Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005843.1 Hibiscus syriacus cultivar Beakdansim tig00013709_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: 86484
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1622 original size:45 final size:46
Alignment explanation
Indices: 1552--1661 Score: 141
Period size: 45 Copynumber: 2.3 Consensus size: 46
1542 CCATGCTTTG
* * *
1552 TTATTCACAAAAATAATCCTAACCGCTTGATATCTAATTCGCATGC-
1 TTATTCA-AAAAACAAACCTAACCGCATGATATCTAATTCGCATGCA
* *
1598 TTGTTCAAAAAACAAACCTAACCGCATGATATCTAGTTCGCATGCA
1 TTATTCAAAAAACAAACCTAACCGCATGATATCTAATTCGCATGCA
1644 TTTATTCGAAAAAACAAA
1 -TTATTC-AAAAAACAAA
1662 AATAAATGAC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
45 34 0.62
46 6 0.11
47 5 0.09
48 10 0.18
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (46 bp):
TTATTCAAAAAACAAACCTAACCGCATGATATCTAATTCGCATGCA
Found at i:9238 original size:13 final size:13
Alignment explanation
Indices: 9220--9246 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9210 TTACAGACGC
9220 GCATATGAAGACT
1 GCATATGAAGACT
9233 GCATATGAAGACT
1 GCATATGAAGACT
9246 G
1 G
9247 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:23019 original size:42 final size:42
Alignment explanation
Indices: 22960--23079 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
22950 TTTCCTCGAA
*
22960 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
23002 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
*
23044 TTCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
23080 TGTAATTCAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:23320 original size:14 final size:14
Alignment explanation
Indices: 23279--23325 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
23269 ATATTTAAAA
23279 TATATTTATTAATAT
1 TATATTT-TTAATAT
* * *
23294 AATA-ATATAATAT
1 TATATTTTTAATAT
23307 TATATTTTTAATAT
1 TATATTTTTAATAT
23321 TATAT
1 TATAT
23326 AAATAATCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
13 9 0.36
14 13 0.52
15 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TATATTTTTAATAT
Found at i:23341 original size:30 final size:28
Alignment explanation
Indices: 23279--23426 Score: 92
Period size: 28 Copynumber: 5.2 Consensus size: 28
23269 ATATTTAAAA
23279 TATATTTATTAATATAATAATATAATAT
1 TATATTTATTAATATAATAATATAATAT
23307 TATATTT-TTAATATTATATAA-ATAATCAAT
1 TATATTTATTAATA-TA-ATAATATAAT--AT
* * *
23337 TATATTATAATAATATAA-GATATTATAT
1 TATATT-TATTAATATAATAATATAATAT
* * *
23365 TTTATTTTAATAATAT-ATAATA-AATTTT
1 TATA-TTTATTAATATAATAATATAA-TAT
* * *
23393 TTTATATATTAATAATGAATAATATTAT-T
1 TATATTTATTAAT-AT-AATAATATAATAT
23422 TATAT
1 TATAT
23427 ATTCAATAAT
Statistics
Matches: 95, Mismatches: 11, Indels: 27
0.71 0.08 0.20
Matches are distributed among these distances:
27 15 0.16
28 39 0.41
29 12 0.13
30 20 0.21
31 4 0.04
32 5 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (28 bp):
TATATTTATTAATATAATAATATAATAT
Found at i:23408 original size:23 final size:26
Alignment explanation
Indices: 23381--23438 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
23371 TTAATAATAT
*
23381 ATAATA-AAT-TTTTTTATATATT-A
1 ATAATATAATATTATTTATATATTCA
23404 ATAATGAATAATATTATTTATATATTCA
1 ATAAT--ATAATATTATTTATATATTCA
23432 ATAATAT
1 ATAATAT
23439 TTTAGTAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 5 0.17
25 1 0.03
26 5 0.17
27 12 0.41
28 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (26 bp):
ATAATATAATATTATTTATATATTCA
Found at i:23679 original size:20 final size:20
Alignment explanation
Indices: 23601--23670 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
23591 TTTCCAGATG
23601 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
23621 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
23641 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
23661 TTTTCCAGAA
1 TTTTCCAGAA
23671 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:23679 original size:40 final size:40
Alignment explanation
Indices: 23601--23679 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
23591 TTTCCAGATG
* **
23601 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
23641 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
23680 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:23689 original size:15 final size:15
Alignment explanation
Indices: 23653--23734 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
23643 TTACAGAAAT
**
23653 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
23668 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
23682 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
23697 GTAATTCAAATTCTA
1 GTAATTCAAATTCCA
23712 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
