Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014829.1 Kokia drynarioides strain JFW-HI SEQ_129871, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 469256
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 555 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:2445 original size:20 final size:21
Alignment explanation
Indices: 2400--2446 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
2390 GATAAAATAA
2400 TCACTCAATTTTCAATTCAAG
1 TCACTCAATTTTCAATTCAAG
*
2421 T-ACTCAATTTTTAATTC-AG
1 TCACTCAATTTTCAATTCAAG
2440 TCACTCA
1 TCACTCA
2447 CTTTCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 3 0.12
20 20 0.83
21 1 0.04
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.40
Consensus pattern (21 bp):
TCACTCAATTTTCAATTCAAG
Found at i:3279 original size:8 final size:8
Alignment explanation
Indices: 3268--3295 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3258 CTTTTTCTCT
3268 TTTTTTTA
1 TTTTTTTA
3276 TTTTTTTA
1 TTTTTTTA
3284 TTTTTTTA
1 TTTTTTTA
3292 TTTT
1 TTTT
3296 CTCCTTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTA
Found at i:3279 original size:16 final size:17
Alignment explanation
Indices: 3260--3298 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3250 TTTTTTCTCT
3260 TTTTCTCT-TTTTTTTA
1 TTTTCTCTATTTTTTTA
*
3276 TTTT-TTTATTTTTTTA
1 TTTTCTCTATTTTTTTA
3292 TTTTCTC
1 TTTTCTC
3299 CTTCTTCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
15 2 0.11
16 16 0.84
17 1 0.05
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTCTCTATTTTTTTA
Found at i:9329 original size:1 final size:1
Alignment explanation
Indices: 9323--9348 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
9313 TCCTTATAAA
9323 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
9349 GACACTGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:9775 original size:31 final size:31
Alignment explanation
Indices: 9732--9800 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
9722 AAAGTATCAA
*
9732 ATTAAAA-AAAACTCAAATGTCAAAGTGAAC
1 ATTAAAATAAAACTCAAATATCAAAGTGAAC
* * * * *
9762 ATTAAAATTAAACTCAGATATCATATTGAAT
1 ATTAAAATAAAACTCAAATATCAAAGTGAAC
9793 ATTAAAAT
1 ATTAAAAT
9801 CAAATTGAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.29
Consensus pattern (31 bp):
ATTAAAATAAAACTCAAATATCAAAGTGAAC
Found at i:10624 original size:17 final size:16
Alignment explanation
Indices: 10602--10640 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
10592 GCCCAATTAT
*
10602 TTTAAAATTAAGTTTA
1 TTTAAAATTAAATTTA
*
10618 TTCTAAATTTAAATTTA
1 TT-TAAAATTAAATTTA
10635 TTTAAA
1 TTTAAA
10641 TTTATTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (16 bp):
TTTAAAATTAAATTTA
Found at i:10639 original size:10 final size:10
Alignment explanation
Indices: 10624--10675 Score: 59
Period size: 10 Copynumber: 4.8 Consensus size: 10
10614 TTTATTCTAA
10624 ATTTAAATTT
1 ATTTAAATTT
10634 ATTTAAATTT
1 ATTTAAATTT
10644 ATTATAAATTT
1 ATT-TAAATTT
*
10655 AAATTTAAAATTC
1 --ATTT-AAATTT
10668 ATTTAAAT
1 ATTTAAAT
10676 AATGTCTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 17 0.46
11 11 0.30
12 1 0.03
13 8 0.22
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:10639 original size:27 final size:27
Alignment explanation
Indices: 10609--10661 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
10599 TATTTTAAAA
* *
10609 TTAAGTTTATTCTAAATTTAAATTTAT
1 TTAAATTTATTATAAATTTAAATTTAT
10636 TTAAATTTATTATAAATTTAAATTTA
1 TTAAATTTATTATAAATTTAAATTTA
10662 AAATTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
TTAAATTTATTATAAATTTAAATTTAT
Found at i:10671 original size:17 final size:17
Alignment explanation
Indices: 10621--10675 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
10611 AAGTTTATTC
*
10621 TAAATTT-AAATTTATT
1 TAAATTTAAAATTAATT
** *
10637 TAAATTTATTATAAATT
1 TAAATTTAAAATTAATT
*
10654 TAAATTTAAAATTCATT
1 TAAATTTAAAATTAATT
10671 TAAAT
1 TAAAT
10676 AATGTCTAGT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
16 7 0.23
17 23 0.77
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TAAATTTAAAATTAATT
Found at i:12525 original size:29 final size:29
Alignment explanation
Indices: 12481--12820 Score: 385
Period size: 29 Copynumber: 11.6 Consensus size: 29
12471 CCCTAAACGA
* *
12481 TCCAAAAATTCTATTTTTACCCCCGAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
* **
12510 TCCAAAAATCCCATTTTTGACCCTAAAACT
1 TCCAAAAATTCCATTTTT-ACCCCCAAACT
*
12540 TCCAAAAATTCCATTTTTACCCCCGAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
* * *
12569 TCCAAAAATCCCATTTTTGACCTCAAAACT
1 TCCAAAAATTCCATTTTT-ACCCCCAAACT
* *
12599 TCCAAAAA-TCTCATTTTGACCCCAAAACT
1 TCCAAAAATTC-CATTTTTACCCCCAAACT
* *
12628 TCCAAAAATTCTATTTTTACCCTCAAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
*
12657 TCCAAAAATTCCATTTTTGACCCCGAAACT
1 TCCAAAAATTCCATTTTT-ACCCCCAAACT
*
12687 TCCAAAAATTCCATTTGTACCCCCAAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
* **
12716 TCCAAAAATTCCATTTTGACCCTGAAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
* * *
12745 TCCAAAAATTCTATTTTTACCCTCGAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
* * * **
12774 TCGAAAAATCCCATTTTTGACTCTGAAACT
1 TCCAAAAATTCCATTTTT-ACCCCCAAACT
12804 TCCAAAAATTACCATTT
1 TCCAAAAATT-CCATTT
12821 CACCCTCGAG
Statistics
Matches: 263, Mismatches: 41, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
29 166 0.63
30 91 0.35
31 6 0.02
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCCCCAAACT
Found at i:12826 original size:88 final size:89
Alignment explanation
Indices: 12481--12820 Score: 433
Period size: 88 Copynumber: 3.9 Consensus size: 89
12471 CCCTAAACGA
* * *
12481 TCCAAAAATTCTATTTTT-ACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTAAAACTTCCAA
1 TCCAAAAATTCCATTTTTGACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAA
*
12545 AAATTCCATTTTTACCCCCG-AACT
66 AAATTCCATTTTTA-CCCTGAAACT
* * *
12569 TCCAAAAATCCCATTTTTGA-CCTCAAAACTTCCAAAAATCTCA-TTTTGACCCCAAAACTTCCA
1 TCCAAAAATTCCATTTTTGACCCTC-GAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCA
* *
12632 AAAATTCTATTTTTACCCTCAAACT
65 AAAATTCCATTTTTACCCTGAAACT
* * *
12657 TCCAAAAATTCCATTTTTGACCC-CGAAACTTCCAAAAATTCCATTTGT-ACCCCCAAACTTCCA
1 TCCAAAAATTCCATTTTTGACCCTCG-AACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCA
*
12720 AAAATTCCATTTTGACCCTGAAACT
65 AAAATTCCATTTTTACCCTGAAACT
* * * **
12745 TCCAAAAATTCTATTTTT-ACCCTCGAACTTCGAAAAATCCCATTTTTGACTCTGAAACTTCCAA
1 TCCAAAAATTCCATTTTTGACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAA
12809 AAATTACCATTT
66 AAATT-CCATTT
12821 CACCCTCGAG
Statistics
Matches: 218, Mismatches: 25, Indels: 17
0.84 0.10 0.07
Matches are distributed among these distances:
87 26 0.12
88 164 0.75
89 28 0.13
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (89 bp):
TCCAAAAATTCCATTTTTGACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAA
AAATTCCATTTTTACCCTGAAACT
Found at i:12829 original size:59 final size:58
Alignment explanation
Indices: 12481--12820 Score: 398
Period size: 59 Copynumber: 5.8 Consensus size: 58
12471 CCCTAAACGA
* * * * *
12481 TCCAAAAATTCTATTTTTACCCCCG-AACTTCCAAAAATCCCATTTTTGACCCTAAAACT
1 TCCAAAAATCCCATTTTGA-CCCCGAAACTTCCAAAAATTCCATTTTT-ACCCTCAAACT
* * *
12540 TCCAAAAATTCCATTTTTACCCCCG-AACTTCCAAAAATCCCATTTTTGA-CCTCAAAACT
1 TCCAAAAATCCCATTTTGA-CCCCGAAACTTCCAAAAATTCCATTTTT-ACCCTC-AAACT
* * *
12599 TCCAAAAATCTCATTTTGACCCCAAAACTTCCAAAAATTCTATTTTTACCCTCAAACT
1 TCCAAAAATCCCATTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACT
* * *
12657 TCCAAAAATTCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTGTACCCCCAAACT
1 TCCAAAAATCCCA-TTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACT
* * * *
12716 TCCAAAAATTCCATTTTGACCCTGAAACTTCCAAAAATTCTATTTTTACCCTCGAACT
1 TCCAAAAATCCCATTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACT
* * *
12774 TCGAAAAATCCCATTTTTGACTCTGAAACTTCCAAAAATTACCATTT
1 TCCAAAAATCCCA-TTTTGACCCCGAAACTTCCAAAAATT-CCATTT
12821 CACCCTCGAG
Statistics
Matches: 252, Mismatches: 23, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
58 75 0.30
59 172 0.68
60 5 0.02
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (58 bp):
TCCAAAAATCCCATTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCAAACT
Found at i:12836 original size:29 final size:29
Alignment explanation
Indices: 12804--12868 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
12794 CTCTGAAACT
*
12804 TCCAAAAATTACCATTTCACCCTCGAGAA
1 TCCAAAAATTACCATTTCACCCCCGAGAA
** *
12833 TCC-AAAATTACCATTTTGCCCCCGAGTA
1 TCCAAAAATTACCATTTCACCCCCGAGAA
12861 TCCAAAAA
1 TCCAAAAA
12869 GTCTCATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 24 0.77
29 7 0.23
ACGTcount: A:0.37, C:0.31, G:0.08, T:0.25
Consensus pattern (29 bp):
TCCAAAAATTACCATTTCACCCCCGAGAA
Found at i:15901 original size:15 final size:15
Alignment explanation
Indices: 15881--15929 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
15871 GCGATAAACA
15881 ACACAGAATAATATC
1 ACACAGAATAATATC
*
15896 ACACAG-ATAACA-C
1 ACACAGAATAATATC
15909 A-ACAGAAAATAATATC
1 ACACAG--AATAATATC
15925 ACACA
1 ACACA
15930 AGGTGTGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
12 4 0.15
13 2 0.07
14 5 0.19
15 11 0.41
16 2 0.07
17 3 0.11
ACGTcount: A:0.57, C:0.22, G:0.06, T:0.14
Consensus pattern (15 bp):
ACACAGAATAATATC
Found at i:15919 original size:29 final size:28
Alignment explanation
Indices: 15873--15929 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
15863 ATCAACGTGC
*
15873 GATAAACAACACAGAATAATATCACACA
1 GATAAACAACACAAAATAATATCACACA
*
15901 GATAACACAACAGAAAATAATATCACACA
1 GATAA-ACAACACAAAATAATATCACACA
15930 AGGTGTGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.58, C:0.21, G:0.07, T:0.14
Consensus pattern (28 bp):
GATAAACAACACAAAATAATATCACACA
Found at i:19857 original size:18 final size:18
