Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000931.1 Hibiscus syriacus cultivar Beakdansim tig00001857_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 102355
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1236 original size:60 final size:61
Alignment explanation
Indices: 1158--1274 Score: 166
Period size: 60 Copynumber: 1.9 Consensus size: 61
1148 TTATAACCTC
*
1158 ATAAACAATTTATCTTATTAGTGAGTTTAGTAATTCAAA-GAGAGATTTATTTTTTAACTTG
1 ATAAACAATTTATATTATTAGTGAGTTTAGTAATT-AAACGAGAGATTTATTTTTTAACTTG
* * * *
1219 ATAAATAATTTA-ATTATTAGTGATTTTAGTAATTAAACGTGAGTTTTATTTTTTAA
1 ATAAACAATTTATATTATTAGTGAGTTTAGTAATTAAACGAGAGATTTATTTTTTAA
1275 TTTATTAGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 3 0.06
60 36 0.72
61 11 0.22
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.47
Consensus pattern (61 bp):
ATAAACAATTTATATTATTAGTGAGTTTAGTAATTAAACGAGAGATTTATTTTTTAACTTG
Found at i:1310 original size:44 final size:43
Alignment explanation
Indices: 1227--1316 Score: 126
Period size: 44 Copynumber: 2.1 Consensus size: 43
1217 TGATAAATAA
* *** *
1227 TTTAATTATTAGTGATTTTAGTAATTAAACGTGAGTTTTATTT
1 TTTAATTATTAGTGACTTTAGTAATTAAAAAAGAATTTTATTT
1270 TTTAATTTATTAGTGACTTTAGTAATTAAAAAAGAATTTTATTT
1 TTTAA-TTATTAGTGACTTTAGTAATTAAAAAAGAATTTTATTT
1314 TTT
1 TTT
1317 TAGAAGTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 5 0.12
44 36 0.88
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.53
Consensus pattern (43 bp):
TTTAATTATTAGTGACTTTAGTAATTAAAAAAGAATTTTATTT
Found at i:12886 original size:30 final size:30
Alignment explanation
Indices: 12850--12928 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 30
12840 TATTATTTTT
* * *
12850 TAATATTTTTGGTAATTTTTTAGCGTCTAG
1 TAATATTTTTGATAATTTTTTAGAGTCTAA
12880 TAATA-TTTTGATAATTTTTTAGAGTCTAA
1 TAATATTTTTGATAATTTTTTAGAGTCTAA
* * *
12909 TAATATGTTCGATTATTTTT
1 TAATATTTTTGATAATTTTT
12929 GTTGAAAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 26 0.62
30 16 0.38
ACGTcount: A:0.28, C:0.05, G:0.13, T:0.54
Consensus pattern (30 bp):
TAATATTTTTGATAATTTTTTAGAGTCTAA
Found at i:14651 original size:20 final size:19
Alignment explanation
Indices: 14619--14665 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
14609 TAATGATTAT
14619 TTTAAAATAATTTGATATA
1 TTTAAAATAATTTGATATA
* *
14638 TTTAATAATTATTTGATAATC
1 TTTAA-AATAATTTGAT-ATA
14659 TTTAAAA
1 TTTAAAA
14666 ATCTAACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 12 0.50
21 7 0.29
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
TTTAAAATAATTTGATATA
Found at i:15491 original size:11 final size:11
Alignment explanation
Indices: 15475--15539 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
15465 AAAATTCAAG
15475 AGCTCGATTGA
1 AGCTCGATTGA
*
15486 AGCTCGAGACTCG-
1 AGCTC--GA-TTGA
15499 AGCTCGATTGA
1 AGCTCGATTGA
* *
15510 AGCTCAATTTTA
1 AGCTCGA-TTGA
*
15522 AGCTCGATTCA
1 AGCTCGATTGA
15533 AGCTCGA
1 AGCTCGA
15540 ACTCAAACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
10 2 0.05
11 23 0.53
12 9 0.21
13 7 0.16
14 2 0.05
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (11 bp):
AGCTCGATTGA
Found at i:15544 original size:29 final size:31
Alignment explanation
Indices: 15512--15580 Score: 79
Period size: 35 Copynumber: 2.2 Consensus size: 31
15502 TCGATTGAAG
15512 CTCAA-TT-TTAAGCTCGATTCAAGCTCGAA
1 CTCAACTTATTAAGCTCGATTCAAGCTCGAA
*
15541 CTCAAACTTAAACTTGAGCTCGATTCAAGCTCGAA
1 CTC-AACTT--A-TTAAGCTCGATTCAAGCTCGAA
15576 CTCAA
1 CTCAA
15581 ACTCGAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
29 3 0.09
30 2 0.06
31 2 0.06
34 2 0.06
35 24 0.73
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (31 bp):
CTCAACTTATTAAGCTCGATTCAAGCTCGAA
Found at i:17440 original size:15 final size:15
Alignment explanation
Indices: 17417--17457 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
17407 TTAATAGTAG
*
17417 GTTTAATCTTATATT
1 GTTTCATCTTATATT
17432 GTTTCATCTTATATT
1 GTTTCATCTTATATT
17447 GTTTCATCTTA
1 GTTTCATCTTA
17458 ATGTATGTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.07, T:0.59
Consensus pattern (15 bp):
GTTTCATCTTATATT
Found at i:17605 original size:7 final size:7
Alignment explanation
Indices: 17589--17686 Score: 110
Period size: 7 Copynumber: 14.1 Consensus size: 7
17579 AGCATAAATA
17589 AAACCCT
1 AAACCCT
*
17596 AAACCTT
1 AAACCCT
* *
17603 AAATCAT
1 AAACCCT
**
17610 AAATACT
1 AAACCCT
*
17617 AAATCCT
1 AAACCCT
*
17624 AAATCCT
1 AAACCCT
17631 AAACCCT
1 AAACCCT
17638 AAACCCT
1 AAACCCT
17645 AAA-CCT
1 AAACCCT
17651 AAACCCT
1 AAACCCT
17658 AAACCAC-
1 AAACC-CT
17665 AAACCCT
1 AAACCCT
17672 AAACCCT
1 AAACCCT
17679 AAACCCT
1 AAACCCT
17686 A
1 A
17687 TCACATAATT
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
6 7 0.09
7 73 0.90
8 1 0.01
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:17772 original size:32 final size:31
Alignment explanation
Indices: 17721--17780 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
17711 TTGTAATATA
* * *
17721 TAATTTTTAAAATTTTATAATTATCAATAATG
1 TAATTTTAAAAAATCTATAATTAT-AATAATG
17753 TAATTTTAAAAAATCTATAATTATAATA
1 TAATTTTAAAAAATCTATAATTATAATA
17781 TAACATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 4 0.16
32 21 0.84
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (31 bp):
TAATTTTAAAAAATCTATAATTATAATAATG
Found at i:19939 original size:40 final size:40
Alignment explanation
Indices: 19882--19989 Score: 171
Period size: 40 Copynumber: 2.7 Consensus size: 40
19872 ATTTGGAAAA
* *
19882 TCGCAATGCGATACTGACTATCGCAACGCGATGCTGACTT
