Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002724.1 Hibiscus syriacus cultivar Beakdansim tig00005618_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: 116615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3690 original size:64 final size:61
Alignment explanation
Indices: 3554--3709 Score: 201
Period size: 64 Copynumber: 2.5 Consensus size: 61
3544 TGCACTAAGA
*
3554 GTGCATCGATGCATCAAGTGCATTCGATGTT-TCAAAATAGCTGGCATCGATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCTCAAAATAGCTGGCATCGATGCATGGTTG
* *
3614 GTGCATCGATGCATCAAATGCATTCGATGTTCTCATAAA-ATCTCAGTGCATCGGTGCATGG-TG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCTCA-AAATAGCT--G-GCATCGATGCATGGTTG
* *
3677 TGTGTATCGATGCATGAAATGCATTCGATGTTC
1 -GTGCATCGATGCATCAAATGCATTCGATGTTC
3710 AATTTAATTC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
60 30 0.35
61 6 0.07
62 3 0.04
63 3 0.04
64 43 0.51
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (61 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTCTCAAAATAGCTGGCATCGATGCATGGTTG
Found at i:3727 original size:64 final size:64
Alignment explanation
Indices: 3554--3759 Score: 196
Period size: 64 Copynumber: 3.3 Consensus size: 64
3544 TGCACTAAGA
* * *
3554 GTGCATCGATGCATCAAGTGCATTCGATGTT-TCAA-AATAGCT--G-GCATCGATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCT-AATAAAATCTCAGTGCATCGATGCATGGTTG
* *
3614 GTGCATCGATGCATCAAATGCATTCGATGTTCTCATAAAATCTCAGTGCATCGGTGCATGG-TG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCTAATAAAATCTCAGTGCATCGATGCATGGTTG
* * ** *
3677 TGTGTATCGATGCATGAAATGCATTCGATGTTC-AATTTAAT-TCATGGTGCATCGATGTATGGA
1 -GTGCATCGATGCATCAAATGCATTCGATGTTCTAATAAAATCTCA--GTGCATCGATGCATGG-
3740 TTG
62 TTG
*
3743 ATGCATCTG-TGCATCAA
1 GTGCATC-GATGCATCAA
3760 TCTGAAAATT
Statistics
Matches: 120, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
60 31 0.26
61 6 0.05
62 3 0.03
63 8 0.07
64 57 0.47
65 12 0.10
66 3 0.03
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTCTAATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:4228 original size:11 final size:11
Alignment explanation
Indices: 4203--4256 Score: 64
Period size: 11 Copynumber: 5.3 Consensus size: 11
4193 GGGTAAATAG
4203 AAATAAAT-A-
1 AAATAAATAAT
4212 AAATAAATAAT
1 AAATAAATAAT
4223 AAATAAATAAT
1 AAATAAATAAT
4234 -AATAATATAAT
1 AAATAA-ATAAT
4245 -AAT-AATAAT
1 AAATAAATAAT
4254 AAA
1 AAA
4257 CAATAAGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
9 13 0.32
10 9 0.22
11 19 0.46
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:4234 original size:3 final size:3
Alignment explanation
Indices: 4208--4255 Score: 55
Period size: 3 Copynumber: 15.7 Consensus size: 3
4198 AATAGAAATA
4208 AAT AA- AAT AAAT AAT AAAT AAAT AAT AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
4254 AA
1 AA
4256 ACAATAAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.10
3 27 0.66
4 10 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:4398 original size:12 final size:11
Alignment explanation
Indices: 4383--4429 Score: 58
Period size: 12 Copynumber: 4.0 Consensus size: 11
4373 TGGAAAAATG
4383 TATATATAATAA
1 TATA-ATAATAA
4395 TATAATAATAA
1 TATAATAATAA
4406 TAATAATAATAGA
1 T-ATAATAATA-A
*
4419 TAAAATAATAA
1 TATAATAATAA
4430 GAGAGAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 9 0.28
12 21 0.66
13 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
TATAATAATAA
Found at i:4449 original size:3 final size:3
Alignment explanation
Indices: 4388--4429 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
4378 AAATGTATAT
4388 ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA GATA A-A ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA A
4430 GAGAGAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:4568 original size:3 final size:3
Alignment explanation
Indices: 4560--4607 Score: 71
Period size: 3 Copynumber: 15.7 Consensus size: 3
4550 AAATATAAAT
4560 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA GT-A TATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TA-A TAA TAA TAA
4606 TA
1 TA
4608 GTAAGAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.02
3 37 0.88
4 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5008 original size:37 final size:37
Alignment explanation
Indices: 4956--5063 Score: 179
Period size: 34 Copynumber: 3.0 Consensus size: 37
4946 ATGCTTATGG
*
4956 ATCATA-TTTTAGGAGTTTGAATCATAGTAAAATTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
4992 ATCATATTTTTAGGAGTTTGAATCAT-GTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
5028 A--ATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
