Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002532.1 Hibiscus syriacus cultivar Beakdansim tig00005147_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: 96186
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:436 original size:21 final size:21
Alignment explanation
Indices: 412--461 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
402 GTTAGGGGAA
** *
412 TTACGTGATGAGGTTGGTGCT
1 TTACGTGATGAGGTCAGTACT
*
433 TTACGTCATGAGGTCAGTACT
1 TTACGTGATGAGGTCAGTACT
454 TTACGTGA
1 TTACGTGA
462 AGATAATGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.30, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:2432 original size:19 final size:20
Alignment explanation
Indices: 2400--2437 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2390 TATTTTCGGT
*
2400 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTATCGCG
2420 TTGCGAA-TTGACTATCGC
1 TTGCGAATTTGACTATCGC
2438 AACGCTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCG
Found at i:2749 original size:18 final size:18
Alignment explanation
Indices: 2723--2763 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2713 AGGTGAAGCC
* *
2723 GATTGTGATTGGGATTTT
1 GATTTTGATTGCGATTTT
2741 GATTTTGATTGCGATTTT
1 GATTTTGATTGCGATTTT
2759 GATTT
1 GATTT
2764 CCTTTTGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.02, G:0.27, T:0.54
Consensus pattern (18 bp):
GATTTTGATTGCGATTTT
Found at i:5034 original size:24 final size:24
Alignment explanation
Indices: 5000--5053 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
4990 CCATCACATC
5000 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
5024 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
5048 ATCAAA
1 ATCAAA
5054 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:5067 original size:24 final size:24
Alignment explanation
Indices: 5000--5067 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
4990 CCATCACATC
* * *
5000 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
5024 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
5048 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
5068 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:5967 original size:19 final size:19
Alignment explanation
Indices: 5925--6066 Score: 64
Period size: 19 Copynumber: 7.4 Consensus size: 19
5915 AAACATTTGT
* **
5925 GTTGCGAAATTAAA-ACAT
1 GTTGCGAAATTAAATTCGC
5943 GTTGCGAAATTAAATTCGC
1 GTTGCGAAATTAAATTCGC
* *
5962 GTTGCGAATTTAAAATTC-A
1 GTTGCGAAATT-AAATTCGC
* *
5981 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAAATT--AAATTCGC
** *
6002 AATGCG-ATTTACATATTCGC
1 GTTGCGAAATTA-A-ATTCGC
*
6022 GTTGCGAAATTGGAAA--C-T
1 GTTGCGAAATT--AAATTCGC
6040 GTTGC-AAATTAGAATTCGC
1 GTTGCGAAATTA-AATTCGC
6059 GTTGCGAA
1 GTTGCGAA
6067 TTTGTTGGTC
Statistics
Matches: 94, Mismatches: 16, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
15 1 0.01
16 2 0.02
17 5 0.05
18 21 0.22
19 29 0.31
20 26 0.28
21 8 0.09
22 1 0.01
23 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (19 bp):
GTTGCGAAATTAAATTCGC
Found at i:5979 original size:20 final size:20
Alignment explanation
Indices: 5943--6029 Score: 74
Period size: 19 Copynumber: 4.4 Consensus size: 20
5933 ATTAAAACAT
*
5943 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTAAAATTCGC
*
5962 GTTGCGAATTTAAAATTC-A
1 GTTGCGAATTTAAAATTCGC
5981 GTTGCGAATTTGGAAAA-TCGC
1 GTTGCGAATTT--AAAATTCGC
** *
6002 AATGCG-ATTTACATATTCGC
1 GTTGCGAATTTA-AAATTCGC
6022 GTTGCGAA
1 GTTGCGAA
6030 ATTGGAAACT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
18 1 0.02
19 23 0.43
20 20 0.38
21 9 0.17
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTTAAAATTCGC
Found at i:21078 original size:2 final size:2
Alignment explanation
Indices: 21071--21095 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21061 GATCTCATTA
21071 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
21096 GTATTTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:27794 original size:17 final size:17
