Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003097.1 Hibiscus syriacus cultivar Beakdansim tig00006465_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: 95018
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:420 original size:18 final size:18
Alignment explanation
Indices: 394--436 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
384 GTTTCGGATT
*
394 TTCGGTTGAATTTAGATA
1 TTCGATTGAATTTAGATA
412 TTCGATTGAATTTAGATA
1 TTCGATTGAATTTAGATA
430 TTCGATT
1 TTCGATT
437 TACATTCGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.47
Consensus pattern (18 bp):
TTCGATTGAATTTAGATA
Found at i:1049 original size:21 final size:21
Alignment explanation
Indices: 1025--1075 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1015 TTGTTCAAAT
1025 GATCAATCCTTTAGACAAAAA
1 GATCAATCCTTTAGACAAAAA
* * * *
1046 GATCGATCCTTTTGACCAAAG
1 GATCAATCCTTTAGACAAAAA
1067 GATCAATCC
1 GATCAATCC
1076 CCTTGATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (21 bp):
GATCAATCCTTTAGACAAAAA
Found at i:1081 original size:21 final size:20
Alignment explanation
Indices: 1020--1096 Score: 57
Period size: 21 Copynumber: 3.8 Consensus size: 20
1010 ATTTTTTGTT
* *
1020 CAAATGATCAAT-CCTTTAGA
1 CAAAAGATCAATCCCCTT-GA
* **
1040 CAAAAAGATCGATCCTTTTGA
1 C-AAAAGATCAATCCCCTTGA
*
1061 CCAAAGGATCAATCCCCTTGA
1 -CAAAAGATCAATCCCCTTGA
*
1082 TAAAAGATCAATCCC
1 CAAAAGATCAATCCC
1097 TTCGATACTA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 14 0.31
21 26 0.58
22 5 0.11
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.25
Consensus pattern (20 bp):
CAAAAGATCAATCCCCTTGA
Found at i:4933 original size:2 final size:2
Alignment explanation
Indices: 4890--4924 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
4880 TTCACAACAA
4890 AT AT -T 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
4925 GAGATATATC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:18666 original size:17 final size:17
Alignment explanation
Indices: 18636--18675 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
18626 ATACTTTAGT
*
18636 TATATTTTTTATTAAAAA
1 TATA-TTTTAATTAAAAA
*
18654 TATATTTTAATTAAATA
1 TATATTTTAATTAAAAA
18671 TATAT
1 TATAT
18676 AAGTTTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATTTTAATTAAAAA
Found at i:18996 original size:2 final size:2
Alignment explanation
Indices: 18989--19046 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
18979 TTCTACATAC
18989 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
19031 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
19047 TTCCTTTTTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19609 original size:19 final size:20
Alignment explanation
Indices: 19585--19634 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
19575 AATGACCAAC
19585 AAAATCGCAACACGAAATA-
1 AAAATCGCAACACGAAATAG
* **
19604 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACACGAAATAG
19624 AAAATCGCAAC
1 AAAATCGCAAC
19635 GGTCAAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.50, C:0.22, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAATAG
Found at i:19629 original size:20 final size:20
Alignment explanation
Indices: 19604--19832 Score: 204
Period size: 20 Copynumber: 11.2 Consensus size: 20
19594 ACACGAAATA
*
19604 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
19624 AAAATCGCAACG-G--TCAAAAG
1 AAAATCGCAACGCGATTC---AG
19644 AAAATCGCAACGCGATATTCCA-
1 AAAATCGCAACGCG--ATT-CAG
* * *
19666 AGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
19686 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
19708 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
19728 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
19748 AGAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
19768 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
19788 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
19808 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
19828 AAAAT
1 AAAAT
19833 GAGTAAATTC
Statistics
Matches: 178, Mismatches: 13, Indels: 36
0.78 0.06 0.16
Matches are distributed among these distances:
17 1 0.01
19 7 0.04
20 133 0.75
21 4 0.02
22 29 0.16
23 2 0.01
25 1 0.01
26 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:19793 original size:60 final size:60
Alignment explanation
Indices: 19668--19825 Score: 255
Period size: 60 Copynumber: 2.6 Consensus size: 60
19658 ATATTCCAAG
* * *
19668 AATCGCAATGCGATT-AAGAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCCA-AGAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTAAGAA
19730 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAA
19790 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
19826 AGAAAATGAG
Statistics
Matches: 92, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
60 62 0.67
62 29 0.32
