Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005142.1 Hibiscus syriacus cultivar Beakdansim tig00011581_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: 103565
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:13187 original size:22 final size:22
Alignment explanation
Indices: 13159--13202 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
13149 TGGACTAAGT
13159 TGTGAAATAGATAATTAATCTA
1 TGTGAAATAGATAATTAATCTA
13181 TGTGAAATAGATAATTAATCTA
1 TGTGAAATAGATAATTAATCTA
13203 CATGAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (22 bp):
TGTGAAATAGATAATTAATCTA
Found at i:13208 original size:22 final size:22
Alignment explanation
Indices: 13161--13210 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
13151 GACTAAGTTG
**
13161 TGAAATAGATAATTAATCTATG
1 TGAAATAGATAATTAATCTACA
13183 TGAAATAGATAATTAATCTACA
1 TGAAATAGATAATTAATCTACA
13205 TGAAAT
1 TGAAAT
13211 TCTCTATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (22 bp):
TGAAATAGATAATTAATCTACA
Found at i:14608 original size:18 final size:19
Alignment explanation
Indices: 14585--14626 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
14575 GTAATAAAAT
*
14585 ATTAAAATAA-TAAAAGCG
1 ATTAAAATAAGTAAAAGCA
14603 ATT-AAATAAGTAAAAGCA
1 ATTAAAATAAGTAAAAGCA
14621 ATTAAA
1 ATTAAA
14627 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (19 bp):
ATTAAAATAAGTAAAAGCA
Found at i:16137 original size:82 final size:82
Alignment explanation
Indices: 16000--16163 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
15990 CAATGTGTTT
16000 GGGGTAAAGAAACGCTCAATGTCAGAATCGACACGATATTACCATAAGCCTGCAAGTAAATCAAA
1 GGGGTAAAGAAACGCTCAATGTCAGAATCGACACGATATTACCATAAGCCTGCAAGTAAATCAAA
16065 TCTCCACTACTAATAAG
66 TCTCCACTACTAATAAG
16082 GGGGTAAAGAAACGCTCAATGTCAGAATCGACACGATATTACCATAAGCCTGCAAGTAAATCAAA
1 GGGGTAAAGAAACGCTCAATGTCAGAATCGACACGATATTACCATAAGCCTGCAAGTAAATCAAA
16147 TCTCCACTACTAATAAG
66 TCTCCACTACTAATAAG
16164 AACAAGATGC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (82 bp):
GGGGTAAAGAAACGCTCAATGTCAGAATCGACACGATATTACCATAAGCCTGCAAGTAAATCAAA
TCTCCACTACTAATAAG
Found at i:18096 original size:13 final size:13
Alignment explanation
Indices: 18078--18117 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
18068 TGCTTGAGTG
18078 AATAAAAATATAA
1 AATAAAAATATAA
18091 AATAAAAATA-AA
1 AATAAAAATATAA
18103 AATGAAAAAATATAA
1 AAT--AAAAATATAA
18118 CGGAATTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.21
13 10 0.42
14 7 0.29
15 2 0.08
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AATAAAAATATAA
Found at i:18098 original size:6 final size:6
Alignment explanation
Indices: 18078--18111 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
18068 TGCTTGAGTG
18078 AATAAA AATATAA AATAAA AATAAA AATGAAA AA
1 AATAAA AATA-AA AATAAA AATAAA AAT-AAA AA
18112 ATATAACGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 15 0.58
7 11 0.42
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:19632 original size:21 final size:21
Alignment explanation
Indices: 19583--19624 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
19573 TTCCTGGGAT
*
19583 AGTGGTAACCTCTCGACAATC
1 AGTGCTAACCTCTCGACAATC
19604 AGTGCTAACCTCTCGACAATC
1 AGTGCTAACCTCTCGACAATC
19625 GATTCTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.24
Consensus pattern (21 bp):
AGTGCTAACCTCTCGACAATC
Found at i:21028 original size:17 final size:17
Alignment explanation
Indices: 20995--21036 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
20985 GGAATTTTGG
20995 TAAT-AAAATATTAAAA
1 TAATAAAAATATTAAAA
21011 TAATAAAAATGATT-AAA
1 TAATAAAAAT-ATTAAAA
21028 TAAGTAAAA
1 TAA-TAAAA
21037 GCAATTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (17 bp):
TAATAAAAATATTAAAA
Found at i:24526 original size:19 final size:19
Alignment explanation
Indices: 24502--24567 Score: 105