5063 A
1 A
5064 AAGTTATGTT
Statistics
Matches: 69, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
34 23 0.33
35 11 0.16
36 16 0.23
37 19 0.28
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:7456 original size:54 final size:53
Alignment explanation
Indices: 7380--7482 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
7370 CGGCTTGACT
* *
7380 TAAGAATTTATAGAGTCGTTGAACATTTTTTTCATTTTCTAAAACTACGACTTC
1 TAAGAATTTATAAAGTCATTGAACA-TTTTTTCATTTTCTAAAACTACGACTTC
* *
7434 TAAGAATTTATAAATTCATTGAACATTTTTTCATTTTTTAAAACTACGA
1 TAAGAATTTATAAAGTCATTGAACATTTTTTCATTTTCTAAAACTACGA
7483 TTTCAGAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 23 0.51
54 22 0.49
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.44
Consensus pattern (53 bp):
TAAGAATTTATAAAGTCATTGAACATTTTTTCATTTTCTAAAACTACGACTTC
Found at i:8001 original size:20 final size:20
Alignment explanation
Indices: 7976--8015 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
7966 TGTTTGCAAC
7976 ATTTTAGCTCATGTCATGTT
1 ATTTTAGCTCATGTCATGTT
*
7996 ATTTTAGCTCATGTTATGTT
1 ATTTTAGCTCATGTCATGTT
8016 TACATTAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.53
Consensus pattern (20 bp):
ATTTTAGCTCATGTCATGTT
Found at i:8910 original size:20 final size:19
Alignment explanation
Indices: 8864--8912 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
8854 TGGCAAAGAG
8864 CATGTATTTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
* *
8883 AATATATTTTCATTAAAAAT
1 CATGTATTTTCATT-AAAAT
8903 CATGTATTTT
1 CATGTATTTT
8913 TAAAGGGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:9008 original size:33 final size:33
Alignment explanation
Indices: 8966--9040 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
8956 GCCTAAACCC
8966 TTTGAAAACTATAAATAGGACATTAGTTTGTCA
1 TTTGAAAACTATAAATAGGACATTAGTTTGTCA
*
8999 TTTGAAAACTATAAATAGGCCATTAGTTTGTCA
1 TTTGAAAACTATAAATAGGACATTAGTTTGTCA
9032 TTTGAAAAC
1 TTTGAAAAC
9041 AATCATTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (33 bp):
TTTGAAAACTATAAATAGGACATTAGTTTGTCA
Found at i:26654 original size:19 final size:20
Alignment explanation
Indices: 26627--26664 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
26617 TGAAAATGAT
26627 TTGACTTTGAAAG-CAAAAG
1 TTGACTTTGAAAGTCAAAAG
*
26646 TTGATTTTGAAAGTCAAAA
1 TTGACTTTGAAAGTCAAAA
26665 TGAAATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (20 bp):
TTGACTTTGAAAGTCAAAAG
Found at i:29481 original size:3 final size:3
Alignment explanation
Indices: 29473--29505 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
29463 ATAAAATATG
29473 TAA TAA TAA TAA GTAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TA
29506 CTTATATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:29488 original size:13 final size:13
Alignment explanation
Indices: 29463--29505 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
29453 ATGGGGTGCT
*
29463 ATAA-AATATGTA
1 ATAATAATAAGTA
29475 ATAATAATAAGTA
1 ATAATAATAAGTA
29488 ATAATAATAA-TA
1 ATAATAATAAGTA
29500 ATAATA
1 ATAATA
29506 CTTATATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 12 0.41
13 17 0.59
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (13 bp):
ATAATAATAAGTA
Found at i:30059 original size:113 final size:112
Alignment explanation
Indices: 29701--30107 Score: 627
Period size: 113 Copynumber: 3.6 Consensus size: 112
29691 ATCTATTCCA
* * * *
29701 TCTGAAGGGAATATCAAATCTTTGAGAAGAGAGACATGTTCCGCTTACTCTGAAGGGACTATCAG
1 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAT
* * *
29766 ATCTGGGGAAGTTGATCCATTGAATCGAAGCAGAGTTGTTCCACTTAC
66 ATCTGGGG-AGTTAATCCATTGAATCGAAGAAGACTTGTTCCACTTAC
*
29814 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCTCTTACTCTGAAGGGAATATCAT
1 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAT
29879 ATCTGGGGAGTTAATCCATTGAATCGAAGAAGACTTGTTCCACTTAC
66 ATCTGGGGAGTTAATCCATTGAATCGAAGAAGACTTGTTCCACTTAC
* * *
29926 TCTGAAGGGAATATCAAATCTTAGAAAAAAGAGACATGTTACGCTTACTCTGAAGGGAATATCAT
1 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAT
* * *
29991 ATCTGAGGGAGTTAATCCATTGAAT-TAGGGTAGACTTGTTCCACTTAC
66 ATCTG-GGGAGTTAATCCATTGAATCGA-AGAAGACTTGTTCCACTTAC
* * *
30039 TCTGAAGGGAATATCAAATCTTGGATAAGAGAGACATGTTTCGCTTACTCTGAAGGGAATATCAA
1 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAT
30104 ATCT
66 ATCT
30108 TGGATAAGAG
Statistics
Matches: 272, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
112 103 0.38
113 169 0.62
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (112 bp):
TCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAT
ATCTGGGGAGTTAATCCATTGAATCGAAGAAGACTTGTTCCACTTAC
