Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_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: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 29
Found at i:6839049 original size:65 final size:62
Alignment explanation
Indices: 6838959--6839089 Score: 172
Period size: 65 Copynumber: 2.1 Consensus size: 62
6838949 ACACCCTTTT
* * *
6838959 GAATGCATTTTTGTACCGATTCACAAGCCATGCATCGATGCACTCTTGAATATTTTGAAACATC
1 GAATGCATTTTTATACCGATGCACAAGCCATGCATCGATGC-CTCCTGAATATTTTG-AACATC
* * * *
6839023 GAATTCATTTTCTATACCGATGCACAAGCCATGTATCGATGCCTCCTGACTCTTTTGAACATC
1 GAATGCATTTT-TATACCGATGCACAAGCCATGCATCGATGCCTCCTGAATATTTTGAACATC
6839086 GAAT
1 GAAT
6839090 ATAATTAGTG
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
63 10 0.17
64 22 0.37
65 27 0.46
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (62 bp):
GAATGCATTTTTATACCGATGCACAAGCCATGCATCGATGCCTCCTGAATATTTTGAACATC
Found at i:6839108 original size:63 final size:65
Alignment explanation
Indices: 6838970--6839110 Score: 171
Period size: 65 Copynumber: 2.2 Consensus size: 65
6838960 AATGCATTTT
* * * *
6838970 TGTACCGATTCACAAGCCATGCATCGATGCACTCTTGAATATTTTGAAACATCGAATTCATTTTC
1 TGTACCGATGCACAAGCCATGCATCGATGCACTCCTGAATATTTTGAAACATCGAATTCAATTAC
* * * *
6839035 TATACCGATGCACAAGCCATGTATCGATGC-CTCCTGACTCTTTTG-AACATCGAATAT-AATTA
1 TGTACCGATGCACAAGCCATGCATCGATGCACTCCTGAATATTTTGAAACATCGAAT-TCAATTA
*
6839097 G
65 C
6839098 TGTACCGATGCAC
1 TGTACCGATGCAC
6839111 CCCTAGTAGT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
63 25 0.38
64 13 0.20
65 27 0.42
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (65 bp):
TGTACCGATGCACAAGCCATGCATCGATGCACTCCTGAATATTTTGAAACATCGAATTCAATTAC
Found at i:6839527 original size:33 final size:33
Alignment explanation
Indices: 6839490--6839566 Score: 120
Period size: 33 Copynumber: 2.3 Consensus size: 33
6839480 CCTTTCATGC
* *
6839490 ATGCACCCATATGCATTATTC-TTTATGCCGATA
1 ATGCACCCATATACA-TATTCATTTATGCCAATA
6839523 ATGCACCCATATACATATTCATTTATGCCAATA
1 ATGCACCCATATACATATTCATTTATGCCAATA
6839556 ATGCACCCATA
1 ATGCACCCATA
6839567 GTATTTCAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 5 0.12
33 36 0.88
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (33 bp):
ATGCACCCATATACATATTCATTTATGCCAATA
Found at i:6839968 original size:2 final size:2
Alignment explanation
Indices: 6839957--6839995 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
6839947 TATTCAAAGG
6839957 AT AT AT -T 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
6839996 TATTAATTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6840083 original size:20 final size:19
Alignment explanation
Indices: 6840054--6840104 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
6840044 ATACTTACCC
*
6840054 TGGTATCGATA-TTCTATATA
1 TGGTACCGATACTT-TATA-A
*
6840074 TGGTACCGATACTTTATAG
1 TGGTACCGATACTTTATAA
6840093 TGGTACCGATAC
1 TGGTACCGATAC
6840105 CACTAGTCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
20 14 0.50
21 2 0.07
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (19 bp):
TGGTACCGATACTTTATAA
Found at i:6847771 original size:24 final size:24
Alignment explanation
Indices: 6847735--6847785 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
6847725 TAACCTTGAT
* *
6847735 GGAAAATGCGGTGGCACGTCATAG
1 GGAAAAGGCGGTGGCACATCATAG
*
6847759 GGAAAAGGTGGTGGCACATCATAG
1 GGAAAAGGCGGTGGCACATCATAG
6847783 GGA
1 GGA
6847786 GATAGCGTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.14, G:0.39, T:0.16
Consensus pattern (24 bp):
GGAAAAGGCGGTGGCACATCATAG
Found at i:6850169 original size:24 final size:23
Alignment explanation
Indices: 6850125--6850170 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
6850115 ATTTGAAAAT
*
6850125 AAAAGAAAAATGAAAAGAACTTG
1 AAAAGAAAAAAGAAAAGAACTTG
6850148 AAAAGTAAAAAAGAGAAA-AACTT
1 AAAAG-AAAAAAGA-AAAGAACTT
6850171 TTATAAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 12 0.60
25 3 0.15
ACGTcount: A:0.67, C:0.04, G:0.15, T:0.13
Consensus pattern (23 bp):
AAAAGAAAAAAGAAAAGAACTTG
Found at i:6852724 original size:20 final size:21
Alignment explanation
Indices: 6852702--6852741 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
6852692 CGATACTCTT
6852702 TTTTG-GGTATCAATA-TTCC
1 TTTTGTGGTATCAATACTTCC
6852721 TTTTGTGGTATCAATACTTCC
1 TTTTGTGGTATCAATACTTCC
6852742 CTAAGTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (21 bp):
TTTTGTGGTATCAATACTTCC
Found at i:6858109 original size:23 final size:23
Alignment explanation
Indices: 6858065--6858112 Score: 89
Period size: 22 Copynumber: 2.1 Consensus size: 23
6858055 AAGACTATAA
6858065 CATACCCTATTCTCGTTCTTTTT
1 CATACCCTATTCTCGTTCTTTTT
6858088 CATA-CCTATTCTCGTTCTTTTT
1 CATACCCTATTCTCGTTCTTTTT
6858110 CAT
1 CAT
6858113 TACGGTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.15, C:0.29, G:0.04, T:0.52
Consensus pattern (23 bp):
CATACCCTATTCTCGTTCTTTTT
Found at i:6859873 original size:36 final size:36
Alignment explanation
Indices: 6859787--6860028 Score: 225
Period size: 36 Copynumber: 6.6 Consensus size: 36
6859777 GGAAAATACG
*
6859787 TATATAATATATAGTTTTTTTAAAACATTTTTGAAAAAA
1 TATATAATATATAG--TTTTTAAAACATTTTTG-AAAAT
*
6859826 TATATATTATATAGTTTTTAAAACATTTTTGAAAAT
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
6859862 TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
**
6859898 TATATAATATATTTTATTTTAGAAA-ATCATTTTGAAAA-
1 TATATAATATATAGT-TTTTA-AAACAT--TTTTGAAAAT
* *
6859936 TATATCATATATAGTTTTTTAAAAAATATTTTTG--AA-
1 TATATAATATATAG-TTTTT--AAAACATTTTTGAAAAT
*
6859972 -A-A-CATATATAG-TTTTAAAA-ATATTTTGAAAAT
