Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007150.1 Hibiscus syriacus cultivar Beakdansim tig00018700_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: 115162
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:4267 original size:15 final size:17
Alignment explanation
Indices: 4242--4275 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
4232 TAAAGGTCCT
4242 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
4258 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
4274 AA
1 AA
4276 CATATTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:4362 original size:25 final size:22
Alignment explanation
Indices: 4333--4378 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
4323 TTTTTAACCC
4333 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
4358 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
4379 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:8132 original size:9 final size:9
Alignment explanation
Indices: 8120--8170 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
8110 TTTTTTGAAA
*
8120 TTTTGGCTT
1 TTTTTGCTT
*
8129 TTTTGGCTT
1 TTTTTGCTT
**
8138 TTTTTTTTGT
1 TTTTTGCT-T
8148 TTTTTGCTT
1 TTTTTGCTT
8157 TTTTTGCTT
1 TTTTTGCTT
8166 TTTTT
1 TTTTT
8171 TTTTCTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
9 29 0.81
10 7 0.19
ACGTcount: A:0.00, C:0.08, G:0.14, T:0.78
Consensus pattern (9 bp):
TTTTTGCTT
Found at i:8140 original size:1 final size:1
Alignment explanation
Indices: 8136--8199 Score: 65
Period size: 1 Copynumber: 64.0 Consensus size: 1
8126 CTTTTTTGGC
* ** ** * *
8136 TTTTTTTTTTGTTTTTTGCTTTTTTTGCTTTTTTTTTTTCTTTTTTTTTCTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
8200 AAAAAAATAG
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.06, G:0.05, T:0.89
Consensus pattern (1 bp):
T
Found at i:8142 original size:28 final size:28
Alignment explanation
Indices: 8110--8171 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
8100 TTGTTTGCAA
8110 TTTTTTGAAATTTTGGCTTTTTTGGCTT
1 TTTTTTGAAATTTTGGCTTTTTTGGCTT
**** * *
8138 TTTTTTTTGTTTTTTGCTTTTTTTGCTT
1 TTTTTTGAAATTTTGGCTTTTTTGGCTT
8166 TTTTTT
1 TTTTTT
8172 TTTCTTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.05, C:0.06, G:0.13, T:0.76
Consensus pattern (28 bp):
TTTTTTGAAATTTTGGCTTTTTTGGCTT
Found at i:8171 original size:10 final size:10
Alignment explanation
Indices: 8127--8193 Score: 59
Period size: 10 Copynumber: 6.7 Consensus size: 10
8117 AAATTTTGGC
*
8127 TTTTTTGGCT
1 TTTTTTTGCT
8137 TTTTTTT--T
1 TTTTTTTGCT
8145 TGTTTTTTGC-
1 T-TTTTTTGCT
8155 TTTTTTTGCTTT
1 TTTTTTTGC--T
*
8167 TTTTTTTTCT
1 TTTTTTTGCT
*
8177 TTTTTTTTCT
1 TTTTTTTGCT
8187 TTTTTTT
1 TTTTTTT
8194 TTTTTTAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
8 2 0.04
9 14 0.29
10 25 0.51
12 8 0.16
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (10 bp):
TTTTTTTGCT
Found at i:8172 original size:28 final size:28
Alignment explanation
Indices: 8120--8173 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
8110 TTTTTTGAAA
8120 TTTTGGCTTTTTTGGCTTTTTTTTTTGT
1 TTTTGGCTTTTTTGGCTTTTTTTTTTGT
* *
8148 TTTTTGCTTTTTTTGCTTTTTTTTTT
1 TTTTGGCTTTTTTGGCTTTTTTTTTT
8174 TCTTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.00, C:0.07, G:0.13, T:0.80
Consensus pattern (28 bp):
TTTTGGCTTTTTTGGCTTTTTTTTTTGT
Found at i:8174 original size:29 final size:28
Alignment explanation
Indices: 8120--8181 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
8110 TTTTTTGAAA
* *
8120 TTTTGGCTTTTTTGGCTTTTTTTTTTGT
1 TTTTTGCTTTTTTGGCTTTTTTTTTTCT
*
8148 TTTTTGCTTTTTTTGCTTTTTTTTTTTCT
1 TTTTTGCTTTTTTGGC-TTTTTTTTTTCT
8177 TTTTT
1 TTTTT
8182 TTTCTTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 14 0.47
29 16 0.53
ACGTcount: A:0.00, C:0.08, G:0.11, T:0.81
Consensus pattern (28 bp):
TTTTTGCTTTTTTGGCTTTTTTTTTTCT
Found at i:8179 original size:28 final size:27
Alignment explanation
Indices: 8120--8199 Score: 89
Period size: 28 Copynumber: 3.1 Consensus size: 27
8110 TTTTTTGAAA
* *
8120 TTTTGGCTTTTTTGGCTTTTTTTTTTGT
1 TTTTTGCTTTTTTTGCTTTTTTTTTT-T
8148 TTTTTGCTTTTTTTGC--TTTTTTTTT
1 TTTTTGCTTTTTTTGCTTTTTTTTTTT
*
8173 TTCTT--TTTTTTT-CTTTTTTTTTTT
1 TTTTTGCTTTTTTTGCTTTTTTTTTTT
8197 TTT
1 TTT
8200 AAAAAAATAG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
22 1 0.02
23 7 0.15
24 11 0.24
25 5 0.11
26 8 0.17
28 14 0.30
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (27 bp):
TTTTTGCTTTTTTTGCTTTTTTTTTTT
Found at i:9073 original size:25 final size:22
Alignment explanation
Indices: 9044--9089 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
9034 TTTTTAACCC
9044 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
9069 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
9090 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:10991 original size:60 final size:56
Alignment explanation
Indices: 10892--11066 Score: 154
Period size: 60 Copynumber: 2.9 Consensus size: 56
10882 ATATGATCTC
* *
10892 TATTTTAAATTAGTCCCTAAACTTTTAA-ATAATCTAATTTTATCCCTAAACTATAACTA
1 TATTCTAAATTAGTCCC-AAACTTTTAACAT-TTC-AATTTTATCCC-AAACTATAACTA
* * *
10951 TCATTCTAAATTAGTCCTCAAACTTTTGAACATTTCAATTTTATCCCCAACCCATGACCTA
1 T-ATTCTAAATTAGTCC-CAAACTTTT-AACATTTCAATTTTAT-CCCAAACTAT-AACTA
* * * *
11012 TATTTTAAATTAGTCCCCAAACTTTTTAAACATTCCAATTTCATCCCAAATTATA
1 TATTCTAAATTAGT-CCCAAAC-TTTT-AACATTTCAATTTTATCCCAAACTATA
11067 TGTATATACT
Statistics
Matches: 96, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
59 2 0.02
60 59 0.61
61 33 0.34
62 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.39
Consensus pattern (56 bp):
TATTCTAAATTAGTCCCAAACTTTTAACATTTCAATTTTATCCCAAACTATAACTA
Found at i:13832 original size:2 final size:2
Alignment explanation
Indices: 13820--13849 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
13810 TTGGTTAAAC
13820 TA TA T- 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