1 TCGCAACGCGATTCTGACTATCGCAACGCGATGCTGACTT
* *
19922 TCGCAACGCGATTCTGACTTTCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTATCGCAACGCGATGCTGACTT
*
19962 TCGCAACGAGATTCTGACTATCGCAACG
1 TCGCAACGCGATTCTGACTATCGCAACG
19990 AGATAATACA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 62 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (40 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGATGCTGACTT
Found at i:19993 original size:20 final size:20
Alignment explanation
Indices: 19881--19989 Score: 155
Period size: 20 Copynumber: 5.5 Consensus size: 20
19871 AATTTGGAAA
* *
19881 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATTCTGACT
*
19901 ATCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTCTGACT
*
19921 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
19941 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
19961 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
19981 ATCGCAACG
1 ATCGCAACG
19990 AGATAATACA
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:20637 original size:19 final size:19
Alignment explanation
Indices: 20595--20658 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
20585 AAATGAAAAT
20595 CGCATTGCGATTTTC--TG
1 CGCATTGCGATTTTCATTG
20612 -G--TTGCGATTTTCATTG
1 CGCATTGCGATTTTCATTG
*
20628 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTG
20647 CGCATTGCGATT
1 CGCATTGCGATT
20659 CTCTCGTTGC
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 11 0.27
16 3 0.07
17 1 0.02
19 26 0.63
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTG
Found at i:22294 original size:41 final size:42
Alignment explanation
Indices: 22249--22340 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
22239 CCTCTTCAAC
*
22249 GATGACAGTGGCCTCTTGAACG-GTGG-GGGTGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGG-GACTCTTGAGG
* *
22290 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
22332 GATGACAGG
1 GATGACAGG
22341 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
41 20 0.44
42 22 0.49
43 3 0.07
ACGTcount: A:0.21, C:0.15, G:0.41, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:22307 original size:21 final size:21
Alignment explanation
Indices: 22279--22336 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
22269 CGGTGGGGGT
*
22279 GACTCTTGAGGGATGATAGGG
1 GACTCTTGAGGGATGAGAGGG
* **
22300 GCCTCTTGAACGATTG-GAGGG
1 GACTCTTGAGGGA-TGAGAGGG
22321 GACTCTTGAGGGATGA
1 GACTCTTGAGGGATGA
22337 CAGGTGAGTC
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.22, C:0.14, G:0.40, T:0.24
Consensus pattern (21 bp):
GACTCTTGAGGGATGAGAGGG
Found at i:22703 original size:20 final size:20
Alignment explanation
Indices: 22678--22716 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
22668 GAAGAATAGT
22678 TTACTTTCACAACACGAAAC
1 TTACTTTCACAACACGAAAC
* *
22698 TTACTTTCGCAACGCGAAA
1 TTACTTTCACAACACGAAA
22717 ATGACTATCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (20 bp):
TTACTTTCACAACACGAAAC
Found at i:22727 original size:20 final size:20
Alignment explanation
Indices: 22704--22749 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
22694 AAACTTACTT
22704 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
* *
22724 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGAAAATGACTA
22744 TCGCAA
1 TCGCAA
22750 TGCAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:22776 original size:14 final size:14
Alignment explanation
Indices: 22759--22817 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
22749 ATGCAAAATT
22759 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
22773 AAAATCGCAATACGAAATG
1 AAAATCGC-A-ACG--A-C
22792 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
22806 AAAATCACAACG
1 AAAATCGCAACG
22818 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 19 0.51
15 2 0.05
16 3 0.08
17 3 0.08
18 2 0.05
19 8 0.22
ACGTcount: A:0.53, C:0.24, G:0.14, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:22796 original size:33 final size:33
Alignment explanation
Indices: 22743--22811 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
22733 GGAAATGGCT
* *
22743 ATCGCAATGCAAAATTAAAATCGCAACGACAAA
1 ATCGCAATACAAAATGAAAATCGCAACGACAAA
*
22776 ATCGCAATACGAAATGAAAATCGCAACGACAAA
1 ATCGCAATACAAAATGAAAATCGCAACGACAAA
22809 ATC
1 ATC
22812 ACAACGCGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.51, C:0.22, G:0.13, T:0.14
Consensus pattern (33 bp):
ATCGCAATACAAAATGAAAATCGCAACGACAAA
Found at i:22822 original size:33 final size:33
Alignment explanation
Indices: 22754--22822 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
22744 TCGCAATGCA
* * *
22754 AAATTAAAATCGCAACGACAAAATCGCAATACG
1 AAATGAAAATCGCAACGACAAAATCACAACACG
*
22787 AAATGAAAATCGCAACGACAAAATCACAACGCG
1 AAATGAAAATCGCAACGACAAAATCACAACACG
22820 AAA
1 AAA
22823 CACAAATCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.54, C:0.22, G:0.13, T:0.12
Consensus pattern (33 bp):
AAATGAAAATCGCAACGACAAAATCACAACACG
Found at i:22830 original size:33 final size:33
Alignment explanation
Indices: 22754--22833 Score: 99
Period size: 33 Copynumber: 2.4 Consensus size: 33
22744 TCGCAATGCA
* * *
22754 AAATTAAAATCGCAACGACAAAATCGCAATACG
1 AAATCAAAATCGCAACGACAAAATCACAACACG
* *
22787 AAATGAAAATCGCAACGACAAAATCACAACGCG
1 AAATCAAAATCGCAACGACAAAATCACAACACG
22820 AAA-CACAAATCGCA
1 AAATCA-AAATCGCA
22834 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.02
33 40 0.98
ACGTcount: A:0.53, C:0.24, G:0.12, T:0.11
Consensus pattern (33 bp):
AAATCAAAATCGCAACGACAAAATCACAACACG