Found at i:30086 original size:48 final size:48
Alignment explanation
Indices: 30029--30150 Score: 217
Period size: 48 Copynumber: 2.5 Consensus size: 48
30019 GGTAGACTTG
* *
30029 TTCCACTTACTCTGAAGGGAATATCAAATCTTGGATAAGAGAGACATG
1 TTCCGCTTACTCTGAAGGGAATATCAAATCTTGGATAAGAGAGACATA
*
30077 TTTCGCTTACTCTGAAGGGAATATCAAATCTTGGATAAGAGAGACATA
1 TTCCGCTTACTCTGAAGGGAATATCAAATCTTGGATAAGAGAGACATA
30125 TTCCGCTTACTCTGAAGGGAATATCA
1 TTCCGCTTACTCTGAAGGGAATATCA
30151 GATCAGGAGG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (48 bp):
TTCCGCTTACTCTGAAGGGAATATCAAATCTTGGATAAGAGAGACATA
Found at i:30092 original size:225 final size:225
Alignment explanation
Indices: 29701--30107 Score: 647
Period size: 225 Copynumber: 1.8 Consensus size: 225
29691 ATCTATTCCA
* * * * *
29701 TCTGAAGGGAATATCAAATCTTTGAGAAGAGAGACATGTTCCGCTTACTCTGAAGGGACTATCAG
1 TCTGAAGGGAATATCAAATCTTAGAAAAAAGAGACATGTTACGCTTACTCTGAAGGGAATATCAG
* * *
29766 ATCTGGGGAAGTTGATCCATTGAATCGAAGCAGAGTTGTTCCACTTACTCTGAAGGGAATATCAA
66 ATCTGGGGAAGTTAATCCATTGAATAGAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAA
* *
29831 ATCTTGGAAAAGAGAGACATGTTCCTCTTACTCTGAAGGGAATATCATATCTGGGGAGTTAATCC
131 ATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAAATCTGGGGAGTTAATCC
29896 ATTGAATCGAAGAAGACTTGTTCCACTTAC
196 ATTGAATCGAAGAAGACTTGTTCCACTTAC
*
29926 TCTGAAGGGAATATCAAATCTTAGAAAAAAGAGACATGTTACGCTTACTCTGAAGGGAATATCAT
1 TCTGAAGGGAATATCAAATCTTAGAAAAAAGAGACATGTTACGCTTACTCTGAAGGGAATATCAG
* *
29991 ATCTGAGGG-AGTTAATCCATTGAATTAG-GGTAGACTTGTTCCACTTACTCTGAAGGGAATATC
66 ATCTG-GGGAAGTTAATCCATTGAA-TAGAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATC
* *
30054 AAATCTTGGATAAGAGAGACATGTTTCGCTTACTCTGAAGGGAATATCAAATCT
129 AAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAAATCT
30108 TGGATAAGAG
Statistics
Matches: 165, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
225 160 0.97
226 5 0.03
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (225 bp):
TCTGAAGGGAATATCAAATCTTAGAAAAAAGAGACATGTTACGCTTACTCTGAAGGGAATATCAG
ATCTGGGGAAGTTAATCCATTGAATAGAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAA
ATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAAATCTGGGGAGTTAATCC
ATTGAATCGAAGAAGACTTGTTCCACTTAC
Found at i:31297 original size:12 final size:12
Alignment explanation
Indices: 31280--31318 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
31270 TTGAACCCTC
31280 CTTTTATTTTTT
1 CTTTTATTTTTT
31292 CTTTTATTTTTT
1 CTTTTATTTTTT
**
31304 CTCAT-TTTTTT
1 CTTTTATTTTTT
31315 CTTT
1 CTTT
31319 CCTTTCCTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (12 bp):
CTTTTATTTTTT
Found at i:31312 original size:28 final size:28
Alignment explanation
Indices: 31281--31348 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
31271 TGAACCCTCC
*
31281 TTTTATTTTTTCTTTTATTTT-TTCTCAT
1 TTTTATTTTTTCTTTCATTTTCTT-TCAT
* *
31309 TTTT-TTCTTTCCTTTCCTTTTCTTTCAT
1 TTTTATT-TTTTCTTTCATTTTCTTTCAT
31337 TTTTCATTTTTT
1 TTTT-ATTTTTT
31349 TCAGGCGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
27 2 0.06
28 23 0.72
29 5 0.16
30 2 0.06
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.76
Consensus pattern (28 bp):
TTTTATTTTTTCTTTCATTTTCTTTCAT
Found at i:34905 original size:25 final size:24
Alignment explanation
Indices: 34867--34932 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 24
34857 AATCTATCCC
* *
34867 ATATCAAAATAGAATGAAATAATAAT
1 ATATAAAAAAAGAATGAAA-AA-AAT
* *
34893 ATAT-AAAAAAGAAAGAAAGAAAT
1 ATATAAAAAAAGAATGAAAAAAAT
34916 ATATAAATAAAAGAATG
1 ATATAAA-AAAAGAATG
34933 GAAGGGATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 7 0.21
24 3 0.09
25 20 0.59
26 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.21
Consensus pattern (24 bp):
ATATAAAAAAAGAATGAAAAAAAT
Found at i:38527 original size:11 final size:11
Alignment explanation
Indices: 38513--38542 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
38503 TGCAATGTAC
38513 ATGCAATATGA
1 ATGCAATATGA
*
38524 ATGCAAGATGA
1 ATGCAATATGA
38535 ATGCAATA
1 ATGCAATA
38543 CGAGGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.10, G:0.20, T:0.23
Consensus pattern (11 bp):
ATGCAATATGA
Found at i:42933 original size:11 final size:11
Alignment explanation
Indices: 42917--42951 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
42907 AAACCAAAAG
42917 TTCAAATGG-AA
1 TTCAAA-GGTAA
42928 TTCAAAGGTAA
1 TTCAAAGGTAA
42939 TTCAAAGGTAA
1 TTCAAAGGTAA
42950 TT
1 TT
42952 TAAAAGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 2 0.09
11 21 0.91
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (11 bp):
TTCAAAGGTAA
Found at i:46608 original size:16 final size:16