13850 CAATTTCGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:26207 original size:22 final size:22
Alignment explanation
Indices: 26181--26230 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
26171 ATGATGTTCA
26181 CATTTCTTTTAAGGTTTTATTT
1 CATTTCTTTTAAGGTTTTATTT
*
26203 CATTTCTTTTAGGGTTTTATTT
1 CATTTCTTTTAAGGTTTTATTT
*
26225 CGTTTC
1 CATTTC
26231 ATATTTATAT
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:0.14, C:0.12, G:0.12, T:0.62
Consensus pattern (22 bp):
CATTTCTTTTAAGGTTTTATTT
Found at i:27873 original size:21 final size:21
Alignment explanation
Indices: 27849--27916 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
27839 GGAAACGGAT
27849 TGAAAGG-TTAAGACCTTTCGA
1 TGAAAGGATTAA-ACCTTTCGA
* *
27870 TGAAAGGATTTAACCTTTTGA
1 TGAAAGGATTAAACCTTTCGA
*
27891 TGAAAGGGATT-AACCTTTTGA
1 TGAAA-GGATTAAACCTTTCGA
27912 TGAAA
1 TGAAA
27917 TGGCTTAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 35 0.81
22 8 0.19
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.32
Consensus pattern (21 bp):
TGAAAGGATTAAACCTTTCGA
Found at i:27924 original size:21 final size:20
Alignment explanation
Indices: 27861--27935 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 20
27851 AAAGGTTAAG
*
27861 ACCTTTCGATGAAAGGATTTA
1 ACCTTTTGATGAAAGGA-TTA
27882 ACCTTTTGATGAAAGGGATTA
1 ACCTTTTGATGAAA-GGATTA
*
27903 ACCTTTTGATGAAATGGCTTA
1 ACCTTTTGATGAAA-GGATTA
* *
27924 ATCTTTTCATGA
1 ACCTTTTGATGA
27936 TGGGAATTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 45 0.94
22 3 0.06
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
ACCTTTTGATGAAAGGATTA
Found at i:30250 original size:28 final size:27
Alignment explanation
Indices: 30194--30255 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
30184 AGAAAATCAT
30194 AAAAAAAAAGAAATTAAAGCACTCCAA
1 AAAAAAAAAGAAATTAAAGCACTCCAA
** **
30221 AAGAAAAAAAGAAATTCCAGCACTTTAA
1 AA-AAAAAAAGAAATTAAAGCACTCCAA
30249 AAAAAAA
1 AAAAAAA
30256 GAAAAGAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 7 0.23
28 23 0.77
ACGTcount: A:0.66, C:0.13, G:0.08, T:0.13
Consensus pattern (27 bp):
AAAAAAAAAGAAATTAAAGCACTCCAA
Found at i:30260 original size:5 final size:5
Alignment explanation
Indices: 30247--30283 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
30237 CCAGCACTTT
*
30247 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG -AAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
30284 GTTGAAGCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:36691 original size:3 final size:3
Alignment explanation
Indices: 36683--36736 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
36673 ATATATATAT
36683 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
36730 -TA TTA TT
1 TTA TTA TT
36737 CTAGAGCGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.08
3 45 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:36937 original size:7 final size:7
Alignment explanation
Indices: 36927--36998 Score: 51
Period size: 7 Copynumber: 10.6 Consensus size: 7
36917 TCCTAATTCC
36927 TAAATCT
1 TAAATCT
36934 TAAATC-
1 TAAATCT
36940 TAAATCT
1 TAAATCT
* *
36947 TAAACCA
1 TAAATCT
* * *
36954 CAAACCC
1 TAAATCT
36961 TAAATCT
1 TAAATCT
36968 TAAATC-
1 TAAATCT
* *
36974 TAAACCC
1 TAAATCT
36981 TAAAT-T
1 TAAATCT
36987 CTAAATCT
1 -TAAATCT
36995 TAAA
1 TAAA
36999 CCCTAAACAC
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
6 11 0.22
7 39 0.76
8 1 0.02
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (7 bp):
TAAATCT
Found at i:36944 original size:13 final size:13
Alignment explanation
Indices: 36926--36950 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36916 GTCCTAATTC
36926 CTAAATCTTAAAT
1 CTAAATCTTAAAT
36939 CTAAATCTTAAA
1 CTAAATCTTAAA
36951 CCACAAACCC
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
CTAAATCTTAAAT
Found at i:36963 original size:21 final size:20
Alignment explanation
Indices: 36939--36985 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
36929 AATCTTAAAT
36939 CTAAATCTTAAACCACAAACC
1 CTAAATCTTAAACC-CAAACC
* *
36960 CTAAATCTTAAATCTAAACC
1 CTAAATCTTAAACCCAAACC
36980 CTAAAT
1 CTAAAT
36986 TCTAAATCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.26
Consensus pattern (20 bp):
CTAAATCTTAAACCCAAACC
Found at i:36977 original size:27 final size:28
Alignment explanation
Indices: 36925--36998 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
36915 AGTCCTAATT
* *
36925 CCTAAATCTTAAATC-TAAATCTTAAAC
1 CCTAAACCCTAAATCTTAAATCTTAAAC
36952 CAC-AAACCCTAAATCTTAAATC-TAAAC
1 C-CTAAACCCTAAATCTTAAATCTTAAAC
**
36979 CCTAAATTCTAAATCTTAAA
1 CCTAAACCCTAAATCTTAAA
36999 CCCTAAACAC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
26 1 0.03
27 32 0.80
28 7 0.17
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (28 bp):
CCTAAACCCTAAATCTTAAATCTTAAAC
Found at i:37000 original size:21 final size:21
Alignment explanation
Indices: 36955--37005 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
36945 CTTAAACCAC
36955 AAACCCTAAATCTTAAATC-T
1 AAACCCTAAATCTTAAATCTT
36975 AAACCCTAAAT-TCTAAATCTT
1 AAACCCTAAATCT-TAAATCTT
36996 AAACCCTAAA
1 AAACCCTAAA
37006 CACTAACCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.03
20 17 0.59
21 11 0.38
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (21 bp):
AAACCCTAAATCTTAAATCTT
Found at i:37004 original size:14 final size:14
Alignment explanation
Indices: 36955--37005 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
36945 CTTAAACCAC
36955 AAACCCTAAATCTT
1 AAACCCTAAATCTT
* * *
36969 AAA-TCTAAACCCT
1 AAACCCTAAATCTT
**
36982 AAATTCTAAATCTT
1 AAACCCTAAATCTT
36996 AAACCCTAAA
1 AAACCCTAAA
37006 CACTAACCAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (14 bp):
AAACCCTAAATCTT
Found at i:37011 original size:21 final size:19
Alignment explanation
Indices: 36955--37011 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
36945 CTTAAACCAC
*
36955 AAACCCTAAATCTTAAATCT
1 AAACCCTAAA-CCTAAATCT
*
36975 AAACCCTAAATTCTAAATCTT