Period size: 19 Copynumber: 3.5 Consensus size: 19
24492 CTTGTAACCG
24502 TAACCCTAACCCTAACCAT
1 TAACCCTAACCCTAACCAT
**
24521 TAACCCTAATTCTAACCAT
1 TAACCCTAACCCTAACCAT
24540 TAACCCTAACCCTAACCAT
1 TAACCCTAACCCTAACCAT
*
24559 TAACTCTAA
1 TAACCCTAA
24568 TTTTAACTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.38, C:0.36, G:0.00, T:0.26
Consensus pattern (19 bp):
TAACCCTAACCCTAACCAT
Found at i:24544 original size:38 final size:38
Alignment explanation
Indices: 24502--24582 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 38
24492 CTTGTAACCG
24502 TAACCCTAACCCTAACCATTAACCCTAATTCTAACCAT
1 TAACCCTAACCCTAACCATTAACCCTAATTCTAACCAT
* * *
24540 TAACCCTAACCCTAACCATTAACTCTAATTTTAACTAT
1 TAACCCTAACCCTAACCATTAACCCTAATTCTAACCAT
24578 TAACC
1 TAACC
24583 ATCATTTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (38 bp):
TAACCCTAACCCTAACCATTAACCCTAATTCTAACCAT
Found at i:24562 original size:7 final size:6
Alignment explanation
Indices: 24496--24556 Score: 59
Period size: 6 Copynumber: 9.8 Consensus size: 6
24486 TCAAAACTTG
* * ** *
24496 TAACCG TAACCC TAACCC TAACCAT TAACCC TAATTC TAACCAT TAACCC
1 TAACCC TAACCC TAACCC TAACC-C TAACCC TAACCC TAACC-C TAACCC
24546 TAACCC TAACC
1 TAACCC TAACC
24557 ATTAACTCTA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
6 34 0.77
7 10 0.23
ACGTcount: A:0.36, C:0.39, G:0.02, T:0.23
Consensus pattern (6 bp):
TAACCC
Found at i:24574 original size:19 final size:19
Alignment explanation
Indices: 24502--24582 Score: 99
Period size: 19 Copynumber: 4.3 Consensus size: 19
24492 CTTGTAACCG
**
24502 TAACCCTAACCCTAACCAT
1 TAACCCTAATTCTAACCAT
24521 TAACCCTAATTCTAACCAT
1 TAACCCTAATTCTAACCAT
**
24540 TAACCCTAACCCTAACCAT
1 TAACCCTAATTCTAACCAT
* * *
24559 TAACTCTAATTTTAACTAT
1 TAACCCTAATTCTAACCAT
24578 TAACC
1 TAACC
24583 ATCATTTTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (19 bp):
TAACCCTAATTCTAACCAT
Found at i:26114 original size:39 final size:39
Alignment explanation
Indices: 26061--26149 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 39
26051 ATCATCTCGT
* * *
26061 GCTCGTTAAAAAAAATTTGTTGCTCAATTAGGTGCTCGTTAA
1 GCTCGTT--AAAAAACTTGTTGCTCAACT-CGTGCTCGTTAA
* **
26103 GCTCGTTAAAAAACTTGTTGTTTGACTCGTGCTCGTTAA
1 GCTCGTTAAAAAACTTGTTGCTCAACTCGTGCTCGTTAA
26142 GCTCGTTA
1 GCTCGTTA
26150 CTCGTCTCGT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 19 0.46
40 15 0.37
42 7 0.17
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (39 bp):
GCTCGTTAAAAAACTTGTTGCTCAACTCGTGCTCGTTAA
Found at i:30427 original size:21 final size:20
Alignment explanation
Indices: 30379--30433 Score: 92
Period size: 20 Copynumber: 2.7 Consensus size: 20
30369 TTATTTCTTG
*
30379 ATAATCTTACATTCTCACTA
1 ATAAACTTACATTCTCACTA
30399 ATAAACTTACATTCTCACTA
1 ATAAACTTACATTCTCACTA
30419 ATAAAACTTACATTC
1 AT-AAACTTACATTC
30434 CGTGAACCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 21 0.64
21 12 0.36
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAACTTACATTCTCACTA
Found at i:35041 original size:42 final size:42
Alignment explanation
Indices: 34977--35096 Score: 204
Period size: 42 Copynumber: 2.9 Consensus size: 42
34967 TTTCCCCAAA
* * * *
34977 TTCCGGTGTTTGTTGCATGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
35019 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
35061 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
35097 TGTAATTCAT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:35298 original size:22 final size:23
Alignment explanation
Indices: 35267--35322 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
35257 TTTTCATCAA
*
35267 AATAATTATTAAAATATTTA-AAT
1 AATATTTATT-AAATATTTATAAT
35290 -ATATTTATT-AATATTTATAAT
1 AATATTTATTAAATATTTATAAT
35311 AATATTATATTA
1 AATATT-TATTA
35323 TTTTTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 8 0.29