Found at i:22851 original size:19 final size:19
Alignment explanation
Indices: 22829--22895 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
22819 GAAACACAAA
22829 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
22848 TCGCGTTGCTATTTT-A--
1 TCGCATTGCGATTTTCATT
22864 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
22881 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
22896 GTCGTTGCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 9 0.22
15 1 0.03
16 3 0.08
17 3 0.08
18 1 0.03
19 23 0.57
ACGTcount: A:0.13, C:0.19, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:22876 original size:33 final size:33
Alignment explanation
Indices: 22834--22921 Score: 140
Period size: 33 Copynumber: 2.7 Consensus size: 33
22824 ACAAATCGCA
* *
22834 TTGCGATTTTCATTTCGCGTTGCTATTTTATCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTATCG
*
22867 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTATCG
*
22900 TTGCGATTTTTATTTCGCATTG
1 TTGCGATTTTCATTTCGCATTG
22922 TGATAGCCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTATCG
Found at i:22952 original size:20 final size:20
Alignment explanation
Indices: 22923--22964 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
22913 TTCGCATTGT
22923 GATAGCCATTTCCGCGTTGC
1 GATAGCCATTTCCGCGTTGC
* * *
22943 GATAGTCATTTTCGTGTTGC
1 GATAGCCATTTCCGCGTTGC
22963 GA
1 GA
22965 AAGTAAACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (20 bp):
GATAGCCATTTCCGCGTTGC
Found at i:23892 original size:15 final size:16
Alignment explanation
Indices: 23872--23901 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23862 ATCCAAATCT
23872 ACAAACAATA-TAATA
1 ACAAACAATAGTAATA
23887 ACAAACAATAGTAAT
1 ACAAACAATAGTAAT
23902 TGTTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.13, G:0.03, T:0.20
Consensus pattern (16 bp):
ACAAACAATAGTAATA
Found at i:24896 original size:20 final size:20
Alignment explanation
Indices: 24848--24906 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
24838 AATAGTTTCT
* *
24848 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
24868 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
24888 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
24907 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:25181 original size:22 final size:22
Alignment explanation
Indices: 25155--25198 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
25145 GATGGAGATA
25155 GACGGATTTCGCCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* *
25177 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
25199 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:25413 original size:20 final size:20
Alignment explanation
Indices: 25385--25457 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
25375 GATTATGTAT
*
25385 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
25405 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
25425 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
25445 TATCGCATTGCGA
1 TATCGCGTTGCGA
25458 TTTTGTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:25470 original size:61 final size:59
Alignment explanation
Indices: 25405--25523 Score: 154
Period size: 61 Copynumber: 2.0 Consensus size: 59
25395 CGAAAGTCAG
25405 TATCGCGTTGCGA-AA-GTAAGTATCGCGTTGCGAA-AGTCAGTATCGCATTGCGATTTTGTAT
1 TATCGCGTTGCGATAATG-AAG-ATCGCGTTGCGAATAG-C-G-ATCGCATTGCGATTTTGTAT
*
25466 TATCGCGTTGCGATAATGGAGATCGCGTTGCGAATTAGCGATCGCATTGCGATTTTGT
1 TATCGCGTTGCGATAATGAAGATCGCGTTGCGAA-TAGCGATCGCATTGCGATTTTGT
25524 TGGTCATTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 9
0.84 0.02 0.14
Matches are distributed among these distances:
60 18 0.34
61 27 0.51
62 5 0.09
63 3 0.06
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.33
Consensus pattern (59 bp):
TATCGCGTTGCGATAATGAAGATCGCGTTGCGAATAGCGATCGCATTGCGATTTTGTAT
Found at i:25510 original size:19 final size:20
Alignment explanation
Indices: 25467--25518 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
25457 ATTTTGTATT
*
25467 ATCGCGTTGCGATAATGGAG
1 ATCGCGTTGCGATAATAGAG
* *
25487 ATCGCGTTGCGA-ATTAGCG
1 ATCGCGTTGCGATAATAGAG
*
25506 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
25519 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGATAATAGAG
Found at i:28788 original size:22 final size:22
Alignment explanation
Indices: 28758--28818 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
28748 TATAATCAGA
28758 TTTAG-GTTTTAGGGTTTAAGG
1 TTTAGAGTTTTAGGGTTTAAGG
* * *
28779 TTTATAGTTTTATGGTTTATGG
1 TTTAGAGTTTTAGGGTTTAAGG
*
28801 TTTAGAG-TTTAGAGTTTA
1 TTTAGAGTTTTAGGGTTTA
28819 TTACAAATAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 13 0.39
22 20 0.61
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.52
Consensus pattern (22 bp):
TTTAGAGTTTTAGGGTTTAAGG
Found at i:28895 original size:21 final size:22
Alignment explanation
Indices: 28871--28915 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
28861 ATAAGTACAA
28871 TTTAGGGTCGATGGTTTA-GAT
1 TTTAGGGTCGATGGTTTATGAT
**
28892 TTTAGGGTTTATGGTTTATGAT
1 TTTAGGGTCGATGGTTTATGAT
28914 TT
1 TT
28916 ATGGTTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.18, C:0.02, G:0.29, T:0.51
Consensus pattern (22 bp):
TTTAGGGTCGATGGTTTATGAT
Found at i:28909 original size:14 final size:15
Alignment explanation
Indices: 28891--28929 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
28881 ATGGTTTAGA
28891 TTTTAGGGTTTATGG
1 TTTTAGGGTTTATGG
* *
28906 -TTTATGATTTATGG
1 TTTTAGGGTTTATGG
28920 TTTTAGGGTT