Alignment explanation
Indices: 27765--27806 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
27755 AAATACATTA
*
27765 ATAT-TAATTTATAAAT
1 ATATATAATATATAAAT
* *
27781 TTATATAATATATATAT
1 ATATATAATATATAAAT
27798 ATATATAAT
1 ATATATAAT
27807 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATAATATATAAAT
Found at i:28099 original size:23 final size:23
Alignment explanation
Indices: 28073--28120 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
28063 ATTTATCTTT
*
28073 TAAATTTCATAAAAAATTATATA
1 TAAATTTCATAAAAAAGTATATA
* *
28096 TAAATTTTATTAAAAAGTATATA
1 TAAATTTCATAAAAAAGTATATA
28119 TA
1 TA
28121 TATTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAATTTCATAAAAAAGTATATA
Found at i:28504 original size:6 final size:6
Alignment explanation
Indices: 28493--28535 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
28483 GTTGAGTGAC
* * *
28493 GGGGAA GGGGAA GGGGAA GGGGAA GAGGAA GAGGAA GAGGAA G
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA G
28536 AATTAATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:28731 original size:31 final size:31
Alignment explanation
Indices: 28690--28796 Score: 135
Period size: 31 Copynumber: 3.5 Consensus size: 31
28680 AGTTACGTCA
*
28690 GGGACCATATTACAAACGGACTAAATGTTGG
1 GGGACCATATTGCAAACGGACTAAATGTTGG
* *
28721 GGGACTATATTGCAAATGGACTAAATGTT-G
1 GGGACCATATTGCAAACGGACTAAATGTTGG
* *
28751 GGGACCATATTGCAAACAGATTAAATGTTGG
1 GGGACCATATTGCAAACGGACTAAATGTTGG
* **
28782 GAGACTGTATTGCAA
1 GGGACCATATTGCAA
28797 GTTTTAAAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 26 0.40
31 39 0.60
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (31 bp):
GGGACCATATTGCAAACGGACTAAATGTTGG
Found at i:31392 original size:31 final size:31
Alignment explanation
Indices: 31357--31424 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
31347 CAGTTACATC
31357 GGGGACCATATTGCAAACAGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
*
31388 GGGGACCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
*
31419 AGGGAC
1 GGGGAC
31425 TGTATTGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:37464 original size:35 final size:35
Alignment explanation
Indices: 37418--37489 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 35
37408 AGGGCTGGGT
* * * * *
37418 CTGGGCTTTACTCCTCCCTTCTCTTTTACGTGTGG
1 CTGGGCTTTACTCATCACTTCCCTTTAACCTGTGG
37453 CTGGGCTTTACTCATCACTTCCCTTTAACCTGTGG
1 CTGGGCTTTACTCATCACTTCCCTTTAACCTGTGG
37488 CT
1 CT
37490 ATGGCGTTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.10, C:0.32, G:0.18, T:0.40
Consensus pattern (35 bp):
CTGGGCTTTACTCATCACTTCCCTTTAACCTGTGG
Found at i:41937 original size:20 final size:20
Alignment explanation
Indices: 41912--41951 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41902 GTTTTAAATA
* *
41912 TAATTTTAGAAATATATTTG
1 TAATTTTAAAAATAAATTTG
41932 TAATTTTAAAAATAAATTTG
1 TAATTTTAAAAATAAATTTG
41952 AAAATTCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
TAATTTTAAAAATAAATTTG
Found at i:42996 original size:15 final size:15
Alignment explanation
Indices: 42976--43004 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42966 TTTAAGGTTA
42976 GTTATGTAAAATTAT
1 GTTATGTAAAATTAT
42991 GTTATGTAAAATTA
1 GTTATGTAAAATTA
43005 CATTAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (15 bp):
GTTATGTAAAATTAT
Found at i:44497 original size:147 final size:144
Alignment explanation
Indices: 44215--44503 Score: 418
Period size: 147 Copynumber: 2.0 Consensus size: 144
44205 AAAAATTGAT
* * *
44215 AAAAGCTATGCCTCAATCTTCACAATAATCGACAGCTGCTGAAATCAAGATCAGTCCAGAAAAAG
1 AAAAACTATGCCTCAATCTTCACAATAATCGACAGCTGCTGAAATCAACAACAGTCCAGAAAAAG
* *
44280 AAATAATTTAAGATCACAATTTCTCAGTAAAAACCAAGCAAATGACACAAAGACGGCAACAGATA
66 AAATAATTTAAGATCACAATTTCTCAGTAAAAACCAAGCAAAGGACACAAAGAAGGCAACAGATA
44345 ATATAGCAAAATAC
131 ATATAGCAAAATAC
** * *
44359 AAAAACTATGCCTCAATCTTCATGATAATCTACAGCTGCTGAAATCAACAACAGTCCAGGAAAAG
