Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 142 of 193
Found at i:44372707 original size:28 final size:28
Alignment explanation
Indices: 44372676--44372733 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
44372666 TATACCGGTG
44372676 TAAGTAGACTCCTCCTTTTATTTTTTTA
1 TAAGTAGACTCCTCCTTTTATTTTTTTA
44372704 TAAGTAGACTCCTCCTTTTATTTTTTTA
1 TAAGTAGACTCCTCCTTTTATTTTTTTA
44372732 TA
1 TA
44372734 TATATAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.53
Consensus pattern (28 bp):
TAAGTAGACTCCTCCTTTTATTTTTTTA
Found at i:44374559 original size:31 final size:31
Alignment explanation
Indices: 44374497--44374559 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
44374487 CAACCCAGTT
* * *
44374497 ACTTAAATAAAAACTTTCAAGTAGTTTAATA
1 ACTTAAATAAAAACTTACAAATAGTTCAATA
*
44374528 ACTTAAATGAAAACTTACAAATA-TTGCAATA
1 ACTTAAATAAAAACTTACAAATAGTT-CAATA
44374559 A
1 A
44374560 TCATTTTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (31 bp):
ACTTAAATAAAAACTTACAAATAGTTCAATA
Found at i:44376520 original size:10 final size:10
Alignment explanation
Indices: 44376480--44376555 Score: 72
Period size: 10 Copynumber: 7.8 Consensus size: 10
44376470 TTCTAAAATC
44376480 TTAATAATAAT
1 TTAATAAT-AT
44376491 TTAAT-AT-T
1 TTAATAATAT
44376499 TTAATAAATAT
1 TTAAT-AATAT
44376510 TTAATAATAT
1 TTAATAATAT
*
44376520 TT-ATAATGT
1 TTAATAATAT
44376529 TT-ATAA-ATT
1 TTAATAATA-T
*
44376538 TTAATAAGAT
1 TTAATAATAT
44376548 TTAATAAT
1 TTAATAAT
44376556 TTGTTATATT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
8 6 0.11
9 15 0.27
10 23 0.41
11 12 0.21
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (10 bp):
TTAATAATAT
Found at i:44376554 original size:29 final size:29
Alignment explanation
Indices: 44376475--44376557 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
44376465 TAAGTTTCTA
*
44376475 AAATCTTAATAATAATTTAAT-ATTTTAAT
1 AAATTTTAATAA-AATTTAATAATTTTAAT
*
44376504 AAATATTTAATAATATTT-ATAATGTTT-AT
1 AAAT-TTTAATAAAATTTAATAAT-TTTAAT
*
44376533 AAATTTTAATAAGATTTAATAATTT
1 AAATTTTAATAAAATTTAATAATTT
44376558 GTTATATTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
28 16 0.34
29 21 0.45
30 10 0.21
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (29 bp):
AAATTTTAATAAAATTTAATAATTTTAAT
Found at i:44376556 original size:19 final size:19
Alignment explanation
Indices: 44376455--44376557 Score: 72
Period size: 19 Copynumber: 5.4 Consensus size: 19
44376445 GATTTTTCTT
* *
44376455 ATAATTTTTATAAGTTTCTA
1 ATAATTTTAATAAGATT-TA
* *
44376475 A-AATCTTAATAATAATTTA
1 ATAATTTTAATAA-GATTTA
*
44376494 AT-ATTTTAATAAATATTTA
1 ATAATTTTAAT-AAGATTTA
44376513 ATAATATTT-ATAATG-TTT-
1 ATAAT-TTTAATAA-GATTTA
44376531 ATAAATTTTAATAAGATTTA
1 AT-AATTTTAATAAGATTTA
44376551 ATAATTT
1 ATAATTT
44376558 GTTATATTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 21
0.70 0.07 0.22
Matches are distributed among these distances:
18 6 0.09
19 46 0.70
20 11 0.17
21 3 0.05
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (19 bp):
ATAATTTTAATAAGATTTA
Found at i:44379239 original size:18 final size:17
Alignment explanation
Indices: 44379213--44379265 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
44379203 TTTAGACCAC
*
44379213 AATTAAAAATTATAAAA
1 AATTTAAAATTATAAAA
*
44379230 TAATTTAAAAATATAAAA
1 -AATTTAAAATTATAAAA
*
44379248 AAATTAAAATT-TAAAA
1 AATTTAAAATTATAAAA
44379264 AA
1 AA
44379266 AATCAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 7 0.23
17 9 0.29
18 15 0.48
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AATTTAAAATTATAAAA
Found at i:44379267 original size:17 final size:17
Alignment explanation
Indices: 44379213--44379274 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
44379203 TTTAGACCAC
*
44379213 AATTAAAAATTATAAAATA
1 AATT-AAAATT-TAAAAAA
* *
44379232 ATTTAAAA-ATATAAAAA
1 AATTAAAATTTA-AAAAA
44379249 AATTAAAATTTAAAAAA
1 AATTAAAATTTAAAAAA
*
44379266 AATCAAAAT
1 AATTAAAAT
44379275 AATAATTTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 2 0.06
17 24 0.69
18 6 0.17
19 3 0.09
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
AATTAAAATTTAAAAAA
Found at i:44379364 original size:28 final size:30
Alignment explanation
Indices: 44379340--44379393 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
44379330 TTTTATAATT
44379340 TTATTTT-AATTT-T-TTTTCAAATATATA
1 TTATTTTAAATTTATGTTTTCAAATATATA
*
44379367 TTATTTTAAATTTATGTTTTCTAATAT
1 TTATTTTAAATTTATGTTTTCAAATAT
44379394 GAAATTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.30
28 5 0.22
29 1 0.04
30 10 0.43
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (30 bp):
TTATTTTAAATTTATGTTTTCAAATATATA
Found at i:44380186 original size:22 final size:23
Alignment explanation
Indices: 44380149--44380219 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
44380139 AAAACCACAA
44380149 TATATTTTTATATCAATTTTTTT
1 TATATTTTTATATCAATTTTTTT
* *
44380172 TATATTTTTA-CTCAATTTTTTA
1 TATATTTTTATATCAATTTTTTT
* * *
44380194 CAAATTTTTTATAT-AATTATTTT
1 TATA-TTTTTATATCAATTTTTTT
44380217 TAT
1 TAT
44380220 CCGCATCGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
22 12 0.32
23 24 0.65
24 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.65
Consensus pattern (23 bp):
TATATTTTTATATCAATTTTTTT
Found at i:44384548 original size:19 final size:17
Alignment explanation
Indices: 44384524--44384560 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
44384514 AAAAAGAAAT
44384524 TAAAATAAATAATATATTA
1 TAAAAT-AAT-ATATATTA
44384543 TAAAATAATATATATTA
1 TAAAATAATATATATTA
44384560 T
1 T
44384561 CTGTTAAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 3 0.17
19 6 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATAATATATATTA
Found at i:44385493 original size:18 final size:18
Alignment explanation
Indices: 44385470--44385512 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
44385460 GTTCAATGTG
44385470 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
44385488 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
44385506 TAATTAA
1 TAATTAA
44385513 AAACCTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:44386370 original size:75 final size:75
Alignment explanation
Indices: 44386265--44386429 Score: 285
Period size: 75 Copynumber: 2.2 Consensus size: 75
44386255 TTTAATGGTC
*
44386265 TTACTGATGTGGCCGTTAGTTGACTAACGGTGCTGATGTGATAAAATTTTTTCCACCTTGGCAAG
1 TTACTGATGT-G--GTTAGTTGACTAACGGTGCTGATGTGACAAAATTTTTTCCACCTTGGCAAG
44386330 TCTACATATGCAG
63 TCTACATATGCAG
*
44386343 TTACTGATGTGGTTAGTTGACTAACGGTGCTGATGTGACAAATTTTTTTCCACCTTGGCAAGTCT
1 TTACTGATGTGGTTAGTTGACTAACGGTGCTGATGTGACAAAATTTTTTCCACCTTGGCAAGTCT
44386408 ACATATGCAG
66 ACATATGCAG
44386418 TTACTGATGTGG
1 TTACTGATGTGG
44386430 CACTATTTTG
Statistics
Matches: 85, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
75 74 0.87
77 1 0.01
78 10 0.12
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (75 bp):
TTACTGATGTGGTTAGTTGACTAACGGTGCTGATGTGACAAAATTTTTTCCACCTTGGCAAGTCT
ACATATGCAG
Found at i:44386481 original size:9 final size:9
Alignment explanation
Indices: 44386467--44386539 Score: 50
Period size: 9 Copynumber: 8.2 Consensus size: 9
44386457 GCAAATGATT
44386467 TTAAAATTA
1 TTAAAATTA
44386476 TTAAAATTA
1 TTAAAATTA
44386485 TT----TT-
1 TTAAAATTA
*
44386489 TTAAAA-AA
1 TTAAAATTA
44386497 TATAAAATTA
1 T-TAAAATTA
44386507 TTAAAATTA
1 TTAAAATTA
44386516 TTTTAAAATTAA
1 --TTAAAATT-A
44386528 TTTAAAATTA
1 -TTAAAATTA
44386538 TT
1 TT
44386540 TTTTAAAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
8 1 0.02
9 26 0.50
10 3 0.06
11 17 0.33
12 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAAAATTA
Found at i:44386506 original size:31 final size:30
Alignment explanation
Indices: 44386468--44386570 Score: 125
Period size: 31 Copynumber: 3.7 Consensus size: 30
44386458 CAAATGATTT
44386468 TAAAATTATTAAAATTATTTTTTAAAAAATA
1 TAAAATTATTAAAATTATTTTTT-AAAAATA
44386499 TAAAATTATTAAAATTA--TTTT-AAAAT-
1 TAAAATTATTAAAATTATTTTTTAAAAATA
44386525 T--AA-T-TTAAAATTATTTTTT-AAAATA
1 TAAAATTATTAAAATTATTTTTTAAAAATA
*
44386550 TAAAATTATTCAAATTATTTT
1 TAAAATTATTAAAATTATTTT
44386571 AATATTTTAA
Statistics
Matches: 64, Mismatches: 1, Indels: 16
0.79 0.01 0.20
Matches are distributed among these distances:
22 9 0.14
23 1 0.02
24 11 0.17
25 1 0.02
26 1 0.02
27 7 0.11
28 1 0.02
29 16 0.25
31 17 0.27
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTAAAAATA
Found at i:44386523 original size:11 final size:11
Alignment explanation
Indices: 44386459--44386541 Score: 70
Period size: 11 Copynumber: 7.9 Consensus size: 11
44386449 CCACGTCAGC
*
44386459 AAATGATTTTA
1 AAATTATTTTA
44386470 AAATTA--TTA
1 AAATTATTTTA
44386479 AAATTATTTTTTA
1 AAATTA--TTTTA
* *
44386492 AAA--AATATA
1 AAATTATTTTA
44386501 AAATTA--TTA
1 AAATTATTTTA
44386510 AAATTATTTTA
1 AAATTATTTTA
*
44386521 AAATTAATTTA
1 AAATTATTTTA
44386532 AAATTATTTT
1 AAATTATTTT
44386542 TTAAAATATA
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
9 23 0.40
11 29 0.50
13 6 0.10
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:44386543 original size:24 final size:20
Alignment explanation
Indices: 44386499--44386559 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
44386489 TTAAAAAATA
44386499 TAAAATTATTAAAATTATTT
1 TAAAATTATTAAAATTATTT
44386519 TAAAATTAATTTAAAATTATTTTT
1 TAAAATT-A-TTAAAATTA--TTT
44386543 TAAAA-TA-TAAAATTATT
1 TAAAATTATTAAAATTATT
44386560 CAAATTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.05
20 15 0.41
21 1 0.03
22 10 0.27
23 1 0.03
24 8 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATTATTAAAATTATTT
Found at i:44386581 original size:53 final size:52
Alignment explanation
Indices: 44386459--44386572 Score: 180
Period size: 51 Copynumber: 2.2 Consensus size: 52
44386449 CCACGTCAGC
*
44386459 AAATGATTTTAAAATT-A-TTAAAATTATTTTTTAAAAAATATAAAATTATTA
1 AAATTATTTTAAAATTAATTTAAAATTATTTTTT-AAAAATATAAAATTATTA
*
44386510 AAATTATTTTAAAATTAATTTAAAATTATTTTTT-AAAATATAAAATTATTC