1 TATATAATATATAGTTTTTAAAACAT-TTTTGAAAAT
*
6860004 ATATATAATATATAATTTTTGAAAA
1 -TATATAATATATAGTTTTT-AAAA
6860029 AACCATTTTT
Statistics
Matches: 175, Mismatches: 10, Indels: 37
0.79 0.05 0.17
Matches are distributed among these distances:
28 2 0.01
29 9 0.05
31 6 0.03
33 9 0.05
34 2 0.01
35 2 0.01
36 61 0.35
37 28 0.16
38 27 0.15
39 26 0.15
40 3 0.02
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
Found at i:6859946 original size:38 final size:38
Alignment explanation
Indices: 6859787--6860068 Score: 195
Period size: 36 Copynumber: 7.5 Consensus size: 38
6859777 GGAAAATACG
* *
6859787 TATATAATATATAGTTTTTT-TAAAACATTTTTGAAAAAA
1 TATATAATATATAGTTTTTTAAAAAATATTTTTG--AAAA
* *
6859826 TATATATTATATAG-TTTTT--AAAACATTTTTGAAAA
1 TATATAATATATAGTTTTTTAAAAAATATTTTTGAAAA
*
6859861 TTATATAATATATAG-TTTTT--AAAACATTTTTGAAAA
1 -TATATAATATATAGTTTTTTAAAAAATATTTTTGAAAA
* *
6859897 TTATATAATATAT-TTTATTTTAGAAAATCA-TTTTGAAAA
1 -TATATAATATATAGTT-TTTTAAAAAAT-ATTTTTGAAAA
*
6859936 TATATCATATATAGTTTTTTAAAAAATATTTTTG--AA
1 TATATAATATATAGTTTTTTAAAAAATATTTTTGAAAA
*
6859972 -A-A-CATATATAG--TTTT-AAAAATA-TTTTGAAAATA
1 TATATAATATATAGTTTTTTAAAAAATATTTTTG-AAA-A
* * *
6860005 TATATAATATATAATTTTTGAAAAAACCATTTTTTGAAAACA
1 TATATAATATATAGTTTTTTAAAAAA-TA-TTTTTG-AAA-A
*
6860047 TATATATGCTATATAGTTTTTT
1 TATATA--ATATATAGTTTTTT
6860069 TTTAAAAATA
Statistics
Matches: 205, Mismatches: 15, Indels: 41
0.79 0.06 0.16
Matches are distributed among these distances:
29 5 0.02
30 7 0.03
31 4 0.02
32 1 0.00
33 10 0.05
34 2 0.01
35 6 0.03
36 57 0.28
37 17 0.08
38 34 0.17
39 33 0.16
40 2 0.01
42 16 0.08
44 11 0.05
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (38 bp):
TATATAATATATAGTTTTTTAAAAAATATTTTTGAAAA
Found at i:6860000 original size:29 final size:32
Alignment explanation
Indices: 6859941--6860010 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 32
6859931 GAAAATATAT
6859941 CATATATAGTTTTTTAAAAAATATTTTTGAAAA
1 CATATATAG-TTTTTAAAAAATATTTTTGAAAA
6859974 CATATATAG-TTTT-AAAAATA-TTTTGAAAA
1 CATATATAGTTTTTAAAAAATATTTTTGAAAA
*
6860003 TATATATA
1 CATATATA
6860011 ATATATAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 16 0.44
30 7 0.19
31 4 0.11
33 9 0.25
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (32 bp):
CATATATAGTTTTTAAAAAATATTTTTGAAAA
Found at i:6860023 original size:69 final size:71
Alignment explanation
Indices: 6859914--6860052 Score: 196
Period size: 69 Copynumber: 2.0 Consensus size: 71
6859904 ATATATTTTA
* * * *
6859914 TTTTAGAAAATCATTTTGAAAATATATCATATATAGTTTTTTAAAAAA-TA-TTTTTGAAAACAT
1 TTTTAGAAAATCATTTTGAAAATATATAATATATAATTTTTGAAAAAACCATTTTTTGAAAACAT
6859977 ATATAG
66 ATATAG
6859983 TTTTA-AAAAT-ATTTTGAAAATATATATAATATATAATTTTTGAAAAAACCATTTTTTGAAAAC
1 TTTTAGAAAATCATTTTG-AAA-ATATATAATATATAATTTTTGAAAAAACCATTTTTTGAAAAC
6860046 ATATATA
64 ATATATA
6860053 TGCTATATAG
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
67 6 0.10
68 8 0.13
69 29 0.47
70 1 0.02
71 18 0.29
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (71 bp):
TTTTAGAAAATCATTTTGAAAATATATAATATATAATTTTTGAAAAAACCATTTTTTGAAAACAT
ATATAG
Found at i:6860086 original size:17 final size:17
Alignment explanation
Indices: 6860064--6860118 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
6860054 GCTATATAGT
* *
6860064 TTTTTTTTAAAAATATA
1 TTTTTTTGAAAAACATA
6860081 TTTTTTTGAAAAACATA
1 TTTTTTTGAAAAACATA
*
6860098 TATATTTTGAAAAACAT-
1 T-TTTTTTGAAAAACATA
6860115 TTTT
1 TTTT
6860119 AAACATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 2 0.06
17 17 0.52
18 14 0.42
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (17 bp):
TTTTTTTGAAAAACATA
Found at i:6860098 original size:19 final size:19
Alignment explanation
Indices: 6860057--6860114 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
6860047 TATATATGCT
**
6860057 ATATAGTTTTTTTTTAAAA-
1 ATATA-TTTTTTTGAAAAAC
6860076 ATATATTTTTTTGAAAAAC
1 ATATATTTTTTTGAAAAAC
*
6860095 ATATA-TATTTTGAAAAAC
1 ATATATTTTTTTGAAAAAC
6860113 AT
1 AT
6860115 TTTTAAACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
18 25 0.71
19 10 0.29
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (19 bp):
ATATATTTTTTTGAAAAAC
Found at i:6861791 original size:12 final size:13
Alignment explanation
Indices: 6861769--6861797 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6861759 CAAATCGATG
6861769 TTTTAAATTTTAA
1 TTTTAAATTTTAA
6861782 TTTT-AATTTTAA
1 TTTTAAATTTTAA
6861794 TTTT
1 TTTT
6861798 TGCAACTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:6863129 original size:22 final size:22
Alignment explanation
Indices: 6863081--6863134 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
6863071 TTCAGCTATT
* *
6863081 ATAACTCCTGAAATTATATCAT
1 ATAACTCCTGAAATTAAATCAA
* * *
6863103 GTAACCCCTGGAATTAAATCAA
1 ATAACTCCTGAAATTAAATCAA
6863125 ATAACTCCTG
1 ATAACTCCTG
6863135 TAACTCATGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (22 bp):
ATAACTCCTGAAATTAAATCAA
Found at i:6863413 original size:6 final size:6
Alignment explanation
Indices: 6863402--6863426 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6863392 GACACGTATT
6863402 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
6863427 GCCGAGCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:6867167 original size:14 final size:14
Alignment explanation
Indices: 6867148--6867175 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6867138 GGTAGCTTTA
6867148 TTTTCATTAAATTG
1 TTTTCATTAAATTG
6867162 TTTTCATTAAATTG
1 TTTTCATTAAATTG
6867176 AGTTTTTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (14 bp):
TTTTCATTAAATTG