1 TTTTAGGGTT
28930 CATTACAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.15, C:0.00, G:0.28, T:0.56
Consensus pattern (15 bp):
TTTTAGGGTTTATGG
Found at i:28916 original size:21 final size:20
Alignment explanation
Indices: 28870--28922 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
28860 GATAAGTACA
**
28870 ATTTAGGGTCGATGGTTTAG
1 ATTTAGGGTTTATGGTTTAG
28890 ATTTTAGGGTTTATGGTTTATG
1 A-TTTAGGGTTTATGGTTTA-G
*
28912 ATTTATGGTTT
1 ATTTAGGGTTT
28923 TAGGGTTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 25 0.89
22 2 0.07
ACGTcount: A:0.19, C:0.02, G:0.28, T:0.51
Consensus pattern (20 bp):
ATTTAGGGTTTATGGTTTAG
Found at i:32916 original size:17 final size:17
Alignment explanation
Indices: 32896--32937 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
32886 ATATAATATT
32896 AATTAATTTTAAAATGA
1 AATTAATTTTAAAATGA
32913 AATTAATATTTTAAAATGA
1 AATT-A-ATTTTAAAATGA
*
32932 TATTAA
1 AATTAA
32938 AGTTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 2 0.09
19 15 0.68
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (17 bp):
AATTAATTTTAAAATGA
Found at i:32925 original size:19 final size:19
Alignment explanation
Indices: 32901--32937 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
32891 ATATTAATTA
32901 ATTTTAAAATGAAATTAAT
1 ATTTTAAAATGAAATTAAT
*
32920 ATTTTAAAATGATATTAA
1 ATTTTAAAATGAAATTAA
32938 AGTTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
ATTTTAAAATGAAATTAAT
Found at i:34016 original size:19 final size:18
Alignment explanation
Indices: 33974--34016 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
33964 ACATAAAATT
* * *
33974 TTAAAATGGACATCTATT
1 TTAAAATAGACAACTATA
33992 TTAAAATAGACAACTAATA
1 TTAAAATAGACAACT-ATA
34011 TTAAAA
1 TTAAAA
34017 AATTCGGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (18 bp):
TTAAAATAGACAACTATA
Found at i:36502 original size:2 final size:2
Alignment explanation
Indices: 36495--36537 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
36485 TAATATCTAA
36495 AT AT AT AT AT AT 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 AT AT
36537 A
1 A
36538 AATACGTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36659 original size:11 final size:11
Alignment explanation
Indices: 36639--36676 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
36629 TATAAAAAAC
36639 ATAATAAAAATA
1 ATAAT-AAAATA
36651 A-AATGAAAATA
1 ATAAT-AAAATA
36662 ATAATAAAATA
1 ATAATAAAATA
36673 ATAA
1 ATAA
36677 AAGGATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (11 bp):
ATAATAAAATA
Found at i:38010 original size:18 final size:18
Alignment explanation
Indices: 37987--38040 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 18
37977 GTCAATTTGA
*
37987 ATTGTGGATGTC-ACCTTC
1 ATTGTGGAAGTCGA-CTTC
38005 ATTGT-GAAGTCGACTTC
1 ATTGTGGAAGTCGACTTC
* *
38022 ATTGT-GAAATCGAGTTC
1 ATTGTGGAAGTCGACTTC
38039 AT
1 AT
38041 CTTGAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 26 0.81
18 6 0.19
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (18 bp):
ATTGTGGAAGTCGACTTC
Found at i:38023 original size:17 final size:17
Alignment explanation
Indices: 38001--38040 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
37991 TGGATGTCAC
*
38001 CTTCATTGTGAAGTCGA
1 CTTCATTGTGAAATCGA
38018 CTTCATTGTGAAATCGA
1 CTTCATTGTGAAATCGA
*
38035 GTTCAT
1 CTTCAT
38041 CTTGAAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (17 bp):
CTTCATTGTGAAATCGA
Found at i:38578 original size:84 final size:84
Alignment explanation
Indices: 38483--39193 Score: 791
Period size: 84 Copynumber: 8.4 Consensus size: 84
38473 AATTTCTTTA
* * *
38483 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTGTATTCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT-GTGCCTTTGAGCTGAGCGTAGTCG
*
38548 TACTCGAAGGTCTTTGG-TG
65 AACTCGAAGGTCTTTGGTTG
** * * * * * * * *
38567 ATAGATAACCCTTCTAGCCTTGATTTATACTGTAAATGATGTG-CTCTTGAAGCTGAGTGTAATC
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCT-TTG-AGCTGAGCGTAGTC
*
38631 GAACTTGAAGGTCTTTGGTTG
64 GAACTCGAAGGTCTTTGGTTG
* * * * *
38652 GCAGATAACCCTTATCGACTTAAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGA
38717 ACTCGAAGGTCTTT-GTTG
66 ACTCGAAGGTCTTTGGTTG
* * * *
38735 GCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCG
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTTG-AGCTGAGCGTAGTCG
*
38800 AACTTGAAGGTCTTTGGTTG
65 AACTCGAAGGTCTTTGGTTG
* * * * *
38820 GCAGATAGCCCTTTTCGACTTAAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGCGTAGTCAA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGA
38885 ACTCGAAGGTCTTTTGG-TG
66 ACTCGAAGGTC-TTTGGTTG
* * * * * * ** * * * * * *
38904 ACAAATAACCCTTCTAGCCTTGAGTTATGTTATAAACGATGTGCCCTCGAAGCTGAGTGTAATCA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTTG-AGCTGAGCGTAGTCG
*
38969 AACTTGAAGGTCTTTGGTTG
65 AACTCGAAGGTCTTTGGTTG
* * * *
38989 GCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGA
* *
39054 ACTCGGAGGTCTTTGGATG
66 ACTCGAAGGTCTTTGGTTG
* * * * *
39073 GCAAATAACCCTTCTCGATTTAAGTTATGCTGTAAATGTTGTGCTTTTGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGA
*
39138 ACTCGAAGGTCTTTTGTTG
66 ACTCGAAGGTCTTTGGTTG
* * * *
39157 GCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAAT
1 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
39194 AGTTTCTTTA
Statistics
Matches: 520, Mismatches: 98, Indels: 18
0.82 0.15 0.03
Matches are distributed among these distances:
82 2 0.00
83 52 0.10
84 314 0.60
85 150 0.29
86 2 0.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (84 bp):
GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGA
ACTCGAAGGTCTTTGGTTG
Found at i:38745 original size:168 final size:168
Alignment explanation
Indices: 38483--39171 Score: 921
Period size: 168 Copynumber: 4.1 Consensus size: 168
38473 AATTTCTTTA
* ** *
38483 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTGTATTCG
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGAT-GTGCCTTGGAGCTGAGCATAGTCG
* * * * * * *
38548 TACTCGAAGGTCTTTGGTGATAGATAACCCTTCTAGCCTTGATTTATACTGTAAATGATGTGCTC
65 AACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGTGCCC
* *
38613 TTGAAGCTGAGTGTAATCGAACTTGAAGGTCTTTGGTTG
130 TCGAAGCTGAGCGTAATCGAACTTGAAGGTCTTTGGTTG
* *
38652 GCAGATAACCCTTATCGACTTAAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGA
* * * *
38717 ACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATGATGTGCCCT
66 ACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGTGCCCT
*
38782 CGAAGCTGAGCGTAGTCGAACTTGAAGGTCTTTGGTTG
131 CGAAGCTGAGCGTAATCGAACTTGAAGGTCTTTGGTTG
* * * * * *
38820 GCAGATAGCCCTTTTCGACTTAAGCTATGCTGTAAATGATGTGCCTTTGAGCTGAGCGTAGTCAA
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGA
* * * *
38885 ACTCGAAGGTCTTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATGTTATAAACGATGTGCCC
66 ACTCGAAGGTC-TTTGGTGACAAATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGTGCCC
* *
38950 TCGAAGCTGAGTGTAATCAAACTTGAAGGTCTTTGGTTG
130 TCGAAGCTGAGCGTAATCGAACTTGAAGGTCTTTGGTTG
* * *
38989 GCAGATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGA
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGA
* * * ** * **
39054 ACTCGGAGGTCTTTGGATGGCAAATAACCCTTCTCGATTTAAGTTATGCTGTAAATGTTGTGCTT
66 ACTCGAAGGTCTTTGG-TGACAAATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGTGCCC
* * * *
39119 TTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTG
130 TCGAAGCTGAGCGTAATCGAACTTGAAGGTCTTTGGTTG
39157 GCAGATAACCCTTCT
1 GCAGATAACCCTTCT
39172 AGCCTTGAGT
Statistics
Matches: 455, Mismatches: 63, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
168 231 0.51
169 224 0.49
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (168 bp):
GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGA
ACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGTGCCCT
CGAAGCTGAGCGTAATCGAACTTGAAGGTCTTTGGTTG
Found at i:38966 original size:337 final size:337
Alignment explanation
Indices: 38483--39193 Score: 1057
Period size: 337 Copynumber: 2.1 Consensus size: 337
38473 AATTTCTTTA
* * * *
38483 GCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTGTATTCG
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGGTGCCTTTGAGCTGAGCGTAGTCA
* * * * * * *
38548 TACTCGAAGGTCTTTGGTGATAGATAACCCTTCTAGCCTTGATTTATACTGTAAATGATGTGCTC
66 AACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATACTATAAACGATGTGCCC
* *
38613 TTGAAGCTGAGTGTAATCGAACTTGAAGGTCTTTGGTTGGCAGATAACCCTTATCGACTTAAGCT
131 TCGAAGCTGAGTGTAATCAAACTTGAAGGTCTTTGGTTGGCAGATAACCCTTATCGACTTAAGCT
* * *
38678 ATGTTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTT-GTTGGCAGATA
196 ATGTTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGATGGCAAATA
* *
38742 ACCCTTCTAGCCTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTTGA
261 ACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCG-AGCTGAGCGTAGTCGAACTCGA
38807 AGGTCTTTGGTTG
325 AGGTCTTTGGTTG
* *
38820 GCAGATAGCCCTTTTCGACTTAAGCTATGCTGTAAATGAT-GTGCCTTTGAGCTGAGCGTAGTCA
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGGTGCCTTTGAGCTGAGCGTAGTCA
**
38884 AACTCGAAGGTCTTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATGTTATAAACGATGTGCC
66 AACTCGAAGGTC-TTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATACTATAAACGATGTGCC
* *
38949 CTCGAAGCTGAGTGTAATCAAACTTGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGT
130 CTCGAAGCTGAGTGTAATCAAACTTGAAGGTCTTTGGTTGGCAGATAACCCTTATCGACTTAAGC
*
39014 TATGTTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGGAGGTCTTTGGATGGCAAAT
195 TATGTTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGATGGCAAAT
* * * * ** *
39079 AACCCTTCTCGATTTAAGTTATGCTGTAAATGTTGTGCTTTTGAGCTGAGCGTAGTCGAACTCGA
260 AACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAGCTGAGCGTAGTCGAACTCGA
*
39144 AGGTCTTTTGTTG
325 AGGTCTTTGGTTG
* * * *
39157 GCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAAT
1 GCAGATAACCCTTCTCGACTTAAGCTATGCTGTAAAT
39194 AGTTTCTTTA
Statistics
Matches: 333, Mismatches: 39, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
336 32 0.10
337 258 0.77
338 43 0.13
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (337 bp):
GCAGATAACCCTTCTCGACTTAAGCTATGCTGTAAATGATGGTGCCTTTGAGCTGAGCGTAGTCA
AACTCGAAGGTCTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATACTATAAACGATGTGCCC
TCGAAGCTGAGTGTAATCAAACTTGAAGGTCTTTGGTTGGCAGATAACCCTTATCGACTTAAGCT
ATGTTGCAAATGATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGATGGCAAATA
ACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAGCTGAGCGTAGTCGAACTCGAA
GGTCTTTGGTTG
Found at i:40212 original size:95 final size:95
Alignment explanation
Indices: 40049--40304 Score: 424
Period size: 95 Copynumber: 2.7 Consensus size: 95
40039 GGCTAGCTGA
* * *
40049 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATAGTA
1 ATCCATAGAGCCAGGGCGTTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATAGTA
40114 TAATTACCTTTATCAGGCTAGATGAATATT
66 TAATTACCTTTATCAGGCTAGATGAATATT
* *
40144 ATCCATAGAGCCAGGGCGTTTAACCAATTTCTCTAGAGGGACAACTCAAGCTTTATTATATAGTA
1 ATCCATAGAGCCAGGGCGTTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATAGTA
* *
40209 TAATTACCTTTGTCAGGCTAGCTGAATATT
66 TAATTACCTTTATCAGGCTAGATGAATATT
* *
40239 ATCCATAGAGCCGGGGCTTTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATA-TA
1 ATCCATAGAGCCAGGGCGTTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATAGTA
40303 TA
66 TA
40305 TAATATTATA
Statistics
Matches: 151, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
94 4 0.03
95 147 0.97
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (95 bp):
ATCCATAGAGCCAGGGCGTTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATAGTA
TAATTACCTTTATCAGGCTAGATGAATATT
Found at i:44304 original size:15 final size:15
Alignment explanation
Indices: 44271--44316 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
44261 TAGAATAAAA
44271 AATAATAATAATA-T
1 AATAATAATAATAGT
44285 GAATAATAATAATAGT
1 -AATAATAATAATAGT
*
44301 AATATTAA-AA-AGT
1 AATAATAATAATAGT
44314 AAT
1 AAT
44317 CTAATATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 6 0.21
14 2 0.07
15 20 0.69
16 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.33
Consensus pattern (15 bp):
AATAATAATAATAGT
Found at i:44597 original size:11 final size:11
Alignment explanation
Indices: 44561--44602 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
44551 AACATAACAG
44561 AAATAA-AATAA
1 AAATAATAAT-A
* *
44572 AAATAAAAAGA
1 AAATAATAATA
44583 AAATAATAATA
1 AAATAATAATA
44594 AAATAATAA
1 AAATAATAA
44603 AAGGATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 25 0.93
12 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (11 bp):
AAATAATAATA
Found at i:47098 original size:50 final size:49
Alignment explanation
Indices: 47003--47149 Score: 188
Period size: 50 Copynumber: 2.9 Consensus size: 49
46993 TTTTGTATCG
*
47003 CTTAGATATG-GTTGAATCGAAAAAAATAATTATGCTAGCATTGGTTGAATCA
1 CTTAGATA-GAGTTGAAT-TAAAAAAA-AATTATGCTAGCATTGGTT-AATCA
*
47055 CTTAGATAGAGTTGAATTAAAAAAAAATTATGCTAGCACTGGTTAATCA
1 CTTAGATAGAGTTGAATTAAAAAAAAATTATGCTAGCATTGGTTAATCA
* * * *
47104 ATTAGATATAGTTGAATTGAATAAAAAATTATGCTATCATTGGTTA
1 CTTAGATAGAGTTGAATT-AAAAAAAAATTATGCTAGCATTGGTTA
47150 CACAGGCTTG
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
49 21 0.24
50 42 0.49
51 8 0.09
52 15 0.17
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (49 bp):
CTTAGATAGAGTTGAATTAAAAAAAAATTATGCTAGCATTGGTTAATCA
Found at i:48544 original size:9 final size:9
Alignment explanation
Indices: 48530--48559 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
48520 AACTGGTTCA
48530 CGGTTCAAT
1 CGGTTCAAT
48539 CGGTTCAAT
1 CGGTTCAAT
*
48548 CGGTTGAAT
1 CGGTTCAAT
48557 CGG
1 CGG
48560 CCGATCCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (9 bp):
CGGTTCAAT
Found at i:50820 original size:2 final size:2
Alignment explanation
Indices: 50813--50857 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
50803 CTCCGGTCTT
50813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50855 TA T
1 TA T
50858 TTTTTTTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:62657 original size:21 final size:21
Alignment explanation
Indices: 62627--62676 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
62617 CATTTTGCTT
*
62627 CTCTCTCTAAAGA-ATAAGAAG
1 CTCTCACTAAAGAGA-AAGAAG
*
62648 CTCTCACTAAAGAGAGAGAAG
1 CTCTCACTAAAGAGAAAGAAG
62669 CTCTCACT
1 CTCTCACT
62677 TCTCTCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (21 bp):
CTCTCACTAAAGAGAAAGAAG
Found at i:63650 original size:45 final size:45
Alignment explanation
Indices: 63586--63709 Score: 230
Period size: 45 Copynumber: 2.8 Consensus size: 45
63576 GATGGAAATG
63586 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
63631 TTGAAAACATCATGCACTGAAGGGTTTACAGATGATCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
63676 TTGAAAACATCATGCACTGAAGGGCTTACAGATG
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATG
63710 TGGGAAATAG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (45 bp):
TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
Found at i:64396 original size:22 final size:21
Alignment explanation
Indices: 64371--64422 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 21
64361 AATAAAGCTT
*
64371 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTG-AAAGAAAATCTA
64393 TCATCTTTG--AGAAAATCTA
1 TCATCTTTGAAAGAAAATCTA
64412 TCATCTTTGAA
1 TCATCTTTGAA
64423 GAATGTAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 18 0.67
22 9 0.33
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (21 bp):
TCATCTTTGAAAGAAAATCTA
Found at i:64887 original size:55 final size:55
Alignment explanation
Indices: 64790--64895 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 55
64780 ATCACTGGTT
* *
64790 CGTAAAACATTTGACAATACATTCATCCTTTCCTGTGGCTTCTGCACAGATGTTC
1 CGTAAAACATTTGACAATACATTAATCCTTTCCTGTGACTTCTGCACAGATGTTC
* * *
64845 CGTAAAACATTTGACAATACATTAATCTTTTCTTGTGACTTCTGCCCAGAT
1 CGTAAAACATTTGACAATACATTAATCCTTTCCTGTGACTTCTGCACAGAT
64896 TTCTCATCAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (55 bp):
CGTAAAACATTTGACAATACATTAATCCTTTCCTGTGACTTCTGCACAGATGTTC
Found at i:65760 original size:17 final size:17
Alignment explanation
Indices: 65726--65760 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
65716 TATTTGCTCA
* *
65726 ACATAATGATCTTTAAC
1 ACATAATGATATTCAAC
65743 ACATAATGATATTCAAC
1 ACATAATGATATTCAAC
65760 A
1 A
65761 TGCCCCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (17 bp):
ACATAATGATATTCAAC
Found at i:68332 original size:32 final size:32
Alignment explanation
Indices: 68293--68359 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