1 AAATTATTTTAAAATTAATTTAAAATTATTTTTTAAAAATATAAAATTATTA
44386561 AAATTATTTTAA
1 AAATTATTTTAA
44386573 TATTTTAATC
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
51 43 0.73
52 1 0.02
53 15 0.25
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (52 bp):
AAATTATTTTAAAATTAATTTAAAATTATTTTTTAAAAATATAAAATTATTA
Found at i:44387188 original size:12 final size:12
Alignment explanation
Indices: 44387171--44387195 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44387161 GGGGAATAGA
44387171 AAAAAAAAACCC
1 AAAAAAAAACCC
44387183 AAAAAAAAACCC
1 AAAAAAAAACCC
44387195 A
1 A
44387196 CCGAAAGGAA
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:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACCC
Found at i:44387277 original size:72 final size:72
Alignment explanation
Indices: 44387174--44387314 Score: 230
Period size: 72 Copynumber: 2.0 Consensus size: 72
44387164 GAATAGAAAA
* *
44387174 AAAAAACCCAAAAAAAAACCCACCGAAAGGAAAATAAGAAGAAGGGGAAGGGGGAGA-GGGAAGG
1 AAAAAACCCAAAAAAAAACCCACCGAAAGGAAAATAAGAAGAAGGGGAAGGAGAAGAGGGGAAGG
44387238 GGAACAG
66 GGAACAG
* *
44387245 AAAAAACCCAGAAAAAAAACCCATCGAAAGGAAAATAAGAGGAAGGGGAAGGAGAAGAGGGGAAG
1 AAAAAACCCA-AAAAAAAACCCACCGAAAGGAAAATAAGAAGAAGGGGAAGGAGAAGAGGGGAAG
44387310 GGGAA
65 GGGAA
44387315 AAGGGGATGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
71 10 0.16
72 43 0.67
73 11 0.17
ACGTcount: A:0.54, C:0.11, G:0.33, T:0.02
Consensus pattern (72 bp):
AAAAAACCCAAAAAAAAACCCACCGAAAGGAAAATAAGAAGAAGGGGAAGGAGAAGAGGGGAAGG
GGAACAG
Found at i:44387307 original size:14 final size:14
Alignment explanation
Indices: 44387287--44387321 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
44387277 AAATAAGAGG
44387287 AAGGGGAAGGAGAA
1 AAGGGGAAGGAGAA
* *
44387301 GAGGGGAAGGGGAA
1 AAGGGGAAGGAGAA
44387315 AAGGGGA
1 AAGGGGA
44387322 TGATGATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (14 bp):
AAGGGGAAGGAGAA
Found at i:44388859 original size:30 final size:29
Alignment explanation
Indices: 44388825--44388884 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 29
44388815 TAAAACCCCT
44388825 AATTAGAATTTTT-TAGAAAATTAAGGACTA
1 AATTAGAATTTTTAT-G-AAATTAAGGACTA
*
44388855 AATTAGAATTTTTATGAATTTAAGGACTA
1 AATTAGAATTTTTATGAAATTAAGGACTA
44388884 A
1 A
44388885 TTTGTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 13 0.46
30 14 0.50
31 1 0.04
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.38
Consensus pattern (29 bp):
AATTAGAATTTTTATGAAATTAAGGACTA
Found at i:44388867 original size:29 final size:30
Alignment explanation
Indices: 44388825--44388884 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
44388815 TAAAACCCCT
44388825 AATTAGAATTTTTTA-GAAAATTAAGGACTA
1 AATTAGAATTTTTTATG-AAATTAAGGACTA
*
44388855 AATTAGAA-TTTTTATGAATTTAAGGACTA
1 AATTAGAATTTTTTATGAAATTAAGGACTA
44388884 A
1 A
44388885 TTTGTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.38
Consensus pattern (30 bp):
AATTAGAATTTTTTATGAAATTAAGGACTA
Found at i:44388893 original size:29 final size:29
Alignment explanation
Indices: 44388845--44388904 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
44388835 TTTTAGAAAA
44388845 TTAAGGACTAAATTAGAATTTTTA-TGAAT
1 TTAAGGACTAAATTAGAA-TTTTAGTGAAT
*
44388874 TTAAGGACT-AATTTGTAATTTTAGTGAAT
1 TTAAGGACTAAATTAG-AATTTTAGTGAAT
44388903 TT
1 TT
44388905 TGGGGGTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 10 0.36
29 18 0.64
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (29 bp):
TTAAGGACTAAATTAGAATTTTAGTGAAT
Found at i:44390525 original size:25 final size:25
Alignment explanation
Indices: 44390491--44390569 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
44390481 CGAAGTACTT
**
44390491 AACAGAAGCGCATAAGCCCTGGGGA
1 AACAGAAGCGCATAAGTGCTGGGGA
*
44390516 AACAGAAGCGCATAAGTGCTGGAGA
1 AACAGAAGCGCATAAGTGCTGGGGA
* *
44390541 AACAAAAGCACATAAGTGCT-GGGA
1 AACAGAAGCGCATAAGTGCTGGGGA
44390565 AACAG
1 AACAG
44390570 TAGGCACACA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 7 0.15
25 40 0.85
ACGTcount: A:0.42, C:0.19, G:0.29, T:0.10
Consensus pattern (25 bp):
AACAGAAGCGCATAAGTGCTGGGGA
Found at i:44390576 original size:25 final size:24
Alignment explanation
Indices: 44390491--44390609 Score: 100
Period size: 25 Copynumber: 4.9 Consensus size: 24
44390481 CGAAGTACTT
* **
44390491 AACAGAAGCGCATAAGCCCTGGGGA
1 AACAGAAGCACATAAGTGCT-GGGA
*
44390516 AACAGAAGCGCATAAGTGCTGGAGA
1 AACAGAAGCACATAAGTGCTGG-GA
*
44390541 AACAAAAGCACATAAGTGCTGGGA
1 AACAGAAGCACATAAGTGCTGGGA
* *
44390565 AACAGTAGGCACACACAGTGCT--G-
1 AACAG-AAGCACATA-AGTGCTGGGA
*
44390588 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACATA-AGTGCTG
44390610 ATCAGAAACA
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
22 15 0.18
23 5 0.06
24 9 0.11
25 47 0.57
26 6 0.07
ACGTcount: A:0.39, C:0.22, G:0.28, T:0.11
Consensus pattern (24 bp):
AACAGAAGCACATAAGTGCTGGGA
Found at i:44390599 original size:22 final size:22
Alignment explanation
Indices: 44390573--44390641 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
44390563 GAAACAGTAG
44390573 GCACACACAGTGCTGAACAGAA
1 GCACACACAGTGCTGAACAGAA
*
44390595 GCACACACAGTGCTGATCAGAA
1 GCACACACAGTGCTGAACAGAA
*
44390617 ACACACACAGTGCTGAACAGTAA
1 GCACACACAGTGCTGAACAG-AA
44390640 GC
1 GC
44390642 GCGCTAGCGT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 39 0.93
23 3 0.07
ACGTcount: A:0.39, C:0.28, G:0.22, T:0.12
Consensus pattern (22 bp):
GCACACACAGTGCTGAACAGAA
Found at i:44393766 original size:11 final size:11
Alignment explanation
Indices: 44393752--44393789 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
44393742 AATTTTTTAA
*
44393752 CACAACTTTAT
1 CACAACTTCAT
44393763 CACAACTTCAT
1 CACAACTTCAT
44393774 CACAACTTCAT
1 CACAACTTCAT
44393785 CACAA
1 CACAA
44393790 TGTAAACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.39, C:0.34, G:0.00, T:0.26
Consensus pattern (11 bp):
CACAACTTCAT
Found at i:44394127 original size:31 final size:31
Alignment explanation
Indices: 44393983--44394128 Score: 113
Period size: 31 Copynumber: 4.8 Consensus size: 31
44393973 CCTAAGTTGG
* * * *
44393983 AAAAAAAAATTT-AGGTACCTTAAAAGTTGAT
1 AAAAAAAAATTTGAGG-CCCTTAAAAGCTAAA
* **
44394014 AAAAAAAATTTTGA-GCTTTTAAAAGCTAAA
1 AAAAAAAAATTTGAGGCCCTTAAAAGCTAAA
* * ***
44394044 AAAAATAAAATTTGGGGCACTTAAAAGCTGGT
1 AAAAA-AAAATTTGAGGCCCTTAAAAGCTAAA
* *
44394076 AAAAAAAAA-TT--GGCCTTTAAAAGTTAAA
1 AAAAAAAAATTTGAGGCCCTTAAAAGCTAAA
44394104 AAAAAAAAATTTGAGGCCCTTAAAA
1 AAAAAAAAATTTGAGGCCCTTAAAA
44394129 ACTGAAATAC
Statistics
Matches: 88, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
28 20 0.23
29 2 0.02
30 16 0.18
31 33 0.38
32 17 0.19
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.26
Consensus pattern (31 bp):
AAAAAAAAATTTGAGGCCCTTAAAAGCTAAA
Found at i:44400322 original size:14 final size:14
Alignment explanation
Indices: 44400303--44400329 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44400293 ATGATGGTTA
44400303 ATTTTTAGGGTTTG
1 ATTTTTAGGGTTTG
44400317 ATTTTTAGGGTTT
1 ATTTTTAGGGTTT
44400330 TAAGGTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (14 bp):
ATTTTTAGGGTTTG
Found at i:44400501 original size:14 final size:14
Alignment explanation
Indices: 44400479--44400509 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
44400469 AGGTTAAATG
*
44400479 CGAATAGGCGTTAT
1 CGAAAAGGCGTTAT
44400493 CGAAAAGGCGTTAT
1 CGAAAAGGCGTTAT
44400507 CGA
1 CGA
44400510 GGATACTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (14 bp):
CGAAAAGGCGTTAT
Found at i:44400599 original size:14 final size:14
Alignment explanation
Indices: 44400583--44400872 Score: 319
Period size: 14 Copynumber: 20.5 Consensus size: 14
44400573 GTAAATGAAT
*
44400583 GCCACACCGGTAAT
1 GCCACACCGGTAAC
44400597 GCCACACCGGTAAC
1 GCCACACCGGTAAC
*
44400611 GCCACACCGATAAC
1 GCCACACCGGTAAC
44400625 GCCACACCGGTAAC
1 GCCACACCGGTAAC
44400639 GCCACACCGGTAAC
1 GCCACACCGGTAAC
*
44400653 GCCTCACCGGTAAC
1 GCCACACCGGTAAC
* *
44400667 ACCACACCGATAAC
1 GCCACACCGGTAAC
* *
44400681 ACCACACCAGTAAC
1 GCCACACCGGTAAC
* *
44400695 GCCACACCGATAAT
1 GCCACACCGGTAAC
* *
44400709 ACCACACTGGTAAC
1 GCCACACCGGTAAC
44400723 GCCACACCGGTAAC
1 GCCACACCGGTAAC
*
44400737 ACCACACACCGGTAAC
1 -GC-CACACCGGTAAC
* * * *
44400753 CCCATAACGATAAAC
1 GCCACACCGGT-AAC
* *
44400768 GCCTCACCGATAAC
1 GCCACACCGGTAAC
*
44400782 GCTACACCGGTAAC
1 GCCACACCGGTAAC
* *
44400796 ACCACACCGATAAC
1 GCCACACCGGTAAC
*
44400810 GCCACACTGGTAAC
1 GCCACACCGGTAAC
*
44400824 GCCTCACCGGTAAC
1 GCCACACCGGTAAC
*
44400838 GCCACACCGATAAC
1 GCCACACCGGTAAC
* *
44400852 GTCACACCGATAAC
1 GCCACACCGGTAAC
44400866 GCCACAC
1 GCCACAC
44400873 AAAAAACCCT
Statistics
Matches: 231, Mismatches: 42, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
14 206 0.89
15 13 0.06
16 12 0.05
ACGTcount: A:0.33, C:0.41, G:0.16, T:0.10
Consensus pattern (14 bp):
GCCACACCGGTAAC
Found at i:44412519 original size:31 final size:30
Alignment explanation
Indices: 44412457--44412614 Score: 138
Period size: 30 Copynumber: 5.2 Consensus size: 30
44412447 TTCTATAATC
* * **
44412457 ATATTTTGACCCTCAAACTTTTTTAAAATT
1 ATATTTTTACCCTCAAACTTCTCAAAAATT
* * *
44412487 ATATTTTTACCTTCGAACTTCCCAAAAAATT
1 ATATTTTTACCCTCAAACTTCTC-AAAAATT
* *
44412518 ATATTTTGACCCTCAAACATCTCAAAAATT
1 ATATTTTTACCCTCAAACTTCTCAAAAATT
* * *
44412548 ACA-TTTTAGCCCCCTAACTTCTCAAAAATT
1 ATATTTTTA-CCCTCAAACTTCTCAAAAATT
* * * *
44412578 ATATTTTGACCCCCTAACTTCTTAAAAATT
1 ATATTTTTACCCTCAAACTTCTCAAAAATT
*
44412608 ACATTTT
1 ATATTTT
44412615 GTGCCCCCGA
Statistics
Matches: 104, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
29 4 0.04
30 72 0.69
31 28 0.27
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (30 bp):
ATATTTTTACCCTCAAACTTCTCAAAAATT
Found at i:44412522 original size:61 final size:61
Alignment explanation
Indices: 44412457--44412626 Score: 202
Period size: 61 Copynumber: 2.8 Consensus size: 61
44412447 TTCTATAATC
* * * **
44412457 ATATTTTGACCCTCAAACTTTTTTAAAATTATATTTTTA-CCTTCGAACTTCCCAAAAAATT