Alignment explanation
Indices: 19834--19882 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
19824 TTATCAAAAA
*
19834 TTTCTTTCTTTTTTTCTT
1 TTTCTTTCTTTTTTTCAT
*
19852 TTTCTTCCTTTTTTTCAT
1 TTTCTTTCTTTTTTTCAT
*
19870 TTTGTTTCTTTTT
1 TTTCTTTCTTTTT
19883 CAAATGACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTCTTTCTTTTTTTCAT
Found at i:19877 original size:10 final size:8
Alignment explanation
Indices: 19838--19882 Score: 54
Period size: 9 Copynumber: 5.1 Consensus size: 8
19828 CAAAAATTTC
19838 TTTCTTTT
1 TTTCTTTT
19846 TTTCTTTT
1 TTTCTTTT
19854 TCTTCCTTTT
1 T-TT-CTTTT
19864 TTTCATTTT
1 TTTC-TTTT
19873 GTTTCTTTT
1 -TTTCTTTT
19882 T
1 T
19883 CAAATGACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 11 0.33
9 12 0.36
10 10 0.30
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTCTTTT
Found at i:29537 original size:7 final size:7
Alignment explanation
Indices: 29525--29551 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
29515 TCTTGATGAT
29525 TTCTTCA
1 TTCTTCA
29532 TTCTTCA
1 TTCTTCA
29539 TTCTTCA
1 TTCTTCA
29546 TTCTTC
1 TTCTTC
29552 TATTTATAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.30, G:0.00, T:0.59
Consensus pattern (7 bp):
TTCTTCA
Found at i:50013 original size:81 final size:81
Alignment explanation
Indices: 49878--50037 Score: 277
Period size: 80 Copynumber: 2.0 Consensus size: 81
49868 TAAATCAACT
* *
49878 ACTCGAATAAATAATCCCCATTTTTTTAGTGAAAAAGCTTTGGACCTAATAAAAAAATATTCATT
1 ACTCGAATAAATAATCCCCATTTTTTCAGTGAAAAAGCTTTGGACCGAATAAAAAAATATTCATT
49943 TAATAAATCAAATAAA
66 TAATAAATCAAATAAA
* *
49959 ACTCGAATAAATAATCCCCA-TTTTTCAGTGAAAAAGCTTTGGACCGGATAAAAAATTATTCATT
1 ACTCGAATAAATAATCCCCATTTTTTCAGTGAAAAAGCTTTGGACCGAATAAAAAAATATTCATT
50023 TAATAAATCAAATAA
66 TAATAAATCAAATAA
50038 TCATAAGATA
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
80 55 0.73
81 20 0.27
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (81 bp):
ACTCGAATAAATAATCCCCATTTTTTCAGTGAAAAAGCTTTGGACCGAATAAAAAAATATTCATT
TAATAAATCAAATAAA
Found at i:51031 original size:2 final size:2
Alignment explanation
Indices: 51024--51053 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
51014 CAACATTTCT
51024 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
51054 ATTAATAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64843 original size:22 final size:22
Alignment explanation
Indices: 64816--64864 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
64806 TTAAAATTAT
64816 TAAATA-TTAAAATAAAATAAAA
1 TAAATATTTAAAA-AAAATAAAA
*
64838 TAAATATTTTAAAAAAATAAAA
1 TAAATATTTAAAAAAAATAAAA
64860 -AAATA
1 TAAATA
64865 ATATTGGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 5 0.20
22 15 0.60
23 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAATATTTAAAAAAAATAAAA
Found at i:65733 original size:21 final size:19
Alignment explanation
Indices: 65704--65838 Score: 84
Period size: 21 Copynumber: 7.0 Consensus size: 19
65694 ATAAAAATAA
*
65704 AAAATATTTTTCAAAAATT
1 AAAATATTTTTAAAAAATT
*
65723 AAAATTAATTTTT--AAATTT
1 AAAA-T-ATTTTTAAAAAATT
*
65742 AAAATATTTATAAAAAATT
1 AAAATATTTTTAAAAAATT
*
65761 CAAATTTATGTTTTAAAAAATAT
1 -AAA-ATAT-TTTTAAAAAAT-T
*
65784 ATAAAAATTTTTAAAAAATCT
1 A-AAATATTTTTAAAAAAT-T
* * *
65805 AAAAAATATATAAAAAA-T
1 AAAATATTTTTAAAAAATT
65823 -AAA-A-TTTTAAAAAATT
1 AAAATATTTTTAAAAAATT
65839 CTAAAATAAT
Statistics
Matches: 94, Mismatches: 12, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
15 8 0.09
16 2 0.02
17 8 0.09
18 2 0.02
19 18 0.19
20 18 0.19
21 22 0.23
22 13 0.14
23 3 0.03
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (19 bp):
AAAATATTTTTAAAAAATT
Found at i:65734 original size:20 final size:20
Alignment explanation
Indices: 65696--65734 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
65686 TTACAAAAAT
*
65696 AAAAATAAAAAATATTTTTC
1 AAAAATAAAAAATAATTTTC
* *
65716 AAAAATTAAAATTAATTTT
1 AAAAATAAAAAATAATTTT
65735 TAAATTTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAAATAAAAAATAATTTTC
Found at i:65758 original size:38 final size:39
Alignment explanation
Indices: 65704--65777 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 39
65694 ATAAAAATAA
* *
65704 AAAATATTTTTCAAAAATTAAAATTAAT-TTTTAAATTT
1 AAAATATTTATAAAAAATTAAAATTAATGTTTTAAATTT
* *
65742 AAAATATTTATAAAAAATTCAAATTTATGTTTTAAA
1 AAAATATTTATAAAAAATTAAAATTAATGTTTTAAA
65778 AAATATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 24 0.77
39 7 0.23
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (39 bp):
AAAATATTTATAAAAAATTAAAATTAATGTTTTAAATTT
Found at i:65790 original size:11 final size:11
Alignment explanation
Indices: 65774--65823 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 11
65764 ATTTATGTTT
65774 TAAAAAATATA
1 TAAAAAATATA
*
65785 T-AAAAAT-TT
1 TAAAAAATATA
* *
65794 TTAAAAA-ATC
1 TAAAAAATATA
65804 TAAAAAATATA
1 TAAAAAATATA
65815 TAAAAAATA
1 TAAAAAATA
65824 AAATTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 2 0.06
10 18 0.56
11 12 0.38
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAAAAATATA
Found at i:65794 original size:20 final size:20
Alignment explanation
Indices: 65771--65823 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
65761 CAAATTTATG
65771 TTTTAAAAAATATATAAAAAT
1 TTTTAAAAAATATA-AAAAAT
*
65792 TTTTAAAAAATCTAAAAAAT
1 TTTTAAAAAATATAAAAAAT
* *
65812 ATATAAAAAATA
1 TTTTAAAAAATA
65824 AAATTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
TTTTAAAAAATATAAAAAAT
Found at i:68326 original size:31 final size:31
Alignment explanation
Indices: 68290--68368 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 31
68280 TTTTGAGTCC
*
68290 AATTTGGTACTTAAACTTGATACT-TTTTTCT
1 AATTTGGTACTTAAACTTGACACTCTTTTT-T
* * *
68321 AATTTGATACCT-AACTCGACACTCTTTTTT
1 AATTTGGTACTTAAACTTGACACTCTTTTTT
*
68351 AATTTGGTATTTAAACTT
1 AATTTGGTACTTAAACTT
68369 TTTTGGATCT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
30 19 0.50
31 19 0.50
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (31 bp):
AATTTGGTACTTAAACTTGACACTCTTTTTT
Found at i:68407 original size:58 final size:59
Alignment explanation
Indices: 68318--68431 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 59
68308 GATACTTTTT
* *
68318 TCTAATTTGATACCTAACTCGACACTCTTTTT-TAATTTGGTATTTAAACTTTTTTGGA
1 TCTAATTTGATACCTAACTCGACACTCTTTTTCTAATTTAGTACTTAAACTTTTTTGGA
* * * *
68376 TCTAATTTGATACCTGAACTTGAC-TTTTTTTTCTAATTTAGTACTTAATCTTTTTT
1 TCTAATTTGATACCT-AACTCGACACTCTTTTTCTAATTTAGTACTTAAACTTTTTT
68432 TAATATTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 21 0.44
59 27 0.56
ACGTcount: A:0.25, C:0.15, G:0.09, T:0.52
Consensus pattern (59 bp):
TCTAATTTGATACCTAACTCGACACTCTTTTTCTAATTTAGTACTTAAACTTTTTTGGA
Found at i:68620 original size:29 final size:29
Alignment explanation
Indices: 68588--68677 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 29
68578 AACTGAATCT
*
68588 AAAAAAAATTAGGTACCAAATTAGGAAAA
1 AAAAAAAATTAAGTACCAAATTAGGAAAA
* * * *
68617 AAAACCAAGTTCAAGTACCAAATTGGGTAAA
1 AAAA-AAAATT-AAGTACCAAATTAGGAAAA
**
68648 AAAAAAGTTTAAGTACCAAATTA-GAAAA
1 AAAAAAAATTAAGTACCAAATTAGGAAAA
68676 AA
1 AA
68678 GTGTCAAGTT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
28 6 0.12
29 16 0.33
30 7 0.14
31 20 0.41
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (29 bp):
AAAAAAAATTAAGTACCAAATTAGGAAAA
Found at i:68636 original size:31 final size:30
Alignment explanation
Indices: 68600--68729 Score: 117
Period size: 31 Copynumber: 4.4 Consensus size: 30
68590 AAAAAATTAG
68600 GTACCAAATTAGGAAAAAAAACCAAGTTCAA
1 GTACCAAATTAGGAAAAAAAA-CAAGTTCAA
* * *
68631 GTACCAAATTGGGTAAAAAAA-AAGTTTAA
1 GTACCAAATTAGGAAAAAAAACAAGTTCAA
**
68660 GTACCAAATTA-GAAAAAAGTGTCAAGTTCAA
1 GTACCAAATTAGGAAAAAA--AACAAGTTCAA
* * *
68691 GTACC-AATTTGAGTAAAAAAA-AA-TTTAA
1 GTACCAAATTAG-GAAAAAAAACAAGTTCAA
68719 GTACCAAATTA
1 GTACCAAATTA
68730 AAAAATATAT
Statistics
Matches: 79, Mismatches: 14, Indels: 14
0.74 0.13 0.13
Matches are distributed among these distances:
28 15 0.19
29 23 0.29
30 4 0.05
31 31 0.39
32 6 0.08
ACGTcount: A:0.52, C:0.12, G:0.14, T:0.23
Consensus pattern (30 bp):
GTACCAAATTAGGAAAAAAAACAAGTTCAA
Found at i:68677 original size:60 final size:59
Alignment explanation
Indices: 68588--68734 Score: 199
Period size: 60 Copynumber: 2.5 Consensus size: 59
68578 AACTGAATCT
* * *
68588 AAAAAAAA-TTAGGTACCAAATTAGGAAAAAAAACCAAGTTCAAGTACCAAATTGGGTA
1 AAAAAAAATTTAAGTACCAAATTAGAAAAAAAAACCAAGTTCAAGTACCAAATTGAGTA
**** *
68646 AAAAAAAAGTTTAAGTACCAAATTAGAAAAAAGTGTCAAGTTCAAGTACCAATTTGAGTA
1 AAAAAAAA-TTTAAGTACCAAATTAGAAAAAAAAACCAAGTTCAAGTACCAAATTGAGTA
68706 AAAAAAAATTTAAGTACCAAATTA-AAAAA
1 AAAAAAAATTTAAGTACCAAATTAGAAAAA
68735 TATATATTAA
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
58 13 0.16
59 16 0.20
60 50 0.63
ACGTcount: A:0.55, C:0.10, G:0.13, T:0.22
Consensus pattern (59 bp):
AAAAAAAATTTAAGTACCAAATTAGAAAAAAAAACCAAGTTCAAGTACCAAATTGAGTA
Found at i:68750 original size:60 final size:60
Alignment explanation
Indices: 68588--68759 Score: 192
Period size: 60 Copynumber: 2.9 Consensus size: 60
68578 AACTGAATCT
* * * *
68588 AAAAAAAA--TTAGGTACCAAATTAGGAAAAAAA-ACCAAGTTCAAGTACCAAATTGGGTA
1 AAAAAAAAGTTTAAGTACCAAATTA-GAAAAAAATATCAAATTCAAGTACCAAATTGAGTA
* * * *
68646 AAAAAAAAGTTTAAGTACCAAATTAGAAAAAAGTGTCAAGTTCAAGTACCAATTTGAGTA
1 AAAAAAAAGTTTAAGTACCAAATTAGAAAAAAATATCAAATTCAAGTACCAAATTGAGTA
* *
68706 AAAAAAAA-TTTAAGTACCAAATTA-AAAAATATATATTAAATTCAAATACCAAAT
1 AAAAAAAAGTTTAAGTACCAAATTAGAAAAA-A-ATATCAAATTCAAGTACCAAAT
68760 GTTATATTAA
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
58 13 0.13
59 24 0.25
60 60 0.62
ACGTcount: A:0.55, C:0.10, G:0.11, T:0.24
Consensus pattern (60 bp):
AAAAAAAAGTTTAAGTACCAAATTAGAAAAAAATATCAAATTCAAGTACCAAATTGAGTA
Found at i:69283 original size:142 final size:138
Alignment explanation