1 AAACCCTAAA-CCTAAATC-T
36996 AAACCCTAAACACTAA
1 AAACCCTAAAC-CTAA
37012 CCATACAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (19 bp):
AAACCCTAAACCTAAATCT
Found at i:40951 original size:40 final size:40
Alignment explanation
Indices: 40888--40968 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
40878 ATAGGAGTCA
* * *
40888 AATATTGCACCGAAGTGCCGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAAGTGCCGAGGTCGAGCTTTACCCACCT
* * *
40928 AATAATGCACCGTAGTGCTGAGGTCGGGCTTTACCCACCT
1 AATAATGCACCGAAGTGCCGAGGTCGAGCTTTACCCACCT
40968 A
1 A
40969 GTACACCGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCCGAGGTCGAGCTTTACCCACCT
Found at i:58126 original size:21 final size:20
Alignment explanation
Indices: 58102--58159 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 20
58092 ATCCTCGCTA
58102 TGTATCGATACACTATGAATG
1 TGTATCGATACACT-TGAATG
*
58123 TGTACCGATACATTCCTTGAATG
1 TGTATCGATACA---CTTGAATG
58146 TGTATCGATACACT
1 TGTATCGATACACT
58160 CAAGAGTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 2 0.06
21 11 0.34
23 17 0.53
24 2 0.06
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (20 bp):
TGTATCGATACACTTGAATG
Found at i:58672 original size:13 final size:13
Alignment explanation
Indices: 58654--58687 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
58644 TATTATGATG
58654 TTTCAAACAATA-T
1 TTTCAAA-AATAGT
58667 TTTCAAAAATAGT
1 TTTCAAAAATAGT
58680 TTTCAAAA
1 TTTCAAAA
58688 TTGCCCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (13 bp):
TTTCAAAAATAGT
Found at i:68521 original size:47 final size:45
Alignment explanation
Indices: 68453--68577 Score: 162
Period size: 47 Copynumber: 2.8 Consensus size: 45
68443 ATAAAATCTA
*
68453 TTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * *
68498 TTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATAC
1 TTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * *
68545 TTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTT
68578 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 23 0.32
45 9 0.13
46 2 0.03
47 37 0.52
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:68726 original size:40 final size:40
Alignment explanation
Indices: 68682--68803 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
68672 ACCGTAGTGC
*
68682 TACACATAAGGTCGTTCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
68722 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
68762 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
68802 TA
1 TA
68804 TAAACCTGCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:72570 original size:6 final size:6
Alignment explanation
Indices: 72554--72658 Score: 70
Period size: 6 Copynumber: 17.3 Consensus size: 6
72544 TCTCTCATTT
* * * *
72554 TTTTCTC TTTTTC -TTTTC TTTCTC GTTTTC ATTTT- TTTTTC TTCTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* * * * * * *
72601 GTTTTC ATTTTC ATTTTC ATTTTC TATTTTT TTTTTC TTCTTC TGTTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC T-TTTTC
72651 TTTTTC TT
1 TTTTTC TT
72659 CTTATAATAT
Statistics
Matches: 78, Mismatches: 16, Indels: 9
0.76 0.16 0.09
Matches are distributed among these distances:
5 9 0.12
6 56 0.72
7 13 0.17
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:72593 original size:23 final size:24
Alignment explanation
Indices: 72561--72611 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
72551 TTTTTTTCTC
72561 TTTTTCTTTTCTT-TCTCGTTTTCA
1 TTTTTCTTTTCTTCT-TCGTTTTCA
72585 TTTTT-TTTTCTTCTTCGTTTTCA
1 TTTTTCTTTTCTTCTTCGTTTTCA
72608 TTTT
1 TTTT
72612 CATTTTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.75
Consensus pattern (24 bp):
TTTTTCTTTTCTTCTTCGTTTTCA
Found at i:72593 original size:29 final size:29
Alignment explanation
Indices: 72561--72617 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
72551 TTTTTTTCTC
*
72561 TTTTTCTT-TTC-TTTCTCGTTTTCATTTT
1 TTTTTCTTCTTCGTTT-TCATTTTCATTTT
72589 TTTTTCTTCTTCGTTTTCATTTTCATTTT
1 TTTTTCTTCTTCGTTTTCATTTTCATTTT
72618 CATTTTCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 8 0.31
29 15 0.58
30 3 0.12
ACGTcount: A:0.05, C:0.18, G:0.04, T:0.74
Consensus pattern (29 bp):
TTTTTCTTCTTCGTTTTCATTTTCATTTT
Found at i:72606 original size:35 final size:34
Alignment explanation
Indices: 72538--72623 Score: 102
Period size: 34 Copynumber: 2.5 Consensus size: 34
72528 AAATATTTTT
* *
72538 TTTTCATCTCTCATTTTTTTCTCTTTTTCTTTTC-
1 TTTTCAT-TTTCATTTTTTTCTCTTCTTCTTTTCA
* *
72572 TTTCTCGTTTTCATTTTTTTTTCTTCTTCGTTTTCA
1 TTT-TCATTTTCATTTTTTTCTCTTCTTC-TTTTCA
72608 TTTTCATTTTCATTTT
1 TTTTCATTTTCATTTT
72624 CTATTTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
34 21 0.48
35 20 0.45
36 3 0.07
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (34 bp):
TTTTCATTTTCATTTTTTTCTCTTCTTCTTTTCA
Found at i:72636 original size:19 final size:19
Alignment explanation
Indices: 72559--72656 Score: 73
Period size: 19 Copynumber: 5.4 Consensus size: 19
72549 CATTTTTTTC
*
72559 TCTTTTTC-TTTTCT-TTC
1 TCTTTTTCATTTTCTATTT
*
72576 TCGTTTTCATTTT-T-TTT
1 TCTTTTTCATTTTCTATTT
* *
72593 TCTTCTTCGTTTTC-ATTT
1 TCTTTTTCATTTTCTATTT
*
72611 TCATTTTCATTTTCTATTT
1 TCTTTTTCATTTTCTATTT
* *
72630 TTTTTTTC-TTCTTCTGTTT
1 TCTTTTTCATT-TTCTATTT
*
72649 TTTTTTTC
1 TCTTTTTC
72657 TTCTTATAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
17 20 0.31
18 20 0.31
19 25 0.38
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.74
Consensus pattern (19 bp):
TCTTTTTCATTTTCTATTT
Found at i:72641 original size:16 final size:17
Alignment explanation
Indices: 72629--72660 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
72619 ATTTTCTATT
72629 TTTTTTTTCTTCTTCTG
1 TTTTTTTTCTTCTTCTG
72646 TTTTTTTT-TTCTTCT
1 TTTTTTTTCTTCTTCT
72661 TATAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTTTTTTCTTCTTCTG
Found at i:72657 original size:19 final size:19
Alignment explanation
Indices: 72585--72661 Score: 75
Period size: 19 Copynumber: 3.8 Consensus size: 19
