Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006434.1 Hibiscus syriacus cultivar Beakdansim tig00015533_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: 105000
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:3148 original size:22 final size:22
Alignment explanation
Indices: 3123--3164 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3113 CAATTCATTT
3123 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
3145 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
3165 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:3499 original size:8 final size:8
Alignment explanation
Indices: 3482--3524 Score: 61
Period size: 8 Copynumber: 5.4 Consensus size: 8
3472 ATTTTTTTAC
3482 AAAA-AAA
1 AAAACAAA
3489 AAAACAAA
1 AAAACAAA
*
3497 AAAGCAAA
1 AAAACAAA
3505 AAACACAAA
1 AAA-ACAAA
3514 AAAACAAA
1 AAAACAAA
3522 AAA
1 AAA
3525 GCCAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
7 4 0.12
8 21 0.66
9 7 0.22
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (8 bp):
AAAACAAA
Found at i:3507 original size:17 final size:17
Alignment explanation
Indices: 3485--3524 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3475 TTTTTACAAA
*
3485 AAAAAAAACAAAAAAGC
1 AAAAAAAACAAAAAAAC
*
3502 AAAAAACACAAAAAAAC
1 AAAAAAAACAAAAAAAC
3519 AAAAAA
1 AAAAAA
3525 GCCAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (17 bp):
AAAAAAAACAAAAAAAC
Found at i:3530 original size:17 final size:16
Alignment explanation
Indices: 3482--3531 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
3472 ATTTTTTTAC
3482 AAAAA-AAAAAA-CAA
1 AAAAACAAAAAACCAA
*
3496 AAAAGCAAAAAACACAA
1 AAAAACAAAAAAC-CAA
3513 AAAAACAAAAAAGCCAA
1 AAAAACAAAAAA-CCAA
3530 AA
1 AA
3532 TTTCAAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 4 0.13
15 6 0.20
17 19 0.63
18 1 0.03
ACGTcount: A:0.82, C:0.14, G:0.04, T:0.00
Consensus pattern (16 bp):
AAAAACAAAAAACCAA
Found at i:7778 original size:22 final size:22
Alignment explanation
Indices: 7753--7794 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
7743 CAATTCATTT
7753 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
7775 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
7795 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:8323 original size:21 final size:22
Alignment explanation
Indices: 8250--8345 Score: 90
Period size: 23 Copynumber: 4.3 Consensus size: 22
8240 GTTGAGGGTT
* *
8250 CTATATGGTCCTTCGGGACAATC
1 CTATGTGGTCCTTCGGGACAA-A
* *
8273 CTATGTAGTCCTTTGGGACAAAA
1 CTATGTGGTCCTTCGGGAC-AAA
8296 CTATGTGGTCCTTCGGGACAAA
1 CTATGTGGTCCTTCGGGACAAA
8318 -TATGTGG-CACTTCGGTG-CAAA
1 CTATGTGGTC-CTTCGG-GACAAA
*
8339 TTATGTG
1 CTATGTG
8346 AGTTGTGGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
20 1 0.02
21 17 0.27
22 10 0.16
23 33 0.52
24 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (22 bp):
CTATGTGGTCCTTCGGGACAAA
Found at i:13413 original size:41 final size:41
Alignment explanation
Indices: 13366--13454 Score: 99
Period size: 41 Copynumber: 2.2 Consensus size: 41
13356 GTACTTTAGC
* *
13366 GGCGTTTGTATAA-AAATGCTGCAATATGGTTCATATATAGT
1 GGCGTTTGTATAACAAATGCCGCAATA-GGTTCATACATAGT
* * * *
13407 GGCGTTTTTTTAACAAATGCCGTAATAGGTTCATCCATAGT
1 GGCGTTTGTATAACAAATGCCGCAATAGGTTCATACATAGT
*
13448 GGTGTTT
1 GGCGTTT
13455 ATCAACAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 29 0.73
42 11 0.28
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.38
Consensus pattern (41 bp):
GGCGTTTGTATAACAAATGCCGCAATAGGTTCATACATAGT
Found at i:13578 original size:82 final size:82
Alignment explanation
Indices: 13471--13650 Score: 190
Period size: 82 Copynumber: 2.2 Consensus size: 82
13461 AAATGTTGTG
* * *
13471 ACATAGTAGTACTTTAGCGTTGTTTGTAT-AAAA-A-TGGCATAATAGGGTTCAAATATAGTG-C
1 ACATAGTAGTATTTTAGCGTCGTTTGTATCAAAACACT-GC--AATAGAGTTCAAATATAGTGAC
*
13532 TGTTTTTTAACAAACTCCGCA
63 T-TTTTTTAACAAACACCGCA
**
13553 ACATAGTAGTATTTTAGC-TACGTTTGTATCAAAACACTGCAATAGAGTTCATCTATAGTGACCT
1 ACATAGTAGTATTTTAGCGT-CGTTTGTATCAAAACACTGCAATAGAGTTCAAATATAGTGA-CT
13617 TTTTTTAACAAACACCGCA
64 TTTTTTAACAAACACCGCA
* * *
13636 AAAGAGTATTATTTT
1 ACATAGTAGTATTTT
13651 TTTAATTATG
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
81 1 0.01
82 42 0.51
83 34 0.41
84 5 0.06
85 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (82 bp):