23727 GTAATTCA
1 GTAATTCA
23735 TTTTCTGGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 46 0.79
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:23705 original size:30 final size:30
Alignment explanation
Indices: 23653--23734 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
23643 TTACAGAAAT
23653 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
23682 GTAATTCATTTTCCAGTAATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
23712 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
23735 TTTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:30584 original size:21 final size:21
Alignment explanation
Indices: 30559--30634 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
30549 GATACTGACT
*
30559 ATCGCATCGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
* * * *
30580 ATCGCAATGTGATACTGAC--T
1 ATCGCAACGCGATAAT-ACAAA
30600 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
30621 ATCGCAACGCGATA
1 ATCGCAACGCGATA
30635 CTGACTTTCG
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 26 0.60
22 2 0.05
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:30613 original size:20 final size:20
Alignment explanation
Indices: 30539--30714 Score: 133
Period size: 20 Copynumber: 8.7 Consensus size: 20
30529 AATTTGGAAA
* *
30539 ATCGCAATGTGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
30559 ATCGCATCGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
30580 ATCGCAATGTGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
30600 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
30621 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
30641 TTCGCAACACGATTA-TGACT
1 ATCGCAACGCGA-TACTGACT
* *
30661 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
30681 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
30701 ATCGCAACGAGATA
1 ATCGCAACGCGATA
30715 ATACAGAATC
Statistics
Matches: 125, Mismatches: 23, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
19 5 0.04
20 87 0.70
21 29 0.23
22 4 0.03
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:30648 original size:41 final size:41
Alignment explanation
Indices: 30536--30689 Score: 177
Period size: 41 Copynumber: 3.8 Consensus size: 41
30526 GCGAATTTGG
* * *
30536 AAAATCGCAATGTGATACTGACTATCGCATCGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
30577 AAAATCGCAATGTGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
30618 AAAATCGCAACGCGATACTGACTTTCGCAACACGATTATGAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAAT-AC
** * *
30660 --TTTCGCAACGCGATTCTGACTTTCGCAACG
1 AAAATCGCAACGCGATACTGACTATCGCAACG
30690 AGATTCTGAC
Statistics
Matches: 102, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
40 26 0.25
41 74 0.73
42 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:31481 original size:24 final size:24
Alignment explanation
Indices: 31454--31507 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
31444 GTATTCGAAA
*
31454 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
31478 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
31502 TTTGAT
1 TTTGAT
31508 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:31699 original size:12 final size:12
Alignment explanation
Indices: 31682--31706 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31672 ATATAATCCT
31682 GAAGAAGAAAAA
1 GAAGAAGAAAAA
31694 GAAGAAGAAAAA
1 GAAGAAGAAAAA
31706 G
1 G
31707 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:34051 original size:19 final size:20
Alignment explanation
Indices: 34009--34063 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
33999 CAATCATCTT
*
34009 AATGTCTATCGCAACGCAGA
1 AATGACTATCGCAACGCAGA
*
34029 AATGACTATCGCAATGC-GA
1 AATGACTATCGCAACGCAGA
**
34048 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
34064 AGAGAATCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCAGA
Found at i:34083 original size:33 final size:33
Alignment explanation
Indices: 34036--34129 Score: 134
Period size: 33 Copynumber: 2.8 Consensus size: 33
34026 AGAAATGACT
34036 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
34069 ATCGTAATGCGAAATGAAAAGCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
34102 ATCACAAAGCGAAATGAAAATCACAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
34130 CGAATTTAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:34190 original size:14 final size:15
Alignment explanation
Indices: 34139--34170 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
34129 GCGAATTTAG
34139 TTTCG-CGTTGCGAT
1 TTTCGTCGTTGCGAT
34153 TTT-GTCGTTGCGAT
1 TTTCGTCGTTGCGAT
34167 TTTC
1 TTTC
34171 ATTTTCGCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.06
14 15 0.94
ACGTcount: A:0.06, C:0.19, G:0.25, T:0.50