Alignment explanation
Indices: 46587--46622 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
46577 AAATTGGACA
46587 CCAAATTACAACATAT
1 CCAAATTACAACATAT
*
46603 CCAAATTACAACATGT
1 CCAAATTACAACATAT
46619 CCAA
1 CCAA
46623 CCGACCCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.47, C:0.28, G:0.03, T:0.22
Consensus pattern (16 bp):
CCAAATTACAACATAT
Found at i:49729 original size:21 final size:21
Alignment explanation
Indices: 49705--49747 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
49695 TACACATTCC
49705 CATCAATATATATATACATGA
1 CATCAATATATATATACATGA
49726 CATCAATATATATATACATGA
1 CATCAATATATATATACATGA
49747 C
1 C
49748 CACAAGCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (21 bp):
CATCAATATATATATACATGA
Found at i:50480 original size:19 final size:19
Alignment explanation
Indices: 50456--50500 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
50446 TGGGAAAGAA
50456 ACATCTGCCAGTAATTAAC
1 ACATCTGCCAGTAATTAAC
*
50475 ACATCTGTCAGTAATTAAC
1 ACATCTGCCAGTAATTAAC
50494 ACATCTG
1 ACATCTG
50501 AAGGTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (19 bp):
ACATCTGCCAGTAATTAAC
Found at i:51109 original size:258 final size:257
Alignment explanation
Indices: 50586--51281 Score: 927
Period size: 258 Copynumber: 2.7 Consensus size: 257
50576 TTAAAATATT
* * * * * *
50586 TTAAATGAGAAACTTTGAAAAT-AACTTTCTCATTTTCTTACAAATACCATATGAAAGCATCTTG
1 TTAAATGAGAAACTTTGAAAATCAA-TTTCCCA-TTT-TT-CAAAT-TCATGTGAAAACATCATA
* * * *
50650 CTTGAAGGTCTTATAGATGGCTCGAAAGACTTATCATCTTGCTCGAAAGATTGACAGATGACCCG
61 CTTGAAGGTCTTACAGATGGC-CCAAAGACTTATCATATTGCTCGAAAGAATGACAGATGACCCG
* * **
50715 AAGGATTTAATCATTATGCTTGAAAGACTTACTGATGGCCCGAAA-GACTTATTAATTTTGGAAA
125 AAGGATTTAATCATTATGCTCGAAAGACTTACTGATGGCCCCAAAGGACTTACAAATTTTGGAAA
*
50779 TAGTCTACTGGGTAAGAAATTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAA
190 TAGTCTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAA
*
50844 GTA
255 ATA
* * **
50847 TTAAATGAGAAACTTTGAAAATCAATTTCCCATTTTTCAAATTCACGTGAAAACATCCTACCCGA
1 TTAAATGAGAAACTTTGAAAATCAATTTCCCATTTTTCAAATTCATGTGAAAACATCATACTTGA
* * **
50912 AGGTCTTACAGATGGCCCAAAGGACTTATCATATTGCTTGAGAGAATGATTGATGACCCGAAGGA
66 AGGTCTTACAGATGGCCCAAA-GACTTATCATATTGCTCGAAAGAATGACAGATGACCCGAAGGA
* *
50977 TTTAATTATTATGCTCGAAAGACTTACTGATGGCCCCAAAGGACTTACAAATTTTGGAAATAGTT
130 TTTAATCATTATGCTCGAAAGACTTACTGATGGCCCCAAAGGACTTACAAATTTTGGAAATAGTC
51042 TACTGGGTAAGAAACTTTGGAAATCACTTTCTTA-TTCTTCAAAAATTTCATTTTCTGAAAATA
195 TACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTT-TTCAAAAATTTCATTTTCTGAAAATA
* **
51105 TTAAATGGGAAACTTTGAAAATCGCTTTCCCATTTTTCAAATTCATGTGAAAACATCATACTTGA
1 TTAAATGAGAAACTTTGAAAATCAATTTCCCATTTTTCAAATTCATGTGAAAACATCATACTTGA
* * * * *
51170 AGGTTTTAC-GAATGGCTCGAATGACTTATCATCA-TGCTCGAAAGACTTACAGATGACCCGAAG
66 AGGTCTTACAG-ATGGC-CCAAAGACTTATCAT-ATTGCTCGAAAGAATGACAGATGACCCGAAG
* *
51233 GATTTAATCATCATGCTCGAAAGACTTACTGATGG-CCCGAAGGACTTAC
128 GATTTAATCATTATGCTCGAAAGACTTACTGATGGCCCCAAAGGACTTAC
51282 TAAGTAAGAA
Statistics
Matches: 384, Mismatches: 44, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
256 4 0.01
257 120 0.31
258 221 0.58
259 6 0.02
260 3 0.01
261 28 0.07
262 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (257 bp):
TTAAATGAGAAACTTTGAAAATCAATTTCCCATTTTTCAAATTCATGTGAAAACATCATACTTGA
AGGTCTTACAGATGGCCCAAAGACTTATCATATTGCTCGAAAGAATGACAGATGACCCGAAGGAT
TTAATCATTATGCTCGAAAGACTTACTGATGGCCCCAAAGGACTTACAAATTTTGGAAATAGTCT
ACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATA
Found at i:51210 original size:21 final size:21
Alignment explanation
Indices: 51184--51260 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
51174 TTTACGAATG
*
51184 GCTCGAATGACTTATCATCAT
1 GCTCGAAAGACTTATCATCAT
*
51205 GCTCGAAAGACTTA-CA-GAT
1 GCTCGAAAGACTTATCATCAT
* * *
51224 GACCCGAAGGATTTAATCATCAT
1 G-CTCGAAAGACTT-ATCATCAT
51247 GCTCGAAAGACTTA
1 GCTCGAAAGACTTA
51261 CTGATGGCCC
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
19 3 0.07
20 11 0.26
21 15 0.35
22 11 0.26
23 3 0.07
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (21 bp):
GCTCGAAAGACTTATCATCAT
Found at i:51244 original size:42 final size:42
Alignment explanation
Indices: 51197--51276 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
51187 CGAATGACTT
51197 ATCATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTA
1 ATCATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTA
* *
51239 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGA
1 ATCATCATGCTCGAAAGACTTACAGATGACCCGAAGGA
51277 CTTACTAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (42 bp):
ATCATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTA
Found at i:51632 original size:237 final size:237
Alignment explanation
Indices: 51048--51856 Score: 995
Period size: 239 Copynumber: 3.4 Consensus size: 237
51038 AGTTTACTGG
** * * *
51048 GTAAGAAACTTTGGAAATCACTTTCTTAT-TCTTCAAAAATTTCATTTTCTGAAAA-TATTAAAT
1 GTAAGAAACTTTGGAAATCGTTTTCTT-TCTTTTCAAAAATTTCATTTTCAGAAAAGTTTTAAAT
* * * * * *
51111 GGGAAACTTTGAAAATCGCTTTCCCA-TTTTTCAAATTCATGTGAAAACATCATACTTGAAGGT-
65 GAGAAACTTTGGAAATCGCTTTCTCATTTTTTGAAATTCATGTGAAAACATCCT-CCTGAAGGTC
* * * * * * * *
51174 TTTACGAATGGCTCGAATGACTTATCATCATGCTCGAAAGACTTACAGATGACCCGAAGGATTTA
129 TTT-TGGAT-GCCCGAAGGACTTATAATCTTGCTCGAAAGACTGATAGATGACCCGAAGGATTTA
51239 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAA
192 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAA
* * * *
51285 GTAAGAAACTTTGGAAATCGTTTTTCTTACTTCTCAAAATTTTCATTTTCAG-AAAGTATTCAAA
1 GTAAGAAACTTTGGAAATCG-TTTTCTTTCTTTTCAAAAATTTCATTTTCAGAAAAGT-TTTAAA
* * * * * *
51349 TGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAATAATGTGAAAATATCCTGCCTGAAGCT
64 TGAGAAACTTTGGAAATCGCTTTCTCATTTTTTGAAATTCATGTGAAAACATCCT-CCTGAAGGT
* **
51414 CTTTTGGATAGCCCGAAGGACTTATAATCTTTCTTAAAAGACTGATAGATGA-CCGAAGGATTTA
128 CTTTTGGAT-GCCCGAAGGACTTATAATCTTGCTCGAAAGACTGATAGATGACCCGAAGGATTTA
* *
51478 ATCATCATGATCTAAAGACTTACTGATGGCCCGAA-GACTTACTAA
192 ATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAA
* *
51523 GTAAGAAACTTTGGAAATTGTTTTATTTCTTTTCAAAAATTTCATTTTCAGAAAAGTTTTAAATG
1 GTAAGAAACTTTGGAAATCGTTTTCTTTCTTTTCAAAAATTTCATTTTCAGAAAAGTTTTAAATG
*
51588 AGAAACTTTGGAAATCGCTTTCTCATTTTTTGAAATTCATGTGAAAACATCCTACTCGAAGGTCT
66 AGAAACTTTGGAAATCGCTTTCTCATTTTTTGAAATTCATGTGAAAACATCCTCCT-GAAGGTCT
* * * *
51653 TATGGATGACCCGAAGGACTTATTATCTTGCTCGAAAGGCTGATAGATGACCCGAAGAATTTAAT
130 TTTGGATG-CCCGAAGGACTTATAATCTTGCTCGAAAGACTGATAGATGACCCGAAGGATTTAAT
* *
51718 CATCATGCTCGAAAGACTTATTGAT-GCCCTGAAGGACTTACTGA
194 CATCATGCTCGAAAGACTTACTGATGGCCC-GAAGGACTTACTAA
* * * * * * * *
51762 CTAAAAAAATTTGGAAATTGTTTTCTTACTTTTCAAAAACTTCATTTTCAAAAAAGATTTAAATG
1 GTAAGAAACTTTGGAAATCGTTTTCTTTCTTTTCAAAAATTTCATTTTCAGAAAAGTTTTAAATG
*
51827 AGATACTTTGGAAATCGCTTTCTCATTTTT
66 AGAAACTTTGGAAATCGCTTTCTCATTTTT
51857 AAAAATAACT
Statistics
Matches: 491, Mismatches: 69, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
236 3 0.01
237 157 0.32
238 97 0.20
239 167 0.34
240 64 0.13
241 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (237 bp):
GTAAGAAACTTTGGAAATCGTTTTCTTTCTTTTCAAAAATTTCATTTTCAGAAAAGTTTTAAATG
AGAAACTTTGGAAATCGCTTTCTCATTTTTTGAAATTCATGTGAAAACATCCTCCTGAAGGTCTT
TTGGATGCCCGAAGGACTTATAATCTTGCTCGAAAGACTGATAGATGACCCGAAGGATTTAATCA
TCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACTAA
Found at i:51702 original size:41 final size:41
Alignment explanation
Indices: 51657--51757 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 41
51647 AGGTCTTATG
* * *
51657 GATGACCCGAAGGACTTATTATCTTGCTCGAAAGGCTGATA
1 GATGACCCGAAGGACTTATCATCATGCTCGAAAGACTGATA
* * * *
51698 GATGACCCGAAGAATTTAATCATCATGCTCGAAAGACTTATT
1 GATGACCCGAAGGACTT-ATCATCATGCTCGAAAGACTGATA
51740 GATG-CCCTGAAGGACTTA
1 GATGACCC-GAAGGACTTA
51758 CTGACTAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 19 0.39
42 30 0.61
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCATGCTCGAAAGACTGATA
Found at i:61050 original size:22 final size:22
Alignment explanation
Indices: 60985--61040 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
60975 CCGAAACTCC
*
60985 AACTCTA-AA-CTTACAAAAAT
1 AACTCTATAACCTCACAAAAAT
61005 AACTCTATAACCTCACAAAAAT
1 AACTCTATAACCTCACAAAAAT
61027 AACTCTATAACCTC
1 AACTCTATAACCTC
61041 CCCCAAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 7 0.21
21 2 0.06
22 24 0.73
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (22 bp):
AACTCTATAACCTCACAAAAAT
Found at i:61917 original size:2 final size:2
Alignment explanation
Indices: 61910--61941 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
61900 AATTACTTAT
*
61910 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61942 CACATACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:62940 original size:41 final size:42
Alignment explanation
Indices: 62871--62986 Score: 110
Period size: 41 Copynumber: 2.8 Consensus size: 42
62861 TACCATATGA
* * * * *
62871 AATCATCTTGCTCGAAGGTCTTATAGATGGCTCAAAAGACTT
1 AATCATCTTGCTTGAAAGACTTACAGATGGCCCAAAAGACTT
* * * * *
62913 -ATCATCTTGCTTGAAAGACTGACAGATGACCCGAATGATTT
1 AATCATCTTGCTTGAAAGACTTACAGATGGCCCAAAAGACTT
*
62954 AATCAT-TATGCTTGAAAGACTTACTGATGGCCC
1 AATCATCT-TGCTTGAAAGACTTACAGATGGCCC
62987 GAAGTTTCTT
