176 GAATGAAAAAA
1 G-ATGAAAAAA
19126187 TGAGAAAATG
Statistics
Matches: 42, Mismatches: 3, Indels: 13
0.72 0.05 0.22
Matches are distributed among these distances:
17 3 0.07
18 10 0.24
19 3 0.07
21 1 0.02
22 11 0.26
23 5 0.12
24 9 0.21
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (22 bp):
GATGAAAAAAAAAAGAAAAGAT
Found at i:19126156 original size:10 final size:10
Alignment explanation
Indices: 19126139--19126171 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
19126129 AAAAGATGAT
19126139 GAAAAAAAAA
1 GAAAAAAAAA
*
19126149 -AGAAAAAAA
1 GAAAAAAAAA
19126158 GAAAAAAAAA
1 GAAAAAAAAA
19126168 GAAA
1 GAAA
19126172 GAATGAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:19126198 original size:16 final size:15
Alignment explanation
Indices: 19126117--19126206 Score: 52
Period size: 16 Copynumber: 6.1 Consensus size: 15
19126107 CAATAGATGA
19126117 AAAATGAAAAAA-A-
1 AAAATGAAAAAAGAG
19126130 AAAGATGATGAAAAA-A-
1 AAA-ATGA--AAAAAGAG
19126146 AAAA-GAAAAAA-AG
1 AAAATGAAAAAAGAG
*
19126159 AAAA--AAAAAGAAAG
1 AAAATGAAAAA-AGAG
19126173 AATGAATGAAAAAATGAG
1 AA--AATGAAAAAA-GAG
19126191 AAAATGAAAAAAGAG
1 AAAATGAAAAAAGAG
19126206 A
1 A
19126207 TTCAAATTGA
Statistics
Matches: 65, Mismatches: 1, Indels: 20
0.76 0.01 0.23
Matches are distributed among these distances:
12 11 0.17
13 8 0.12
14 10 0.15
15 5 0.08
16 21 0.32
17 1 0.02
18 9 0.14
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.08
Consensus pattern (15 bp):
AAAATGAAAAAAGAG
Found at i:19126201 original size:37 final size:35
Alignment explanation
Indices: 19126113--19126202 Score: 85
Period size: 38 Copynumber: 2.5 Consensus size: 35
19126103 TCAACAATAG
19126113 ATGAAAAATG-AAAAAAAAAAGATGATGAAAAAAAA
1 ATGAAAAATGAAAAAAAAAAAGA-GATGAAAAAAAA
* * *
19126148 AAGAAAAAAAGAAAAAAAAAGAA-AGAATGAATGAAAAA
1 ATG-AAAAATGAAAAAAAAA-AAGAG-ATGAA-AAAAAA
19126186 ATGAGAAAATGAAAAAA
1 ATGA-AAAATGAAAAAA
19126203 GAGATTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
35 2 0.05
36 7 0.16
37 15 0.34
38 20 0.45
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (35 bp):
ATGAAAAATGAAAAAAAAAAAGAGATGAAAAAAAA
Found at i:19127563 original size:44 final size:44
Alignment explanation
Indices: 19127470--19127552 Score: 118
Period size: 43 Copynumber: 1.9 Consensus size: 44
19127460 GCCTTTGAAC
* *
19127470 TCAAATGAAAAAGCTTTGAATTTTTGGATGTGAATTTCCAAAAT
1 TCAAATGAAAAAGCTTTGAACTTTTGGATATGAATTTCCAAAAT
19127514 TCAAATG-AAAAGCTTT-AGACTTTTGGATATGAA-TTCCAA
1 TCAAATGAAAAAGCTTTGA-ACTTTTGGATATGAATTTCCAA
19127553 GTTTGCCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
42 7 0.19
43 22 0.61
44 7 0.19
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (44 bp):
TCAAATGAAAAAGCTTTGAACTTTTGGATATGAATTTCCAAAAT
Found at i:19127627 original size:16 final size:16
Alignment explanation
Indices: 19127606--19127636 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
19127596 TGTTTGATGC
19127606 GAGTCTTACAGGTTGT
1 GAGTCTTACAGGTTGT
19127622 GAGTCTTACAGGTTG
1 GAGTCTTACAGGTTG
19127637 CAAATGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.13, G:0.32, T:0.35
Consensus pattern (16 bp):
GAGTCTTACAGGTTGT
Found at i:19127886 original size:42 final size:41
Alignment explanation
Indices: 19127808--19128145 Score: 505
Period size: 41 Copynumber: 8.1 Consensus size: 41
19127798 TGATTGTCAG
*
19127808 GGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGA
*
19127849 GGAGCAATTTACTTTTCCAAAGTCGTGGTGCCCCTGTTTAGA
1 GGAGCAATTTA-TTTTCCAAAGTCGTGGTGCCTCTGTTTAGA
*
19127891 GGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGA
* * *
19127932 AGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTATTTAGA
1 GGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGA
* * *
19127973 GGAGCAATTTACTTTCCAAAGTCGTGGTACTTCTGTTTAGA
1 GGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGA
*
19128014 GGAGCAATTTACTTTTCCAAAGTCGTGGTGCCACTGTTTAGA
1 GGAGCAATTTA-TTTTCCAAAGTCGTGGTGCCTCTGTTTAGA
*
19128056 GGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGA
1 GGAGCAATTTATTTTCC-AAAGTCGTGGTGCCTCTGTTTAGA
* * *
19128098 GGAGCAATTTATGTTTCTCAAAGTCGTTGAGCCTCTATTTAGA
1 GGAGCAATTTAT-TTTC-CAAAGTCGTGGTGCCTCTGTTTAGA
19128141 GGAGC
1 GGAGC
19128146 TTTGGTCAAA
Statistics
Matches: 270, Mismatches: 22, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
41 129 0.48
42 110 0.41
43 30 0.11
44 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (41 bp):
GGAGCAATTTATTTTCCAAAGTCGTGGTGCCTCTGTTTAGA
Found at i:19127948 original size:83 final size:83
Alignment explanation
Indices: 19127808--19128145 Score: 509
Period size: 83 Copynumber: 4.1 Consensus size: 83
19127798 TGATTGTCAG
* *
19127808 GGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTC
1 GGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTC
* *
19127873 GTGGTGCCCCTGTTTAGA
66 GTGGTGCCTCTATTTAGA
* * * *
19127891 GGAGCAATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAAGAGCAATTTA-TTTTTCAAAGTC
1 GGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTC
19127955 GTGGTGCCTCTATTTAGA
66 GTGGTGCCTCTATTTAGA
* *
19127973 GGAGCAATTTACTTTCCAAAGTCGTGGTACTTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTC
1 GGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTC
* *
19128038 GTGGTGCCACTGTTTAGA
66 GTGGTGCCTCTATTTAGA
19128056 GGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTA-TGTTTCTCAAA
1 GGAGCAATTTACTTTCC-AAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACT-TTTC-CAAA
* *
19128120 GTCGTTGAGCCTCTATTTAGA
63 GTCGTGGTGCCTCTATTTAGA
19128141 GGAGC
1 GGAGC
19128146 TTTGGTCAAA
Statistics
Matches: 233, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
82 74 0.32
83 96 0.41
84 37 0.16
85 26 0.11
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (83 bp):
GGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTC
GTGGTGCCTCTATTTAGA
Found at i:19128164 original size:1 final size:1
Alignment explanation
Indices: 19128153--19128240 Score: 86
Period size: 1 Copynumber: 88.0 Consensus size: 1
19128143 AGCTTTGGTC
* * * * * * *
19128153 AAAAAACAAAAAAAAACAAAAAAAAAATAAAAAAAACAAAAAAAAACAAAAAAACACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
19128218 CAAAAAAACAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAA
19128241 TGACAATGTT
Statistics
Matches: 67, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.89, C:0.10, G:0.00, T:0.01
Consensus pattern (1 bp):
A
Found at i:19128240 original size:10 final size:10
Alignment explanation
Indices: 19128153--19128233 Score: 116
Period size: 10 Copynumber: 8.4 Consensus size: 10
19128143 AGCTTTGGTC
19128153 AAAAAACAAA
1 AAAAAACAAA
19128163 AAAAAACAAA
1 AAAAAACAAA
19128173 AAAAAA-ATAA
1 AAAAAACA-AA
19128183 AAAAAACAAA
1 AAAAAACAAA
19128193 AAAAAACAAA
1 AAAAAACAAA
*
19128203 AAAACAC-AA
1 AAAAAACAAA
19128212 AAAAAAC--A
1 AAAAAACAAA
19128220 AAAAAACAAA
1 AAAAAACAAA
19128230 AAAA
1 AAAA
19128234 CAAAAAATGA
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
8 8 0.12
9 9 0.14
10 47 0.72
11 1 0.02
ACGTcount: A:0.89, C:0.10, G:0.00, T:0.01
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:19128439 original size:3 final size:3
Alignment explanation
Indices: 19128404--19128564 Score: 63
Period size: 3 Copynumber: 52.3 Consensus size: 3
19128394 TTCTATCTGG
* *
19128404 TAT TAT TTT TAT T-T TAT GTAT T-G TAT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TA-T TAT TAT TAT TAT TAT
*
19128449 TAT TAT GTAT TAA TA- TAT ATAT CT-T TATT TATT TATT TATT TAT T-T
1 TAT TAT -TAT TAT TAT TAT -TAT -TAT TA-T TA-T TA-T TA-T TAT TAT
* * * *
19128495 T-T TTT TGT TAA TAT T-T ATAT GTAT T-T TAT T-T ATAT AAT TAT ATATT
1 TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT -TAT TAT TAT -TA-T
19128541 TAT TAT TA- TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
19128565 TTTTAAAATA
Statistics
Matches: 127, Mismatches: 13, Indels: 36
0.72 0.07 0.20
Matches are distributed among these distances:
2 16 0.13
3 73 0.57
4 37 0.29
5 1 0.01
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:19128452 original size:22 final size:22
Alignment explanation
Indices: 19128404--19128564 Score: 88