Indices: 69116--69409 Score: 346
Period size: 142 Copynumber: 2.1 Consensus size: 138
69106 ATTTTGAGAC
** *
69116 AAAAACATTTTTAAACAAATTGTTTTTTGAA-AG-AAAAAATGCTTCTTCC-AAACTAAAAA-TT
1 AAAAACATTCCTAAACAAACTGTTTTTT-AAGAGAAAAAAATGCTTC-TCCTAAA-TAAAAATTT
* ** * * * *
69177 GGCCTAAATTCACTTTTTTTTAAAAGA-TAAAAATTTTAACTTCTTTTCAAAAATGTTTTTTTTT
63 GACCTAAAAACAC-TTTTTCTAAAA-ATTAAAAATTTTAACTTC-TCT-AAAAAT-ATTTTTTCT
* * *
69241 TTCAAAAAATATTTTTG
123 CTC-AAAAATACTTTTA
*
69258 AAAAATATTCCTAAACAAACTGTTTTTTAAGAGAAAAAAATGCTTCTCCTAAATAAAAATTTGAC
1 AAAAACATTCCTAAACAAACTGTTTTTTAAGAGAAAAAAATGCTTCTCCTAAATAAAAATTTGAC
69323 CTAAAAACACTTTTTCTAAAAATTAAAAATTTTAACTTCTCTAAAAATATTTTTTCTCTCAAAAA
66 CTAAAAACACTTTTTCTAAAAATTAAAAATTTTAACTTCTCTAAAAATATTTTTTCTCTCAAAAA
69388 TACTTTTA
131 TACTTTTA
69396 AAAAACATTCCTAA
1 AAAAACATTCCTAA
69410 GGCAAAAAAT
Statistics
Matches: 132, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
138 24 0.18
139 9 0.07
140 6 0.05
141 5 0.04
142 61 0.46
143 27 0.20
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.39
Consensus pattern (138 bp):
AAAAACATTCCTAAACAAACTGTTTTTTAAGAGAAAAAAATGCTTCTCCTAAATAAAAATTTGAC
CTAAAAACACTTTTTCTAAAAATTAAAAATTTTAACTTCTCTAAAAATATTTTTTCTCTCAAAAA
TACTTTTA
Found at i:69379 original size:17 final size:19
Alignment explanation
Indices: 69359--69394 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
69349 AAATTTTAAC
69359 TTCTCT-AAAAATA-TTTT
1 TTCTCTCAAAAATACTTTT
69376 TTCTCTCAAAAATACTTTT
1 TTCTCTCAAAAATACTTTT
69395 AAAAAACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (19 bp):
TTCTCTCAAAAATACTTTT
Found at i:69581 original size:25 final size:25
Alignment explanation
Indices: 69527--69584 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
69517 GTAAGAAGGA
* * *
69527 AACAAAAAGTTGGTTGTTGAATGTG
1 AACACAAAGTTGGATGTGGAATGTG
69552 AACACAAAGTTGGATGTGGAATGTG
1 AACACAAAGTTGGATGTGGAATGTG
69577 AACACAAA
1 AACACAAA
69585 TGTTATGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (25 bp):
AACACAAAGTTGGATGTGGAATGTG
Found at i:70518 original size:31 final size:31
Alignment explanation
Indices: 70483--70553 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
70473 TGGAGTCAAG
**
70483 ACTAAAATTTTA-AATTTTGAAAAGTACAAAA
1 ACTAAAATTTTACAA-TTCAAAAAGTACAAAA
70514 ACTAAAA-TTTACCAATTCAAAAAGTACAAAA
1 ACTAAAATTTTA-CAATTCAAAAAGTACAAAA
*
70545 ATTAAAATT
1 ACTAAAATT
70554 AATCAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 4 0.12
31 27 0.79
32 3 0.09
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.30
Consensus pattern (31 bp):
ACTAAAATTTTACAATTCAAAAAGTACAAAA
Found at i:70567 original size:31 final size:31
Alignment explanation
Indices: 70502--70567 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
70492 TTAAATTTTG
* * *
70502 AAAAGTACAAAAACTAAAATTTACCAATTCA
1 AAAAGTACAAAAACTAAAATTAACCAAATAA
* *
70533 AAAAGTACAAAAATTAAAATTAATCAAATAA
1 AAAAGTACAAAAACTAAAATTAACCAAATAA
70564 AAAA
1 AAAA
70568 TATAAAGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.65, C:0.11, G:0.03, T:0.21
Consensus pattern (31 bp):
AAAAGTACAAAAACTAAAATTAACCAAATAA
Found at i:73913 original size:364 final size:365
Alignment explanation
Indices: 73240--73969 Score: 1311
Period size: 364 Copynumber: 2.0 Consensus size: 365
73230 CTATACATTG
* *
73240 ATGCAAGTTTTCAATAATAATATAAGAATTGTTTAACCTCATGTAATGATATAATTGTTAAAAGT
1 ATGCAAGTTTTCAATAATAATATAAGAATTGTTTAACCCCATGTAATGATATAATGGTTAAAAGT
73305 GTTTATCATTTCAGGTGTGACATGAGTTTAAAGCGCTCTAATCACGTTTATTGTTCAGGCTTTTA
66 GTTTATCATTTCAGGTGTGACATGAGTTTAAAGCGCTCTAATCACGTTTATTGTTCAGGCTTTTA
73370 CTATATTATTGTAATTCACCAAAAAAAAAAATAAGAATTACTAATTCTGTTAATTAAGTTATAAA
131 CTATATTATTGTAATTCACC-AAAAAAAAAATAAGAATTACTAATTCTGTTAATTAAGTTATAAA
* *
73435 GTGCAACGAAAATTTTAATCCTCATCATATATAAATGGTGGGTATGGAAATGTGGAATGTGAGTC
195 GTGCAACGAAAAATTTAATCCTCATCATATACAAATGGTGGGTATGGAAATGTGGAATGTGAGTC
* **
73500 ATTTACTTCATTAGGGTAGGTGGAAGACTGTTGAATTCGGTGTCTTAAGTGTAGTATTTTCGTCT
260 ATTTACTTCATTAGGGTAGGTGGAAGACTGTTGAATCCGGTACCTTAAGTGTAGTATTTTCGTCT
*
73565 ATGTATACTTGTAATTTTTTGAACAAATATATTAATAAAAT
325 ATGTATACTTGTAATTTTTCGAACAAATATATTAATAAAAT
73606 ATGCAAGTTTTCAATAATAATATAAGAATTGTTTAACCCCATGTAATGATATAATGGTTAAAAGT
1 ATGCAAGTTTTCAATAATAATATAAGAATTGTTTAACCCCATGTAATGATATAATGGTTAAAAGT
* * * *
73671 GTTTATCGTTTCAGGTGTGACATGAGTTTAAATCGCTCTAATCATGTTTGTTGTTC-GGACTTTT
66 GTTTATCATTTCAGGTGTGACATGAGTTTAAAGCGCTCTAATCACGTTTATTGTTCAGG-CTTTT
*
73735 ACTATATTATTGTAATTCACC-AAAAAAAAATAAGAATTGCTAATTCTGTTAATTAAGTTATAAA
130 ACTATATTATTGTAATTCACCAAAAAAAAAATAAGAATTACTAATTCTGTTAATTAAGTTATAAA
73799 GTGCAACGAAAAATTTAATCCTCATCATATACAAATGGTGGGTATGGAAATGTGGAATGTGAGTC
195 GTGCAACGAAAAATTTAATCCTCATCATATACAAATGGTGGGTATGGAAATGTGGAATGTGAGTC
73864 ATTTACTTCATTAGGGTAGGTGGAAGACTGTTGAATCCGGTACCTTAAGTGTAGTATTTTCGTCT
260 ATTTACTTCATTAGGGTAGGTGGAAGACTGTTGAATCCGGTACCTTAAGTGTAGTATTTTCGTCT
73929 ATGTATACTTGTAATTTTTCGAACAAATATATTAATAAAAT
325 ATGTATACTTGTAATTTTTCGAACAAATATATTAATAAAAT
73970 TATTCATGAA
Statistics
Matches: 350, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
364 207 0.59
365 2 0.01
366 141 0.40
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (365 bp):
ATGCAAGTTTTCAATAATAATATAAGAATTGTTTAACCCCATGTAATGATATAATGGTTAAAAGT
GTTTATCATTTCAGGTGTGACATGAGTTTAAAGCGCTCTAATCACGTTTATTGTTCAGGCTTTTA
CTATATTATTGTAATTCACCAAAAAAAAAATAAGAATTACTAATTCTGTTAATTAAGTTATAAAG
TGCAACGAAAAATTTAATCCTCATCATATACAAATGGTGGGTATGGAAATGTGGAATGTGAGTCA
TTTACTTCATTAGGGTAGGTGGAAGACTGTTGAATCCGGTACCTTAAGTGTAGTATTTTCGTCTA
TGTATACTTGTAATTTTTCGAACAAATATATTAATAAAAT
Found at i:76882 original size:97 final size:97
Alignment explanation
Indices: 76721--76912 Score: 284
Period size: 97 Copynumber: 2.0 Consensus size: 97
76711 AGGATATTCA
* *
76721 ATTATTTCGATTTGAAGAAAATTCACACCTAGTAAGTTAAGGCACAATTTTTCAAAATCAGAAAT
1 ATTATTTCGATTTGAAGAAAATTCACACCTAGCAAGTTAAGGCACAAATTTTCAAAATCAGAAAT
76786 -AAAGAAACATTGCCTCGA-TTTAAAGGTTTTTG
66 AAAAG-AACATTGCCTCGATTTTAAA-GTTTTTG
*
76818 ATTATTTCGATTTGAAGAAAAATT-GCACCTAGCAAGTTAAGGCACAAATTTTCAAAACTC-GAA
1 ATTATTTCGATTTGAAG-AAAATTCACACCTAGCAAGTTAAGGCACAAATTTTCAAAA-TCAGAA
*
76881 ATAAAAGAATATTGCCTCGATTTTAAAGTTTT
64 ATAAAAGAACATTGCCTCGATTTTAAAGTTTT
76913 CATAAAGATA
Statistics
Matches: 87, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
97 69 0.79
98 18 0.21
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (97 bp):
ATTATTTCGATTTGAAGAAAATTCACACCTAGCAAGTTAAGGCACAAATTTTCAAAATCAGAAAT
AAAAGAACATTGCCTCGATTTTAAAGTTTTTG
Found at i:76937 original size:97 final size:97
Alignment explanation
Indices: 76730--76937 Score: 230
Period size: 97 Copynumber: 2.1 Consensus size: 97
76720 AATTATTTCG
* *
76730 ATTTGAAGAAAATTCACACCTAGTAAGTTAAGGCACAATTTTTCAAAATCAGAAATAAAGAAACA
1 ATTTGAAGAAAATTCACACCTAGCAAGTTAAGGCACAAATTTTCAAAATCAGAAATAAAGAAACA
* * ** *
76795 TTGCCTCGATTTAAAGGTTTTTGATTATTTCG
66 TTGCCTCGATTTAAAGGTTTTTCATAAGATCA
*
76827 ATTTGAAGAAAAATT-GCACCTAGCAAGTTAAGGCACAAATTTTCAAAACTC-GAAATAAA-AGA
1 ATTTGAAG-AAAATTCACACCTAGCAAGTTAAGGCACAAATTTTCAAAA-TCAGAAATAAAGA-A
*
76889 ATATTGCCTCGATTTTAAA-G-TTTTCATAAAGAT-A
63 ACATTGCCTCGA-TTTAAAGGTTTTTCAT-AAGATCA
76923 ATTTTGAAAGAAAAT
1 A-TTTG-AAGAAAAT
76938 GTAAAATTTT
Statistics
Matches: 95, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
96 8 0.08
97 70 0.74
98 17 0.18
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (97 bp):
ATTTGAAGAAAATTCACACCTAGCAAGTTAAGGCACAAATTTTCAAAATCAGAAATAAAGAAACA
TTGCCTCGATTTAAAGGTTTTTCATAAGATCA
Found at i:77154 original size:28 final size:28
Alignment explanation
Indices: 77123--77184 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
77113 AAAATGAGAT
* *
77123 TTTTGGATACCCGAGGGTAAAATGGTAA
1 TTTTGGACACCCGAGGGGAAAATGGTAA
* *
77151 TTTTGGACACTCGGGGGGAAAATGGTAA
1 TTTTGGACACCCGAGGGGAAAATGGTAA
77179 TTTTGG
1 TTTTGG
77185 GAACGTTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.32, T:0.31
Consensus pattern (28 bp):
TTTTGGACACCCGAGGGGAAAATGGTAA
Found at i:77232 original size:59 final size:59
Alignment explanation
Indices: 77169--77484 Score: 340
Period size: 59 Copynumber: 5.4 Consensus size: 59
77159 ACTCGGGGGG
* *** * *
77169 AAAATGGTAATTTTGGGAACGTTCAAGGTCAAAAATGGCATTTTTAGACA-TTCGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGA-AGTTCGAGGGT
** * *
77228 AAAATGGTAA-TTTTAAAAAAATCAAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT
* ***
77286 AAAATGGTAATTTTTAGAAAAATTGGGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT
* * *
77345 AAAATTGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAGTTC-AGAGGT
1 AAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAG-GGT
* * *
77404 AAAATTGTAATTTTTGGAAAAAATCGAGAGT-AAAAATGGAATTTTGGGAGAGTTCGA-GGT
1 AAAATGGTAATTTTTGG-AAAAATCAAG-GTCAAAAATGGAATTTTTGGA-AGTTCGAGGGT
77464 AAAAAATGG-AA-TTTTGGAAAA
1 --AAAATGGTAATTTTTGGAAAA
77485 GTTTCGGGGT
Statistics
Matches: 226, Mismatches: 22, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
57 1 0.00
58 49 0.22
59 124 0.55
60 36 0.16
61 9 0.04
62 7 0.03
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGT
Found at i:77241 original size:28 final size:28
Alignment explanation
Indices: 77134--77242 Score: 94
Period size: 28 Copynumber: 3.8 Consensus size: 28
77124 TTTGGATACC
* *
77134 CGAGGGTAAAATGGTAATTTTGGACACT
1 CGAGGGTAAAATGGTAATTTTAGACATT
* * * *
77162 CGGGGGGAAAATGGTAATTTTGGGAACGTT
1 CGAGGGTAAAATGGTAATTTT-AG-ACATT
* * *
77192 C-AAGGTCAAAAATGGCATTTTTAGACATT
1 CGAGGGT--AAAATGGTAATTTTAGACATT
77221 CGAGGGTAAAATGGTAATTTTA
1 CGAGGGTAAAATGGTAATTTTA
77243 AAAAAATCAA
Statistics
Matches: 62, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
28 32 0.52
29 9 0.15
30 9 0.15
31 12 0.19
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.29
Consensus pattern (28 bp):
CGAGGGTAAAATGGTAATTTTAGACATT
Found at i:77330 original size:30 final size:28