ACATAGTAGTATTTTAGCGTCGTTTGTATCAAAACACTGCAATAGAGTTCAAATATAGTGACTTT
TTTTAACAAACACCGCA
Found at i:16832 original size:44 final size:44
Alignment explanation
Indices: 16716--16830 Score: 142
Period size: 43 Copynumber: 2.6 Consensus size: 44
16706 GTTTTCTACT
* * * * *
16716 AAAACGCCGCTATAGATCATGATCTTTTGCGGCATTTTTTATTA
1 AAAACGCCGCTATTGAGCTTGACCTTTTACGGCATTTTTTATTA
* **
16760 AAAATGTTGCTATTGAGCTTGACCTTTTACGGCA-TTTTTATTA
1 AAAACGCCGCTATTGAGCTTGACCTTTTACGGCATTTTTTATTA
*
16803 AAAACGCCGCTATTGAGCTTGACATTTT
1 AAAACGCCGCTATTGAGCTTGACCTTTT
16831 TAAGAAAAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
43 33 0.56
44 26 0.44
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (44 bp):
AAAACGCCGCTATTGAGCTTGACCTTTTACGGCATTTTTTATTA
Found at i:16839 original size:33 final size:33
Alignment explanation
Indices: 16792--16863 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
16782 CCTTTTACGG
** * * *
16792 CATTTTTATTAAAAACGCCGCTATTGAGCTTGA
1 CATTTTTAAGAAAAACACCGCTATAGAGCTAGA
*
16825 CATTTTTAAGAAAAACACGGCTATAGAGCTAGA
1 CATTTTTAAGAAAAACACCGCTATAGAGCTAGA
16858 -ATTTTT
1 CATTTTT
16864 GCGGCGTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 6 0.18
33 27 0.82
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (33 bp):
CATTTTTAAGAAAAACACCGCTATAGAGCTAGA
Found at i:17589 original size:2 final size:2
Alignment explanation
Indices: 17578--17650 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
17568 AATTTTAGAT
17578 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17619 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17651 AATAAGATTA
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18521 original size:24 final size:24
Alignment explanation
Indices: 18489--18544 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
18479 CTATTCTTTC
18489 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
18513 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
18537 GCTTCAAT
1 GCTTCAAT
18545 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:19991 original size:31 final size:31
Alignment explanation
Indices: 19906--20001 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
19896 TTAAAAAACA
* *
19906 TAAGATATTGTCACTTTT-ATTTTTATGTAAT
1 TAAGATATGGTCA-TTTTCATTTTTATTTAAT
* *
19937 TAAGATATGGTCACTTTCGTTTTTATTTAAT
1 TAAGATATGGTCATTTTCATTTTTATTTAAT
* *
19968 TAAGATATGGTCATTTTCTTTTTTGTTTAAT
1 TAAGATATGGTCATTTTCATTTTTATTTAAT
19999 TAA
1 TAA
20002 AATGTGTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 3 0.05
31 54 0.95
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.54
Consensus pattern (31 bp):
TAAGATATGGTCATTTTCATTTTTATTTAAT
Found at i:22282 original size:18 final size:18
Alignment explanation
Indices: 22259--22304 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
22249 CTTCCTCTTG
22259 GTATCGATACCCACTTAA
1 GTATCGATACCCACTTAA
*
22277 GTATCGATACCCATTTAA
1 GTATCGATACCCACTTAA
22295 GTATCGATAC
1 GTATCGATAC
22305 TACTTGCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (18 bp):
GTATCGATACCCACTTAA
Found at i:28410 original size:21 final size:21
Alignment explanation
Indices: 28366--28411 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28356 GATCAAAAAT
* *
28366 TTTTATTTATTTTCTGTAATA
1 TTTTATTTATTTTATATAATA
28387 TTTTATTATATTTTATATAA-A
1 TTTTATT-TATTTTATATAATA
28408 TTTT
1 TTTT
28412 GTTTTCAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTATTTATTTTATATAATA
Found at i:28668 original size:23 final size:23
Alignment explanation
Indices: 28642--28706 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
28632 AGTCGAGGGT
*
28642 TCTATGCGGTCTTTCGGGACAAA
1 TCTATGCGGTCCTTCGGGACAAA
* *
28665 TCTATGTGGTCCTTCGGGACAAT
1 TCTATGCGGTCCTTCGGGACAAA
* * *
28688 TCAATGTGGTCCTTTGGGA
1 TCTATGCGGTCCTTCGGGA
28707 GAATTTCTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.20, G:0.28, T:0.34
Consensus pattern (23 bp):
TCTATGCGGTCCTTCGGGACAAA
Found at i:28711 original size:23 final size:23
Alignment explanation
Indices: 28649--28711 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
28639 GGTTCTATGC
* * *
28649 GGTCTTTCGGGACAAATCTATGT
1 GGTCCTTCGGGACAATTCAATGT
28672 GGTCCTTCGGGACAATTCAATGT
1 GGTCCTTCGGGACAATTCAATGT
* *
28695 GGTCCTTTGGGAGAATT
1 GGTCCTTCGGGACAATT
28712 TCTTCGTAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCAATGT
Found at i:35010 original size:18 final size:17
Alignment explanation
Indices: 34978--35013 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
34968 TTTCATAATG
34978 CTAAAATGGTATCGATA
1 CTAAAATGGTATCGATA
*
34995 CTAAAGTGGATATCGATA
1 CTAAAATGG-TATCGATA
35013 C
1 C
35014 CATAGAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (17 bp):
CTAAAATGGTATCGATA
Found at i:41953 original size:12 final size:12
Alignment explanation
Indices: 41924--41961 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
41914 AATTATTAAA
41924 ATATTTAA-AAT
1 ATATTTAATAAT
*
41935 ATATTTATTAAT
1 ATATTTAATAAT
*
41947 ATTTTTAATAAT
1 ATATTTAATAAT
41959 ATA
1 ATA
41962 ATAGTATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:41953 original size:23 final size:23
Alignment explanation
Indices: 41906--41963 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
41896 CATTTTAATC
41906 AAAATATTAATTATTAAAATATTT
1 AAAATA-TAATTATTAAAATATTT
* * *
41930 AAAATATATTTATTAATATTTTT
1 AAAATATAATTATTAAAATATTT
41953 AATAATATAAT
1 AA-AATATAAT
41964 AGTATATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATATAATTATTAAAATATTT
Found at i:41956 original size:21 final size:21
Alignment explanation
Indices: 41912--41987 Score: 63
Period size: 22 Copynumber: 3.8 Consensus size: 21
41902 AATCAAAATA
41912 TTAAT-TAT-TAA-AATATTT
1 TTAATATATATAATAATATTT
** * *
41930 AAAATATATTTATTAATATTT
1 TTAATATATATAATAATATTT
41951 TTAATA-ATATAATAGTATATTT
1 TTAATATATATAATA--ATATTT
41973 TTAATAT-TATAATAA
1 TTAATATATATAATAA
41988 AATAATAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
18 3 0.07
19 3 0.07
20 9 0.20
21 11 0.24
22 19 0.42
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (21 bp):
TTAATATATATAATAATATTT
Found at i:41970 original size:22 final size:22
Alignment explanation
Indices: 41945--41986 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
41935 ATATTTATTA
41945 ATATTTTTAATAATATAATAGT
1 ATATTTTTAATAATATAATAGT
*
41967 ATATTTTTAATATTATAATA
1 ATATTTTTAATAATATAATA
41987 AAATAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATTTTTAATAATATAATAGT
Found at i:42001 original size:18 final size:18
Alignment explanation
Indices: 41978--42012 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41968 TATTTTTAAT
41978 ATTATAATAAAATAATAA
1 ATTATAATAAAATAATAA
* *
41996 ATTATATTATAATAATA
1 ATTATAATAAAATAATA
42013 TAATATAAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTATAATAAAATAATAA
Found at i:42025 original size:23 final size:23
Alignment explanation
Indices: 41976--42029 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
41966 TATATTTTTA
*
41976 ATATTATAATAAAATAATAAATT
1 ATATTATAATAAAATAATAAATG
*
41999 ATATTATAATAATATAATATAA-G
1 ATATTATAATAAAATAATA-AATG
42022 ATATTATA
1 ATATTATA
42030 TTTTTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 26 0.93
24 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAATAAATG
Found at i:42059 original size:31 final size:31
Alignment explanation
Indices: 41929--42059 Score: 103
Period size: 31 Copynumber: 4.3 Consensus size: 31
41919 TTAAAATATT
* *
41929 TAAAATATATTTATTAATATTTTTAATA-AT-A
1 TAAATTATATTT-TTAATA-TTATAATATATAA
* *
41960 TAATAGTATATTTTTAATATTATAATAAAATAA
1 TAA-ATTATATTTTTAATATTATAAT-ATATAA
* *
41993 TAAATTATA-TTATAATAATATAATATA-AGA
1 TAAATTATATTTTTAATATTATAATATATA-A
* *
42023 T--ATTATATTTTTATTTTTATAATATATAA
1 TAAATTATATTTTTAATATTATAATATATAA
42052 TAAATTAT
1 TAAATTAT
42060 TAATAAAATT
Statistics
Matches: 81, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
28 6 0.07
29 17 0.21
30 11 0.14
31 28 0.35
32 15 0.19
33 4 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.50
Consensus pattern (31 bp):
TAAATTATATTTTTAATATTATAATATATAA
Found at i:42191 original size:23 final size:22
Alignment explanation
Indices: 42164--42214 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
42154 ATTATCTAAT
* *
42164 AATATTTTAATAAATATATTTAA
1 AATATATTAATAAATAT-TTAAA
*
42187 AATATATTAATTAATATTTAAA
1 AATATATTAATAAATATTTAAA
42209 AATATA
1 AATATA
42215 ATATAACACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATATTAATAAATATTTAAA
Found at i:49273 original size:19 final size:18
Alignment explanation
Indices: 49249--49297 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
49239 TCATTGGCTT
49249 TTCTTTCTTTTTGAAATTC
1 TTCTTTCTTTTTG-AATTC
*