68283 TGAAGAAATG
* * * *
68293 GTTGTTATGCTTATCTGGTATAGATACTTCTT
1 GTTGTTATGCTCATCTCGTAGAAATACTTCTT
68325 GTTGTTATGCTCATCTCGTAGAAATACTTCTT
1 GTTGTTATGCTCATCTCGTAGAAATACTTCTT
68357 GTT
1 GTT
68360 TCCAGACTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (32 bp):
GTTGTTATGCTCATCTCGTAGAAATACTTCTT
Found at i:71924 original size:43 final size:42
Alignment explanation
Indices: 71831--71914 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 42
71821 TGTGCATCAA
* *
71831 ACAAAACTTTACATATAGGGGACAACTTTCAGTCCTATCTTT
1 ACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTT
* * *
71873 AACAAAACTTTACATATAGGGGATAACTTTCCCTCTTAACTT
1 -ACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTT
71915 CTCTAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (42 bp):
ACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTT
Found at i:73330 original size:26 final size:28
Alignment explanation
Indices: 73295--73353 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 28
73285 ATACTTGAAA
*
73295 ATAAACATTAATAAAA-AATAA-TATAT
1 ATAAACATTAAGAAAATAATAAGTATAT
* *
73321 ATAAATATTAGGAAAATAATAAGTATAT
1 ATAAACATTAAGAAAATAATAAGTATAT
73349 ATAAA
1 ATAAA
73354 AATTTTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 13 0.46
27 5 0.18
28 10 0.36
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (28 bp):
ATAAACATTAAGAAAATAATAAGTATAT
Found at i:74143 original size:2 final size:2
Alignment explanation
Indices: 74136--74165 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
74126 AATCAAAAAC
74136 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
74166 GATTAAAATA
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):
AT
Found at i:75391 original size:35 final size:35
Alignment explanation
Indices: 75350--75418 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
75340 TTCATGTTCA
75350 AAATTCCAAAACACTTCAATTACATTCTAAACCCG
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCG
*
75385 AAATTCCAAAATACTTCAATTACATTCTAAACCC
1 AAATTCCAAAACACTTCAATTACATTCTAAACCC
75419 TAATGAAGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.43, C:0.28, G:0.01, T:0.28
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACCCG
Found at i:76645 original size:14 final size:14
Alignment explanation
Indices: 76609--76646 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
76599 CGATGAAGCC
76609 AAAGATTCCAAACA
1 AAAGATTCCAAACA
* *
76623 ATA-ATTCCAAATA
1 AAAGATTCCAAACA
76636 AAAGATTCCAA
1 AAAGATTCCAA
76647 TGCTCAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.55, C:0.18, G:0.05, T:0.21
Consensus pattern (14 bp):
AAAGATTCCAAACA
Found at i:79134 original size:15 final size:15
Alignment explanation
Indices: 79116--79164 Score: 89
Period size: 15 Copynumber: 3.3 Consensus size: 15
79106 TCAAGGATTC
79116 GATTTATCAAAATTT
1 GATTTATCAAAATTT
79131 GATTTATCAAAATTT
1 GATTTATCAAAATTT
*
79146 GATTTATCAAAATTC
1 GATTTATCAAAATTT
79161 GATT
1 GATT
79165 CCTCTTACCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (15 bp):
GATTTATCAAAATTT
Found at i:87431 original size:21 final size:21
Alignment explanation
Indices: 87405--87452 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
87395 GCATTGAGGA
* *
87405 GTGACTGACAGTGTGACGGTG
1 GTGACTGACAGCGCGACGGTG
* *
87426 GTGACTGGCGGCGCGACGGTG
1 GTGACTGACAGCGCGACGGTG
87447 GTGACT
1 GTGACT
87453 AGCGTGCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.19, G:0.46, T:0.21
Consensus pattern (21 bp):
GTGACTGACAGCGCGACGGTG
Found at i:87704 original size:42 final size:42
Alignment explanation
Indices: 87564--88040 Score: 253
Period size: 42 Copynumber: 11.5 Consensus size: 42
87554 CAAGGTGGCG
* * * *
87564 TTTTAATAATAAACGCCACTAACGTGCACCTCTATTGCGGCA
1 TTTTTATAACAAACGCCACTAACGTTCACCTCTATTACGGCA
** * * * * * * *
87606 TTTGAACAACAAACACCACTAAGGTACGA-ATCTATTACAG-T
1 TTTTTATAACAAACGCCACTAACGTTC-ACCTCTATTACGGCA
** * *
87647 TTTTTA-ATACAAACGCCACTAATATTCACCTCTATTATGACA
1 TTTTTATA-ACAAACGCCACTAACGTTCACCTCTATTACGGCA
* * * ** *
87689 TTTTTATAACAAACGCCACGAACATTGAGATCTATAACGGC-
1 TTTTTATAACAAACGCCACTAACGTTCACCTCTATTACGGCA
* * * * ** *
87730 GTTTTAGTGACAAACGTCACTAAGGTTTGCCTCTATTACGGTA
1 TTTTTA-TAACAAACGCCACTAACGTTCACCTCTATTACGGCA
* **
87773 TTTTTATAACAAACGCCACTAACGTACGGCTCTA-TAGCGGCA
1 TTTTTATAACAAACGCCACTAACGTTCACCTCTATTA-CGGCA
* * * **
87815 -TTTTAGTGACAAACGCCACTAAGGTTGACCTCTATTGTGGCA
1 TTTTTA-TAACAAACGCCACTAACGTTCACCTCTATTACGGCA
* * * * * *
87857 TTTTCATAATAAACGCCACTAA-GTT-GCTTCTATTGCGGCG
1 TTTTTATAACAAACGCCACTAACGTTCACCTCTATTACGGCA
* * * *
87897 TTTTTATAACAAACGCCACTAAGGTACGA-CTCTA-TAGTGGCG
1 TTTTTATAACAAACGCCACTAACGTTC-ACCTCTATTA-CGGCA
* * * * *
87939 TTTTAATGACAAACACCACTAAGGTTCACCTCTATTGCGGC-
1 TTTTTATAACAAACGCCACTAACGTTCACCTCTATTACGGCA
* * * *
87980 CTTTTAGTAACAAACACCACTGA-GTT-TCCTCTATTACGG-A
1 TTTTTA-TAACAAACGCCACTAACGTTCACCTCTATTACGGCA
88020 GTTTTTTATAACAAACGCCAC
1 --TTTTTATAACAAACGCCAC
88041 CAAGGTACGG
Statistics
Matches: 329, Mismatches: 85, Indels: 43
0.72 0.19 0.09
Matches are distributed among these distances:
40 44 0.13
41 64 0.19
42 208 0.63
43 13 0.04
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Consensus pattern (42 bp):
TTTTTATAACAAACGCCACTAACGTTCACCTCTATTACGGCA
Found at i:87876 original size:84 final size:83
Alignment explanation
Indices: 87655--88040 Score: 304
Period size: 84 Copynumber: 4.6 Consensus size: 83
87645 GTTTTTTAAT
** * * * * * *
87655 ACAAACGCCACTAATATTCACCTCTATTATGACATTTTTATAACAAACGCCACGAACATTGAGAT