72575 CTCGTTTTCA
*
72585 TTTTTTTTTCTTCTTCGTTT
1 TTTTTTTTTCTTCTTC-TAT
72605 TCATTTTCATTTTCATT-TTCTAT
1 T--TTTT--TTTTC-TTCTTCTAT
*
72628 TTTTTTTTTCTTCTTCTGT
1 TTTTTTTTTCTTCTTCTAT
72647 TTTTTTTTTCTTCTT
1 TTTTTTTTTCTTCTT
72662 ATAATATATA
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
18 2 0.04
19 25 0.51
20 1 0.02
21 4 0.08
22 4 0.08
23 3 0.06
24 8 0.16
25 2 0.04
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.77
Consensus pattern (19 bp):
TTTTTTTTTCTTCTTCTAT
Found at i:73766 original size:6 final size:6
Alignment explanation
Indices: 73755--73785 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
73745 ACACTTGTAT
73755 CATGAC CATGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC CATGAC C
73786 TATGGGTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.35, G:0.16, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:75599 original size:47 final size:45
Alignment explanation
Indices: 75529--75654 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
75519 TATAAAATCT
*
75529 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
75574 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
75621 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
75655 GCATGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 37 0.51
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:75814 original size:40 final size:40
Alignment explanation
Indices: 75759--75880 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
75749 ACCGTAGTGC
75759 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
*
75799 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
75839 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
75879 TA
1 TA
75881 TAAACCTGCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:83811 original size:20 final size:20
Alignment explanation
Indices: 83786--83831 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
83776 GTCTGATTGC
* *
83786 TCCTCTACTCGTTATATCAT
1 TCCTCTACTCATTATAGCAT
83806 TCCTCTACTCATTATAGCAT
1 TCCTCTACTCATTATAGCAT
83826 TCCTCT
1 TCCTCT
83832 GCTTTTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.33, G:0.04, T:0.43
Consensus pattern (20 bp):
TCCTCTACTCATTATAGCAT
Found at i:90183 original size:183 final size:183
Alignment explanation
Indices: 89875--90224 Score: 628
Period size: 183 Copynumber: 1.9 Consensus size: 183
89865 ATTAAATCCG
89875 TAAAGCTGAGCTATTCCACTAAGGCAATTGATTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGATTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
89940 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTGCTT
90005 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCGGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCGGTGATTTGTCCCTC
*
90058 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGATTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
90123 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTGTTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTGCTT
*
90188 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTT
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTT
90225 TAGTTAAACC
Statistics
Matches: 159, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
183 159 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGATTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCAGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCGGTGATTTGTCCCTC
Found at i:91414 original size:36 final size:36
Alignment explanation
Indices: 91307--91422 Score: 99
Period size: 36 Copynumber: 3.2 Consensus size: 36
91297 ATGCAGATGA
** * *
91307 TTATCTCACTTGAGATTGTTTTTCTTAGAACAGA-CT
1 TTATCTCACTCAAGATTGTTTTTCTTAAAACA-ATAT
* * * ** *
91343 TTGTCTCACTTAAGATTGTTTTACTCGAAAGAATAT
1 TTATCTCACTCAAGATTGTTTTTCTTAAAACAATAT
* *
91379 TTATTTCCCTCAAGATTGTTTTTCTTAAAACAATATT
1 TTATCTCACTCAAGATTGTTTTTCTTAAAACAATA-T
91416 TTATCTC
1 TTATCTC
91423 GCTTGAGATA
Statistics
Matches: 61, Mismatches: 17, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
35 1 0.02
36 53 0.87
37 7 0.11
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (36 bp):
TTATCTCACTCAAGATTGTTTTTCTTAAAACAATAT
Found at i:91569 original size:37 final size:37
Alignment explanation
Indices: 91502--91588 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
91492 ATTGAAAACA
** * *
91502 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
91538 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
91575 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
91589 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 12 0.27
37 33 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:91591 original size:102 final size:105
Alignment explanation
Indices: 91407--91654 Score: 369
Period size: 102 Copynumber: 2.4 Consensus size: 105
91397 TTTTTCTTAA
* * * *
91407 AACAATATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACA
1 AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGACA
*
91472 GTTTCTCTTTAAACATAAACATTGAAAACATTTCCCTT-G
66 GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
* * *
91511 AA-ATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAA-TTTTGTCTCCCTTGAGAC
1 AACA-AAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGAC
91573 AGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
65 AGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
* *
91614 AACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
91655 TAAACATTGA
Statistics
Matches: 130, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
102 55 0.42
103 40 0.31
104 35 0.27
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (105 bp):
AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTGAGACA
GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
Found at i:91644 original size:66 final size:66
Alignment explanation
Indices: 91538--91717 Score: 278
Period size: 66 Copynumber: 2.8 Consensus size: 66
91528 CTTGAGATAG
*