49268 TTCTTT-TTTTCTGAATTT
1 TTCTTTCTTTT-TGAATTC
*
49286 TTTTTTCTTTTT
1 TTCTTTCTTTTT
49298 ATCTTTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.10, C:0.12, G:0.04, T:0.73
Consensus pattern (18 bp):
TTCTTTCTTTTTGAATTC
Found at i:63780 original size:7 final size:7
Alignment explanation
Indices: 63758--63790 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
63748 TCTTCATTCA
63758 TTATTAT
1 TTATTAT
63765 TTATGTAT
1 TTAT-TAT
63773 TTATTAT
1 TTATTAT
63780 TTATT-T
1 TTATTAT
63786 TTATT
1 TTATT
63791 TATCTTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (7 bp):
TTATTAT
Found at i:63793 original size:25 final size:26
Alignment explanation
Indices: 63741--63793 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 26
63731 ATATTTTCCC
*
63741 ATGTATTTCTTCATTCATTATTATTT
1 ATGTATTTATTCATTCATTATTATTT
* *
63767 ATGTATTTATT-ATTTATTTTTATTT
1 ATGTATTTATTCATTCATTATTATTT
63792 AT
1 AT
63794 CTTGATATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.66
Consensus pattern (26 bp):
ATGTATTTATTCATTCATTATTATTT
Found at i:68190 original size:34 final size:30
Alignment explanation
Indices: 68152--68220 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
68142 TTGATATAAC
68152 AATTTAAGGAAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--AAAAAT-GTTTTTGGACTT-AATTG
*
68186 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAAAAAAATGTTTTTGGACTTAATTG
68215 AATTTA
1 AATTTA
68221 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 12 0.36
31 5 0.15
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAAAAAAATGTTTTTGGACTTAATTG
Found at i:68231 original size:29 final size:30
Alignment explanation
Indices: 68162--68220 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
68152 AATTTAAGGA
68162 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAC
68193 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
68221 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAC
Found at i:68326 original size:21 final size:21
Alignment explanation
Indices: 68300--68398 Score: 114
Period size: 21 Copynumber: 4.7 Consensus size: 21
68290 AGGGTGTCAA
*
68300 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCATGC
*
68321 AGTGCATCCATGCATCCC-TGT
1 AGTGCATCCATGCA-CCCATGC
*
68342 AGTGCATCCATGCACCTACAT-T
1 AGTGCATCCATGCACC--CATGC
*
68364 AGTGCATCAATGCA-CCATGC
1 AGTGCATCCATGCACCCATGC
68384 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
68399 TCAAACACCG
Statistics
Matches: 68, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.04
20 15 0.22
21 31 0.46
22 18 0.26
23 1 0.01
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCATGC
Found at i:68482 original size:20 final size:20
Alignment explanation
Indices: 68422--68492 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
68412 TCAATTAGTT
*
68422 CATCGATGCATCCT-TCTGTG
1 CATCAATGCATCCTGT-TGTG
* **
68442 CATCAATGTATCAAGGTTGTG
1 CATCAATGCATC-CTGTTGTG
68463 CATCAATGCATCCTGTTGTG
1 CATCAATGCATCCTGTTGTG
*
68483 CATCCATGCA
1 CATCAATGCA
68493 CGAAGGCTGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 25 0.61
21 15 0.37
22 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (20 bp):
CATCAATGCATCCTGTTGTG
Found at i:69579 original size:28 final size:30
Alignment explanation
Indices: 69510--69568 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
69500 CAATTTTAGG
69510 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
*
69541 CAAAATATTTTTGGACTT-AATT-AATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
69569 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 6 0.22
29 4 0.15
30 11 0.41
31 6 0.22
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:69674 original size:21 final size:21
Alignment explanation
Indices: 69648--69808 Score: 261
Period size: 21 Copynumber: 7.7 Consensus size: 21
69638 AGGGTGTCAA
69648 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
69669 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
69690 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
69711 AGTGCATCCATGCACCCTTGC
1 AGTGCATCCATGCACCCCTGC
*
69732 AGTGCATCGATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
69753 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
* * *
69774 AGTGAATCGATGCA-CCATGC
1 AGTGCATCCATGCACCCCTGC
69794 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