1 ACAAACGCCACTAAGGTTGACCTCTATTATGGCATTTTTATAACAAACGCCACTAACGTCG-GCT
* * *
87720 CTATAACGGCGTTTTAGTG
65 CTATAGCGGCATTTTAGTA
* * *
87739 ACAAACGTCACTAAGGTTTG-CCTCTATTACGGTATTTTTATAACAAACGCCACTAACGTACGGC
1 ACAAACGCCACTAAGG-TTGACCTCTATTATGGCATTTTTATAACAAACGCCACTAACGT-CGGC
*
87803 TCTATAGCGGCATTTTAGTG
64 TCTATAGCGGCATTTTAGTA
* * * *
87823 ACAAACGCCACTAAGGTTGACCTCTATTGTGGCATTTTCATAATAAACGCCACTAA-GT-TGCTT
1 ACAAACGCCACTAAGGTTGACCTCTATTATGGCATTTTTATAACAAACGCCACTAACGTCGGC-T
* *
87886 CTATTGCGGCGTTTTTA-TA
65 CTATAGCGGC-ATTTTAGTA
* * * * * * **
87905 ACAAACGCCACTAAGGTACGA-CTCTA-TAGTGGCGTTTTAATGACAAACACCACTAAGGTTCAC
1 ACAAACGCCACTAAGGT-TGACCTCTATTA-TGGCATTTTTATAACAAACGCCACTAACG-TCGG
* *
87968 CTCTATTGCGGCCTTTTAGTA
63 CTCTATAGCGGCATTTTAGTA
* * * *
87989 ACAAACACCACTGA-GTT-TCCTCTATTACGG-AGTTTTTTATAACAAACGCCAC
1 ACAAACGCCACTAAGGTTGACCTCTATTATGGCA--TTTTTATAACAAACGCCAC
88041 CAAGGTACGG
Statistics
Matches: 245, Mismatches: 42, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
81 3 0.01
82 62 0.25
83 38 0.16
84 138 0.56
85 4 0.02
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (83 bp):
ACAAACGCCACTAAGGTTGACCTCTATTATGGCATTTTTATAACAAACGCCACTAACGTCGGCTC
TATAGCGGCATTTTAGTA
Found at i:87932 original size:124 final size:124
Alignment explanation
Indices: 87560--88080 Score: 419
Period size: 124 Copynumber: 4.2 Consensus size: 124
87550 ATCCCAAGGT
* * * * * ** *
87560 GGCGTTTTAATAATAAACGCCACTAACGTGCACCTCTATTGCGGCATTTGAACAACAAACACCAC
1 GGCGTTTTAATGACAAACGCCACTAAGGTTCACCTCTATTGCGGCATTTTAGTAACAAACGCCAC
* ** ** * *
87625 TAAGGTACGAATCTATTAC--AGTTTTT-TAATACAAACGCCACTAATATTC-ACCTCTATTA-T
66 TAA-GT-TGCCTCTATTACGGAGTTTTTAT-A-ACAAACGCCACTAAGGTACGA-CTCTA-TAGC
* * * * * ** * ** ** * * *
87685 GACATTTTTATAACAAACGCCACGAACATTGAGATCTATAACGGCGTTTTAGTGACAAACGTCAC
1 GGCGTTTTAATGACAAACGCCACTAAGGTTCACCTCTATTGCGGCATTTTAGTAACAAACGCCAC
* *
87750 TAAGGTTTGCCTCTATTACGGTA-TTTTTATAACAAACGCCACTAACGTACGGCTCTATAGC
66 TAA-G-TTGCCTCTATTACGG-AGTTTTTATAACAAACGCCACTAAGGTACGACTCTATAGC
* * * * *
87811 GGCATTTTAGTGACAAACGCCACTAAGGTTGACCTCTATTGTGGCATTTTCA-TAATAAACGCCA
1 GGCGTTTTAATGACAAACGCCACTAAGGTTCACCTCTATTGCGGCATTTT-AGTAACAAACGCCA
* * * *
87875 CTAAGTTGCTTCTATTGCGGCGTTTTTATAACAAACGCCACTAAGGTACGACTCTATAGT
65 CTAAGTTGCCTCTATTACGGAGTTTTTATAACAAACGCCACTAAGGTACGACTCTATAGC
* * *
87935 GGCGTTTTAATGACAAACACCACTAAGGTTCACCTCTATTGCGGCCTTTTAGTAACAAACACCAC
1 GGCGTTTTAATGACAAACGCCACTAAGGTTCACCTCTATTGCGGCATTTTAGTAACAAACGCCAC
* * * * * *
88000 TGAGTTTCCTCTATTACGGAGTTTTTTATAACAAACGCCACCAAGGTACGGA-TTTTTAAC
66 TAAGTTGCCTCTATTACGGAG-TTTTTATAACAAACGCCACTAAGGTAC-GACTCTATAGC
*
88060 GGCGTTTTATTGACAAACGCC
1 GGCGTTTTAATGACAAACGCC
88081 GCCAATTTTG
Statistics
Matches: 315, Mismatches: 69, Indels: 24
0.77 0.17 0.06
Matches are distributed among these distances:
123 1 0.00
124 119 0.38
125 112 0.36
126 74 0.23
127 7 0.02
128 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (124 bp):
GGCGTTTTAATGACAAACGCCACTAAGGTTCACCTCTATTGCGGCATTTTAGTAACAAACGCCAC
TAAGTTGCCTCTATTACGGAGTTTTTATAACAAACGCCACTAAGGTACGACTCTATAGC
Found at i:98292 original size:37 final size:34
Alignment explanation
Indices: 98219--98292 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 34
98209 TTTTTATATT
98219 TTTAATTTTGTAAAAAAATATAAAATATTATAAA
1 TTTAATTTTGTAAAAAAATATAAAATATTATAAA
* *
98253 TTTAATTTTTTAAAGAAAATATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATATA-AAATATTATA-AA
98290 TTT
1 TTT
98293 GTAATATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
34 13 0.37
35 8 0.23
36 9 0.26
37 5 0.14
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (34 bp):
TTTAATTTTGTAAAAAAATATAAAATATTATAAA
Found at i:99212 original size:24 final size:24
Alignment explanation
Indices: 99158--99213 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
99148 AGAGTTTATT
*
99158 TTTTAAAATAAAAGTTATTTTAAA
1 TTTTAAAATAAAAGTTATTTCAAA
*
99182 TTATAAATATAAAA-TTA-TTCAAA
1 TTTTAAA-ATAAAAGTTATTTCAAA
99205 TATTTAAAA
1 T-TTTAAAA
99214 AAATAAGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
23 7 0.26
24 14 0.52
25 6 0.22
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (24 bp):
TTTTAAAATAAAAGTTATTTCAAA
Found at i:100291 original size:18 final size:18
Alignment explanation
Indices: 100265--100316 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
100255 ACGTAGGATT
*
100265 TGTCTCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
100283 TGTCCCGAAGAACCACTA
1 TGTCCCGAAGGACCACTA
*
100301 TGTCCTGAAGGACCAC
1 TGTCCCGAAGGACCAC
100317 ATATCACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:100411 original size:21 final size:21
Alignment explanation
Indices: 100364--100440 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
100354 CATATACACA
* *
100364 TTCCAATGGACCAAATA-AGTG
1 TTCCAAAGGACCACATATA-TG
* *
100385 TACCAAAGTACCACATATATG
1 TTCCAAAGGACCACATATATG
**
100406 TTCCAAAGGATTACATATATG
1 TTCCAAAGGACCACATATATG
*
100427 -TCCTGAAGGACCAC
1 TTCC-AAAGGACCAC
100441 GTAGAACCAT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 3 0.07
21 39 0.91
22 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (21 bp):
TTCCAAAGGACCACATATATG
Found at i:101365 original size:20 final size:20
Alignment explanation
Indices: 101324--101362 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
101314 AATTGCCTGT
*
101324 AGTATCGGTACCTACTAACC
1 AGTATCGGTACCTACCAACC
*
101344 AGTATCGTTA-CTACCAACC
1 AGTATCGGTACCTACCAACC
101363 CAGAATTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.26
Consensus pattern (20 bp):
AGTATCGGTACCTACCAACC
Done.