Alignment explanation
Indices: 77281--77484 Score: 90
Period size: 30 Copynumber: 6.9 Consensus size: 28
77271 TGGAAGTTCG
77281 GGGGT-AAAATGGTAATTTTTAGAAAAATT
1 GGGGTAAAAATGG-AATTTTT-GAAAAATT
* *
77310 GGGGTCAAAAATGGAATTTTTG-GAAGTT
1 GGGGT-AAAAATGGAATTTTTGAAAAATT
* * *
77338 CGAGGGTAAAATTGTAATTTTTGGAAAAATC
1 -G-GGGTAAAAATGGAATTTTT-GAAAAATT
* * *
77369 GAGGTTAAAAATGGAATTTTTG-GAAGTT
1 G-GGGTAAAAATGGAATTTTTGAAAAATT
* * * *
77397 CAGAGGTAAAATTGTAATTTTTGGAAAAAATC
1 --GGGGTAAAAATGGAATTTTT-G-AAAAATT
* * * * *
77429 GAGAGTAAAAATGGAATTTTGGGAGAGTT
1 G-GGGTAAAAATGGAATTTTTGAAAAATT
* *
77458 CGAGGTAAAAAATGGAATTTTGGAAAA
1 -GGGGT-AAAAATGGAATTTTTGAAAA
77485 GTTTCGGGGT
Statistics
Matches: 128, Mismatches: 33, Indels: 27
0.68 0.18 0.14
Matches are distributed among these distances:
28 7 0.05
29 41 0.32
30 53 0.41
31 24 0.19
32 3 0.02
ACGTcount: A:0.40, C:0.03, G:0.26, T:0.31
Consensus pattern (28 bp):
GGGGTAAAAATGGAATTTTTGAAAAATT
Found at i:77419 original size:29 final size:28
Alignment explanation
Indices: 77266--77467 Score: 145
Period size: 29 Copynumber: 6.8 Consensus size: 28
77256 CAAAAATGGG
* *
77266 ATTTTTGGAAGTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTC-GAGGTAAAATTGTA
* * * * *
77295 ATTTTTAGAAAAATT-GGGGTCAAAAATGGA
1 ATTTTT-G-GAAGTTCGAGGT-AAAATTGTA
77325 ATTTTTGGAAGTTCGAGGGTAAAATTGTA
1 ATTTTTGGAAGTTCGA-GGTAAAATTGTA
** * *
77354 ATTTTTGGAAAAATCGAGGTTAAAAATGGA
1 ATTTTTGG-AAGTTCGAGG-TAAAATTGTA
77384 ATTTTTGGAAGTTCAGAGGTAAAATTGTA
1 ATTTTTGGAAGTTC-GAGGTAAAATTGTA
** * *
77413 ATTTTTGGAAAAAATCGAGAGTAAAAATGGA
1 ATTTTTGG--AAGTTCGAG-GTAAAATTGTA
*
77444 ATTTTGGGAGAGTTCGAGGTAAAA
1 ATTTTTGGA-AGTTCGAGGTAAAA
77468 AATGGAATTT
Statistics
Matches: 136, Mismatches: 25, Indels: 24
0.74 0.14 0.13
Matches are distributed among these distances:
28 4 0.03
29 57 0.42
30 51 0.38
31 24 0.18
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (28 bp):
ATTTTTGGAAGTTCGAGGTAAAATTGTA
Found at i:77500 original size:30 final size:30
Alignment explanation
Indices: 77316--77487 Score: 135
Period size: 30 Copynumber: 5.8 Consensus size: 30
77306 AATTGGGGTC
77316 AAAAATGGAATTTTTGG--AAGTTCGAGGGT-
1 AAAAATGGAA-TTTTGGAAAAGTTCGA-GGTA
* * * *
77345 AAAATTGTAATTTTTGGAAAA-ATCGAGGTT
1 AAAAATGGAA-TTTTGGAAAAGTTCGAGGTA
77375 AAAAATGGAATTTTTGG--AAGTTCAGAGGT-
1 AAAAATGGAA-TTTTGGAAAAGTTC-GAGGTA
* * **
77404 AAAATTGTAATTTTTGGAAAAAATCGAGAGT-
1 AAAAATGGAA-TTTTGGAAAAGTTCGAG-GTA
* *
77435 AAAAATGGAATTTTGGGAGAGTTCGAGGTA
1 AAAAATGGAATTTTGGAAAAGTTCGAGGTA
77465 AAAAATGGAATTTTGGAAAAGTT
1 AAAAATGGAATTTTGGAAAAGTT
77488 TCGGGGTCAA
Statistics
Matches: 116, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
28 2 0.02
29 37 0.32
30 61 0.53
31 16 0.14
ACGTcount: A:0.40, C:0.03, G:0.26, T:0.31
Consensus pattern (30 bp):
AAAAATGGAATTTTGGAAAAGTTCGAGGTA
Found at i:78637 original size:3 final size:3
Alignment explanation
Indices: 78631--78675 Score: 63
Period size: 3 Copynumber: 14.3 Consensus size: 3
78621 TAAAAAAAGA
*
78631 TAT TAT TAT TAT TAA TAT TAT TGAT TAT TAT TGAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT T-AT TAT TAT TAT T
78676 TAATGTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:78661 original size:10 final size:9
Alignment explanation
Indices: 78631--78675 Score: 63
Period size: 10 Copynumber: 4.8 Consensus size: 9
78621 TAAAAAAAGA
78631 TATTATTAT
1 TATTATTAT
*
78640 TATTAATAT
1 TATTATTAT
78649 TATTGATTAT
1 TATT-ATTAT
78659 TATTGATTAT
1 TATT-ATTAT
78669 TATTATT
1 TATTATT
78676 TAATGTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 15 0.45
10 18 0.55
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (9 bp):
TATTATTAT
Found at i:79434 original size:17 final size:15
Alignment explanation
Indices: 79412--79470 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 15
79402 ATTAAAATTA
79412 AAATTTAAAACCATTTT
1 AAATTTAAAA-CA-TTT
79429 AAATTTAACTAA-ATTT
1 AAATTTAA--AACATTT
79445 AAATTTAAAACAAGTTT
1 AAATTTAAAAC-A-TTT
79462 AAATTTAAA
1 AAATTTAAA
79471 TTCAGAAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 2 0.05
16 12 0.32
17 21 0.57
19 2 0.05
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.39
Consensus pattern (15 bp):
AAATTTAAAACATTT
Found at i:79449 original size:33 final size:33
Alignment explanation
Indices: 79406--79469 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
79396 TTTCAAATTA
* *
79406 AAATTAAAATTTAAAACCATTTTAAATTTAACT
1 AAATTAAAATTTAAAACAAGTTTAAATTTAACT
*
79439 AAATTTAAATTTAAAACAAGTTTAAATTTAA
1 AAATTAAAATTTAAAACAAGTTTAAATTTAA
79470 ATTCAGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (33 bp):
AAATTAAAATTTAAAACAAGTTTAAATTTAACT
Found at i:79589 original size:17 final size:17
Alignment explanation
Indices: 79566--79675 Score: 132
Period size: 17 Copynumber: 6.4 Consensus size: 17
79556 GATTTTATTT
*
79566 ATTTAAATTTATAATAA
1 ATTTAAATTTAAAATAA
*
79583 TTTTAAATTTAAAAATAA
1 ATTTAAATTT-AAAATAA
* *
79601 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAAATAA
79618 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
* * *
79635 ATCTAAATTTAAGACAA
1 ATTTAAATTTAAAATAA
79652 ATTT-AATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
79669 ATTTAAA
1 ATTTAAA
79676 AATGAGTTTG
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
16 3 0.04
17 58 0.75
18 16 0.21
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:79593 original size:6 final size:6
Alignment explanation
Indices: 79566--79646 Score: 71
Period size: 6 Copynumber: 14.0 Consensus size: 6
79556 GATTTTATTT
* ** *
79566 ATTTAA ATTTATA A--TAA TTTTAA ATTTAA AAATAA ATTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
79613 A-TTAA ATTTAA ATTTAA A-ATAA ATCTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
79647 GACAAATTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
4 1 0.02
5 11 0.18
6 46 0.77
7 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:79641 original size:23 final size:23
Alignment explanation
Indices: 79598--79646 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
79588 AATTTAAAAA
*
79598 TAAATTTAAACTTAAATTAAATT
1 TAAATTTAAACATAAATTAAATT
79621 TAAATTTAAA-ATAAATCTAAATT
1 TAAATTTAAACATAAAT-TAAATT
79644 TAA
1 TAA
79647 GACAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAATTTAAACATAAATTAAATT
Found at i:88621 original size:25 final size:25
Alignment explanation
Indices: 88585--88641 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
88575 GTCGTGCCAA
*
88585 TCACATTGTTGTTAAGGCTTTACCT
1 TCACATTATTGTTAAGGCTTTACCT
88610 TCACATTATTGTTAAGGCTTTACCT
1 TCACATTATTGTTAAGGCTTTACCT
*
88635 TCCCATT
1 TCACATT
88642 GTAATTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (25 bp):
TCACATTATTGTTAAGGCTTTACCT
Found at i:96855 original size:101 final size:98
Alignment explanation
Indices: 96733--96922 Score: 258
Period size: 99 Copynumber: 1.9 Consensus size: 98
96723 AAACCTATAG
* *
96733 TAGTATATATAAACATTAAAAAAATGTTAAAATGAC-CATATATAAAATTTTAATAACTAAAAAT
1 TAGTATATATAAACATT--AAAAATATTAAAATGACAC-TATATAAAATTTTAATAAATAAAAAT
96797 ATTAAATGAAAAATAA-TATAAATATATTGTTAATAC
63 ATTAAATGAAAAA-AATTATAAATATATTGTTAATAC
* * *
96833 TAGTATGATGTAAACATTAAAAATATTAAGATGATACTATATAAAATTTTAATAAATAAAAATAT
1 TAGTAT-ATATAAACATTAAAAATATTAAAATGACACTATATAAAATTTTAATAAATAAAAATAT
* *
96898 TAAATTAAAAAAATTATATATATAT
65 TAAATGAAAAAAATTATAAATATAT
96923 ATATATATTT
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
98 2 0.03
99 61 0.76
100 7 0.09
101 10 0.12
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (98 bp):
TAGTATATATAAACATTAAAAATATTAAAATGACACTATATAAAATTTTAATAAATAAAAATATT
AAATGAAAAAAATTATAAATATATTGTTAATAC
Found at i:96905 original size:53 final size:51
Alignment explanation
Indices: 96848--96946 Score: 121
Period size: 51 Copynumber: 1.9 Consensus size: 51
96838 TGATGTAAAC
*
96848 ATTAAAAATATTAAGATGATACTATATA-AAATTTTAATAAATAA-AAATATTAA
1 ATTAAAAAAATT-AGAT-ATA-TATATATAAATTTTAA-AAATAATAAATATTAA
* *
96901 ATTAAAAAAATTATATATATATATATATATTTTAAAAATAATAAAT
1 ATTAAAAAAATTAGATATATATATATAAATTTTAAAAATAATAAAT
96947 TTTTGTTAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
50 12 0.29
51 15 0.37
52 3 0.07
53 11 0.27
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (51 bp):
ATTAAAAAAATTAGATATATATATATAAATTTTAAAAATAATAAATATTAA
Found at i:100434 original size:102 final size:101
Alignment explanation
Indices: 100280--100604 Score: 402
Period size: 102 Copynumber: 3.2 Consensus size: 101
100270 TATACCACAG
* * * * ** *
100280 TATGTGAGCCCAGCTCTAGTTGGATTACCCAATGATTTGCTCCCAGCGCTAGTCGGATAAACCGA
1 TATGTGAGCCCAGCTCTAGTTTGATTAACCAACGATTTGCGCCCAGCGCTAGTCAAATAAACTGA
* **
100345 CGATTATGACACCCAGTGCCTAGCGGATAAATTGCGA
66 CG-TTATGGCACCCAGTGCCTAGCGGATAAACAGCGA
* * *
100382 TATGTGAGCCCAGCTCTGGTTTGATTAACCAACGATTTGCGCCCAGCGCTAGTTAAATAAATTGA
1 TATGTGAGCCCAGCTCTAGTTTGATTAACCAACGATTTGCGCCCAGCGCTAGTCAAATAAACTGA
*
100447 CGGTTATGGCACCCAGTGCCTAGTGGATAAACAGCGA
66 C-GTTATGGCACCCAGTGCCTAGCGGATAAACAGCGA
* * *
100484 TATGTGAGCGCAGCTCTAG-TTGAATTAACCAACGTTTTGCGCCCAGCTCTAGTCAAATAAACTG
1 TATGTGAGCCCAGCTCTAGTTTG-ATTAACCAACGATTTGCGCCCAGCGCTAGTCAAATAAACTG
* * *
100548 ACTGTTATGGCACCCAATGCCTAGCAGATAAACCGCGA
65 AC-GTTATGGCACCCAGTGCCTAGCGGATAAACAGCGA
* *
100586 GA-GTGAGCCCCGCTCTAGT
1 TATGTGAGCCCAGCTCTAGT
100605 CAGTTAAACT
Statistics
Matches: 192, Mismatches: 28, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
101 17 0.09
102 174 0.91
103 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (101 bp):
TATGTGAGCCCAGCTCTAGTTTGATTAACCAACGATTTGCGCCCAGCGCTAGTCAAATAAACTGA
CGTTATGGCACCCAGTGCCTAGCGGATAAACAGCGA
Found at i:101242 original size:136 final size:136
Alignment explanation
Indices: 100906--101274 Score: 628
Period size: 136 Copynumber: 2.8 Consensus size: 136
100896 TTCTTGCTCT
100906 ATATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