Consensus pattern (15 bp):
TTTCGTCGTTGCGAT
Found at i:34331 original size:14 final size:14
Alignment explanation
Indices: 34312--34348 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
34302 CATCAATTAA
34312 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
34326 ACAAATCATCTTTT
1 ACAAATCAACTTTT
34340 ACAAATCAA
1 ACAAATCAA
34349 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:36369 original size:94 final size:94
Alignment explanation
Indices: 36209--36610 Score: 682
Period size: 94 Copynumber: 4.3 Consensus size: 94
36199 GAATAGTTTC
* * * *
36209 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAATAAAGACAAATACTAATTTC
1 AATTGGCAGCAACCGAATAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
*
36274 ACAGTGTTAAAGAATACACAGTTTAGCAC
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
*
36303 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAATAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
*
36368 ACAGTGTTAAAGAATATACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
36397 AATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAATAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
36461 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAAGAATACACAGTTTAGCAG
*
36490 AATTGGCAGCAACTGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTT
1 AATTGGCAGCAACCGAATAAATTTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTT
* *
36554 CACATTGTTAAAGAATAAACAGTTTAGCAG
65 CACAGTGTTAAAGAATACACAGTTTAGCAG
*
36584 TATTGGCAGCAACCGAATAAATTTACT
1 AATTGGCAGCAACCGAATAAATTTACT
36611 AAGCAATCTA
Statistics
Matches: 294, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
93 110 0.37
94 184 0.63
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
AATTGGCAGCAACCGAATAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
ACAGTGTTAAAGAATACACAGTTTAGCAG
Found at i:36542 original size:187 final size:187
Alignment explanation
Indices: 36209--36610 Score: 689
Period size: 187 Copynumber: 2.1 Consensus size: 187
36199 GAATAGTTTC
* * * *
36209 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAATAAAGACAAATACTAATTTC
1 AATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
36274 ACAGTGTTAAAGAATACACAGTTTAGCACAATTGGCAGCAACCGAACAAATTTACTTTCAACCAA
65 ACAGTGTTAAAGAATACACAGTTTAGCACAATTGGCAGCAACCGAACAAATTTACTTTCAACCAA
*
36339 AAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATATACAGTTTAGCAG
130 AAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAG
36397 AATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCA
1 AATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCA
* * *
36462 CAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACTGAATAAATTTAC-TTCAACCAAA
66 CAGTGTTAAAGAATACACAGTTTAGCACAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAA
*
36526 AGACAAAACAAAAGACAAATACTAACTTCACATTGTTAAAGAATAAACAGTTTAGCAG
131 AGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAG
*
36584 TATTGGCAGCAACCGAATAAATTTACT
1 AATTGGCAGCAACCGAATAAATTTACT
36611 AAGCAATCTA
Statistics
Matches: 203, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
186 19 0.09
187 160 0.79
188 24 0.12
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (187 bp):
AATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCA
CAGTGTTAAAGAATACACAGTTTAGCACAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAA
AGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAG
Found at i:38364 original size:19 final size:19
Alignment explanation
Indices: 38297--38376 Score: 115
Period size: 20 Copynumber: 4.1 Consensus size: 19
38287 TCTTTTGGTT
*
38297 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
38316 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
38336 GGAAATGAAAATCGCAACGC
1 -GAAATGAAAATCGCAACGC
* *
38356 GAAAAGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
38375 GA
1 GA
38377 TTTTGGTTTC
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
19 21 0.38
20 33 0.59
21 2 0.04
ACGTcount: A:0.49, C:0.17, G:0.24, T:0.10
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:38405 original size:19 final size:19
Alignment explanation
Indices: 38372--38456 Score: 81
Period size: 19 Copynumber: 4.7 Consensus size: 19
38362 AAAATCGCAA
**
38372 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
38391 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
38410 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
**
38424 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
38444 TGCGATTTTCATT
1 TGCGATTTTCATT
38457 CTCGAAACTA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
14 10 0.19
16 2 0.04
17 3 0.06
19 23 0.43
20 15 0.28
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:39026 original size:20 final size:20