91538 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
91603 A
66 A
*
91604 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
91669 A
66 A
* * *
91670 TTTCCCTT-GAA-ATAAA--TTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
91718 AAATTTTGTC
Statistics
Matches: 108, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
63 29 0.27
64 1 0.01
65 6 0.06
66 72 0.67
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (66 bp):
TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
A
Found at i:91713 original size:34 final size:36
Alignment explanation
Indices: 91669--91754 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 36
91659 CATTGAAAGC
* * *
91669 ATTTCCCTTGAAA-TAAA-TTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACA
*
91703 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAAA-TTTGTCTCCCTTGAGACA
*
91740 ATTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
91755 TAAACATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
34 12 0.28
35 3 0.07
37 28 0.65
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACA
Found at i:91732 original size:100 final size:102
Alignment explanation
Indices: 91604--91883 Score: 467
Period size: 100 Copynumber: 2.8 Consensus size: 102
91594 ATTGAAAACA
* *
91604 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAGC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
91669 ATTTCCCTTGAAAT-AA-ATTGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAG
*
91704 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
*
91769 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAG
* * *
91806 TTTCCCTTGAAAC-AAATTTTGTCTCCTTTGAGACAGTTTCTATTGAAACATAAACTTTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
91870 AGTTTCCCTTGAAA
66 A-TTTCCCTTGAAA
91884 CAAAATCTTT
Statistics
Matches: 169, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
100 76 0.45
101 50 0.30
102 43 0.25
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAG
Found at i:91747 original size:166 final size:169
Alignment explanation
Indices: 91434--91819 Score: 622
Period size: 166 Copynumber: 2.3 Consensus size: 169
91424 CTTGAGATAG
* * *
91434 TTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAGTTTCTCTTTAAACATAAACATTGAAA
1 TTTCCCTTGGAACAGAAA-TTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
*
91499 ACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
65 ACATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTC
*
91564 CCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
130 CCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
* *
91604 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAG
1 TTTCCCTTGGAACAGAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
91668 CATTTCCCTTGAAAT-AA-ATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
66 CATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
91731 CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
131 CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
* * *
91770 TTTCCCTT-GAA-ATG-AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-GAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACA
91820 AATTTTGTCT
Statistics
Matches: 204, Mismatches: 10, Indels: 9
0.91 0.04 0.04
Matches are distributed among these distances:
164 1 0.00
165 36 0.18
166 91 0.45
167 2 0.01
168 59 0.29
169 3 0.01
170 12 0.06
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (169 bp):
TTTCCCTTGGAACAGAAATTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
CATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
Found at i:91817 original size:36 final size:36
Alignment explanation
Indices: 91770--91855 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
91760 ATTGAAAACA
** *
91770 TTTCCCTTGAAATGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACAG
91806 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
**
91842 TTTCTATTGAAACA
1 TTTCCCTTGAAACA
91856 TAAACTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 42 0.95
37 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
Found at i:91873 original size:30 final size:30
Alignment explanation
Indices: 91838--91896 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
91828 CTCCTTTGAG
*
91838 ACAGTTTCTATTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCATTGAAACA-AAATCTTTGAAA
*
91868 ACAGTTTCCCTTGAAACAAAATCTTTGAA
1 ACAGTTTCCATTGAAACAAAATCTTTGAA
91897 TATGTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (30 bp):
ACAGTTTCCATTGAAACAAAATCTTTGAAA
Found at i:91961 original size:36 final size:36
Alignment explanation
Indices: 91910--92024 Score: 149
Period size: 36 Copynumber: 3.1 Consensus size: 36
91900 GTTTTACATT
* *
91910 AAACAAATTTCGTCTCTCTTGAGACGGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
91946 AAACAAATTTTGTCTCTCTTAAGACATGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTG
* *
91983 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTATTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
92020 AAACA
1 AAACA
92025 TCAATCCTTG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
36 24 0.36
37 23 0.34
38 20 0.30
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:92113 original size:36 final size:35
Alignment explanation
Indices: 92066--92154 Score: 137
Period size: 33 Copynumber: 2.6 Consensus size: 35
92056 CCTTGATACA
*
92066 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAA-AAACCTTTGAAAAT
*
92102 GTTTCTCTTGAAACGC--AAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
92135 GTTTCTCTTGAAACACAAAA
1 GTTTCTCTTGAAACACAAAA
92155 CCTTTGAGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
33 28 0.58
34 3 0.06
35 2 0.04
36 15 0.31
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.30
Consensus pattern (35 bp):
GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
Found at i:92130 original size:33 final size:32
Alignment explanation
Indices: 92066--92179 Score: 140
Period size: 31 Copynumber: 3.4 Consensus size: 32