1 AAAAACTATGCCTCAATCTTCACAATAATCGACAGCTGCTGAAATCAACAACAGTCCAGAAAAAG
* * * *
44424 AATTTACGCTTTGAGATCACAATTTCTCTA-TCAAAACCAAGCAAAGGACACAAAGAAGGCAACA
66 AA-ATA--ATTTAAGATCACAATTTCTC-AGTAAAAACCAAGCAAAGGACACAAAGAAGGCAACA
44488 GATAATATAGCAAAAT
127 GATAATATAGCAAAAT
44504 TAAAAGACCT
Statistics
Matches: 128, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
144 60 0.47
145 2 0.02
147 65 0.51
148 1 0.01
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.20
Consensus pattern (144 bp):
AAAAACTATGCCTCAATCTTCACAATAATCGACAGCTGCTGAAATCAACAACAGTCCAGAAAAAG
AAATAATTTAAGATCACAATTTCTCAGTAAAAACCAAGCAAAGGACACAAAGAAGGCAACAGATA
ATATAGCAAAATAC
Found at i:44979 original size:16 final size:17
Alignment explanation
Indices: 44958--44991 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
44948 CATAAAAATA
44958 AAATTATTGAA-ATATT
1 AAATTATTGAATATATT
*
44974 AAATTATTTAATATATT
1 AAATTATTGAATATATT
44991 A
1 A
44992 CTGAGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AAATTATTGAATATATT
Found at i:45263 original size:53 final size:52
Alignment explanation
Indices: 45195--45493 Score: 293
Period size: 53 Copynumber: 5.7 Consensus size: 52
45185 TTGATTATAT
* *
45195 TTACACCT-ATGTAAGTATGTGTTGATTTCTAAGATATTAAGAGATGTACATAC
1 TTACA-CTGATGTAAGTATGTGTTAATTT-TAAGATATTGAGAGATGTACATAC
* * * * * **
45248 TTACACTGATCTAAGTGTGTGTTGATTCCTAATATATTGAGAGATGTACATTT
1 TTACACTGATGTAAGTATGTGTTAATT-TTAAGATATTGAGAGATGTACATAC
* * *
45301 TTACACTGATATAAGTGTGTGTTAATTTTAAGATATTGAGAGATGCACATAC
1 TTACACTGATGTAAGTATGTGTTAATTTTAAGATATTGAGAGATGTACATAC
* * * * *
45353 TTACA-TTACTGTAAGTATTTGTTAATTGTTAAGATATTAAGATATGCACATAC
1 TTACACTGA-TGTAAGTATGTGTTAATT-TTAAGATATTGAGAGATGTACATAC
* * *
45406 TTACACTGGTGTAAGTATTTGTTAATTGTTAAGATATTGAGAGATGTACATAT
1 TTACACTGATGTAAGTATGTGTTAATT-TTAAGATATTGAGAGATGTACATAC
* **
45459 TTATA-TCGGCGTAAGTATGTGTTAA--TTAAGATATT
1 TTACACT-GATGTAAGTATGTGTTAATTTTAAGATATT
45494 TTTTTTATTT
Statistics
Matches: 211, Mismatches: 29, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
50 10 0.05
51 2 0.01
52 43 0.20
53 155 0.73
54 1 0.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (52 bp):
TTACACTGATGTAAGTATGTGTTAATTTTAAGATATTGAGAGATGTACATAC
Found at i:45351 original size:105 final size:105
Alignment explanation
Indices: 45206--45485 Score: 294
Period size: 105 Copynumber: 2.6 Consensus size: 105
45196 TACACCTATG
* * *
45206 TAAGTATGTGTTGATTTCTAAGATATTAAGAGATGTACATACTTACACTGA-TCTAAGTGTGTGT
1 TAAGTATGTGTTAATTT-TAAGATATTGAGAGATGTACATACTTACA-TGACTCTAAGTATGTGT
* * * * **
45270 TGATTCCTAATATATTGAGAGATGTACATTTTTACACTGATA
64 TAATTCCTAAGATATTAAGAGATGCACATACTTACACTGATA
* * * * *
45312 TAAGTGTGTGTTAATTTTAAGATATTGAGAGATGCACATACTTACATTACTGTAAGTATTTGTTA
1 TAAGTATGTGTTAATTTTAAGATATTGAGAGATGTACATACTTACATGACTCTAAGTATGTGTTA
** * * *
45377 ATTGTTAAGATATTAAGATATGCACATACTTACACTGGTG
66 ATTCCTAAGATATTAAGAGATGCACATACTTACACTGATA
* * * * *
45417 TAAGTATTTGTTAATTGTTAAGATATTGAGAGATGTACATATTTATATCGGC-GTAAGTATGTGT
1 TAAGTATGTGTTAATT-TTAAGATATTGAGAGATGTACATACTTACAT-GACTCTAAGTATGTGT
45481 TAATT
64 TAATT
45486 AAGATATTTT
Statistics
Matches: 144, Mismatches: 27, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
104 2 0.01
105 82 0.57
106 59 0.41
107 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.40
Consensus pattern (105 bp):
TAAGTATGTGTTAATTTTAAGATATTGAGAGATGTACATACTTACATGACTCTAAGTATGTGTTA
ATTCCTAAGATATTAAGAGATGCACATACTTACACTGATA
Found at i:45483 original size:158 final size:156
Alignment explanation
Indices: 45204--45493 Score: 368
Period size: 158 Copynumber: 1.8 Consensus size: 156
45194 TTTACACCTA
* * *
45204 TGTAAGTATGTGTTGATTTCTAAGATATTAAGAGATGTACATACTTACACTGATCTAAGTGTGTG
1 TGTAAGTATGTGTTAATTTCTAAGATATTAAGAGATGCACATACTTACACTGATCTAAGTATGTG
* * * * *
45269 TTGATTCCTAATATATTGAGAGATGTACATTTTTACACTGATATAAGTGTGTGTTAATTTTAAGA
66 TTAATTCCTAAGATATTGAGAGATGTACATATTTACACTGACATAAGTATGTGTTAA--TTAAGA
45334 TATTGAGAGATGCACATACTTACATTAC
129 TATTGAGAGATGCACATACTTACATTAC