1 ATATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
* *
100971 GTTCAATATAATTCACATGGCAAAAAGC--------ATTTATTTATTTCTAGCCACCAAATATGC
66 GTTCAATATAATTCACATAGCAAAAAGCATTTATTTATTTATTTATTTCCAGCCACCAAATATGC
101028 ATATCA
131 ATATCA
101034 ATATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
1 ATATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
101099 GTTCAATATAATTCACATAGCAAAAAGCATTTATTTATTTATTTATTTCCAGCCACCAAATATGC
66 GTTCAATATAATTCACATAGCAAAAAGCATTTATTTATTTATTTATTTCCAGCCACCAAATATGC
*
101164 ATATTA
131 ATATCA
* *
101170 ATATATATAAAAATTCAAATATTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
1 ATATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
*
101235 GTTCAATATAATTCACATAGCACAAAGCATTTATTTATTT
66 GTTCAATATAATTCACATAGCAAAAAGCATTTATTTATTT
101275 TTGTTAATGA
Statistics
Matches: 227, Mismatches: 6, Indels: 8
0.94 0.02 0.03
Matches are distributed among these distances:
128 92 0.41
136 135 0.59
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.38
Consensus pattern (136 bp):
ATATATATAACAATTCAAATCTTTCATTAATCCTTTGTATTCAACTCATTTCAACAATCCAAAAT
GTTCAATATAATTCACATAGCAAAAAGCATTTATTTATTTATTTATTTCCAGCCACCAAATATGC
ATATCA
Found at i:114092 original size:24 final size:24
Alignment explanation
Indices: 114065--114123 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
114055 TTTAGCCCAC
*
114065 ACGAACCCATAATGATTAGCTCTT
1 ACGAACCCAGAATGATTAGCTCTT
* * *
114089 ACGAGCCTAGAATGGTTAGCTCTT
1 ACGAACCCAGAATGATTAGCTCTT
* *
114113 ATGAGCCCAGA
1 ACGAACCCAGA
114124 CAGAGTTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (24 bp):
ACGAACCCAGAATGATTAGCTCTT
Found at i:117619 original size:14 final size:13
Alignment explanation
Indices: 117592--117626 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
117582 AAATACATTT
*
117592 AAATAAAAATATA
1 AAATAAAAAGATA
117605 AAATAGAAAAGATA
1 AAATA-AAAAGATA
117619 AAATAAAA
1 AAATAAAA
117627 TACATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (13 bp):
AAATAAAAAGATA
Found at i:127685 original size:27 final size:24
Alignment explanation
Indices: 127628--127682 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
127618 GGTGGAGGTG
*
127628 TTGGTGGGCTGTTGATGATGTTAC
1 TTGGTGGGCTGTGGATGATGTTAC
127652 TTGGTGGGCTGTGGATGATGTTAC
1 TTGGTGGGCTGTGGATGATGTTAC
127676 TTGGTGG
1 TTGGTGG
127683 TGGAGGTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.11, C:0.07, G:0.42, T:0.40
Consensus pattern (24 bp):
TTGGTGGGCTGTGGATGATGTTAC
Found at i:128498 original size:40 final size:40
Alignment explanation
Indices: 128443--128524 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
128433 AATAAGTTGC
128443 ATTTACTGTTTAGGATATTGGAGAATGTAATCATATCAGT
1 ATTTACTGTTTAGGATATTGGAGAATGTAATCATATCAGT
128483 ATTTACTGTTTAGGATATTGGAGAATGTAATCATATCAGT
1 ATTTACTGTTTAGGATATTGGAGAATGTAATCATATCAGT
128523 AT
1 AT
128525 ATTCAAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (40 bp):
ATTTACTGTTTAGGATATTGGAGAATGTAATCATATCAGT
Found at i:129085 original size:5 final size:5
Alignment explanation
Indices: 129076--129108 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
129066 CTTTTCTTAT
*
129076 TTCTT TTCT- TTCTC TTCTC TTCTC TTCTC TTCT
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC TTCT
129109 TCATTAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (5 bp):
TTCTC
Found at i:134115 original size:42 final size:42
Alignment explanation
Indices: 134052--134612 Score: 664
Period size: 42 Copynumber: 13.4 Consensus size: 42
134042 GAAAACATTT
* * * *
134052 ATTGCATTTAAAGGCCTAGGTGTGAAGGTCCATTTACTTTTC
1 ATTGCATTTAGAGGCCAAGGTGTGGAGGCCCATTTACTTTTC
* * * *
134094 ATCGCATTCAGTGGCCAAGGTGTGGAGACCCATTTACTTTTC
1 ATTGCATTTAGAGGCCAAGGTGTGGAGGCCCATTTACTTTTC
* *
134136 ATTGCATTTACAGGCTCAA-GTGTGGAGGTCCATTTACTTTTC
1 ATTGCATTTAGAGGC-CAAGGTGTGGAGGCCCATTTACTTTTC
* * *
134178 ATTACATTTAGAGGCCCACGG-GTGGAGGTCCATTTACTTTTC
1 ATTGCATTTAGAGG-CCAAGGTGTGGAGGCCCATTTACTTTTC
* * *
134220 ATTGCATTTAGCTGTCC-AGGTGTGGGGGCCCATTTACTTTTC
1 ATTGCATTTAG-AGGCCAAGGTGTGGAGGCCCATTTACTTTTC
* * *
134262 ATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTTCTC
1 ATTGCATTTAGAGGCCAAGGTGTGGAGGCCCATTTACTTTTC
* * **
134304 ATTGCATTTAGAAGCCTAGGTGTAAAGGCCCATTTACTTTTC
1 ATTGCATTTAGAGGCCAAGGTGTGGAGGCCCATTTACTTTTC
* * *
134346 ATTGCATTTAGATGCCCAGGTGTGGATGCCCATTTACTTTTC
1 ATTGCATTTAGAGGCCAAGGTGTGGAGGCCCATTTACTTTTC
* *** *
134388 ATTACATTTAGAGGTTGAGGTGTGGAGGTCCATTTACTTTTC
1 ATTGCATTTAGAGGCCAAGGTGTGGAGGCCCATTTACTTTTC
*
134430 ATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTC
1 ATTGCATTTAGAGGCCAAGGTGTGGAGGCCCATTTACTTTTC
* *
134472 ATTGTATTTAGAGGCCCAA-GTGTGGAGGCTCATTTACTTTTC
1 ATTGCATTTAGAGG-CCAAGGTGTGGAGGCCCATTTACTTTTC
* *
134514 ATTGCATTTAGAGGCCTAA-GTGTGGAGGTCCATTTGCTTTTC
1 ATTGCATTTAGAGGCC-AAGGTGTGGAGGCCCATTTACTTTTC
* * * * *
134556 ATTGCATTTAAAGGCCTAGGTGTGAAGGCCCGTTTACTTTTT
1 ATTGCATTTAGAGGCCAAGGTGTGGAGGCCCATTTACTTTTC
*
134598 ATTGCATTTGGAGGC
1 ATTGCATTTAGAGGC
134613 TTAGGCGTAG
Statistics
Matches: 444, Mismatches: 66, Indels: 18
0.84 0.12 0.03
Matches are distributed among these distances:
41 8 0.02
42 427 0.96
43 9 0.02
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (42 bp):
ATTGCATTTAGAGGCCAAGGTGTGGAGGCCCATTTACTTTTC
Found at i:134285 original size:126 final size:126
Alignment explanation
Indices: 134052--134606 Score: 740
Period size: 126 Copynumber: 4.4 Consensus size: 126
134042 GAAAACATTT
* * * * * *
134052 ATTGCATTTAAAGGCCTAGGTGTGAAGGTCCATTTACTTTTCATCGCATTCAG-TGGCCAAGGTG
1 ATTGCATTTAGAGGCCCAGGTGTGAAGGCCCATTTACTTTTCATTGCATTTAGAT-GCCCAGGTG
* *
134116 TGGAGACCCATTTACTTTTCATTGCATTTACAGGCTCAAGTGTGGAGGTCCATTTACTTTTC
65 TGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCTCAAGTGTGGAGGTCCATTTACTTTTC
* * * * *
134178 ATTACATTTAGAGGCCCACGG-GTGGAGGTCCATTTACTTTTCATTGCATTTAGCTGTCCAGGTG
1 ATTGCATTTAGAGGCCCA-GGTGTGAAGGCCCATTTACTTTTCATTGCATTTAGATGCCCAGGTG
* * *
134242 TGGGGGCCCATTTACTTTTCATTGCATTTAGAGGC-CTAGGTGTGGAGGTCCATTTACTTCTC
65 TGGAGGCCCATTTACTTTTCATTGCATTTAGAGGCTC-AAGTGTGGAGGTCCATTTACTTTTC
* * *
134304 ATTGCATTTAGAAGCCTAGGTGTAAAGGCCCATTTACTTTTCATTGCATTTAGATGCCCAGGTGT
1 ATTGCATTTAGAGGCCCAGGTGTGAAGGCCCATTTACTTTTCATTGCATTTAGATGCCCAGGTGT
* * * * *
134369 GGATGCCCATTTACTTTTCATTACATTTAGAGGTTGAGGTGTGGAGGTCCATTTACTTTTC
66 GGAGGCCCATTTACTTTTCATTGCATTTAGAGGCTCAAGTGTGGAGGTCCATTTACTTTTC
* * * *
134430 ATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTTTTCATTGTATTTAGAGGCCCAAGTGT
1 ATTGCATTTAGAGGCCCAGGTGTGAAGGCCCATTTACTTTTCATTGCATTTAGATGCCCAGGTGT
* *
134495 GGAGGCTCATTTACTTTTCATTGCATTTAGAGGC-CTAAGTGTGGAGGTCCATTTGCTTTTC
66 GGAGGCCCATTTACTTTTCATTGCATTTAGAGGCTC-AAGTGTGGAGGTCCATTTACTTTTC
* * * *
134556 ATTGCATTTAAAGGCCTAGGTGTGAAGGCCCGTTTACTTTTTATTGCATTT
1 ATTGCATTTAGAGGCCCAGGTGTGAAGGCCCATTTACTTTTCATTGCATTT
134607 GGAGGCTTAG
Statistics
Matches: 376, Mismatches: 47, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
125 3 0.01
126 370 0.98
127 3 0.01
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (126 bp):
ATTGCATTTAGAGGCCCAGGTGTGAAGGCCCATTTACTTTTCATTGCATTTAGATGCCCAGGTGT
GGAGGCCCATTTACTTTTCATTGCATTTAGAGGCTCAAGTGTGGAGGTCCATTTACTTTTC
Found at i:135818 original size:151 final size:150
Alignment explanation
Indices: 135658--136142 Score: 631
Period size: 148 Copynumber: 3.2 Consensus size: 150
135648 ATTTTTTTAG
* * *
135658 AAAAGTTTAAATCTTTAAACAAATTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGA-TTTTTTTAACTATTTCGAAATAAAAGTTTAGATT
*
135723 TTTAAGAAAGTAGTGATTTTCATTAAAAAAGGAAAAAAGTTTATATTTTTAAAAATAAAAAAACT
65 TTTAAGAAAGTAGTGATTTTCATTAAAAAAAGAAAAAAGTTTATATTTTTAAAAATAAAAAAA-T
*
135788 ATTTTTTAGTTATTTTAAAGAA
129 TTTTTTTAGTTATTTTAAAGAA
* *
135810 AAAA-TTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCAAAATAAAAGTTTGGATTT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTAGATTT
* *
135874 TTAGGTAAAGTAGTGATTTTCATTAAAAAAAAGAAAGAAAGTTTATATTTTTAAAAAT---AAAT
66 TTAAG-AAAGTAGTGATTTTCATT-AAAAAAAGAAA-AAAGTTTATATTTTTAAAAATAAAAAAA
135936 TTTTTTTTAGTTA-TTTAAA-AA
128 TTTTTTTTAGTTATTTTAAAGAA
* * * * *
135957 AAAAGCTTAAAATTTTAAATAAAATTTTGATTTTTTCAACTATTTCGGAATAAAAGTTTAGATTT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTAGATTT
* * * * * *** *
136022 TTAAGAAAGTAATGATTTTCATTAAAAAACGAAGAAAGTTCAGAATTAAAAAAAATAAAAATATG
66 TTAAGAAAGTAGTGATTTTCATTAAAAAAAGAAAAAAGTTTA-TATTTTTAAAAATAAAAAAAT-
* *
136087 TTTTTTTAGTGATTTTAAGGAA
129 TTTTTTTAGTTATTTTAAAGAA
*
136109 AAAAGCTTAAATTTTTAAATAAAGTTTTGATTTT
1 AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTT
136143 GAAGTAAAAT
Statistics
Matches: 291, Mismatches: 31, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
145 7 0.02
146 18 0.06
147 23 0.08
148 63 0.22
149 15 0.05
150 51 0.18
151 45 0.15
152 48 0.16
153 21 0.07
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.42
Consensus pattern (150 bp):
AAAAGTTTAAATTTTTAAATAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTAGATTT
TTAAGAAAGTAGTGATTTTCATTAAAAAAAGAAAAAAGTTTATATTTTTAAAAATAAAAAAATTT
TTTTTAGTTATTTTAAAGAA
Found at i:136046 original size:298 final size:291
Alignment explanation
Indices: 135550--136142 Score: 741
Period size: 298 Copynumber: 2.0 Consensus size: 291
135540 AGTTTTAATT
* *
135550 TTTTTTTAAACAATTTCGAAATAAAAGCTTTGATTTTTAAGTAAAATAGTGATTTTCTTCAAAAA
1 TTTTTTTAAACAATTTCAAAATAAAAGCTTTGATTTTTAAGTAAAATAGTGATTTTCTTAAAAAA
* * *
135615 ATAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTTAGAAAAGTTTAAATCTTTAAACAA
66 AAAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTTAAAAAAGTTAAAATCTTTAAACAA
* * *
135680 ATTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAAGTAGTGATTTTCA
131 AATTTTGATTTTTTTCAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAAGTAATGATTTTCA
* * * *** *
135745 TTAAAAAAGGAAAAAAGTTTA-TATTTTTAAAAATAAAAAAACT-ATTTTTTAGTTATTTTAAAG