Period size: 22 Copynumber: 7.2 Consensus size: 22
19128394 TTCTATCTGG
19128404 TATTATT-TTTATT-TTATGTAT
1 TATTATTATTTATTATTAT-TAT
*
19128425 T-GTATTATTTATTATTATTAT
1 TATTATTATTTATTATTATTAT
* *
19128446 TATTATTATGTATTAATA-TAT
1 TATTATTATTTATTATTATTAT
19128467 ATATCT-TTATTTATTTATTTATTTAT
1 -TAT-TATTATTTA-TTA-TTA-TTAT
* * *
19128493 T-TTTTTTTGTTAATATT-TATAT
1 TATTATTAT-TTATTATTAT-TAT
*
19128515 GTATT-TTATTTA-TATAATTAT
1 -TATTATTATTTATTATTATTAT
19128536 ATATTTATTATTATATTATTATTAT
1 -TA-TTATTATT-TATTATTATTAT
19128561 TATT
1 TATT
19128565 TTTTAAAATA
Statistics
Matches: 109, Mismatches: 12, Indels: 36
0.69 0.08 0.23
Matches are distributed among these distances:
20 4 0.04
21 23 0.21
22 35 0.32
23 18 0.17
24 14 0.13
25 12 0.11
26 3 0.03
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (22 bp):
TATTATTATTTATTATTATTAT
Found at i:19128479 original size:4 final size:4
Alignment explanation
Indices: 19128472--19128544 Score: 51
Period size: 4 Copynumber: 17.5 Consensus size: 4
19128462 TATATATATC
*
19128472 TTTA TTTA TTTA TTTA TTTA TTT- TTT- TTTG TTAATA TTTA TATGTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTTA T-T-TA
* * *
19128518 TTTTA TTTA TATA ATTA TATA TTTA TT
1 -TTTA TTTA TTTA TTTA TTTA TTTA TT
19128545 ATTATATTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
3 6 0.11
4 40 0.71
5 3 0.05
6 6 0.11
7 1 0.02
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:19129636 original size:27 final size:28
Alignment explanation
Indices: 19129600--19129653 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
19129590 TTTAATATTT
19129600 TTTTATCTTTATCTTA-TTTTTATTTTTG
1 TTTTATCTTT-TCTTATTTTTTATTTTTG
*
19129628 TTTTA-CTTTTTTTATTTTTTATTTTT
1 TTTTATCTTTTCTTATTTTTTATTTTT
19129654 TTATTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 15 0.62
28 5 0.21
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.80
Consensus pattern (28 bp):
TTTTATCTTTTCTTATTTTTTATTTTTG
Found at i:19129642 original size:52 final size:48
Alignment explanation
Indices: 19129586--19129689 Score: 120
Period size: 52 Copynumber: 2.1 Consensus size: 48
19129576 TTAGATTATA
*
19129586 TTTATTTAATATTTTTTTATCTTTATCTT-ATTTTTATTTTTGTTTTACTTTT
1 TTTATTTAATATTTTTTTAT-TTT-TCTTCACTTTTA-TTTT-TTTTA-TTTT
** *
19129638 TTTATTTTTTATTTTTTTATTTTTTTTCACTTTTATTTTTTTTATTTT
1 TTTATTTAATATTTTTTTATTTTTCTTCACTTTTATTTTTTTTATTTT
19129686 TTTA
1 TTTA
19129690 AAAATAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
48 8 0.17
49 5 0.11
50 7 0.15
51 9 0.19
52 18 0.38
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.79
Consensus pattern (48 bp):
TTTATTTAATATTTTTTTATTTTTCTTCACTTTTATTTTTTTTATTTT
Found at i:19129653 original size:16 final size:16
Alignment explanation
Indices: 19129598--19129687 Score: 69
Period size: 16 Copynumber: 5.4 Consensus size: 16
19129588 TATTTAATAT
*
19129598 TTTTTTATCTTTATCTTA
1 TTTTTTAT-TTT-TTTTA
19129616 -TTTTTATTTTTGTTTTA
1 TTTTTTA-TTTT-TTTTA
*
19129633 CTTTTTT-TATTTTTTA
1 -TTTTTTATTTTTTTTA
19129649 TTTTTTTATTTTTTTTCA
1 -TTTTTTATTTTTTTT-A
*
19129667 -CTTTTATTTTTTTTA
1 TTTTTTATTTTTTTTA
19129682 TTTTTT
1 TTTTTT
19129688 TAAAAATAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
15 1 0.02
16 28 0.47
17 23 0.39
18 2 0.03
19 5 0.08
ACGTcount: A:0.12, C:0.06, G:0.01, T:0.81
Consensus pattern (16 bp):
TTTTTTATTTTTTTTA
Found at i:19129679 original size:33 final size:35
Alignment explanation
Indices: 19129616--19129689 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 35
19129606 CTTTATCTTA
* *
19129616 TTTTTATTTTTGTTTTACTTTTTTTATTTTTTATT
1 TTTTTATTTTTGTTTCACTTTTATTATTTTTTATT
19129651 TTTTTATTTTT-TTTCACTTTTATT-TTTTTTATT
1 TTTTTATTTTTGTTTCACTTTTATTATTTTTTATT
19129684 TTTTTA
1 TTTTTA
19129690 AAAATAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 15 0.41
34 11 0.30
35 11 0.30
ACGTcount: A:0.12, C:0.04, G:0.01, T:0.82
Consensus pattern (35 bp):
TTTTTATTTTTGTTTCACTTTTATTATTTTTTATT
Found at i:19129680 original size:25 final size:23
Alignment explanation
Indices: 19129586--19129688 Score: 89
Period size: 25 Copynumber: 4.1 Consensus size: 23
19129576 TTAGATTATA
*
19129586 TTTATTTAATATTTTTTTATCTTTAT
1 TTTATTTTAT-TTTTTTTAT-TTT-T
* *
19129612 CTTATTTTTATTTTTGTTTTACTTTT
1 TTTA-TTTTA-TTTT-TTTTATTTTT
*
19129638 TTTATTTTTTATTTTTTTATTTTT
1 TTTATTTTAT-TTTTTTTATTTTT
19129662 TTTCACTTTTATTTTTTTTATTTTT
1 TTT-A-TTTTATTTTTTTTATTTTT
19129687 TT
1 TT
19129689 AAAAATAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
24 13 0.20
25 23 0.36
26 12 0.19
27 10 0.16
28 6 0.09
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.80
Consensus pattern (23 bp):
TTTATTTTATTTTTTTTATTTTT
Found at i:19130045 original size:58 final size:57
Alignment explanation
Indices: 19129706--19130203 Score: 424
Period size: 59 Copynumber: 8.5 Consensus size: 57
19129696 AAAAAAATAG
* * *
19129706 GGAAAAGTTGAAAGTATCAA-TTTTCTTTGAAAATCAAAATTTTCAAAAAA-ATATTTTTA
1 GGAAAAGTTGAAAGTATCAATTTTTC-TTAAAAAT--AAATTTTCAAAAAAGGT-TTTTGA
* *
19129765 GGGAAAGGTTGAAAG--T--A--TTCCTTAAAAATAAATTTTCAAAAAAGGATTTTTTGA
1 -GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAGG--TTTTTGA
* * * ** *
19129819 GGAAAAGTTGAAAGTATAAATTTTTTTTTAAAATCAAAATTTTCAAAAAATATATTT-A
1 GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT--AAATTTTCAAAAAAGGTTTTTGA
* *
19129877 GGGAAAAGTTAAAAGTATCAATTTTCCTTAAAAAAAAAATAAATTTTCAAAAACAAAGGATTTTT
1 -GGAAAAGTTGAAAGTATCAATTTTTCTT-----AAAAATAAATTTTC--AAA-AAAGG-TTTTT
*
19129942 GG
56 GA
* * * *
19129944 GGAAAAATTAAAAGTATCAATTTTTCTTTAAAAATAAAATTTCAAAAAGAGGTTCTTGA
1 GGAAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAAATTTTCAAAAA-AGGTTTTTGA
*
19130003 GAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAAGGGTTTTTGA
1 GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTC-AAAAAA-GGTTTTTGA
* * **
19130062 GGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTCCAAAAAATATTTTT-A
1 GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAGGTTTTTGA
* * ** *
19130118 GGGAAAAGTTGAAAGTATCAATTTTCCTAAAAAAATAAA-TTTCAAAAAAATATTTTTTGG
1 -GGAAAAGTTGAAAGTATCAATTTTTCT-TAAAAATAAATTTTC-AAAAAA-GGTTTTTGA
19130178 GGAAAAGTTGAAAGTATCAATTTTTC
1 GGAAAAGTTGAAAGTATCAATTTTTC
19130204 CTACACAAGA
Statistics
Matches: 365, Mismatches: 42, Indels: 63
0.78 0.09 0.13
Matches are distributed among these distances:
52 14 0.04
53 13 0.04
54 12 0.03
55 5 0.01
56 2 0.01
57 36 0.10
58 39 0.11
59 149 0.41
60 19 0.05
61 14 0.04
62 21 0.06
64 8 0.02
65 3 0.01
66 28 0.08
67 2 0.01
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (57 bp):
GGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAGGTTTTTGA
Found at i:19131888 original size:63 final size:65
Alignment explanation
Indices: 19131767--19131891 Score: 157
Period size: 63 Copynumber: 2.0 Consensus size: 65
19131757 AATTTTGTTG
* *
19131767 AAGGAATTATTGAAGGTATTTTTGATAAAAAAAATGCCTTCAATAATCCTCTGAAAAAATTTGGA
1 AAGGAATTATTGAAGGTATTTTTGATAAAAAAAACGCCTTCAATAATCCTCTCAAAAAATTTGGA
* * ** *
19131832 AAGG-ATTATTGAATGTATTTTT-TTATCAAAAACGCCTTCAATAAT-TTCTCATAAAAATTT
1 AAGGAATTATTGAAGGTATTTTTGATAAAAAAAACGCCTTCAATAATCCTCTCA-AAAAATTT
19131892 ATTTAGGGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 4 0.08
63 27 0.52
64 17 0.33
65 4 0.08
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (65 bp):
AAGGAATTATTGAAGGTATTTTTGATAAAAAAAACGCCTTCAATAATCCTCTCAAAAAATTTGGA
Found at i:19131958 original size:156 final size:156
Alignment explanation
Indices: 19131759--19132076 Score: 627
Period size: 156 Copynumber: 2.0 Consensus size: 156
19131749 CTCTTCCAAA
19131759 TTTTGTTGAAGGAATTATTGAAGGTATTTTTGATAAAAAAAATGCCTTCAATAATCCTCTGAAAA
1 TTTTGTTGAAGGAATTATTGAAGGTATTTTTGATAAAAAAAATGCCTTCAATAATCCTCTGAAAA
*
19131824 AATTTGGAAAGGATTATTGAATGTATTTTTTTATCAAAAACGCCTTCAATAATTTCTCATAAAAA
66 AATTTGGAAAGGATTATTGAAGGTATTTTTTTATCAAAAACGCCTTCAATAATTTCTCATAAAAA
19131889 TTTATTTAGGGGATTATTAAAGGCAT
131 TTTATTTAGGGGATTATTAAAGGCAT
19131915 TTTTGTTGAAGGAATTATTGAAGGTATTTTTGATAAAAAAAATGCCTTCAATAATCCTCTGAAAA
1 TTTTGTTGAAGGAATTATTGAAGGTATTTTTGATAAAAAAAATGCCTTCAATAATCCTCTGAAAA
19131980 AATTTGGAAAGGATTATTGAAGGTATTTTTTTATCAAAAACGCCTTCAATAATTTCTCATAAAAA