1 ATATTTTGACCCTCAAACTTCTTAAAAATTACATTTTTAGCCCCCGAACTTCCC-AAAAATT
* * * *
44412518 ATATTTTGACCCTCAAACATCTCAAAAATTACA-TTTTAGCCCCCTAACTTCTCAAAAATT
1 ATATTTTGACCCTCAAACTTCTTAAAAATTACATTTTTAGCCCCCGAACTTCCCAAAAATT
* *
44412578 ATATTTTGACCCCCTAACTTCTTAAAAATTACATTTTGT-GCCCCCGAAC
1 ATATTTTGACCCTCAAACTTCTTAAAAATTACATTTT-TAGCCCCCGAAC
44412627 ATCTAAAAAA
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
60 41 0.45
61 50 0.54
62 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.37
Consensus pattern (61 bp):
ATATTTTGACCCTCAAACTTCTTAAAAATTACATTTTTAGCCCCCGAACTTCCCAAAAATT
Found at i:44412649 original size:29 final size:29
Alignment explanation
Indices: 44412511--44412737 Score: 176
Period size: 30 Copynumber: 7.7 Consensus size: 29
44412501 GAACTTCCCA
* * *
44412511 AAAAATTA-TATTTTGACCCTCAAACATCT
1 AAAAATTACCATTTTG-CCCCCGAACATCT
* *
44412540 CAAAAATTA-CATTTTAGCCCCCTAACTTCT
1 -AAAAATTACCATTTT-GCCCCCGAACATCT
* * *
44412570 CAAAAATTA-TATTTTGACCCCCTAACTTCTT
1 -AAAAATTACCATTTTG-CCCCCGAACATC-T
44412601 AAAAATTA-CATTTTGTGCCCCCGAACATCT
1 AAAAATTACCA-TTT-TGCCCCCGAACATCT
* * *
44412631 AAAAAATACCATTTTGCCCCCGAACTTCC
1 AAAAATTACCATTTTGCCCCCGAACATCT
* * *
44412660 AAAAATCA-CATTTTTTACCCTCGAACATCT
1 AAAAATTACCA--TTTTGCCCCCGAACATCT
* * *
44412690 AAAAATTACCATTTTGCCCCTGAGCATCC
1 AAAAATTACCATTTTGCCCCCGAACATCT
44412719 AAAAATTACCATTTTGCCC
1 AAAAATTACCATTTTGCCC
44412738 TCAAATTTCC
Statistics
Matches: 165, Mismatches: 23, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
28 2 0.01
29 52 0.32
30 90 0.55
31 19 0.12
32 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAAATTACCATTTTGCCCCCGAACATCT
Found at i:44412651 original size:60 final size:58
Alignment explanation
Indices: 44412540--44412737 Score: 211
Period size: 59 Copynumber: 3.3 Consensus size: 58
44412530 TCAAACATCT
* * * * *
44412540 CAAAAATTACATTTTAGCCCCCTAACTTCTCAAAAATTA-TATTTTGACCCCCTAACTTC
1 CAAAAATTACATTTTTGCCCCCGAACATCT-AAAAATTACCATTTTG-CCCCCGAACTTC
* *
44412599 TTAAAAATTACATTTTGTGCCCCCGAACATCTAAAAAATACCATTTTGCCCCCGAACTTC
1 -CAAAAATTACATTTT-TGCCCCCGAACATCTAAAAATTACCATTTTGCCCCCGAACTTC
* * * * * *
44412659 CAAAAATCACATTTTTTACCCTCGAACATCTAAAAATTACCATTTTGCCCCTGAGCATC
1 CAAAAATTACA-TTTTTGCCCCCGAACATCTAAAAATTACCATTTTGCCCCCGAACTTC
44412718 CAAAAATTACCA-TTTTGCCC
1 CAAAAATTA-CATTTTTGCCC
44412738 TCAAATTTCC
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
58 7 0.06
59 54 0.46
60 38 0.32
61 18 0.15
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (58 bp):
CAAAAATTACATTTTTGCCCCCGAACATCTAAAAATTACCATTTTGCCCCCGAACTTC
Found at i:44417984 original size:11 final size:10
Alignment explanation
Indices: 44417968--44418047 Score: 58
Period size: 10 Copynumber: 7.6 Consensus size: 10
44417958 AAAAGATAAT
44417968 AAAAAAAGAG
1 AAAAAAAGAG
44417978 AAGAAAAAGA-
1 AA-AAAAAGAG
*
44417988 AAAAATAA-AT
1 AAAAA-AAGAG
44417998 AAAAAAAGAAG
1 AAAAAAAG-AG
*
44418009 AAGAAAAAGAAC
1 AA-AAAAAG-AG
44418021 AAAAACAAGA-
1 AAAAA-AAGAG
44418031 ACAAAAAAGAG
1 A-AAAAAAGAG
44418042 AAAAAA
1 AAAAAA
44418048 GAAAAGGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 18
0.75 0.03 0.23
Matches are distributed among these distances:
9 6 0.10
10 21 0.36
11 19 0.32
12 13 0.22
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:44417999 original size:30 final size:32
Alignment explanation
Indices: 44417942--44418024 Score: 107
Period size: 31 Copynumber: 2.6 Consensus size: 32
44417932 CGGAATCGAT
* *
44417942 GAAGAAAAATAAATAAAAAAGATAATAAAAAAA
1 GAAGAAGAA-AAAGAAAAAAGATAATAAAAAAA
*
44417975 G-AGAAGAAAAAGAAAAAATA-AATAAAAAAA
1 GAAGAAGAAAAAGAAAAAAGATAATAAAAAAA
44418005 GAAGAAGAAAAAGAACAAAA
1 GAAGAAGAAAAAGAA-AAAA
44418025 ACAAGAACAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
30 11 0.24
31 23 0.51
32 10 0.22
33 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.13, T:0.07
Consensus pattern (32 bp):
GAAGAAGAAAAAGAAAAAAGATAATAAAAAAA
Found at i:44418003 original size:31 final size:30
Alignment explanation
Indices: 44417968--44418052 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
44417958 AAAAGATAAT
*
44417968 AAAAAAAGAGAAGAAAAAGAAAAAATA-AAT
1 AAAAAAAGAGAAGAAAAAGAAAAAA-ACAAG
44417998 AAAAAAAGAAGAAGAAAAAGAACAAAAACAAG
1 AAAAAAAG-AGAAGAAAAAGAA-AAAAACAAG
44418030 AACAAAAA-AG-AGAAAAAAGAAAA
1 AA-AAAAAGAGAAG-AAAAAGAAAA
44418053 GGAAATGTTG
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
30 12 0.24
31 24 0.49
32 8 0.16
33 5 0.10
ACGTcount: A:0.80, C:0.04, G:0.14, T:0.02
Consensus pattern (30 bp):
AAAAAAAGAGAAGAAAAAGAAAAAAACAAG
Found at i:44418031 original size:43 final size:41
Alignment explanation
Indices: 44417946--44418050 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 41
44417936 ATCGATGAAG
* * *
44417946 AAAAATAAATAAAAAAGATAATAAAAAAAGAGAAGAAAAAGA
1 AAAAATAAATAAAAAA-AGAAGAAAAAAAGAGAAAAAAAAGA
44417988 AAAAATAAATAAAAAAAGAAGAAGAAAAAGA-ACAAAAACAAGA
1 AAAAATAAATAAAAAAAGAAGAA-AAAAAGAGA-AAAAA-AAGA
* *
44418031 ACAAA-AAAGAGAAAAAAGAA
1 AAAAATAAATA-AAAAAAGAA
44418051 AAGGAAATGT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
41 6 0.11
42 31 0.57
43 17 0.31
ACGTcount: A:0.79, C:0.03, G:0.12, T:0.06
Consensus pattern (41 bp):
AAAAATAAATAAAAAAAGAAGAAAAAAAGAGAAAAAAAAGA
Found at i:44419117 original size:49 final size:49
Alignment explanation
Indices: 44418966--44419117 Score: 132
Period size: 49 Copynumber: 3.1 Consensus size: 49
44418956 ATGAGTCACG
*
44418966 GTACCATGAAGATTTGAAAGGAAAA-GTTGAGGTCGCAATAGCAA-ACCCTA
1 GTACCATGAAGATTTG-AAGGAAAAGGTTGAGGTCGCAA-AG-AAGAACCTA
* * * * * * * * *
44419016 -TACCATAAAGATTTGAAGGGAAAGTTTGACGCCGTAATGACGAA-CTCG
1 GTACCATGAAGATTTGAAGGAAAAGGTTGAGGTCGCAAAGAAGAACCT-A
* *
44419064 GTACCATGAAGAGTTGAAGGAAAAGGTTGAGGTCACAAAGAAGAACCTA
1 GTACCATGAAGATTTGAAGGAAAAGGTTGAGGTCGCAAAGAAGAACCTA
44419113 GTACC
1 GTACC
44419118 TTAGAATCAT
Statistics
Matches: 76, Mismatches: 21, Indels: 11
0.70 0.19 0.10
Matches are distributed among these distances:
47 3 0.04
48 9 0.12
49 62 0.82
50 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.20
Consensus pattern (49 bp):
GTACCATGAAGATTTGAAGGAAAAGGTTGAGGTCGCAAAGAAGAACCTA
Found at i:44419470 original size:39 final size:39
Alignment explanation
Indices: 44419427--44419506 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
44419417 TTTTATCCCA
*
44419427 AGCCTAGGGCAAATCACCATCAGCCAATCTCTTACCTCG
1 AGCCTAGGGCAAATCACCATCAGCCAATCTCTTACCCCG
* *
44419466 AGCCTAGGGTAGATCACCATCAGCCAATCTCTTACCCCG
1 AGCCTAGGGCAAATCACCATCAGCCAATCTCTTACCCCG
44419505 AG
1 AG
44419507 ATAGGGGCAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.35, G:0.17, T:0.20
Consensus pattern (39 bp):
AGCCTAGGGCAAATCACCATCAGCCAATCTCTTACCCCG
Found at i:44419541 original size:39 final size:39
Alignment explanation
Indices: 44419489--44419600 Score: 136
Period size: 39 Copynumber: 2.9 Consensus size: 39
44419479 TCACCATCAG
* *
44419489 CCAATCTCTTACCCCGA-GATAGGGGCAGATTGTAACCAT
1 CCAATCTCTTACCCCGACCAT-GGGGCAGATTGCAACCAT
* * * **
44419528 CCGATCTTTTACCCCGACCATGGGGTAGATCACAACCAT
1 CCAATCTCTTACCCCGACCATGGGGCAGATTGCAACCAT
*
44419567 CCAATCTCTTACCCCGATCATGGGGCAGATTGCA
1 CCAATCTCTTACCCCGACCATGGGGCAGATTGCA
44419601 GTTATCCAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
39 57 0.97
40 2 0.03
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (39 bp):
CCAATCTCTTACCCCGACCATGGGGCAGATTGCAACCAT
Found at i:44419972 original size:208 final size:207
Alignment explanation
Indices: 44419617--44420558 Score: 1011
Period size: 208 Copynumber: 4.5 Consensus size: 207
44419607 CAAAACAAAC
* * * * *
44419617 GAGGCGGTCATCTTCCTGATGAGATACTGAAAAGTAGACCAAATTAAGGAAACAAAGCTCAAAGT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAAAGT
* * * * * *
44419682 GAGCAAATCTTCGAACCCTAGCTTCCTAATGAGATACTAAGAAGCATGTCGAAGCAATAAAGCAG
66 GAGCAAA-CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAGCGG
* ** *
44419747 TTACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCTATCTTCCTGATGAAATACAAAGAAGT
130 TCACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAAAGAAGT
* * *
44419812 GGATCAAAATAAC
195 GAATTAAAATAAT
* * * * *
44419825 GAGGCGGTCATTTTCCTGATGAAATACTGAGAAGTAAACCAAATCAATGAAACAAAGCTCAAAGT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAAAGT
* ** * * *
44419890 GAGCAAATCTTTGAACCCCAGCTTTTTGATTAGATATTGAGAAGCAGGTCAAAGTAATAAAGCGG
66 GAGCAAA-CTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAGCGG
* * *
44419955 TTACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAGAGAAGC
130 TCACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAAAGAAGT
* *
44420020 GAATTGAAACAAT
195 GAATTAAAATAAT
* *
44420033 GAGGTGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAAT-ACAT-AAAGCGAAGCTCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCA-ATGAAA-CGAAGCTCAA-
* * * * *
44420096 ACGAATGAG---ACTTCAAACCCCATCTTCCTGATGAGATA-TAGAGAAG-TGGATCGAACCAAT
63 A-G--TGAGCAAACTTCGAACCCCAGCTTCCTGATGAGATACT-GAGAAGCAGG-TCAAAGCAAT
* * * *
44420156 -AAGTGGTCATCTTCCTGACGAGATGCAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACA
123 AAAGCGGTCACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACA
* * *
44420220 AAAAAGTGGATTGAAATAAT
188 AAGAAGTGAATTAAAATAAT
* * * * * *
44420240 AAGGCGGTCATCTTTCTGACGAGATACAGAGAAGTAGACCAAATCGATAAAACGAAGCTCAATGT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAAAGT
* * ** *
44420305 GAGTGAAACTTCGAACCCCCATCTTCCTGATGAGATACTGAGAAGTGGGTCAAAGCAATAAAACG
66 GAG-CAAACTTCGAA-CCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAGCG
** * * * *
44420370 GTCGTCTTCCCGATGAGATACAGAAAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAG
129 GTCACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAAAGAAG
*
44420435 TGAATTAAAACAAAT
194 TGAATTAAAA-TAAT
* * *
44420450 GAGGCGGTTATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAAAGT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAAAGT
* * * * *
44420515 GAGTGAAACTT-GAAACCCCTATCTGCTTGATGAGATACAGAGAA
66 GAG-CAAACTTCG-AACCCC-AGCTTCCTGATGAGATACTGAGAA
44420559 ATAGATCAAG