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
41 32 0.54
42 27 0.46
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (42 bp):
AATCATCTTGCTTGAAAGACTTACAGATGGCCCAAAAGACTT
Found at i:64073 original size:2 final size:2
Alignment explanation
Indices: 64066--64134 Score: 76
Period size: 2 Copynumber: 35.5 Consensus size: 2
64056 TAAATTAATG
64066 TA TA TA TA TA TA TA TA TGA T- TA CT- TA -A T- TA CT- TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA -TA TA TA TA TA -TA TA TA TA
64104 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64135 TACCATAAGC
Statistics
Matches: 59, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
1 5 0.08
2 50 0.85
3 4 0.07
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:70870 original size:18 final size:19
Alignment explanation
Indices: 70834--70871 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
70824 TATTCATGAG
70834 GTATCGATACCTGAAGGGTA
1 GTATCGATACC-GAAGGGTA
70854 GTATCGATACC-AAGGGTA
1 GTATCGATACCGAAGGGTA
70872 CTGATACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
GTATCGATACCGAAGGGTA
Found at i:71637 original size:22 final size:22
Alignment explanation
Indices: 71609--71650 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
71599 AGTCGAGGGT
71609 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
71631 TACATAGGTCCTTCGGGACA
1 TACATAGGTCCTTCGGGACA
71651 AATTTCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGACATA
Found at i:75500 original size:25 final size:25
Alignment explanation
Indices: 75466--75548 Score: 123
Period size: 25 Copynumber: 3.4 Consensus size: 25
75456 ACTATAGGAA
*
75466 GGGGAGCCAAGGTTGGAAGAGAGTT
1 GGGGAGCCAAGGTTGGAAGAGAGCT
*
75491 GGGGAGCCAATGTTGGAAGAGAGCT
1 GGGGAGCCAAGGTTGGAAGAGAGCT
75516 -GGGAGCCAAGGTTGGAAGAGAGCT
1 GGGGAGCCAAGGTTGGAAGAGAGCT
* *
75540 AGAGAGCCA
1 GGGGAGCCA
75549 CCTATAAGGA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 23 0.43
25 30 0.57
ACGTcount: A:0.30, C:0.12, G:0.45, T:0.13
Consensus pattern (25 bp):
GGGGAGCCAAGGTTGGAAGAGAGCT
Found at i:79678 original size:13 final size:13
Alignment explanation
Indices: 79660--79684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
79650 CCTGAAGGAA
79660 GAAAAATGAAAAT
1 GAAAAATGAAAAT
79673 GAAAAATGAAAA
1 GAAAAATGAAAA
79685 AATGAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (13 bp):
GAAAAATGAAAAT
Found at i:79687 original size:8 final size:8
Alignment explanation
Indices: 79668--79717 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
79658 AAGAAAAATG
79668 AAAATG-A
1 AAAATGAA
79675 AAAATGAA
1 AAAATGAA
79683 AAAATGAA
1 AAAATGAA
*
79691 AAAAGAGAA
1 AAAA-TGAA
*
79700 AAAAAGAA
1 AAAATGAA
79708 AAAA-GAA
1 AAAATGAA
79715 AAA
1 AAA
79718 GAAAAAACAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
7 12 0.30
8 21 0.52
9 7 0.17
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.06
Consensus pattern (8 bp):
AAAATGAA
Found at i:79688 original size:15 final size:15
Alignment explanation
Indices: 79668--79729 Score: 65
Period size: 16 Copynumber: 4.1 Consensus size: 15
79658 AAGAAAAATG
*
79668 AAAATGAAAAATGAA
1 AAAATGAAAAAAGAA
79683 AAAATGAAAAAAGAGAA
1 AAAATG-AAAAA-AGAA
*
79700 AAAAAGAAAAAAG-A
1 AAAATGAAAAAAGAA
*
79714 AAAA-GAAAAAACAA
1 AAAATGAAAAAAGAA
79728 AA
1 AA
79730 TGGGAGTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
13 7 0.17
14 8 0.20
15 8 0.20
16 10 0.24
17 8 0.20
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.05
Consensus pattern (15 bp):
AAAATGAAAAAAGAA
Found at i:79701 original size:7 final size:7
Alignment explanation
Indices: 79658--79729 Score: 58
Period size: 7 Copynumber: 10.0 Consensus size: 7
79648 TGCCTGAAGG
79658 AAGAAAA
1 AAGAAAA
*
79665 ATG-AAA
1 AAGAAAA
*
79671 ATGAAAA
1 AAGAAAA
*
79678 ATGAAAA
1 AAGAAAA
79685 AATGAAAAA
1 AA-G-AAAA
79694 AGAGAAAAA
1 A-AG-AAAA
79703 AAGAAAA
1 AAGAAAA
79710 AAG-AAA
1 AAGAAAA
79716 AAGAAAA
1 AAGAAAA
*
79723 AACAAAA
1 AAGAAAA
79730 TGGGAGTTCA
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
6 12 0.21
7 29 0.51
8 3 0.05
9 12 0.21
10 1 0.02
ACGTcount: A:0.79, C:0.01, G:0.14, T:0.06
Consensus pattern (7 bp):
AAGAAAA
Found at i:81207 original size:135 final size:135
Alignment explanation
Indices: 80962--81546 Score: 527
Period size: 135 Copynumber: 4.3 Consensus size: 135
80952 GCAAATTGAA
* * * ** * * *
80962 CTCGATTAAATCTTCCCTGAAGAACAGTGGAATAAATCAACGTCCCCATATCTAATTTTCCTTAA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTAATTTTCCCTCA
** * * * ** * * *
81027 AGAAATAGTGGAACAGATC-CCCTCTCTTTTCAGATTTGATCTTCCCTGAGTAGCAATGGAACAA
66 AGAAGCAGCGAAACAAATCACTATCTCTTTCCATATTTGATCTTCCCTGAGTAG-AGTGGAACAA