66 AATTTGGAAAGGATTATTGAAGGTATTTTTTTATCAAAAACGCCTTCAATAATTTCTCATAAAAA
19132045 TTTATTTAGGGGATTATTAAAGGCAT
131 TTTATTTAGGGGATTATTAAAGGCAT
19132071 TTTTGT
1 TTTTGT
19132077 CCAAAAATAC
Statistics
Matches: 161, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 161 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (156 bp):
TTTTGTTGAAGGAATTATTGAAGGTATTTTTGATAAAAAAAATGCCTTCAATAATCCTCTGAAAA
AATTTGGAAAGGATTATTGAAGGTATTTTTTTATCAAAAACGCCTTCAATAATTTCTCATAAAAA
TTTATTTAGGGGATTATTAAAGGCAT
Found at i:19132095 original size:64 final size:66
Alignment explanation
Indices: 19131990--19132127 Score: 156
Period size: 65 Copynumber: 2.1 Consensus size: 66
19131980 AATTTGGAAA
* * * * * * * *
19131990 GGATTATTGAAGGTATTTTTTTATCAAAAACGCCTTCAATAATTTCT-CATAAAAA-TTTATTTA
1 GGATTATTAAAGGCATTTTTGTACCAAAAACACCTTCAATAATCTATACA-AAAAATTTTATTGA
19132053 GG
65 GG
* *
19132055 GGATTATTAAAGGCATTTTTGT-CCAAAAATACCTTTAATAATCTATACAAAAAATTTTATTGAG
1 GGATTATTAAAGGCATTTTTGTACCAAAAACACCTTCAATAATCTATACAAAAAATTTTATTGAG
19132119 G
66 G
19132120 GGATTATT
1 GGATTATT
19132128 GAAATTAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
64 23 0.38
65 38 0.62
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (66 bp):
GGATTATTAAAGGCATTTTTGTACCAAAAACACCTTCAATAATCTATACAAAAAATTTTATTGAG
G
Found at i:19132262 original size:62 final size:61
Alignment explanation
Indices: 19132132--19132320 Score: 209
Period size: 62 Copynumber: 3.1 Consensus size: 61
19132122 ATTATTGAAA
* * * * *
19132132 TTAATAATCCCTTTAACAAAATTTGAAAGGGATTATTGAATGCATTTTTG-TCAAAAATACT
1 TTAATAAT-CCTCTAAAAAAATTTGGAAGGGATTATTGAAAGTATTTTTGATCAAAAATACT
* * *
19132193 TTCAATAATCCTCTAAAAAAATTTGGAAGGGATTATTAAAAGTGTTTTTGATAAAAAATACAT
1 TT-AATAATCCTCTAAAAAAATTTGGAAGGGATTATTGAAAGTATTTTTGATCAAAAATAC-T
* * * * * * *
19132256 TTAATAATCCCCTAAAAAAATTTAGAAAGAATTATTGAAGGTATTTTTGATCAGAAATACC
1 TTAATAATCCTCTAAAAAAATTTGGAAGGGATTATTGAAAGTATTTTTGATCAAAAATACT
19132317 TTAA
1 TTAA
19132321 ATAACCCCAT
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
61 40 0.37
62 64 0.60
63 3 0.03
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (61 bp):
TTAATAATCCTCTAAAAAAATTTGGAAGGGATTATTGAAAGTATTTTTGATCAAAAATACT
Found at i:19133791 original size:35 final size:35
Alignment explanation
Indices: 19133725--19133793 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
19133715 ATGATGTATG
* * * *
19133725 GGTGCATATGGGTATGTGTTTGGTTGTGTTGAAAT
1 GGTGCACATAGGTATGTGTTTAGTTGAGTTGAAAT
*
19133760 GGTGCACATAGGTATGTGTTTATTTGAGTTGAAA
1 GGTGCACATAGGTATGTGTTTAGTTGAGTTGAAA
19133794 ATACTCCATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.22, C:0.04, G:0.33, T:0.41
Consensus pattern (35 bp):
GGTGCACATAGGTATGTGTTTAGTTGAGTTGAAAT
Found at i:19134662 original size:2 final size:2
Alignment explanation
Indices: 19134655--19134681 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19134645 ATTGTTCAGA
19134655 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
19134682 AGATTTGAGA
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:19137513 original size:16 final size:16
Alignment explanation
Indices: 19137479--19137549 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 16
19137469 AAACTATGAT
*
19137479 AAATTATTTATTATTA
1 AAATTATTTAATATTA
19137495 AAATTA-TTAATATTA
1 AAATTATTTAATATTA
* * *
19137510 AAAATAGTTATATTTTA
1 AAATTATTTA-ATATTA
*
19137527 ATAATAATATTTAATCTTA
1 A-AAT--TATTTAATATTA
19137546 AAAT
1 AAAT
19137550 ATCATCGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
15 13 0.30
16 9 0.20
17 6 0.14
18 5 0.11
19 6 0.14
20 5 0.11
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (16 bp):
AAATTATTTAATATTA
Found at i:19137713 original size:22 final size:24
Alignment explanation
Indices: 19137672--19137730 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 24
19137662 ATTAGAATAA
*
19137672 TAATATTCAAAAT-ATTAATA-TT-
1 TAATATT-AAAATAATAAATATTTG
*
19137694 TATTATTAAAATAATAAATATTTG
1 TAATATTAAAATAATAAATATTTG
19137718 TAATATTAAAATA
1 TAATATTAAAATA
19137731 GTAATATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 5 0.16
22 12 0.39
23 2 0.06
24 12 0.39
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
TAATATTAAAATAATAAATATTTG
Found at i:19137755 original size:28 final size:30
Alignment explanation
Indices: 19137706--19137774 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 30
19137696 TTATTAAAAT
19137706 AATAA-ATATTTGTAATATTAAAATAGT-AA
1 AATAATATATTTGTAATATTAAAATA-TAAA
* *
19137735 TATAATATATTTGTCA-A-TAAAATATAAA
1 AATAATATATTTGTAATATTAAAATATAAA
19137763 AATAATATATTT
1 AATAATATATTT
19137775 TAAATTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 1 0.03
28 20 0.57
29 5 0.14
30 9 0.26
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (30 bp):
AATAATATATTTGTAATATTAAAATATAAA
Found at i:19137985 original size:26 final size:26
Alignment explanation
Indices: 19137941--19137991 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
19137931 AGTACTCCAA
* * * *
19137941 AAGTTATTAAATGATAATAATATAGC
1 AAGTCATTAAATCACAATAACATAGC
19137967 AAGTCATTAAATCACAATAACATAG
1 AAGTCATTAAATCACAATAACATAG
19137992 TGATCAATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (26 bp):
AAGTCATTAAATCACAATAACATAGC
Found at i:19138012 original size:24 final size:24
Alignment explanation
Indices: 19137981--19138026 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
19137971 CATTAAATCA
19137981 CAATAACATAGTGATCAATTGTGG
1 CAATAACATAGTGATCAATTGTGG
19138005 CAATAACATAGTGATCAATTGT
1 CAATAACATAGTGATCAATTGT
19138027 AGACAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (24 bp):
CAATAACATAGTGATCAATTGTGG
Found at i:19141499 original size:120 final size:119
Alignment explanation
Indices: 19141374--19141613 Score: 399
Period size: 120 Copynumber: 2.0 Consensus size: 119
19141364 TTTAGAACTA
* *
19141374 TACTATGCTAATAATAATTTTAATACATTTAACTTTTATGCTTAATTTATATTAAGATTAATTAT
1 TACTATGCTAATAATAATTTTAATACATTTAACTTTTATGCTTAATTGAGATTAAGATTAATTAT
* * * *
19141439 ATTTACGTAATTACACTCAGTTGAGTTTAGGGTGATTAGCATTATACTAATTAAT
66 ATTTAAGTAACTACACTC-GATGAGTTTAGGGTGATTAGCATTAAACTAATTAAT
* *
19141494 TACTATGCTAATAATAATTTTAATACATTTAATTTTTATGCTTAATTGAGATTAAGGTTAATTAT
1 TACTATGCTAATAATAATTTTAATACATTTAACTTTTATGCTTAATTGAGATTAAGATTAATTAT
19141559 ATTTAAGTAACTACACTCGATGAGTTTAGGGTGATTAGCATTAAACTAATTAAT
66 ATTTAAGTAACTACACTCGATGAGTTTAGGGTGATTAGCATTAAACTAATTAAT
19141613 T
1 T
19141614 TAATAATGTC
Statistics
Matches: 112, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
119 35 0.31
120 77 0.69
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (119 bp):
TACTATGCTAATAATAATTTTAATACATTTAACTTTTATGCTTAATTGAGATTAAGATTAATTAT
ATTTAAGTAACTACACTCGATGAGTTTAGGGTGATTAGCATTAAACTAATTAAT
Found at i:19142540 original size:2 final size:2
Alignment explanation
Indices: 19142533--19142561 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
19142523 GGGAAGGTTT
19142533 TA TA TA TA TA T- 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
19142562 AATAGCTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19143793 original size:3 final size:3
Alignment explanation
Indices: 19143785--19143825 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
19143775 TTGCCCAAAT
19143785 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19143826 CTTTGTGACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19145433 original size:3 final size:3
Alignment explanation
Indices: 19145425--19145477 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
19145415 AAAAACTATA
19145425 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19145473 AAT AA
1 AAT AA
19145478 AATTATATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19151631 original size:3 final size:3
Alignment explanation
Indices: 19151623--19151656 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
19151613 TTTATAACAT
*
19151623 TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19151657 CATCATCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:19151661 original size:3 final size:3
Alignment explanation