Statistics
Matches: 624, Mismatches: 89, Indels: 40
0.83 0.12 0.05
Matches are distributed among these distances:
203 4 0.01
205 1 0.00
207 139 0.22
208 302 0.48
209 78 0.12
210 96 0.15
212 4 0.01
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (207 bp):
GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAACGAAGCTCAAAGT
GAGCAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAGCGGT
CACCTTCCTGATGAGATACAGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAAAGAAGTG
AATTAAAATAAT
Found at i:44420281 original size:85 final size:84
Alignment explanation
Indices: 44420118--44420284 Score: 228
Period size: 85 Copynumber: 2.0 Consensus size: 84
44420108 TCAAACCCCA
* * * * * *
44420118 TCTTCCTGATGAGATATAGAGAAGTGGATCGAACCAATAAGTGGTCATCTTCCTGACGAGATGCA
1 TCTTCCTGATGAGATACAAAAAAGTGGATCGAAACAATAAGCGGTCATCTTCCTGACGAGATACA
44420183 GAGAAGTGAACCAAATCCG
66 GAGAAGTGAACCAAATCCG
* * *
44420202 TCTTCCTGATGAGATACAAAAAAGTGGATTGAAATAATAAGGCGGTCATCTTTCTGACGAGATAC
1 TCTTCCTGATGAGATACAAAAAAGTGGATCGAAACAATAA-GCGGTCATCTTCCTGACGAGATAC
44420267 AGAGAAGT-AGACCAAATC
65 AGAGAAGTGA-ACCAAATC
44420285 GATAAAACGA
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
84 35 0.49
85 37 0.51
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (84 bp):
TCTTCCTGATGAGATACAAAAAAGTGGATCGAAACAATAAGCGGTCATCTTCCTGACGAGATACA
GAGAAGTGAACCAAATCCG
Found at i:44422195 original size:30 final size:30
Alignment explanation
Indices: 44422161--44422242 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 30
44422151 TTAGACCCCT
*
44422161 AAACTTTTTTATAATTATATTTTAACCTAC
1 AAACTTTTTTAAAATTATATTTTAACCTAC
* * *
44422191 AAACTTTTCTAAAATTATATTTTTACCTTC
1 AAACTTTTTTAAAATTATATTTTAACCTAC
* *
44422221 GAAC-TTTTAAAAATTATATTTT
1 AAACTTTTTTAAAATTATATTTT
44422243 GACCCTTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 16 0.36
30 29 0.64
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (30 bp):
AAACTTTTTTAAAATTATATTTTAACCTAC
Found at i:44422315 original size:60 final size:59
Alignment explanation
Indices: 44422229--44422397 Score: 171
Period size: 60 Copynumber: 2.8 Consensus size: 59
44422219 TCGAACTTTT
* *
44422229 AAAAATTATATTTTGACCCTTAAACTTCTAAAAAATTACATTTTAACCC-CATAACTTCTC
1 AAAAATTACATTTTGACCCTTAAACTTCTAAAAAATTACATTTTAACCCTCA-AACATC-C
* * *
44422289 AAAAATTACATTTTGACCCCTT-AACTTCTTAAAAATTATATTTTTACCCTCAAACATCC
1 AAAAATTACATTTTGA-CCCTTAAACTTCTAAAAAATTACATTTTAACCCTCAAACATCC
* * * ** * *
44422348 AAAAATCACATTTTTTATCCTCGAACATCCAAAAAATTACCATTTTAACC
1 AAAAATTACA-TTTTGACCCTTAAACTTCTAAAAAATTA-CATTTTAACC
44422398 TTGAACTTTA
Statistics
Matches: 90, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
59 13 0.14
60 62 0.69
61 15 0.17
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.36
Consensus pattern (59 bp):
AAAAATTACATTTTGACCCTTAAACTTCTAAAAAATTACATTTTAACCCTCAAACATCC
Found at i:44422352 original size:29 final size:30
Alignment explanation
Indices: 44422180--44422393 Score: 150
Period size: 30 Copynumber: 7.1 Consensus size: 30
44422170 TATAATTATA
* * * *
44422180 TTTTAACCTACAAACTTTTCTAAAATTATAT
1 TTTTACCCT-CAAACTTCTCAAAAATTACAT
* * * *
44422211 TTTTACCTTCGAACTT-TTAAAAATTATAT
1 TTTTACCCTCAAACTTCTCAAAAATTACAT
* * *
44422240 TTTGACCCTTAAACTTCTAAAAAATTACAT
1 TTTTACCCTCAAACTTCTCAAAAATTACAT
*
44422270 TTTAACCC-CATAACTTCTCAAAAATTACAT
1 TTTTACCCTCA-AACTTCTCAAAAATTACAT
* * * *
44422300 TTTGACCC-CTTAACTTCTTAAAAATTATAT
1 TTTTACCCTC-AAACTTCTCAAAAATTACAT
* *
44422330 TTTTACCCTCAAACATC-CAAAAATCACATT
1 TTTTACCCTCAAACTTCTCAAAAATTACA-T
* * *
44422360 TTTTATCCTCGAACATC-CAAAAAATTACCAT
1 TTTTACCCTCAAACTTCTC-AAAAATTA-CAT
44422391 TTT
1 TTT
44422394 AACCTTGAAC
Statistics
Matches: 149, Mismatches: 27, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
29 32 0.21
30 96 0.64
31 19 0.13
32 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.39
Consensus pattern (30 bp):
TTTTACCCTCAAACTTCTCAAAAATTACAT
Found at i:44422394 original size:30 final size:29
Alignment explanation
Indices: 44422330--44422458 Score: 107
Period size: 30 Copynumber: 4.3 Consensus size: 29
44422320 AAAATTATAT
* *
44422330 TTTTACCCTCAAACATCCAAAAATCA-CA
1 TTTTACCCTCGAACATCCAAAAATTACCA
*
44422358 TTTTTTATCCTCGAACATCCAAAAAATTACCA
1 --TTTTACCCTCGAACATCC-AAAAATTACCA
* * * **
44422390 TTTTAACCTTGAACTTTAACAAAATTACCA
1 TTTTACCCTCGAACATCCA-AAAATTACCA
* * *
44422420 TTTTGCCCCCGAGCATCCAAAAATTACCA
1 TTTTACCCTCGAACATCCAAAAATTACCA
*
44422449 TTTTGCCCTC
1 TTTTACCCTC
44422459 AAAATTCCAA
Statistics
Matches: 79, Mismatches: 17, Indels: 7
0.77 0.17 0.07
Matches are distributed among these distances:
29 20 0.25
30 50 0.63
31 7 0.09
32 2 0.03
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.32
Consensus pattern (29 bp):
TTTTACCCTCGAACATCCAAAAATTACCA
Found at i:44422405 original size:90 final size:88
Alignment explanation
Indices: 44422201--44422416 Score: 206
Period size: 90 Copynumber: 2.4 Consensus size: 88
44422191 AAACTTTTCT
* * * * *
44422201 AAAATTATATTTTTACCTTCGAACTTTTAAAAATTATATTTTGACCCTTAAACTTCTAAAAAATT
1 AAAATTACATTTTAACCTT-GAACTTTTAAAAATTATATTTTGACCCTCAAACATCTAAAAAATC
* *
44422266 ACATTTTAACCCCATAACTTCTCA
65 ACATTTTAACCCCAGAACATCTCA
* * *
44422290 AAAATTACATTTTGACCCCTT-AACTTCTTAAAAATTATATTTTTACCCTCAAACATC-CAAAAA
1 AAAATTACATTTT-A-ACCTTGAACTT-TTAAAAATTATATTTTGACCCTCAAACATCTAAAAAA
* *
44422353 TCACATTTTTTATCCTC-GAACATC-CAA
63 TCACA--TTTTAACCCCAGAACATCTC-A
*
44422380 AAAATTACCATTTTAACCTTGAACTTTAACAAAATTA
1 AAAATTA-CATTTTAACCTTGAACTTTTA-AAAATTA
44422417 CCATTTTGCC
Statistics
Matches: 104, Mismatches: 14, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
89 33 0.32
90 53 0.51
91 18 0.17
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.38
Consensus pattern (88 bp):
AAAATTACATTTTAACCTTGAACTTTTAAAAATTATATTTTGACCCTCAAACATCTAAAAAATCA
CATTTTAACCCCAGAACATCTCA
Found at i:44422467 original size:29 final size:29
Alignment explanation
Indices: 44422410--44422470 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
44422400 GAACTTTAAC
**
44422410 AAAATTACCATTTTGCCCCCGAGCATCCA
1 AAAATTACCATTTTGCCCCCGAAAATCCA
*
44422439 AAAATTACCATTTTGCCCTC-AAAATTCCA
1 AAAATTACCATTTTGCCCCCGAAAA-TCCA
44422468 AAA
1 AAA
44422471 TTCACATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.38, C:0.30, G:0.07, T:0.26
Consensus pattern (29 bp):
AAAATTACCATTTTGCCCCCGAAAATCCA
Found at i:44425694 original size:18 final size:18
Alignment explanation
Indices: 44425673--44425715 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
44425663 TTTACAGTTG
44425673 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
44425691 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
44425709 TAATTAA
1 TAATTAA
44425716 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:44427020 original size:21 final size:18
Alignment explanation
Indices: 44426983--44427021 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
44426973 AGTTGATGTT
44426983 TTTAAAAAATAAAATATA
1 TTTAAAAAATAAAATATA
44427001 TTTAAAATAATGATAAATATA
1 TTTAAAA-AAT-A-AAATATA
44427022 AAAATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 1 0.06
21 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TTTAAAAAATAAAATATA
Found at i:44427073 original size:24 final size:24
Alignment explanation
Indices: 44427017--44427075 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
44427007 ATAATGATAA
*
44427017 ATATAAAAATATATATTTTATTAT
1 ATATAAATATATATATTTTATTAT
*
44427041 ATGATTAAATATTTATTATTTTATT-T
1 AT-A-TAAATATATA-TATTTTATTAT
44427067 ATATAAATA
1 ATATAAATA
44427076 AAAAGTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 8 0.27
25 2 0.07
26 11 0.37
27 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
ATATAAATATATATATTTTATTAT
Found at i:44427084 original size:28 final size:26
Alignment explanation
Indices: 44427013--44427085 Score: 65
Period size: 28 Copynumber: 2.6 Consensus size: 26
44427003 TAAAATAATG
*
44427013 ATAAATATAAAAATATATATTTTATTAT
1 ATAAATA-AAAATTAT-TATTTTATTAT
* * *
44427041 ATGATTAAATATTTATTATTTTATTTAT
1 ATAAATAAA-AATTATTATTTTA-TTAT
44427069 ATAAATAAAAAGTTATT
1 ATAAATAAAAA-TTATT
44427086 GATTAAAATG
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
27 10 0.29
28 25 0.71
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (26 bp):
ATAAATAAAAATTATTATTTTATTAT
Found at i:44429328 original size:7 final size:7
Alignment explanation
Indices: 44429316--44429387 Score: 58
Period size: 7 Copynumber: 10.6 Consensus size: 7
44429306 TTCGAAAAAA
44429316 TCAACGG
1 TCAACGG
*
44429323 TCAACGA
1 TCAACGG
*
44429330 TCAACGA
1 TCAACGG
*
44429337 TCAA-AG
1 TCAACGG
*
44429343 TCAATGG
1 TCAACGG
44429350 TCAACGG
1 TCAACGG
*
44429357 TCAA-AG
1 TCAACGG
*
44429363 TTAACGG
1 TCAACGG
**
44429370 TCAACAA
1 TCAACGG
44429377 TCAACGG
1 TCAACGG
44429384 TCAA
1 TCAA
44429388 TCAAAACCAG
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
6 8 0.16
7 42 0.84
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (7 bp):
TCAACGG
Found at i:44429353 original size:20 final size:20
Alignment explanation
Indices: 44429322--44429380 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
44429312 AAAATCAACG
*
44429322 GTCAACGATCAACGATCAAA
1 GTCAACGGTCAACGATCAAA
* *
44429342 GTCAATGGTCAACGGTCAAA
1 GTCAACGGTCAACGATCAAA
* *
44429362 GTTAACGGTCAACAATCAA
1 GTCAACGGTCAACGATCAA
44429381 CGGTCAATCA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
GTCAACGGTCAACGATCAAA
Found at i:44431407 original size:30 final size:31
Alignment explanation
Indices: 44431371--44431443 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 31
44431361 CAAGTGGTTT
44431371 TAAAATTATTAAAAATAATT-TTTTGAAATA
1 TAAAATTATTAAAAATAATTATTTTGAAATA
* *
44431401 TAAAATTATT--ATATTATTATTTTGAAATA
1 TAAAATTATTAAAAATAATTATTTTGAAATA
44431430 TAAAATTATTAAAA
1 TAAAATTATTAAAA
44431444 TAGAACGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.16
29 20 0.54
30 10 0.27
31 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (31 bp):
TAAAATTATTAAAAATAATTATTTTGAAATA