Found at i:6869335 original size:6 final size:6
Alignment explanation
Indices: 6869324--6869359 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
6869314 GACACGTATT
*
6869324 ACCACG ACCACG A-CACG ACCACG ACCACG AGCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
6869360 GCCGAGCCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.36, C:0.44, G:0.19, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:6869342 original size:11 final size:12
Alignment explanation
Indices: 6869324--6869359 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
6869314 GACACGTATT
6869324 ACCACGACCACG
1 ACCACGACCACG
6869336 A-CACGACCACG
1 ACCACGACCACG
*
6869347 ACCACGAGCACG
1 ACCACGACCACG
6869359 A
1 A
6869360 GCCGAGCCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.36, C:0.44, G:0.19, T:0.00
Consensus pattern (12 bp):
ACCACGACCACG
Found at i:6869346 original size:17 final size:18
Alignment explanation
Indices: 6869324--6869359 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
6869314 GACACGTATT
6869324 ACCACGACCACGA-CACG
1 ACCACGACCACGAGCACG
6869341 ACCACGACCACGAGCACG
1 ACCACGACCACGAGCACG
6869359 A
1 A
6869360 GCCGAGCCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.36, C:0.44, G:0.19, T:0.00
Consensus pattern (18 bp):
ACCACGACCACGAGCACG
Found at i:6869367 original size:5 final size:5
Alignment explanation
Indices: 6869351--6869390 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
6869341 ACCACGACCA
* *
6869351 CGAGC ACGAGC CGAGC CGAGC CGAGC CGTGC CGAGA CGAG
1 CGAGC -CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
6869391 ACGGACGGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.23, C:0.35, G:0.40, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:6876072 original size:21 final size:21
Alignment explanation
Indices: 6876007--6876073 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
6875997 TTTCTATAAA
* *
6876007 CCTTTA-GAAAAGAGATCAATT
1 CCTTTATGAAAAAAGATTAA-T
*
6876028 CCTTT-TGAAAAATGA-T-AT
1 CCTTTATGAAAAAAGATTAAT
6876046 CTCTTTATGAAAAAAGATTAAT
1 C-CTTTATGAAAAAAGATTAAT
6876068 CCTTTA
1 CCTTTA
6876074 GGTTTAATGC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
18 2 0.05
19 5 0.14
20 9 0.24
21 18 0.49
22 3 0.08
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.36
Consensus pattern (21 bp):
CCTTTATGAAAAAAGATTAAT
Found at i:6877351 original size:60 final size:61
Alignment explanation
Indices: 6877241--6877363 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 61
6877231 ATTTTGCAAC
* ** * *
6877241 TTTTAATAGTCGAGGGACTCAACAAAGTAATGCTCTATGCTTAGAGGACCATTT-TATATT
1 TTTTAATAGTCGAGGAACTCAACAAAGTAATGCTCTATAATCAGAAGACCATTTATATATT
* * *
6877301 TTTTAATAGTTGAGGAACTCAACAAATTAATG-TCCTATAATCGGAAGACCATTTATATATT
1 TTTTAATAGTCGAGGAACTCAACAAAGTAATGCT-CTATAATCAGAAGACCATTTATATATT
6877362 TT
1 TT
6877364 ACTTTTTATT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 1 0.02
60 44 0.83
61 8 0.15
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (61 bp):
TTTTAATAGTCGAGGAACTCAACAAAGTAATGCTCTATAATCAGAAGACCATTTATATATT
Found at i:6879246 original size:22 final size:21
Alignment explanation
Indices: 6879221--6879279 Score: 86
Period size: 22 Copynumber: 2.9 Consensus size: 21
6879211 GAGGTCAACC
6879221 GGTCAACGGTCGGGTCGAGTCG
1 GGTCAACGGTCGGGTC-AGTCG
6879243 GGTCAACGGTCGGGTCAGTCG
1 GGTCAACGGTCGGGTCAGTCG
*
6879264 GGTC--TGGTCGGGTCAG
1 GGTCAACGGTCGGGTCAG
6879280 ACCGGTTGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 11 0.31
21 9 0.25
22 16 0.44
ACGTcount: A:0.12, C:0.22, G:0.46, T:0.20
Consensus pattern (21 bp):
GGTCAACGGTCGGGTCAGTCG
Found at i:6879254 original size:12 final size:12
Alignment explanation
Indices: 6879221--6879259 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
6879211 GAGGTCAACC
6879221 GGTCAACGGTCG
1 GGTCAACGGTCG
*
6879233 GGTCGA--GTCG
1 GGTCAACGGTCG
6879243 GGTCAACGGTCG
1 GGTCAACGGTCG
6879255 GGTCA
1 GGTCA
6879260 GTCGGGTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.39
12 14 0.61
ACGTcount: A:0.15, C:0.23, G:0.44, T:0.18
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:6888541 original size:25 final size:25
Alignment explanation
Indices: 6888513--6888562 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
6888503 CACGAGTAAA
*
6888513 TGTTCGGCCATGATTTTGGATGTCC
1 TGTTCGACCATGATTTTGGATGTCC
6888538 TGTTCGACCATGATTTTGGATGTCC
1 TGTTCGACCATGATTTTGGATGTCC
6888563 CATCAACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.14, C:0.20, G:0.26, T:0.40
Consensus pattern (25 bp):
TGTTCGACCATGATTTTGGATGTCC
Found at i:6891343 original size:21 final size:22
Alignment explanation
Indices: 6891319--6891363 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
6891309 TGAGTTTTAA
6891319 AAAAT-AATAAATATTTTAA-AT
1 AAAATGAATAAA-ATTTTAATAT
*
6891340 AAAATGATTAAAATTTTAATAT
1 AAAATGAATAAAATTTTAATAT
6891362 AA
1 AA
6891364 CATATTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAATGAATAAAATTTTAATAT
Found at i:6891467 original size:14 final size:15
Alignment explanation
Indices: 6891439--6891467 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6891429 AATTAAATTA
6891439 TTATAAATATATTTT
1 TTATAAATATATTTT
6891454 TTATAAAT-TATTTT
1 TTATAAATATATTTT
6891468 ATCCCACCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATAAATATATTTT
Found at i:6894511 original size:3 final size:3
Alignment explanation
Indices: 6894444--6894499 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
6894434 ATATTAAATA
6894444 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6894492 AAT AAT AA
1 AAT AAT AA