196 TTAAAAAACGAAAAAAGTTCAGAATTAAAAAAAATAAAAAAA-TGATTTTTTAGTGATTTTAAAG
*
135808 AAAAAA-TTTAAATTTTTAAATAAAGTTTTGA
260 AAAAAAGCTTAAATTTTTAAATAAAGTTTTGA
* * *
135839 TTTTTTT-AACTATTTCAAAATAAAAG-TTTGGATTTTTAGGTAAAGTAGTGATTTTCATTAAAA
1 TTTTTTTAAACAATTTCAAAATAAAAGCTTT-GATTTTTAAGTAAAATAGTGATTTTC-TT--AA
* ** * *
135902 AAAAGAAAGAAAGTTTATATTTTTAAAAATAAATTTTTTTTTAGTTATTTAAAAAAAAAGCTTAA
62 AAAA-AAAGAAAGTTTAGATTTTTAAAAATAAA-AATCTATT--TT-TTT---AAAAAAG-TTAA
* *
135967 AAT-TTTAAATAAAATTTTGA-TTTTTTCAACTATTTCGGAATAAAAGTTTAGATTTTTAAGAAA
118 AATCTTTAAACAAAATTTTGATTTTTTTCAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAA
* * *
136030 GTAATGATTTTCATTAAAAAACGAAGAAAGTTCAGAATTAAAAAAAATAAAAATATGTTTTTTTA
183 GTAATGATTTTCATTAAAAAACGAAAAAAGTTCAGAATTAAAAAAAATAAAAAAATGATTTTTTA
*
136095 GTGATTTTAAGGAAAAAAGCTTAAATTTTTAAATAAAGTTTTGA
248 GTGATTTTAAAGAAAAAAGCTTAAATTTTTAAATAAAGTTTTGA
136139 TTTT
1 TTTT
136143 GAAGTAAAAT
Statistics
Matches: 258, Mismatches: 30, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
287 3 0.01
288 41 0.16
289 9 0.03
291 5 0.02
292 26 0.10
293 4 0.02
295 2 0.01
296 3 0.01
298 72 0.28
299 59 0.23
300 34 0.13
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (291 bp):
TTTTTTTAAACAATTTCAAAATAAAAGCTTTGATTTTTAAGTAAAATAGTGATTTTCTTAAAAAA
AAAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTTAAAAAAGTTAAAATCTTTAAACAA
AATTTTGATTTTTTTCAACTATTTCGAAATAAAAGTTTAGATTTTTAAGAAAGTAATGATTTTCA
TTAAAAAACGAAAAAAGTTCAGAATTAAAAAAAATAAAAAAATGATTTTTTAGTGATTTTAAAGA
AAAAAGCTTAAATTTTTAAATAAAGTTTTGA
Found at i:138311 original size:16 final size:16
Alignment explanation
Indices: 138290--138339 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
138280 TGATGGGGAT
138290 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
138306 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
138321 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
138336 ATTA
1 ATTA
138340 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:142333 original size:27 final size:27
Alignment explanation
Indices: 142300--142352 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
142290 TCAGCAAGTT
*
142300 TCAGCTTGCTTT-TTGTTTCGGATTTCC
1 TCAGCTTGCTTTGTTG-CTCGGATTTCC
*
142327 TCAGCTTTCTTTGTTGCTCGGATTTC
1 TCAGCTTGCTTTGTTGCTCGGATTTC
142353 AACTCCCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.08, C:0.23, G:0.19, T:0.51
Consensus pattern (27 bp):
TCAGCTTGCTTTGTTGCTCGGATTTCC
Found at i:144595 original size:6 final size:6
Alignment explanation
Indices: 144584--144613 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
144574 CTTTTGTTTT
*
144584 AGTCAC AGTCAC AGTCAC AGTCAC ACTCAC
1 AGTCAC AGTCAC AGTCAC AGTCAC AGTCAC
144614 TTTGCAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.37, G:0.13, T:0.17
Consensus pattern (6 bp):
AGTCAC
Found at i:148769 original size:3 final size:3
Alignment explanation
Indices: 148761--148790 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
148751 CTTGTGAAAC
148761 AAG AAG AAG AAG AAG AAG AAG AAG -AG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
148791 GCAAAAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:167356 original size:1 final size:1
Alignment explanation
Indices: 167308--167336 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
167298 TTCTTTCACC
167308 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
167337 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:185168 original size:21 final size:22
Alignment explanation
Indices: 185144--185190 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
185134 CGATCTAAGG
185144 AAAAATAAAAGA-AACAAAATT
1 AAAAATAAAAGATAACAAAATT
* *
185165 AAAAATAAAAGATAATAGAATT
1 AAAAATAAAAGATAACAAAATT
185187 AAAA
1 AAAA
185191 GAAACAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGATAACAAAATT
Found at i:185203 original size:22 final size:22
Alignment explanation
Indices: 185144--185204 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
185134 CGATCTAAGG
185144 AAAAATAAAAGAAACA-A-AATT
1 AAAAATAAAAGAAA-ATAGAATT
*
185165 AAAAATAAAAGATAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
185187 AAAAGA-AACAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
185205 GGAAGTCGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
22 18 0.53
23 1 0.03
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:185906 original size:19 final size:19
Alignment explanation
Indices: 185882--185924 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
185872 AAACATAAAT
185882 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
185901 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
185920 TAAAT
1 TAAAT
185925 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:195028 original size:12 final size:12
Alignment explanation
Indices: 195013--195039 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
195003 GCAAATCATG
195013 AGAAAAATCTAA
1 AGAAAAATCTAA
195025 AGAAAAATCTAA
1 AGAAAAATCTAA
195037 AGA
1 AGA
195040 TTTTTCATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.11, T:0.15
Consensus pattern (12 bp):
AGAAAAATCTAA
Found at i:195311 original size:16 final size:16
Alignment explanation
Indices: 195290--195342 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
195280 ATATGTATAT
* *
195290 AAGAAATAAAAGAATA
1 AAGAAACAAAAGAAAA
* *
195306 AAGAAAGAAAAAAAAA
1 AAGAAACAAAAGAAAA
*
195322 AAGAAACAAAAGAAGA
1 AAGAAACAAAAGAAAA
195338 AAGAA
1 AAGAA
195343 CAGAGGCTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (16 bp):
AAGAAACAAAAGAAAA
Found at i:195791 original size:17 final size:18
Alignment explanation
Indices: 195769--195804 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
195759 TAAATGAGTT
195769 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
195786 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
195804 A
1 A
195805 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:199198 original size:16 final size:16
Alignment explanation
Indices: 199162--199205 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
199152 GAGTAAAGAG
* *
199162 GTATATGATGATATAT
1 GTATATGATGAAAAAT
*
199178 ATATATGATGAAAAAT
1 GTATATGATGAAAAAT
199194 GTATATG-TGAAA
1 GTATATGATGAAA
199206 TATTATGTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (16 bp):
GTATATGATGAAAAAT
Found at i:199463 original size:22 final size:22
Alignment explanation
Indices: 199445--199524 Score: 142
Period size: 22 Copynumber: 3.6 Consensus size: 22
199435 TTTAGCATTG
199445 TGTGTGCTTCTATTCAGCACTA
1 TGTGTGCTTCTATTCAGCACTA
199467 TGTGTGCTTCTATTCAGCACTA
1 TGTGTGCTTCTATTCAGCACTA
* *
199489 TGTGTGCTTCTGTTCAGCACTG
1 TGTGTGCTTCTATTCAGCACTA
199511 TGTGTGCTTCTATT
1 TGTGTGCTTCTATT
199525 TCCCCAGCAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (22 bp):
TGTGTGCTTCTATTCAGCACTA
Found at i:199565 original size:21 final size:21
Alignment explanation
Indices: 199539--199586 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
199529 CAGCAGTTAT
199539 GTACTTCT-GTTAAGTACTTTG
1 GTACTTCTAG-TAAGTACTTTG
199560 GTACTTCTAGTAAGTACTTTG
1 GTACTTCTAGTAAGTACTTTG
199581 GTACTT
1 GTACTT
199587 TATGTTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.46
Consensus pattern (21 bp):
GTACTTCTAGTAAGTACTTTG
Found at i:199659 original size:15 final size:15
Alignment explanation
Indices: 199639--199671 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
199629 AATGGGCTAA
199639 AATGAGAAAAATGTG
1 AATGAGAAAAATGTG
199654 AATGAGAAAAATGTG
1 AATGAGAAAAATGTG
199669 AAT
1 AAT
199672 CAAAGTATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (15 bp):
AATGAGAAAAATGTG
Found at i:202462 original size:22 final size:22
Alignment explanation
Indices: 202434--202479 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
202424 TATGACAGAG
202434 TTAGCTCGGAATTCATCAATAC
1 TTAGCTCGGAATTCATCAATAC
202456 TTAGCTCGGAATTCATCAATAC
1 TTAGCTCGGAATTCATCAATAC
202478 TT
1 TT
202480 CTATCTACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (22 bp):
TTAGCTCGGAATTCATCAATAC
Found at i:212746 original size:14 final size:14
Alignment explanation
Indices: 212729--212770 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
212719 CGCAAATCTA
212729 ATTTTAAAAATATT
1 ATTTTAAAAATATT
*
212743 A-TTTAAAAATAAT
1 ATTTTAAAAATATT
212756 ATTGTTAAAAGATAT
1 ATT-TTAAAA-ATAT
212771 AATCACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 12 0.52
14 2 0.09
15 6 0.26
16 3 0.13
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (14 bp):
ATTTTAAAAATATT
Found at i:216986 original size:18 final size:18
Alignment explanation
Indices: 216963--216997 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
216953 ACTACTTCTG
* *
216963 ATTTTAATTAGTGATATA
1 ATTTTAAGTAGAGATATA
216981 ATTTTAAGTAGAGATAT
1 ATTTTAAGTAGAGATAT
216998 TCATGGATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (18 bp):
ATTTTAAGTAGAGATATA
Found at i:217174 original size:23 final size:23
Alignment explanation
Indices: 217148--217198 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
217138 TAATATATAT
217148 ATATATATATATTATT-TTTAAAA
1 ATATATAT-TATTATTCTTTAAAA
*
217171 ATATA-ATTATTCTTCTTTAAAA
1 ATATATATTATTATTCTTTAAAA
*
217193 ACATAT
1 ATATAT
217199 CTTAGATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.25
22 13 0.54
23 5 0.21
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATATATTATTATTCTTTAAAA
Found at i:217699 original size:2 final size:2
Alignment explanation
Indices: 217687--217718 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
217677 TGACTAACAA
*
217687 AT AT TT 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 AT AT AT
217719 GATTCCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:218852 original size:3 final size:3
Alignment explanation
Indices: 218844--218869 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