Found at i:44431567 original size:75 final size:75
Alignment explanation
Indices: 44431482--44431623 Score: 223
Period size: 75 Copynumber: 1.9 Consensus size: 75
44431472 AATTGGTAAG
* *
44431482 TTTCTCTCTTCAAATCCTTTTATTTCTTTATTTAATCCATCACATATCATCCGCAAATCTG-TTT
1 TTTCTCTCTTCAAATACTTTTATTTCTTTATTGAATCCATCACATATCATCCGCAAAT-TGATTT
44431546 TTGAGTTTTTT
65 TTGAGTTTTTT
* * *
44431557 TTTCTCTCTTCAAATATTTTTATTTTTTTATTGAATCCATCACATATCATCTGCAAATTGATTTT
1 TTTCTCTCTTCAAATACTTTTATTTCTTTATTGAATCCATCACATATCATCCGCAAATTGATTTT
44431622 TG
66 TG
44431624 TACAGTTTGT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 2 0.03
75 59 0.97
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (75 bp):
TTTCTCTCTTCAAATACTTTTATTTCTTTATTGAATCCATCACATATCATCCGCAAATTGATTTT
TGAGTTTTTT
Found at i:44431916 original size:23 final size:23
Alignment explanation
Indices: 44431885--44431928 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
44431875 TTGTTTATGA
44431885 TTGTCGAATTTGGGGATTTTGAG
1 TTGTCGAATTTGGGGATTTTGAG
*
44431908 TTGTTGAATTTGGGGATTTTG
1 TTGTCGAATTTGGGGATTTTG
44431929 GGTTTTGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (23 bp):
TTGTCGAATTTGGGGATTTTGAG
Found at i:44432599 original size:28 final size:29
Alignment explanation
Indices: 44432568--44432641 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 29
44432558 AAATATATTT
*
44432568 TAATATAATAATTTTATATTTCAAA-ATA
1 TAATATAATAATTTTATATTTCAAAGAAA
*
44432596 TAATACAATAATTTTATATTTCAAAGAAA
1 TAATATAATAATTTTATATTTCAAAGAAA
*
44432625 TAATTTTAATAATTTTA
1 TAA-TATAATAATTTTA
44432642 AAATCATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 24 0.60
29 5 0.12
30 11 0.28
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (29 bp):
TAATATAATAATTTTATATTTCAAAGAAA
Found at i:44433189 original size:93 final size:94
Alignment explanation
Indices: 44433016--44433189 Score: 226
Period size: 93 Copynumber: 1.9 Consensus size: 94
44433006 TTTATTTAAT
* * * * *
44433016 TCTTTCATGCTTTATGAATTACAAAATTTCTTTGAAACTTTTTTATGTTTTAAGTAATTCTTTCT
1 TCTTTCATGATTTATGAATTACAAAATTTCTTTAAAACTATTTTATGTATTAAGTAATTCTTTCA
* * *
44433081 TGAATCAGAACTTAATCAACTCTGAGATC
66 TCAATCAAAAATTAATCAACTCTGAGATC
**
44433110 TCTTTCATGATTTATGAATTACTTAATTT-TTTAAAAAC-ATTTTATGTATTAAGTAATTCTTTC
1 TCTTTCATGATTTATGAATTACAAAATTTCTTT-AAAACTATTTTATGTATTAAGTAATTCTTTC
*
44433173 ATCTATCAAAAATTAAT
65 ATCAATCAAAAATTAAT
44433190 TTTTTTAGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
93 38 0.56
94 30 0.44
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (94 bp):
TCTTTCATGATTTATGAATTACAAAATTTCTTTAAAACTATTTTATGTATTAAGTAATTCTTTCA
TCAATCAAAAATTAATCAACTCTGAGATC
Found at i:44433271 original size:56 final size:58
Alignment explanation
Indices: 44433211--44433341 Score: 153
Period size: 58 Copynumber: 2.3 Consensus size: 58
44433201 TCTTTCATGT
* * *
44433211 TTTACGAATTACTTAATATCT-TAGAAAC-TGTCATATTTTAAATAATTCTTTTATAC
1 TTTACGAATTACTTAATATCTGTAAAAACGTGTCATATTTTAAATAACTATTTTATAC
* * * * *
44433267 TTTACGAATTACTTAAT-TTTGTAAAAACGTTTTCATGTTTTAAGTAACTATTTTATAT
1 TTTACGAATTACTTAATATCTGTAAAAACG-TGTCATATTTTAAATAACTATTTTATAC
44433325 TTTACGAATTA-TTAATA
1 TTTACGAATTACTTAATA
44433342 ATCCTTTCAT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
55 2 0.03
56 23 0.37
57 5 0.08
58 33 0.52
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (58 bp):
TTTACGAATTACTTAATATCTGTAAAAACGTGTCATATTTTAAATAACTATTTTATAC
Found at i:44434681 original size:5 final size:5
Alignment explanation
Indices: 44434673--44434705 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
44434663 CTTTGCTTGA
44434673 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
44434706 TACAGTCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:44437877 original size:5 final size:5
Alignment explanation
Indices: 44437848--44437905 Score: 55
Period size: 5 Copynumber: 10.8 Consensus size: 5
44437838 CTTAATCGTT
*
44437848 TTAATA TTAAA TT-AA TATAATA TTAAA TTAAA TTTAATA TTAAA TTTAA
1 TTAA-A TTAAA TTAAA T-TAA-A TTAAA TTAAA -TTAA-A TTAAA TTAAA
44437897 TTAAA TTAA
1 TTAAA TTAA
44437906 TAGAATATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
4 3 0.07
5 23 0.51
6 16 0.36
7 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (5 bp):
TTAAA
Found at i:44437884 original size:22 final size:21
Alignment explanation
Indices: 44437848--44437914 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 21
44437838 CTTAATCGTT
44437848 TTAATATTAAATTAATATAATA
1 TTAA-ATTAAATTAATATAATA
44437870 TTAAATTAAATTTAATATTAA-A
1 TTAAATTAAA-TTAATA-TAATA
* *
44437892 TTTAATTAAATTAATAGAATA
1 TTAAATTAAATTAATATAATA
44437913 TT
1 TT
44437915 TATCTACAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
20 2 0.05
21 15 0.38
22 20 0.50
23 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (21 bp):
TTAAATTAAATTAATATAATA
Found at i:44437887 original size:17 final size:16
Alignment explanation
Indices: 44437847--44437898 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 16
44437837 ACTTAATCGT
44437847 TTTAATATTAAATTAA
1 TTTAATATTAAATTAA
*
44437863 TATAATATTAAATTAAA
1 TTTAATATTAAATT-AA
44437880 TTTAATATTAAATTTAA
1 TTTAATATTAAA-TTAA
44437897 TT
1 TT
44437899 AAATTAATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
16 13 0.41
17 17 0.53
18 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAATATTAAATTAA
Found at i:44437978 original size:20 final size:18
Alignment explanation
Indices: 44437931--44437979 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
44437921 CAAGATAAAC
44437931 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
44437948 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
44437968 ATTAAATTAATA
1 ATTAAATTAATA
44437980 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:44445908 original size:10 final size:10
Alignment explanation
Indices: 44445893--44445917 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
44445883 TTCCAGATAT
44445893 AAAGTATAGA
1 AAAGTATAGA
44445903 AAAGTATAGA
1 AAAGTATAGA
44445913 AAAGT
1 AAAGT
44445918 GTCTATAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (10 bp):
AAAGTATAGA
Found at i:44450321 original size:2 final size:2
Alignment explanation
Indices: 44450314--44450339 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44450304 ATGGGATCTT
44450314 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
44450340 AAGAGATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44451774 original size:5 final size:5
Alignment explanation
Indices: 44451766--44451800 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
44451756 ATGAATGAGA
*
44451766 TGAAG TGAAG TGGAG TGAAG TGAAG TGAAG TGAAG
1 TGAAG TGAAG TGAAG TGAAG TGAAG TGAAG TGAAG
44451801 AAGTAGATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.43, T:0.20
Consensus pattern (5 bp):
TGAAG
Found at i:44455283 original size:22 final size:22
Alignment explanation
Indices: 44455258--44455362 Score: 133
Period size: 22 Copynumber: 4.8 Consensus size: 22
44455248 ATTATATTGT
44455258 TGTTTTGGTTGCTATTTTTTAC
1 TGTTTTGGTTGCTATTTTTTAC
*
44455280 TGTTTTGGTTGCTATTTTTTGC
1 TGTTTTGGTTGCTATTTTTTAC
* * *
44455302 TGTTTTGG-TGTTGTGTTTTTAT
1 TGTTTTGGTTGCTAT-TTTTTAC
*
44455324 TGTTTTGGTT-CTTTTTTTTAC
1 TGTTTTGGTTGCTATTTTTTAC
*
44455345 TGTTTTTGTTGCTATTTT
1 TGTTTTGGTTGCTATTTT
44455363 GGTGCTATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
21 19 0.27
22 50 0.71
23 1 0.01
ACGTcount: A:0.06, C:0.07, G:0.20, T:0.68
Consensus pattern (22 bp):
TGTTTTGGTTGCTATTTTTTAC
Found at i:44455396 original size:23 final size:23
Alignment explanation
Indices: 44455345--44455415 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
44455335 TTTTTTTTAC
* * *
44455345 TGTTTTTGTTGCTATTTTGGTGC
1 TGTTTTTATTGCTATTTTGATGT
* * *
44455368 TATTTTTTTTACTATTTTGATGT
1 TGTTTTTATTGCTATTTTGATGT
*
44455391 TGTTTTTATTGTTATTTTTGATGT
1 TGTTTTTATTGCTA-TTTTGATGT
44455415 T
1 T
44455416 ATTTCTTCTA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 28 0.74
24 10 0.26
ACGTcount: A:0.11, C:0.04, G:0.17, T:0.68
Consensus pattern (23 bp):
TGTTTTTATTGCTATTTTGATGT
Found at i:44455397 original size:24 final size:24
Alignment explanation
Indices: 44455382--44455456 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
44455372 TTTTTTACTA
44455382 TTTTGATGTTGTTTTTATTGTTAT
1 TTTTGATGTTGTTTTTATTGTTAT
* * *
44455406 TTTTGATGTTATTTCTT-CTATTAT
1 TTTTGATGTTGTTT-TTATTGTTAT
* * **
44455430 TTTTGTTGCTGTTTTGGTTGTTAT
1 TTTTGATGTTGTTTTTATTGTTAT
44455454 TTT
1 TTT
44455457 GGTTGTTTGG
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
23 1 0.03
24 37 0.93
25 2 0.05
ACGTcount: A:0.11, C:0.04, G:0.16, T:0.69
Consensus pattern (24 bp):
TTTTGATGTTGTTTTTATTGTTAT
Found at i:44456049 original size:39 final size:41
Alignment explanation
Indices: 44455967--44456059 Score: 109
Period size: 39 Copynumber: 2.3 Consensus size: 41
44455957 CATTAAAAAA
* * * *
44455967 TATTAATATTAAAAAACACTATCATAAATATACTAAATGTTT
1 TATT-ATATTAAAAAACACTATAATAAATAAAATAAATATTT
*
44456009 TATTATATTAAAAAACAC-A-AATAAATAAAATCAATATTT
1 TATTATATTAAAAAACACTATAATAAATAAAATAAATATTT
*
44456048 TATTGTATTAAA
1 TATTATATTAAA
44456060 TATAATACTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 26 0.58
40 1 0.02
41 14 0.31
42 4 0.09
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.38
Consensus pattern (41 bp):
TATTATATTAAAAAACACTATAATAAATAAAATAAATATTT
Found at i:44456191 original size:26 final size:26
Alignment explanation
Indices: 44456159--44456228 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 26
44456149 GGGTTAGTGA
44456159 TTTAATATAAATATATATCA-TTATTT
1 TTTAATATAAATATATAT-ATTTATTT
*
44456185 TTTAATATATATAATTAATATATTTATTT
1 TTTAATATAAAT-A-T-ATATATTTATTT
*
44456214 TATAATAT-AATATAT
1 TTTAATATAAATATAT
44456229 TCAGGCTGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
25 2 0.05
26 12 0.32
27 2 0.05
28 4 0.11
29 17 0.46
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTAATATAAATATATATATTTATTT
Found at i:44460391 original size:13 final size:15