Indices: 19151655--19151689 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
19151645 TATTAATATT
* *
19151655 ATC ATC ATC ATC ACC ATC ATC GTC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
19151690 TATTATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.34, G:0.03, T:0.31
Consensus pattern (3 bp):
ATC
Found at i:19153088 original size:36 final size:35
Alignment explanation
Indices: 19153041--19153112 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
19153031 TTTTCATCTA
* *
19153041 TGTGTGTTCTTCTTTTATTTATAGCTATGGAGTCTT
1 TGTGTGTTCTTCTCTCATTTATAGCTATGGAG-CTT
*
19153077 TGTGTGTTCTTCTCTCATTTATAGTTATGGAGCTT
1 TGTGTGTTCTTCTCTCATTTATAGCTATGGAGCTT
19153112 T
1 T
19153113 ATTTATAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 4 0.12
36 29 0.88
ACGTcount: A:0.14, C:0.12, G:0.19, T:0.54
Consensus pattern (35 bp):
TGTGTGTTCTTCTCTCATTTATAGCTATGGAGCTT
Found at i:19153521 original size:10 final size:10
Alignment explanation
Indices: 19153506--19153534 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
19153496 AAATATGTTC
19153506 AAAATTTATT
1 AAAATTTATT
19153516 AAAATTTATT
1 AAAATTTATT
19153526 AAAATTTAT
1 AAAATTTAT
19153535 ATACTTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
AAAATTTATT
Found at i:19155482 original size:7 final size:8
Alignment explanation
Indices: 19155465--19155513 Score: 53
Period size: 8 Copynumber: 5.6 Consensus size: 8
19155455 AAGGGCATGC
19155465 AAAGAAAA
1 AAAGAAAA
19155473 AAAGAAAA
1 AAAGAAAA
*
19155481 AAAGGGAAAG
1 AAA--GAAAA
19155491 AAAGAAAAA
1 AAAG-AAAA
19155500 AAAGAAGAA
1 AAAGAA-AA
19155509 AAAGA
1 AAAGA
19155514 TGAAAATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
8 14 0.40
9 14 0.40
10 7 0.20
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:19155483 original size:9 final size:9
Alignment explanation
Indices: 19155465--19155513 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
19155455 AAGGGCATGC
19155465 AAAG-AAAA
1 AAAGAAAAA
19155473 AAAGAAAAA
1 AAAGAAAAA
* * *
19155482 AAGGGAAAG
1 AAAGAAAAA
19155491 AAAGAAAAA
1 AAAGAAAAA
*
19155500 AAAGAAGAA
1 AAAGAAAAA
19155509 AAAGA
1 AAAGA
19155514 TGAAAATAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
8 4 0.12
9 29 0.88
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:19155512 original size:22 final size:22
Alignment explanation
Indices: 19155465--19155513 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
19155455 AAGGGCATGC
**
19155465 AAAGAAAAAAAGAAAAAAAGGG
1 AAAGAAAAAAAGAAAAAAAGAA
*
19155487 AAAGAAAGAAAA-AAAAGAAGAA
1 AAAGAAA-AAAAGAAAAAAAGAA
19155509 AAAGA
1 AAAGA
19155514 TGAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (22 bp):
AAAGAAAAAAAGAAAAAAAGAA
Found at i:19156064 original size:16 final size:15
Alignment explanation
Indices: 19156008--19156065 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
19155998 ATGAGAAGGT
*
19156008 AAGGAAAGGGAAAGAA
1 AAGGAAA-GGAAAAAA
* *
19156024 AATGAAA-GAAAGAA
1 AAGGAAAGGAAAAAA
19156038 AA--AAAGGAAAAAA
1 AAGGAAAGGAAAAAA
19156051 AAGGAAAGGGAAAAA
1 AAGGAAA-GGAAAAA
19156066 TGATAAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
12 3 0.08
13 8 0.22
14 9 0.25
15 3 0.08
16 13 0.36
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.02
Consensus pattern (15 bp):
AAGGAAAGGAAAAAA
Found at i:19156090 original size:25 final size:22
Alignment explanation
Indices: 19156028--19156111 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 22
19156018 AAAGAAAATG
*
19156028 AAAGAAAGAAAAAAAGGAAAAAA
1 AAAGAAAG-AAAAAATGAAAAAA
* *
19156051 AAGGAAAGGGAAAAATGATAAAAGA
1 AAAGAAA-GAAAAAATGA-AAAA-A
19156076 AAAGAAAGAACAAAATGAAATAAA
1 AAAGAAAGAA-AAAATGAAA-AAA
*
19156100 AAAAAAAGAAAA
1 AAAGAAAGAAAA
19156112 GGAAATAAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
23 15 0.30
24 19 0.38
25 16 0.32
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (22 bp):
AAAGAAAGAAAAAATGAAAAAA
Found at i:19158174 original size:39 final size:39
Alignment explanation
Indices: 19158109--19158202 Score: 143
Period size: 39 Copynumber: 2.4 Consensus size: 39
19158099 GAATGAGTAC
* * * *
19158109 AAGAATTTTAAGACTTCTTGGCAGAATTTTAATTTTTGA
1 AAGAATTTCAAGACCTCTAGGCAGAATTTTAATTTTGGA
*
19158148 AAGAATTTCAAGACCTCTAGGTAGAATTTTAATTTTGGA
1 AAGAATTTCAAGACCTCTAGGCAGAATTTTAATTTTGGA
19158187 AAGAATTTCAAGACCT
1 AAGAATTTCAAGACCT
19158203 TCGAGCATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (39 bp):
AAGAATTTCAAGACCTCTAGGCAGAATTTTAATTTTGGA
Found at i:19158512 original size:14 final size:13
Alignment explanation
Indices: 19158503--19158536 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
19158493 AAAAAGAATG
19158503 AAAAAAAAA-GAA
1 AAAAAAAAATGAA
19158515 AAAAAAATAATGAA
1 AAAAAAA-AATGAA
19158529 AAAAAAAA
1 AAAAAAAA
19158537 GACAAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 7 0.35
13 3 0.15
14 10 0.50
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (13 bp):
AAAAAAAAATGAA
Found at i:19158518 original size:12 final size:12
Alignment explanation
Indices: 19158493--19158550 Score: 55
Period size: 12 Copynumber: 4.6 Consensus size: 12
19158483 TGGAGCTTGG
19158493 AAAAAGAATGAAAA
1 AAAAAGAA--AAAA
19158507 AAAAAGAAAAAA
1 AAAAAGAAAAAA
19158519 AAATAATG-AAAAA
1 AAA-AA-GAAAAAA
* *
19158532 AAAAAGACAAAC
1 AAAAAGAAAAAA
19158544 AAAAAGA
1 AAAAAGA
19158551 TCTTGTGTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 1 0.03
12 19 0.49
13 10 0.26
14 9 0.23
ACGTcount: A:0.81, C:0.03, G:0.10, T:0.05
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:19160750 original size:6 final size:6
Alignment explanation
Indices: 19160739--19160763 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19160729 GGTAACTTAA
19160739 AAATGC AAATGC AAATGC AAATGC A
1 AAATGC AAATGC AAATGC AAATGC A
19160764 TAAATGGGAC
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:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
AAATGC
Found at i:19160809 original size:19 final size:20
Alignment explanation
Indices: 19160776--19160819 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
19160766 AATGGGACCA
19160776 AGGGTTGATTTTAGGGTTTG
1 AGGGTTGATTTTAGGGTTTG
* *
19160796 AGGGTTGA-TTTAGGTTTTT
1 AGGGTTGATTTTAGGGTTTG
19160815 AGGGT
1 AGGGT
19160820 CTAGGGTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (20 bp):
AGGGTTGATTTTAGGGTTTG
Found at i:19160852 original size:18 final size:18
Alignment explanation
Indices: 19160831--19160868 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
19160821 TAGGGTAAGT
19160831 TTAGGGTCTTG-GTTAGGG
1 TTAGGGT-TTGAGTTAGGG
*
19160849 TTAGGGTTTGATTTAGGG
1 TTAGGGTTTGAGTTAGGG
19160867 TT
1 TT
19160869 TAGGTTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.13, C:0.03, G:0.39, T:0.45
Consensus pattern (18 bp):
TTAGGGTTTGAGTTAGGG
Found at i:19160910 original size:24 final size:24
Alignment explanation
Indices: 19160860--19160944 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
19160850 TAGGGTTTGA
* *
19160860 TTTAGGGTTTAGGTTAGTTTAATG
1 TTTAAGGTTTAGGTTAGTTTAAGG
* *
19160884 TTTAAGGTTTGGGTTAGTTTAGGG
1 TTTAAGGTTTAGGTTAGTTTAAGG
* * *
19160908 TTTGAGATTTAAGGTTTTAGTTCAAGG
1 TTTAAGGTTT-AGG--TTAGTTTAAGG
*
19160935 TTTAGGGTTT
1 TTTAAGGTTT
19160945 GTTTTAGGGT
Statistics
Matches: 46, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
24 28 0.61
25 2 0.04
27 16 0.35
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.48
Consensus pattern (24 bp):
TTTAAGGTTTAGGTTAGTTTAAGG
Found at i:19160989 original size:12 final size:12
Alignment explanation
Indices: 19160933--19160970 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
19160923 TTTAGTTCAA
19160933 GGTTTAGGGTTT
1 GGTTTAGGGTTT
*
19160945 GTTTTAGGGTTT
1 GGTTTAGGGTTT
*
19160957 GGTTTATGGTTT
1 GGTTTAGGGTTT
19160969 GG
1 GG
19160971 AGGGGTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.08, C:0.00, G:0.39, T:0.53
Consensus pattern (12 bp):
GGTTTAGGGTTT
Found at i:19161000 original size:28 final size:29
Alignment explanation
Indices: 19160947--19161002 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 29
19160937 TAGGGTTTGT
*
19160947 TTTAGGGTTTGGTTTATGGTTTGGAGGGG