63 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (60 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAGAA
Found at i:19939 original size:6 final size:6
Alignment explanation
Indices: 19928--20002 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
19918 GACACGTATT
19928 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
19976 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
20003 CGAGACGAGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:20509 original size:6 final size:6
Alignment explanation
Indices: 20498--20548 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
20488 TCTCGTCTCG
20498 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
20546 GGT
1 GGT
20549 AATACGTGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:20669 original size:20 final size:20
Alignment explanation
Indices: 20644--21049 Score: 365
Period size: 20 Copynumber: 20.2 Consensus size: 20
20634 GAATTTACTC
20644 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
20664 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
20684 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
20704 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
20724 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
20744 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
* *
20764 ATTCTT-GGAATCGTGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
* *
20784 ATTTTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
20804 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
20824 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
20844 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
20864 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
20884 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
20904 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* * *
20926 ATTCTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
20946 ATTCTT-GGAATATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
20968 ATTTTCTTTTG-A-C-CGTTGCG
1 ATTTTC---TGAATCGCGTTGCG
* *
20988 ATTTT-T--TTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
*
21006 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
21026 ATTTT-T-ATTTCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
21045 ATTTT
1 ATTTT
21050 GTTGGTCATT
Statistics
Matches: 318, Mismatches: 40, Indels: 57
0.77 0.10 0.14
Matches are distributed among these distances:
16 2 0.01
18 13 0.04
19 27 0.08
20 225 0.71
21 22 0.07
22 28 0.09
25 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:20706 original size:40 final size:40
Alignment explanation
Indices: 20651--20948 Score: 410
Period size: 40 Copynumber: 7.4 Consensus size: 40
20641 CTCATTTTCT
20651 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
20691 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
20731 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
* *
20771 GAATCGTGTTGCGATTTTCTTAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
*
20811 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTT-G
20851 GAATCGCGTTGCGA--TTCTTGGAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGATTTTCTT--AATCGCGTTGCGA--TTCTTG
***
20892 -AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTCT-
1 GAATCGCGTTGCGATT-TTCTTA-ATCGCGTTGCGATTCT-TG
* *
20933 TAATCGCATTGCGATT
1 GAATCGCGTTGCGATT
20949 CTTGGAATAT
Statistics
Matches: 237, Mismatches: 9, Indels: 22
0.88 0.03 0.08
Matches are distributed among these distances:
38 5 0.02
39 2 0.01
40 196 0.83
41 2 0.01
42 28 0.12
43 4 0.02
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (40 bp):
GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
Found at i:21002 original size:18 final size:18
Alignment explanation
Indices: 20961--21010 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
20951 TGGAATATCG
* *
20961 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGA-TTT-TTTTCAA
20981 CGTTGCGATTTTTTTCAA
1 CGTTGCGATTTTTTTCAA
20999 CGTTGCGATTTT
1 CGTTGCGATTTT
21011 CTAAATCGCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 17 0.61
19 3 0.11
20 8 0.29
ACGTcount: A:0.12, C:0.18, G:0.20, T:0.50
Consensus pattern (18 bp):
CGTTGCGATTTTTTTCAA
Found at i:21646 original size:21 final size:21
Alignment explanation
Indices: 21622--21717 Score: 79
Period size: 20 Copynumber: 4.7 Consensus size: 21
21612 CGATTTTCCC
*
21622 AATTCGTAATGCGAATAAGTA
1 AATTCGCAATGCGAATAAGTA
* ** *
21643 AATT-GCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTA
*
21663 AAATCGCAATGCGAATAAGTA
1 AATTCGCAATGCGAATAAGTA
* ** *
21684 AA-TCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTA
*
21704 AAATCGCAATGCGA
1 AATTCGCAATGCGA
21718 TACTGACTAT
Statistics
Matches: 58, Mismatches: 15, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
20 30 0.52
21 28 0.48
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.20
Consensus pattern (21 bp):