92056 CCTTGATACA
92066 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAAC-C--AAA-AAACCTTTGAAATT
*
92102 GTTTCTCTTGAAACGCAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAAC-CAAAAAACCTTTGAAATT
* *
92135 GTTTCTCTTGAAA-CACAAAACCTTTGAGATT
1 GTTTCTCTTGAAACCAAAAAACCTTTGAAATT
*
92166 GTTTCCCTTGAAAC
1 GTTTCTCTTGAAAC
92180 AAATTTCATC
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
31 27 0.38
33 26 0.37
34 3 0.04
36 15 0.21
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.32
Consensus pattern (32 bp):
GTTTCTCTTGAAACCAAAAAACCTTTGAAATT
Found at i:92227 original size:67 final size:67
Alignment explanation
Indices: 92135--92321 Score: 221
Period size: 67 Copynumber: 2.7 Consensus size: 67
92125 CTTTGAAAAT
*
92135 GTTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTCATCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCATCTCCCTTGAGA
92200 CA
66 CA
* * * **
92202 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCCTTAAAACAAAATTTTGTCTCCCTTGAG
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAAC-AAATTTCATCTCCCTTGAG
* *
92267 GCT
65 ACA
* ** * * *
92270 GTTTCTCATGAAACAACATTTATCTTTAAGATCGTTTCCCTTGAAACGAATT
1 GTTTCTCTTGAAAC-ACA-AAATCTTTGAGATTGTTTCCCTTGAAACAAATT
92322 CTGTCTTTTT
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
67 41 0.41
68 31 0.31
69 7 0.07
70 21 0.21
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (67 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCATCTCCCTTGAGA
CA
Found at i:92833 original size:106 final size:107
Alignment explanation
Indices: 92640--92872 Score: 326
Period size: 106 Copynumber: 2.2 Consensus size: 107
92630 GGTTTTAGCT
*
92640 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
** * *
92705 CGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCCCAATTTC
66 CGAAGGGACGGCTGACTATCAACAAAACAATTTCCCAATTCC
* ** * *
92746 GGAGCCAATTTCAACTTCACATTGAAGTG-CATTGGACTCGAGACAGCACAAGTTCAACTTCACA
1 AGAGCCAATTTCAACTTCACAGCGAAG-GACATTGGACTCAAGACAACACAAGTTCAACTTCACA
*
92810 ACGAAGGGACGGCTGACTATCAACAAAACAATTTCCCAGTTCC
65 ACGAAGGGACGGCTGACTATCAACAAAACAATTTCCCAATTCC
* *
92853 AGAACCAACTTCAACTTCAC
1 AGAGCCAATTTCAACTTCAC
92873 GACAGAAGAT
Statistics
Matches: 111, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
106 77 0.69
107 34 0.31
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.21
Consensus pattern (107 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGGCTGACTATCAACAAAACAATTTCCCAATTCC
Found at i:94471 original size:20 final size:21
Alignment explanation
Indices: 94430--94471 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
94420 GTTTTATATA
94430 TTTCTATATATATTTCTTATT
1 TTTCTATATATATTTCTTATT
94451 TTTCTAT-TATTATTT-TTATT
1 TTTCTATATA-TATTTCTTATT
94471 T
1 T
94472 AATACTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTCTATATATATTTCTTATT
Found at i:98727 original size:183 final size:183
Alignment explanation
Indices: 98419--98768 Score: 637
Period size: 183 Copynumber: 1.9 Consensus size: 183
98409 ATTAAATCCG
98419 TAAAGCTGAGCTATTCCACTAAGGCAATTGATTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGATTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** *
98484 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
98549 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCGGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCGGTGATTTGTCCCTC
*
98602 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGATTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* *
98667 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGTTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
98732 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTT
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTT
98769 TAGTTAAACC
Statistics
Matches: 160, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 160 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGATTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCGGTGATTTGTCCCTC
Found at i:100122 original size:37 final size:37
Alignment explanation
Indices: 100047--100133 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 37
100037 ATTGAAAACA
** * * *
100047 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTCAGACAG
100083 TTTCCCTTGAAACAAAATTTTGTCTCCCTTCAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTCAGACAG
*
100120 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
100134 TAAACATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 12 0.27
37 32 0.73
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTCAGACAG
Found at i:100141 original size:102 final size:105
Alignment explanation
Indices: 99952--100199 Score: 351
Period size: 102 Copynumber: 2.4 Consensus size: 105
99942 TTTTTCTTAA
* * * * * * *
99952 AACAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTGTCACTTGAGACT
1 AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTCAGACA
*
100017 GTTTCTCTTTAAACATAAACATTGAAAACATTTCCCTT-G
66 GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
* * *
100056 AA-ATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAA-TTTTGTCTCCCTTCAGAC
1 AACA-AAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTCAGAC
100118 AGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
65 AGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
*
100159 AACAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACA
1 AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACA
100200 TAAACATTGA
Statistics
Matches: 128, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
102 52 0.41
103 41 0.32
104 35 0.27
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (105 bp):
AACAAAATTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAGAAAGTTTTGTCTCACTTCAGACA
GTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGG
Found at i:100189 original size:66 final size:66
Alignment explanation
Indices: 100083--100262 Score: 269