1 TTTAAGGTTTGGTTTATGGTTTGGAGGGG
19160976 TTTAAGGTTTGG-TTATGGTTTGGAGGG
1 TTTAAGGTTTGGTTTATGGTTTGGAGGG
19161003 TGGTTTTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.12, C:0.00, G:0.43, T:0.45
Consensus pattern (29 bp):
TTTAAGGTTTGGTTTATGGTTTGGAGGGG
Found at i:19168107 original size:13 final size:14
Alignment explanation
Indices: 19168085--19168113 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
19168075 GATAAGATTA
19168085 TTTTATTTATAATT
1 TTTTATTTATAATT
19168099 TTTTA-TTATAATT
1 TTTTATTTATAATT
19168112 TT
1 TT
19168114 ACAATAATTC
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTATTTATAATT
Found at i:19168180 original size:11 final size:11
Alignment explanation
Indices: 19168164--19168201 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19168154 TATTTATAAG
19168164 TATAAATTTTA
1 TATAAATTTTA
19168175 TATAAAATTTTA
1 TAT-AAATTTTA
19168187 -ATAAATTTTA
1 TATAAATTTTA
*
19168197 CATAA
1 TATAA
19168202 TTATAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.32
11 9 0.36
12 8 0.32
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
TATAAATTTTA
Found at i:19169091 original size:16 final size:17
Alignment explanation
Indices: 19169059--19169096 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
19169049 TATTTTTACA
19169059 AAAAGAAAAACAAAATT
1 AAAAGAAAAACAAAATT
* *
19169076 TAAAGACAAA-AAAATT
1 AAAAGAAAAACAAAATT
19169092 AAAAG
1 AAAAG
19169097 CATTGAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (17 bp):
AAAAGAAAAACAAAATT
Found at i:19169470 original size:28 final size:28
Alignment explanation
Indices: 19169417--19169470 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
19169407 TAATATAAAA
*
19169417 AAATAAAAAATAAAATAAATATTATATT
1 AAATAAAAAATAAAATAAATACTATATT
* *
19169445 AAATAAATATTAAAATTAAA-ACTATA
1 AAATAAAAAATAAAA-TAAATACTATA
19169471 AACAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 18 0.82
29 4 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (28 bp):
AAATAAAAAATAAAATAAATACTATATT
Found at i:19169673 original size:12 final size:12
Alignment explanation
Indices: 19169656--19169704 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
19169646 TTTTTATATC
19169656 TTTTATATTTAT
1 TTTTATATTTAT
19169668 TTTTATCA-TTAT
1 TTTTAT-ATTTAT
*
19169680 TGTTATATTT-T
1 TTTTATATTTAT
*
19169691 TATTAT-TTTAT
1 TTTTATATTTAT
19169702 TTT
1 TTT
19169705 ATTGTTGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
10 3 0.10
11 10 0.32
12 17 0.55
13 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (12 bp):
TTTTATATTTAT
Found at i:19170590 original size:8 final size:8
Alignment explanation
Indices: 19170577--19170618 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
19170567 AAATCAATCG
19170577 ATAAAAAA
1 ATAAAAAA
19170585 ATAAAAAA
1 ATAAAAAA
19170593 A-AATAAAA
1 ATAA-AAAA
**
19170601 ATACCAAA
1 ATAAAAAA
19170609 ATAAAAAA
1 ATAAAAAA
19170617 AT
1 AT
19170619 TTGATTGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 2 0.07
8 25 0.89
9 1 0.04
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (8 bp):
ATAAAAAA
Found at i:19170787 original size:2 final size:2
Alignment explanation
Indices: 19170780--19170810 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19170770 GATAACTTTA
19170780 AT AT 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 AT AT A
19170811 ATTTTAGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19171016 original size:12 final size:12
Alignment explanation
Indices: 19170995--19171024 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19170985 GAAAATAAAA
19170995 AATAAACAAATC
1 AATAAACAAATC
*
19171007 AATAAGCAAATC
1 AATAAACAAATC
19171019 AATAAA
1 AATAAA
19171025 TAAAAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.67, C:0.13, G:0.03, T:0.17
Consensus pattern (12 bp):
AATAAACAAATC
Found at i:19171157 original size:12 final size:12
Alignment explanation
Indices: 19171140--19171164 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19171130 TTTTCATGCC
19171140 TTAATTAATTTT
1 TTAATTAATTTT
19171152 TTAATTAATTTT
1 TTAATTAATTTT
19171164 T
1 T
19171165 ATGTCTTACA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTAATTAATTTT
Found at i:19171207 original size:441 final size:442
Alignment explanation
Indices: 19170378--19171226 Score: 1144
Period size: 441 Copynumber: 1.9 Consensus size: 442
19170368 ATTTCATCAT
* * * *
19170378 TGGAAAATTATTCATTTATTTCCATTTTTTTAAATTCACATGATACAAATAAATAAATATAATTA
1 TGGAAAATTATTAATTTATTTCCATTTTTTAAAATTCACATGACACAAATAAATAAATAGAATTA
* * * *
19170443 TAAAAAATTTACAAATTTATTTGTCTAACACATATTGTTGATTTTTTTTAAGTTGTTAAATGATT
66 TAAAAAATTTACAAATCTATTTGTCTAACACATATTGTTGAGTTTTTCTAAGTTGTCAAATGATT
* * * * *
19170508 AAAACATATTCTTAATATAAAATTTTAAATATGTAAGTAGATAAAAAAAATCAATAAGCAAATCA
131 AAAACAGATTCTTAATATAAAATTTTAAATATGAAAATAAAAAAAAAAAATCAATAAGCAAATCA
* *
19170573 ATCGATAAAAAAATAAAAAAAAATAAAAATACCAAAATAAAAAAATTTGATTGTCATGCATCAAA
196 ATC-ATAAAAAAATAAAAAAAAATAAAAATACCAAAATAAAAAAATCTGATTGTCATACATCAAA
* * *
19170638 CACAAAGAAAAAATACAAAAGATTCTTTCTCCAAATCACCCCAACCAAAATTTTTCATGCTTTAA
260 CACAAAGAAAAAATACAAAAAAATCTTTCTCCAAATCACCCCAACCAAAATTTTTCATGCCTTAA
* * ** * *
19170703 TTAACCTTTTAATTATTTTTTATGTCTTACCTTAAATGTTTTTGAATTTGAGGAATCTCACATTT
325 TTAACCTTTTAATTAATTTTTATGTCTTACATTAAATGTCCTTGAAATTAAGGAATCTCACATTT
19170768 GAGATAACTTTAATATATATATATATATATATATATATATATAATTTTAGCAC
390 GAGATAACTTTAATATATATATATATATATATATATATATATAATTTTAGCAC
* *
19170821 TGGAAAATTATTAATTTATTTCCTATTTTTTAAAATTTACATGACACAAATAACTAAATAGAATT
1 TGGAAAATTATTAATTTATTTCC-ATTTTTTAAAATTCACATGACACAAATAAATAAATAGAATT
* *
19170886 AT-AAAAA-TTACAAATCTATTTGTCTAACACATATT-TTTAGTTTTTCTATGTTGTCAAATGAT
65 ATAAAAAATTTACAAATCTATTTGTCTAACACATATTGTTGAGTTTTTCTAAGTTGTCAAATGAT
*
19170948 TAAAACAGATTTTTAATATAAAATTTTAATTATCTATGAAAATAAAAAATAAACAAATCAATAAG
130 TAAAACAGATTCTTAATATAAAATTTTAA--A--TATGAAAATAAAAAA-AAA-AAATCAATAAG
* * * * * *
19171013 CAAATCAAT-A-AATAAAA-AAATAAAAAT-AAAATACCTAAATAAAAGAA-CTGATTTTCATAT
189 CAAATCAATCATAAAAAAATAAAAAAAAATAAAAATACCAAAATAAAAAAATCTGATTGTCATAC
* *
19171073 GTCCAAA-ACAAAGAAAAAAATACAAAAAAAAT-TTTCTTCAAATCA-CCCAACCAAAATTTTTC
254 AT-CAAACACAAAG-AAAAAATAC-AAAAAAATCTTTCTCCAAATCACCCCAACCAAAATTTTTC
** **
19171135 ATGCCTTAATTAATTTTTTAATTAATTTTTATGTCTTACATTACGTGTCCTTGAAATTAAGGAAT
316 ATGCCTTAATTAACCTTTTAATTAATTTTTATGTCTTACATTAAATGTCCTTGAAATTAAGGAAT
*
19171200 TTCACATTTGAGATAACTTTAATATAT
381 CTCACATTTGAGATAACTTTAATATAT
19171227 TGTTTTAGAT
Statistics
Matches: 354, Mismatches: 42, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
441 162 0.46
442 70 0.20
443 43 0.12
444 44 0.12
445 12 0.03
446 3 0.01
447 20 0.06
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.37
Consensus pattern (442 bp):
TGGAAAATTATTAATTTATTTCCATTTTTTAAAATTCACATGACACAAATAAATAAATAGAATTA
TAAAAAATTTACAAATCTATTTGTCTAACACATATTGTTGAGTTTTTCTAAGTTGTCAAATGATT
AAAACAGATTCTTAATATAAAATTTTAAATATGAAAATAAAAAAAAAAAATCAATAAGCAAATCA
ATCATAAAAAAATAAAAAAAAATAAAAATACCAAAATAAAAAAATCTGATTGTCATACATCAAAC
ACAAAGAAAAAATACAAAAAAATCTTTCTCCAAATCACCCCAACCAAAATTTTTCATGCCTTAAT
TAACCTTTTAATTAATTTTTATGTCTTACATTAAATGTCCTTGAAATTAAGGAATCTCACATTTG
AGATAACTTTAATATATATATATATATATATATATATATATAATTTTAGCAC
Found at i:19172878 original size:29 final size:28
Alignment explanation
Indices: 19172845--19172974 Score: 130
Period size: 29 Copynumber: 4.7 Consensus size: 28
19172835 AATTTTACTA
19172845 ATTAATAATATTATATTAATAAATAATAT
1 ATTAATAATATTATATTAATAAAT-ATAT
*
19172874 ATTAATAAATATTATTATGAATAAATATTAT
1 ATTAAT-AATATTA-TATTAATAAATA-TAT
*
19172905 ACTAAT-ATATTAATATTAATAAATA-AT
1 ATTAATAATATT-ATATTAATAAATATAT
19172932 ATT-AT-A-A-TATATTAATAAATAT-T
1 ATTAATAATATTATATTAATAAATATAT
*
19172955 ATTAATAAATAATATATTAA
1 ATTAAT-AATATTATATTAA
19172975 AATATTAATA
Statistics
Matches: 87, Mismatches: 4, Indels: 21
0.78 0.04 0.19
Matches are distributed among these distances:
23 17 0.20
24 3 0.03
25 1 0.01
26 4 0.05
27 5 0.06
28 8 0.09
29 22 0.25
30 9 0.10
31 18 0.21
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.44
Consensus pattern (28 bp):
ATTAATAATATTATATTAATAAATATAT