81091 GTCTGC
130 GTCTGC
* * * * *
81097 CTCGATTCTATTTTCCCTTAAGAACAGTGGAATGAGTTAACATTTCCAGATCTAATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTAATTTTCCCTCA
* * * * * *
81162 AGAAGTAGCGAAACAAATGACTAT-TTTTTCCATATTTGATTTTCCCTAAGGAAGAGTGGAACAA
66 AGAAGCAGCGAAACAAATCACTATCTCTTTCCATATTTGATCTTCCCTGA-GTAGAGTGGAACAA
* *
81226 ATCTAC
130 GTCTGC
* *
81232 CTTGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTAATTTTCCCTCA
* * *
81297 AGAAGCAGCGAAACATATCCCTCTCTCTTTCCATATTTGATCTTCCCTGAGTA-ATTGTGGAACA
66 AGAAGCAGCGAAACAAATCACTATCTCTTTCCATATTTGATCTTCCCTGAGTAGA--GTGGAACA
81361 AGTCTGC
129 AGTCTGC
* * * * * * * * ** *
81368 TTTGGTTCAATCTTCCCTGAAGAACAATGTAATGAATCAATATTT-CATATCTGATTTTTTCTAA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTAATTTTCCCTCA
* * * * * * * * * *
81432 AAAAGCAGGGGAACATATC-C-CTCTCTTTCCAGATTTGTTCTTCCCT-AGGTAACAATGGAACT
66 AGAAGCAGCGAAACAAATCACTATCTCTTTCCATATTTGATCTTCCCTGA-GT-AGAGTGGAACA
*
81494 AGTCTAC
129 AGTCTGC
* *
81501 CTCGATTCAATCTTCCCTGAATAACATTGGAATGAATCAACATTTC
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTC
81547 TCGATCTGAT
Statistics
Matches: 370, Mismatches: 71, Indels: 19
0.80 0.15 0.04
Matches are distributed among these distances:
132 1 0.00
133 76 0.21
134 3 0.01
135 210 0.57
136 80 0.22
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (135 bp):
CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTAATTTTCCCTCA
AGAAGCAGCGAAACAAATCACTATCTCTTTCCATATTTGATCTTCCCTGAGTAGAGTGGAACAAG
TCTGC
Found at i:81535 original size:269 final size:270
Alignment explanation
Indices: 80962--81556 Score: 642
Period size: 270 Copynumber: 2.2 Consensus size: 270
80952 GCAAATTGAA
* * * ** * * *
80962 CTCGATTAAATCTTCCCTGAAGAACAGTGGAATAAATCAACGTCCCCATATCTAATTTTCCTTAA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTAA
* * * * *
81027 AGAAATAGTGGAACAGATCCCCTCTCTTTTCAGATTTGATCTTCCCTGAGTAGCAATGGAACAAG
66 AGAAACAGCGAAACAGATCCCCTCTCTTTCCAGATTTGATCTTCCCTGAGTAACAATGGAACAAG
* * * * * *
81092 TCTGCCTCGATTCTATTTTCCCTTAAGAACAGTGGAATGAGTTAACATTTCCAGATCTAATTTTC
131 TCTGCCTCGATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACATTTCCAGATCTAATTTTC
* * * * * * * * *
81157 CCTCAAGAAGTAGCGAAACAAATGACTATTTTTTCCATATTTGATTTTCCCTAAGGAAGAGTGGA
196 CCTAAAAAAGCAGCGAAACAAATCACTACTCTTTCCAGATTTGATTTTCCCTAAGGAACAATGGA
81222 ACAAATCTAC
261 ACAAATCTAC
* *
81232 CTTGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTAA
* * * ***
81297 AGAAGCAGCGAAACATATCCCTCTCTCTTTCCATATTTGATCTTCCCTGAGTAATTGTGGAACAA
66 AGAAACAGCGAAACAGATCCC-CTCTCTTTCCAGATTTGATCTTCCCTGAGTAACAATGGAACAA
* * * * * * *
81362 GTCTGCTTTGGTTCAATCTTCCCTGAAGAACAATGTAATGAATCAATATTT-CATATCTGATTTT
130 GTCTGCCTCGATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACATTTCCAGATCTAATTTT
** * * * *
81426 TTCTAAAAAAGCAGGGGAACATATCCCT-CTCTTTCCAGATTTG-TTCTTCCCT-AGGTAACAAT
195 CCCTAAAAAAGCAGCGAAACAAATCACTACTCTTTCCAGATTTGATT-TTCCCTAAGG-AACAAT
* *
81488 GGAACTAGTCTAC
258 GGAACAAATCTAC
* *
81501 CTCGATTCAATCTTCCCTGAATAACATTGGAATGAATCAACATTTCTC-GATCTGAT
1 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTC-CAGATCTGAT
81557 CTACACTGAA
Statistics
Matches: 267, Mismatches: 54, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
268 5 0.02
269 84 0.31
270 101 0.38
271 77 0.29
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (270 bp):
CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTAA
AGAAACAGCGAAACAGATCCCCTCTCTTTCCAGATTTGATCTTCCCTGAGTAACAATGGAACAAG
TCTGCCTCGATTCAATCTTCCCTGAAGAACAATGGAATGAATCAACATTTCCAGATCTAATTTTC
CCTAAAAAAGCAGCGAAACAAATCACTACTCTTTCCAGATTTGATTTTCCCTAAGGAACAATGGA
ACAAATCTAC
Found at i:81719 original size:3 final size:3
Alignment explanation
Indices: 81711--81736 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
81701 TTTGTCCCGC
81711 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
81737 ATTTATGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:83878 original size:7 final size:8
Alignment explanation
Indices: 83851--83883 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
83841 CTATATTTAT
83851 TTAAAATA
1 TTAAAATA
83859 TTAAAATA
1 TTAAAATA
83867 TTAAAA-A
1 TTAAAATA
83874 TT-AAATA
1 TTAAAATA
83881 TTA
1 TTA
83884 TATTAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 3 0.13
7 6 0.26
8 14 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TTAAAATA
Found at i:93506 original size:24 final size:24
Alignment explanation
Indices: 93479--93539 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 24
93469 GGAACTCCTC
*
93479 GTCCAAATTACATAAAACTTAAAA
1 GTCCATATTACATAAAACTTAAAA
**
93503 GTCCATATT--ATGTAACTTAAAA