6894500 AAGTAAATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6894526 original size:19 final size:19
Alignment explanation
Indices: 6894443--6894526 Score: 80
Period size: 21 Copynumber: 4.2 Consensus size: 19
6894433 GATATTAAAT
6894443 AAATAATAATAATAATAATAA
1 AAATAATAATAATAA-AA-AA
*
6894464 TAATAATAATAATAATAATAA
1 AAATAATAATAATAA-AA-AA
* **
6894485 TAATAATAATAATAAAAGT
1 AAATAATAATAATAAAAAA
6894504 AAATAAT-ATATATAAAAAA
1 AAATAATAATA-ATAAAAAA
6894523 AAAT
1 AAAT
6894527 CAAAGAAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
18 3 0.05
19 16 0.29
20 2 0.04
21 35 0.62
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (19 bp):
AAATAATAATAATAAAAAA
Found at i:6894563 original size:11 final size:11
Alignment explanation
Indices: 6894534--6894567 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
6894524 AATCAAAGAA
6894534 ATTAAATTAAA-
1 ATTAAA-TAAAT
6894545 ATTAAATAAAT
1 ATTAAATAAAT
6894556 ATTAAATAAAT
1 ATTAAATAAAT
6894567 A
1 A
6894568 AGAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATTAAATAAAT
Found at i:6895797 original size:3 final size:3
Alignment explanation
Indices: 6895789--6895824 Score: 54
Period size: 3 Copynumber: 11.3 Consensus size: 3
6895779 AAAAAATGAA
6895789 AAT AAT AAT AAT AAAT AAT AAT AAT AAAT AAT AAT A
1 AAT AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT A
6895825 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 25 0.81
4 6 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6895806 original size:13 final size:13
Alignment explanation
Indices: 6895788--6895824 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
6895778 TAAAAAATGA
6895788 AAATAATAATAAT
1 AAATAATAATAAT
6895801 AAATAATAATAAT
1 AAATAATAATAAT
6895814 AAATAATAATA
1 AAATAATAATA
6895825 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:6895965 original size:71 final size:72
Alignment explanation
Indices: 6895889--6896072 Score: 220
Period size: 71 Copynumber: 2.6 Consensus size: 72
6895879 TTTTTTTCTT
* * *
6895889 AAACTATATAATATACGAATGTTTTCAACATGTTTTCAAAAATATTATATAAGTTTTCAAAAACG
1 AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAAATATAATATAAGTTTTCAAAAACG
6895954 TTTT-AA
66 TTTTCAA
* * ** *
6895960 AAACTATATAATATATAAATGTTTTCAAAATGTTTTCAAAACTATAATATGTGTTTTCAAAAATG
1 AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAAATATAATATAAGTTTTCAAAAACG
6896025 TTTTCAA
66 TTTTCAA
* *
6896032 AAA-T-TAT-ATATA-TAAT-TTTTCAAAATGATTTT-AAAATTATA
1 AAACTATATAATATACAAATGTTTTCAAAATG-TTTTCAAAAATATA
6896073 TATTATATAT
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
67 19 0.19
68 7 0.07
69 5 0.05
70 3 0.03
71 62 0.61
72 5 0.05
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.42
Consensus pattern (72 bp):
AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAAATATAATATAAGTTTTCAAAAACG
TTTTCAA
Found at i:6895992 original size:11 final size:11
Alignment explanation
Indices: 6895976--6896000 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6895966 TATAATATAT
6895976 AAATGTTTTCA
1 AAATGTTTTCA
6895987 AAATGTTTTCA
1 AAATGTTTTCA
6895998 AAA
1 AAA
6896001 CTATAATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:6896028 original size:12 final size:12
Alignment explanation
Indices: 6896011--6896035 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6896001 CTATAATATG
6896011 TGTTTTCAAAAA
1 TGTTTTCAAAAA
6896023 TGTTTTCAAAAA
1 TGTTTTCAAAAA
6896035 T
1 T
6896036 TATATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TGTTTTCAAAAA
Found at i:6896072 original size:33 final size:33
Alignment explanation
Indices: 6895910--6896086 Score: 155
Period size: 33 Copynumber: 5.1 Consensus size: 33
6895900 TATACGAATG
* * *
6895910 TTTTCAACATGTTTTCAAAAATAT-TATATAAG
1 TTTTCAAAATGTTTTCAAAATTATATATATAAT
* *
6895942 TTTTCAAAAACGTTTTAAAAACTATATAATATATAAAT
1 TTTTC-AAAATGTTTTCAAAA-T-TAT-ATATAT-AAT
* *
6895980 GTTTTCAAAATGTTTTCAAAACTATA-ATAT-GT
1 -TTTTCAAAATGTTTTCAAAATTATATATATAAT
6896012 GTTTTCAAAAATGTTTTCAAAAATTATATATATAAT
1 -TTTTC-AAAATGTTTTC-AAAATTATATATATAAT
6896048 TTTTCAAAATGATTTT-AAAATTATATATTATATAT
1 TTTTCAAAATG-TTTTCAAAATTATATA-TATA-AT
6896083 TTTT
1 TTTT
6896087 TTAAAACGTT
Statistics
Matches: 120, Mismatches: 11, Indels: 25
0.77 0.07 0.16
Matches are distributed among these distances:
32 12 0.10
33 34 0.28
34 22 0.18
35 23 0.19
36 4 0.03
37 5 0.04
38 15 0.12
39 5 0.04
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (33 bp):
TTTTCAAAATGTTTTCAAAATTATATATATAAT
Found at i:6897068 original size:165 final size:163
Alignment explanation
Indices: 6896789--6897416 Score: 1067
Period size: 165 Copynumber: 3.8 Consensus size: 163
6896779 TGATATGACT
* * * *
6896789 TCGAAGTTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATAC
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTC
* *
6896854 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCC
66 TGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGG-TGGCAGATAACCC
6896919 TTCTTGACTTAAGTTATGCTGCAAATGGTGTGCCC
129 TTCTTGACTTAAGTTATGCTGCAAATGGTGTGCCC
6896954 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTC
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTC
* *
6897019 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCC
66 TGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGG-TGGCAGATAACCC
6897084 TTCTTGACTTAAGTTATGCTGCAAATGGTGTGCCC
129 TTCTTGACTTAAGTTATGCTGCAAATGGTGTGCCC
6897119 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTC
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTC
6897184 TGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGTCACAGATAACC
66 TGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGG---CAGATAACC
* * * * *
6897249 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
128 CTTCTTGACTTAAGTTATGCTGCAAATGGTGTGCCC
6897285 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTC
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTC
*
6897350 TGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGCAGATAGCCCTT
66 TGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGCAGATAACCCTT
6897415 CT
131 CT
6897417 GGTCTTGAGC
Statistics
Matches: 446, Mismatches: 14, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
163 16 0.04
164 4 0.01
165 268 0.60
166 158 0.35
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (163 bp):
TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTC
TGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGCAGATAACCCTT
CTTGACTTAAGTTATGCTGCAAATGGTGTGCCC
Found at i:6897397 original size:331 final size:328
Alignment explanation
Indices: 6896789--6897416 Score: 1071
Period size: 331 Copynumber: 1.9 Consensus size: 328
6896779 TGATATGACT
* *
6896789 TCGAAGTTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATAC
1 TCGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATAC
*
6896854 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCC
66 TGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCC
* *
6896919 TTCTTGACTTAAGTTATGCTGCAAATGGTGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGT
131 TTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGT
*
6896984 CTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTA
196 CTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGCGTA
6897049 GTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGGTG
261 GTCGAACTCAAAGGTC-TTGG-TGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGGTG
6897114 TGCCC
324 TGCCC
* *
6897119 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTC
1 TCGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATAC
*
6897184 TGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGG-TGGTCACAGATAA
66 TGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG---CAGATAA
* * *
6897247 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
128 CCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
6897312 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGC
193 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGC
* *
6897377 GTAGTCGAACTCGAAGGTCTTGGTGGCAGATAGCCCTTCT
258 GTAGTCGAACTCAAAGGTCTTGGTGGCAGATAACCCTTCT
6897417 GGTCTTGAGC
Statistics
Matches: 281, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
328 3 0.01
329 20 0.07
330 109 0.39
331 149 0.53
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (328 bp):
TCGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATAC
TGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCC
TTCTAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGT
CTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTAGAGCTGAGCGTA
GTCGAACTCAAAGGTCTTGGTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGGTGTG
CCC
Found at i:6902574 original size:3 final size:3
Alignment explanation
Indices: 6902522--6902562 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
6902512 AATAAATCAA
6902522 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6902563 AAGTAAATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6902625 original size:11 final size:11
Alignment explanation
Indices: 6902596--6902629 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
6902586 AATCAAAGAA
6902596 ATTAAATTAAA-
1 ATTAAA-TAAAT
6902607 ATTAAATAAAT
1 ATTAAATAAAT
6902618 ATTAAATAAAT
1 ATTAAATAAAT
6902629 A
1 A
6902630 AGAAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.18
11 18 0.82
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATTAAATAAAT
Found at i:6903867 original size:3 final size:3
Alignment explanation
Indices: 6903859--6903889 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
6903849 AAAAAATGAA
6903859 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6903890 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6904054 original size:12 final size:12
Alignment explanation
Indices: 6904037--6904099 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
6904027 TATAATATAT
6904037 AAATGTTTTCAA
1 AAATGTTTTCAA
6904049 AAATGTTTTCAA
1 AAATGTTTTCAA
* * ** *
6904061 AACTATAAT-AT
1 AAATGTTTTCAA
**
6904072 ATGTGTTTTCAA
1 AAATGTTTTCAA
6904084 AAATGTTTTCAA
1 AAATGTTTTCAA
6904096 AAAT
1 AAAT
6904100 TATATATATA
Statistics
Matches: 37, Mismatches: 13, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
11 5 0.14
12 32 0.86
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (12 bp):
AAATGTTTTCAA
Found at i:6904079 original size:35 final size:35
Alignment explanation
Indices: 6903968--6904152 Score: 157
Period size: 35 Copynumber: 5.2 Consensus size: 35
6903958 TAATATACGA
* *
6903968 ATGTTTTC-AACATGTTTTCAAAA--ATATTATAT
1 ATGTTTTCAAAAATGTTTTCAAAACTATAATATAT
* * *
6904000 AAGTTTTCAAAAACGTTTTAAAAACTATATAATATAT
1 ATGTTTTCAAAAATGTTTTCAAAAC--TATAATATAT
6904037 AAATGTTTTCAAAAATGTTTTCAAAACTATAATATAT
1 --ATGTTTTCAAAAATGTTTTCAAAACTATAATATAT
* *
6904074 GTGTTTTCAAAAATGTTTTCAAAAAT-TATATATAT
1 ATGTTTTCAAAAATGTTTTCAAAACTATA-ATATAT
* *
6904109 AAT-TTTTC-AAAATGATTTTAAAAATTATATATTATAT
1 -ATGTTTTCAAAAATG-TTTTCAAAACTATA-A-TATAT
*
6904146 ATATTTT
1 ATGTTTT
6904153 TTTAAAACGT
Statistics
Matches: 127, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
32 7 0.06
33 12 0.09
34 8 0.06
35 44 0.35
36 7 0.06
37 27 0.21
39 22 0.17
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.45
Consensus pattern (35 bp):