Alignment explanation
Indices: 44460359--44460395 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
44460349 TGGGTAAGAG
44460359 TTTTGATTTGAGGAT
1 TTTTGATTTGAGGAT
*
44460374 TTTTG-TTT-AGGGT
1 TTTTGATTTGAGGAT
44460387 TTTTGATTT
1 TTTTGATTT
44460396 TTGAGATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 9 0.45
14 6 0.30
15 5 0.25
ACGTcount: A:0.14, C:0.00, G:0.24, T:0.62
Consensus pattern (15 bp):
TTTTGATTTGAGGAT
Found at i:44461067 original size:28 final size:28
Alignment explanation
Indices: 44461025--44461099 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
44461015 ATTTTAATAT
*
44461025 AATAATTTTAATAATTTTATATTTCAAAA
1 AATAATTATAATAATTTTATATTT-AAAA
*
44461054 TATAA-TATAATAATTTTATATTTAAAA
1 AATAATTATAATAATTTTATATTTAAAA
*
44461081 AATAATTTTAATAATTTTA
1 AATAATTATAATAATTTTA
44461100 AAATTATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
27 8 0.20
28 29 0.71
29 4 0.10
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (28 bp):
AATAATTATAATAATTTTATATTTAAAA
Found at i:44462437 original size:13 final size:13
Alignment explanation
Indices: 44462419--44462448 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
44462409 AACAGCTTCC
44462419 GAGCCCAAATCAA
1 GAGCCCAAATCAA
44462432 GAGCCCAAATCAA
1 GAGCCCAAATCAA
44462445 GAGC
1 GAGC
44462449 ATATGGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.43, C:0.30, G:0.20, T:0.07
Consensus pattern (13 bp):
GAGCCCAAATCAA
Found at i:44468456 original size:24 final size:25
Alignment explanation
Indices: 44468411--44468461 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
44468401 TCCCTAAATC
* *
44468411 TTAAAAAAATAACTTATTTGACCAA
1 TTAAAAAAATAACATATATGACCAA
* *
44468436 TTAAAAAAA-GACATATATGACTAA
1 TTAAAAAAATAACATATATGACCAA
44468460 TT
1 TT
44468462 TAACCACATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.53, C:0.10, G:0.06, T:0.31
Consensus pattern (25 bp):
TTAAAAAAATAACATATATGACCAA
Found at i:44488178 original size:30 final size:29
Alignment explanation
Indices: 44488152--44488427 Score: 172
Period size: 30 Copynumber: 9.2 Consensus size: 29
44488142 TAAAAATGGG
44488152 ATTTTTAGAAGTTTGAGGGATCAAAATGTA
1 ATTTTTAGAAGTTTGAGGG-TCAAAATGTA
*
44488182 ATTTTTAGAAAGTATTG-GGGTCAAAATATA
1 ATTTTTAG-AAGT-TTGAGGGTCAAAATGTA
44488212 ATTTTTAAGAAGTTTTGA-GGTCAAAATGTA
1 ATTTTT-AGAAG-TTTGAGGGTCAAAATGTA
** * *
44488242 ATATTGGAAAAGTTTTG-GGGTCAAAATGCA
1 AT-TTTTAGAAG-TTTGAGGGTCAAAATGTA
* * **
44488272 A-TATTAGAAGAGTTTTAGGGTCAAAACATA
1 ATTTTTAG-A-AGTTTGAGGGTCAAAATGTA
* * *
44488302 ATTTTGGAAAAGTTTTG-GAGTCAAAATGTA
1 ATTTT-TAGAAG-TTTGAGGGTCAAAATGTA
* * * *
44488332 ATTTTGGAAAAGTTTTAGGGTTAAAATGTA
1 ATTTT-TAGAAGTTTGAGGGTCAAAATGTA
*
44488362 A-TTTTAGAAAAGTTTTG-GGGTTAAAATGTA
1 ATTTTTAG--AAG-TTTGAGGGTCAAAATGTA
* *
44488392 ATTTCTAAAAAGTTTTG-GGGTCAAAATGTA
1 ATTT-TTAGAAG-TTTGAGGGTCAAAATGTA
44488422 ATTTTT
1 ATTTTT
44488428 GGACTATTTG
Statistics
Matches: 196, Mismatches: 31, Indels: 39
0.74 0.12 0.15
Matches are distributed among these distances:
28 3 0.02
29 11 0.06
30 153 0.78
31 23 0.12
32 6 0.03
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (29 bp):
ATTTTTAGAAGTTTGAGGGTCAAAATGTA
Found at i:44488216 original size:60 final size:59
Alignment explanation
Indices: 44488152--44488426 Score: 279
Period size: 60 Copynumber: 4.6 Consensus size: 59
44488142 TAAAAATGGG
* *
44488152 ATTTTTAGAAGTTTGAGGGATCAAAATGTAATTTTTAG-AAAGTATTGGGGTCAAAATATA
1 ATTTTTAGAAGTTTGAGGG-TCAAAATGTAA-TTTTAGAAAAGTTTTGGGGTCAAAATGTA
* * *
44488212 ATTTTTAAGAAGTTTTGA-GGTCAAAATGTAATATTGGAAAAGTTTTGGGGTCAAAATGCA
1 ATTTTT-AGAAG-TTTGAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTCAAAATGTA
* * ** * *
44488272 A-TATTAGAAGAGTTTTAGGGTCAAAACATAATTTTGGAAAAGTTTTGGAGTCAAAATGTA
1 ATTTTTAG-A-AGTTTGAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTCAAAATGTA
* * * * *
44488332 ATTTTGGAAAAGTTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTTGGGGTTAAAATGTA
1 ATTTT-TAGAAGTTTGAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTCAAAATGTA
* *
44488392 ATTTCTAAAAAGTTTTG-GGGTCAAAATGTAATTTT
1 ATTT-TTAGAAG-TTTGAGGGTCAAAATGTAATTTT
44488427 TGGACTATTT
Statistics
Matches: 181, Mismatches: 24, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
58 2 0.01
59 12 0.07
60 147 0.81
61 14 0.08
62 6 0.03
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (59 bp):
ATTTTTAGAAGTTTGAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTCAAAATGTA
Found at i:44488424 original size:90 final size:89
Alignment explanation
Indices: 44488160--44488426 Score: 338
Period size: 90 Copynumber: 3.0 Consensus size: 89
44488150 GGATTTTTAG
* * *
44488160 AAGTTTGAGGGATCAAAATGTAATTTTTAG-AAAGTATTGGGGTCAAAATATAATTTTTAAGAAG
1 AAGTTTTAGGG-TCAAAATGTAA-TTTTAGAAAAGTTTTGGGGTCAAAATATAA-TTTTAAAAAG
* *
44488224 TTTTGAGGTCAAAATGTAATATTGGAA
63 TTTTGGGGTCAAAATGTAATTTTGGAA
* * * * * * *
44488251 AAGTTTTGGGGTCAAAATGCAATATTAGAAGAGTTTTAGGGTCAAAACATAATTTTGGAAAAGTT
1 AAGTTTTAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTCAAAATATAATTTT-AAAAAGTT
*
44488316 TTGGAGTCAAAATGTAATTTTGGAA
65 TTGGGGTCAAAATGTAATTTTGGAA
* * *
44488341 AAGTTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTTGGGGTTAAAATGTAATTTCTAAAAAGTT
1 AAGTTTTAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTCAAAATATAATTT-TAAAAAGTT
44488406 TTGGGGTCAAAATGTAATTTT
65 TTGGGGTCAAAATGTAATTTT
44488427 TGGACTATTT
Statistics
Matches: 149, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
89 9 0.06
90 130 0.87
91 10 0.07
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (89 bp):
AAGTTTTAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTCAAAATATAATTTTAAAAAGTTT
TGGGGTCAAAATGTAATTTTGGAA
Found at i:44490283 original size:6 final size:6
Alignment explanation
Indices: 44490266--44490317 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
44490256 TAAATTCAAG
* * * * *
44490266 TTAAAT TCAAAT TTAAAT TTAAAA TTGAAT TTAAA- ATAAAT TTAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
44490313 TTAAA
1 TTAAA
44490318 ATAATTTTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (6 bp):
TTAAAT
Found at i:44490296 original size:12 final size:12
Alignment explanation
Indices: 44490266--44490317 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
44490256 TAAATTCAAG
* *
44490266 TTAAATTCAAAT
1 TTAAATTTAAAA
44490278 TTAAATTTAAAA
1 TTAAATTTAAAA
*
44490290 TTGAATTTAAAA
1 TTAAATTTAAAA
44490302 -TAAATTTAAAA
1 TTAAATTTAAAA
44490313 TTAAA
1 TTAAA
44490318 ATAATTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 10 0.29
12 25 0.71
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (12 bp):
TTAAATTTAAAA
Found at i:44490309 original size:11 final size:11
Alignment explanation
Indices: 44490279--44490313 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
44490269 AATTCAAATT
44490279 TAAATTTAAAA
1 TAAATTTAAAA
*
44490290 TTGAATTTAAAA
1 -TAAATTTAAAA
44490302 TAAATTTAAAA
1 TAAATTTAAAA
44490313 T
1 T
44490314 TAAAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:44490923 original size:92 final size:92
Alignment explanation
Indices: 44490662--44491507 Score: 1414
Period size: 92 Copynumber: 9.2 Consensus size: 92
44490652 ATCTTACTCT
* * *
44490662 TACTTCAATTTCAA-AGG-GACGAAAATGATGTTGGTGCTTTATCTTGCTCTTACTTCAATTTCA
1 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
44490725 GATG-GACGAAGGCTTGATATCCAGCTC
66 GA-GAGACGAAGGCTTGATATCCAGCTC
* *
44490752 TACTTCAATTTCAAGAGGATAGGAAAA-GATGTCGGTGCTTCATCTTACTCTTACTTCAATTTCA
1 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
*
44490816 GAGAGACAAAGGCTTGATATCCAGCTC
66 GAGAGACGAAGGCTTGATATCCAGCTC
* *
44490843 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGTTTCATCTTACTCTTACTTCAATTTCA
1 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
*
44490908 GAGAGAC-AAGGGCTTGATATCCAACTC
66 GAGAGACGAA-GGCTTGATATCCAGCTC
44490935 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
1 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
*
44491000 GAGGGACGAAGGCTTGATATCCAGCTC
66 GAGAGACGAAGGCTTGATATCCAGCTC
44491027 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
1 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
* * *
44491092 GAGGGACGAAGGCTTGTTATCCAGCTT
66 GAGAGACGAAGGCTTGATATCCAGCTC
* *
44491119 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTACTCTTACTTCAATTCCA
1 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
*
44491184 GAGAGACGAAGGCTTGTTATCCAGCTC
66 GAGAGACGAAGGCTTGATATCCAGCTC
44491211 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
1 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
*
44491276 GAGGGACGAAGGCTTGATATCCAGCTC
66 GAGAGACGAAGGCTTGATATCCAGCTC
44491303 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
1 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
* * *
44491368 GAGGGACGAAGGCTTGTTATCCAGCTT
66 GAGAGACGAAGGCTTGATATCCAGCTC
** *
44491395 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTCACTCTTACTTCAATTCCA
1 TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
* *
44491460 GAGAGACGAAGGCTTGTTATCCAGCTT
66 GAGAGACGAAGGCTTGATATCCAGCTC
44491487 TACTTCAATTTCAAGAGGATA
1 TACTTCAATTTCAAGAGGATA
44491508 AAAATCTGAC
Statistics
Matches: 721, Mismatches: 29, Indels: 10
0.95 0.04 0.01
Matches are distributed among these distances:
90 15 0.02
91 90 0.12
92 614 0.85
93 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (92 bp):
TACTTCAATTTCAAGAGGATAGGAAAATGATGTTGGTGCTTCATCTTGCTCTTACTTCAATTTCA
GAGAGACGAAGGCTTGATATCCAGCTC
Found at i:44491584 original size:40 final size:40
Alignment explanation
Indices: 44491539--44491699 Score: 119
Period size: 40 Copynumber: 3.7 Consensus size: 40
44491529 TATCTTACTC
44491539 TTACTATAACTTC-AGAGAGATAAAAATTCATTATCCAACT
1 TTACTATAACTTCAAGAG-GATAAAAATTCATTATCCAACT
* * **
44491579 TTACTATAACTTTAAAAGGATAAAAATTTGACATTTGAAAATTCATCTTGCT
1 TTACTATAACTTCAAGAGGATAAAAA-TT--CA-TT----A-TC--C-AACT
* *
44491631 CTTACTATAACTTC-AGAGAGATGAAGATTCATTATCCAACT
1 -TTACTATAACTTCAAGAG-GATAAAAATTCATTATCCAACT