218834 ATTATCATAT
218844 TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TC
218870 TATGTTGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:221343 original size:5 final size:5
Alignment explanation
Indices: 221333--221374 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
221323 AGTGCTTCTC
221333 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TC
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TC
221375 TTCTTACGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TCCTT
Found at i:243650 original size:20 final size:20
Alignment explanation
Indices: 243625--243664 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
243615 CTATAATTAA
243625 AATCTCTAAAAATCAGCTAT
1 AATCTCTAAAAATCAGCTAT
* *
243645 AATCTCTAAAGATTAGCTAT
1 AATCTCTAAAAATCAGCTAT
243665 TCAATGTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (20 bp):
AATCTCTAAAAATCAGCTAT
Found at i:253225 original size:2 final size:2
Alignment explanation
Indices: 253212--253249 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
253202 ACCAATGACA
*
253212 AT AT AT AC AT AT 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 AT AT AT AT AT AT
253250 GGATGGCTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:258535 original size:1 final size:1
Alignment explanation
Indices: 258497--258521 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
258487 TAAGATTTAT
258497 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
258522 CTAAAAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:273325 original size:19 final size:19
Alignment explanation
Indices: 273301--273341 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
273291 TCTGAATGTT
* *
273301 TTCCATTTCTTTATTTCTA
1 TTCCATCTCTTTATTTCGA
*
273320 TTCCATCTGTTTATTTCGA
1 TTCCATCTCTTTATTTCGA
273339 TTC
1 TTC
273342 AAACACGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.22, G:0.05, T:0.59
Consensus pattern (19 bp):
TTCCATCTCTTTATTTCGA
Found at i:277543 original size:6 final size:6
Alignment explanation
Indices: 277532--277576 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
277522 ACAACAATGA
* *
277532 CTCACT CTCACT CTCACT CTTACT CTCACT CTCACT TTCACT CTC
1 CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTCACT CTC
277577 TTACATGTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.16, C:0.47, G:0.00, T:0.38
Consensus pattern (6 bp):
CTCACT
Found at i:277758 original size:3 final size:3
Alignment explanation
Indices: 277750--277779 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
277740 TCCTCAATGT
277750 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC ACC
277780 TTCCTTCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:278871 original size:41 final size:41
Alignment explanation
Indices: 278804--278899 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
278794 AAATTTTATT
* * *
278804 TTAAGAAGAATTCTAGTCACCTAATTCTAACAACCTTCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAACCTCCACC
* *
278845 TTAACAAGAATTCTAGTTACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAACCTCCACC
*
278886 TTGACAAGAATTCT
1 TTAACAAGAATTCT
278900 CTATGAACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.36, C:0.26, G:0.07, T:0.30
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAACCTCCACC
Found at i:282934 original size:20 final size:18
Alignment explanation
Indices: 282890--282928 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
282880 TTTATTTTTT
*
282890 AATTGTAT-TTTTCTTAA
1 AATTGTATGATTTCTTAA
282907 AATTGTATGATTTCTTAA
1 AATTGTATGATTTCTTAA
282925 AATT
1 AATT
282929 ATGTATAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (18 bp):
AATTGTATGATTTCTTAA
Found at i:284975 original size:6 final size:6
Alignment explanation
Indices: 284951--285003 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
284941 GGTTGCCCTC
* * * * * *
284951 ATCATT GTCATC ATGATT ATCATT ATCATT ATCATC AACATC ATCATT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
284999 ATCAT
1 ATCAT
285004 CATCTTCTAC
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.42
Consensus pattern (6 bp):
ATCATT
Found at i:284987 original size:9 final size:9
Alignment explanation
Indices: 284949--285006 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
284939 ATGGTTGCCC
*
284949 TCATCATTG
1 TCATCATTA
*
284958 TCATCATGA
1 TCATCATTA
*
284967 TTATCA-T-
1 TCATCATTA
284974 T-ATCATTA
1 TCATCATTA
**
284982 TCATCAACA
1 TCATCATTA
284991 TCATCATTA
1 TCATCATTA
285000 TCATCAT
1 TCATCAT
285007 CTTCTACTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
6 4 0.11
7 2 0.05
8 1 0.03
9 31 0.82
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.41
Consensus pattern (9 bp):
TCATCATTA
Found at i:292506 original size:16 final size:16
Alignment explanation
Indices: 292485--292516 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
292475 CTTTCGTTTG
292485 TTTACTCATTTAGCGA
1 TTTACTCATTTAGCGA
292501 TTTACTCATTTAGCGA
1 TTTACTCATTTAGCGA
292517 AAAGTCGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (16 bp):
TTTACTCATTTAGCGA
Found at i:295369 original size:44 final size:44
Alignment explanation
Indices: 295308--295391 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
295298 AAAAAAATTT
* * **
295308 TAATTTTATTTCATTCAAGATAAAAAATAAATCAATTAAAAATA
1 TAATCTTATTTCATTCAAAATAAAAAATAAAAAAATTAAAAATA
295352 TAATCTTATTT-ACTTCAAAATAAAAAATAAAAAAATTAAA
1 TAATCTTATTTCA-TTCAAAATAAAAAATAAAAAAATTAAA
295392 TTAAATTCGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 1 0.03
44 34 0.97
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.35
Consensus pattern (44 bp):
TAATCTTATTTCATTCAAAATAAAAAATAAAAAAATTAAAAATA
Found at i:295810 original size:13 final size:13
Alignment explanation
Indices: 295788--295834 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
295778 TAATATAAAT
*
295788 ATTAACTATTTCA
1 ATTAAATATTTCA
295801 ATTAAATA-TTCA
1 ATTAAATATTTCA
**
295813 AAAAAACTATTTCA
1 ATTAAA-TATTTCA
295827 ATTAAATA
1 ATTAAATA
295835 CGTACAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
12 8 0.30
13 11 0.41
14 8 0.30
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTAAATATTTCA
Found at i:298636 original size:19 final size:20
Alignment explanation
Indices: 298598--298643 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
298588 GATCTGAAAC
* *
298598 AAGGAAAAATAATGTAAATA
1 AAGGGAAAATAATATAAATA
298618 AAGGGAAAATAA-ATAAATA
1 AAGGGAAAATAATATAAATA
298637 AAGGGAA
1 AAGGGAA
298644 GACATTGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (20 bp):
AAGGGAAAATAATATAAATA
Found at i:303794 original size:45 final size:43
Alignment explanation
Indices: 303685--303803 Score: 134
Period size: 43 Copynumber: 2.7 Consensus size: 43
303675 TATTTTGCTT
** *
303685 AAAAAAAAG-GATTAAGATGAAAACCCGTAAAGGGCATCTCGA
1 AAAAAAAAGAGATCGAGATGAAAACCCGCAAAGGGCATCTCGA
* *
303727 AAAAAAAAGAGATCGAGATGAAAACCCGCAAAGGGTATCTTGA
1 AAAAAAAAGAGATCGAGATGAAAACCCGCAAAGGGCATCTCGA
* *
303770 AACAAAAAG-GAATTTCGAGTTGAAAACCCGCAAA
1 AAAAAAAAGAG-A--TCGAGATGAAAACCCGCAAA
303804 AGGTGACTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
42 10 0.15
43 37 0.56
45 19 0.29
ACGTcount: A:0.50, C:0.15, G:0.21, T:0.14
Consensus pattern (43 bp):
AAAAAAAAGAGATCGAGATGAAAACCCGCAAAGGGCATCTCGA
Found at i:304881 original size:85 final size:85
Alignment explanation
Indices: 304736--304896 Score: 232
Period size: 85 Copynumber: 1.9 Consensus size: 85
304726 TTAAACATCT
* * * * *
304736 TCTTCCTGATGAGATACAAAGAAGTGGGTCAAAGCAATAAAGCGGCCATCTTTCTGATGAGTTAC
1 TCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATAAAGCGGCCATCTTCCTAATGAGATAC
304801 AAAGAAGTAGACCAAATTCG
66 AAAGAAGTAGACCAAATTCG
* * * * *
304821 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAAGCGGTCATCTTCCTAATGAGATAT
1 TCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATAAAGCGGCCATCTTCCTAATGAGATAC
304886 AAAGAAGTAGA
66 AAAGAAGTAGA
304897 TCAATTCAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 66 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAAAGAAGTGGATCAAAACAATAAAGCGGCCATCTTCCTAATGAGATAC
AAAGAAGTAGACCAAATTCG
Found at i:304892 original size:48 final size:48
Alignment explanation
Indices: 304821--304912 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
304811 ACCAAATTCG
* * * *
304821 TCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAAGCGGTCA
1 TCTTCCTAATGAGATACAAAGAAGTAGATCAAAACAATGAAGCGGTCA
* **
304869 TCTTCCTAATGAGATATAAAGAAGTAGATCAATTCAATGAAGCG
1 TCTTCCTAATGAGATACAAAGAAGTAGATCAAAACAATGAAGCG
304913 AAGCTCAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (48 bp):
TCTTCCTAATGAGATACAAAGAAGTAGATCAAAACAATGAAGCGGTCA
Found at i:305089 original size:85 final size:85
Alignment explanation
Indices: 304945--305109 Score: 233
Period size: 85 Copynumber: 1.9 Consensus size: 85
304935 TCAAACCCTA
* ** *
304945 TCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGATCATCTTTTGGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGAATCAAAGCAATAAAGAGATCATCTTCTGGATGAGATAC
305010 AAAGAAGTAGACCAAATTCG
66 AAAGAAGTAGACCAAATTCG
* * * *
305030 TCTTCCTGATGAGATACAGAGAAGTGAATTAAATCAATGAAGCGATCATCTTCCT-GATGAGATA
1 TCTTCCTGATGAGATACAGAGAAGTGAATCAAAGCAATAAAGAGATCATCTT-CTGGATGAGATA
*
305094 CAGAGAAGTAGACCAA
65 CAAAGAAGTAGACCAA
305110 TTCAATAAAG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
85 69 0.99
86 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAGAAGTGAATCAAAGCAATAAAGAGATCATCTTCTGGATGAGATAC
AAAGAAGTAGACCAAATTCG
Found at i:305103 original size:209 final size:207
Alignment explanation
Indices: 304736--305311 Score: 722
Period size: 209 Copynumber: 2.8 Consensus size: 207
304726 TTAAACATCT
* * ** *
304736 TCTTCCTGATGAGATACAAAGAAGTGGGTCAAAGCAATAAAGCGGCCATCTTTCTGATGAGTTAC
1 TCTT-CTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGATCATCTTTCTGATGAGATAC
*
304801 AAAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAAGCGG
65 AAAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAAGCGA
* * * *
304866 TCATCTTCCTAATGAGATATAAAGAAGTAGATCAATTCAATGAAGCGAAGCTCAATGAGAGTAAA
130 TCATCTTCCTGATGAGATACAGAGAAGTAGATCAATTCAATAAAGCGAAGCTCAATGAGAGTAAA
*
304931 ACTTTCAAACCCTA
195 AC-TTCAAACCCCA
304945 TCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGATCATCTTT-TGGATGAGATA
1 TCTTC-TGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGATCATCTTTCT-GATGAGATA
* *
305009 CAAAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGAATTAAATCAATGAAGCG
64 CAAAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAAGCG
* * * *
305074 ATCATCTTCCTGATGAGATACAGAGAAGTAGACCAATTCAATAAAGTGAAGCTCAATGTGAGTGA
129 ATCATCTTCCTGATGAGATACAGAGAAGTAGATCAATTCAATAAAGCGAAGCTCAATGAGAGTAA
*
305139 AACTTCCAACCCCA
194 AACTTCAAACCCCA
* ** * * * * *
305153 TCTTC--CT--GAT-CAGAGAAGTGGGTTGAAGCAATAAAGTGTTCAT-TTTCTTGACGAAATGC
1 TCTTCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGATCATCTTTC-TGATGAGATAC
* * * * *
305212 AGAGATGT-GAACCAAATCCATCTTCCTGATAAGATACAGAGACA-TGGATTAAAACAATGAAGC
65 AAAGAAGTAG-ACCAAATTCGTCTTCCTGATGAGATACAGAGA-AGTGGATTAAAACAATGAAGC
*
305275 GGA-CATCTTTCTGATGAGATACAGAGAAGTAGATCAA
128 -GATCATCTTCCTGATGAGATACAGAGAAGTAGATCAA
305312 GAAATGAAGC
Statistics
Matches: 325, Mismatches: 35, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
201 4 0.01
202 120 0.37
203 7 0.02
205 1 0.00
208 16 0.05
209 177 0.54
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.24
Consensus pattern (207 bp):
TCTTCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGAGATCATCTTTCTGATGAGATACA
AAGAAGTAGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATTAAAACAATGAAGCGAT
CATCTTCCTGATGAGATACAGAGAAGTAGATCAATTCAATAAAGCGAAGCTCAATGAGAGTAAAA
CTTCAAACCCCA
Found at i:305823 original size:12 final size:12
Alignment explanation
Indices: 305806--305837 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
305796 ACATTAGCAG
305806 CTGCCACCGCCA
1 CTGCCACCGCCA
305818 CTGCCACCGCCA
1 CTGCCACCGCCA
305830 CTGCCACC
1 CTGCCACC
305838 TGCAAAGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.59, G:0.16, T:0.09
Consensus pattern (12 bp):
CTGCCACCGCCA
Found at i:307326 original size:30 final size:30
Alignment explanation
Indices: 307287--307622 Score: 262
Period size: 30 Copynumber: 11.3 Consensus size: 30
307277 CACTATTTTC
* * *
307287 TTTCTAAAATTACATTTTGACCCTTGAACT
1 TTTCAAAAATCACATTTTGACCCTTAAACT
* *
307317 TTTCAAAAATTACATTTTGA-CTTTCAAACT
1 TTTCAAAAATCACATTTTGACCCTT-AAACT
* * *
307347 CTTCCAAAATCACATTTTTTGACCTTTAAACT
1 TTTCAAAAATCACA--TTTTGACCCTTAAACT
* * * *
307379 ATTCAAAAATTACATTTTAACCAC-TGAACT
1 TTTCAAAAATCACATTTTGACC-CTTAAACT
* * * * *
307409 TTCCTAAAATCCCA-TTTAACCCCTAAACT
1 TTTCAAAAATCACATTTTGACCCTTAAACT
*
307438 TTTCCAAAATCACATTTTGACACC-TAAAC-
1 TTTCAAAAATCACATTTTGAC-CCTTAAACT
* * **
307467 TTCCCAAAATCACATTTTGACCCCCAAACT
1 TTTCAAAAATCACATTTTGACCCTTAAACT
* * *
307497 TTTCAAAAATCA-AATTTAACCCCTAAA-T
1 TTTCAAAAATCACATTTTGACCCTTAAACT
*
307525 TATTCAAAAATTC-CATTTTCATCCC-TAAACTT
1 T-TTCAAAAA-TCACATTTTGA-CCCTTAAAC-T
307557 TTTC-AAAATCACATTTTGACCCTTAAAC-
1 TTTCAAAAATCACATTTTGACCCTTAAACT
* *
307585 TTTCTAAAATCACATTTTAACCCTTAAACT
1 TTTCAAAAATCACATTTTGACCCTTAAACT
307615 TTTCAAAA
1 TTTCAAAA
307623 CTCCCAAACT
Statistics
Matches: 252, Mismatches: 34, Indels: 40
0.77 0.10 0.12
Matches are distributed among these distances:
28 9 0.04
29 98 0.39
30 109 0.43
31 8 0.03
32 24 0.10
33 4 0.02
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (30 bp):
TTTCAAAAATCACATTTTGACCCTTAAACT
Found at i:307468 original size:59 final size:59
Alignment explanation
Indices: 307286--307622 Score: 251
Period size: 59 Copynumber: 5.7 Consensus size: 59
307276 CCACTATTTT
* * * * * * * **
307286 CTTT-CTAAAATTACATTTTGACCCTTGAACTTTTCAAAAATTACATTTTGACTTTCAAA
1 CTTTCCTAAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTAACCCT-AAA
* ** * * * *
307345 CTCTTCC-AAAATCACATTTTTTGACCTTTAAACTATTCAAAAATTACATTTTAACCACTGAA
1 CT-TTCCTAAAATCACA--TTTTAACCCCTAAACTTTTCCAAAATCACATTTTAACC-CTAAA
* *
307407 CTTTCCTAAAATCCCA-TTTAACCCCTAAACTTTTCCAAAATCACATTTTGACACCTAAA
1 CTTTCCTAAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTAAC-CCTAAA
* * * * *
307466 C-TTCCCAAAATCACATTTTGACCCCCAAACTTTTCAAAAATCA-AATTTAACCCCTAAA
1 CTTTCCTAAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTAA-CCCTAAA
* * * * * *
307524 -TTATTCAAAAATTC-CATTTTCATCCCTAAACTTTTTCAAAATCACATTTTGACCCTTAAA
1 CTT-TCCTAAAA-TCACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTAACCC-TAAA
*
307584 CTTT-CTAAAATCACATTTTAACCCTTAAACTTTT-CAAAA
1 CTTTCCTAAAATCACATTTTAACCCCTAAACTTTTCCAAAA
307623 CTCCCAAACT
Statistics
Matches: 225, Mismatches: 37, Indels: 33
0.76 0.13 0.11
Matches are distributed among these distances:
58 31 0.14
59 118 0.52
60 23 0.10
61 7 0.03
62 45 0.20
63 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.36
Consensus pattern (59 bp):
CTTTCCTAAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTAACCCTAAA
Found at i:307678 original size:77 final size:78
Alignment explanation
Indices: 307546--307699 Score: 238
Period size: 77 Copynumber: 2.0 Consensus size: 78
307536 TCCATTTTCA
* * * * *
307546 TCCCTAAACTTTTTCAAAATCACATTTTGACCCTTAAACTTTCTAAAATCACATTTTAACCCTTA
1 TCCCTAAACTTTTCCAAAATCACATTTTAACCCTTAAACTTCCCAAAATCACATTTTAACCCTCA
307611 AACTTTTCAAAAC
66 AACTTTTCAAAAC
* *
307624 TCCC-AAACTTTTCCAAAATCACATTTTAACCCTTAAACTTCCCAAAATTACATTTTGACCCTCA
1 TCCCTAAACTTTTCCAAAATCACATTTTAACCCTTAAACTTCCCAAAATCACATTTTAACCCTCA
307688 AACTTTTCAAAA
66 AACTTTTCAAAA
307700 GTCACATTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
77 65 0.94
78 4 0.06
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.35
Consensus pattern (78 bp):
TCCCTAAACTTTTCCAAAATCACATTTTAACCCTTAAACTTCCCAAAATCACATTTTAACCCTCA
AACTTTTCAAAAC
Found at i:307709 original size:30 final size:29
Alignment explanation
Indices: 307627--307714 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
307617 TCAAAACTCC
*
307627 CAAACTTTTCCAAAATCACATTTTAACCCT
1 CAAACTTTT-CAAAATCACATTTTGACCCT
* ** *
307657 TAAACTTCCCAAAATTACATTTTGACCCT
1 CAAACTTTTCAAAATCACATTTTGACCCT
307686 CAAACTTTTCAAAAGTCACATTTTGACCC
1 CAAACTTTTCAAAA-TCACATTTTGACCC
307715 CGAATTGTCT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
29 29 0.60
30 19 0.40
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
CAAACTTTTCAAAATCACATTTTGACCCT
Found at i:310593 original size:17 final size:17
Alignment explanation
Indices: 310571--310626 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
310561 GGGATGCCAT
310571 CTAGCTCGCCACCTTTG
1 CTAGCTCGCCACCTTTG
*
310588 CTAGCTCGCCA--TTTCA
1 CTAGCTCGCCACCTTT-G
* *
310604 CTAGCTTGCCACCTCTG
1 CTAGCTCGCCACCTTTG
310621 CTAGCT
1 CTAGCT
310627 TGCACGCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 3 0.09
16 10 0.31
17 17 0.53
18 2 0.06
ACGTcount: A:0.14, C:0.39, G:0.16, T:0.30
Consensus pattern (17 bp):
CTAGCTCGCCACCTTTG
Found at i:311503 original size:28 final size:28
Alignment explanation
Indices: 311472--311525 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
311462 TGGATGGTCA
311472 ATTTAAAAAAATTCACAATTAAGTGACC
1 ATTTAAAAAAATTCACAATTAAGTGACC
* * *
311500 ATTTAATAAAATTCATAATTGAGTGA
1 ATTTAAAAAAATTCACAATTAAGTGA
311526 TAAAAGAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.33
Consensus pattern (28 bp):
ATTTAAAAAAATTCACAATTAAGTGACC
Found at i:314972 original size:28 final size:28
Alignment explanation
Indices: 314926--314985 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
314916 TTAAGATGAG
*
314926 TATATAAAAATTTTCAATAAATAAAA-AA
1 TATATAAAAATTTTAAAT-AATAAAATAA
*
314954 TATAT-AAAATTATTAAATATTAAAATAA
1 TATATAAAAATT-TTAAATAATAAAATAA
314982 TATA
1 TATA
314986 ATATAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
TATATAAAAATTTTAAATAATAAAATAA
Found at i:315021 original size:32 final size:31
Alignment explanation
Indices: 314943--315021 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 31
314933 AAATTTTCAA
* *
314943 TAAATAAAAAATATATAAAATTATTAAATAT
1 TAAAAAAAAAAAATATAAAATTATTAAATAT
* * * *
314974 TAAAATAATATAATATAAATATTTTTTAAAT-T
1 TAAAAAAAAAAAATATAAA-A-TTATTAAATAT
315006 TAAAAAAAAAAAATAT
1 TAAAAAAAAAAAATAT
315022 GAACGATCCT
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
31 14 0.38
32 15 0.41
33 8 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (31 bp):
TAAAAAAAAAAAATATAAAATTATTAAATAT
Found at i:318488 original size:16 final size:16
Alignment explanation
Indices: 318463--318495 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
318453 TTGTCACAGG
318463 CTTCTCAGGTGGGAAT
1 CTTCTCAGGTGGGAAT
*
318479 CTTCTTAGGTGGGAAT
1 CTTCTCAGGTGGGAAT
318495 C
1 C
318496 CAAGAAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.33
Consensus pattern (16 bp):
CTTCTCAGGTGGGAAT
Found at i:325545 original size:18 final size:18
Alignment explanation
Indices: 325522--325559 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
325512 TCAAATTCAC
325522 TTCCAAATC-AATGTCTAT
1 TTCCAAATCTAAT-TCTAT
*
325540 TTCCAATTCTAATTCTAT
1 TTCCAAATCTAATTCTAT
325558 TT
1 TT
325560 TAATTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.29, C:0.21, G:0.03, T:0.47
Consensus pattern (18 bp):
TTCCAAATCTAATTCTAT
Found at i:333127 original size:24 final size:24
Alignment explanation
Indices: 333087--333142 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
333077 ACAGCAGCAG
* *
333087 CAACAGCAGAATTCACAACTGCAA
1 CAACAGCAAAATCCACAACTGCAA
*
333111 CAGCAGCAAAATCCACAACTGCAA
1 CAACAGCAAAATCCACAACTGCAA
333135 CAACAGCA
1 CAACAGCA
333143 GCTTCCGCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.46, C:0.32, G:0.12, T:0.09
Consensus pattern (24 bp):
CAACAGCAAAATCCACAACTGCAA
Done.