Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 98 of 199
Found at i:29887702 original size:20 final size:20
Alignment explanation
Indices: 29887677--29887737 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
29887667 TTTGTTTTTC
29887677 TTTATTTCATTTTTCTCTTT
1 TTTATTTCATTTTTCTCTTT
*
29887697 TTTATTT--GTTTT-TC---
1 TTTATTTCATTTTTCTCTTT
*
29887711 TTTATTTCATTTTTCTATTT
1 TTTATTTCATTTTTCTCTTT
29887731 TTTATTT
1 TTTATTT
29887738 GTTTATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
14 7 0.22
16 4 0.12
17 3 0.09
18 4 0.12
20 14 0.44
ACGTcount: A:0.11, C:0.10, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTATTTCATTTTTCTCTTT
Found at i:29887737 original size:15 final size:15
Alignment explanation
Indices: 29887652--29887737 Score: 64
Period size: 17 Copynumber: 5.2 Consensus size: 15
29887642 TTGTTTGTCC
*
29887652 TTTTTCTGTTTTTTA
1 TTTTTCTCTTTTTTA
*
29887667 TTTGTTTTTCTTTATTTCA
1 -TT-TTTCTCTTT-TTT-A
29887686 TTTTTCTCTTTTTTA
1 TTTTTCTCTTTTTTA
*
29887701 TTTGTTTTTCTTTATTTCA
1 -TT-TTTCTCTTT-TTT-A
*
29887720 TTTTTCTATTTTTTA
1 TTTTTCTCTTTTTTA
29887735 TTT
1 TTT
29887738 GTTTATTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
15 5 0.09
16 10 0.18
17 30 0.53
18 10 0.18
19 2 0.04
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.78
Consensus pattern (15 bp):
TTTTTCTCTTTTTTA
Found at i:29887961 original size:10 final size:10
Alignment explanation
Indices: 29887946--29887988 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
29887936 ATGGAGGACC
*
29887946 AAAAAATAAA
1 AAAAAATGAA
29887956 AAAAAATTGAA
1 AAAAAA-TGAA
29887967 AAAAAATGAGA
1 AAAAAATGA-A
*
29887978 AAAAATTGAA
1 AAAAAATGAA
29887988 A
1 A
29887989 GTTGAATTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 11 0.38
11 18 0.62
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (10 bp):
AAAAAATGAA
Found at i:29887968 original size:11 final size:11
Alignment explanation
Indices: 29887954--29887988 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
29887944 CCAAAAAATA
29887954 AAAAAAAATTG
1 AAAAAAAATTG
29887965 AAAAAAAA-TG
1 AAAAAAAATTG
*
29887975 AGAAAAAATTG
1 AAAAAAAATTG
29887986 AAA
1 AAA
29887989 GTTGAATTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.14
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:29887970 original size:21 final size:21
Alignment explanation
Indices: 29887946--29887988 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
29887936 ATGGAGGACC
29887946 AAAAAATAAAAAAAAATTGAA
1 AAAAAATAAAAAAAAATTGAA
* *
29887967 AAAAAATGAGAAAAAATTGAA
1 AAAAAATAAAAAAAAATTGAA
29887988 A
1 A
29887989 GTTGAATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (21 bp):
AAAAAATAAAAAAAAATTGAA
Found at i:29888320 original size:18 final size:18
Alignment explanation
Indices: 29888297--29888336 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
29888287 TTATAGTTTG
29888297 TATTTTGTATTTTATAGT
1 TATTTTGTATTTTATAGT
29888315 TATTTTGTATTTTATAGT
1 TATTTTGTATTTTATAGT
29888333 TATT
1 TATT
29888337 GTAATATAAT
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:0.23, C:0.00, G:0.10, T:0.68
Consensus pattern (18 bp):
TATTTTGTATTTTATAGT
Found at i:29893580 original size:24 final size:22
Alignment explanation
Indices: 29893532--29893606 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
29893522 TTTTATAACG
* *
29893532 TTAAAAAATTATATTTAAAATT
1 TTAAAAAATAATATTTAAAAAT
29893554 TTAAAAAATAATATTATAAAACAT
1 TTAAAAAATAATATT-TAAAA-AT
* *
29893578 TTAAAATAT-ACATTTAAAATAT
1 TTAAAAAATAATATTTAAAA-AT
*
29893600 TTTAAAA
1 TTAAAAA
29893607 CAAATAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 26 0.59
23 9 0.20
24 9 0.20
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAAAATAATATTTAAAAAT
Found at i:29893590 original size:13 final size:13
Alignment explanation
Indices: 29893574--29893599 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29893564 ATATTATAAA
29893574 ACATTTAAAATAT
1 ACATTTAAAATAT
29893587 ACATTTAAAATAT
1 ACATTTAAAATAT
29893600 TTTAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATTTAAAATAT
Found at i:29893603 original size:23 final size:22
Alignment explanation
Indices: 29893536--29893606 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 22
29893526 ATAACGTTAA
29893536 AAAAT-TATATTT-AAAATTTT
1 AAAATATATATTTAAAAATTTT
*
29893556 AAAAAATAATATTATAAAACA-TTT
1 AAAATAT-ATATT-TAAAA-ATTTT
*
29893580 AAAATATACATTTAAAATATTTT
1 AAAATATATATTTAAAA-ATTTT
29893603 AAAA
1 AAAA
29893607 CAAATAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
20 4 0.10
21 1 0.02
22 11 0.27
23 12 0.29
24 12 0.29
25 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATATATATTTAAAAATTTT
Found at i:29895452 original size:25 final size:24
Alignment explanation
Indices: 29895424--29895636 Score: 121
Period size: 25 Copynumber: 8.8 Consensus size: 24
29895414 AATAAATGGA
* *
29895424 TCTCTTGAGCTTTCCGTTATTTGGC
1 TCTCATGAGCTTCCCGTTA-TTGGC
**
29895449 TCTCACAAGCTTCCCGTTAATTGGC
1 TCTCATGAGCTTCCCGTT-ATTGGC
*
29895474 TCTCATGAGCTTCCCGATTAATGGC
1 TCTCATGAGCTTCCCG-TTATTGGC
* *
29895499 TCTCCA-GAGCTTCTCGATATTGGC
1 TCT-CATGAGCTTCCCGTTATTGGC
* * * *
29895523 TCGCATGAGCTTCTCGATATTGAC
1 TCTCATGAGCTTCCCGTTATTGGC
* ** *
29895547 TCGCATGAGCTTCTCCAAT-TTGAC
1 TCTCATGAGCTTC-CCGTTATTGGC
* **
29895571 TCT--TGAGCTTCCCATTATACAGC
1 TCTCATGAGCTTCCCGTTAT-TGGC
*
29895594 TCAT-ATGAGCTTCCCGTTATATGAC
1 TC-TCATGAGCTTCCCGTTAT-TGGC
** *
29895619 TCGGAAGAGCTTCCCGTT
1 TCTCATGAGCTTCCCGTT
29895637 TACATGCTCG
Statistics
Matches: 153, Mismatches: 25, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.03
22 9 0.06
23 5 0.03
24 46 0.30
25 84 0.55
26 5 0.03
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.35
Consensus pattern (24 bp):
TCTCATGAGCTTCCCGTTATTGGC
Found at i:29895532 original size:24 final size:24
Alignment explanation
Indices: 29895468--29895561 Score: 118
Period size: 24 Copynumber: 3.9 Consensus size: 24
29895458 CTTCCCGTTA
* *
29895468 ATTGGCTCTCATGAGCTTCCCGATT
1 ATTGGCTCGCATGAGCTTCTCGA-T
* *
29895493 AATGGCTCTCCA-GAGCTTCTCGAT
1 ATTGGCTC-GCATGAGCTTCTCGAT
29895517 ATTGGCTCGCATGAGCTTCTCGAT
1 ATTGGCTCGCATGAGCTTCTCGAT
*
29895541 ATTGACTCGCATGAGCTTCTC
1 ATTGGCTCGCATGAGCTTCTC
29895562 CAATTTGACT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
23 2 0.03
24 40 0.66
25 17 0.28
26 2 0.03
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.33
Consensus pattern (24 bp):
ATTGGCTCGCATGAGCTTCTCGAT
Found at i:29895535 original size:49 final size:50
Alignment explanation
Indices: 29895445--29895540 Score: 133
Period size: 49 Copynumber: 1.9 Consensus size: 50
29895435 TTCCGTTATT
* *
29895445 TGGCTCTCACAAGCTTCCCGTTAATTGGCTCTCATGAGCTTCCCGATTAA
1 TGGCTCTCACAAGCTTCCCGATAATTGGCTCGCATGAGCTTCCCGATTAA
* *
29895495 TGGCTCTC-CAGAGCTTCTCGAT-ATTGGCTCGCATGAGCTTCTCGAT
1 TGGCTCTCACA-AGCTTCCCGATAATTGGCTCGCATGAGCTTCCCGAT
29895541 ATTGACTCGC
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
49 24 0.59
50 17 0.41
ACGTcount: A:0.18, C:0.29, G:0.21, T:0.32
Consensus pattern (50 bp):
TGGCTCTCACAAGCTTCCCGATAATTGGCTCGCATGAGCTTCCCGATTAA
Found at i:29895653 original size:25 final size:25
Alignment explanation
Indices: 29895574--29895653 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
29895564 ATTTGACTCT
* *
29895574 TGAGCTTCCCATTATACA-GCTCATA
1 TGAGCTTCCCGTT-TACATGCTCGTA
* *
29895599 TGAGCTTCCCG-TTATATGACTCGGA
1 TGAGCTTCCCGTTTACATG-CTCGTA
*
29895624 AGAGCTTCCCGTTTACATGCTCGTA
1 TGAGCTTCCCGTTTACATGCTCGTA
29895649 TGAGC
1 TGAGC
29895654 ATACATGTAC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
23 3 0.07
24 2 0.05
25 33 0.75
26 6 0.14
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (25 bp):
TGAGCTTCCCGTTTACATGCTCGTA
Found at i:29900165 original size:39 final size:39
Alignment explanation
Indices: 29900111--29900185 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
29900101 TCACTCTTCC
29900111 CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCTCA
1 CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCTCA
29900150 CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATC
1 CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATC
29900186 ACTTGTCACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (39 bp):
CTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCTCA
Found at i:29900211 original size:51 final size:51
Alignment explanation
Indices: 29900147--29900298 Score: 241
Period size: 51 Copynumber: 3.0 Consensus size: 51
29900137 ACCACTTATC
*
29900147 TCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTG
1 TCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTGTCACTTG
* * * **
29900198 TCACTGATTAGATAAGTATAGCTGAAGCTATCACTTATCACTTACCACTTG
1 TCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTGTCACTTG
*
29900249 TCACTGATCAGATAAGTGTAGCTGAAGCTACTACTTATCACTTGTCACTT
1 TCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTGTCACTT
29900299 ATCAGAAGTA
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 89 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (51 bp):
TCACTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTGTCACTTG
Found at i:29904311 original size:13 final size:13
Alignment explanation
Indices: 29904281--29904320 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
29904271 GCCCATATTA
*
29904281 AATTTTTTTAGAT
1 AATTTTTTTAAAT
* *
29904294 TATTTTATTAAAT
1 AATTTTTTTAAAT
29904307 AATTTTTTTAAAT
1 AATTTTTTTAAAT
29904320 A
1 A
29904321 TAATAAATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (13 bp):
AATTTTTTTAAAT
Found at i:29904607 original size:34 final size:33