44491672 TTACTATAACTTCAAGAGGATAAAAATT
1 TTACTATAACTTCAAGAGGATAAAAATT
44491700 TGACATTTAA
Statistics
Matches: 93, Mismatches: 12, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
40 41 0.44
41 11 0.12
42 1 0.01
43 2 0.02
44 4 0.04
45 1 0.01
48 1 0.01
49 4 0.04
50 2 0.02
51 1 0.01
52 7 0.08
53 18 0.19
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (40 bp):
TTACTATAACTTCAAGAGGATAAAAATTCATTATCCAACT
Found at i:44491601 original size:93 final size:93
Alignment explanation
Indices: 44491476--44491748 Score: 417
Period size: 93 Copynumber: 2.9 Consensus size: 93
44491466 CGAAGGCTTG
* * *
44491476 TTATCCAGCTTTACT-TCAA-TTTCAAGAGGATAAAAATCTGACATTTAAAGCTTTATCTTACTC
1 TTATCCAACTTTACTAT-AACTTT-AAGAGGATAAAAATTTGACATTTAAAGCTTTATCTTGCTC
44491539 TTACTATAACTTCAGAGAGATAAAAATTCA
64 TTACTATAACTTCAGAGAGATAAAAATTCA
* * *
44491569 TTATCCAACTTTACTATAACTTTAAAAGGATAAAAATTTGACATTTGAAA-ATTCATCTTGCTCT
1 TTATCCAACTTTACTATAACTTTAAGAGGATAAAAATTTGACATTT-AAAGCTTTATCTTGCTCT
* *
44491633 TACTATAACTTCAGAGAGATGAAGATTCA
65 TACTATAACTTCAGAGAGATAAAAATTCA
*
44491662 TTATCCAACTTTACTATAACTTCAAGAGGATAAAAATTTGACATTTAAAGCTTTATCTTGCTCTT
1 TTATCCAACTTTACTATAACTTTAAGAGGATAAAAATTTGACATTTAAAGCTTTATCTTGCTCTT
44491727 ACTATAACTTCAGAGAGATAAA
66 ACTATAACTTCAGAGAGATAAA
44491749 GACTTTTCCC
Statistics
Matches: 163, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
92 3 0.02
93 153 0.94
94 7 0.04
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (93 bp):
TTATCCAACTTTACTATAACTTTAAGAGGATAAAAATTTGACATTTAAAGCTTTATCTTGCTCTT
ACTATAACTTCAGAGAGATAAAAATTCA
Found at i:44494053 original size:18 final size:18
Alignment explanation
Indices: 44494030--44494068 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
44494020 ATCTTGACCC
44494030 TTTCTTCTTC-TTCTCTTT
1 TTTCTTCTTCTTTC-CTTT
*
44494048 TTTCTTTTTCTTTCCTTT
1 TTTCTTCTTCTTTCCTTT
44494066 TTT
1 TTT
44494069 ATTTGGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTCTTCTTCTTTCCTTT
Found at i:44498647 original size:30 final size:29
Alignment explanation
Indices: 44498582--44498896 Score: 360
Period size: 30 Copynumber: 10.5 Consensus size: 29
44498572 GTTCGGGGGA
* *
44498582 TCAAAATGTAATTTTTCAGAAAGTATTAAGG
1 TCAAAATGTAA-TTTT-AGAAAGTTTTAGGG
* * * *
44498613 TTAAAATATAATTTTTAGGAAGTTTTGGGG
1 TCAAAATGTAA-TTTTAGAAAGTTTTAGGG
* * *
44498643 TTAAAATGTAATATTAGAAAAGTTTTGGGG
1 TCAAAATGTAATTTTAG-AAAGTTTTAGGG
*
44498673 TCAAAATGTAATATTAGAAGAGTTTTAGGG
1 TCAAAATGTAATTTTAGAA-AGTTTTAGGG
* *
44498703 TCAAAATGTAATTTTGGAAAAGTTTTGGGG
1 TCAAAATGTAATTTTAG-AAAGTTTTAGGG
*
44498733 TCAAAATGTAATATTAGAAGAGTTTTAGGG
1 TCAAAATGTAATTTTAGAA-AGTTTTAGGG
* *
44498763 TCAAAATGTAATTTTGGAAAGTTTTAAGG
1 TCAAAATGTAATTTTAGAAAGTTTTAGGG
* *
44498792 TTAAAATGTAATTTTGGAAAAGTTTTAGGG
1 TCAAAATGTAATTTTAG-AAAGTTTTAGGG
*
44498822 TCAAAATGTAATTTTAGAAAAGTTTTGGGG
1 TCAAAATGTAATTTTAG-AAAGTTTTAGGG
* *
44498852 TTAAAATGTAATTTCTAAAAAGTTTTAGGG
1 TCAAAATGTAATTT-TAGAAAGTTTTAGGG
44498882 TCAAAATGTAATTTT
1 TCAAAATGTAATTTT
44498897 TGGACTGTTT
Statistics
Matches: 249, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
29 35 0.14
30 196 0.79
31 18 0.07
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (29 bp):
TCAAAATGTAATTTTAGAAAGTTTTAGGG
Found at i:44498819 original size:119 final size:119
Alignment explanation
Indices: 44498632--44498896 Score: 379
Period size: 119 Copynumber: 2.2 Consensus size: 119
44498622 AATTTTTAGG
* * * ** *
44498632 AAGTTTTGGGGTTAAAATGTAATATTAGAAAAGTTTTGGGGTCAAAATGTAATATTAGAAGAGTT
1 AAGTTTTAGGGTCAAAATGTAAT-TTTGAAAAGTTTTAAGGTCAAAATGTAATATTAGAAAAGTT
*
44498697 TTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATAT-TAGAA
65 TTAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTCAAAATGTAATATCTA-AA
* * * * *
44498752 GAGTTTTAGGGTCAAAATGTAATTTTGGAAAGTTTTAAGGTTAAAATGTAATTTTGGAAAAGTTT
1 AAGTTTTAGGGTCAAAATGTAATTTTGAAAAGTTTTAAGGTCAAAATGTAATATTAGAAAAGTTT
* *
44498817 TAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTTAAAATGTAATTTCTAAA
66 TAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTCAAAATGTAATATCTAAA
44498871 AAGTTTTAGGGTCAAAATGTAATTTT
1 AAGTTTTAGGGTCAAAATGTAATTTT
44498897 TGGACTGTTT
Statistics
Matches: 129, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
119 107 0.83
120 22 0.17
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (119 bp):
AAGTTTTAGGGTCAAAATGTAATTTTGAAAAGTTTTAAGGTCAAAATGTAATATTAGAAAAGTTT
TAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTCAAAATGTAATATCTAAA
Found at i:44500780 original size:6 final size:6
Alignment explanation
Indices: 44500761--44500795 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
44500751 AATTCAAGTT
*
44500761 AAATTCA AATTTA AAATTA AAATTA AAATTA AAAT
1 AAATT-A AAATTA AAATTA AAATTA AAATTA AAAT
44500796 AATTTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 22 0.85
7 4 0.15
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (6 bp):
AAATTA
Found at i:44501290 original size:7 final size:8
Alignment explanation
Indices: 44501278--44501327 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
44501268 TCTAAAATAC
44501278 ATACAT-T
1 ATACATAT
44501285 ATACATAT
1 ATACATAT
*
44501293 ATATATAT
1 ATACATAT
*
44501301 ATATATAT
1 ATACATAT
*
44501309 ATATATAT
1 ATACATAT
*
44501317 ATATATAT
1 ATACATAT
44501325 ATA
1 ATA
44501328 TCTATTGATG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
7 6 0.15
8 35 0.85
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (8 bp):
ATACATAT
Found at i:44501296 original size:2 final size:2
Alignment explanation
Indices: 44501284--44501328 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
44501274 ATACATACAT
*
44501284 TA TA CA TA TA TA TA TA 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 TA
44501326 TA T
1 TA T
44501329 CTATTGATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:44506508 original size:34 final size:34
Alignment explanation
Indices: 44506470--44506549 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 34
44506460 CTCTAAAACA
* * *
44506470 AGCTAATAACCTCAACTTTTTACTCTCACTAACG
1 AGCTAACAAACTCAACTTTCTACTCTCACTAACG
* * * *
44506504 AGCTAACAAATTCAACTTTCTACTTTCATTAACA
1 AGCTAACAAACTCAACTTTCTACTCTCACTAACG
*
44506538 AGTTAACAAACT
1 AGCTAACAAACT
44506550 TCCTAGAATC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.33
Consensus pattern (34 bp):
AGCTAACAAACTCAACTTTCTACTCTCACTAACG
Found at i:44507337 original size:55 final size:54
Alignment explanation
Indices: 44507278--44507382 Score: 140
Period size: 55 Copynumber: 1.9 Consensus size: 54
44507268 AATAACATCC
* * *
44507278 AAACAACAAAAATCA-CAACCAAAATAGCAGCAAAAATAACAGCAAACAACATTAA
1 AAACAACAAAAAT-AGCAACAAAAACAGCAACAAAAATAACAGCAAA-AACATTAA
* *
44507333 AAACAACAAAAATAGCAACAAAAACAGCAATAAAAATAACAGTAAAAACA
1 AAACAACAAAAATAGCAACAAAAACAGCAACAAAAATAACAGCAAAAACA
44507383 ACACGAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
54 5 0.11
55 39 0.89
ACGTcount: A:0.67, C:0.19, G:0.06, T:0.09
Consensus pattern (54 bp):
AAACAACAAAAATAGCAACAAAAACAGCAACAAAAATAACAGCAAAAACATTAA
Found at i:44507339 original size:43 final size:43
Alignment explanation
Indices: 44507265--44507356 Score: 116
Period size: 43 Copynumber: 2.1 Consensus size: 43
44507255 AAACGCATAA
* *
44507265 AAAAATAACATCCAAACAACAAAAATCACAACCAAAATAGCAGC
1 AAAAATAACATCCAAACAACAAAAA-CACAACAAAAATAGCAAC
*
44507309 AAAAATAACA-GCAAACAACATTAAAA-ACAACAAAAATAGCAAC
1 AAAAATAACATCCAAACAACA--AAAACACAACAAAAATAGCAAC
44507352 AAAAA
1 AAAAA
44507357 CAGCAATAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 29 0.67
44 10 0.23
45 4 0.09
ACGTcount: A:0.66, C:0.21, G:0.04, T:0.09
Consensus pattern (43 bp):
AAAAATAACATCCAAACAACAAAAACACAACAAAAATAGCAAC
Found at i:44507417 original size:21 final size:20
Alignment explanation
Indices: 44507397--44507487 Score: 55
Period size: 22 Copynumber: 4.5 Consensus size: 20
44507387 GAAAATAACA
*
44507397 ACCAAAAGAATAAAAAAAAC
1 ACCAAAACAATAAAAAAAAC
*
44507417 ACCAAAACAGT---AAAAAC
1 ACCAAAACAATAAAAAAAAC
*
44507434 A-CAAAAGCAACAAAAAACAAC
1 ACCAAAA-CAATAAAAAA-AAC
* * *
44507455 AATCACAACAGTAAAAAAACAGC
1 -ACCAAAACAATAAAAAAA-A-C
44507478 ACCAAAACAA
1 ACCAAAACAA
44507488 CAATAGAATT
Statistics
Matches: 52, Mismatches: 10, Indels: 16
0.67 0.13 0.21
Matches are distributed among these distances:
16 5 0.10
17 9 0.17
20 12 0.23
21 4 0.08
22 17 0.33
23 5 0.10
ACGTcount: A:0.68, C:0.22, G:0.05, T:0.04
Consensus pattern (20 bp):
ACCAAAACAATAAAAAAAAC
Found at i:44508955 original size:18 final size:18
Alignment explanation
Indices: 44508932--44508970 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
44508922 TTACTCACTT
*
44508932 AATAATCATATGATTAAA
1 AATAATCATATAATTAAA
**
44508950 AATAATGTTATAATTAAA
1 AATAATCATATAATTAAA
44508968 AAT
1 AAT
44508971 TTAATAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (18 bp):
AATAATCATATAATTAAA
Found at i:44508983 original size:13 final size:13
Alignment explanation
Indices: 44508965--44508989 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44508955 TGTTATAATT
44508965 AAAAATTTAATAA
1 AAAAATTTAATAA
44508978 AAAAATTTAATA
1 AAAAATTTAATA
44508990 GAATTGAAAC
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAATTTAATAA
Found at i:44510495 original size:4 final size:4
Alignment explanation
Indices: 44510470--44510523 Score: 54
Period size: 4 Copynumber: 13.2 Consensus size: 4
44510460 TTTCCATCCT
* * * * *
44510470 TATA GTATA TATA CATA CATA TATA TATA TATA TATG TATA TGTA TATG
1 TATA -TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
44510519 TATA T
1 TATA T
44510524 GTGTGTGTGG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
4 37 0.90
5 4 0.10
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (4 bp):
TATA
Found at i:44510499 original size:6 final size:6
Alignment explanation
Indices: 44510470--44510523 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
44510460 TTTCCATCCT
* * * * *
44510470 TATAGTA TATATA CATACA TATATA TATATA TATATG TATATG TATATG
1 TATA-TA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