AATTCGCAATGCGAATAAGTA
Found at i:21657 original size:20 final size:20
Alignment explanation
Indices: 21632--21698 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
21622 AATTCGTAAT
*
21632 GCGAATAAGTAAATTGCAAC
1 GCGAATAAGTAAATCGCAAC
** * *
21652 GCGAATTGGGAAAATCGCAAT
1 GCGAA-TAAGTAAATCGCAAC
21673 GCGAATAAGTAAATCGCAAC
1 GCGAATAAGTAAATCGCAAC
21693 GCGAAT
1 GCGAAT
21699 TGGGAAAATC
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 22 0.59
21 15 0.41
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (20 bp):
GCGAATAAGTAAATCGCAAC
Found at i:21731 original size:20 final size:20
Alignment explanation
Indices: 21706--21800 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
21696 AATTGGGAAA
*
21706 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
21726 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
** *
21747 ATCGCAACAAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
21767 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
21787 TTCGCAACGCGATA
1 ATCGCAACGCGATA
21801 ATACATAATC
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 46 0.78
21 13 0.22
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:21732 original size:41 final size:41
Alignment explanation
Indices: 21629--21717 Score: 169
Period size: 41 Copynumber: 2.2 Consensus size: 41
21619 CCCAATTCGT
*
21629 AATGCGAATAAGTAAATTGCAACGCGAATTGGGAAAATCGC
1 AATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGC
21670 AATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGC
1 AATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGC
21711 AATGCGA
1 AATGCGA
21718 TACTGACTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.18
Consensus pattern (41 bp):
AATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCGC
Found at i:22016 original size:22 final size:22
Alignment explanation
Indices: 21988--22031 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
21978 CACTCTCTCA
21988 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
22010 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
22032 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:22320 original size:20 final size:20
Alignment explanation
Indices: 22295--22332 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22285 CGATTCTCTC
22295 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
22315 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
22333 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:23672 original size:18 final size:18
Alignment explanation
Indices: 23651--23695 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
23641 TCCACTTCGG
**
23651 GAGCCATCACCTCGTCCA
1 GAGCCATCACCTCACCCA
*
23669 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
23687 GAGCCATCA
1 GAGCCATCA
23696 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:24223 original size:19 final size:19
Alignment explanation
Indices: 24201--24294 Score: 77
Period size: 19 Copynumber: 5.5 Consensus size: 19
24191 GAAATTGCTA
24201 CGCAATGCGAAATGAAAAT
1 CGCAATGCGAAATGAAAAT
*
24220 CGCAA--CG--A-CAAAAT
1 CGCAATGCGAAATGAAAAT
24234 CGCAATGCGAAATG-AAAT
1 CGCAATGCGAAATGAAAAT
24252 CGCAA--C---A-GCAAAAT
1 CGCAATGCGAAATG-AAAAT
*
24266 CGCAACGCGAAATGAAAAT
1 CGCAATGCGAAATGAAAAT
24285 CGCAATGCGA
1 CGCAATGCGA
24295 TTTGTGTTTC
Statistics
Matches: 59, Mismatches: 3, Indels: 26
0.67 0.03 0.30
Matches are distributed among these distances:
12 1 0.02
13 1 0.02
14 19 0.32
15 1 0.02
16 4 0.07
17 2 0.03
18 10 0.17
19 20 0.34
20 1 0.02
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
CGCAATGCGAAATGAAAAT
Found at i:24234 original size:14 final size:14
Alignment explanation
Indices: 24215--24272 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
24205 ATGCGAAATG
24215 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
24229 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
24245 ATGAAATCGCAAC-AGC
1 A--AAATCGCAACGA-C
24261 AAAATCGCAACG
1 AAAATCGCAACG
24273 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 6 0.17
18 9 0.25
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:24257 original size:32 final size:33
Alignment explanation
Indices: 24201--24289 Score: 146
Period size: 32 Copynumber: 2.7 Consensus size: 33
24191 GAAATTGCTA
24201 CGCAATGCGAAATGAAAATCGCAAC-GACAAAAT
1 CGCAATGCGAAATGAAAATCGCAACAG-CAAAAT
24234 CGCAATGCGAAATG-AAATCGCAACAGCAAAAT
1 CGCAATGCGAAATGAAAATCGCAACAGCAAAAT
*
24266 CGCAACGCGAAATGAAAATCGCAA
1 CGCAATGCGAAATGAAAATCGCAA
24290 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
32 29 0.55
33 24 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
CGCAATGCGAAATGAAAATCGCAACAGCAAAAT
Found at i:24325 original size:14 final size:14
Alignment explanation
Indices: 24306--24363 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
24296 TTGTGTTTCG
24306 CGTTGCGATTTTGC
1 CGTTGCGATTTTGC
*