Alignment explanation
Indices: 29904559--29904633 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 33
29904549 AATAACTGCG
* *
29904559 AAACAACAATAAAACACCA-CAAAAAGCAGCACCA
1 AAACAAC-ATAAAACACCATAAAAAAACAGCA-CA
*
29904593 AAACAACATCAAAACAGCATAAAAAAACAGCACA
1 AAACAACAT-AAAACACCATAAAAAAACAGCACA
29904627 AAA-AACA
1 AAACAACA
29904634 GTATCACCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 6 0.17
34 20 0.56
35 10 0.28
ACGTcount: A:0.65, C:0.25, G:0.05, T:0.04
Consensus pattern (33 bp):
AAACAACATAAAACACCATAAAAAAACAGCACA
Found at i:29910110 original size:16 final size:17
Alignment explanation
Indices: 29910091--29910125 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
29910081 CAATTAAATA
29910091 AATTG-GAAATAAATTC
1 AATTGAGAAATAAATTC
29910107 AATTGAGAAATAAATTC
1 AATTGAGAAATAAATTC
29910124 AA
1 AA
29910126 ATTTCGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.29
Consensus pattern (17 bp):
AATTGAGAAATAAATTC
Found at i:29912053 original size:22 final size:22
Alignment explanation
Indices: 29912028--29912076 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
29912018 GCAAAAATCG
*
29912028 ATCAATCATGTATACTTACCAT
1 ATCAATCATGCATACTTACCAT
29912050 ATCAATCATGCATACTTACCAT
1 ATCAATCATGCATACTTACCAT
*
29912072 TTCAA
1 ATCAA
29912077 CCCCCCACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (22 bp):
ATCAATCATGCATACTTACCAT
Found at i:29920812 original size:15 final size:15
Alignment explanation
Indices: 29920792--29920829 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
29920782 TAATTCAATA
29920792 AATAAAATATTATTT
1 AATAAAATATTATTT
*
29920807 AATAAAAGATTATTT
1 AATAAAATATTATTT
29920822 AATAAAAT
1 AATAAAAT
29920830 TTAATTTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
AATAAAATATTATTT
Found at i:29923583 original size:26 final size:27
Alignment explanation
Indices: 29923516--29923584 Score: 77
Period size: 26 Copynumber: 2.5 Consensus size: 27
29923506 TAGAAAATGC
* *
29923516 ATGTATATGCATGGATTATAAAATATGGA
1 ATGTATAT--ATGTATTATAAAATATGAA
* *
29923545 ATATATATATGTATTATAAAATGT-AA
1 ATGTATATATGTATTATAAAATATGAA
29923571 ATGTATATATGTAT
1 ATGTATATATGTAT
29923585 ACATGTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 14 0.40
27 14 0.40
29 7 0.20
ACGTcount: A:0.43, C:0.01, G:0.14, T:0.41
Consensus pattern (27 bp):
ATGTATATATGTATTATAAAATATGAA
Found at i:29923698 original size:2 final size:2
Alignment explanation
Indices: 29923691--29923716 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29923681 GAAAATATGC
29923691 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
29923717 TAAAAACTAT
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):
AT
Found at i:29923774 original size:3 final size:3
Alignment explanation
Indices: 29923766--29923816 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
29923756 AAAACGTAAC
*
29923766 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29923814 AAT
1 AAT
29923817 GCAATATAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:29925894 original size:19 final size:19
Alignment explanation
Indices: 29925870--29925918 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
29925860 TGAGAGTTTC
*
29925870 TTTTATATTTCTTATTCTG
1 TTTTATATTTCCTATTCTG
* *
29925889 TTTTATTAGTTCCTCTTCTG
1 TTTTA-TATTTCCTATTCTG
*
29925909 TTTAATATTT
1 TTTTATATTT
29925919 TGAAGCTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.16, C:0.12, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTTATATTTCCTATTCTG
Found at i:29927190 original size:13 final size:13
Alignment explanation
Indices: 29927172--29927233 Score: 115
Period size: 13 Copynumber: 4.8 Consensus size: 13
29927162 ACACTCAAAT
29927172 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
29927185 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
29927198 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
*
29927211 TTCTAAAAAGCAC
1 TTCTCAAAAGCAC
29927224 TTCTCAAAAG
1 TTCTCAAAAG
29927234 TAATAAAGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:29935990 original size:17 final size:17
Alignment explanation
Indices: 29935970--29936004 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29935960 AATGGCATAG
29935970 AAATAATAT-AAACAAAT
1 AAATAA-ATGAAACAAAT
29935987 AAATAAATGAAACAAAT
1 AAATAAATGAAACAAAT
29936004 A
1 A
29936005 TACATAAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (17 bp):
AAATAAATGAAACAAAT
Found at i:29936418 original size:18 final size:18
Alignment explanation
Indices: 29936388--29936422 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29936378 ATATATATAG
29936388 ATTAAAAATAATAAATAC
1 ATTAAAAATAATAAATAC
29936406 ATTATAAAA-AATAAATA
1 ATTA-AAAATAATAAATA
29936423 TGTATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
ATTAAAAATAATAAATAC
Found at i:29937431 original size:13 final size:13
Alignment explanation
Indices: 29937413--29937442 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29937403 TTAGCAGAGT
*
29937413 AAAAAAATAATAG
1 AAAAAAATAAAAG
29937426 AAAAAAATAAAAG
1 AAAAAAATAAAAG
29937439 AAAA
1 AAAA
29937443 TAAAACGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (13 bp):
AAAAAAATAAAAG
Found at i:29939061 original size:7 final size:7
Alignment explanation
Indices: 29939049--29939073 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29939039 TAGTCAATTG
29939049 GTATTTA
1 GTATTTA
29939056 GTATTTA
1 GTATTTA
29939063 GTATTTA
1 GTATTTA
29939070 GTAT
1 GTAT
29939074 CATGTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (7 bp):
GTATTTA
Found at i:29939752 original size:18 final size:18
Alignment explanation
Indices: 29939725--29939764 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
29939715 CAGGTGCGTT
*
29939725 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
29939743 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
29939761 TCCT
1 TCCT
29939765 TTTCCGAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:29940044 original size:21 final size:21
Alignment explanation
Indices: 29940020--29940068 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
29940010 AGATGCTGTA
* *
29940020 CCGGAAGAACCAGAATCC-CCG
1 CCGGAAGAACAACAA-CCACCG
*
29940041 CCGGAGGAACAACAACCACCG
1 CCGGAAGAACAACAACCACCG
29940062 CCGGAAG
1 CCGGAAG
29940069 CTAGACAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.35, C:0.37, G:0.27, T:0.02
Consensus pattern (21 bp):
CCGGAAGAACAACAACCACCG
Found at i:29940221 original size:25 final size:24
Alignment explanation
Indices: 29940193--29940309 Score: 95
Period size: 25 Copynumber: 5.0 Consensus size: 24
29940183 TATTTTGATA
29940193 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAA-T
29940218 TTATTTGATGTAATAAAAT--AAT
1 TTATTTGATGTAATAAAATAGAAT
* * ** *
29940240 TT-TTT--T-TAGTTATTTTG-AT
1 TTATTTGATGTAATAAAATAGAAT
29940259 ATTATTTGATGTGTAATAAAATAGAAGT
1 -TTATTTGA--TGTAATAAAATAGAA-T
29940287 TTATTTGATGTAATAAAATAGAA
1 TTATTTGATGTAATAAAATAGAA
29940310 AATTTTTAAT
Statistics
Matches: 72, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
18 5 0.07
19 3 0.04
20 2 0.03
21 6 0.08
22 3 0.04
23 2 0.03
25 35 0.49
26 6 0.08
27 9 0.12
28 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (24 bp):
TTATTTGATGTAATAAAATAGAAT
Found at i:29940314 original size:22 final size:23
Alignment explanation
Indices: 29940270--29940314 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
29940260 TTATTTGATG
*
29940270 TGTAATAAAATAGAAGTTTATTTGA
1 TGTAATAAAATAGAA--TAATTTGA
29940295 TGTAATAAAATAGAA-AATTT
1 TGTAATAAAATAGAATAATTT
29940315 TTAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
25 15 0.79
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (23 bp):
TGTAATAAAATAGAATAATTTGA
Found at i:29940329 original size:9 final size:9
Alignment explanation
Indices: 29940311--29940348 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
29940301 AAAATAGAAA
*
29940311 ATTTTTAAT
1 ATTTTGAAT
29940320 ATTTTGAAT
1 ATTTTGAAT
29940329 ATTTTGAAT
1 ATTTTGAAT
29940338 ATTTTG-AT
1 ATTTTGAAT
29940346 ATT
1 ATT
29940349 ATTTGAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
8 5 0.18
9 23 0.82
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (9 bp):
ATTTTGAAT
Found at i:29940332 original size:67 final size:66
Alignment explanation
Indices: 29940175--29940331 Score: 224
Period size: 69 Copynumber: 2.3 Consensus size: 66
29940165 TTGTACAAAT
* *
29940175 ATTTTGAATATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAAT
1 ATTTTTAATATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAAA
*
29940240 T
66 A
* *
29940241 TTTTTTAGTTATTTTGATATTATTTGATGTGTAATAAAATAGAAGTTTATTTGATGTAATAAAAT
1 ATTTTTA-ATATTTTGATATTATTTGA--TGTAATAAAATAGAAGTTTATTTGATGTAATAAAAT
29940306 AGAAA
63 A-AAA
29940311 ATTTTTAATATTTTGAATATT
1 ATTTTTAATATTTTG-ATATT
29940332 TTGAATATTT
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
66 5 0.06
67 18 0.23
69 44 0.56
70 12 0.15
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (66 bp):
ATTTTTAATATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATAAAATAAA
A
Found at i:29940414 original size:23 final size:23
Alignment explanation
Indices: 29940379--29940730 Score: 415
Period size: 23 Copynumber: 15.6 Consensus size: 23
29940369 ATTAATACCC
29940379 TTAACTTAAAAACCCTAACCTAAT
1 TTAA-TTAAAAACCCTAACCTAAT
*
29940403 TTAATTAAAAACCTTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
*
29940426 TTAATTAAAAACCCTAACCTGAT
1 TTAATTAAAAACCCTAACCTAAT
* *
29940449 TTACTTAAAAACCCTAACC---C
1 TTAATTAAAAACCCTAACCTAAT
* *
29940469 TTAACCCT-AAAACCTTAACCTAAT
1 TTAA--TTAAAAACCCTAACCTAAT