21 3 0.11
22 13 0.46
23 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATTTATTAAATATTTATAAT
Found at i:35333 original size:22 final size:22
Alignment explanation
Indices: 35279--35322 Score: 65
Period size: 20 Copynumber: 2.0 Consensus size: 22
35269 TAATTATTAA
35279 AATATTTA-AAT-ATATTTATT
1 AATATTTATAATAATATTTATT
35299 AATATTTATAATAATATTATATT
1 AATATTTATAATAATATT-TATT
35322 A
1 A
35323 TTTTTTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.38
21 3 0.14
22 5 0.24
23 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATATTTATAATAATATTTATT
Found at i:35354 original size:31 final size:32
Alignment explanation
Indices: 35271--35367 Score: 94
Period size: 31 Copynumber: 3.1 Consensus size: 32
35261 CATCAAAATA
* *
35271 ATTAT-TAAAATATTTAAATATATTTATTAAT
1 ATTATATAAAATAATTAATTATATTTATTAAT
*
35302 ATT-TATAATAAT-ATTATATTAT-TTTTTTAAT
1 ATTATATAA-AATAATTA-ATTATATTTATTAAT
* *
35333 ATTATATAAAATAATCAATTATATTATAATAAT
1 ATTATATAAAATAATTAATTATATT-TATTAAT
35366 AT
1 AT
35368 AAGATATTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
30 1 0.02
31 28 0.53
32 17 0.32
33 7 0.13
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (32 bp):
ATTATATAAAATAATTAATTATATTTATTAAT
Found at i:35368 original size:28 final size:28
Alignment explanation
Indices: 35336--35403 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
35326 TTTTAATATT
35336 ATATAAAATAATCAATTATATTATAATA
1 ATATAAAATAATCAATTATATTATAATA
* * ** * *
35364 ATATAAGATATTTTATTTTATTTTAATA
1 ATATAAAATAATCAATTATATTATAATA
*
35392 ATATATAATAAT
1 ATATAAAATAAT
35404 TTTTTTATAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (28 bp):
ATATAAAATAATCAATTATATTATAATA
Found at i:35419 original size:30 final size:29
Alignment explanation
Indices: 35352--35454 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 29
35342 AATAATCAAT
35352 TATATTATAATAATATA-AGATATTTTATTT-
1 TATATT-TAATAATATATA-ATATTTT-TTTA
35382 TAT-TTTAATAATATATAATAATTTTTTTA
1 TATATTTAATAATATATAAT-ATTTTTTTA
*
35411 TATATTTAATAATGA-ATAATA-TTATTTA
1 TATATTTAATAAT-ATATAATATTTTTTTA
35439 TATATTTCAATAATAT
1 TATATTT-AATAATAT
35455 TTTAGTAAAA
Statistics
Matches: 65, Mismatches: 1, Indels: 15
0.80 0.01 0.19
Matches are distributed among these distances:
28 29 0.45
29 18 0.28
30 17 0.26
31 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (29 bp):
TATATTTAATAATATATAATATTTTTTTA
Found at i:35710 original size:20 final size:20
Alignment explanation
Indices: 35652--35701 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
35642 TTTTCAGATG
35652 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
35672 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
35692 TTTTCCAGAA
1 TTTTCCAGAA
35702 TTCAAATTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:35720 original size:15 final size:15
Alignment explanation
Indices: 35684--35780 Score: 124
Period size: 15 Copynumber: 6.5 Consensus size: 15
35674 TTCCAGAAAT
**
35684 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
35699 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
35713 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
35728 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
*
35743 GTAATTCAAACTCCA
1 GTAATTCAAATTCCA
* *
35758 GTAATTCAAACTCTA
1 GTAATTCAAATTCCA
35773 GTAATTCA
1 GTAATTCA
35781 TTTTTCGGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
14 12 0.16
15 61 0.84
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:35736 original size:30 final size:30
Alignment explanation
Indices: 35684--35784 Score: 150
Period size: 30 Copynumber: 3.4 Consensus size: 30
35674 TTCCAGAAAT
35684 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
35713 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*** * *
35743 GTAATTCAAACTCCAGTAATTCAAACTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