ATGTTTTCAAAAATGTTTTCAAAACTATAATATAT
Found at i:6904804 original size:43 final size:44
Alignment explanation
Indices: 6904714--6904834 Score: 165
Period size: 43 Copynumber: 2.8 Consensus size: 44
6904704 TCCCCCTTGG
* * * *
6904714 TGTGACCAAGATGGTTCGACTCTCTTGCATGAATTTGGCTCCTA
1 TGTGAACATGATGGTTCGACTATCTTGCATGAACTTGGCTCCTA
*
6904758 TGTGAACATGATGGTTCGACTATCTT-TATGAACTTGGCTTCC-A
1 TGTGAACATGATGGTTCGACTATCTTGCATGAACTTGGC-TCCTA
*
6904801 TGTGAACATGATGTTTCGACTATCTTGCATGAAC
1 TGTGAACATGATGGTTCGACTATCTTGCATGAAC
6904835 ATGCATGGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 36 0.53
44 32 0.47
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (44 bp):
TGTGAACATGATGGTTCGACTATCTTGCATGAACTTGGCTCCTA
Found at i:6906524 original size:17 final size:17
Alignment explanation
Indices: 6906481--6906532 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
6906471 TTAGTAATAG
*
6906481 AAACTCTTTAAATTAAT
1 AAACTCTCTAAATTAAT
**
6906498 --ACTCGGTAAATTAAT
1 AAACTCTCTAAATTAAT
*
6906513 AAACTCTCTAAAATAAT
1 AAACTCTCTAAATTAAT
6906530 AAA
1 AAA
6906533 TTTGTCCAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (17 bp):
AAACTCTCTAAATTAAT
Found at i:6907711 original size:14 final size:14
Alignment explanation
Indices: 6907685--6907719 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
6907675 TACAAAATAA
6907685 AAATAAT-TAAAAT
1 AAATAATATAAAAT
*
6907698 ATATAATATAAAAT
1 AAATAATATAAAAT
6907712 AAATAATA
1 AAATAATA
6907720 ACATAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATAATATAAAAT
Found at i:6914168 original size:20 final size:20
Alignment explanation
Indices: 6914122--6914169 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
6914112 CCAGCTCACC
*
6914122 AGTATCAATACCAAGCATTT
1 AGTATCGATACCAAGCATTT
* * *
6914142 GGTATCGATACCGAGCTTTT
1 AGTATCGATACCAAGCATTT
6914162 AGTATCGA
1 AGTATCGA
6914170 CACTATAACC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTATCGATACCAAGCATTT
Found at i:6916437 original size:3 final size:3
Alignment explanation
Indices: 6916429--6916454 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6916419 GACATATAAA
6916429 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
6916455 CACAAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:6918862 original size:20 final size:20
Alignment explanation
Indices: 6918828--6918886 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
6918818 TGCTCAACCA
*
6918828 CTTTGGGTATTGATACTAAGC
1 CTTT-GGTATGGATACTAAGC
* *
6918849 CTTTGGTATGGATACCCAATC
1 CTTTGGTATGGATA-CTAAGC
6918870 C-TTGGTATGGATACTAA
1 CTTTGGTATGGATACTAA
6918887 TTCATCCGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.09
20 21 0.64
21 9 0.27
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (20 bp):
CTTTGGTATGGATACTAAGC
Found at i:6918949 original size:21 final size:21
Alignment explanation
Indices: 6918873--6918948 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
6918863 CCCAATCCTT
6918873 GGTATGGATACTAATTCATCC
1 GGTATGGATACTAATTCATCC
* *
6918894 GGTATGGATACCAACTCATCC
1 GGTATGGATACTAATTCATCC
* * * *
6918915 GGAATGAATACTAGTTTATCC
1 GGTATGGATACTAATTCATCC
6918936 GGTATGGATACTA
1 GGTATGGATACTA
6918949 GCCTACTGGT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (21 bp):
GGTATGGATACTAATTCATCC
Found at i:6918980 original size:20 final size:20
Alignment explanation
Indices: 6918957--6919006 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
6918947 TAGCCTACTG
6918957 GTATCGATACCAAGCATCTA
1 GTATCGATACCAAGCATCTA
* * *
6918977 GTATCGATATCAATCTTCTA
1 GTATCGATACCAAGCATCTA
6918997 GTATCGATAC
1 GTATCGATAC
6919007 TAAAACCCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (20 bp):
GTATCGATACCAAGCATCTA
Found at i:6920384 original size:27 final size:25
Alignment explanation
Indices: 6920345--6920407 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 25
6920335 ATAAGTTTGT
6920345 AAAAAATTGAAGTTAA-AAGATCAAATTG
1 AAAAAA-T-AAGTTAAGAA-AT-AAATTG
6920373 AATAAAATAAGTTAATGAAATAAATTG
1 AA-AAAATAAGTTAA-GAAATAAATTG
6920400 AAAAAATA
1 AAAAAATA
6920408 GTAAATTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
26 6 0.19
27 15 0.47
28 5 0.16
29 6 0.19
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.25
Consensus pattern (25 bp):
AAAAAATAAGTTAAGAAATAAATTG
Found at i:6920406 original size:13 final size:14
Alignment explanation
Indices: 6920367--6920407 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
6920357 TTAAAAGATC
6920367 AAATTGAATAAAAT
1 AAATTGAATAAAAT
* *
6920381 AAGTT-AATGAAAT
1 AAATTGAATAAAAT
6920394 AAATTGAA-AAAAT
1 AAATTGAATAAAAT
6920407 A
1 A
6920408 GTAAATTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (14 bp):
AAATTGAATAAAAT
Found at i:6928001 original size:17 final size:17
Alignment explanation
Indices: 6927979--6928014 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
6927969 TATATGGTTT
6927979 GAGAAAATAAAAAATTA
1 GAGAAAATAAAAAATTA
*
6927996 GAGAAAATCAAAAATTA
1 GAGAAAATAAAAAATTA
6928013 GA
1 GA
6928015 AACTCAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.67, C:0.03, G:0.14, T:0.17
Consensus pattern (17 bp):
GAGAAAATAAAAAATTA
Found at i:6928261 original size:23 final size:23
Alignment explanation
Indices: 6928235--6928279 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
6928225 CTTAGTTAGA
*
6928235 GTATAAATACTTCTTCTTCTTGT
1 GTATAAATACTTATTCTTCTTGT
6928258 GTATAAATACTTATTCTTCTTG
1 GTATAAATACTTATTCTTCTTG
6928280 GGGTATCGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (23 bp):
GTATAAATACTTATTCTTCTTGT
Found at i:6929346 original size:26 final size:23
Alignment explanation