Alignment explanation
Indices: 39003--39219 Score: 138
Period size: 20 Copynumber: 10.7 Consensus size: 20
38993 CGATAGTCAG
39003 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
39023 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
39043 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* *
39064 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
39084 ATTCGCATTGCGAATTATGAA
1 ATTCGCATTGCGATTTACG-T
* ** *
39105 AATCGCAACGCGA-ATACGT
1 ATTCGCATTGCGATTTACGT
* * *
39124 AAATCGCATTGTGATTT-TGT
1 -ATTCGCATTGCGATTTACGT
* *
39144 ATTATCGCGTTGCGATAGT-CAGT
1 A-T-TCGCATTGCGAT-TTAC-GT
*
39167 A-TCGCATTGCGATTTTC-T
1 ATTCGCATTGCGATTTACGT
* *
39185 AAATTCGTATTGCGATTTACTT
1 --ATTCGCATTGCGATTTACGT
39207 ATTCGCATTGCGA
1 ATTCGCATTGCGA
39220 ATTGGGAAAA
Statistics
Matches: 151, Mismatches: 33, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
18 1 0.01
19 2 0.01
20 90 0.60
21 53 0.35
22 2 0.01
23 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:39055 original size:41 final size:40
Alignment explanation
Indices: 39003--39096 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
38993 CGATAGTCAG
* *
39003 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
* * *
39043 AATTCGCATTGCGATTTACTTAATCGCGTTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
39084 ATTCGCATTGCGA
1 ATTCGCATTGCGA
39097 ATTATGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 13 0.27
41 35 0.73
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTAATCGCATTGCGATTTACCT
Found at i:39109 original size:41 final size:41
Alignment explanation
Indices: 38977--39234 Score: 113
Period size: 41 Copynumber: 6.3 Consensus size: 41
38967 CGAATGACGC
* * *
38977 TATGTAAATCGCATTGCGATAGT-CAG-ATTCGCATTGCGATT
1 TATGAAAATCGCATTGCGAT-TTAC-GTATTCGCATTGCGAAT
* * * * * *
39018 TACG-TATTCGCATTGCGATTTTCCTAATTCGCATTGCGATT
1 TATGAAAATCGCATTGCGATTTACGT-ATTCGCATTGCGAAT
* *
39059 TACT--TAATCGCGTTGCGATTTACGTATTCGCATTGCGAAT
1 TA-TGAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
** * * *
39099 TATGAAAATCGCAACGCGA-ATACGTAAATCGCATTGTG-AT
1 TATGAAAATCGCATTGCGATTTACGT-ATTCGCATTGCGAAT
* ** * *
39139 TTTGTATTATCGCGTTGCGATAGT-CAGTA-TCGCATTGCG-AT
1 TATG-AAAATCGCATTGCGAT-TTAC-GTATTCGCATTGCGAAT
* * * * *
39180 TTTCTAAATTCGTATTGCGATTTACTTATTCGCATTGCGAAT
1 TAT-GAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
**
39222 TGGGAAAATCGCA
1 TATGAAAATCGCA
39235 ATTCGCAATG
Statistics
Matches: 163, Mismatches: 39, Indels: 30
0.70 0.17 0.13
Matches are distributed among these distances:
39 2 0.01
40 43 0.26
41 110 0.67
42 5 0.03
43 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (41 bp):
TATGAAAATCGCATTGCGATTTACGTATTCGCATTGCGAAT
Found at i:39111 original size:61 final size:60
Alignment explanation
Indices: 39005--39219 Score: 193
Period size: 61 Copynumber: 3.5 Consensus size: 60
38995 ATAGTCAGAT
* * * *
39005 TCGCATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACTTAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGATTAT-CAAAATCGCATTGCGATTTACTAAA
* * ** *
39066 TCGCGTTGCGATTTACGTATTCGCATTGCGAATTATGAAAATCGCAACGCGA-ATACGTAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCG-ATTATCAAAATCGCATTGCGATTTAC-TAAA
* * * ** *
39127 TCGCATTGTGATTT-TGTATTATCGCGTTGCGA-TAGTCAGTATCGCATTGCGATTTTCTAAA
1 TCGCATTGCGATTTACGTA-T-TCGCATTGCGATTA-TCAAAATCGCATTGCGATTTACTAAA
* *
39188 TTCGTATTGCGATTTACTTATTCGCATTGCGA
1 -TCGCATTGCGATTTACGTATTCGCATTGCGA
39220 ATTGGGAAAA
Statistics
Matches: 121, Mismatches: 25, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
60 8 0.07
61 83 0.69
62 28 0.23
63 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (60 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGATTATCAAAATCGCATTGCGATTTACTAAA
Found at i:39198 original size:21 final size:20
Alignment explanation
Indices: 39168--39219 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
39158 ATAGTCAGTA
*
39168 TCGCATTGCGATTTTCTAAAT
1 TCGCATTGCGATTTACT-AAT
* *
39189 TCGTATTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
39209 TCGCATTGCGA
1 TCGCATTGCGA
39220 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:39239 original size:28 final size:28
Alignment explanation
Indices: 39207--39262 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
39197 CGATTTACTT
*
39207 ATTCGCATTGCG-AATTGGGAAAATCGCA
1 ATTCGCAATGCGAAATT-GGAAAATCGCA
39235 ATTCGCAATGCGAAATTGGAAAATCGCA
1 ATTCGCAATGCGAAATTGGAAAATCGCA
39263 TTGCGATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 22 0.85
29 4 0.15
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (28 bp):
ATTCGCAATGCGAAATTGGAAAATCGCA
Found at i:40701 original size:77 final size:77
Alignment explanation
Indices: 40537--40694 Score: 183