69809 TCAAACAGCG
Statistics
Matches: 129, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
20 17 0.13
21 112 0.87
ACGTcount: A:0.21, C:0.38, G:0.20, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:69854 original size:20 final size:20
Alignment explanation
Indices: 69829--69901 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
69819 AATGGAATTA
69829 GTGCATCGATGCATCCTTAT
1 GTGCATCGATGCATCCTTAT
69849 GTGCATCGATGCATCCTTAT
1 GTGCATCGATGCATCCTTAT
*
69869 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTAT
*
69889 GTGCATCCATGCA
1 GTGCATCGATGCA
69902 CGAAGGTTGC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTAT
Found at i:70043 original size:21 final size:21
Alignment explanation
Indices: 70014--70053 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
70004 TATTAGTAGA
70014 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCC-AACGGCTCC
*
70036 AAAA-CATCTCCAACGGCT
1 AAAATCATCCCCAACGGCT
70054 ATATACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:70757 original size:29 final size:28
Alignment explanation
Indices: 70724--70783 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 28
70714 CAATTTAAGG
70724 AAAAATGGTTTTTCGACTTGAATTGAATTT
1 AAAAAT-GTTTTTCGACTT-AATTGAATTT
*
70754 AAAAAATGTTTTTGGACTTAATTGAATTT
1 -AAAAATGTTTTTCGACTTAATTGAATTT
70783 A
1 A
70784 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 1 0.04
29 10 0.36
30 11 0.39
31 6 0.21
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (28 bp):
AAAAATGTTTTTCGACTTAATTGAATTT
Found at i:70794 original size:29 final size:30
Alignment explanation
Indices: 70724--70783 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
70714 CAATTTAAGG
70724 AAAAATGGTTTTTCGACTTGAATTGAATTTA
1 AAAAAT-GTTTTTCGACTTGAATTGAATTTA
*
70755 AAAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAAATGTTTTTCGACTTGAATTGAATTTA
70784 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.37, C:0.05, G:0.15, T:0.43
Consensus pattern (30 bp):
AAAAATGTTTTTCGACTTGAATTGAATTTA
Found at i:70919 original size:21 final size:21
Alignment explanation
Indices: 70863--70926 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
70853 AGGGTGTCAA
*
70863 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCATCCCTGC
70884 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
70905 AGTGCATCCATGCATCCATGC
1 AGTGCATCCATGCATCCCTGC
70926 A
1 A
70927 CCTTCACTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:71015 original size:20 final size:20
Alignment explanation
Indices: 70990--71057 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
70980 AATGTAATTA
70990 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
**
71010 GTGCATCGATGCATCAAGGT-T
1 GTGCATCGATGCATC--CTTCT
* *
71031 GTGCATCAATGCATCCTGCT
1 GTGCATCGATGCATCCTTCT
71051 GTGCATC
1 GTGCATC
71058 CTTGCACGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 23 0.59
21 15 0.38
22 1 0.03
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:72758 original size:2 final size:2
Alignment explanation
Indices: 72751--72777 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
72741 ATTTGCGTAT
72751 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
72778 CTTATTAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72924 original size:34 final size:34
Alignment explanation
Indices: 72864--72929 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
72854 GGCACATAAT
* *
72864 TTATATATTATATTATTATTAGTTATGTGTGTGG
1 TTATATATTATAATATTATTAGTTATGGGTGTGG
72898 TTATATATATATAA-ATATATTA-TTATGGGTGT
1 TTATATAT-TATAATAT-TATTAGTTATGGGTGT
72930 ATGTGTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 19 0.68
35 9 0.32
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (34 bp):
TTATATATTATAATATTATTAGTTATGGGTGTGG
Found at i:74002 original size:33 final size:33
Alignment explanation
Indices: 73960--74037 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
73950 TTTAAATAGT
* *
73960 TATTATTTTTTA-TATTAAT-ATATTTATGTAAA
1 TATTATTTTTTATTA-AAATAATATTTATATAAA
*
73992 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATTAAAATAATATTTATATAAA
74025 TATTATTTATTTA
1 TATTATTT-TTTA
74038 GAATTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.38
33 21 0.52
34 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTTATTAAAATAATATTTATATAAA
Found at i:74199 original size:17 final size:17