29940493 TTAATTAAAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
*
29940516 TTAATT-AAAACCTTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
29940538 TTAATTAAAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
29940561 TTAATTAAAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
*
29940584 TTAATTAAAAACCCTAACC---C
1 TTAATTAAAAACCCTAACCTAAT
* *
29940604 TTAACCCT-CAAACCCTAACCTAAT
1 TTAA--TTAAAAACCCTAACCTAAT
*
29940628 TAAATTAAAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
*
29940651 TAAATTAAAAACCCTAACCTAAT
1 TTAATTAAAAACCCTAACCTAAT
* *
29940674 TTAATTAAAAACACTAACC---C
1 TTAATTAAAAACCCTAACCTAAT
*
29940694 TTAACCCT-AAAACCCTAACCTAAT
1 TTAA--TTAAAAACCCTAACCTAAT
29940718 TTAATTAAAAACC
1 TTAATTAAAAACC
29940731 TTTGGTCACG
Statistics
Matches: 282, Mismatches: 27, Indels: 39
0.81 0.08 0.11
Matches are distributed among these distances:
20 11 0.04
21 33 0.12
22 27 0.10
23 196 0.70
24 15 0.05
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (23 bp):
TTAATTAAAAACCCTAACCTAAT
Found at i:29940472 original size:90 final size:90
Alignment explanation
Indices: 29940378--29940730 Score: 418
Period size: 90 Copynumber: 3.9 Consensus size: 90
29940368 CATTAATACC
*
29940378 CTTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCTTAACCTAATTTAATTAAAAACCCTAA
1 CTTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATT-AAAACCCTAA
* *
29940443 CCTGATTTACTTAAAAACCCTAACC-
65 CCTAATTTAATTAAAAACCCTAACCA
* * *
29940468 CTTAACCCT-AAAACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAACCTTAA
1 CTTAA-CTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAACCCTAA
29940532 CCTAATTTAATTAAAAACCCTAACCTAA
65 CCTAATTTAATTAAAAACCCTAACC--A
* * * *
29940560 TTTAA-TTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC---CTTAACCCTCAAACCCTA
1 CTTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAA--TTAAAACCCTA
*
29940621 ACCTAATTAAATTAAAAACCCTAACCTA
64 ACCTAATTTAATTAAAAACCCTAACC-A
* * * * *
29940649 ATTAAATTAAAAACCCTAACCTAATTTAATTAAAAACACTAACC---CTTAACCCTAAAACCCTA
1 CTTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAA--TTAAAACCCTA
29940711 ACCTAATTTAATTAAAAACC
64 ACCTAATTTAATTAAAAACC
29940731 TTTGGTCACG
Statistics
Matches: 236, Mismatches: 19, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
88 4 0.02
89 37 0.16
90 155 0.66
91 36 0.15
92 4 0.02
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (90 bp):
CTTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAACCCTAAC
CTAATTTAATTAAAAACCCTAACCA
Found at i:29940493 original size:67 final size:67
Alignment explanation
Indices: 29940410--29940669 Score: 373
Period size: 67 Copynumber: 3.9 Consensus size: 67
29940400 AATTTAATTA
* * *
29940410 AAAACCTTAACCTAATTTAATTAAAAACCCTAACCTGATTTACTTAAAAACCCTAACCCTTAACC
1 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAACC
29940475 CT
66 CT
* * *
29940477 AAAACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATT-AAAACCTTAACCTAATTTA
1 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC---CTTA
*
29940541 A--TT
63 ACCCT
29940544 AAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAAC
1 -AAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAAC
29940609 CCT
65 CCT
* * *
29940612 CAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAACC
1 AAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC
29940670 TAATTTAATT
Statistics
Matches: 174, Mismatches: 12, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
66 15 0.09
67 99 0.57
68 45 0.26
69 15 0.09
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (67 bp):
AAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCCTTAACC
CT
Found at i:29940634 original size:135 final size:136
Alignment explanation
Indices: 29940379--29940730 Score: 543
Period size: 135 Copynumber: 2.6 Consensus size: 136
29940369 ATTAATACCC
* *
29940379 TTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCTTAACCTAATTTAATTAAAAACCCTAAC
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAC
* * * *
29940444 CTGATTTACTTAAAAACCCTAACCCTTAACCCTAAAACCTTAACCTAATTTAATTAAAAACCCTA
66 CTAATTTAATTAAAAACCCTAACCCTTAACCCTAAAACCCTAACCTAATTAAATTAAAAACCCTA
29940509 ACCTAA
131 ACCTAA
* *
29940515 TTTAATT-AAAACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAC
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAC
*
29940579 CTAATTTAATTAAAAACCCTAACCCTTAACCCTCAAACCCTAACCTAATTAAATTAAAAACCCTA
66 CTAATTTAATTAAAAACCCTAACCCTTAACCCTAAAACCCTAACCTAATTAAATTAAAAACCCTA
29940644 ACCTAA
131 ACCTAA
* * *
29940650 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACACTAACC---CTTAACCCT-AAAACCCTA
1 TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAA--TTAAAAACCCTA
29940711 ACCTAATTTAATTAAAAACC
64 ACCTAATTTAATTAAAAACC
29940731 TTTGGTCACG
Statistics
Matches: 199, Mismatches: 14, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
133 4 0.02
134 29 0.15
135 128 0.64
136 38 0.19
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (136 bp):
TTAAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAC
CTAATTTAATTAAAAACCCTAACCCTTAACCCTAAAACCCTAACCTAATTAAATTAAAAACCCTA
ACCTAA
Found at i:29940706 original size:67 final size:67
Alignment explanation
Indices: 29940379--29940730 Score: 366
Period size: 67 Copynumber: 5.2 Consensus size: 67
29940369 ATTAATACCC
*
29940379 TTAACTTAAAAACCCTAACCTAATTTAATTAAAAACCTTAACCTAATTTAATTAAAAACCCTAAC
1 TTAA-TTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC-AA-TTAATTAAAAACCCTAAC
*
29940444 CTGAT
63 CTAAT
* * * *
29940449 TTACTTAAAAACCCTAACC---CTTAACCCT-AAAACCTTAACCTAATTTAATTAAAAACCCTAA
1 TTAATTAAAAACCCTAACCTAATTTAA--TTAAAAACCCTAACC-AA-TTAATTAAAAACCCTAA
29940510 CCTAAT
62 CCTAAT
*
29940516 TTAATT-AAAACCTTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC
1 TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACC-AA-TTAATTAAAAACCCTAACC
29940580 TAAT
64 TAAT
* * *
29940584 TTAATTAAAAACCCTAACC---CTTAACCCT-CAAACCCTAACCTAATTAAATTAAAAACCCTAA
1 TTAATTAAAAACCCTAACCTAATTTAA--TTAAAAACCCTAACC-AATT-AATTAAAAACCCTAA
29940645 CCTAAT
62 CCTAAT
* * * *
29940651 TAAATTAAAAACCCTAACCTAATTTAATTAAAAACACTAACC-CTTAACCCT-AAAACCCTAACC
1 TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCAATTAA--TTAAAAACCCTAACC
29940714 TAAT
64 TAAT
29940718 TTAATTAAAAACC
1 TTAATTAAAAACC
29940731 TTTGGTCACG
Statistics
Matches: 245, Mismatches: 21, Indels: 35
0.81 0.07 0.12
Matches are distributed among these distances:
66 23 0.09
67 127 0.52
68 48 0.20
69 40 0.16
70 7 0.03
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (67 bp):
TTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCAATTAATTAAAAACCCTAACCTA
AT
Found at i:29949699 original size:20 final size:20
Alignment explanation
Indices: 29949676--29949722 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
29949666 AGGCGAAATT
*
29949676 GTGCAATTAGAGGCACCGAA
1 GTGCAATTAGAGGCACCAAA
*
29949696 GTGCAAATAGAGGCACCAAA
1 GTGCAATTAGAGGCACCAAA
29949716 GTGCAAT
1 GTGCAAT
29949723 CTCGTACAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.19, G:0.28, T:0.15
Consensus pattern (20 bp):
GTGCAATTAGAGGCACCAAA
Found at i:29961419 original size:16 final size:16
Alignment explanation
Indices: 29961398--29961428 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29961388 ATCAGGTTGA
*
29961398 GAAAATTATTTAATTG
1 GAAAATTAATTAATTG
29961414 GAAAATTAATTAATT
1 GAAAATTAATTAATT
29961429 TATAATGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
GAAAATTAATTAATTG
Found at i:29964028 original size:24 final size:25
Alignment explanation
Indices: 29963999--29964045 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
29963989 TCCTCCCCCT
29963999 TCTCTA-ACATTTTTT-TTTCTTTTC
1 TCTCTATAC-TTTTTTCTTTCTTTTC
*
29964023 TCTCTATTCTTTTTTCTTTCTTT
1 TCTCTATACTTTTTTCTTTCTTT
29964046 GAAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (25 bp):
TCTCTATACTTTTTTCTTTCTTTTC
Found at i:29964948 original size:13 final size:14
Alignment explanation
Indices: 29964925--29964959 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
29964915 CACGTTAACA
29964925 CTGTATATCTGTAT
1 CTGTATATCTGTAT
29964939 CTGT-TATCTGTAT
1 CTGTATATCTGTAT
*
29964952 ATGTATAT
1 CTGTATAT
29964960 GGGGCAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.51
Consensus pattern (14 bp):
CTGTATATCTGTAT
Found at i:29965973 original size:21 final size:21
Alignment explanation
Indices: 29965947--29965987 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29965937 GCTTGAAAGC
29965947 TGAACAAAAGCTCATAAGAGT
1 TGAACAAAAGCTCATAAGAGT
* *
29965968 TGAACAGAAGTTCATAAGAG
1 TGAACAAAAGCTCATAAGAG
29965988 CTGATCCACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.12, G:0.22, T:0.20
Consensus pattern (21 bp):
TGAACAAAAGCTCATAAGAGT
Found at i:29981106 original size:15 final size:15
Alignment explanation
Indices: 29981071--29981099 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29981061 TGAAACATGT
29981071 GAAAATATGAAATTA
1 GAAAATATGAAATTA
29981086 GAAAATA-GAAATTA
1 GAAAATATGAAATTA
29981100 TTAAAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (15 bp):
GAAAATATGAAATTA
Found at i:29999215 original size:70 final size:70
Alignment explanation
Indices: 29999098--29999358 Score: 233
Period size: 70 Copynumber: 3.7 Consensus size: 70
29999088 TTAACTTTCG
* * * * * * * *
29999098 CTAACTATGTTGGAGGCTAC-GATTTTTATTCTGTGAGCCTTAGTATGACAACTTGGAGTTTTGC
1 CTAACTATGTTGAAGGCTGCAGTTTTTTATCCTGCGAGCCTTAGTATGACAGCTAGGAGCTTTGC
29999162 TCTCT
66 TCTCT
* * *
29999167 CTAACTTTGTTGAAGGCTGCCGTTTTTTATCCTGCGAGCCTTAGTATGAGAGCTAGGAGCTTTGC
1 CTAACTATGTTGAAGGCTGCAGTTTTTTATCCTGCGAGCCTTAGTATGACAGCTAGGAGCTTTGC