35773 GTAATTCATTTT
1 GTAATTCATTTT
35785 TCGGAAAACC
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
29 16 0.25
30 47 0.75
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:46533 original size:32 final size:31
Alignment explanation
Indices: 46497--46572 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
46487 GGGGCCGTGA
*
46497 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
46529 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
46560 AGCCTACCTAAGA
1 GGCCTACCTAAGA
46573 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:46555 original size:63 final size:63
Alignment explanation
Indices: 46449--46572 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
46439 CCCTAAGGGA
* * *
46449 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
46512 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
46573 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:47472 original size:5 final size:5
Alignment explanation
Indices: 47462--47521 Score: 57
Period size: 5 Copynumber: 11.2 Consensus size: 5
47452 AACGGTCAAC
* * *
47462 GGTCG GGTCG GGTCG GGTCAAC GGTCA GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
47511 GGTCG GGTCG G
1 GGTCG GGTCG G
47522 ACCGGTCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
5 38 0.83
7 8 0.17
ACGTcount: A:0.08, C:0.22, G:0.52, T:0.18
Consensus pattern (5 bp):
GGTCG
Found at i:47483 original size:22 final size:22
Alignment explanation
Indices: 47455--47521 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
47445 AACGGTCAAC
47455 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
47477 GGTCAACGGTCAGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
47499 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
47521 G
1 G
47522 ACCGGTCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.10, C:0.22, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:47500 original size:27 final size:29
Alignment explanation
Indices: 47448--47502 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 29
47438 GAAAGTCAAC
47448 GGTCAACGGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCAACGGTCGGGTCGGGTCG
47477 GGTCAACGGTC-A-GGTCGGGTCGGGTC
1 GGTCAACGGTCAACGGTCGGGTCGGGTC
47503 AACGGTCGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 14 0.54
28 1 0.04
29 11 0.42
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (29 bp):
GGTCAACGGTCAACGGTCGGGTCGGGTCG
Found at i:47534 original size:9 final size:9
Alignment explanation
Indices: 47522--47593 Score: 90
Period size: 9 Copynumber: 7.7 Consensus size: 9
47512 GTCGGGTCGG
47522 ACCGGTCAA
1 ACCGGTCAA
*
47531 ACCGGCTCAG
1 ACCGG-TCAA
47541 ACCGGTCAA
1 ACCGGTCAA
*
47550 ACCGGTTCAG
1 ACCGG-TCAA
47560 ACCGGTCAA
1 ACCGGTCAA
*
47569 ACCGGTTCGA
1 ACCGG-TCAA
47579 ACCGGTCAA
1 ACCGGTCAA
47588 ACCGGT
1 ACCGGT
47594 TTTCCAGCAG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
9 30 0.56
10 24 0.44
ACGTcount: A:0.26, C:0.33, G:0.26, T:0.14
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:47543 original size:19 final size:19
Alignment explanation
Indices: 47521--47594 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
47511 GGTCGGGTCG
*
47521 GACCGGTCAAACCGGCTCA
1 GACCGGTCAAACCGGTTCA
47540 GACCGGTCAAACCGGTTCA
1 GACCGGTCAAACCGGTTCA
47559 GACCGGTCAAACCGGTTC-
1 GACCGGTCAAACCGGTTCA
47577 GAACCGGTCAAACCGGTT
1 G-ACCGGTCAAACCGGTT
47595 TTCCAGCAGC
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
18 1 0.02
19 52 0.98
ACGTcount: A:0.26, C:0.32, G:0.27, T:0.15
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCA
Found at i:53883 original size:32 final size:31
Alignment explanation
Indices: 53847--53922 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
53837 GGGGCCGTGA
*
53847 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