24320 CGTTGCGATTTCATTTC
1 CGTTGCGA-TT--TTGC
*
24337 GCGTTGCGATTTTGT
1 -CGTTGCGATTTTGC
24352 CGTTGCGATTTT
1 CGTTGCGATTTT
24364 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
15 4 0.11
17 5 0.14
18 8 0.22
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGC
Found at i:24370 original size:33 final size:32
Alignment explanation
Indices: 24301--24421 Score: 134
Period size: 32 Copynumber: 3.5 Consensus size: 32
24291 GCGATTTGTG
24301 TTTCGCGTTGCGATTTTGCCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGCCGTTGCGATTTCA
*
24333 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGCCGTTGCGA-TTTCA
* * *
24366 TTTCGCATTGCGATAGCCATTTCCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGAT-----TTTGC-CGTTGCGAT-TTCA
24405 TTTCGCGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
24422 AAGTTTCGTG
Statistics
Matches: 75, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
32 26 0.35
33 18 0.24
34 3 0.04
38 4 0.05
39 24 0.32
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.43
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGCCGTTGCGATTTCA
Found at i:24378 original size:19 final size:19
Alignment explanation
Indices: 24320--24437 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
24310 GCGATTTTGC
24320 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
24338 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
24352 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
24371 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
24391 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
24410 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
24430 TGTTGCGA
1 CGTTGCGA
24438 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:26445 original size:14 final size:14
Alignment explanation
Indices: 26426--26479 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
26416 CGAAATGGCT
26426 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
26440 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
26459 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
26473 ATCGCAA
1 ATCGCAA
26480 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:26497 original size:33 final size:33
Alignment explanation
Indices: 26407--26484 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
26397 AAAACAGATT
* ***
26407 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
26440 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
26473 ATCGCAATGCGA
1 ATCGCAATGCGA
26485 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:26528 original size:20 final size:20
Alignment explanation
Indices: 26503--26580 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
26493 TCGCATTGCG
*
26503 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
26523 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
26543 ATTTTCGCATTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
26563 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
26581 TCAAATGAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:27667 original size:24 final size:24
Alignment explanation
Indices: 27640--27693 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
27630 GTATTCGAAA
* *
27640 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
27664 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
27688 TTTGAT
1 TTTGAT
27694 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:30204 original size:19 final size:19
Alignment explanation
Indices: 30182--30312 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
30172 GGAAATTACT
30182 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
30201 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
30215 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
30234 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
* *
30248 TTCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
30267 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
30281 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
30300 ATCGCAACGCGAA
1 ATCGCAATGCGAA
30313 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 27 0.33
15 3 0.04
16 5 0.06
17 5 0.06
18 3 0.04
19 39 0.48
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:30224 original size:33 final size:33
Alignment explanation
Indices: 30182--30308 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
30172 GGAAATTACT
30182 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
30215 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
30247 TTTCGCAATGCAAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
30281 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
30309 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:30289 original size:66 final size:66
Alignment explanation
Indices: 30183--30315 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
30173 GAAATTACTA
* *