Period size: 77 Copynumber: 2.0 Consensus size: 77
40527 TTAATATTTT
* * * ** *
40537 TTAATATTTTTGGTAAAGCGCTACCTAAAACATTATTTTTTACCGGAAATATTAATACTGGGCGC
1 TTAATATTTTCGATAAAACGCTACCTAAAACATTATTTTTTACCAAAAATATTAATACTGGACGC
*
40602 TACCTAAAATGT
66 TACCTAAAATGA
* * * * *
40614 TTAATATTTTCGATAAAACGCTACCTAAAATATTATTTTTTCTATCAAAAATGTTAATATTGGAT
1 TTAATATTTTCGATAAAACGCTACCTAAAACATTA-TTTTT-TACCAAAAATATTAATACTGGAC
40679 GCTACCTAAAAT-A
64 GCTACCTAAAATGA
40692 TTA
1 TTA
40695 TTTTTTCTAC
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
77 31 0.46
78 8 0.12
79 28 0.42
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (77 bp):
TTAATATTTTCGATAAAACGCTACCTAAAACATTATTTTTTACCAAAAATATTAATACTGGACGC
TACCTAAAATGA
Found at i:45591 original size:16 final size:14
Alignment explanation
Indices: 45561--45594 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
45551 TTATATTTTC
45561 ATAATTATTTTTAA
1 ATAATTATTTTTAA
45575 ATAATTATATATTTAA
1 ATAATTAT-T-TTTAA
45591 ATAA
1 ATAA
45595 AATGAGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 1 0.06
16 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAATTATTTTTAA
Found at i:47085 original size:47 final size:47
Alignment explanation
Indices: 47016--47155 Score: 181
Period size: 47 Copynumber: 3.0 Consensus size: 47
47006 GCCATAAAAA
*
47016 CACTGACAATGCCCCACGAGGGCAACTAAGGTAGCCTAACTACACAC
1 CACTGACAATGCCCCACGAGGGCAACTGAGGTAGCCTAACTACACAC
* * * *
47063 CACTGATAATGCCCCACGAGGGCAACTGAGGTAACTTAGCTACACAC
1 CACTGACAATGCCCCACGAGGGCAACTGAGGTAGCCTAACTACACAC
* ** * * *
47110 CATTGGGAATGCCCCACTAGGGCAACTGAGGTAGCCTTACCACACA
1 CACTGACAATGCCCCACGAGGGCAACTGAGGTAGCCTAACTACACA
47156 TTAGCATAAC
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 79 1.00
ACGTcount: A:0.31, C:0.31, G:0.21, T:0.16
Consensus pattern (47 bp):
CACTGACAATGCCCCACGAGGGCAACTGAGGTAGCCTAACTACACAC
Found at i:48757 original size:13 final size:13
Alignment explanation
Indices: 48739--48772 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
48729 GATGATGGTC
48739 TTGATGAAGGATG
1 TTGATGAAGGATG
*
48752 TTGATGATGGATG
1 TTGATGAAGGATG
*
48765 ATGATGAA
1 TTGATGAA
48773 ATGGCAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
TTGATGAAGGATG
Found at i:54968 original size:16 final size:15
Alignment explanation
Indices: 54927--54968 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
54917 GGATGTAAAG
*
54927 GCATCTTGATGGGAA
1 GCATCTTCATGGGAA
54942 GCATCTTCATGGGAA
1 GCATCTTCATGGGAA
54957 GCATCATTCATG
1 GCATC-TTCATG
54969 AAAGGTCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (15 bp):
GCATCTTCATGGGAA
Found at i:56700 original size:62 final size:62
Alignment explanation
Indices: 56629--56752 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
56619 GTCTTGTAGC
56629 AATCAAGAAGGATTATGCAGTCGTACATATTCTATTGTCAAAGTTGGCATTACCTTTGCCAG
1 AATCAAGAAGGATTATGCAGTCGTACATATTCTATTGTCAAAGTTGGCATTACCTTTGCCAG
56691 AATCAAGAAGGATTATGCAGTCGTACATATTCTATTGTCAAAGTTGGCATTACCTTTGCCAG
1 AATCAAGAAGGATTATGCAGTCGTACATATTCTATTGTCAAAGTTGGCATTACCTTTGCCAG
56753 TTTTCAAAGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (62 bp):
AATCAAGAAGGATTATGCAGTCGTACATATTCTATTGTCAAAGTTGGCATTACCTTTGCCAG
Found at i:57538 original size:182 final size:180
Alignment explanation
Indices: 57083--57746 Score: 807
Period size: 182 Copynumber: 3.6 Consensus size: 180
57073 ATACAAATGA
* * * * * *
57083 AAAATGTATCGTTCCATAGCAATATAATAGGTAAAAATATGATAAAATCGGTTTC-ATTATGATA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA-CGGTATCGA-AATGATA
** * * *
57147 AAACCGGTAAACCGCTACTGGATATATCGAAAGTATCGATTA-GATTTAA-ATAAGTATCGACAC
64 AAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGA-TACG--TTAATATAAGTATCGACAC
* *
57210 TTTTGGAATTTAAAAGAGAAGAAGTAATAGCGCCTATAAAGTGTCGATACTTTATTTAT
126 TTTTCGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATAC----TTTAT
* * * * *
57269 AAAAACGTATCAATCCATAATAATATAACAGGTATAAGTATGACAAAACTGGTCA-CGAAATGAT
1 -AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC-GGT-ATCGAAATGAT
57333 AAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACGTTAATATAAGTATCGACACTT
63 AAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACGTTAATATAAGTATCGACACTT
* * *
57398 TTTGAATTTAAAAGAGAAGAAGTTATAGAGCCTATAATGTGTCGATACTTTAT
128 TTCGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
* *
57451 ACAAATGTATCGATCCATAGCAATATAACAGGTAAGAATATGACAAAACAGGTATCGAAATGATA
1 A-AAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC-GGTATCGAAATGATA
* * * **
57516 AAACCGGTAAAAAACTACCGGATATAGTGAAAGTGTCGATAAATTAATATAAGTATCGACAC-TT
64 AAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACGTTAATATAAGTATCGACACTTT
*
57580 TCGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAT
129 TCG-AATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
* * *
57633 GAAAATGTATCGATCTATAACAATATAATAGGTAAAAATATGACAAAACCGGTATCGAAATGACA
1 -AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAA-CGGTATCGAAATGATA
* * * * *
57698 AAACCGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGGTACTTTAATA
64 AAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACGTTAATA
57747 AGTATGCGTA
Statistics
Matches: 416, Mismatches: 51, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
181 6 0.01
182 257 0.62
183 2 0.00
185 4 0.01
186 63 0.15
187 83 0.20
188 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.28
Consensus pattern (180 bp):
AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACGGTATCGAAATGATAAA
ACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACGTTAATATAAGTATCGACACTTTTC
GAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAT
Found at i:59389 original size:158 final size:158
Alignment explanation
Indices: 59084--59400 Score: 618
Period size: 158 Copynumber: 2.0 Consensus size: 158
59074 GGAATTGTGC
59084 CGATCCTTGATGGAGCAATTTGATGTCAAACAATGTAGTGCTAAATATGGCGATTATTTATTCCC
1 CGATCCTTGATGGAGCAATTTGATGTCAAACAATGTAGTGCTAAATATGGCGATTATTTATTCCC
59149 TCTGGGGGTATCGACTGCTGCAGCTGTCTTGGGGGTATAAACAAAGGCAAAAGTGTTGTAGAAGT
66 TCTGGGGGTATCGACTGCTGCAGCTGTCTTGGGGGTATAAACAAAGGCAAAAGTGTTGTAGAAGT
59214 CTGTAGGAGTAAGACTGGAAAGCACTTG
131 CTGTAGGAGTAAGACTGGAAAGCACTTG
59242 CGATCCTTGATGGAGCAATTTGATGTCAAACAATGTAGTGCTAAATATGGCGATTATTTATTCCC
1 CGATCCTTGATGGAGCAATTTGATGTCAAACAATGTAGTGCTAAATATGGCGATTATTTATTCCC
59307 TCTGGGGGTATCGACTGCTGCAGCTGTCTT-GGGGTATAAACAAAGGCAAAAGTGTTGTAGAAGT
66 TCTGGGGGTATCGACTGCTGCAGCTGTCTTGGGGGTATAAACAAAGGCAAAAGTGTTGTAGAAGT
59371 CTGTAGGAGTAAGAACTGGAAAGCACTTG
131 CTGTAGGAGTAAG-ACTGGAAAGCACTTG
59400 C
1 C
59401 CTCCAAATAT
Statistics
Matches: 158, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
157 47 0.30
158 111 0.70
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (158 bp):
CGATCCTTGATGGAGCAATTTGATGTCAAACAATGTAGTGCTAAATATGGCGATTATTTATTCCC
TCTGGGGGTATCGACTGCTGCAGCTGTCTTGGGGGTATAAACAAAGGCAAAAGTGTTGTAGAAGT
CTGTAGGAGTAAGACTGGAAAGCACTTG
Found at i:59776 original size:22 final size:22
Alignment explanation
Indices: 59725--59780 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
59715 ATGTTTTTGT
*
59725 TTTTTTTATATAAAATGATGGTA
1 TTTTATTATATAAAATGAT-GTA
*
59748 TAGTTATTATATAAAATGAT-TAA
1 T-TTTATTATATAAAATGATGT-A
59771 TTTTATTATA
1 TTTTATTATA
59781 AATTCAGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.32
23 3 0.11
24 16 0.57
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTTTATTATATAAAATGATGTA
Found at i:60452 original size:20 final size:21
Alignment explanation
Indices: 60422--60462 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
60412 GAGAAAATTT
60422 GAAGAAGAAAAGATGGAGGAA
1 GAAGAAGAAAAGATGGAGGAA
60443 GAAG-AGAAAAGATGGAGGAA
1 GAAGAAGAAAAGATGGAGGAA
60463 ATGAGGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.39, T:0.05
Consensus pattern (21 bp):
GAAGAAGAAAAGATGGAGGAA
Found at i:60786 original size:17 final size:17
Alignment explanation
Indices: 60764--60799 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
60754 TTTAAATATT
*
60764 TCATGAAAATATATTAA
1 TCATGAAAAGATATTAA
60781 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
60798 TC
1 TC
60800 CTAATGATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (17 bp):
TCATGAAAAGATATTAA
Found at i:62352 original size:15 final size:15
Alignment explanation
Indices: 62334--62368 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
62324 TATAAAAAGT
62334 ATCGATCCCAAAAAC
1 ATCGATCCCAAAAAC
62349 ATCGATCCCAAAAAC
1 ATCGATCCCAAAAAC
62364 ATCGA
1 ATCGA
62369 GACCCATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.31, G:0.09, T:0.14
Consensus pattern (15 bp):
ATCGATCCCAAAAAC
Found at i:62374 original size:16 final size:15
Alignment explanation
Indices: 62334--62374 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
62324 TATAAAAAGT
*
62334 ATCGATCCCAAAAAC
1 ATCGAACCCAAAAAC
*
62349 ATCGATCCCAAAAAC
1 ATCGAACCCAAAAAC
62364 ATCGAGACCCA
1 ATCGA-ACCCA
62375 TAATTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.44, C:0.34, G:0.10, T:0.12
Consensus pattern (15 bp):
ATCGAACCCAAAAAC
Found at i:62687 original size:198 final size:198
Alignment explanation
Indices: 62349--63091 Score: 1267
Period size: 198 Copynumber: 3.8 Consensus size: 198
62339 TCCCAAAAAC
62349 ATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATGAATCTAACCGGT
1 ATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATGAATCTAACCGGT
* ** * * *
62414 CTAAATATAATGGTTTATGAAAAAAC-AGATGTACATAAAGTATTGACACTTATTTAATTTGTGG