53879 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
53910 AGCCTACCTAAGA
1 GGCCTACCTAAGA
53923 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:53905 original size:63 final size:63
Alignment explanation
Indices: 53799--53922 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
53789 CCCTAAGGGA
* * *
53799 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
53862 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
53923 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:54804 original size:7 final size:7
Alignment explanation
Indices: 54792--54816 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54782 GTCAAAGAAA
54792 GTCAACG
1 GTCAACG
54799 GTCAACG
1 GTCAACG
54806 GTCAACG
1 GTCAACG
54813 GTCA
1 GTCA
54817 GGTCGGGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:54833 original size:22 final size:22
Alignment explanation
Indices: 54805--54849 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
54795 AACGGTCAAC
54805 GGTCAACGGTCAGGTCGGGTCG
1 GGTCAACGGTCAGGTCGGGTCG
*
54827 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCAGGTCGGGTCG
54849 G
1 G
54850 ACCGGTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.22, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCAGGTCGGGTCG
Found at i:54862 original size:9 final size:9
Alignment explanation
Indices: 54850--54922 Score: 83
Period size: 9 Copynumber: 7.7 Consensus size: 9
54840 GTCGGGTCGG
54850 ACCGGTCAA
1 ACCGGTCAA
*
54859 ACCGGCTCAG
1 ACCGG-TCAA
54869 ACCGGTCAA
1 ACCGGTCAA
*
54878 ACCGGTTCGA
1 ACCGG-TCAA
54888 ACCGGTCAA
1 ACCGGTCAA
54897 ACCGGTTCAAA
1 ACCGG-TC-AA
*
54908 ACTGGTCAA
1 ACCGGTCAA
54917 ACCGGT
1 ACCGGT
54923 TTTCCAGCAG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
9 28 0.52
10 20 0.37
11 6 0.11
ACGTcount: A:0.29, C:0.32, G:0.25, T:0.15
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:54871 original size:19 final size:19
Alignment explanation
Indices: 54849--54923 Score: 98
Period size: 19 Copynumber: 3.9 Consensus size: 19
54839 GGTCGGGTCG
*
54849 GACCGGTCAAACCGGCTCA
1 GACCGGTCAAACCGGTTCA
54868 GACCGGTCAAACCGGTTC-
1 GACCGGTCAAACCGGTTCA
54886 GAACCGGTCAAACCGGTTCAA
1 G-ACCGGTCAAACCGGTTC-A
* *
54907 AACTGGTCAAACCGGTT
1 GACCGGTCAAACCGGTT
54924 TTCCAGCAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.02
19 34 0.68
20 15 0.30
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.16
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCA
Found at i:56754 original size:14 final size:13
Alignment explanation
Indices: 56722--56755 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
56712 AACACTGCGA
*
56722 ACAAACAAAAATT
1 ACAAAAAAAAATT
56735 ACAAAAAAAAATT
1 ACAAAAAAAAATT
*
56748 CCAAAAAA
1 ACAAAAAA
56756 GAAAAGCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.12
Consensus pattern (13 bp):
ACAAAAAAAAATT
Found at i:58633 original size:35 final size:35
Alignment explanation
Indices: 58594--58661 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
58584 TGGTTTGGGT
*
58594 TGTGTTCTTCAGC-AGGTCACTATGTCAGTTTTCTA
1 TGTGTTATTCAGCTA-GTCACTATGTCAGTTTTCTA
* *
58629 TGTGTTATTCAGCTATTCACTATGTTAGTTTTC
1 TGTGTTATTCAGCTAGTCACTATGTCAGTTTTC
58662 CGTGTGCGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 28 0.97
36 1 0.03
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (35 bp):
TGTGTTATTCAGCTAGTCACTATGTCAGTTTTCTA
Found at i:58675 original size:35 final size:35
Alignment explanation
Indices: 58610--58676 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
58600 CTTCAGCAGG
* *
58610 TCACTATGTCAGTTTTCTATGTGTTATTCAGCTAT
1 TCACTATGTCAGTTTTCCATGTGGTATTCAGCTAT
* *
58645 TCACTATGTTAGTTTTCCGTGTGCGT-TTCAGC
1 TCACTATGTCAGTTTTCCATGTG-GTATTCAGC
58677 GTTTCAGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 26 0.96
36 1 0.04
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.46