Alignment explanation
Indices: 74177--74230 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
74167 AATGTTAATA
74177 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
74194 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
74211 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
74228 TTT
1 TTT
74231 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:75790 original size:21 final size:21
Alignment explanation
Indices: 75760--75807 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
75750 GCATGGGTAC
* *
75760 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
75781 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
75802 ATGCCA
1 ATGCCA
75808 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:75837 original size:21 final size:20
Alignment explanation
Indices: 75811--75904 Score: 116
Period size: 21 Copynumber: 4.5 Consensus size: 20
75801 TATGCCATCT
* *
75811 CCGCAGGGTTACATTCCGAGC
1 CCGCA-GGTTACATGCCTAGC
*
75832 CCGCAGGGTTACATTCCTAGC
1 CCGCA-GGTTACATGCCTAGC
75853 CCGCCAGGTTACATGCCTAGC
1 CCG-CAGGTTACATGCCTAGC
75874 CCGCCAGGTTACATGCCTAGC
1 CCG-CAGGTTACATGCCTAGC
75895 CCGCATGGTT
1 CCGCA-GGTT
75905 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.26, T:0.21
Consensus pattern (20 bp):
CCGCAGGTTACATGCCTAGC
Found at i:76479 original size:39 final size:39
Alignment explanation
Indices: 76427--76504 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 39
76417 AAATGTTTTT
76427 AAAATACAAATTATATT-ATTCGAAATTTAAAATAAAAATA
1 AAAATACAAATTAT-TTAATT-GAAATTTAAAATAAAAATA
* * *
76467 AAAATA-ATATTATTTAAATTTAAATTTAAAATATAAAT
1 AAAATACAAATTATTT-AATTGAAATTTAAAATAAAAAT
76505 TATAGTATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
38 2 0.06
39 22 0.67
40 9 0.27
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (39 bp):
AAAATACAAATTATTTAATTGAAATTTAAAATAAAAATA
Found at i:76486 original size:33 final size:34
Alignment explanation
Indices: 76427--76523 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
76417 AAATGTTTTT
*
76427 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * * *
76461 AAAATAAAAATAATATTATT-TAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
76494 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
76524 CATTAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 27 0.51
34 26 0.49
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:76530 original size:34 final size:33
Alignment explanation
Indices: 76425--76530 Score: 124
Period size: 34 Copynumber: 3.2 Consensus size: 33
76415 ATAAATGTTT
*
76425 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* * *
76459 TAAAAATAAAAATAATATTATT-TAAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
76491 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
76526 TTAAA
1 TTAAA
76531 TTTCAACTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.05
33 24 0.40
34 32 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.39
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:77086 original size:127 final size:127
Alignment explanation
Indices: 76920--77264 Score: 613
Period size: 127 Copynumber: 2.7 Consensus size: 127
76910 TTACCTGATT
76920 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
**
76985 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGC-CCCCCGGGAACGCGCCTTCATGT-CAATAGAGAAATAATAGG
77048 TACTGATATATCTAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
77112 TGACGAAATAATGGAAGGCGCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCCCCCCGGGAACGCGCCTTCATGTCAATAGAGAAATAATAGG
77174 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
77239 TGACGAAATAATGGAAGGAGCCCCCC
66 TGACGAAATAATGGAAGGCGCCCCCC
77265 CCCGAGGGAC
Statistics
Matches: 210, Mismatches: 5, Indels: 5
0.95 0.02 0.02
Matches are distributed among these distances:
125 1 0.00
126 53 0.25
127 138 0.66
128 18 0.09
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (127 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCCCCCCGGGAACGCGCCTTCATGTCAATAGAGAAATAATAGG
Found at i:77309 original size:72 final size:72
Alignment explanation
Indices: 77192--77337 Score: 274
Period size: 72 Copynumber: 2.0 Consensus size: 72
77182 TATCTAGTGT
77192 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
77257 AGCCCCC
66 AGCCCCC
*