Found at i:19172965 original size:36 final size:35
Alignment explanation
Indices: 19172861--19172988 Score: 147
Period size: 36 Copynumber: 3.7 Consensus size: 35
19172851 AATATTATAT
* *
19172861 TAATAAATAATATATTAATAAATATTATT-ATGAA
1 TAATATATAATATATTAATAAATATTATTAATAAA
* * *
19172895 TAA-ATAT--TATACTAATATATTAATATTAATAAA
1 TAATATATAATATATTAATA-AATATTATTAATAAA
19172928 TAATATTATAATATATTAATAAATATTATTAATAAA
1 TAATA-TATAATATATTAATAAATATTATTAATAAA
*
19172964 TAATATATTAAAATATTAATAAATA
1 TAATATA-TAATATATTAATAAATA
19172989 ACATAAAGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
31 9 0.12
32 7 0.09
33 10 0.13
34 4 0.05
35 5 0.06
36 34 0.44
37 9 0.12
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (35 bp):
TAATATATAATATATTAATAAATATTATTAATAAA
Found at i:19172995 original size:68 final size:68
Alignment explanation
Indices: 19172867--19173000 Score: 175
Period size: 68 Copynumber: 2.0 Consensus size: 68
19172857 ATATTAATAA
* * * *
19172867 ATAATATATTAATAAATATTATTATGAATAAATATTATACTAATATATTAATATTAATAAATAAT
1 ATAATATATTAATAAATATTATTATGAATAAATAATATACTAAAATATTAATATAAATAAAGAAT
19172932 ATT
66 ATT
*
19172935 ATAATATATTAATAAATATTA-T-T-AATAAATAATATATTAAAATATTAATAAATAACATAAAG
1 ATAATATATTAATAAATATTATTATGAATAAATAATATACTAAAATATTAAT--ATAA-ATAAAG
19172997 AATA
63 AATA
19173001 CTAAATAGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
65 23 0.40
66 1 0.02
67 4 0.07
68 30 0.52
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (68 bp):
ATAATATATTAATAAATATTATTATGAATAAATAATATACTAAAATATTAATATAAATAAAGAAT
ATT
Found at i:19173099 original size:15 final size:15
Alignment explanation
Indices: 19173079--19173118 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
19173069 TATAATTATT
*
19173079 TTTTAATATTAATAA
1 TTTTAATATAAATAA
19173094 TTTTAATAATAAATAA
1 TTTTAAT-ATAAATAA
*
19173110 TTTCAATAT
1 TTTTAATAT
19173119 GTTTTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTAATATAAATAA
Found at i:19173151 original size:17 final size:18
Alignment explanation
Indices: 19173105--19173151 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
19173095 TTTAATAATA
19173105 AATAATTTCAATATGTTTT
1 AATAATTT-AATATGTTTT
*
19173124 AATAA-TAAATAT-TTTT
1 AATAATTTAATATGTTTT
*
19173140 TATAATTTAATA
1 AATAATTTAATA
19173152 GTTATATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 8 0.33
17 10 0.42
18 1 0.04
19 5 0.21
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
AATAATTTAATATGTTTT
Found at i:19173610 original size:22 final size:21
Alignment explanation
Indices: 19173585--19173637 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
19173575 TGGAGCAAAT
19173585 GTTGAAAAATCTTGAAGAACCA
1 GTTGAAAAA-CTTGAAGAACCA
* *
19173607 GTTGAACAAACTTGAAGAGCTA
1 GTTGAA-AAACTTGAAGAACCA
19173629 GTTGAAAAA
1 GTTGAAAAA
19173638 ATATTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 22 0.79
23 3 0.11
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (21 bp):
GTTGAAAAACTTGAAGAACCA
Found at i:19175127 original size:18 final size:19
Alignment explanation
Indices: 19175106--19175151 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
19175096 TTTACTGTTG
* *
19175106 TTATTTCTTATT-TAGTTT
1 TTATTTCTAATTCTAATTT
19175124 TTA-TTCTAATTCTAATTT
1 TTATTTCTAATTCTAATTT
19175142 TTAATTTCTA
1 TT-ATTTCTA
19175152 TTATTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.30
18 10 0.43
19 1 0.04
20 5 0.22
ACGTcount: A:0.24, C:0.09, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATTTCTAATTCTAATTT
Found at i:19177005 original size:3 final size:3
Alignment explanation
Indices: 19176997--19177055 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
19176987 TTTTTAAAAT
19176997 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19177045 TTA TTA TTA TT
1 TTA TTA TTA TT
19177056 GTTAATTTGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:19177536 original size:26 final size:26
Alignment explanation
Indices: 19177481--19177536 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
19177471 AATTTTGACT
* * * *
19177481 AATTATGGTAGGAGAAATATTTCCAT
1 AATTATGATAAGAGAAATATTTCAAC
19177507 AATTATGATAAGAGAAATATTAT-AAC
1 AATTATGATAAGAGAAATATT-TCAAC
19177533 AATT
1 AATT
19177537 TTTGTTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.34
Consensus pattern (26 bp):
AATTATGATAAGAGAAATATTTCAAC
Found at i:19178244 original size:61 final size:61
Alignment explanation
Indices: 19178054--19178225 Score: 159
Period size: 61 Copynumber: 2.8 Consensus size: 61
19178044 GGTAGGGGGC
* ** * ** **
19178054 ATTATAATAATTTTTATTAATTATGGTAAGAAGGATATTTTTTGTAATTATCA-T-AGAAATGTT
1 ATTATAGTAATTTTGGTTAATTATGGT-AGAAAGATA-TTTTCATAATTA-CAGTAAGAAA-AAT
* * * * *
19178117 ATTAAAGTAACTTTGATCAATTATGGTAGAAAGATATTTTCATAATTACAGTAAGAAAAAC
1 ATTATAGTAATTTTGGTTAATTATGGTAGAAAGATATTTTCATAATTACAGTAAGAAAAAT
*
19178178 ATTATAGTAATTTTGGTTAATTATGGTAGCAAAGATATTTTCGTAATT
1 ATTATAGTAATTTTGGTTAATTATGGTAG-AAAGATATTTTCATAATT
19178226 GTGGTAAGAG
Statistics
Matches: 90, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
60 2 0.02
61 36 0.40
62 30 0.33
63 22 0.24
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (61 bp):
ATTATAGTAATTTTGGTTAATTATGGTAGAAAGATATTTTCATAATTACAGTAAGAAAAAT
Found at i:19178290 original size:654 final size:654
Alignment explanation
Indices: 19177171--19178484 Score: 1981
Period size: 654 Copynumber: 2.0 Consensus size: 654
19177161 AATTTCATAT
19177171 GTAATTTAATAAGGATCTTATAGAAAATTTCAAATAAAATATCACATGTCAAATTTCTAAAAAGT
1 GTAATTTAATAAGGATCTTATAGAAAATTTCAAATAAAATATCACATGTCAAATTTCTAAAAAGT
*
19177236 AATGATAAAGGTATTTTAGTAATTTAATATGTGATTAATTTTATATTATATTAAAATTTAATATG
66 AATGATAAAGGTATTTTAGTAATTTAATATGTGATTAATTTTATATTATATTAAAAATTAATATG
*
19177301 CAATTTAATAGGGGCATTTGAGTAATTTTAAAATAAATACCACATATCAACTTGTTATGAAACAC
131 CAATTTAATAGGAGCATTTGAGTAATTTTAAAATAAATACCACATATCAACTTGTTATGAAACAC
* * *
19177366 TTATAAAGATATTTTCATAATTATGGTCGAAGACATTAGAGTAATTTTGGTTAATTATGGTAGAA
196 TTATAAAGATATTTTCATAATTATGGTAGAAGACATTAGAATAATTTTGATTAATTATGGTAGAA
* * *
19177431 AGGATATTTTTCTTAATTATGATAGGAATGTTATTAAAGTAATTTTGACTAATTATGGTAGGAGA
261 AGGATATTTTTCTTAATTATCATAGAAATGTTATTAAAGTAACTTTGACTAATTATGGTAGGAGA
* * * * *
19177496 AATATTTCCATAATTATGATAAGAGAAATATTATAACAATTTTTGTTAATTATGGTAGTAAAGAC
326 AATATTTCCATAATTAAGATAAGAAAAACATTATAACAATTTTGGTTAATTATGGTAGCAAAGAC
* * *
19177561 ATTTTTGTAATTATGGTAAGAGGGTATTATAATAATTTTGACTAATTATGAGAATAAGGTATTTT
391 ATTTTCGTAATTATGGTAAGAGGGTATTATAAAAATTTTGACTAATTATGAGAATAAGGTATTTC
** *
19177626 CGTAATTATAATATAATGGCATTATAGTAAATTTGGATATGCGTCAATTTCTTATCAAATAAATA
456 CGTAATTATAATATAATAACATTATAGTAAATTTGGACATGCGTCAATTTCTTATCAAATAAATA
* * * *
19177691 AAAGGTTATTATAATAATTTTCATACAAATTGTTTTAATGTATAGTTATTGATTATTGATTATTT
521 AAAGGATATTATAATAATTTTCATACAAATTGCTTTAATATATAGTTATTGATTATTAATTATTT
* * *
19177756 TATTTTCAATGTTGGAAAGTGAACAATTTTTTATTTTTTTATTTGAAATGTTTAAACCAAATTAT
586 TATTTTCAATGTTGGAAAGTGAACAATTATTTA-TTTGTTATTTGAAATGTTCAAACCAAATTAT
19177821 TTTGA
650 TTTGA
* * * * *
19177826 GTAATTTAATAAGGGTCTTATAGTAACTTTTAAATAAAATATCACATGTCAAATTTCTCAAAAGT
1 GTAATTTAATAAGGATCTTATAGAAAATTTCAAATAAAATATCACATGTCAAATTTCTAAAAAGT
*
19177891 AATGA-AAATGGTA-TTTAGTAATTTAATATGTGATTAATTTTATATTATATTAAAAATTAATTT
66 AATGATAAA-GGTATTTTAGTAATTTAATATGTGATTAATTTTATATTATATTAAAAATTAATAT
*
19177954 GTAATTTAATA-GAG-ATGTTAGAGTAATTTTAAAATAAAT-CTCACATATCAACTTGTTATGAA
130 GCAATTTAATAGGAGCAT-TT-GAGTAATTTTAAAATAAATAC-CACATATCAACTTGTTATGAA
** * * *
19178016 ACACTTATAAATG-TATTTTCATAATTATGGTAGGGGGCATTATAATAATTTTTATTAATTATGG
192 ACACTTATAAA-GATATTTTCATAATTATGGTAGAAGACATTAGAATAATTTTGATTAATTATGG
19178080 TA-AGAAGGATATTTTT-TGTAATTATCATAGAAATGTTATTAAAGTAACTTTGA-TCAATTATG
256 TAGA-AAGGATATTTTTCT-TAATTATCATAGAAATGTTATTAAAGTAACTTTGACT-AATTATG
* **
19178142 GTA-GA-AAGATATTTTCATAATTACAG-TAAGAAAAACATTATAGTAATTTTGGTTAATTATGG
318 GTAGGAGAA-ATATTTCCATAATTA-AGATAAGAAAAACATTATAACAATTTTGGTTAATTATGG
* *
19178204 TAGCAAAGATATTTTCGTAATTGTGGTAAGAGGGTATTATAAAAATTTT-AGCTAATTATGAGAA
381 TAGCAAAGACATTTTCGTAATTATGGTAAGAGGGTATTATAAAAATTTTGA-CTAATTATGAGAA
*
19178268 T-AGTAGTATTTCCGTAATTATAATATAATAACATTATAGTAAATTTGGACATGTGTCAATTTCT