Consensus pattern (35 bp):
TCACTATGTCAGTTTTCCATGTGGTATTCAGCTAT
Found at i:61254 original size:18 final size:18
Alignment explanation
Indices: 61206--61265 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
61196 TATTAGTTTT
*
61206 TTATTTATTATATATATATA
1 TTATTTA-TATATA-ATAGA
* *
61226 TAATATA-ATATAATAGA
1 TTATTTATATATAATAGA
* *
61243 TTATTTATATATTATGGA
1 TTATTTATATATAATAGA
61261 TTATT
1 TTATT
61266 AGATTTTGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
17 9 0.28
18 18 0.56
20 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
TTATTTATATATAATAGA
Found at i:71454 original size:2 final size:2
Alignment explanation
Indices: 71447--71496 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
71437 GAATTATTGA
71447 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
71489 AT AT AT AT
1 AT AT AT AT
71497 TCTTTATGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74729 original size:15 final size:16
Alignment explanation
Indices: 74701--74730 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
74691 CTCTATATAT
74701 AATAAAAAACACAAAA
1 AATAAAAAACACAAAA
74717 AATAAAAAA-ACAAA
1 AATAAAAAACACAAA
74731 TTACAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (16 bp):
AATAAAAAACACAAAA
Found at i:76598 original size:16 final size:17
Alignment explanation
Indices: 76574--76624 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
76564 GATATATTAA
*
76574 AATAAAATAAAAA-AAT
1 AATATAATAAAAATAAT
*
76590 AATATAATAATAAATATT
1 AATATAATAA-AAATAAT
*
76608 AATAGTAATAAATATAA
1 AATA-TAATAAAAATAA
76625 AAGGGGATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 9 0.32
17 3 0.11
18 10 0.36
19 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
AATATAATAAAAATAAT
Found at i:84911 original size:21 final size:22
Alignment explanation
Indices: 84871--84911 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
84861 TGTGATTTTA
* *
84871 AAAATAAAATAGTTGGATGACC
1 AAAACAAAATAGTTGAATGACC
84893 AAAACAAAAT-GTTGAATGA
1 AAAACAAAATAGTTGAATGA
84912 GAAAGCTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.54, C:0.07, G:0.17, T:0.22
Consensus pattern (22 bp):
AAAACAAAATAGTTGAATGACC
Found at i:85948 original size:31 final size:31
Alignment explanation
Indices: 85877--85954 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
85867 CTTTTAAAAC
** *
85877 TTGCAATATAATCCCCCAATATTTAGTCCGT
1 TTGCAATATGGTCCCCCAACATTTAGTCCGT
85908 TTGCAATATGGTCCCCCAACATTTAGTCCGT
1 TTGCAATATGGTCCCCCAACATTTAGTCCGT
*
85939 TTGTAATATGGTCCCC
1 TTGCAATATGGTCCCC
85955 GACGTAACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGTCCGT
Found at i:87418 original size:39 final size:39
Alignment explanation
Indices: 87375--87479 Score: 210
Period size: 39 Copynumber: 2.7 Consensus size: 39
87365 AGCCATCAGA
87375 AAATTGTAGAGCATGGACCAACATTAATGAGATGATTAT
1 AAATTGTAGAGCATGGACCAACATTAATGAGATGATTAT
87414 AAATTGTAGAGCATGGACCAACATTAATGAGATGATTAT
1 AAATTGTAGAGCATGGACCAACATTAATGAGATGATTAT
87453 AAATTGTAGAGCATGGACCAACATTAA
1 AAATTGTAGAGCATGGACCAACATTAA
87480 AATTGTAGAG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 66 1.00
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (39 bp):
AAATTGTAGAGCATGGACCAACATTAATGAGATGATTAT
Found at i:87485 original size:26 final size:26
Alignment explanation
Indices: 87448--87505 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
87438 TAATGAGATG
87448 ATTATAAATTGTAGAGCATGGACCAAC
1 ATTA-AAATTGTAGAGCATGGACCAAC
87475 ATTAAAATTGTAGAGCATGGACCAAC
1 ATTAAAATTGTAGAGCATGGACCAAC
87501 ATTAA
1 ATTAA
87506 TGAGATGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 27 0.87
27 4 0.13
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (26 bp):
ATTAAAATTGTAGAGCATGGACCAAC
Found at i:91973 original size:15 final size:17
Alignment explanation