Period size: 66 Copynumber: 2.8 Consensus size: 66
100073 CTTGAGATAG
* * *
100083 TTTCCCTTGAAACAAAATTTTGTCTCCCTTCAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
100148 A
66 A
*
100149 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAGC
1 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
100214 A
66 A
* *
100215 TTTCCCTT-GAA-ATAAA--TTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACA
100263 AAATTTTGTC
Statistics
Matches: 107, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
63 30 0.28
64 1 0.01
65 6 0.06
66 70 0.65
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.36
Consensus pattern (66 bp):
TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
A
Found at i:100258 original size:34 final size:36
Alignment explanation
Indices: 100214--100299 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 36
100204 CATTGAAAGC
* * *
100214 ATTTCCCTTGAAA-TAAA-TTGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACA
*
100248 GTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAAA-TTTGTCTCCCTTGAGACA
*
100285 ATTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
100300 TAAACATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
34 12 0.28
35 3 0.07
37 28 0.65
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACA
Found at i:100277 original size:100 final size:102
Alignment explanation
Indices: 100149--100428 Score: 458
Period size: 100 Copynumber: 2.8 Consensus size: 102
100139 ATTGAAAACA
* * *
100149 TTTCCCTTGGAACAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAGC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
100214 ATTTCCCTTGAAAT-AA-ATTGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAG
*
100249 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
*
100314 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
66 ATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAG
* * *
100351 TTTCCCTTGAAAC-AAATTTTGTCTCCTTTGAGACAGTTTCTATTGAAACATAAACTTTGAAAAC
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
100415 AGTTTCCCTTGAAA
66 A-TTTCCCTTGAAA
100429 CAAAATCTTT
Statistics
Matches: 168, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
100 75 0.45
101 50 0.30
102 43 0.26
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAG
Found at i:100292 original size:166 final size:169
Alignment explanation
Indices: 99979--100364 Score: 597
Period size: 166 Copynumber: 2.3 Consensus size: 169
99969 CTTGAGATAG
* * * *
99979 TTTCCCTCGAAACAGAAAGTTTTGTGTCACTTGAGACT-GTTTCTCTTTAAACATAAACATTGAA
1 TTTCCCTTGGAACAGAAA-TTTTGTCTCACTTGAGA-TAGTTTCTCTTGAAACATAAACATTGAA
*
100043 AACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCT
64 AACATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCT
*
100108 CCCTTCAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
129 CCCTTCAGACAATTTCTCTTGAAACATAAACATTGAAAACA
* *
100149 TTTCCCTTGGAACA-AAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAG
1 TTTCCCTTGGAACAGAAATTTTGTCTCACTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAA
100213 CATTTCCCTTGAAAT-AA-ATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
66 CATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
*
100276 CTTGAGACAATTTCTCTTGAAACATAAACATTGAAAACA
131 CTTCAGACAATTTCTCTTGAAACATAAACATTGAAAACA
* *
100315 TTTCCCTT-GAA-ATG-AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTTCCCTTGGAACA-GAAATTTTGTCTCACTTGAGATAGTTTCTCTTGAAACA
100365 AATTTTGTCT
Statistics
Matches: 202, Mismatches: 11, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
164 1 0.00
165 37 0.18
166 90 0.45
167 3 0.01
168 56 0.28
169 3 0.01
170 12 0.06
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (169 bp):
TTTCCCTTGGAACAGAAATTTTGTCTCACTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAA
CATTTCCCTTGAAATGAATATTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCC
CTTCAGACAATTTCTCTTGAAACATAAACATTGAAAACA
Found at i:100362 original size:36 final size:36
Alignment explanation
Indices: 100315--100400 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
100305 ATTGAAAACA
** *
100315 TTTCCCTTGAAATGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCT-TTGAGACAG
100351 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
**
100387 TTTCTATTGAAACA
1 TTTCCCTTGAAACA
100401 TAAACTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
36 42 0.95
37 2 0.05
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCTTTGAGACAG
Found at i:100418 original size:30 final size:30
Alignment explanation
Indices: 100383--100441 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
100373 CTCCTTTGAG
*
100383 ACAGTTTCTATTGAAACATAAA-CTTTGAAA
1 ACAGTTTCCATTGAAACA-AAATCTTTGAAA
*
100413 ACAGTTTCCCTTGAAACAAAATCTTTGAA
1 ACAGTTTCCATTGAAACAAAATCTTTGAA
100442 TATGTTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (30 bp):
ACAGTTTCCATTGAAACAAAATCTTTGAAA
Found at i:100537 original size:38 final size:36
Alignment explanation
Indices: 100455--100569 Score: 158
Period size: 36 Copynumber: 3.1 Consensus size: 36
100445 GTTTTACATT
* *
100455 AAACAAATTTCGTCTCTCTTGAGACGGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
100491 AAACAAATTTTGTCTCTCTTAAGACATGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTG
*
100528 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
100565 AAACA
1 AAACA
100570 TCAATCCTTG
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 24 0.35
37 24 0.35
38 20 0.29
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:100675 original size:33 final size:33
Alignment explanation
Indices: 100611--100725 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
100601 CCTTGATACA
100611 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACAC--AAA-AAACCTTTGAAATT
*
100647 GTTTCTCTTGAAACACAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
100680 GTTTCTCTTGAAACAC--AAAACCTTTGAGATT
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
*
100711 GTTTCCCTTGAAACA
1 GTTTCTCTTGAAACA