29999232 TCT-T
66 TCTCT
* * ** * *
29999236 GCTAACTGTGTTGAAGGCTAAG-ATTTTTTTATCCTGCGAGTTTTAGTATGATAGCTGGGAGCTT
1 -CTAACTATGTTGAAGGCT--GCAGTTTTTTATCCTGCGAGCCTTAGTATGACAGCTAGGAGCTT
* *
29999300 TACTCTCA
63 TGCTCTCT
* ** * * *
29999308 CTAGCTATGTTGGTGGCTGCAATTTTTTAT-CTAACGAACCTTAGTATGACA
1 CTAACTATGTTGAAGGCTGCAGTTTTTTATCCT-GCGAGCCTTAGTATGACA
29999359 CAAATGTTGT
Statistics
Matches: 156, Mismatches: 29, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
69 21 0.13
70 79 0.51
71 55 0.35
72 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.39
Consensus pattern (70 bp):
CTAACTATGTTGAAGGCTGCAGTTTTTTATCCTGCGAGCCTTAGTATGACAGCTAGGAGCTTTGC
TCTCT
Found at i:30043203 original size:36 final size:36
Alignment explanation
Indices: 30043163--30043234 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
30043153 AAGAGTGTGT
30043163 GCTGAAATGGAGACCTACCCTATAAAAAGAAGAAAG
1 GCTGAAATGGAGACCTACCCTATAAAAAGAAGAAAG
30043199 GCTGAAATGGAGACCTACCCTATAAAAAGAAGAAAG
1 GCTGAAATGGAGACCTACCCTATAAAAAGAAGAAAG
30043235 AAAAAGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (36 bp):
GCTGAAATGGAGACCTACCCTATAAAAAGAAGAAAG
Found at i:30043771 original size:17 final size:17
Alignment explanation
Indices: 30043749--30043781 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30043739 CCCGTTAGTG
30043749 AAATAAACT-AAATAAAC
1 AAATAAA-TAAAATAAAC
30043766 AAATAAATAAAATAAA
1 AAATAAATAAAATAAA
30043782 GCCAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATAAATAAAATAAAC
Found at i:30045765 original size:111 final size:111
Alignment explanation
Indices: 30045639--30045859 Score: 352
Period size: 111 Copynumber: 2.0 Consensus size: 111
30045629 TAAATAATCG
* **
30045639 AAAATTTTCTACAATCAAAACGCATAAACCAAAAACTCACTTTCGAGAATTCAATATGCCATGTC
1 AAAATTTTCTACAATCAAAACACATAAACCAAAAACTCACTTTCGAGAATTCAATACACCATGTC
*
30045704 CTAATGTATTGAATGTGATGTGTCGTTTTCTCGAAATGAAGATTTT
66 CTAATGTATTGAATGTGACGTGTCGTTTTCTCGAAATGAAGATTTT
* * * *
30045750 AAAATTTTCTACAATCAAAACACATAAACCAAAAACTCACTTTCGGGAATTCGATACATCGTGTC
1 AAAATTTTCTACAATCAAAACACATAAACCAAAAACTCACTTTCGAGAATTCAATACACCATGTC
* *
30045815 CTAATGTATTGGATGTGACGTGTCGTTTTCTGGAAATGAAGATTT
66 CTAATGTATTGAATGTGACGTGTCGTTTTCTCGAAATGAAGATTT
30045860 AAATAATAAG
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 100 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (111 bp):
AAAATTTTCTACAATCAAAACACATAAACCAAAAACTCACTTTCGAGAATTCAATACACCATGTC
CTAATGTATTGAATGTGACGTGTCGTTTTCTCGAAATGAAGATTTT
Found at i:30057847 original size:44 final size:44
Alignment explanation
Indices: 30057781--30058214 Score: 553
Period size: 44 Copynumber: 9.9 Consensus size: 44
30057771 AATCACAAAA
* * * *
30057781 CCTAGCTCCCTGTCCAGTAGTGGAATAGGTTGAAGATTGTAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * *
30057825 CCTAGCTCCCTGACCAACAGTGGAATAGGTTGAAGATTGTAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * * *
30057869 CCTATCTCCCTGACCAACAGAGGAATAGGTAGAAGATTGCAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * *
30057913 CCTAACTCCCTAACCAACAGTGGAATATGTTGAAGATTGCAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * *
30057957 CCTAACTCCCTGACCAGCAGAGGAGTAGGTAGAAGATTGCAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * *
30058001 CCTAACTTCTTGACCAGCAGTGGAATAGGTTGAGGATTGCAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * *
30058045 CCTAACTCCCTGACCAGCAATGGAATAGGTAGAAGATTTCAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* *
30058089 CCTAACTCCCTGGCCAGCAGTAGAATAGGTTGAAGATTGCAAGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * * *
30058133 CCTAACTCCTTGACCAGCAGTGGAATAGGTGGAAGATTGTATGT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
* * ** * *
30058177 CCTATCTCCCTAAAAAGTAGTGGAATAGGTTAAAGATT
1 CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATT
30058215 ATGGATCCTG
Statistics
Matches: 341, Mismatches: 49, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 341 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (44 bp):
CCTAACTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
Found at i:30058229 original size:44 final size:44
Alignment explanation
Indices: 30058151--30058245 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
30058141 CTTGACCAGC
*
30058151 AGTGGAATAGGTGGAAGATTGTATGTCCTATCTCCCTAAAAAGT
1 AGTGGAATAGGTGAAAGATTGTATGTCCTATCTCCCTAAAAAGT
* * **
30058195 AGTGGAATAGGTTAAAGA-T-TATGGATCCTGTCTCCCTAAGCAGT
1 AGTGGAATAGGTGAAAGATTGTAT-G-TCCTATCTCCCTAAAAAGT
30058239 AGTGGAA
1 AGTGGAA
30058246 CAGATCGAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
42 3 0.07
43 2 0.05
44 39 0.89
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (44 bp):
AGTGGAATAGGTGAAAGATTGTATGTCCTATCTCCCTAAAAAGT
Found at i:30060550 original size:111 final size:111
Alignment explanation
Indices: 30060426--30060646 Score: 361
Period size: 111 Copynumber: 2.0 Consensus size: 111
30060416 TAAATAATCA
* ** *
30060426 AAAATTTTCTACAATCAAAGCGAATAAACCAAAAACTCACTTTCGGGAATTTGATACGTCGTGTC
1 AAAATTTTCTACAATCAAAACGAATAAACCAAAAACTCACTTTCGGGAATTCAATACGTCATGTC
* *
30060491 CTAATGTATTGAATGTGATGTGTCGTTTTCTCAAAATGAAGATTTT
66 CTAATGTATTGAATGTGACGTGTCGGTTTCTCAAAATGAAGATTTT
*
30060537 AAAATTTTCTACAATCAAAACGTATAAACCAAAAACTCACTTTCGGGAATTCAATACGTCATGTC
1 AAAATTTTCTACAATCAAAACGAATAAACCAAAAACTCACTTTCGGGAATTCAATACGTCATGTC
* *
30060602 CTAATGTATTGGATGTGACGTGTCGGTTTCTCGAAATGAAGATTT
66 CTAATGTATTGAATGTGACGTGTCGGTTTCTCAAAATGAAGATTT
30060647 AAATAATAAG
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (111 bp):
AAAATTTTCTACAATCAAAACGAATAAACCAAAAACTCACTTTCGGGAATTCAATACGTCATGTC
CTAATGTATTGAATGTGACGTGTCGGTTTCTCAAAATGAAGATTTT
Found at i:30071712 original size:386 final size:385
Alignment explanation
Indices: 30070989--30071749 Score: 1371
Period size: 386 Copynumber: 2.0 Consensus size: 385
30070979 CATTGGGTTG
30070989 GGATTACTGGATGAATCTTTAGTTCCTTTAATGACCAAGGCATTATCCTGATTAGATTTACTATT
1 GGATTACTGGATGAATCTTTAGTTCCTTTAATGACCAAGGCATTATCCTGATTAGATTTACTATT
30071054 TCATTTGATTTGCGCTATTTTAAAACGTATGCATGCAGTCTCTAGACATAGATGAATATATGCTA
66 TCATTTGATTTGCGCTATTTTAAAACGTATGCATGCAGTCTCTAGACATAGATGAATATATGCTA
* *
30071119 TATCCATAAACTTGATTTAATTTTGAAAAGGTTAGATGAGTTGGATTGTGATCGAATGATACAAG
131 CATCCATAAACTTGATTTAATTCTGAAAAGGTTAGATGAGTTGGATTGTGATCGAATGATACAAG
*
30071184 CGAGTATTCGATAGAATAGTCGTAGCACTCTAGACATAGAACTACGCTCTGTACAGAGAAAGGAA
196 CGAGTATTCGACAGAATAGTCGTAGCACTCTAGACATAGAACTACGCTCTGTACAGAGAAAGGAA
* *
30071249 GAAACAGTGATGGGTATCCTTTTTAAAGCTTGTAGATATGCAAAGCCTTAGGTAGGGTAGCTTGA
261 GAAACAGTGATAGGTATCCTTCTTAAAGCTTGTAGATATGCAAAGCCTTAGGTAGGGTAGCTTGA
* *
30071314 AGTCTAACTCTCGAAAGAAGCAGACTACCTTAGATATGTTGTTGAATGATACTTTTATTTT
326 AGTCTAACTCTCGAAAGAAGCAGACTACCTTAGATATATT-CTGAATGATACTTTTATTTT
*
30071375 GGATTATTGGATGAATCTTTAGTTCCTTTAATGACCAAGGCATTATCCTGATTAGATTTACTATT
1 GGATTACTGGATGAATCTTTAGTTCCTTTAATGACCAAGGCATTATCCTGATTAGATTTACTATT
*
30071440 TCATTTGATTTGCGCTATTTTAAAACGTATGCATGCAGTCTCTAGACATAGATGAATATATGGTA
66 TCATTTGATTTGCGCTATTTTAAAACGTATGCATGCAGTCTCTAGACATAGATGAATATATGCTA
* *
30071505 CGTCCATAAACTTGATTTAATTCTGAAAAGGTTAGATGAGTTGGATTGTGATTGAATGATACAAG
131 CATCCATAAACTTGATTTAATTCTGAAAAGGTTAGATGAGTTGGATTGTGATCGAATGATACAAG
*
30071570 CGAGTATTCGACAGAATAGTCGTAGCACTCTAGACATAGAGCTACGCTCTGTACA-AGGAAAGGA
196 CGAGTATTCGACAGAATAGTCGTAGCACTCTAGACATAGAACTACGCTCTGTACAGA-GAAAGGA
30071634 AGAAACAGTGATAGGTATCCTTCTTAAAGCTTGTAGATATGCAAAGCCTTAGGTAGGGTAGCTTG
260 AGAAACAGTGATAGGTATCCTTCTTAAAGCTTGTAGATATGCAAAGCCTTAGGTAGGGTAGCTTG
* *
30071699 AAGTCTGACTCTCGAAAGAATCAGACTACCTTAGATATATTCTGAATGATA
325 AAGTCTAACTCTCGAAAGAAGCAGACTACCTTAGATATATTCTGAATGATA
30071750 GATTTGTTAA
Statistics
Matches: 360, Mismatches: 14, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
385 10 0.03
386 350 0.97
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (385 bp):
GGATTACTGGATGAATCTTTAGTTCCTTTAATGACCAAGGCATTATCCTGATTAGATTTACTATT
TCATTTGATTTGCGCTATTTTAAAACGTATGCATGCAGTCTCTAGACATAGATGAATATATGCTA
CATCCATAAACTTGATTTAATTCTGAAAAGGTTAGATGAGTTGGATTGTGATCGAATGATACAAG
CGAGTATTCGACAGAATAGTCGTAGCACTCTAGACATAGAACTACGCTCTGTACAGAGAAAGGAA
GAAACAGTGATAGGTATCCTTCTTAAAGCTTGTAGATATGCAAAGCCTTAGGTAGGGTAGCTTGA
AGTCTAACTCTCGAAAGAAGCAGACTACCTTAGATATATTCTGAATGATACTTTTATTTT
Found at i:30072360 original size:19 final size:20
Alignment explanation
Indices: 30072338--30072391 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
30072328 CACTCATTCA
30072338 ATGCTTTTATTCACTCA-CT
1 ATGCTTTTATTCACTCACCT
*
30072357 ATGCTTTTA-TCCCTCACCT
1 ATGCTTTTATTCACTCACCT
30072376 -TGCTTTTATTCACTCA
1 ATGCTTTTATTCACTCA
30072392 ATTTTTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.19, C:0.30, G:0.06, T:0.46
Consensus pattern (20 bp):
ATGCTTTTATTCACTCACCT
Found at i:30072379 original size:18 final size:18
Alignment explanation
Indices: 30072311--30072391 Score: 69
Period size: 19 Copynumber: 4.4 Consensus size: 18
30072301 GTCACTCTTT
*
30072311 TCACTCACAATGC-TTTA
1 TCACTCACTATGCTTTTA
*
30072328 -CACTCATTCAATGCTTTTA
1 TCACTCA--CTATGCTTTTA
30072347 TTCACTCACTATGCTTTTA
1 -TCACTCACTATGCTTTTA
*
30072366 TCCCTCACCT-TGCTTTTA
1 TCACTCA-CTATGCTTTTA
30072384 TTCACTCA
1 -TCACTCA
30072392 ATTTTTTTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
16 6 0.11
18 20 0.37
19 22 0.41
21 6 0.11
ACGTcount: A:0.22, C:0.31, G:0.05, T:0.42
Consensus pattern (18 bp):
TCACTCACTATGCTTTTA
Found at i:30076171 original size:50 final size:50
Alignment explanation
Indices: 30076102--30076294 Score: 190
Period size: 50 Copynumber: 3.7 Consensus size: 50
30076092 TTTTCTGTAT
* * * *
30076102 TGCCAGTGCCATATCCCAGATATGGTCTTACATGGGA-GTGCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCT-CTCATATCGG