* * * * *
45362 TGTAAGTATTTGTTAATTGT-TAAGATATTAAGATATGCACATACTTACACTGGTGTAAGTATTT
1 TGTAAGTATGTGTTAATT-TCTAAGATATTAAGAGATGCACATACTTACACTGATCTAAGTATGT
** * * *
45426 GTTAATTGTTAAGATATTGAGAGATGTACATATTTATA-TCGGCGTAAGTATGTGTTAATTAAGA
65 GTTAATTCCTAAGATATTGAGAGATGTACATATTTACACT-GACATAAGTATGTGTTAATTAAGA
45490 TATT
129 TATT
45494 TTTTTTATTT
Statistics
Matches: 112, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
156 10 0.09
157 1 0.01
158 100 0.89
159 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (156 bp):
TGTAAGTATGTGTTAATTTCTAAGATATTAAGAGATGCACATACTTACACTGATCTAAGTATGTG
TTAATTCCTAAGATATTGAGAGATGTACATATTTACACTGACATAAGTATGTGTTAATTAAGATA
TTGAGAGATGCACATACTTACATTAC
Found at i:46955 original size:24 final size:24
Alignment explanation
Indices: 46906--46956 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
46896 AAAAGTAAAA
*
46906 AGAACTAAAATTTAAATTACTGTT
1 AGAACTAAAATTTAAATTACTATT
* *
46930 AGAATTAAAATTTAAATTAGTATT
1 AGAACTAAAATTTAAATTACTATT
46954 AGA
1 AGA
46957 TCAAAAAGTG
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:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (24 bp):
AGAACTAAAATTTAAATTACTATT
Found at i:51555 original size:2 final size:2
Alignment explanation
Indices: 51548--51603 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
51538 GTTTAAAATG
51548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51590 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
51604 GTGTGTGTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51736 original size:15 final size:15
Alignment explanation
Indices: 51716--51765 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
51706 TATTAAAGGT
51716 AAATTTGAACTTATA
1 AAATTTGAACTTATA
*
51731 AAATTTCAA--TATA
1 AAATTTGAACTTATA
*
51744 CGAATTTGAACTTATA
1 -AAATTTGAACTTATA
51760 AAATTT
1 AAATTT
51766 TAAGGGACGA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 4 0.14
14 7 0.25
15 13 0.46
16 4 0.14
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (15 bp):
AAATTTGAACTTATA
Found at i:51775 original size:29 final size:29
Alignment explanation
Indices: 51717--51776 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
51707 ATTAAAGGTA
* *
51717 AATTTGAACTTATAAAATTTCAATATACG
1 AATTTGAACTTATAAAATTTCAAGAGACG
* *
51746 AATTTGAACTTATAAAATTTTAAGGGACG
1 AATTTGAACTTATAAAATTTCAAGAGACG
51775 AA
1 AA
51777 AATAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (29 bp):
AATTTGAACTTATAAAATTTCAAGAGACG
Found at i:52262 original size:20 final size:20
Alignment explanation
Indices: 52149--52256 Score: 162
Period size: 20 Copynumber: 5.3 Consensus size: 20
52139 GAATATGTAA
* *
52149 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
52169 ATCGCAAACGCGATTCTGACT
1 ATCGC-AACGCGATTCTGACT
*
52190 ATCGCAACGGGATTCTGACT
1 ATCGCAACGCGATTCTGACT
52210 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
52230 GTCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTCTGACT
52250 ATCGCAA
1 ATCGCAA
52257 TACGATTTTC
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
20 62 0.77
21 18 0.22
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:52974 original size:20 final size:20
Alignment explanation
Indices: 52870--52976 Score: 103
Period size: 20 Copynumber: 5.5 Consensus size: 20
52860 AGCATCGCAA
*
52870 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
*
52889 TGCGATTTTCA-TTTCACGT
1 TGCGATTTTCATTTTCGCGT
** **
52908 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
* *
52928 TGCGATAGTT-ATTTTCGTGT
1 TGCGAT-TTTCATTTTCGCGT
*
52948 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
52968 TGCGATTTT
1 TGCGATTTT
52977 AAGTTTTAGA
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
19 27 0.37
20 45 0.62
21 1 0.01
ACGTcount: A:0.15, C:0.16, G:0.22, T:0.47
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:57169 original size:149 final size:148
Alignment explanation
Indices: 56900--57205 Score: 495
Period size: 149 Copynumber: 2.1 Consensus size: 148