100726 AATTTCGTCT
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 27 0.36
33 29 0.39
34 3 0.04
36 16 0.21
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.32
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATT
Found at i:100772 original size:67 final size:67
Alignment explanation
Indices: 100680--100866 Score: 230
Period size: 67 Copynumber: 2.7 Consensus size: 67
100670 CTTTGAAAAT
*
100680 GTTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
100745 CA
66 CA
* * * *
100747 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCCTTAAAACAAAATTTTGTCTCCCTTGAG
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAAC-AAATTTCGTCTCCCTTGAG
* *
100812 GCC
65 ACA
* ** * * *
100815 GTTTCTCATGAAACAACATTTATCTTTAAGATCGTTTCCCTTGAAACGAATT
1 GTTTCTCTTGAAAC-ACA-AAATCTTTGAGATTGTTTCCCTTGAAACAAATT
100867 CTGTATTTTT
Statistics
Matches: 101, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
67 41 0.41
68 32 0.32
69 7 0.07
70 21 0.21
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (67 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGA
CA
Found at i:101048 original size:14 final size:14
Alignment explanation
Indices: 101029--101067 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
101019 TCAGAACTTG
*
101029 AAGATTCTAGAACT
1 AAGATTCCAGAACT
101043 AAGATTCCAGAACT
1 AAGATTCCAGAACT
101057 AAGATTCCAGA
1 AAGATTCCAGA
101068 GAAGCAACCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (14 bp):
AAGATTCCAGAACT
Found at i:101389 original size:106 final size:107
Alignment explanation
Indices: 101198--101430 Score: 342
Period size: 106 Copynumber: 2.2 Consensus size: 107
101188 GGTTTTAGCT
*
101198 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
** *
101263 CGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCCCAATTTC
66 CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
* ** * * *
101304 GGAGCCAATTTCAACTTCACATTGAAGGGCATTGGACTCGAGACAGCACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
*
101369 CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAGTTCC
66 CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
* *
101411 AGAACCAACTTCAACTTCAC
1 AGAGCCAATTTCAACTTCAC
101431 GACAGAAGAT
Statistics
Matches: 112, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
106 79 0.71
107 33 0.29
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (107 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
Found at i:102783 original size:2 final size:2
Alignment explanation
Indices: 102776--102802 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
102766 TTAATATTAG
102776 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
102803 TAAGTATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:103019 original size:20 final size:21
Alignment explanation
Indices: 102969--103019 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
102959 TTATATTTTG
*
102969 TTCTATATATTTCTATATATAT
1 TTCT-TATTTTTCTATATATAT
102991 TTCTTATTTTTCTAT-TATTAT
1 TTCTTATTTTTCTATATA-TAT
103012 TT-TTATTT
1 TTCTTATTT
103020 AATACTATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 8 0.30
21 15 0.56
22 4 0.15
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.69
Consensus pattern (21 bp):
TTCTTATTTTTCTATATATAT
Found at i:106732 original size:2 final size:2
Alignment explanation
Indices: 106712--106750 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
106702 TCTTATAATT
* * *
106712 TA TA TA CA TA CA TA CA 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 TA TA TA TA T
106751 TATTTTCTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:109344 original size:125 final size:125
Alignment explanation
Indices: 109129--109365 Score: 341
Period size: 125 Copynumber: 1.9 Consensus size: 125
109119 CTATCAAAGC
* * * * *
109129 AATGGAACAAAAGAATGTTAGAGGTGCCTAACATTGGCTCTAGCATTAAACAAGGAGAAATACTG
1 AATGGAACAAAAGAATATTAGAGGTACCCAACATTGGCACTAGCATTAAACAAGGAGAAATACTA
109194 GAGATGCCCAACATTAGCTCCAGCAAAGGAATAAAGTTAAAAAAATGGCTTTAGTAATGA
66 GAGATGCCCAACATTAGCTCCAGCAAAGGAATAAAGTTAAAAAAATGGCTTTAGTAATGA
* *
109254 AATGGAACAAAATAATATTAGAGGTACCCAACATTGGCACTAGCATTAAACAATGAGAAATACTA
1 AATGGAACAAAAGAATATTAGAGGTACCCAACATTGGCACTAGCATTAAACAAGGAGAAATACTA
* * * * * *
109319 GAGGA-GCCCGATATTGGGTCTAGCAAAGGAATAAAGTTAAAATAATG
66 GA-GATGCCCAACATTAGCTCCAGCAAAGGAATAAAGTTAAAAAAATG
109366 TTGCTACAAC
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
125 96 0.98
126 2 0.02
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (125 bp):
AATGGAACAAAAGAATATTAGAGGTACCCAACATTGGCACTAGCATTAAACAAGGAGAAATACTA
GAGATGCCCAACATTAGCTCCAGCAAAGGAATAAAGTTAAAAAAATGGCTTTAGTAATGA
Found at i:109587 original size:17 final size:17
Alignment explanation
Indices: 109565--109601 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
109555 AGAACTAAAT
*
109565 AATGAGTTAAAAATCTG
1 AATGAGTTAAAAATATG
109582 AATGAGTTAAAAATATG
1 AATGAGTTAAAAATATG
109599 AAT
1 AAT
109602 TGGGGTCGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.16, T:0.30
Consensus pattern (17 bp):
AATGAGTTAAAAATATG
Found at i:109881 original size:3 final size:3
Alignment explanation
Indices: 109873--109906 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
109863 TTTCATCCCA
109873 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
109907 AATAATTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:110010 original size:23 final size:24
Alignment explanation
Indices: 109935--110010 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
109925 TTTATTACAG
* * * *
109935 GCCCAATTATAAAGCATACCAGGA
1 GCCCAGTTACAAAGCAAACCCGGA
* * *
109959 GCCTAGTTACAAAGCAGACCCGAA
1 GCCCAGTTACAAAGCAAACCCGGA
* *
109983 CCCCAGTTAC-AAGCAAACTCGGA
1 GCCCAGTTACAAAGCAAACCCGGA
110006 GCCCA
1 GCCCA
110011 ACAAGTCACC
Statistics
Matches: 40, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
23 14 0.35
24 26 0.65
ACGTcount: A:0.37, C:0.32, G:0.18, T:0.13
Consensus pattern (24 bp):
GCCCAGTTACAAAGCAAACCCGGA
Done.