* * *** *
30076152 TGCCCATGCCATGTCCCAGACATAGTCTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
30076202 TGCCAACGCCATGTACCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
30076258 TGCCAATGCCATGTCCCATACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
30076295 TCTCATTCCC
Statistics
Matches: 114, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
50 76 0.67
51 1 0.01
53 2 0.02
56 35 0.31
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:30078105 original size:27 final size:27
Alignment explanation
Indices: 30078046--30078342 Score: 317
Period size: 27 Copynumber: 11.4 Consensus size: 27
30078036 CCCAGTATTT
** *
30078046 GTAAAATGACTATAATA-ACCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
30078072 GTAAAATGACCGTAATACCCTTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
30078099 GTGAAATGACCGTAATACCCCTGTAAG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
30078126 GTAAAATGATCGTAATACCCCTGTAAG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
30078153 GTAAAAT----G--AT---CTTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
30078171 GTAAAATGACCGTAATACCCTTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* * *
30078198 GTAAAATAACCGTAATGCCCCTATAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
30078225 GTAAAATGACCATAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* ** *
30078252 GTAAAATGGCCGTAACGCCCCTGTATG
1 GTAAAATGACCGTAATACCCCTGTAGG
* * *
30078279 GTAAAATGACCATAATGCCGCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
* *
30078306 GTAAAATAACCGTAATGCCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
30078333 GTAAAATGAC
1 GTAAAATGAC
30078343 TATTTTGCCT
Statistics
Matches: 228, Mismatches: 33, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
18 13 0.06
21 2 0.01
22 1 0.00
23 1 0.00
24 2 0.01
26 15 0.07
27 194 0.85
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (27 bp):
GTAAAATGACCGTAATACCCCTGTAGG
Found at i:30078192 original size:99 final size:99
Alignment explanation
Indices: 30078066--30078259 Score: 316
Period size: 99 Copynumber: 2.0 Consensus size: 99
30078056 TATAATAACC
* * *
30078066 TGTAGGGTAAAATGACCGTAATACCCTTGTAGGGTGAAATGACCGTAATACCCCTGTAAGGTAAA
1 TGTAGGGTAAAATGACCGTAATACCCTTGTAGGGTAAAATAACCGTAATACCCCTATAAGGTAAA
* *
30078131 ATGATCGTAATACCCCTGTAAGGTAAAATGATCT
66 ATGACCATAATACCCCTGTAAGGTAAAATGATCT
* *
30078165 TGTAGGGTAAAATGACCGTAATACCCTTGTAGGGTAAAATAACCGTAATGCCCCTATAGGGTAAA
1 TGTAGGGTAAAATGACCGTAATACCCTTGTAGGGTAAAATAACCGTAATACCCCTATAAGGTAAA
*
30078230 ATGACCATAATACCCCTGTAGGGTAAAATG
66 ATGACCATAATACCCCTGTAAGGTAAAATG
30078260 GCCGTAACGC
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 87 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (99 bp):
TGTAGGGTAAAATGACCGTAATACCCTTGTAGGGTAAAATAACCGTAATACCCCTATAAGGTAAA
ATGACCATAATACCCCTGTAAGGTAAAATGATCT
Found at i:30078212 original size:72 final size:72
Alignment explanation
Indices: 30078091--30078233 Score: 214
Period size: 72 Copynumber: 2.0 Consensus size: 72
30078081 CCGTAATACC
* * * *
30078091 CTTGTAGGGTGAAATGACCGTAATACCCCTGTAAGGTAAAATGATCGTAATACCCCTGTAAGGTA
1 CTTGTAGGGTAAAATGACCGTAATACCCCTGTAAGGTAAAATAACCGTAATACCCCTATAAGGTA
30078156 AAATGAT
66 AAATGAT
* * * *
30078163 CTTGTAGGGTAAAATGACCGTAATACCCTTGTAGGGTAAAATAACCGTAATGCCCCTATAGGGTA
1 CTTGTAGGGTAAAATGACCGTAATACCCCTGTAAGGTAAAATAACCGTAATACCCCTATAAGGTA
30078228 AAATGA
66 AAATGA
30078234 CCATAATACC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (72 bp):
CTTGTAGGGTAAAATGACCGTAATACCCCTGTAAGGTAAAATAACCGTAATACCCCTATAAGGTA
AAATGAT
Found at i:30078394 original size:24 final size:24
Alignment explanation
Indices: 30078361--30078479 Score: 141
Period size: 24 Copynumber: 5.0 Consensus size: 24
30078351 CTATCGGGGT
30078361 TAAATGATTGATTTGTCTGTGATG
1 TAAATGATTGATTTGTCTGTGATG
* * *
30078385 TAAATAATTGATTTGTCCGAGATG
1 TAAATGATTGATTTGTCTGTGATG
* * *
30078409 TAAATGATCGATTTGTCTCTGATT
1 TAAATGATTGATTTGTCTGTGATG
*
30078433 TACATGATTGATTTGTCTGTGAT-
1 TAAATGATTGATTTGTCTGTGATG
* *
30078456 TAGTATGACTGATTTGTCTGTGAT
1 TA-AATGATTGATTTGTCTGTGAT
30078480 TTGTATGACT
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
23 2 0.03
24 78 0.98
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.45
Consensus pattern (24 bp):
TAAATGATTGATTTGTCTGTGATG
Found at i:30078480 original size:24 final size:24
Alignment explanation
Indices: 30078418--30078490 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
30078408 GTAAATGATC
* * *
30078418 GATTTGTCTCTGATTTA-CATGATT
1 GATTTGTCTGTGA-TTAGTATGACT
30078442 GATTTGTCTGTGATTAGTATGACT
1 GATTTGTCTGTGATTAGTATGACT
*
30078466 GATTTGTCTGTGATTTGTATGACT
1 GATTTGTCTGTGATTAGTATGACT
30078490 G
1 G
30078491 GTTCTAAGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.19, C:0.10, G:0.23, T:0.48
Consensus pattern (24 bp):
GATTTGTCTGTGATTAGTATGACT
Found at i:30078481 original size:11 final size:11
Alignment explanation
Indices: 30078441--30078483 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
30078431 TTTACATGAT
30078441 TGATTTGTCTG
1 TGATTTGTCTG
* *
30078452 TGATTAGTATG
1 TGATTTGTCTG
30078463 ACTGATTTGTCTG
1 --TGATTTGTCTG
30078476 TGATTTGT
1 TGATTTGT
30078484 ATGACTGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 17 0.65
13 9 0.35
ACGTcount: A:0.16, C:0.07, G:0.26, T:0.51
Consensus pattern (11 bp):
TGATTTGTCTG
Found at i:30078594 original size:27 final size:27
Alignment explanation
Indices: 30078556--30078620 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
30078546 ATGGAAGAAG
30078556 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTGGTGGCT-TGGCCACATA
30078581 TCACTGTTACTGGTGGCTTGGCCACATA
1 T-ACTGTTACTGGTGGCTTGGCCACATA
*
30078609 TACTGTTGCTGG
1 TACTGTTACTGG
30078621 CAGCTTTGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 1 0.03
26 5 0.14
27 27 0.77
28 2 0.06
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCCACATA
Found at i:30078626 original size:27 final size:27
Alignment explanation
Indices: 30078574--30078626 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
30078564 TGGTGGCTCT
**
30078574 GCCACAATCACTGTTACTGGTGGCTTG
1 GCCACAATCACTGTTACTGGCAGCTTG
*
30078601 GCCACATAT-ACTGTTGCTGGCAGCTT
1 GCCACA-ATCACTGTTACTGGCAGCTT
30078627 TGCTGCGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTGTTACTGGCAGCTTG
Found at i:30078642 original size:26 final size:26
Alignment explanation
Indices: 30078608--30078661 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
30078598 TTGGCCACAT
* *
30078608 ATACTGTTGCTGGCAGCTTTGCTGCG
1 ATACTGTTGCTAGCAGCTATGCTGCG
30078634 ATACTGTTGCTAGCAGCTATGCTGCG
1 ATACTGTTGCTAGCAGCTATGCTGCG
30078660 AT
1 AT
30078662 GCTACTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (26 bp):
ATACTGTTGCTAGCAGCTATGCTGCG
Found at i:30078705 original size:32 final size:32
Alignment explanation
Indices: 30078664--30078770 Score: 146
Period size: 32 Copynumber: 3.4 Consensus size: 32
30078654 GCTGCGATGC
30078664 TACTGATGGCTTTGTGCCGATCATATTA-TCAT
1 TACTGATGGCTTTGTGCCGATCATATTACT-AT
* * *
30078696 TACTGATGGCTGTGTGTCGGTCATATTACTAT
1 TACTGATGGCTTTGTGCCGATCATATTACTAT
*
30078728 TACTGATGGCTTTGTGCCAATCATATTACTA-
1 TACTGATGGCTTTGTGCCGATCATATTACTAT
*
30078759 TACTTATGGCTT
1 TACTGATGGCTT
30078771 GTAGCCATTC
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
31 11 0.17
32 54 0.82
33 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACTAT
Found at i:30078792 original size:22 final size:22
Alignment explanation
Indices: 30078762--30078823 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
30078752 ATTACTATAC
30078762 TTATGGCTTGTAGCCATTC-TGT
1 TTATGGCTT-TAGCCATTCTTGT
* *
30078784 TTATAGCTTATAGCTA-TCTTGT
1 TTATGGCTT-TAGCCATTCTTGT
30078806 TTATGGCTCTTAGCCATT
1 TTATGGCT-TTAGCCATT
30078824 TTGGTTACTG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.06
22 28 0.88
23 2 0.06
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (22 bp):
TTATGGCTTTAGCCATTCTTGT
Found at i:30079345 original size:21 final size:22
Alignment explanation
Indices: 30079321--30079372 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
30079311 AATAAATACC
30079321 AAAAATTTATTTTAAAA-ATTA
1 AAAAATTTATTTTAAAATATTA
** *
30079342 AAAAAAGTATTTTAAAATATTT
1 AAAAATTTATTTTAAAATATTA
*
30079364 AAATATTTA
1 AAAAATTTA
30079373 AATTTTTAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAAATTTATTTTAAAATATTA
Found at i:30079369 original size:8 final size:8
Alignment explanation
Indices: 30079356--30079404 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
30079346 AAGTATTTTA
30079356 AAATATTT
1 AAATATTT
30079364 AAATATTT
1 AAATATTT
*
30079372 AAATTTTT
1 AAATATTT
*
30079380 AAA-A--A
1 AAATATTT
*
30079385 AAATTTTT
1 AAATATTT
30079393 AAATATTT
1 AAATATTT
30079401 AAAT
1 AAAT
30079405 TAAAATAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
5 3 0.09
8 29 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
AAATATTT
Found at i:30079393 original size:21 final size:21
Alignment explanation
Indices: 30079364--30079403 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30079354 TAAAATATTT
*
30079364 AAATATTTAAATTTTTAAAAA
1 AAATATTTAAATATTTAAAAA
*
30079385 AAATTTTTAAATATTTAAA
1 AAATATTTAAATATTTAAA
30079404 TTAAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATATTTAAATATTTAAAAA
Found at i:30079414 original size:29 final size:29
Alignment explanation
Indices: 30079355--30079423 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
30079345 AAAGTATTTT
**
30079355 AAAATATTTAAATATTTAAATTTTTAAAA
1 AAAATATTTAAATATTTAAATTTAAAAAA