56890 GAGTCGAGGG
* * * ** * *
56900 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGGGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
*
56965 CTTGGTCCTTAGTATATGTATATGATTATTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCTTAGTATATGTATATGATTATTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
*
57030 ATGGCACTACGGTGCAAT
131 AAGGCACTACGGTGCAAT
* *
57048 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
*
57113 ACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCTTAGTATATGTATATGATTATTAAGGAATGATATGTGGTCCTTATGGACATTATTA
57178 TAAGGCACTACGGTGCAAT
130 TAAGGCACTACGGTGCAAT
57197 TCTACGCGG
1 TCTACGCGG
57206 CACTACGGTG
Statistics
Matches: 145, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
148 47 0.32
149 98 0.68
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCTTAGTATATGTATATGATTATTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
AAGGCACTACGGTGCAAT
Found at i:57211 original size:23 final size:22
Alignment explanation
Indices: 57181--57241 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 22
57171 ATTATTATAA
57181 GGCACTACGGTGCAATTCTACG
1 GGCACTACGGTGCAATTCTACG
*
57203 CGGCACTACGGTGTAATTCTACG
1 -GGCACTACGGTGCAATTCTACG
* *
57226 TGCACTTCGGTGCAAT
1 GGCACTACGGTGCAAT
57242 GATACGAGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
GGCACTACGGTGCAATTCTACG
Found at i:62467 original size:22 final size:23
Alignment explanation
Indices: 62401--62461 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
62391 ATTATTATAA
62401 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
62424 GGCACTACGGTGCAATTCTACG-
1 GGCACTACGGTGCAATTCTACGC
* *
62446 TGCACTTCGGTGCAAT
1 GGCACTACGGTGCAAT
62462 GATACGAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:63271 original size:18 final size:18
Alignment explanation
Indices: 63248--63297 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
63238 TTTACTCGTA
63248 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
63266 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
63284 ATTTCACTTAGATT
1 ATTTCACTTAGATT
63298 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:63470 original size:20 final size:20
Alignment explanation
Indices: 63445--63492 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
63435 TAGTATACTT
63445 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
63465 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
63485 TCGCAACG
1 TCGCAACG
63493 AAAGTATCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:63577 original size:18 final size:19
Alignment explanation
Indices: 63535--63581 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
63525 GCGATTCTCT
63535 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
63555 CGTTGCGATAGTCA-TTCG
1 CGTTGCGATAGTCATTTCG
*
63573 TGTTGCGAT
1 CGTTGCGAT
63582 TTTAAGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
20 14 0.54
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:64101 original size:18 final size:19
Alignment explanation
Indices: 64062--64103 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
64052 CTCACCTGTC
64062 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
64083 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
64101 ATC
1 ATC
64104 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:64157 original size:42 final size:42
Alignment explanation
Indices: 64086--64167 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
64076 CTCCCCTATC
*
64086 GTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACT
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCACT
** *
64128 GTTCAAGAGGCCACTATCATCGTTGAAGAGGTCCCTCCCA
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
64168 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (42 bp):
GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACT
Found at i:65480 original size:14 final size:14
Alignment explanation
Indices: 65443--65504 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