30183 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
30248 T
66 T
*
30249 TCGCAATGCAAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
30314 T
66 T
30315 T
1 T
30316 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:30490 original size:14 final size:14
Alignment explanation
Indices: 30471--30507 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
30461 CATCAATTAA
30471 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
30485 ACAAATCACCTTTT
1 ACAAATCAACTTTT
30499 ACAAATCAA
1 ACAAATCAA
30508 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:31932 original size:21 final size:21
Alignment explanation
Indices: 31866--31932 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
31856 GTGAATCGGG
*
31866 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
31886 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
31908 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
31929 CTCT
1 CTCT
31933 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:31951 original size:42 final size:42
Alignment explanation
Indices: 31866--31988 Score: 124
Period size: 42 Copynumber: 2.9 Consensus size: 42
31856 GTGAATCGGG
* * * * *
31866 CTCTTGAATGGTGGGA-GGGACCTCTTCAACG-ATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGAATGATAGGGGC
31908 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
* * * * *
31950 CTCTTCAACGATAGGAGTGGACTCTTGAGGAATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
31989 CGAGTCGGGC
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.88
43 4 0.06
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
Found at i:34007 original size:20 final size:19
Alignment explanation
Indices: 33976--34036 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
33966 TCTTTTGGTT
33976 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
33995 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
34016 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
34035 GA
1 GA
34037 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:34058 original size:33 final size:33
Alignment explanation
Indices: 34001--34097 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 33
33991 ACGAGATAAT
*
34001 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
34035 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
34068 GACAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
34098 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 43 0.75
34 14 0.25
ACGTcount: A:0.40, C:0.25, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:34131 original size:19 final size:19
Alignment explanation
Indices: 34098--34178 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
34088 AAAATCGCAA
**
34098 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
34117 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
34136 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
34150 TGCGATAGTTATTTTCGCGT
1 TGCGATTTTTA-TTTCGCGT
34170 TGCGATTTT
1 TGCGATTTT
34179 CATTCTAGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 22 0.44
20 12 0.24
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:34768 original size:41 final size:41
Alignment explanation
Indices: 34716--34793 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
34706 CGAAAGTCAG
* * *
34716 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
*
34757 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
34794 CCCAATTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:34790 original size:20 final size:20
Alignment explanation
Indices: 34697--34790 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
34687 CGCTATGTAA
* *
34697 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
34717 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* ** * *
34737 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTAAGT
*
34758 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
34778 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
34791 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:34809 original size:41 final size:41
Alignment explanation
Indices: 34716--34811 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
34706 CGAAAGTCAG
* * * ** *
34716 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
*
34757 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
34799 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
34812 TTACTTATTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:35431 original size:12 final size:12
Alignment explanation
Indices: 35414--35464 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 12
35404 CTATCGCAAA
35414 TTCGCGTTGCAT
1 TTCGCGTTGCAT
35426 TTCGCGTTGCGAT
1 TTCGCGTTGC-AT
35439 AGTT-GAACGTTGCAT
1 --TTCG--CGTTGCAT
35454 TTCGCGTTGCA
1 TTCGCGTTGCA
35465 ATAGTTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
12 17 0.52
13 4 0.12
14 2 0.06
