Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008629.1 Hibiscus syriacus cultivar Beakdansim tig00111598_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: 200978
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5894 original size:16 final size:16
Alignment explanation
Indices: 5870--5902 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5860 TATCGCCGAC
*
5870 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
5886 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
5902 C
1 C
5903 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:10170 original size:20 final size:19
Alignment explanation
Indices: 10147--10193 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
10137 CAAAGAACAT
10147 TATCAATA-TTGTTCTTTCAG
1 TATCAATACTT-TT-TTTCAG
* *
10167 TATCGATACTTTTTTTTAG
1 TATCAATACTTTTTTTCAG
10186 TATCAATA
1 TATCAATA
10194 ATCATGACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 12 0.52
20 9 0.39
21 2 0.09
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (19 bp):
TATCAATACTTTTTTTCAG
Found at i:10795 original size:21 final size:21
Alignment explanation
Indices: 10762--10827 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 21
10752 TCATGAAGTC
* *
10762 ACTCAACCACTTTAGGTATTGAT
1 ACTCAAGC-CTTTA-GTATGGAT
10785 A-TCAAGCCTTTAGTATGGAT
1 ACTCAAGCCTTTAGTATGGAT
* *
10805 ACTCAA-TCTTTGGTATGGAT
1 ACTCAAGCCTTTAGTATGGAT
10825 ACT
1 ACT
10828 AGTCCTCTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 23 0.61
21 9 0.24
22 5 0.13
23 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (21 bp):
ACTCAAGCCTTTAGTATGGAT
Found at i:10862 original size:20 final size:20
Alignment explanation
Indices: 10839--10907 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
10829 GTCCTCTAAT
*
10839 ATGGAGACCAATTTTTCAGG
1 ATGGAGACCAATTTTTCTGG
10859 ATGGAGACC-ATTTATT-TGG
1 ATGGAGACCAATTT-TTCTGG
*
10878 TATGGAGA-CAAGTTTTTCTGT
1 -ATGGAGACCAA-TTTTTCTGG
10899 ATGGAGACC
1 ATGGAGACC
10908 CAGTGATCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
19 7 0.17
20 28 0.68
21 6 0.15
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (20 bp):
ATGGAGACCAATTTTTCTGG
Found at i:11029 original size:26 final size:26
Alignment explanation
Indices: 11000--11050 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
10990 GGAGGTACCG
*
11000 ATACCTATACTCTAGTATCGATACTT
1 ATACCTATACTCCAGTATCGATACTT
*
11026 ATACCTATACTCCATTATCGATACT
1 ATACCTATACTCCAGTATCGATACT
11051 GAAGCCCTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.37
Consensus pattern (26 bp):
ATACCTATACTCCAGTATCGATACTT
Found at i:16452 original size:20 final size:20
Alignment explanation
Indices: 16429--16496 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
16419 TCCTCTAGTT
16429 TGGAGACCAGTTTTTCGGTA
1 TGGAGACCAGTTTTTCGGTA
* * *
16449 TGGAGACCA-TTCCTCCGGTT
1 TGGAGACCAGTT-TTTCGGTA
** *
16469 TGGAGATAAGTTTTTCAGTA
1 TGGAGACCAGTTTTTCGGTA
16489 TGGAGACC
1 TGGAGACC
16497 CAGTGGTCTC
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
19 2 0.06
20 31 0.89
21 2 0.06
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (20 bp):
TGGAGACCAGTTTTTCGGTA
Found at i:16463 original size:40 final size:40
Alignment explanation
Indices: 16405--16496 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
16395 TCAAGCCTTT
* * *
16405 GGTATGGATACCAGTCCTCTAGTTTGGAGACCAGTTTTTC
1 GGTATGGAGACCAGTCCTCCAGTTTGGAGACAAGTTTTTC
* * *
16445 GGTATGGAGACCATTCCTCCGGTTTGGAGATAAGTTTTTC
1 GGTATGGAGACCAGTCCTCCAGTTTGGAGACAAGTTTTTC
*
16485 AGTATGGAGACC
1 GGTATGGAGACC
16497 CAGTGGTCTC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (40 bp):
GGTATGGAGACCAGTCCTCCAGTTTGGAGACAAGTTTTTC
Found at i:39312 original size:31 final size:31
Alignment explanation
Indices: 39274--39360 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
39264 CCCGAAAGAC
* *
39274 AGTCCATAGGTCCCGAAAAACCTAGGTAATA
1 AGTCCATATGTCCCGAAAAACATAGGTAATA
* *
39305 AGTCCATATGTCCCGAAGAACATAGGTAATC
1 AGTCCATATGTCCCGAAAAACATAGGTAATA
*
39336 AGTCCATATGTCCCGAAGAACATAG
1 AGTCCATATGTCCCGAAAAACATAG
39361 ATAACCCTCG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (31 bp):