44510519 TATAT
1 TATAT
44510524 GTGTGTGTGG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
6 38 0.90
7 4 0.10
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (6 bp):
TATATA
Found at i:44510524 original size:6 final size:6
Alignment explanation
Indices: 44510489--44510525 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
44510479 TATACATACA
* *
44510489 TATATA TATATA TATATG TATATG TATATG TATATG T
1 TATATG TATATG TATATG TATATG TATATG TATATG T
44510526 GTGTGTGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:44512278 original size:20 final size:20
Alignment explanation
Indices: 44512253--44512293 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
44512243 GTCCTCTTCT
44512253 TTTATTAGATGAGG-GATTAA
1 TTTATTAGATG-GGAGATTAA
44512273 TTTATTAGATGGGAGATTAA
1 TTTATTAGATGGGAGATTAA
44512293 T
1 T
44512294 CGGGTCGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (20 bp):
TTTATTAGATGGGAGATTAA
Found at i:44516661 original size:25 final size:26
Alignment explanation
Indices: 44516628--44516679 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
44516618 AAATTTGATT
*
44516628 TAATCTTTTAAATATTAT-AAA-TATA
1 TAATATTTTAAA-ATTATGAAATTATA
44516653 TAATATTTTAAAATTATGAAATTATA
1 TAATATTTTAAAATTATGAAATTATA
44516679 T
1 T
44516680 TTTTATTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 5 0.21
25 14 0.58
26 5 0.21
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
TAATATTTTAAAATTATGAAATTATA
Found at i:44521734 original size:18 final size:18
Alignment explanation
Indices: 44521711--44521750 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
44521701 GAGAAACATA
44521711 CAAGGAATCTCTATGTTG
1 CAAGGAATCTCTATGTTG
44521729 CAAGGAATCTCTATGTTG
1 CAAGGAATCTCTATGTTG
44521747 CAAG
1 CAAG
44521751 CAATTTGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (18 bp):
CAAGGAATCTCTATGTTG
Found at i:44532856 original size:21 final size:21
Alignment explanation
Indices: 44532830--44532871 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
44532820 GTTGTGGTTG
44532830 GGGCTCAATTATTCATAGTTA
1 GGGCTCAATTATTCATAGTTA
44532851 GGGCTCAATTATTCATAGTTA
1 GGGCTCAATTATTCATAGTTA
44532872 AGTATGTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (21 bp):
GGGCTCAATTATTCATAGTTA
Found at i:44535802 original size:20 final size:21
Alignment explanation
Indices: 44535785--44535865 Score: 105
Period size: 20 Copynumber: 4.0 Consensus size: 21
44535775 ATCATTGACT
44535785 GTTGACTTTGACCGTTGA-TC
1 GTTGACTTTGACCGTTGACTC
*
44535805 GTTGACAGTTGACCGTTGA-TC
1 GTTGAC-TTTGACCGTTGACTC
*
44535826 GTTGACTTTGATCGTTGAC-C
1 GTTGACTTTGACCGTTGACTC
*
44535846 GTTGACTTTGACCATTGACT
1 GTTGACTTTGACCGTTGACT
44535866 TTTTTCGAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
20 34 0.64
21 19 0.36
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (21 bp):
GTTGACTTTGACCGTTGACTC
Found at i:44535808 original size:34 final size:32
Alignment explanation
Indices: 44535728--44535857 Score: 102
Period size: 34 Copynumber: 3.8 Consensus size: 32
44535718 ATTGATCGGT
**
44535728 CGTTGA-CAGTTGACCATTGACCATTGACAGTTGA
1 CGTTGATC-GTTGA-CATTGACTGTTGAC-GTTGA
* *
44535762 TCGTTGACCGTTGATCATTGACTGTTGACTTTGA
1 -CGTTGATCGTTGA-CATTGACTGTTGACGTTGA
*
44535796 CCGTTGATCGTTGACAGTTGACCGTTGATCGTTGA
1 -CGTTGATCGTTGACA-TTGACTGTTGA-CGTTGA
* *
44535831 CTTTGATCGTTGACCGTTGACT-TTGAC
1 CGTTGATCGTTGA-CATTGACTGTTGAC
44535858 CATTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
32 1 0.01
33 6 0.08
34 43 0.54
35 29 0.36
36 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (32 bp):
CGTTGATCGTTGACATTGACTGTTGACGTTGA
Found at i:44535808 original size:41 final size:42
Alignment explanation
Indices: 44535751--44535865 Score: 146
Period size: 41 Copynumber: 2.8 Consensus size: 42
44535741 CCATTGACCA
* *
44535751 TTGACAGTTGATCGTTGACCGTTGATCATTGACT-GTTGACT
1 TTGACCGTTGATCGTTGACCGTTGACCATTGACTCGTTGACT
* *
44535792 TTGACCGTTGATCGTTGACAGTTGACCGTTGA-TCGTTGACT
1 TTGACCGTTGATCGTTGACCGTTGACCATTGACTCGTTGACT
* * *
44535833 TTGATCGTTGACCGTTGA-CTTTGACCATTGACT
1 TTGACCGTTGATCGTTGACCGTTGACCATTGACT
44535866 TTTTTCGAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
40 11 0.17
41 52 0.83
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (42 bp):
TTGACCGTTGATCGTTGACCGTTGACCATTGACTCGTTGACT
Found at i:44535851 original size:7 final size:7
Alignment explanation
Indices: 44535728--44535864 Score: 109
Period size: 7 Copynumber: 20.0 Consensus size: 7
44535718 ATTGATCGGT
44535728 CGTTGAC
1 CGTTGAC
*
44535735 AGTTGAC
1 CGTTGAC
*
44535742 CATTGAC
1 CGTTGAC
*
44535749 CATTGAC
1 CGTTGAC
* *
44535756 AGTTGAT
1 CGTTGAC
44535763 CGTTGAC
1 CGTTGAC
*
44535770 CGTTGAT
1 CGTTGAC
*
44535777 CATTGAC
1 CGTTGAC
*
44535784 TGTTGA-
1 CGTTGAC
*
44535790 CTTTGAC
1 CGTTGAC
*
44535797 CGTTGAT
1 CGTTGAC
44535804 CGTTGAC
1 CGTTGAC
*
44535811 AGTTGAC
1 CGTTGAC
*
44535818 CGTTGAT
1 CGTTGAC
44535825 CGTTGA-
1 CGTTGAC
* *
44535831 CTTTGAT
1 CGTTGAC
44535838 CGTTGAC
1 CGTTGAC
44535845 CGTTGA-
1 CGTTGAC
*
44535851 CTTTGAC
1 CGTTGAC
*
44535858 CATTGAC
1 CGTTGAC
44535865 TTTTTTCGAA
Statistics
Matches: 101, Mismatches: 26, Indels: 6
0.76 0.20 0.05
Matches are distributed among these distances:
6 14 0.14
7 87 0.86
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (7 bp):
CGTTGAC
Found at i:44543646 original size:78 final size:78
Alignment explanation
Indices: 44543511--44543674 Score: 249
Period size: 78 Copynumber: 2.1 Consensus size: 78
44543501 TTGAGTTTAG
* * * *
44543511 TCAACAATGTTAAATGGAGCACTTTTTGGAGTCTAAGGATTTGGTTGAAATTCTTTAAGATTTGA
1 TCAACAATATTAAATGGAGCACTTTTTGGAATCTAAGGATTTGGTTGAAAATATTTAAGATTTGA
44543576 TTGAGAATCTTAA
66 TTGAGAATCTTAA
* *
44543589 TCAACAATATTAAATGGAGCTC-TTTTGAGAATTTAAGGATTTGGTTGAAAATATTTAAGATTTG
1 TCAACAATATTAAATGGAGCACTTTTTG-GAATCTAAGGATTTGGTTGAAAATATTTAAGATTTG
44543653 ATTGAGAATCTTAA
65 ATTGAGAATCTTAA
*
44543667 TTAACAAT
1 TCAACAAT
44543675 TTATATGTTG
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
77 5 0.06
78 73 0.94
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (78 bp):
TCAACAATATTAAATGGAGCACTTTTTGGAATCTAAGGATTTGGTTGAAAATATTTAAGATTTGA
TTGAGAATCTTAA
Found at i:44548981 original size:29 final size:29
Alignment explanation
Indices: 44548939--44549025 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
44548929 CTCAGAGCCC
44548939 CCCATGTGCAATGCTATAAGTTATTTAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
* *
44548968 CCCATGTGCAATGCTACAAGTGATTTAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
*
44548997 CTCATGTGCAATGCTATAAGTTATTTAGA
1 CCCATGTGCAATGCTATAAGTTATTTAGA
44549026 AAGTGCTTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (29 bp):
CCCATGTGCAATGCTATAAGTTATTTAGA
Found at i:44552226 original size:14 final size:15
Alignment explanation
Indices: 44552202--44552237 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
44552192 ATTAAAAAAA
44552202 TTAAGTATTAAATTT
1 TTAAGTATTAAATTT
44552217 TTAA-TATTAAATTT
1 TTAAGTATTAAATTT
44552231 TATAAGT
1 T-TAAGT
44552238 GTCGAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.58
15 7 0.37
16 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TTAAGTATTAAATTT
Found at i:44552291 original size:13 final size:13
Alignment explanation
Indices: 44552273--44552297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44552263 TTTAAATAAG
44552273 TAAATATAATTAA
1 TAAATATAATTAA
44552286 TAAATATAATTA
1 TAAATATAATTA
44552298 TATTGTTTGA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAATATAATTAA
Found at i:44559984 original size:18 final size:17
Alignment explanation
Indices: 44559961--44559994 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
44559951 AAAAGGTAAT
*
44559961 ATTTATGATTATTTTTAA
1 ATTTATAATT-TTTTTAA
44559979 ATTTATAATTTTTTTA
1 ATTTATAATTTTTTTA
44559995 TGGTTATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
ATTTATAATTTTTTTAA
Found at i:44560179 original size:26 final size:26
Alignment explanation
Indices: 44560150--44560202 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
44560140 ATAAATATTA
* *
44560150 TATTGATAAATAAAGTACCTATTTTT
1 TATTGATAAATAAAATACATATTTTT
* * *
44560176 TATTTATGACTAAAATACATATTTTT
1 TATTGATAAATAAAATACATATTTTT
44560202 T
1 T
44560203 TTCTTTGTTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.49
Consensus pattern (26 bp):
TATTGATAAATAAAATACATATTTTT
Found at i:44566072 original size:7 final size:7
Alignment explanation
Indices: 44566060--44566085 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
44566050 ATCAATTTAA
44566060 TTTAAAT
1 TTTAAAT
44566067 TTTAAAT
1 TTTAAAT
44566074 TTTAAAT
1 TTTAAAT
44566081 TTTAA
1 TTTAA
44566086 GTATAATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTAAAT
Found at i:44567476 original size:20 final size:22
Alignment explanation
Indices: 44567453--44567510 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 22
44567443 AAACAACACG
44567453 AAAACAACAAT-CAAAACAAT-
1 AAAACAACAATACAAAACAATA
*
44567473 AAAA-AA-AATACCAAAACAGTA
1 AAAACAACAATA-CAAAACAATA
*
44567494 AAAACAACAACACAAAA
1 AAAACAACAATACAAAA
44567511 TAGCAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 3 0.10
19 2 0.06
20 12 0.39
21 4 0.13
22 7 0.23
23 3 0.10
ACGTcount: A:0.72, C:0.19, G:0.02, T:0.07
Consensus pattern (22 bp):
AAAACAACAATACAAAACAATA
Found at i:44567497 original size:21 final size:21
Alignment explanation
Indices: 44567464--44567554 Score: 96
Period size: 21 Copynumber: 4.3 Consensus size: 21
44567454 AAACAACAAT
*
44567464 CAAAACAAT-AAAAAAAATAC
1 CAAAACAGTAAAAAAAAATAC
*
44567484 CAAAACAGTAAAAACAACA-AC
1 CAAAACAGTAAAAA-AAAATAC
* * *
44567505 ACAAAATAGCAAAAAAAAAAAC
1 -CAAAACAGTAAAAAAAAATAC
*
44567527 CAAAACAGTAAAAAACAATAC
1 CAAAACAGTAAAAAAAAATAC
44567548 CAAAACA
1 CAAAACA
44567555 AGAATATATT
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
20 8 0.14
21 33 0.57
22 17 0.29
ACGTcount: A:0.71, C:0.19, G:0.03, T:0.07
Consensus pattern (21 bp):
CAAAACAGTAAAAAAAAATAC
Done.