1 GTCCATATTACATAAAACTTAAAA
93525 GTCCATA-TACATAAA
1 GTCCATATTACATAAA
93540 CCAAACATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 1 0.03
22 18 0.60
23 3 0.10
24 8 0.27
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.30
Consensus pattern (24 bp):
GTCCATATTACATAAAACTTAAAA
Found at i:104993 original size:17 final size:17
Alignment explanation
Indices: 104971--105005 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
104961 CTAAAGGTGC
*
104971 CCTATGTTATCTCTAGT
1 CCTATGCTATCTCTAGT
104988 CCTATGCTATCTCTAGT
1 CCTATGCTATCTCTAGT
105005 C
1 C
105006 AATGGACTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.29, G:0.11, T:0.43
Consensus pattern (17 bp):
CCTATGCTATCTCTAGT
Found at i:109748 original size:19 final size:20
Alignment explanation
Indices: 109706--109749 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
109696 AATTTGAATT
*
109706 TTTTATAATAATTAACTTTA
1 TTTTATAATAATTAACTGTA
*
109726 TTTTATAATAATTTA-TGTA
1 TTTTATAATAATTAACTGTA
109745 TTTTA
1 TTTTA
109750 AGTTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTATAATAATTAACTGTA
Found at i:109855 original size:29 final size:26
Alignment explanation
Indices: 109811--109863 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 26
109801 ATAAAATTAA
*
109811 ATTAAAAATATATTTTATTGTTATTT
1 ATTAAAAATATATTTTATTCTTATTT
109837 ATTAAAAATATAATTTTTTATTCTTAT
1 ATTAAAAATAT-A--TTTTATTCTTAT
109864 CTAACATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 11 0.48
27 1 0.04
29 11 0.48
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
ATTAAAAATATATTTTATTCTTATTT
Found at i:110227 original size:118 final size:117
Alignment explanation
Indices: 109878--110234 Score: 378
Period size: 118 Copynumber: 3.1 Consensus size: 117
109868 CATAAAAATA
* * *
109878 TATA-TTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTTATATTATTACACATTT--T---
1 TATACTTTTATCTCATATTAACTTTTAAAATTTAATAAAATTTGTATAATTACACATTTGGTCAA
* * *
109937 TTCAT--TTATACTCTATCAATTTAGT--TGAAATTTTAAAAACTAAAATTAATAA
66 TT-ATACTTATATTCTATCAATTTAGTCAT-AAA-TTTAAAAATTAAAATTAAT-T
* ** * *
109989 TAAAAATATATTCTCATTTTAACTTTTAAAATTTAATAAAATTTGTATAATTACACATTTGGTCA
1 TATACTTTTA-TCTCATATTAACTTTTAAAATTTAATAAAATTTGTATAATTACACATTTGGTCA
* * * * * *
110054 CTTTTACTTATATTCTATCAATTTAGTCCTAATTTTAATAATTAAAATTACTT
65 ATTATACTTATATTCTATCAATTTAGTCATAAATTTAAAAATTAAAATTAATT
* *
110107 TATATTTTTATCTCATATTAA-TTTTAAAATTTAATAAAA-TTGATATAATTACACGTTTGGTCA
1 TATACTTTTATCTCATATTAACTTTTAAAATTTAATAAAATTTG-TATAATTACACATTTGGTCA
*
110170 ATTATACTATTATATTCTATCAATTTAGTCATAAATTTAAAAATTAGAATTAATT
65 ATTATAC--TTATATTCTATCAATTTAGTCATAAATTTAAAAATTAAAATTAATT
110225 TATACTTTTA
1 TATACTTTTA
110235 ATATAATAAT
Statistics
Matches: 205, Mismatches: 27, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
111 3 0.01
112 3 0.01
113 46 0.22
115 4 0.02
116 42 0.20
117 11 0.05
118 58 0.28
119 35 0.17
120 2 0.01
121 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (117 bp):
TATACTTTTATCTCATATTAACTTTTAAAATTTAATAAAATTTGTATAATTACACATTTGGTCAA
TTATACTTATATTCTATCAATTTAGTCATAAATTTAAAAATTAAAATTAATT
Found at i:110558 original size:126 final size:121
Alignment explanation
Indices: 110379--110748 Score: 451
Period size: 122 Copynumber: 3.0 Consensus size: 121
110369 AACTTAAAAA
* * * *
110379 TATATATTTTATATCATCTTAGA-TTTTAAAA-TTATTCAAATTGATATAATTACACATTTGGTC
1 TATATATTTTATACCATATTA-ACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTC
* *
110442 AGTTTGACTTATATATTCTATCAATTTAGTCATAATTTTAATAAATTAAAATTACTT
65 ACTTTGACTTATATATTCTATCAATTTAGTCATAATTTTAATAAATTAAAATTAATT
* * *
110499 TATGTTTTTTACCTCACCCCGTATTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTT
1 TATATATTTTA--T-A--CCATATTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTT
** * * *
110564 TTTCACTTATG-CTTTTATATTCTATCAATTTAGTCATAATTTTAAAAAAATTAGAATTAATT
61 GGTCACTT-TGACTTATATATTCTATCAATTTAGTCATAATTTT-AATAAATTAAAATTAATT
* *
110626 TATATATTTTATATCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTCA
1 TATATATTTTATACCATATTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTCA
* * * *
110691 CTTTTACTTATAGATTCTATCAATTTAGTTC-TAATTTTAATAACTTAAAACTAATT
66 CTTTGACTTATATATTCTATCAATTTAG-TCATAATTTTAATAAATTAAAATTAATT
110747 TA
1 TA
110749 ATCTTTGAAT
Statistics
Matches: 211, Mismatches: 28, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
120 9 0.04
121 17 0.08
122 78 0.37
123 3 0.01
124 2 0.01
125 14 0.07
126 62 0.29
127 26 0.12
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (121 bp):
TATATATTTTATACCATATTAACTTTTAAAATTTAATAAAATTGATATAATTACACATTTGGTCA
CTTTGACTTATATATTCTATCAATTTAGTCATAATTTTAATAAATTAAAATTAATT
Done.