65433 TTGCTTGTTT
*
65443 AATTGATTTCTAAA
1 AATTGATTTGTAAA
65457 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
65471 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
65486 TATTGATGTGTAAA
1 AATTGATTTGTAAA
65500 TAATT
1 -AATT
65505 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:65643 original size:20 final size:20
Alignment explanation
Indices: 65603--65656 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
65593 AGGTACACTT
* **
65603 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
* *
65623 TCGTAATGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
65643 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
65657 TCAATTCGCG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.24, G:0.19, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:65724 original size:20 final size:20
Alignment explanation
Indices: 65699--65949 Score: 309
Period size: 20 Copynumber: 12.8 Consensus size: 20
65689 GCGATTTTCT
* *
65699 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
65719 CGTTGCGATAATAAAATTCG
1 CGTTGCGATAGTCAAATTCG
65739 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
65759 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
*
65778 CCGTTGCGATAATCAAATTCG
1 -CGTTGCGATAGTCAAATTCG
65799 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
65819 CGTTGCGATAGACAAATTTG
1 CGTTGCGATAGTCAAATTCG
* *
65839 CATTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
65859 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
65879 CGTTGCG--AGT----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
65893 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
65913 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
65933 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
65950 GAATGTGTAA
Statistics
Matches: 196, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
14 9 0.05
16 2 0.01
18 3 0.02
19 2 0.01
20 178 0.91
21 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:66172 original size:140 final size:140
Alignment explanation
Indices: 65920--66329 Score: 766
Period size: 140 Copynumber: 2.9 Consensus size: 140
65910 TCGCGTTGCG
*
65920 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAAGTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
65985 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66050 AATACACATA
131 AATACACATA
* *
66060 ATAGTCAAATTCGTGTTGCGATATTTAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
*
66125 TAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66190 AATACACATA
131 AATACACATA
*
66200 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
*
66265 TAGCAATGTTCAAACTTAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66330 TACAACGTTT
Statistics
Matches: 261, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 261 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:66412 original size:18 final size:18
Alignment explanation
Indices: 66389--66424 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
66379 AAGCCGGTTG
*
66389 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
66407 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
66425 CCTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:69057 original size:24 final size:24
Alignment explanation
Indices: 69023--69076 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
69013 CTGAAACATC
69023 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
69047 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
69071 ATCAAA
1 ATCAAA
69077 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:69922 original size:20 final size:20
Alignment explanation
Indices: 69897--69964 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
69887 GAAATTCAGT
69897 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* **
69917 GTTGCGACAGTTTGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
69937 GTTGCAATAGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