15 4 0.12
16 6 0.18
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.37
Consensus pattern (12 bp):
TTCGCGTTGCAT
Found at i:35450 original size:28 final size:28
Alignment explanation
Indices: 35418--35473 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
35408 CGCAAATTCG
*
35418 CGTTGCATTTCGCGTTGCGATAGTTGAA
1 CGTTGCATTTCGCGTTGCAATAGTTGAA
35446 CGTTGCATTTCGCGTTGCAATAGTTGAA
1 CGTTGCATTTCGCGTTGCAATAGTTGAA
35474 AATCGCGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.36
Consensus pattern (28 bp):
CGTTGCATTTCGCGTTGCAATAGTTGAA
Found at i:35502 original size:40 final size:41
Alignment explanation
Indices: 35458--35543 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
35448 TTGCATTTCG
35458 CGTTGCAATAGT-TGAAAATCG-CGTTGCGATTTTCCAAATT
1 CGTTGCAATAGTCT-AAAATCGTCGTTGCGATTTTCCAAATT
* * * * *
35498 CGTTGCGATAGTCTACAGTTGTTGTTGCGATTTTCCAAATT
1 CGTTGCAATAGTCTAAAATCGTCGTTGCGATTTTCCAAATT
35539 CGTTG
1 CGTTG
35544 AAAAAAAAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 15 0.38
41 24 0.62
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
CGTTGCAATAGTCTAAAATCGTCGTTGCGATTTTCCAAATT
Found at i:35503 original size:19 final size:19
Alignment explanation
Indices: 35479--35543 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
35469 TTGAAAATCG
35479 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
* * **
35498 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGAT--TTTCCAAAT-T
*
35520 TGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
35539 CGTTG
1 CGTTG
35544 AAAAAAAAGA
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
19 14 0.42
20 5 0.15
21 5 0.15
22 9 0.27
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:35543 original size:22 final size:22
Alignment explanation
Indices: 35480--35543 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
35470 TGAAAATCGC
35480 GTTGCGATTTTCCAAATTC---
1 GTTGCGATTTTCCAAATTCGTT
** * *
35499 GTTGCGATAGTCTACAGTT-GTT
1 GTTGCGATTTTCCA-AATTCGTT
35521 GTTGCGATTTTCCAAATTCGTT
1 GTTGCGATTTTCCAAATTCGTT
35543 G
1 G
35544 AAAAAAAAGA
Statistics
Matches: 32, Mismatches: 8, Indels: 7
0.68 0.17 0.15
Matches are distributed among these distances:
19 11 0.34
20 3 0.09
21 3 0.09
22 15 0.47
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (22 bp):
GTTGCGATTTTCCAAATTCGTT
Found at i:35629 original size:6 final size:6
Alignment explanation
Indices: 35618--35678 Score: 101
Period size: 6 Copynumber: 10.7 Consensus size: 6
35608 AGACACGTAT
35618 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC-C
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
35665 GACC-C GACC-C GACC
1 GACCAC GACCAC GACC
35679 CGAGACGAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.27
6 40 0.73
ACGTcount: A:0.30, C:0.52, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:36334 original size:20 final size:20
Alignment explanation
Indices: 36283--36334 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
36273 ACTGTAGACT
*
36283 ATCGCAACGCAAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
36303 ATCGCAATGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
36323 ATCGCAACGCGA
1 ATCGCAACGCGA
36335 TTTTCAACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:36369 original size:22 final size:22
Alignment explanation
Indices: 36341--36414 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
36331 GCGATTTTCA
36341 ACTATCGCAACGACAACTGTAG
1 ACTATCGCAACGACAACTGTAG
* *
36363 ACTATCGCAACG--AA-TTTGG
1 ACTATCGCAACGACAACTGTAG
** *
36382 AAAATCACAACGACAACTGTAG
1 ACTATCGCAACGACAACTGTAG
36404 ACTATCGCAAC
1 ACTATCGCAAC
36415 TCGAAATGGA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
19 12 0.31
20 2 0.05
21 2 0.05
22 23 0.59
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.19
Consensus pattern (22 bp):
ACTATCGCAACGACAACTGTAG
Found at i:43549 original size:21 final size:22
Alignment explanation
Indices: 43518--43558 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
43508 ATTTTGAAAA
43518 AAATAAAAATAAAATGAAAACT
1 AAATAAAAATAAAATGAAAACT
43540 AAAT-AAAATAAAATGAAAA
1 AAATAAAAATAAAATGAAAA
43559 TGTATGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (22 bp):
AAATAAAAATAAAATGAAAACT
Found at i:44863 original size:15 final size:15
Alignment explanation
Indices: 44843--44872 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44833 AGAAGGTAAA
*
44843 ATTATTTTTTATTAT
1 ATTATTTTTAATTAT
44858 ATTATTTTTAATTAT
1 ATTATTTTTAATTAT
44873 TTGACCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTATTTTTAATTAT
Found at i:50401 original size:26 final size:24
Alignment explanation
Indices: 50351--50402 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 24
50341 GCTCTCTGTT
*
50351 CGAACATAAATGAACGAACATAAA
1 CGAACATAAATGAACGAACACAAA
**
50375 CGAACATATAATCGAACGTTCACAAA
1 CGAACATA-AAT-GAACGAACACAAA
50401 CG
1 CG