77264 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATGAAATAATGGAAGG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
*
77329 CGCCCCC
66 AGCCCCC
77336 CC
1 CC
77338 GGGAACGCGC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.18
Consensus pattern (72 bp):
CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
AGCCCCC
Found at i:77408 original size:200 final size:199
Alignment explanation
Indices: 77066--77465 Score: 755
Period size: 200 Copynumber: 2.0 Consensus size: 199
77056 TATCTAGTGT
77066 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
1 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
77131 GCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCC
66 GCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCC
77196 GAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGAGCC
131 GAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGAGCC
77261 CCCC
196 CCCC
*
77265 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATGAAATAATGGAAGGC
1 CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
77330 GCCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
66 G-CCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCC
* *
77395 CGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTTACGAAATAATGGAAGGCGC
130 CGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGAGC
*
77460 GCCCC
195 CCCCC
77465 C
1 C
77466 GGGAACGCGC
Statistics
Matches: 196, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
199 65 0.33
200 131 0.67
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (199 bp):
CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGC
GCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCCCC
GAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGAGCC
CCCC
Found at i:77495 original size:128 final size:128
Alignment explanation
Indices: 77264--77873 Score: 1035
Period size: 128 Copynumber: 4.8 Consensus size: 128
77254 AGGAGCCCCC
*
77264 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATGAAATAATGGAAGG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
* * *
77329 CGCCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGT
66 CGCGCCCCCGGGAACGCGCCTTCATGTCAATAGAGAAATAATAGGTACTGATATATCTAGTGT
*
77392 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTTACGAAATAATGGAAGG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
**
77457 CGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGGTACTGATATATCTAGTGT
66 CGCGCCCCCGGGAACGCGCCTTCATGT-CAATAGAGAAATAATAGGTACTGATATATCTAGTGT
* *
77520 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATATGACGAAATAATGGAAGG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
* *
77585 CGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGT
66 CGCGCCCCCGGGAACGCGCCTTCATGTCAATAGAGAAATAATAGGTACTGATATATCTAGTGT
*
77648 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATGAAATAATGGAAGG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
* **
77713 CGCGCCCCCGGGAACGCGCCTTAATGTCCCCT-GAGAAATAATAGGTACTGATATATCTAGTGT
66 CGCGCCCCCGGGAACGCGCCTTCATGT-CAATAGAGAAATAATAGGTACTGATATATCTAGTGT
77776 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
* *
77841 CGCGCCCCCGGGAACGTGCCTTCATGTGAATAG
66 CGCGCCCCCGGGAACGCGCCTTCATGTCAATAG
77874 TACTCCGATT
Statistics
Matches: 450, Mismatches: 28, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
127 2 0.00
128 446 0.99
129 2 0.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (128 bp):
CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
CGCGCCCCCGGGAACGCGCCTTCATGTCAATAGAGAAATAATAGGTACTGATATATCTAGTGT
Found at i:77719 original size:256 final size:256
Alignment explanation
Indices: 77264--77874 Score: 1150
Period size: 256 Copynumber: 2.4 Consensus size: 256
77254 AGGAGCCCCC
*
77264 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATGAAATAATGGAAGG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
*
77329 CGCCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
66 CGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
*
77394 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTTACGAAATAATGGAAGGCG
131 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
*
77459 CGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGGTACTGATATATCTAGTGT
196 CGCCCCCGGGAACGCGCCTTAATGTCCCCTGAGAAATAATAGGTACTGATATATCTAGTGT
* *