445 TAAG--GTATTTCCGTAATTATAATATAATAACATTATAGTAAATTTGGACATGCGTCAATTTCT
* * *
19178332 TATCAAATAAATAAAGGGATATTATAATAATTTTCATGCGAATTGCTTTAATATATAGTTATTGA
508 TATCAAATAAATAAAAGGATATTATAATAATTTTCATACAAATTGCTTTAATATATAGTTATTGA
19178397 TTATTAATTATTTTATTTTCAATGTTGGAAAGTGAACAATTATTTATTTGTTATTTGAAATGTTC
573 TTATTAATTATTTTATTTTCAATGTTGGAAAGTGAACAATTATTTATTTGTTATTTGAAATGTTC
19178462 AAACCAAATTATTTTGA
638 AAACCAAATTATTTTGA
19178479 GTAATT
1 GTAATT
19178485 AAAAAATACA
Statistics
Matches: 599, Mismatches: 47, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
652 7 0.01
653 153 0.26
654 369 0.62
655 70 0.12
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.42
Consensus pattern (654 bp):
GTAATTTAATAAGGATCTTATAGAAAATTTCAAATAAAATATCACATGTCAAATTTCTAAAAAGT
AATGATAAAGGTATTTTAGTAATTTAATATGTGATTAATTTTATATTATATTAAAAATTAATATG
CAATTTAATAGGAGCATTTGAGTAATTTTAAAATAAATACCACATATCAACTTGTTATGAAACAC
TTATAAAGATATTTTCATAATTATGGTAGAAGACATTAGAATAATTTTGATTAATTATGGTAGAA
AGGATATTTTTCTTAATTATCATAGAAATGTTATTAAAGTAACTTTGACTAATTATGGTAGGAGA
AATATTTCCATAATTAAGATAAGAAAAACATTATAACAATTTTGGTTAATTATGGTAGCAAAGAC
ATTTTCGTAATTATGGTAAGAGGGTATTATAAAAATTTTGACTAATTATGAGAATAAGGTATTTC
CGTAATTATAATATAATAACATTATAGTAAATTTGGACATGCGTCAATTTCTTATCAAATAAATA
AAAGGATATTATAATAATTTTCATACAAATTGCTTTAATATATAGTTATTGATTATTAATTATTT
TATTTTCAATGTTGGAAAGTGAACAATTATTTATTTGTTATTTGAAATGTTCAAACCAAATTATT
TTGA
Found at i:19182144 original size:44 final size:43
Alignment explanation
Indices: 19182038--19182247 Score: 183
Period size: 44 Copynumber: 4.8 Consensus size: 43
19182028 ATGACTTTTG
* * *
19182038 AAAGGCTCAACGACTTT-AAAAAATAAATAAGGTTCCTCTAAAC
1 AAAGGCTTAATGACTTTGAAAAAA-AAATAAGGCTCCTCTAAAC
* * * * *
19182081 AGAGGCTCAACGACTTTGAAAAAAAAATAAAGCTCCTCTAAGC
1 AAAGGCTTAATGACTTTGAAAAAAAAATAAGGCTCCTCTAAAC
* ** * * *
19182124 AAATGCTTAATGACTTTTGAAAAGTAAATAAGGTTCTTCTAAAT
1 AAAGGCTTAATGAC-TTTGAAAAAAAAATAAGGCTCCTCTAAAC
** *
19182168 AGGGGCTTAACT-ACTTTTGAAAAATAAATAAGGCTCCT-TAAAAC
1 AAAGGCTTAA-TGAC-TTTGAAAAAAAAATAAGGCTCCTCT-AAAC
*
19182212 AAAGGCATAATGACTTTGAAAAAATAAATAAGGCTC
1 AAAGGCTTAATGACTTTGAAAAAA-AAATAAGGCTC
19182248 TTCGATAGTC
Statistics
Matches: 135, Mismatches: 26, Indels: 11
0.78 0.15 0.06
Matches are distributed among these distances:
43 53 0.39
44 81 0.60
45 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (43 bp):
AAAGGCTTAATGACTTTGAAAAAAAAATAAGGCTCCTCTAAAC
Found at i:19182225 original size:88 final size:87
Alignment explanation
Indices: 19182049--19182250 Score: 248
Period size: 88 Copynumber: 2.3 Consensus size: 87
19182039 AAGGCTCAAC
*
19182049 GACTTT-AAAAAATAAATAAGGTTCCTCTAAACAGAGGCTCAACGACTTTGAAAAAAAAATAAAG
1 GACTTTGAAAAAATAAATAAGGTTCTTCTAAACAGAGGCTCAACGACTTTGAAAAAAAAATAAAG
* * *
19182113 CTCCTCTAAGCAAATGCTTAAT
66 CTCCTCTAAACAAAGGCATAAT
* * * * * *
19182135 GACTTTTG-AAAAGTAAATAAGGTTCTTCTAAATAGGGGCTTAACTACTTTTGAAAAATAAATAA
1 GAC-TTTGAAAAAATAAATAAGGTTCTTCTAAACAGAGGCTCAACGAC-TTTGAAAAAAAAATAA
*
19182199 GGCTCCT-TAAAACAAAGGCATAAT
64 AGCTCCTCT-AAACAAAGGCATAAT
*
19182223 GACTTTGAAAAAATAAATAAGGCTCTTC
1 GACTTTGAAAAAATAAATAAGGTTCTTC
19182251 GATAGTCATG
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
86 3 0.03
87 41 0.42
88 54 0.55
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (87 bp):
GACTTTGAAAAAATAAATAAGGTTCTTCTAAACAGAGGCTCAACGACTTTGAAAAAAAAATAAAG
CTCCTCTAAACAAAGGCATAAT
Found at i:19182372 original size:3 final size:3
Alignment explanation
Indices: 19182357--19182530 Score: 172
Period size: 3 Copynumber: 61.7 Consensus size: 3
19182347 TTTTTGGTTG
* * * *
19182357 TTA TTA GTA TTA TTA TTA TTT TTA TTA CTA GTA TTA -TA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
19182403 GTA -TA GTA -TA TT- CTA TTA -TA TTA -TA CTA -TA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
19182444 -TA TTA -TA TTA TTA TTA ATA TTA TTA TTA TCA TTA TTA TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
19182490 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19182531 TTAATTTATT
Statistics
Matches: 145, Mismatches: 15, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
2 21 0.14
3 124 0.86
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:19182424 original size:28 final size:28
Alignment explanation
Indices: 19182388--19182529 Score: 111
Period size: 28 Copynumber: 5.0 Consensus size: 28
19182378 TTATTACTAG
*
19182388 TATTATATTATTATAGTA-TAGTATATTC
1 TATTATATTATTATA-TATTAGTATATTA
*
19182416 TATTATATTA-TACTATATTATTATATTA
1 TATTATATTATTA-TATATTAGTATATTA
19182444 TATTATATTATTATTAATATTA-T-TATTA
1 TATTATATTATTA-T-ATATTAGTATATTA
*
19182472 TCATTATTATTATTAT-TGTTA-T-TATTA
1 T-ATTA-TATTATTATATATTAGTATATTA
*
19182499 TTATTATTATTATTAT-TATTATTATTATTA
1 -TATTA-TATTATTATATATTAGTA-TATTA
19182529 T
1 T
19182530 TTTAATTTAT
Statistics
Matches: 99, Mismatches: 5, Indels: 19
0.80 0.04 0.15
Matches are distributed among these distances:
27 32 0.32
28 38 0.38
29 10 0.10
30 19 0.19
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (28 bp):
TATTATATTATTATATATTAGTATATTA
Found at i:19183227 original size:20 final size:19
Alignment explanation
Indices: 19183195--19183238 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
19183185 GTTTTTCTTA
19183195 TTTTATTTTATTTTT-ATT
1 TTTTATTTTATTTTTAATT
19183213 TTTTGATTTTGATTTTTAATT
1 TTTT-ATTTT-ATTTTTAATT
19183234 TTTTA
1 TTTTA
19183239 ATTATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.17
19 5 0.22
20 7 0.30
21 7 0.30
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTTATTTTATTTTTAATT
Found at i:19193975 original size:72 final size:72
Alignment explanation
Indices: 19193894--19194037 Score: 252
Period size: 72 Copynumber: 2.0 Consensus size: 72
19193884 TGATGTGCCA
*
19193894 ATTTTGACCTCTTTCTTATTCTTCTCATTTTTTAAGTTCACCAATTCAGTTACCTCCTGATGAGG
1 ATTTTGACCTCTTTCTTATTCTTCTCATTTTCTAAGTTCACCAATTCAGTTACCTCCTGATGAGG
19193959 CTTAATT
66 CTTAATT
* * *
19193966 ATTTTGACCTCTTTCTTGTTTTTCTCATTTTCTAAGTTCACCAATTCAGTTACCTCTTGATGAGG
1 ATTTTGACCTCTTTCTTATTCTTCTCATTTTCTAAGTTCACCAATTCAGTTACCTCCTGATGAGG
19194031 CTTAATT
66 CTTAATT
19194038 GGTTTATTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.48
Consensus pattern (72 bp):
ATTTTGACCTCTTTCTTATTCTTCTCATTTTCTAAGTTCACCAATTCAGTTACCTCCTGATGAGG
CTTAATT
Found at i:19198023 original size:50 final size:45
Alignment explanation
Indices: 19197904--19198047 Score: 182
Period size: 44 Copynumber: 3.1 Consensus size: 45
19197894 ATTTTACAAG
* * *
19197904 TTTTATTTTTAAATTTTTCACCATTCGGGCCAATTTAGAATTTTT
1 TTTTATTTTTAAATTTTTCACCATTTGGGTCTATTTAGAATTTTT
19197949 TTTTATTTTTAAA-TTTTCACCATTTGGGTCTATTTAGAATTTTT
1 TTTTATTTTTAAATTTTTCACCATTTGGGTCTATTTAGAATTTTT
* *
19197993 CTATTTGATTTCTAAATTTTTTCCACCATTTGGATCTATTTAGAATTATTT
1 -T-TTT-ATTTTTAAA-TTTTT-CACCATTTGGGTCTATTTAGAATT-TTT
19198044 TTTT
1 TTTT
19198048 GTCTTTTTAT
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
44 28 0.32
45 14 0.16
46 3 0.03
47 8 0.09
49 7 0.08
50 24 0.28
51 3 0.03
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (45 bp):
TTTTATTTTTAAATTTTTCACCATTTGGGTCTATTTAGAATTTTT
Found at i:19198319 original size:5 final size:4
Alignment explanation
Indices: 19198297--19198346 Score: 57
Period size: 4 Copynumber: 12.2 Consensus size: 4
19198287 AATATTTTAA
* *
19198297 AAAT AAAT AAAC AAAT AAAAT AACT AAAT AAAT AAAT AAAAT AAA- AAAT
1 AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT
19198346 A
1 A
19198347 CCAAAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 3 0.08
4 28 0.72
5 8 0.21
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:19198325 original size:21 final size:21
Alignment explanation
Indices: 19198300--19198340 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
19198290 ATTTTAAAAA
19198300 TAAATAAACAAATAAAATAAC
1 TAAATAAACAAATAAAATAAC
*
19198321 TAAATAAATAAATAAAATAA
1 TAAATAAACAAATAAAATAA
19198341 AAAATACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAATAAACAAATAAAATAAC
Found at i:19198336 original size:12 final size:12
Alignment explanation
Indices: 19198297--19198346 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 12
19198287 AATATTTTAA
*