Indices: 91933--91969 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
91923 TTCAGGCCAT
91933 ACAAATAGGACCAAAAC
1 ACAAATAGGACCAAAAC
91950 ATGCAAATAGGACCAAAAC
1 A--CAAATAGGACCAAAAC
91969 A
1 A
91970 AATAATGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.06
19 17 0.94
ACGTcount: A:0.57, C:0.22, G:0.14, T:0.08
Consensus pattern (17 bp):
ACAAATAGGACCAAAAC
Found at i:93075 original size:15 final size:15
Alignment explanation
Indices: 93022--93076 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
93012 ACCTTCTTTC
*
93022 TAATATTTATGAAAA
1 TAATATTTATTAAAA
93037 TAATATAATT-TTAAAA
1 TAATAT--TTATTAAAA
*
93053 T--GATTTATTAAAA
1 TAATATTTATTAAAA
93066 TAATATTTATT
1 TAATATTTATT
93077 TCTATTACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
12 2 0.06
13 7 0.22
14 2 0.06
15 13 0.41
16 6 0.19
17 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (15 bp):
TAATATTTATTAAAA
Found at i:93545 original size:60 final size:60
Alignment explanation
Indices: 93399--93531 Score: 189
Period size: 60 Copynumber: 2.2 Consensus size: 60
93389 AAACTCGGGC
* *
93399 AAAAG-TACACAAATGGTCC-TCGACTATAGGGTGATGATTTGTTGAGTCCCTCAACTATT
1 AAAAGTTACA-AAATGATCCTTCGACTATAGGGTGATGATTTGTTGAGTCCATCAACTATT
* * * *
93458 AAAAGTTACCAAATGATCCTTCGACTATAGGGTGTTGCTTTGTTGAGTCCATCGACTATT
1 AAAAGTTACAAAATGATCCTTCGACTATAGGGTGATGATTTGTTGAGTCCATCAACTATT
93518 AAAAGTTACAAAAT
1 AAAAGTTACAAAAT
93532 AGTCAGTTGA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
59 13 0.20
60 52 0.80
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (60 bp):
AAAAGTTACAAAATGATCCTTCGACTATAGGGTGATGATTTGTTGAGTCCATCAACTATT
Found at i:94246 original size:30 final size:31
Alignment explanation
Indices: 94205--94264 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 31
94195 CTCCCCTTCG
94205 CTCTCCCCATCATTCCCTTCGTCCGCCTGTC
1 CTCTCCCCATCATTCCCTTCGTCCGCCTGTC
94236 CTCT-CCCATCATTCCCTTCGTCCGCCTGT
1 CTCTCCCCATCATTCCCTTCGTCCGCCTGT
94265 TAATTATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.07, C:0.50, G:0.10, T:0.33
Consensus pattern (31 bp):
CTCTCCCCATCATTCCCTTCGTCCGCCTGTC
Found at i:94342 original size:20 final size:20
Alignment explanation
Indices: 94305--94342 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
94295 ATTTAATAAC
*
94305 AAATTTGGGATTATGGTTAA
1 AAATTTGGCATTATGGTTAA
94325 AAATTTGAGCATTA-GGTT
1 AAATTTG-GCATTATGGTT
94343 TATGGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (20 bp):
AAATTTGGCATTATGGTTAA
Found at i:95586 original size:23 final size:23
Alignment explanation
Indices: 95512--95597 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
95502 GAAACTCAAG
*
95512 ACTCGATTGAAGCTCGATTTTGA
1 ACTCGATTCAAGCTCGATTTTGA
** * *
95535 GTTCAATTCAAACTCGATTTTGA
1 ACTCGATTCAAGCTCGATTTTGA
*
95558 GA-TCGATTCAAGCTCGATTGTGA
1 -ACTCGATTCAAGCTCGATTTTGA
95581 ACTCGATTCAAGCTCGA
1 ACTCGATTCAAGCTCGA
95598 CTTAAGCTCG
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
22 1 0.02
23 51 0.98
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (23 bp):
ACTCGATTCAAGCTCGATTTTGA
Found at i:96435 original size:16 final size:17
Alignment explanation
Indices: 96400--96436 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
96390 TATCCCTTGC
96400 ATAATTCAACAAAAATA
1 ATAATTCAACAAAAATA
96417 ATAATT-AA-AAAAATGA
1 ATAATTCAACAAAAAT-A
96433 ATAA
1 ATAA
96437 AAGCAGCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 7 0.37
17 6 0.32
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (17 bp):
ATAATTCAACAAAAATA
Found at i:102700 original size:15 final size:14
Alignment explanation
Indices: 102674--102703 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
102664 TTTATTCATC
102674 AATAATGTATTTTT
1 AATAATGTATTTTT
*
102688 AATAATGTAATTTT
1 AATAATGTATTTTT
102702 AA
1 AA
102704 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTATTTTT
Done.