77520 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATATGACGAAATAATGGAAGG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
77585 CGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
66 CGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
*
77650 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATGAAATAATGGAAGGCG
131 CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
77715 CGCCCCCGGGAACGCGCCTTAATGTCCCCTGAGAAATAATAGGTACTGATATATCTAGTGT
196 CGCCCCCGGGAACGCGCCTTAATGTCCCCTGAGAAATAATAGGTACTGATATATCTAGTGT
77776 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
1 CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
*
77841 CGCGCCCCCGGGAACGTGCCTTCATGTGAATAGT
66 CGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
77875 ACTCCGATTA
Statistics
Matches: 345, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
256 345 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (256 bp):
CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGG
CGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTGTCC
CCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAGGCG
CGCCCCCGGGAACGCGCCTTAATGTCCCCTGAGAAATAATAGGTACTGATATATCTAGTGT
Found at i:77958 original size:8 final size:8
Alignment explanation
Indices: 77945--77985 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
77935 TCACAATCTT
77945 TCAAATTC
1 TCAAATTC
77953 TCAAATTC
1 TCAAATTC
* *
77961 CCAAACTC
1 TCAAATTC
77969 T-AAATTC
1 TCAAATTC
77976 TCAAATTC
1 TCAAATTC
77984 TC
1 TC
77986 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:81001 original size:12 final size:12
Alignment explanation
Indices: 80984--81022 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
80974 TACATAAATA
80984 TATTTAATATAT
1 TATTTAATATAT
*
80996 TATTTAATATAA
1 TATTTAATATAT
*
81008 TAATTAATATTAT
1 TATTTAATA-TAT
81021 TA
1 TA
81023 GTTATATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 19 0.83
13 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TATTTAATATAT
Found at i:81664 original size:25 final size:26
Alignment explanation
Indices: 81630--81680 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
81620 CGTGCCTTCC
81630 ACACGTGGCATCCAACTCAGC-GAAA
1 ACACGTGGCATCCAACTCAGCAGAAA
81655 ACACGTGGCATCCAACTCAGCAGAAA
1 ACACGTGGCATCCAACTCAGCAGAAA
81681 GGGTGCTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.37, C:0.31, G:0.20, T:0.12
Consensus pattern (26 bp):
ACACGTGGCATCCAACTCAGCAGAAA
Found at i:83213 original size:8 final size:8
Alignment explanation
Indices: 83200--83224 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
83190 TTTGTTTTTG
83200 CATGTTTA
1 CATGTTTA
83208 CATGTTTA
1 CATGTTTA
83216 CATGTTTA
1 CATGTTTA
83224 C
1 C
83225 GTACGTATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (8 bp):
CATGTTTA
Found at i:87460 original size:20 final size:19
Alignment explanation
Indices: 87435--87472 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
87425 GAACTAGATA
*
87435 GGGGTTTTAAAACCATCTAG
1 GGGGTTTCAAAACC-TCTAG
87455 GGGGTTTCAAAACCTCTA
1 GGGGTTTCAAAACCTCTA
87473 CTGTAGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (19 bp):
GGGGTTTCAAAACCTCTAG
Found at i:96200 original size:25 final size:25
Alignment explanation
Indices: 96163--96218 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
96153 CACAATGCTA
*
96163 ATGTGGCAGTCCACAATGGATGATG
1 ATGTGGCAATCCACAATGGATGATG
** **
96188 ATGTGGCAATCCATGATGTTTGATG
1 ATGTGGCAATCCACAATGGATGATG
96213 ATGTGG
1 ATGTGG
96219 TAGATAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.12, G:0.32, T:0.30
Consensus pattern (25 bp):
ATGTGGCAATCCACAATGGATGATG
Found at i:98217 original size:2 final size:2
Alignment explanation
Indices: 98210--98256 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
98200 TTTCTATAAC
98210 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
98250 AA TA TA T
1 TA TA TA T
98257 TTTTGCATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:101183 original size:26 final size:26
Alignment explanation
Indices: 101161--101213 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
101151 GTACAAATTT
101161 TACGAGGCACTTTCT-AGTGCAAATAC
1 TACGAGGCACTTT-TGAGTGCAAATAC
*
101187 TACTAGGCACTTTTGAGTGC-AATAC
1 TACGAGGCACTTTTGAGTGCAAATAC
101212 TA
1 TA
101214 TATCTACGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (26 bp):
TACGAGGCACTTTTGAGTGCAAATAC
Done.