Indices: 6929292--6929347 Score: 58
Period size: 26 Copynumber: 2.3 Consensus size: 23
6929282 CTGTTTTCCC
*
6929292 TTCTTTTTCACCATTCTCTTCTT
1 TTCTTTTTCACCATTCTCATCTT
*
6929315 TGTCTTTTTCATTCCTTTCTCATCATT
1 T-TCTTTTTCA--CCATTCTCATC-TT
6929342 TTCTTT
1 TTCTTT
6929348 CTCTCCAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.04
24 9 0.33
26 14 0.52
27 3 0.11
ACGTcount: A:0.09, C:0.27, G:0.02, T:0.62
Consensus pattern (23 bp):
TTCTTTTTCACCATTCTCATCTT
Found at i:6934894 original size:419 final size:410
Alignment explanation
Indices: 6934125--6934954 Score: 1561
Period size: 419 Copynumber: 2.0 Consensus size: 410
6934115 TTTACTAGCC
*
6934125 CATTAAGAGAAGTGCTTCCCATGTGTCATTGCTTTTGTTATTTTGTATTATCGAAGTCAAGTCTA
1 CATTAAGAGAAGTGCTTCCCATGTGTCATTGCTTTTGTTATTTTGTATTATCGAACTCAAGTCTA
6934190 TCTATGTGTTCATCATATTACAAAATGAAGGGTGGGTCTTACGAGATATATTTTTTTCTCATTAT
66 TCTATGTGTTCATCATATTACAAAATGAAGGGTGGGTCTTACGAGATATATTTTTTTCTCATTAT
6934255 GCACTTCAGAACTTCAATACAACAGTGTTTGAAGCCGTACATAAGTATATTAGTTTATTTATCCA
131 GCACTTCAGAACTTCAATACAACAGTGTTTGAAGCCGTACATAAGTATATTAGTTTATTTATCCA
6934320 TACAATGGAAAGGATATTATAGAGATAATATTGTTGTTTTAGATTTTGTATTATAGCCACTCTTT
196 TACAATGGAAAGGATATTATAGAGATAATATTGTTGTTTTAGATTTTGTATTATAGCCACTCTTT
6934385 TTTCTGTTGATGATCATTGTGTGTTCTCTATGTTTACGTATTCATATTTGGCTATGTTGTTTTAC
261 TTTCTGTTGATGATCATTGTGTGTTCTCTATGTTTACGTATTCATATTTGGCTATGTTGTTTTAC
6934450 TGATGGGTTTTAATATTAGATTCCCTTTCATTTTTAGTAATATTATTAGAATTTAATTTATGGAT
326 TGATGGGTTTTAATATTAGATTCCCTTTCATTTTTAGTAATATTATTAGAATTTAATTTATGGAT
6934515 TGGCATCAGTTTTAACGTGT
391 TGGCATCAGTTTTAACGTGT
6934535 CATTAAGAGAAGTGCTTCCCATGTGTCATTGCTTTTGTTATTTTGTATTATGGGGTTTATCGAAC
1 CATTAAGAGAAGTGCTTCCCATGTGTCATTGCTTTTGTTATTTTG---TA------TTATCGAAC
6934600 TCAAGTCTATCTATGTGTTCATCATATTACAAAATGAAGGGTGGGTCTTACGAGATATATTTTTT
57 TCAAGTCTATCTATGTGTTCATCATATTACAAAATGAAGGGTGGGTCTTACGAGATATATTTTTT
*
6934665 TCTCATTATGCACTTCAGAACTTCAATACAACAGTGTTTGATGCCGTACATAAGTATATTAGTTT
122 TCTCATTATGCACTTCAGAACTTCAATACAACAGTGTTTGAAGCCGTACATAAGTATATTAGTTT
6934730 ATTTATCCATACAATGGAAAGGATATTATAGAGATAATATTGTTGTTTTAGATTTTGTATTATAG
187 ATTTATCCATACAATGGAAAGGATATTATAGAGATAATATTGTTGTTTTAGATTTTGTATTATAG
6934795 CCACTCTTTTTTCTGTTGATGATCATTGTGTGTTCTCTATGTTTACGTATTCATATTTGGCTATG
252 CCACTCTTTTTTCTGTTGATGATCATTGTGTGTTCTCTATGTTTACGTATTCATATTTGGCTATG
6934860 TTGTTTTACTGATGGGTTTTAATATTAGATTCCCTTTCATTTTTAGTAATATTATTAGAATTTAA
317 TTGTTTTACTGATGGGTTTTAATATTAGATTCCCTTTCATTTTTAGTAATATTATTAGAATTTAA
6934925 TTTATGGATTGGCATCAGTTTTAACGTGT
382 TTTATGGATTGGCATCAGTTTTAACGTGT
6934954 C
1 C
6934955 TGACCATTTG
Statistics
Matches: 409, Mismatches: 2, Indels: 9
0.97 0.00 0.02
Matches are distributed among these distances:
410 45 0.11
413 2 0.00
419 362 0.89
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (410 bp):
CATTAAGAGAAGTGCTTCCCATGTGTCATTGCTTTTGTTATTTTGTATTATCGAACTCAAGTCTA
TCTATGTGTTCATCATATTACAAAATGAAGGGTGGGTCTTACGAGATATATTTTTTTCTCATTAT
GCACTTCAGAACTTCAATACAACAGTGTTTGAAGCCGTACATAAGTATATTAGTTTATTTATCCA
TACAATGGAAAGGATATTATAGAGATAATATTGTTGTTTTAGATTTTGTATTATAGCCACTCTTT
TTTCTGTTGATGATCATTGTGTGTTCTCTATGTTTACGTATTCATATTTGGCTATGTTGTTTTAC
TGATGGGTTTTAATATTAGATTCCCTTTCATTTTTAGTAATATTATTAGAATTTAATTTATGGAT
TGGCATCAGTTTTAACGTGT
Found at i:6962957 original size:42 final size:42
Alignment explanation
Indices: 6962889--6963088 Score: 206
Period size: 42 Copynumber: 4.7 Consensus size: 42
6962879 GGTTATTAGC
6962889 GGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGT
1 GGCGTTTGT-TCCAAAAACGCCGCTATAGATATGACCTTTTGT
* ** * *
6962932 GGCGTTTGTTCCAAAAATGTTGCTATAGATCTTGATCTTTTGT
1 GGCGTTTGTTCCAAAAACGCCGCTATAGAT-ATGACCTTTTGT
** ** *
6962975 GATGTTT-TTGGAACAAACGCCGCTATAGATCTGACCTTTTGT
1 GGCGTTTGTTCCAA-AAACGCCGCTATAGATATGACCTTTTGT
* * * **
6963017 GGCGTTTGTTCC-AAAATGCCGCTTTAGATATCGACGTTTTAA
1 GGCGTTTGTTCCAAAAACGCCGCTATAGATAT-GACCTTTTGT
*
6963059 GACGTTTGTTCCAAAAACGCCGCTATAGAT
1 GGCGTTTGTTCCAAAAACGCCGCTATAGAT
6963089 CTTCACCTAT
Statistics
Matches: 125, Mismatches: 27, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
41 15 0.12
42 56 0.45
43 54 0.43
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (42 bp):
GGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTTGT
Found at i:6963106 original size:43 final size:43
Alignment explanation
Indices: 6962891--6963108 Score: 203
Period size: 43 Copynumber: 5.1 Consensus size: 43
6962881 TTATTAGCGG
*
6962891 CGTTTGTATCCAAAAACGCCGCTATAGAT-ATGACCTTTTGTGG
1 CGTTTGT-TCCAAAAACGCCGCTATAGATCATGACCTTTTGTGA
* ** * *
6962934 CGTTTGTTCCAAAAATGTTGCTATAGATCTTGATCTTTTGTGA
1 CGTTTGTTCCAAAAACGCCGCTATAGATCATGACCTTTTGTGA
* ** *
6962977 TGTTT-TTGGAACAAACGCCGCTATAGATC-TGACCTTTTGTGG
1 CGTTTGTTCCAA-AAACGCCGCTATAGATCATGACCTTTTGTGA
* * * **
6963019 CGTTTGTTCC-AAAATGCCGCTTTAGAT-ATCGACGTTTTAAGA
1 CGTTTGTTCCAAAAACGCCGCTATAGATCAT-GACCTTTTGTGA
* * * *
6963061 CGTTTGTTCCAAAAACGCCGCTATAGATCTTCACCTATTGCGA
1 CGTTTGTTCCAAAAACGCCGCTATAGATCATGACCTTTTGTGA
6963104 CGTTT
1 CGTTT
6963109 TATTTTCTCA
Statistics
Matches: 137, Mismatches: 31, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
41 15 0.11
42 56 0.41
43 65 0.47
44 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (43 bp):
CGTTTGTTCCAAAAACGCCGCTATAGATCATGACCTTTTGTGA
Found at i:6963108 original size:85 final size:85
Alignment explanation
Indices: 6962891--6963090 Score: 253
Period size: 84 Copynumber: 2.4 Consensus size: 85
6962881 TTATTAGCGG
* **
6962891 CGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGTGGCGTTTGTTCCAAAAATGTTGCT
1 CGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTTGTGGCGTTTGTTCCAAAAATGCCGCT