50403 TAAATGAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 8 0.35
25 3 0.13
26 12 0.52
ACGTcount: A:0.50, C:0.21, G:0.13, T:0.15
Consensus pattern (24 bp):
CGAACATAAATGAACGAACACAAA
Found at i:51267 original size:665 final size:666
Alignment explanation
Indices: 49991--51322 Score: 2477
Period size: 665 Copynumber: 2.0 Consensus size: 666
49981 AATTTTTTTT
49991 TTGTTCATGTTCGTTCATTAAAGAATATAGTTTGTTAATGTCCGTTCATTTACATAATAAACAAA
1 TTGTTCATGTTCGTTCATTAAAGAATATAGTTTGTTAATGTCCGTTCATTTACATAATAAACAAA
*
50056 TATAAACGAACACGAACGAACACAATAAACGAACAACACAAACACAAAAAAAATTATTTGAATTC
66 TATAAACGAACACGAACGAACACAATAAACGAACAACAAAAACACAAAAAAAATTATTTGAATTC
50121 AACAAACGAATGTATAAAAAAATAAACAACAAGAATAACAACTTAAAATTCATTAATATAACCTG
131 AACAAACGAATGTATAAAAAAATAAACAACAAGAATAACAACTTAAAATTCATTAATATAACCTG
*
50186 CAACTTTAGAGTTAATTTGTTCGAATACGACAAAAACATACATAAATCATAAATTAGCTATATAA
196 CAACTTTAGAGTTAATTTGTTCGAATACGACAAAAACATACATAAATCATAAATAAGCTATATAA
*
50251 ACATAATAAAGTCTTAAAGTTAATTTGTTCAACAAAACAATCTTCTTGAAATTCAAACAACTTCA
261 ACATAATAAAATCTTAAAGTTAATTTGTTCAACAAAACAATCTTCTTGAAATTCAAACAACTTCA
*
50316 ATAATCTTCGTAACATATTCAACTTGCTCTCTGTTCGAACATAAATGAACGAACATAAACGAACA
326 ATAATCTTCGTAACATATTCAACTTGCTATCTGTTCGAACATAAATGAACGAACATAAACGAACA
*
50381 TATAATCGAACGTTCACAAACGTAAATGAACGAACGAGCCTTTTGTTCATGTTCGTTCATTTAAT
391 TATAATCGAACGTTCACAAAAGTAAATGAACGAACGAGCCTTTTGTTCATGTTCGTTCATTTAAT
* *
50446 TAAACGAACGTAAAATCATGTTCATGTTCGTTCATTTAATAAATAAATGAACATAAATGAACTTA
456 TAAACGAACATAAAATCATGTTCATGTTCGTTCATTTAATAAATAAACGAACATAAATGAACTTA
* * *
50511 TCGTCACACGATTCATGAACGATTCGCTGAATATTCAATTCATTTACGGGCCACTTCACGCACTT
521 TCATCACACGATTCATGAACAATTCACTGAATATTCAATTCATTTACGGGCCACTTCACGCACTT
50576 AAAAGTCGCTTGGATCTTTGCTTTTCCTAAGGGTCAA-CTTGCATTGAATTAAATCTTACGTCCA
586 AAAAGTCGCTTGGATCTTTGCTTTTCCTAAGGGTCAACCTTGCATTGAATTAAATCTTACGTCCA
*
50640 TTATCATTATTCGTTA
651 TTATCATCATTCGTTA
* * *
50656 TTGTTTATGTTCGTTCATTAAGGAATATAGTTTGTTCATGTCCGTTCATTTACATAATAAACAAA
1 TTGTTCATGTTCGTTCATTAAAGAATATAGTTTGTTAATGTCCGTTCATTTACATAATAAACAAA
*
50721 TATAAACGAACACGAACGAACACAATAAACGAATAACAAAAACACAAAAAAAATTATTTGAATTC
66 TATAAACGAACACGAACGAACACAATAAACGAACAACAAAAACACAAAAAAAATTATTTGAATTC
50786 AACAAACGAATGTATAAAAAAATAAACAACAAGAATAACAACTTAAAATTCATTAATATAACCTG
131 AACAAACGAATGTATAAAAAAATAAACAACAAGAATAACAACTTAAAATTCATTAATATAACCTG
50851 CAACTTTAGAGTTAATTTGTTCGAATACGACAAAAACATACATAAATCATAAATAAGCTATATAA
196 CAACTTTAGAGTTAATTTGTTCGAATACGACAAAAACATACATAAATCATAAATAAGCTATATAA
50916 ACATAATAAAATCTTAAAGTTAATTTGTTCAACAAAACAATCTTCTTGAAATTCAAACAACTTCA
261 ACATAATAAAATCTTAAAGTTAATTTGTTCAACAAAACAATCTTCTTGAAATTCAAACAACTTCA
50981 ATAATCTTCGTAACATATTCAACTTGCTATCTGTTCGAACATAAATGAACGAACATAAACGAACA
326 ATAATCTTCGTAACATATTCAACTTGCTATCTGTTCGAACATAAATGAACGAACATAAACGAACA
51046 TATAATCGAACGTTCACAAAAGTAAATGAACGAACGAGCCTTTTGTTCATGTTCGTTCATTTAAT
391 TATAATCGAACGTTCACAAAAGTAAATGAACGAACGAGCCTTTTGTTCATGTTCGTTCATTTAAT
* *
51111 TAAATGAACATAAAATCATGTTCATGTTCGTTCATTTAATAAATAAACGAACATAAATGAACTTC
456 TAAACGAACATAAAATCATGTTCATGTTCGTTCATTTAATAAATAAACGAACATAAATGAACTTA
* *
51176 TCATCACACGATTTATGAATAATTCACTGAATATTCAATTCATTTACGGGCCACTTCACGCACTT
521 TCATCACACGATTCATGAACAATTCACTGAATATTCAATTCATTTACGGGCCACTTCACGCACTT
51241 AAAAGTCGCTTGGATCTTTGCTTTTCCTAAGGGTCAACCCTTGCATTGAATTAAATCTTACGTCC
586 AAAAGTCGCTTGGATCTTTGCTTTTCCTAAGGGTCAA-CCTTGCATTGAATTAAATCTTACGTCC
51306 ATTATCATCATTCGTTA
650 ATTATCATCATTCGTTA
51323 GGTCATGTAT
Statistics
Matches: 646, Mismatches: 19, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
665 604 0.93
667 42 0.07
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (666 bp):
TTGTTCATGTTCGTTCATTAAAGAATATAGTTTGTTAATGTCCGTTCATTTACATAATAAACAAA
TATAAACGAACACGAACGAACACAATAAACGAACAACAAAAACACAAAAAAAATTATTTGAATTC
AACAAACGAATGTATAAAAAAATAAACAACAAGAATAACAACTTAAAATTCATTAATATAACCTG
CAACTTTAGAGTTAATTTGTTCGAATACGACAAAAACATACATAAATCATAAATAAGCTATATAA
ACATAATAAAATCTTAAAGTTAATTTGTTCAACAAAACAATCTTCTTGAAATTCAAACAACTTCA
ATAATCTTCGTAACATATTCAACTTGCTATCTGTTCGAACATAAATGAACGAACATAAACGAACA
TATAATCGAACGTTCACAAAAGTAAATGAACGAACGAGCCTTTTGTTCATGTTCGTTCATTTAAT
TAAACGAACATAAAATCATGTTCATGTTCGTTCATTTAATAAATAAACGAACATAAATGAACTTA
TCATCACACGATTCATGAACAATTCACTGAATATTCAATTCATTTACGGGCCACTTCACGCACTT
AAAAGTCGCTTGGATCTTTGCTTTTCCTAAGGGTCAACCTTGCATTGAATTAAATCTTACGTCCA
TTATCATCATTCGTTA
Found at i:57064 original size:27 final size:27
Alignment explanation
Indices: 57026--57077 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
57016 TTCAGAGGAA
* *
57026 GTTAGGCGGTTAGGAAACTGTTGAGAG
1 GTTAGGCAGTTAGGAAACGGTTGAGAG
*
57053 GTTAGGCAGTTAGGAAGCGGTTGAG
1 GTTAGGCAGTTAGGAAACGGTTGAG
57078 CTTCTGTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.08, G:0.42, T:0.25
Consensus pattern (27 bp):
GTTAGGCAGTTAGGAAACGGTTGAGAG
Found at i:61638 original size:27 final size:27
Alignment explanation