66 CTAAATACACCGGTTTATGAGAAAACAAG-TGTACATAAAGTATCGACACTTATTTAATTTGTGT
*
62478 CGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGAATGGAAATGTGTCGATACATTTATAAA
130 CGATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGGAAATGTGTCGATACATTTATAAA
62543 AAGT
195 AAGT
*
62547 ATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAGTTATGAATCTAACCGGT
1 ATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATGAATCTAACCGGT
62612 CTAAATACACCGGTTTATGAGAAAACAAGTGTACATAAAGTATCGACACTTATTTAATTTGTGTC
66 CTAAATACACCGGTTTATGAGAAAACAAGTGTACATAAAGTATCGACACTTATTTAATTTGTGTC
* * *
62677 GATACTTTGTGTACGGAGTGATTTCCTTACCAAGTGCATGGAAATGTGTCGATACATTTATAAAA
131 GATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGGAAATGTGTCGATACATTTATAAAA
62742 AGT
196 AGT
62745 ATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATGAATCTAACCGGT
1 ATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATGAATCTAACCGGT
* * *
62810 ATAAATACACCGGTTTATGAGAAAACAGGTGTACATAAAATATCGACACTTATTTAATTTGTGTC
66 CTAAATACACCGGTTTATGAGAAAACAAGTGTACATAAAGTATCGACACTTATTTAATTTGTGTC
* * *
62875 AATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGGAAATATGTCGATACATCTATAAAA
131 GATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGGAAATGTGTCGATACATTTATAAAA
62940 AGT
196 AGT
62943 ATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATGAATCTAACCGGT
1 ATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATGAATCTAACCGGT
*
63008 CTAAATACACCAGTTTATGAGAAAACAAGTGTACATAAAGTATCGACACTCT-TTTAATTTGTGT
66 CTAAATACACCGGTTTATGAGAAAACAAGTGTACATAAAGTATCGACACT-TATTTAATTTGTGT
*
63072 AGATACGTTT-TGTCCAGAAT
130 CGATAC-TTTGTGTCCAGAAT
63092 TTAATGGTCA
Statistics
Matches: 515, Mismatches: 27, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
198 509 0.99
199 6 0.01
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (198 bp):
ATCGATCCCAAAAACATCGAGACCCATAATTATAATGTAATAGGTAAATTATGAATCTAACCGGT
CTAAATACACCGGTTTATGAGAAAACAAGTGTACATAAAGTATCGACACTTATTTAATTTGTGTC
GATACTTTGTGTCCAGAATGATTTCCTTACCAAGTGCATGGAAATGTGTCGATACATTTATAAAA
AGT
Found at i:63587 original size:15 final size:15
Alignment explanation
Indices: 63567--63618 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
63557 AGAATCGGGG
*
63567 CTCTTCTCAACCCAT
1 CTCTTCTCAACCCAC
63582 CTCTTCTCAACCCAC
1 CTCTTCTCAACCCAC
*
63597 CTCTTCTCAACCCAG
1 CTCTTCTCAACCCAC
63612 CTCTTCT
1 CTCTTCT
63619 GAGGAAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.17, C:0.48, G:0.02, T:0.33
Consensus pattern (15 bp):
CTCTTCTCAACCCAC
Found at i:64798 original size:6 final size:6
Alignment explanation
Indices: 64758--64797 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
64748 CAAGCGGTCA
* * *
64758 ATGAAG ATGACG ATGAAG ATGAAG ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
64798 TCCAAACAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.42, C:0.03, G:0.33, T:0.23
Consensus pattern (6 bp):
ATGAAG
Found at i:66751 original size:22 final size:21
Alignment explanation
Indices: 66725--66770 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
66715 AAAAGAAAGG
*
66725 TATACATAATGTATCGATACTT
1 TATACAT-ATGTATCGACACTT
* *
66747 TATACATTTGTGTCGACACTT
1 TATACATATGTATCGACACTT
66768 TAT
1 TAT
66771 GTCCATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (21 bp):
TATACATATGTATCGACACTT
Found at i:67014 original size:197 final size:196
Alignment explanation
Indices: 66230--67361 Score: 1430
Period size: 197 Copynumber: 5.7 Consensus size: 196
66220 ATGATAAGCG
* * *
66230 TCCCAAAAACATCGAGACCCATAATTACAATGTAATAGGTAAAATAACAATGTAACCGGTCTAAA
1 TCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAA
* * * * * *
66295 TATACCAGTGTATGAGAAAAGAGGTATACATAAAGTATCGACACTTTATACATTTGTGTTGATAC
66 TATACCGGT-TATTA-AAAA-AGGTATACATAATGTATCGATACTTTATACATTTGTGTCGACAC
* * * *
66360 TTTGTGTCCATAATGTATTTTCCATCCAAAACAAGTTCAC-AAATAAGTGTCGATACATTTATAT
128 TTTATGTCCATAAT-AAATTT---TCC-AAACAAGTTCACGAAA-AAGTGTCGATACATTTATAA
66424 CAAGTGTCGA
187 CAAGTGTCGA
* * * * * * * *
66434 TCCCAAAAACATCGAAACCCGTAACTATAATGTAATAGGTCACTTTATAATGTAACCGATTTAAA
1 TCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAA
* * * * * * *
66499 TTTATCGGTTTTATGAGAAAATAGGTCTACA-ATATGTATCGACACTTTATTCATTTGTGTCGAT
66 TATACCGG--TTATTA-AAAA-AGGTATACATA-ATGTATCGATACTTTATACATTTGTGTCGAC
* ** * * *
66563 ACATGT-TGTCCATAATGTA-TTTCCAAACCAAGTGCACGAAAAAAGTGTCGATATATTTGTAAC
126 AC-TTTATGTCCATAATAAATTTTCCAAA-CAAGTTCACG-AAAAAGTGTCGATACATTTATAAC
66626 AAGTGTCGA
188 AAGTGTCGA
*
66635 TCCCAAAAACATCGAAACACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAA
1 TCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAA
*
66700 TATACCGGTCATTAAAAAAGAAAGGTATACATAATGTATCGATACTTTATACATTTGTGTCGACA
66 TATACCGGTTATT---AAA-AAAGGTATACATAATGTATCGATACTTTATACATTTGTGTCGACA