19198297 AAATAAATAAAC
1 AAATAAATAAAT
*
19198309 AAATAAAATAACT
1 AAAT-AAATAAAT
19198322 AAATAAATAAAT
1 AAATAAATAAAT
19198334 AAAATAAA-AAAT
1 -AAATAAATAAAT
19198346 A
1 A
19198347 CCAAAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
11 1 0.03
12 15 0.45
13 17 0.52
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (12 bp):
AAATAAATAAAT
Found at i:19199020 original size:19 final size:20
Alignment explanation
Indices: 19199006--19199047 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
19198996 AATTTTAATT
19199006 CAACTCAAACTTTTTCAATC
1 CAACTCAAACTTTTTCAATC
*
19199026 CACCTCAAAC-TTTTCAATC
1 CAACTCAAACTTTTTCAATC
19199045 CAA
1 CAA
19199048 GTTTTACACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (20 bp):
CAACTCAAACTTTTTCAATC
Found at i:19200389 original size:3 final size:3
Alignment explanation
Indices: 19200381--19200415 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19200371 AGCAAACTCT
19200381 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
19200416 GGGTTTCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:19207707 original size:33 final size:34
Alignment explanation
Indices: 19207669--19207744 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
19207659 ATTTTATTTT
* ** * *
19207669 TAAAAATTTATGTATCTTAATA-TTTTTATATAA
1 TAAAAATTTATATATAATAAAATTTTTTAAATAA
19207702 TAAAAATTTATATATAATAAAATTTTTTAAATAA
1 TAAAAATTTATATATAATAAAATTTTTTAAATAA
19207736 -AAAAATTTA
1 TAAAAATTTA
19207745 AGCTTTCAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 27 0.73
34 10 0.27
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (34 bp):
TAAAAATTTATATATAATAAAATTTTTTAAATAA
Found at i:19207713 original size:15 final size:16
Alignment explanation
Indices: 19207692--19207738 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
19207682 ATCTTAATAT
19207692 TTTTATATAATAAAAA
1 TTTTATATAATAAAAA
19207708 TTTATATATAAT-AAAA
1 TTT-TATATAATAAAAA
*
19207724 TTTTTTA-AATAAAAA
1 TTTTATATAATAAAAA
19207739 AATTTAAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 3 0.11
15 7 0.25
16 10 0.36
17 8 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTTATATAATAAAAA
Found at i:19207715 original size:17 final size:17
Alignment explanation
Indices: 19207690--19207744 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
19207680 GTATCTTAAT
*
19207690 ATTTTTATATAATAAAA
1 ATTTATATATAATAAAA
19207707 ATTTATATATAATAAAA
1 ATTTATATATAATAAAA
* * *
19207724 TTTTTTAAATAA-AAAA
1 ATTTATATATAATAAAA
19207740 ATTTA
1 ATTTA
19207745 AGCTTTCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 7 0.22
17 25 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTTATATATAATAAAA
Found at i:19207725 original size:16 final size:16
Alignment explanation
Indices: 19207671--19207726 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
19207661 TTTATTTTTA
* **
19207671 AAAATTTATGTATCTT
1 AAAATTTATATATAAT
* *
19207687 AATATTTTTATATAAT
1 AAAATTTATATATAAT
19207703 AAAAATTTATATATAAT
1 -AAAATTTATATATAAT
19207720 AAAATTT
1 AAAATTT
19207727 TTTAAATAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
16 18 0.56
17 14 0.44
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
AAAATTTATATATAAT
Found at i:19208619 original size:21 final size:23
Alignment explanation
Indices: 19208574--19208620 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
19208564 GAAATATTAG
*
19208574 ATTTTTATTAGGTTACTATTTCA
1 ATTTGTATTAGGTTACTATTTCA
*
19208597 ATTTGTATTTGGTTA-TA-TTCA
1 ATTTGTATTAGGTTACTATTTCA
19208618 ATT
1 ATT
19208621 ATTTCAGGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 2 0.09
23 13 0.59
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (23 bp):
ATTTGTATTAGGTTACTATTTCA
Found at i:19210034 original size:22 final size:21
Alignment explanation
Indices: 19210008--19210083 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 21
19209998 TAGTGAAACA
19210008 ATAATAATATAATAATAAATGC
1 ATAATAATATAATAATAAAT-C
* * *
19210030 ATAATATTTTAATAGTAAATC
1 ATAATAATATAATAATAAATC
* *
19210051 AATTATAATATAATTATAAATCC
1 -ATAATAATATAATAATAAAT-C
*
19210074 ATAACAATAT
1 ATAATAATAT
19210084 GGTACGAAGT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 1 0.02
22 40 0.95
23 1 0.02
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.37
Consensus pattern (21 bp):
ATAATAATATAATAATAAATC
Found at i:19210124 original size:22 final size:22
Alignment explanation
Indices: 19210098--19210207 Score: 87
Period size: 22 Copynumber: 5.0 Consensus size: 22
19210088 CGAAGTTAAA
*
19210098 GATAACTTAATAAAAAATAAGT
1 GATAACTTAATAATAAATAAGT
* * * *
19210120 GATAACTTAGTAATTAATTATT
1 GATAACTTAATAATAAATAAGT
*
19210142 AATAACTTAATAATAAATCAA-T
1 GATAACTTAATAATAAAT-AAGT
* * * *
19210164 GATAATTTAATAGTAAATTAGG
1 GATAACTTAATAATAAATAAGT
* **
19210186 GATAATTTAATAGCAAATAAGT
1 GATAACTTAATAATAAATAAGT
19210208 TTCAATTTAA
Statistics
Matches: 69, Mismatches: 17, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
21 1 0.01
22 67 0.97
23 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.35
Consensus pattern (22 bp):
GATAACTTAATAATAAATAAGT
Found at i:19210183 original size:44 final size:44
Alignment explanation
Indices: 19210099--19210523 Score: 138
Period size: 44 Copynumber: 9.9 Consensus size: 44
19210089 GAAGTTAAAG
** * * * *
19210099 ATAACTTAATAAAAAAT-AAGTGATAACTTAGTAATTAATTATTA
1 ATAACTTAATAGTAAATCAA-TGATAATTTAATAGTAAATTATTA
* ***
19210143 ATAACTTAATAATAAATCAATGATAATTTAATAGTAAATTAGGG
1 ATAACTTAATAGTAAATCAATGATAATTTAATAGTAAATTATTA
* * *
19210187 ATAATTTAATAGCAAAT-AA-GTTTCAATTTAATAGT-AATTAATTA
1 ATAACTTAATAGTAAATCAATG-AT-AATTTAATAGTAAATT-ATTA
* * * * * *
19210231 ATAA--T-A-GGT-ATTC-ATTAAAATTTAAAAGTAAATTAAT-
1 ATAACTTAATAGTAAATCAATGATAATTTAATAGTAAATTATTA
** ** *
19210268 ATAACTTTGTAGTAAATC-ATCGATAATTTAATA-TAAAACAGTA
1 ATAACTTAATAGTAAATCAAT-GATAATTTAATAGTAAATTATTA
* * * * *
19210311 AT-ACTTAATAGTGAAT-TATAGATAATTTAGT-GACAAATAATTA
1 ATAACTTAATAGTAAATCAAT-GATAATTTAATAG-TAAATTATTA
* * ** *
19210354 A-AAATTAACTAGTAAATCAATTATAACATAATAATAAA-TATATA
1 ATAACTTAA-TAGTAAATCAATGATAATTTAATAGTAAATTAT-TA
* * * *
19210398 A-AAATATAATAATAAATCATTGATAATTTAGTAGT-AA--ATTA
1 ATAACT-TAATAGTAAATCAATGATAATTTAATAGTAAATTATTA
** * * * ** * *
19210439 ATAACTTAGCATTAAATCACTAATAACATAATAGTAAAGTAGTA
1 ATAACTTAATAGTAAATCAATGATAATTTAATAGTAAATTATTA
* * * * *
19210483 ATAACTTAGTTGTAAATTAGTGATAATTTAATAATAAATTA
1 ATAACTTAATAGTAAATCAATGATAATTTAATAGTAAATTA
19210524 GTTGATTATT
Statistics
Matches: 276, Mismatches: 78, Indels: 54
0.68 0.19 0.13
Matches are distributed among these distances:
37 4 0.01
38 12 0.04
39 8 0.03
40 1 0.00
41 27 0.10
42 43 0.16
43 34 0.12
44 140 0.51
45 7 0.03
ACGTcount: A:0.50, C:0.05, G:0.08, T:0.36
Consensus pattern (44 bp):
ATAACTTAATAGTAAATCAATGATAATTTAATAGTAAATTATTA
Found at i:19210616 original size:22 final size:22
Alignment explanation
Indices: 19210591--19210695 Score: 90
Period size: 22 Copynumber: 4.8 Consensus size: 22
19210581 AATTTTATAA
*
19210591 TAAATCATTAATAACTTAGTAG
1 TAAATCATTCATAACTTAGTAG
* * * * *
19210613 TAAATCACTAACAA-TCATTAG
1 TAAATCATTCATAACTTAGTAG
19210634 TAAATCATTCATAACTTA--ACG
1 TAAATCATTCATAACTTAGTA-G
* *
19210655 ACAAATCATTCATAAATTAGTAG
1 -TAAATCATTCATAACTTAGTAG
*
19210678 CAAATCATTCATAACTTA
1 TAAATCATTCATAACTTA
19210696 ACTATACATC
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
20 1 0.01
21 17 0.25
22 47 0.70
23 1 0.01
24 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.32
Consensus pattern (22 bp):
TAAATCATTCATAACTTAGTAG
Found at i:19211273 original size:22 final size:22
Alignment explanation
Indices: 19211248--19211313 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
19211238 TCATCAATAG
*
19211248 CTTAATAGTTAATCAATGATAA
1 CTTAATAGTAAATCAATGATAA
*
19211270 CTTAATAGTAAAT-TATGGATAA
1 CTTAATAGTAAATCAAT-GATAA
*
19211292 -TTAATA-TAAAGCAATGATAA
1 CTTAATAGTAAATCAATGATAA
19211312 CT
1 CT
19211314 CGATAATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 9 0.24
21 11 0.30
22 17 0.46
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.35
Consensus pattern (22 bp):
CTTAATAGTAAATCAATGATAA
Done.