* * **
6962956 ATAGATCTTGATCTTTTGTGA
65 ATAGATATCGATCTTTTAAGA
* **
6962977 TGTTT-TTGGAACAAACGCCGCTATAGATCTGACCTTTTGTGGCGTTTGTTCC-AAAATGCCGCT
1 CGTTTGTTCCAA-AAACGCCGCTATAGATCTGACCTTTTGTGGCGTTTGTTCCAAAAATGCCGCT
*
6963040 TTAGATATCGA-CGTTTTAAGA
65 ATAGATATCGATC-TTTTAAGA
6963061 CGTTTGTTCCAAAAACGCCGCTATAGATCT
1 CGTTTGTTCCAAAAACGCCGCTATAGATCT
6963091 TCACCTATTG
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
83 1 0.01
84 48 0.49
85 44 0.45
86 4 0.04
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (85 bp):
CGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGTGGCGTTTGTTCCAAAAATGCCGCTA
TAGATATCGATCTTTTAAGA
Found at i:6966415 original size:14 final size:15
Alignment explanation
Indices: 6966384--6966416 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
6966374 CAAAGAAACA
6966384 CACATATCATCATAT
1 CACATATCATCATAT
*
6966399 CACATAT-ATCATTT
1 CACATATCATCATAT
6966413 CACA
1 CACA
6966417 CCATAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.33
Consensus pattern (15 bp):
CACATATCATCATAT
Found at i:6966589 original size:23 final size:22
Alignment explanation
Indices: 6966563--6966622 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 22
6966553 CTCGTATAAC
6966563 TGCACTGAAGTGCCACGTAGAA
1 TGCACTGAAGTGCCACGTAGAA
* * *
6966585 TTGCACCGTAGTGCCGCGTAGAA
1 -TGCACTGAAGTGCCACGTAGAA
6966608 TGCACTGAAGTGCCA
1 TGCACTGAAGTGCCA
6966623 TATAAGATTG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (22 bp):
TGCACTGAAGTGCCACGTAGAA
Found at i:6971628 original size:14 final size:15
Alignment explanation
Indices: 6971597--6971629 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
6971587 CAAAGAAACA
6971597 CACATATCATCATAT
1 CACATATCATCATAT
*
6971612 CACATAT-ATCATTT
1 CACATATCATCATAT
6971626 CACA
1 CACA
6971630 CCATAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.33
Consensus pattern (15 bp):
CACATATCATCATAT
Found at i:6971794 original size:23 final size:22
Alignment explanation
Indices: 6971776--6971835 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 22
6971766 CTCGTATAAC
6971776 TGCACCGAAGTGCCACGTAGAA
1 TGCACCGAAGTGCCACGTAGAA
* *
6971798 TTGCACCGTAGTGCCGCGTAGAA
1 -TGCACCGAAGTGCCACGTAGAA
*
6971821 TGCACTGAAGTGCCA
1 TGCACCGAAGTGCCA
6971836 TATAAGATTG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (22 bp):
TGCACCGAAGTGCCACGTAGAA
Found at i:6974704 original size:26 final size:24
Alignment explanation
Indices: 6974675--6974726 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
6974665 TTTTGTTCCA
6974675 TAAACAAACATTATAATTTGTATATT
1 TAAACAAA-A-TATAATTTGTATATT
* * *
6974701 TAAATAAAATATAATTTTTTTATT
1 TAAACAAAATATAATTTGTATATT
6974725 TA
1 TA
6974727 TCCAAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 15 0.65
25 1 0.04
26 7 0.30
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (24 bp):
TAAACAAAATATAATTTGTATATT
Found at i:6974895 original size:25 final size:25
Alignment explanation
Indices: 6974867--6974917 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
6974857 TTCAAACTCG
6974867 AAATAAAAAATTGAAGCTCGGCTCA
1 AAATAAAAAATTGAAGCTCGGCTCA
* * * *
6974892 AAATTAAAATTTGAAGTTTGGCTCA
1 AAATAAAAAATTGAAGCTCGGCTCA
6974917 A
1 A
6974918 GCTCAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (25 bp):
AAATAAAAAATTGAAGCTCGGCTCA
Found at i:6979509 original size:35 final size:34
Alignment explanation
Indices: 6979424--6979510 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 34
6979414 AATATAATTT
*
6979424 TAAATATAACAAACTTACAATAAGTATTAAATGG
1 TAAATATAACAAAATTACAATAAGTATTAAATGG
*
6979458 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ATAACAAAATTACAATAA--G-TATTAAATGG
6979496 T-AATA-AACAAAATTA
1 TAAATATAACAAAATTA
6979511 ACTGAAATAC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
34 5 0.11
35 25 0.54
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.29
Consensus pattern (34 bp):
TAAATATAACAAAATTACAATAAGTATTAAATGG
Found at i:6981782 original size:111 final size:111
Alignment explanation
Indices: 6981645--6981866 Score: 417
Period size: 111 Copynumber: 2.0 Consensus size: 111
6981635 ATTACAAAAA
6981645 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
6981710 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
6981756 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
6981821 AATTAAAACATTAAAATGTTACTGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
6981867 ATGATTTCCA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:6982206 original size:50 final size:49
Alignment explanation
Indices: 6982143--6982275 Score: 135
Period size: 50 Copynumber: 2.7 Consensus size: 49
6982133 ATGTCAGATA
*
6982143 ACCGTATAGCGCGGATCAGGGG-GCACGCTATAC-CCACGAGGCGTCAAATC
1 ACCGTATAGCGCGG-TCAGGGGTG--CGCTATACTCCACGAGGCGCCAAATC
* * **
6982193 ACCGTATATCGCGGGGCAGGGGTGCGCTATACTCCACGTTGCGCCAAATC
1 ACCGTATAGCGC-GGTCAGGGGTGCGCTATACTCCACGAGGCGCCAAATC
* * *
6982243 AGCGTATAGCGCGGTGCAGGGGCGCGCTTTACT
1 ACCGTATAGCGCGGT-CAGGGGTGCGCTATACT
6982276 GCTACGGGTG
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
49 10 0.14
50 56 0.81
51 3 0.04
ACGTcount: A:0.21, C:0.29, G:0.32, T:0.18
Consensus pattern (49 bp):
ACCGTATAGCGCGGTCAGGGGTGCGCTATACTCCACGAGGCGCCAAATC
Found at i:6982875 original size:22 final size:22
Alignment explanation
Indices: 6982845--6982886 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6982835 AATATTCTTC
* *
6982845 ATTGGCATTATATAAATATTTG
1 ATTGACATTACATAAATATTTG
*
6982867 ATTGACATTACATACATATT
1 ATTGACATTACATAAATATT
6982887 AGATCGATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (22 bp):
ATTGACATTACATAAATATTTG
Done.