* *
30079384 AAAATTTTTAAATATTTAAATTAAAATAAAA
1 AAAATATTTAAATATTTAAATT-TAA-AAAA
30079415 AAAATATTT
1 AAAATATTT
30079424 TATAAAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 21 0.64
31 12 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AAAATATTTAAATATTTAAATTTAAAAAA
Found at i:30079431 original size:22 final size:22
Alignment explanation
Indices: 30079393--30079452 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 22
30079383 AAAAATTTTT
30079393 AAATA-TTTAAATTAAAATAAAAA
1 AAATATTTTAAA--AAAATAAAAA
30079416 AAATATTTTATAAAAAATAAAAA
1 AAATATTTTA-AAAAAATAAAAA
*
30079439 AAGTATTTTAAAAA
1 AAATATTTTAAAAA
30079453 TATTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
22 4 0.12
23 24 0.71
24 4 0.12
25 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (22 bp):
AAATATTTTAAAAAAATAAAAA
Found at i:30079437 original size:21 final size:23
Alignment explanation
Indices: 30079405--30079454 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
30079395 ATATTTAAAT
30079405 TAAAAT-AAAAAAAA-TATTTTA
1 TAAAATAAAAAAAAAGTATTTTA
30079426 TAAAA-AATAAAAAAAGTATTTTA
1 TAAAATAA-AAAAAAAGTATTTTA
30079449 -AAAATA
1 TAAAATA
30079455 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 6 0.24
22 11 0.44
23 8 0.32
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
TAAAATAAAAAAAAAGTATTTTA
Found at i:30079468 original size:17 final size:17
Alignment explanation
Indices: 30079446--30079530 Score: 55
Period size: 17 Copynumber: 4.8 Consensus size: 17
30079436 AAAAAGTATT
*
30079446 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
**
30079463 TTAAAAA-ATAAAAAAAGTA
1 TTAAAAATAT-TTAAAA--A
*
30079482 TTTTAAAAATATTTTAAAA
1 -TT-AAAAATATTTAAAAA
*
30079501 TTAAAAAAATTTAAAAA
1 TTAAAAATATTTAAAAA
* *
30079518 ATAAATATATTTA
1 TTAAAAATATTTA
30079531 TTATATCGGG
Statistics
Matches: 51, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
16 2 0.04
17 33 0.65
18 2 0.04
19 2 0.04
20 2 0.04
21 8 0.16
22 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:30079475 original size:38 final size:38
Alignment explanation
Indices: 30079426--30079508 Score: 166
Period size: 38 Copynumber: 2.2 Consensus size: 38
30079416 AAATATTTTA
30079426 TAAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAAT
1 TAAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAAT
30079464 TAAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAAT
1 TAAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAAT
30079502 TAAAAAA
1 TAAAAAA
30079509 ATTTAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (38 bp):
TAAAAAATAAAAAAAGTATTTTAAAAATATTTTAAAAT
Found at i:30079477 original size:93 final size:97
Alignment explanation
Indices: 30079333--30079506 Score: 225
Period size: 93 Copynumber: 1.8 Consensus size: 97
30079323 AAATTTATTT
* *** * *
30079333 TAAAAATTAAAAAAAGTATTTTAAAATATTTAAATATTTAAATTTTTAAAAAA-AATTTT-TAAA
1 TAAAAAATAAAAAAAGTATTTTAAAATATTTAAATATTTAAAAAATAAAAAAAGAATTTTAAAAA
30079396 TA-TTT-AAATTAAAATAAAAAAAATATTTTA
66 TATTTTAAAATTAAAATAAAAAAAATATTTTA
*
30079426 TAAAAAATAAAAAAAGTATTTTAAAAATATTTTAAA-A-TTAAAAAATAAAAAAAGTATTTTAAA
1 TAAAAAATAAAAAAAGTATTTT-AAAATA-TTTAAATATTTAAAAAATAAAAAAAGAATTTTAAA
30079489 AATATTTTAAAATTAAAA
64 AATATTTTAAAATTAAAA
30079507 AAATTTAAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
93 33 0.49
94 12 0.18
95 11 0.16
96 3 0.04
97 9 0.13
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (97 bp):
TAAAAAATAAAAAAAGTATTTTAAAATATTTAAATATTTAAAAAATAAAAAAAGAATTTTAAAAA
TATTTTAAAATTAAAATAAAAAAAATATTTTA
Found at i:30082451 original size:32 final size:32
Alignment explanation
Indices: 30082415--30082498 Score: 132
Period size: 32 Copynumber: 2.6 Consensus size: 32
30082405 TCACTTGTCT
30082415 TTTCTTGCAGGGAATCTTTCCTGTTCACGTCA
1 TTTCTTGCAGGGAATCTTTCCTGTTCACGTCA
* * *
30082447 TTTCTTGCAGGGAATCTCTCCTGTTCATGTCT
1 TTTCTTGCAGGGAATCTTTCCTGTTCACGTCA
*
30082479 TTTCTTGCAGGGAATATTTC
1 TTTCTTGCAGGGAATCTTTC
30082499 TTGCAGGGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
TTTCTTGCAGGGAATCTTTCCTGTTCACGTCA
Found at i:30082500 original size:16 final size:16
Alignment explanation
Indices: 30082479--30082509 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
30082469 GTTCATGTCT
30082479 TTTCTTGCAGGGAATA
1 TTTCTTGCAGGGAATA
30082495 TTTCTTGCAGGGAAT
1 TTTCTTGCAGGGAAT
30082510 CTCTCCTGTT
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:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (16 bp):
TTTCTTGCAGGGAATA
Found at i:30082502 original size:48 final size:48
Alignment explanation
Indices: 30082446--30082541 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
30082436 TGTTCACGTC
* *
30082446 ATTTCTTGCAGGGAATCTCTCCTGTTCATGTCTTTTCTTGCAGGGAAT
1 ATTTCTTGCAGGGAATCTCTCCTGTTCACGTCATTTCTTGCAGGGAAT
30082494 ATTTCTTGCAGGGAATCTCTCCTGTTCACGTCATTTCTTGCAGGGAAT
1 ATTTCTTGCAGGGAATCTCTCCTGTTCACGTCATTTCTTGCAGGGAAT
30082542 CTCTCCTGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.40
Consensus pattern (48 bp):
ATTTCTTGCAGGGAATCTCTCCTGTTCACGTCATTTCTTGCAGGGAAT
Found at i:30082548 original size:80 final size:80
Alignment explanation
Indices: 30082415--30082573 Score: 291
Period size: 80 Copynumber: 2.0 Consensus size: 80
30082405 TCACTTGTCT
* * *
30082415 TTTCTTGCAGGGAATCTTTCCTGTTCACGTCATTTCTTGCAGGGAATCTCTCCTGTTCATGTCTT
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGTCATTTCTTGCAGGGAATCTCTCCTGTTCACGTCAT
30082480 TTCTTGCAGGGAATA
66 TTCTTGCAGGGAATA
30082495 TTTCTTGCAGGGAATCTCTCCTGTTCACGTCATTTCTTGCAGGGAATCTCTCCTGTTCACGTCAT
1 TTTCTTGCAGGGAATCTCTCCTGTTCACGTCATTTCTTGCAGGGAATCTCTCCTGTTCACGTCAT
30082560 TTCTTGCAGGGAAT
66 TTCTTGCAGGGAAT
30082574 CTCTCTTGTT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (80 bp):
TTTCTTGCAGGGAATCTCTCCTGTTCACGTCATTTCTTGCAGGGAATCTCTCCTGTTCACGTCAT
TTCTTGCAGGGAATA
Found at i:30082621 original size:36 final size:32
Alignment explanation
Indices: 30082494--30082591 Score: 180
Period size: 32 Copynumber: 3.1 Consensus size: 32
30082484 TGCAGGGAAT
30082494 ATTTCTTGCAGGGAATCTCTCCTGTTCACGTC
1 ATTTCTTGCAGGGAATCTCTCCTGTTCACGTC
30082526 ATTTCTTGCAGGGAATCTCTCCTGTTCACGTC
1 ATTTCTTGCAGGGAATCTCTCCTGTTCACGTC
*
30082558 ATTTCTTGCAGGGAATCTCTCTTGTTCACG-C
1 ATTTCTTGCAGGGAATCTCTCCTGTTCACGTC
30082589 ATT
1 ATT
30082592 ATTTTGTTTG
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
31 4 0.06
32 61 0.94
ACGTcount: A:0.16, C:0.27, G:0.18, T:0.39
Consensus pattern (32 bp):
ATTTCTTGCAGGGAATCTCTCCTGTTCACGTC
Found at i:30082629 original size:36 final size:36
Alignment explanation
Indices: 30082499--30082631 Score: 129
Period size: 32 Copynumber: 3.9 Consensus size: 36
30082489 GGAATATTTC
* * *
30082499 TTGCAGGGAATCTCTCCTGTTCACG--TCA-TTT-C
1 TTGCAGGGAATCTCTCTTGTTCACGCATTATTTTGT
* * *
30082531 TTGCAGGGAATCTCTCCTGTTCACG--TCA-TTT-C
1 TTGCAGGGAATCTCTCTTGTTCACGCATTATTTTGT
30082563 TTGCAGGGAATCTCTCTTGTTCACGCATTATTTTGT
1 TTGCAGGGAATCTCTCTTGTTCACGCATTATTTTGT
* * *
30082599 TTGCAGGGAATCTTTCTTGTTCATGTATTATTT
1 TTGCAGGGAATCTCTCTTGTTCACGCATTATTT
30082632 CTTTTTGGAC
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
32 56 0.62
34 2 0.02
35 3 0.03
36 30 0.33
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.43
Consensus pattern (36 bp):
TTGCAGGGAATCTCTCTTGTTCACGCATTATTTTGT
Found at i:30085466 original size:20 final size:23
Alignment explanation
Indices: 30085431--30085475 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
30085421 GAGCAAATCG
30085431 TTGATTCTATTTCTTTTTTG-AT
1 TTGATTCTATTTCTTTTTTGTAT
30085453 TTGA-TCTA-TTCTTTTTTGTAT
1 TTGATTCTATTTCTTTTTTGTAT
30085474 TT
1 TT
30085476 CTCTTTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 8 0.36
22 4 0.18
ACGTcount: A:0.13, C:0.09, G:0.09, T:0.69
Consensus pattern (23 bp):
TTGATTCTATTTCTTTTTTGTAT
Found at i:30091389 original size:42 final size:42
Alignment explanation
Indices: 30091339--30091432 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
30091329 CTATATGAAT
* * *
30091339 GGCACTAAGTATGTAAAATTAAAATGATGATGTTGAATAATA
1 GGCACTAAGTATGCAAAATTAAAATAATGATGTTGAATAACA
* ** * * *
30091381 GGCACTAAGTGTGCGGAATTATAATAATGTTGTTGAATAACG
1 GGCACTAAGTATGCAAAATTAAAATAATGATGTTGAATAACA
30091423 GGCACTAAGT
1 GGCACTAAGT
30091433 GTGCGATACC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (42 bp):
GGCACTAAGTATGCAAAATTAAAATAATGATGTTGAATAACA
Found at i:30091433 original size:42 final size:42
Alignment explanation
Indices: 30091355--30091437 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
30091345 AAGTATGTAA
* *
30091355 AATTAAAATGATGATGTTGAATAATAGGCACTAAGTGTGCGG
1 AATTAAAATAATGATGTTGAATAACAGGCACTAAGTGTGCGG
* * *
30091397 AATTATAATAATGTTGTTGAATAACGGGCACTAAGTGTGCG
1 AATTAAAATAATGATGTTGAATAACAGGCACTAAGTGTGCG
30091438 ATACCGAGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.36, C:0.08, G:0.25, T:0.30
Consensus pattern (42 bp):
AATTAAAATAATGATGTTGAATAACAGGCACTAAGTGTGCGG
Found at i:30092685 original size:41 final size:41
Alignment explanation
Indices: 30092628--30092784 Score: 242
Period size: 41 Copynumber: 3.8 Consensus size: 41
30092618 TTTTGTAAGT
30092628 TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAATTATA
30092669 TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAATTATA
* * * *
30092710 TCAGACTTTATGTCTAGCAGGCTTTGTGCCGGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAATTATA
* ** *
30092751 TCGGGCTTGGTGCCTAGCAGGCTTTATGCCGGTG
1 TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTG
30092785 TTATATACAA
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 106 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTTTGTGCCGGTGAATTATA
Found at i:30095089 original size:30 final size:30
Alignment explanation
Indices: 30095055--30095112 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
30095045 TCTCATGGCC
30095055 GTGTGCCACACACGGTCACACCACACATCT
1 GTGTGCCACACACGGTCACACCACACATCT
*
30095085 GTGTGCCACACACGGTCATACCACACAT
1 GTGTGCCACACACGGTCACACCACACAT
30095113 TCGTCCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.38, G:0.17, T:0.17
Consensus pattern (30 bp):
GTGTGCCACACACGGTCACACCACACATCT
Found at i:30095108 original size:15 final size:15
Alignment explanation
Indices: 30095060--30095111 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
30095050 TGGCCGTGTG
*
30095060 CCACACACGGTCACA
1 CCACACACGGTCATA
* * *
30095075 CCACACATCTGT-GTG
1 CCACACA-CGGTCATA
30095090 CCACACACGGTCATA
1 CCACACACGGTCATA
30095105 CCACACA
1 CCACACA
30095112 TTCGTCCATG
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
14 3 0.11
15 22 0.79
16 3 0.11
ACGTcount: A:0.31, C:0.42, G:0.13, T:0.13
Consensus pattern (15 bp):
CCACACACGGTCATA
Found at i:30096593 original size:15 final size:16
Alignment explanation
Indices: 30096562--30096595 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
30096552 TCACATGCTT
30096562 ATATATGTTAAATTTC
1 ATATATGTTAAATTTC
*
30096578 ATATATG-TACATTTC
1 ATATATGTTAAATTTC
30096593 ATA
1 ATA
30096596 CCATTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (16 bp):
ATATATGTTAAATTTC
Found at i:30098477 original size:19 final size:19
Alignment explanation
Indices: 30098453--30098490 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
30098443 TCAAGCACAT
30098453 AAAATCACTAGATGCTCAC
1 AAAATCACTAGATGCTCAC
30098472 AAAATCACTAGATGCTCAC
1 AAAATCACTAGATGCTCAC
30098491 TTACCAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (19 bp):
AAAATCACTAGATGCTCAC
Found at i:30100446 original size:20 final size:18
Alignment explanation
Indices: 30100411--30100450 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
30100401 TGTTTTAAAG
30100411 TTTATAGTTTAATTTTAT
1 TTTATAGTTTAATTTTAT
*
30100429 TTTATAGGTATTAGTTTTAT
1 TTTATA-GT-TTAATTTTAT
30100449 TT
1 TT
30100451 ATCTTTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (18 bp):
TTTATAGTTTAATTTTAT
Found at i:30100465 original size:25 final size:25
Alignment explanation
Indices: 30100415--30100465 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
30100405 TTAAAGTTTA
*
30100415 TAGTTTAATTTTATTTTATAGGTAT
1 TAGTTTAATTTTATTTTATAGATAT
* *
30100440 TAGTTTTATTTATCTTTTA-AGATAT
1 TAGTTTAATTT-TATTTTATAGATAT
30100465 T
1 T
30100466 TTACTTATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.61
Consensus pattern (25 bp):
TAGTTTAATTTTATTTTATAGATAT
Found at i:30112677 original size:18 final size:17
Alignment explanation
Indices: 30112654--30112707 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 17
30112644 AAATCGTGTC
30112654 ATTCATTTCCAACACATT
1 ATTCATTTCCAA-ACATT
*
30112672 ATTCATTTACAAATCATT
1 ATTCATTTCCAAA-CATT
30112690 ATTCAATTTCCAAACATT
1 ATTC-ATTTCCAAACATT
30112708 TTTTTACTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 1 0.03
18 23 0.72
19 8 0.25
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTCATTTCCAAACATT
Found at i:30117033 original size:24 final size:24
Alignment explanation
Indices: 30117001--30117051 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
30116991 TGATATCCTT
*
30117001 AACTGTAGAGTCCACAGAATCTAA
1 AACTATAGAGTCCACAGAATCTAA
* * *
30117025 AACTATAGAGTCCTCATAATCTGA
1 AACTATAGAGTCCACAGAATCTAA
30117049 AAC
1 AAC
30117052 ACTTACATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (24 bp):
AACTATAGAGTCCACAGAATCTAA
Found at i:30131096 original size:45 final size:45
Alignment explanation
Indices: 30131027--30131152 Score: 162
Period size: 45 Copynumber: 2.8 Consensus size: 45
30131017 GTTGGTTGAA
* * *
30131027 AAACAAGTAAGACCATAGCTGAAAGACGCTATGGCATCACAGTTC
1 AAACGAGTAAGACCATAGTTGAAAGACGCTATGGCATCACAATTC
* * **
30131072 AAACGAGTAAGACCATAGTTGAAAGACGTTATGACATTGCAATTC
1 AAACGAGTAAGACCATAGTTGAAAGACGCTATGGCATCACAATTC
* * *
30131117 AAACGTGTAAGACCATTGTTGAAAGACACTATGGCA
1 AAACGAGTAAGACCATAGTTGAAAGACGCTATGGCA
30131153 ACAAGACGAA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (45 bp):
AAACGAGTAAGACCATAGTTGAAAGACGCTATGGCATCACAATTC
Found at i:30131212 original size:46 final size:46
Alignment explanation
Indices: 30131124--30131286 Score: 222
Period size: 46 Copynumber: 3.6 Consensus size: 46
30131114 TTCAAACGTG
* *
30131124 TAAGACCATTGTTGAAAGACACTATGGCAACA-AGACGAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGACAACATA-ACGAAAAATGAA
* * * * *
30131170 TAAAACTATAGTTGAAAGACACTATGACAATATAACGGAAAATAAA
1 TAAGACCATAGTTGAAAGACACTATGACAACATAACGAAAAATGAA
* *
30131216 TAAGACCATTGTTGAAAGACACTATGACAACATGAC-AAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGACAACATAACGAAAAATGAA
30131261 TAAGACCATAGTTGAAAGACACTATG
1 TAAGACCATAGTTGAAAGACACTATG
30131287 GCATCACGAT
Statistics
Matches: 101, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
45 32 0.32
46 68 0.67
47 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (46 bp):
TAAGACCATAGTTGAAAGACACTATGACAACATAACGAAAAATGAA
Found at i:30131262 original size:91 final size:91
Alignment explanation
Indices: 30131124--30131334 Score: 282
Period size: 91 Copynumber: 2.3 Consensus size: 91
30131114 TTCAAACGTG
* *
30131124 TAAGACCATTGTTGAAAGACACTATGGCAACAAGACGAAAAATGAATAAAACTATAGTTGAAAGA
1 TAAGACCATTGTTGAAAGACACTATGACAACAAGACGAAAAATGAATAAAACCATAGTTGAAAGA
*
30131189 CACTATGACAAT-ATAACGGAAAATAAA
66 CACTATGAC-ATCACAACGG-AAATAAA
* *
30131216 TAAGACCATTGTTGAAAGACACTATGACAACATGAC-AAAAATGAATAAGACCATAGTTGAAAGA
1 TAAGACCATTGTTGAAAGACACTATGACAACAAGACGAAAAATGAATAAAACCATAGTTGAAAGA
* * *
30131280 CACTATGGCATCACGATGGAAATAAA
66 CACTATGACATCACAACGGAAATAAA
* * * *
30131306 TAAGACCATGGATGAAAGACGCTACGACA
1 TAAGACCATTGTTGAAAGACACTATGACA
30131335 TTCTTTGAAA
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
90 34 0.32
91 38 0.36
92 34 0.32
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (91 bp):
TAAGACCATTGTTGAAAGACACTATGACAACAAGACGAAAAATGAATAAAACCATAGTTGAAAGA
CACTATGACATCACAACGGAAATAAA
Found at i:30131308 original size:45 final size:45
Alignment explanation
Indices: 30131124--30131334 Score: 224
Period size: 45 Copynumber: 4.6 Consensus size: 45
30131114 TTCAAACGTG
* * * *
30131124 TAAGACCATTGTTGAAAGACACTATGGCAACAAGACGAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGACAACATGACG-AAAATAAA
* * * *
30131170 TAAAACTATAGTTGAAAGACACTATGACAATATAACGGAAAATAAA
1 TAAGACCATAGTTGAAAGACACTATGACAACATGAC-GAAAATAAA
* * *
30131216 TAAGACCATTGTTGAAAGACACTATGACAACATGACAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGACAACATGACGAAAATAAA
* * * * *
30131261 TAAGACCATAGTTGAAAGACACTATGGCATCACGATGGAAATAAA
1 TAAGACCATAGTTGAAAGACACTATGACAACATGACGAAAATAAA
* * * *
30131306 TAAGACCATGGATGAAAGACGCTACGACA
1 TAAGACCATAGTTGAAAGACACTATGACA
30131335 TTCTTTGAAA
Statistics
Matches: 136, Mismatches: 28, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
45 68 0.50
46 67 0.49
47 1 0.01
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.19
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGACAACATGACGAAAATAAA
Found at i:30133682 original size:1 final size:1
Alignment explanation
Indices: 30133678--30133783 Score: 122
Period size: 1 Copynumber: 106.0 Consensus size: 1
30133668 AAAAAATATG
* * * * * * * *
30133678 TTTTTTTTTTTTGTTTTTTGTTTTTTGTTTGTTTTTTTGTTTTTTTTTGTTTTTGTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
**
30133743 GGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
30133784 GTAATGGTTA
Statistics
Matches: 87, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 87 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:30141003 original size:26 final size:27
Alignment explanation
Indices: 30140927--30141011 Score: 90
Period size: 26 Copynumber: 3.3 Consensus size: 27
30140917 AGGGAATCTT
*
30140927 CGAAGAGCCA-ATAATCAAGAAGCTCA
1 CGAAGAGCCATATAATCAGGAAGCTCA
* *
30140953 CAAAGAGCC-TTTAATC-GGAAAGCTCA
1 CGAAGAGCCATATAATCAGG-AAGCTCA
*
30140979 CGAAGAGCCATAT-ATCAGGACGCTCA
1 CGAAGAGCCATATAATCAGGAAGCTCA
30141005 -GAAGAGC
1 CGAAGAGC
30141012 TGTGGTGTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
25 8 0.16
26 37 0.76
27 4 0.08
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (27 bp):
CGAAGAGCCATATAATCAGGAAGCTCA
Found at i:30143914 original size:27 final size:27
Alignment explanation
Indices: 30143862--30143937 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
30143852 ACATAATGCC
*
30143862 ATAACAGTCATTTCATCTCCTA--GGGGT
1 ATAACAGTCATTTTA-C-CCTATGGGGGT
30143889 ATAACAGTCATTTTACCCTATGGGGGT
1 ATAACAGTCATTTTACCCTATGGGGGT
*** *
30143916 ATTTTAGTCATTTTACCTTATG
1 ATAACAGTCATTTTACCCTATG
30143938 AGAGCCTATG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 4 0.10
26 1 0.02
27 37 0.88
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.39
Consensus pattern (27 bp):
ATAACAGTCATTTTACCCTATGGGGGT
Found at i:30143979 original size:27 final size:27
Alignment explanation
Indices: 30143949--30144024 Score: 134
Period size: 27 Copynumber: 2.8 Consensus size: 27
30143939 GAGCCTATGA
30143949 GGGTATTTCGGTCATTTTACCTTACGG
1 GGGTATTTCGGTCATTTTACCTTACGG
* *
30143976 GGGTATTTCGATCATTTTACCTTATGG
1 GGGTATTTCGGTCATTTTACCTTACGG
30144003 GGGTATTTCGGTCATTTTACCT
1 GGGTATTTCGGTCATTTTACCT
30144025 ATTTTAGGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.16, C:0.17, G:0.24, T:0.43
Consensus pattern (27 bp):
GGGTATTTCGGTCATTTTACCTTACGG
Found at i:30144313 original size:20 final size:20