Indices: 61600--61651 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
61590 TTCAGAGGAA
* *
61600 GTTAGGCGGTTAGGAAACTGTTGAGAG
1 GTTAGGCAGTTAGGAAACGGTTGAGAG
*
61627 GTTAGGCAGTTAGGAAGCGGTTGAG
1 GTTAGGCAGTTAGGAAACGGTTGAG
61652 CTTCTGTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.08, G:0.42, T:0.25
Consensus pattern (27 bp):
GTTAGGCAGTTAGGAAACGGTTGAGAG
Found at i:75507 original size:23 final size:23
Alignment explanation
Indices: 75439--75491 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
75429 CAATCTTATA
75439 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
75462 CGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
75485 TGGCACT
1 TGGCACT
75492 TTGGTGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:75622 original size:2 final size:2
Alignment explanation
Indices: 75615--75644 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
75605 AACGTATGTC
75615 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
75645 GATGTGTAAT
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:75678 original size:12 final size:11
Alignment explanation
Indices: 75615--75678 Score: 55
Period size: 10 Copynumber: 6.0 Consensus size: 11
75605 AACGTATGTC
75615 ATATATATAT-
1 ATATATATATG
75625 ATATATATAT-
1 ATATATATATG
75635 ATATATATATG
1 ATATATATATG
* *
75646 ATGTGTAATATG
1 ATATAT-ATATG
*
75658 A-AT-TGTATG
1 ATATATATATG
75667 ATATGATATATG
1 ATAT-ATATATG
75679 TGTGTTATGG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 5 0.11
10 23 0.52
11 5 0.11
12 11 0.25
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (11 bp):
ATATATATATG
Found at i:75950 original size:2 final size:2
Alignment explanation
Indices: 75945--75969 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
75935 TATATATATA
75945 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
75970 TTGCGTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:76719 original size:21 final size:21
Alignment explanation
Indices: 76693--76764 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
76683 AAAATCTCTC
76693 AGTATCGATATTGACCACCTG
1 AGTATCGATATTGACCACCTG
*
76714 AGTATCGATGTTGACCACCTG
1 AGTATCGATATTGACCACCTG
*
76735 AGTATCGATAATGGACC-CC-G
1 AGTATCGAT-ATTGACCACCTG
76755 AGTATCGATA
1 AGTATCGATA
76765 CTCCTTGAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
19 1 0.02
20 10 0.21
21 31 0.66
22 5 0.11
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (21 bp):
AGTATCGATATTGACCACCTG
Found at i:77670 original size:30 final size:29
Alignment explanation
Indices: 77584--77677 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 29
77574 GTAACGATAG
* *
77584 AGTGACTATTTTGTTATAAATTGATAACATT
1 AGTGACCATTTTG-T-TAAATTGATAACGTT
* *
77615 AGTGATCATTTTATATAAATTGATAACGTT
1 AGTGACCATTTTGT-TAAATTGATAACGTT
*
77645 AGTGACCATTTTGTTACAATCGATAACGTT
1 AGTGACCATTTTGTTA-AATTGATAACGTT
77675 AGT
1 AGT
77678 AACAAATTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
29 2 0.04
30 43 0.78
31 10 0.18
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (29 bp):
AGTGACCATTTTGTTAAATTGATAACGTT
Found at i:77954 original size:14 final size:14
Alignment explanation
Indices: 77911--77955 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
77901 AATCAAGTAG
77911 TTTTTAAATATATAT
1 TTTTTAAA-ATATAT
* *
77926 TTTATAAAATTTAT
1 TTTTTAAAATATAT
*
77940 TTTTTAAAAAATAT
1 TTTTTAAAATATAT
77954 TT
1 TT
77956 AAAATAATCA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTTAAAATATAT
Found at i:79177 original size:20 final size:20
Alignment explanation
Indices: 79149--79197 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
79139 GTGATATCGA
79149 TATCAATACCAACCCT-TGAG
1 TATCAATACCAACCCTGT-AG
*
79169 TATCGATACCAACCCTGTAG
1 TATCAATACCAACCCTGTAG
79189 TATCAATAC
1 TATCAATAC
79198 TCTTTGTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.29, G:0.10, T:0.27
Consensus pattern (20 bp):
TATCAATACCAACCCTGTAG
Found at i:80243 original size:22 final size:22
Alignment explanation
Indices: 80196--80243 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
80186 TATAAATTAT
80196 AAAATAATAATTATAAATATGGA
1 AAAATAATAATTATAAATAT-GA
*
80219 AAATTAA-AATT-TAAATATAGA
1 AAAATAATAATTATAAATAT-GA
80240 AAAA
1 AAAA
80244 GTGGACAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 12 0.55
22 4 0.18
23 6 0.27
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (22 bp):
AAAATAATAATTATAAATATGA
Found at i:80552 original size:25 final size:25
Alignment explanation
Indices: 80524--80585 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
80514 AGGTAAATAC
*
80524 AAATTTATAATAGAAAATGCATAAA
1 AAATTTAAAATAGAAAATGCATAAA
80549 AAATTTAAAATAGAAAATGCATAAA
1 AAATTTAAAATAGAAAATGCATAAA
80574 AAATTTAAAATA
1 AAATTTAAAATA
80586 TATAATAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.27
Consensus pattern (25 bp):
AAATTTAAAATAGAAAATGCATAAA
Done.