*
69957 ATTGCGAT
1 GTTGCGAT
69965 TTACATATTC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.29
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:84701 original size:2 final size:2
Alignment explanation
Indices: 84694--84755 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
84684 TTTTCTAACC
84694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
84736 AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT
84756 TAATGTTATT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:87920 original size:24 final size:22
Alignment explanation
Indices: 87888--87933 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
87878 ATAAATTCAA
*
87888 AATTTTAAATAATTTATTTATTAT
1 AATTATAAA-AATTTATTT-TTAT
*
87912 AATTATAAAATTTTATTTTTAT
1 AATTATAAAAATTTATTTTTAT
87934 TTATATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 8 0.40
24 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
AATTATAAAAATTTATTTTTAT
Found at i:91147 original size:76 final size:76
Alignment explanation
Indices: 91007--91152 Score: 206
Period size: 76 Copynumber: 1.9 Consensus size: 76
90997 ATGTGGTAAA
* * * *
91007 TATTCTTTTAGTAAATTACTTAATTTTTTATTTCCTAACCTTTATAATTAATTTTATAGTTTTTC
1 TATTCTTTGAGTAAATTACTTAATTTTTTATTTACTAACCTTTATAATTAATGTTACAGTTTTTC
91072 TTGGATTTTTT
66 TTGGATTTTTT
* *
91083 TATTGTTTGAGTAAATTACTTATTTTTTTATTTATACTAA-CTTTATAATTAATGTTACAG-TTT
1 TATTCTTTGAGTAAATTACTTAATTTTTTA-TT-TACTAACCTTTATAATTAATGTTACAGTTTT
91146 TCTTGGA
64 TCTTGGA
91153 ATTTAAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
76 37 0.60
77 20 0.32
78 5 0.08
ACGTcount: A:0.27, C:0.08, G:0.08, T:0.58
Consensus pattern (76 bp):
TATTCTTTGAGTAAATTACTTAATTTTTTATTTACTAACCTTTATAATTAATGTTACAGTTTTTC
TTGGATTTTTT
Found at i:93701 original size:20 final size:21
Alignment explanation
Indices: 93646--93701 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
93636 TTTGTGGCTC
*
93646 AAAGGATCGATCCCTTTGACC
1 AAAGGATCGATCCCTTTGACA
* *
93667 AAATGATTGAT-CCTTTGA-A
1 AAAGGATCGATCCCTTTGACA
93686 AAAGGATCGATCCCTT
1 AAAGGATCGATCCCTT
93702 GGATAACAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 9 0.31
20 11 0.38
21 9 0.31
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (21 bp):
AAAGGATCGATCCCTTTGACA
Found at i:93790 original size:41 final size:41
Alignment explanation
Indices: 93719--93810 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
93709 AGTGAGTTTG
* *
93719 GGATCGATCCATTAACCAAAAGGATTGATCCCTATAGGAAAA
1 GGATCGATCCATTAA-CAAAAGGATCGATCCCTAGAGGAAAA
* * * *
93761 TGATCGATCCCTTAA-ATAAAGGATCGATCCCTCGATGAAAA
1 GGATCGATCCATTAACA-AAAGGATCGATCCCTAGAGGAAAA
93802 GGATCGATC
1 GGATCGATC
93811 TCTTTGTTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
40 1 0.02
41 28 0.67
42 13 0.31
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (41 bp):
GGATCGATCCATTAACAAAAGGATCGATCCCTAGAGGAAAA
Found at i:93877 original size:22 final size:22
Alignment explanation
Indices: 93832--93874 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
93822 ACGATCGAAA
93832 TTTTTAAAAAAATGATCGATCC
1 TTTTTAAAAAAATGATCGATCC
* *
93854 TTTTTAATAAAA-GATTGATCC
1 TTTTTAAAAAAATGATCGATCC
93875 CTTGTTCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (22 bp):
TTTTTAAAAAAATGATCGATCC
Found at i:96174 original size:64 final size:65
Alignment explanation
Indices: 96052--96176 Score: 173
Period size: 64 Copynumber: 1.9 Consensus size: 65
96042 TGCACCAATC
* *
96052 CATGCATCAATGCACTCAAGATTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACAAGA
1 CATGCATCAATGCACTCAAGATTTTATGAAAACATCGAATGCACTTCATGCATCGATGCACAAGA
* * * *
96117 CATGCATCGATGCACTCAGGCTATTT-TG-AAACATCGAATGCACTTCATGCATTGATGCAC
1 CATGCATCAATGCACTCAAGAT-TTTATGAAAACATCGAATGCACTTCATGCATCGATGCAC
96177 TCTTAGTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 29 0.55
65 21 0.40
66 3 0.06
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (65 bp):
CATGCATCAATGCACTCAAGATTTTATGAAAACATCGAATGCACTTCATGCATCGATGCACAAGA
Done.