Alignment explanation
Indices: 30144290--30144327 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30144280 GCCCATCTCT
* *
30144290 GCCCAATATGGCCTATTACG
1 GCCCAACATGGCCCATTACG
30144310 GCCCAACATGGCCCATTA
1 GCCCAACATGGCCCATTA
30144328 TAGCCGAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.21
Consensus pattern (20 bp):
GCCCAACATGGCCCATTACG
Found at i:30146193 original size:151 final size:151
Alignment explanation
Indices: 30145914--30146216 Score: 491
Period size: 151 Copynumber: 2.0 Consensus size: 151
30145904 TTTCTCACTG
* * *
30145914 AGCTTAGTCCAATACAATGGAGTTCTACATTTATGACCATATAGAGCCTCATACGGTGCCATCTT
1 AGCTCAGTCCAATACAATGGAGTTCTACATTTATGACCATACAGAGCCTCATACGGTGCCATATT
*
30145979 AATACTTGACTGATAACTGTTATTATATGCGAATTCGACTAAAGACAGGTATTTTTCCCAATTGC
66 AATACTTGACTGATAACTATTATTATATGCGAATTCGACTAAAGACAGGTATTTTTCCCAATTGC
*
30146044 CTTTGAATTCTAACACACAGC
131 CTTCGAATTCTAACACACAGC
*
30146065 AGCTCAGTCCAATACAATGGAGTTCTACATTTA-GAACCATACAGAGCCTCATATGGTGCCATAT
1 AGCTCAGTCCAATACAATGGAGTTCTACATTTATG-ACCATACAGAGCCTCATACGGTGCCATAT
* * *
30146129 TAATACTTGACTGATAATTATTATTATATGTGAATTCGACTAAAGGCAGGTATTTTTCCCAATTG
65 TAATACTTGACTGATAACTATTATTATATGCGAATTCGACTAAAGACAGGTATTTTTCCCAATTG
* *
30146194 CCTTCGAATTTTAATACACAGC
130 CCTTCGAATTCTAACACACAGC
30146216 A
1 A
30146217 CCGAAGCATA
Statistics
Matches: 140, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
150 1 0.01
151 139 0.99
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (151 bp):
AGCTCAGTCCAATACAATGGAGTTCTACATTTATGACCATACAGAGCCTCATACGGTGCCATATT
AATACTTGACTGATAACTATTATTATATGCGAATTCGACTAAAGACAGGTATTTTTCCCAATTGC
CTTCGAATTCTAACACACAGC
Found at i:30154284 original size:22 final size:22
Alignment explanation
Indices: 30154258--30154302 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
30154248 CTGGACTACA
* *
30154258 ATACATCGGATAGGACTCAAGC
1 ATACATCAGATAGGACCCAAGC
30154280 ATACATCAGATAGGACCCAAGC
1 ATACATCAGATAGGACCCAAGC
30154302 A
1 A
30154303 AAATAGATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (22 bp):
ATACATCAGATAGGACCCAAGC
Found at i:30156511 original size:17 final size:17
Alignment explanation
Indices: 30156489--30156533 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
30156479 TAAATTGCCT
30156489 TTCTCACAATGTAAACA
1 TTCTCACAATGTAAACA
* *
30156506 TTCTCACAAAGTAAACG
1 TTCTCACAATGTAAACA
*
30156523 TTCTTACAATG
1 TTCTCACAATG
30156534 CCACTTATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (17 bp):
TTCTCACAATGTAAACA
Found at i:30157625 original size:15 final size:16
Alignment explanation
Indices: 30157593--30157625 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
30157583 ACATTCGGTC
*
30157593 ATAGTGAACATGTTGA
1 ATAGTGAACATATTGA
30157609 ATAGTGAA-ATATTGA
1 ATAGTGAACATATTGA
30157624 AT
1 AT
30157626 GAATTTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.33
Consensus pattern (16 bp):
ATAGTGAACATATTGA
Found at i:30171763 original size:19 final size:19
Alignment explanation
Indices: 30171739--30171782 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
30171729 GTAGATTACA
*
30171739 AAAAATGTGGTTAAAT-TTG
1 AAAAAT-TGGTAAAATGTTG
30171758 AAAAATTGGTAAAATGTTG
1 AAAAATTGGTAAAATGTTG
*
30171777 TAAAAT
1 AAAAAT
30171783 AAGGTTCCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (19 bp):
AAAAATTGGTAAAATGTTG
Found at i:30171876 original size:41 final size:41
Alignment explanation
Indices: 30171830--30171939 Score: 175
Period size: 41 Copynumber: 2.7 Consensus size: 41
30171820 CATCAAATGT
*
30171830 AAGGGGTTGCTAAGCGTAGATTCCCCGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGTAGATTCCCCGAATCACTGATCAAA
* * *
30171871 AAGGGGTTGCTAAGTGCAAATTCCCCGAATCACTGATTAAA
1 AAGGGGTTGCTAAGTGTAGATTCCCCGAATCACTGATCAAA
*
30171912 AAGGGGTTGCTACGTGTAGATTCCCCGA
1 AAGGGGTTGCTAAGTGTAGATTCCCCGA
30171940 GGGGTTGCTA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGTAGATTCCCCGAATCACTGATCAAA
Found at i:30171942 original size:26 final size:26
Alignment explanation
Indices: 30171913--30171965 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
30171903 CTGATTAAAA
*
30171913 AGGGGTTGCTACGTG-TAGATTCCCCG
1 AGGGGTTGCTAAGTGCT-GATTCCCCG
30171939 AGGGGTTGCTAAGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
30171965 A
1 A
30171966 ATTATTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTGATTCCCCG
Found at i:30172001 original size:42 final size:43
Alignment explanation
Indices: 30171942--30172092 Score: 161
Period size: 42 Copynumber: 3.6 Consensus size: 43
30171932 TTCCCCGAGG
30171942 GGTTGCTAAGTGCTGATTCC-CCGAATTATTGATTATAAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATTATTGATTATAAAGGT
*
30171984 GGTTGCTAAGTGCTGATTCCACC--ATATACTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGAAT-TA-TTGATTAT-AAAGGT
* * * * * * *
30172027 GGTTGCTATGTGTTGATTCC-CCGTATCACTGAATAT-AAGTT
1 GGTTGCTAAGTGCTGATTCCACCGAATTATTGATTATAAAGGT
30172068 GGTTGCTAAGTGCTGATTCCACCGA
1 GGTTGCTAAGTGCTGATTCCACCGA
30172093 GTAACGGTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
40 3 0.03
41 20 0.22
42 32 0.36
43 28 0.31
44 7 0.08
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACCGAATTATTGATTATAAAGGT
Found at i:30173045 original size:26 final size:26
Alignment explanation
Indices: 30173009--30173084 Score: 143
Period size: 26 Copynumber: 2.9 Consensus size: 26
30172999 TTGATCAAAA
30173009 AGGGGTTGCTAAGTGCAGATTCCCTG
1 AGGGGTTGCTAAGTGCAGATTCCCTG
30173035 AGGGGTTGCTAAGTGCAGATTCCCTG
1 AGGGGTTGCTAAGTGCAGATTCCCTG
*
30173061 AGGGGTTGCTAAGTGCTGATTCCC
1 AGGGGTTGCTAAGTGCAGATTCCC
30173085 CGAATTATTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.18, C:0.20, G:0.34, T:0.28
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCAGATTCCCTG
Found at i:30173111 original size:42 final size:43
Alignment explanation
Indices: 30173064--30173214 Score: 132
Period size: 42 Copynumber: 3.6 Consensus size: 43
30173054 TTCCCTGAGG
*
30173064 GGTTGCTAAGTGCTGATTCC-CCGAATTATTGATTCTAAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGATTCTAAAGGT
* * * * *
30173106 GGTTGCTAGGTGCTGAATCCACCGTATCCTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGATTCT-AAAGGT
* * * * * *
30173149 GGTTGCTATGTGATGATTCC-CCGTATCACTGA-AC-ATAAGTT
1 GGTTGCTAAGTGCTGATTCCACCGAATCATTGATTCTA-AAGGT
*
30173190 GGTTGCTAAGTGCTAATTCCACCGA
1 GGTTGCTAAGTGCTGATTCCACCGA
30173215 GTAACGGTTA
Statistics
Matches: 86, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
39 1 0.01
40 3 0.03
41 17 0.20
42 31 0.36
43 29 0.34
44 5 0.06
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (43 bp):
GGTTGCTAAGTGCTGATTCCACCGAATCATTGATTCTAAAGGT
Found at i:30173153 original size:43 final size:41
Alignment explanation
Indices: 30173061--30173176 Score: 133
Period size: 43 Copynumber: 2.8 Consensus size: 41
30173051 AGATTCCCTG
* *
30173061 AGGGGTTGCTAAGTGCTGATTCCCCGAATTATTGATTCTAA
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTCTAA
* * * *
30173102 AGGTGGTTGCTAGGTGCTGAATCCACCGTATCCTTGATTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGATTCT-AA
* *
30173146 AGGGGTTGCTATGTGATGATTCCCCGTATCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGTATCA
30173177 CTGAACATAA
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 3 0.05
42 25 0.40
43 29 0.47
44 5 0.08
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.33
Consensus pattern (41 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTCTAA
Found at i:30175590 original size:32 final size:32
Alignment explanation
Indices: 30175549--30175616 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
30175539 CTGAACCAAC
30175549 GGCAAGCTGAACTGGCAAACAAGGAGATCAAA
1 GGCAAGCTGAACTGGCAAACAAGGAGATCAAA
*
30175581 GGCAAGCTGAACTGGCAAACAAGGAGATCGAA
1 GGCAAGCTGAACTGGCAAACAAGGAGATCAAA
30175613 GGCA
1 GGCA
30175617 TATAAGACAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.41, C:0.19, G:0.31, T:0.09
Consensus pattern (32 bp):
GGCAAGCTGAACTGGCAAACAAGGAGATCAAA
Found at i:30176316 original size:7 final size:7
Alignment explanation
Indices: 30176304--30176344 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
30176294 TAAAAGGGTC
30176304 AATTTTG
1 AATTTTG
30176311 AATTTTG
1 AATTTTG
30176318 AATTTTG
1 AATTTTG
30176325 AATTTTG
1 AATTTTG
30176332 AATTTTG
1 AATTTTG
30176339 AATTTT
1 AATTTT
30176345 ATGTTGCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (7 bp):
AATTTTG
Found at i:30176437 original size:30 final size:30
Alignment explanation
Indices: 30176401--30176462 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
30176391 TGAATTATTT
* *
30176401 TTAAAAATTTGGTTACTCTTTTTGTAAATA
1 TTAAAAATTAGATTACTCTTTTTGTAAATA
*
30176431 TTAAAAATTAGATTCCTCTTTTTGTAAATA
1 TTAAAAATTAGATTACTCTTTTTGTAAATA
30176461 TT
1 TT
30176463 TTCAAAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (30 bp):
TTAAAAATTAGATTACTCTTTTTGTAAATA
Found at i:30176554 original size:16 final size:15
Alignment explanation
Indices: 30176521--30176562 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
30176511 AGATGATAAT
30176521 TATTAATATATAATTA
1 TATTAAT-TATAATTA
*
30176537 TATTCATTATAATATA
1 TATTAATTATAAT-TA
30176553 TATTAATTAT
1 TATTAATTAT
30176563 GATCAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:30177142 original size:20 final size:20
Alignment explanation
Indices: 30177114--30177152 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
30177104 AATTTTTCTC
30177114 CTAA-ATTTTAATTTTATTAT
1 CTAATATTTTAA-TTTATTAT
*
30177134 CTAATTTTTTAATTTATTA
1 CTAATATTTTAATTTATTA
30177153 AATTATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
CTAATATTTTAATTTATTAT
Done.