*
66765 CTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTCATAACAAGT
127 CTTTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTTATAACAAGT
66830 GTCGA
192 GTCGA
* *
66835 TCCCAAAAACATTGAAACACATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAA
1 TCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAA
*
66900 TATACCGGTTATTAAAGAAAGGTATACATAATGTATTGATACTTTATACATTTGTGTCGACACTT
66 TATACCGGTTATTAAA-AAAGGTATACATAATGTATCGATACTTTATACATTTGTGTCGACACTT
*
66965 TATGTCCATAATAAATTTTCCAAACAAGTTCACTAAAAAGTGTCGATACATTTATAACAAGTGTC
130 TATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTTATAACAAGTGTC
67030 GA
195 GA
*
67032 TCCCAAAAACATCGAAACCCGTAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAA
1 TCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAA
* *
67097 TATACCGGTTATTAAAAATAAGGTATACATAATGTATTGATATTTTATACATTTGTGTCGACACT
66 TATACCGGTTATT-AAAA-AAGGTATACATAATGTATCGATACTTTATACATTTGTGTCGACACT
* *
67162 TTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCG--ACATTTAGAAAAAGTGT
129 TTATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTTATAACAAGTGT
*
67225 CAA
194 CGA
* * * * * *
67228 TCCTAAAAACATCGAAACCCGTAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAA
1 TCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAA
* * * * * * *
67293 TTTACCGGTTTTATGATAAAATAGGTCTACATAATGTATCGATACTTTTTAAATTAGTGTCGATA
66 TATACCGG--TTAT--TAAAAAAGGTATACATAATGTATCGATACTTTATACATTTGTGTCGACA
67358 CTTT
127 CTTT
67362 TTAAAATTAC
Statistics
Matches: 830, Mismatches: 78, Indels: 46
0.87 0.08 0.05
Matches are distributed among these distances:
196 84 0.10
197 192 0.23
198 137 0.17
199 10 0.01
200 120 0.14
201 149 0.18
202 15 0.02
203 2 0.00
204 60 0.07
205 58 0.07
206 3 0.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (196 bp):
TCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAACATAACAATGTAACCGGTCTAAA
TATACCGGTTATTAAAAAAGGTATACATAATGTATCGATACTTTATACATTTGTGTCGACACTTT
ATGTCCATAATAAATTTTCCAAACAAGTTCACGAAAAAGTGTCGATACATTTATAACAAGTGTCG
A
Found at i:71034 original size:198 final size:195
Alignment explanation
Indices: 70521--71043 Score: 575
Period size: 198 Copynumber: 2.6 Consensus size: 195
70511 GTTAGATTTT
** *
70521 GTGTCGATACATTTATAACAAGTATCGATCCC-AAAATCAAAGAGACCGATAATTATAATGTAAT
1 GTGTCGATACATTTA-AA-AAGTATCGATCCCGAAAA-CATCGAAACCGATAATTATAATGTAAT
* * * *
70585 AGGTAAATTTCCAATGTAACCGATAGAAATATACCGGGTTCATGAGAGAATAGGTCAACATAAAG
63 AGGTAAATTTACAATGTAACCGTTA-AAATATACC-GGTTAATGAGAAAATAGGTCAACATAAAG
* * * * *
70650 TATCGACACTTTTTTAATTTGTGTCGATACATTTTTCCAAAATAAATGGCAAACGAGGTGTACGC
126 TATCGACACTCTTTAAATATGTGTCGATACATTTTTCCAAAATAAATGACAAACGAGGTGCACGC
70715 ATAAA
191 ATAAA
* * *
70720 GTGTCGATACATTTGTAAAAAGTATCGATCCTCG-AAACATCGAAATCGATAATTATCATGTAAC
1 GTGTCGATACA-TT-TAAAAAGTATCGATCC-CGAAAACATCGAAACCGATAATTATAATGTAAT
* * * * * * * *
70784 AGGTAAATTTACAATGTATCCGGTTAAAATATACCAGTTAATTAGCAAATAGGTCTAGATTATGT
63 AGGTAAATTTACAATGTAACC-GTTAAAATATACCGGTTAATGAGAAAATAGGTCAACATAAAGT
* *
70849 ATCGACACTCTTTAAATATGTGTCGATACTTTTTTCCAAAATAAA-GCACAAACGAGTTGCACGC
127 ATCGACACTCTTTAAATATGTGTCGATACATTTTTCCAAAATAAATG-ACAAACGAGGTGCACGC
70913 ATAAA
191 ATAAA
* * *
70918 GTGTCGATACATTTAAAATTGTATCGATCCCGAAAACATCGAAACCGATATTTATAATGTAATAA
1 GTGTCGATACATTTAAAA-AGTATCGATCCCGAAAACATCGAAACCGATAATTATAATGTAATAG
* * * ** * * * *
70983 GTCAATTTATAATGTAACTTGTTTTAATTTACCGGTTTTATGATAAAATAGGTCAATATAA
65 GTAAATTTACAATGTAAC-CGTTAAAATATACCGG-TTAATGAGAAAATAGGTCAACATAA
71044 GCGATACCTA
Statistics
Matches: 268, Mismatches: 46, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
196 7 0.03
197 66 0.25
198 110 0.41
199 72 0.27
200 11 0.04
201 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (195 bp):
GTGTCGATACATTTAAAAAGTATCGATCCCGAAAACATCGAAACCGATAATTATAATGTAATAGG
TAAATTTACAATGTAACCGTTAAAATATACCGGTTAATGAGAAAATAGGTCAACATAAAGTATCG
ACACTCTTTAAATATGTGTCGATACATTTTTCCAAAATAAATGACAAACGAGGTGCACGCATAAA
Found at i:71193 original size:28 final size:23
Alignment explanation
Indices: 71122--71195 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
71112 TGCCTATTTT
71122 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTATTAC
*
71145 ATTATATAAGTGCTACCTATTAC
1 ATTATATAAGCGCTACCTATTAC
* *
71168 ATTATATAAGCGCTACCTAATAT
1 ATTATATAAGCGCTACCTATTAC
71191 ATTAT
1 ATTAT
71196 TGTGTTTGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTATTAC
Found at i:72773 original size:2 final size:2
Alignment explanation
Indices: 72766--72793 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
72756 GTAAGCTGAT
72766 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
72794 CACGCACACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.