AGTCCATATGTCCCGAAAAACATAGGTAATA
Found at i:44128 original size:63 final size:63
Alignment explanation
Indices: 44024--44155 Score: 167
Period size: 63 Copynumber: 2.1 Consensus size: 63
44014 CTTCACTGGT
* *
44024 GTATCGGTACACTGCCTATGTATCGGTACACAAATTACATTCG-TAATTTTCCATTTCAAGGGG
1 GTATCGATACACTGCCTATGTATCGGTACACAAATTACATTCGATAATTTTCCA-TTCAAGAGG
* ** * ** *
44087 GTATCGATACACTTCCTATGTATCGGTACACTTATTGCATTCGATGTTTTTTCATTCAAGAGG
1 GTATCGATACACTGCCTATGTATCGGTACACAAATTACATTCGATAATTTTCCATTCAAGAGG
44150 GTATCG
1 GTATCG
44156 GTACCTAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 52 0.88
64 7 0.12
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (63 bp):
GTATCGATACACTGCCTATGTATCGGTACACAAATTACATTCGATAATTTTCCATTCAAGAGG
Found at i:56202 original size:41 final size:39
Alignment explanation
Indices: 56145--56251 Score: 124
Period size: 41 Copynumber: 2.7 Consensus size: 39
56135 ATTCGAGCCT
*
56145 CACCGAAGTGCTTACGCATAAGGTTGCATTAACCCTTTTCG
1 CACCGAAGTGCTTACGCATAAGGTTGCATCAACCC-TTT-G
* ** * *
56186 CACCGAAGTGCTTACGCAGAAGGTTGTGTCGATCCTTTG
1 CACCGAAGTGCTTACGCATAAGGTTGCATCAACCCTTTG
* *
56225 CATCGAAGTACTTACGCATAAGGTTGC
1 CACCGAAGTGCTTACGCATAAGGTTGC
56252 GTCGATCACT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 24 0.43
40 3 0.05
41 29 0.52
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (39 bp):
CACCGAAGTGCTTACGCATAAGGTTGCATCAACCCTTTG
Found at i:56248 original size:39 final size:41
Alignment explanation
Indices: 56145--56258 Score: 142
Period size: 39 Copynumber: 2.8 Consensus size: 41
56135 ATTCGAGCCT
* ** *
56145 CACCGAAGTGCTTACGCATAAGGTTGCATTAACCCTTTTCG
1 CACCGAAGTGCTTACGCATAAGGTTGCGTCGATCCTTTTCG
* *
56186 CACCGAAGTGCTTACGCAGAAGGTTGTGTCGATCC-TTT-G
1 CACCGAAGTGCTTACGCATAAGGTTGCGTCGATCCTTTTCG
* *
56225 CATCGAAGTACTTACGCATAAGGTTGCGTCGATC
1 CACCGAAGTGCTTACGCATAAGGTTGCGTCGATC
56259 ACTGAAGTTC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
39 31 0.49
40 3 0.05
41 29 0.46
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (41 bp):
CACCGAAGTGCTTACGCATAAGGTTGCGTCGATCCTTTTCG
Found at i:60281 original size:12 final size:12
Alignment explanation
Indices: 60264--60289 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
60254 GATTTGTCTC
60264 CTTTTGCATATT
1 CTTTTGCATATT
60276 CTTTTGCATATT
1 CTTTTGCATATT
60288 CT
1 CT
60290 GAAATACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.19, G:0.08, T:0.58
Consensus pattern (12 bp):
CTTTTGCATATT
Found at i:60880 original size:2 final size:2
Alignment explanation
Indices: 60873--60906 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
60863 TCAATCTACA
60873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60907 TTACGAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61118 original size:13 final size:13
Alignment explanation
Indices: 61069--61120 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
61059 AATGACGCTC
61069 AATGCACGTCATA
1 AATGCACGTCATA
*
61082 AATGAACGTCATA
1 AATGCACGTCATA
***
61095 AATGTGTGTCATA
1 AATGCACGTCATA
*
61108 AATGCGCGTCATA
1 AATGCACGTCATA
61121 GATTTATGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (13 bp):
AATGCACGTCATA
Found at i:61728 original size:55 final size:55
Alignment explanation
Indices: 61644--61752 Score: 209
Period size: 55 Copynumber: 2.0 Consensus size: 55
61634 CTGGCTCATC
61644 GCAAGCCAATGTTTGTTCGATAACATAAGTACAAATTAAAATTGCACTCACCTGT
1 GCAAGCCAATGTTTGTTCGATAACATAAGTACAAATTAAAATTGCACTCACCTGT
*
61699 GCAAGCCAATGTTTGTTTGATAACATAAGTACAAATTAAAATTGCACTCACCTG
1 GCAAGCCAATGTTTGTTCGATAACATAAGTACAAATTAAAATTGCACTCACCTG
61753 GTGTCCTCAG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (55 bp):
GCAAGCCAATGTTTGTTCGATAACATAAGTACAAATTAAAATTGCACTCACCTGT
Found at i:72707 original size:20 final size:20
Alignment explanation
Indices: 72674--72712 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
72664 TCAAATACAA
**
72674 AAAATAATGTTAATATTAAC
1 AAAATAATAATAATATTAAC
*
72694 AAAATAATAATAATTTTAA
1 AAAATAATAATAATATTAA
72713 AATATTAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (20 bp):
AAAATAATAATAATATTAAC
Found at i:72776 original size:21 final size:19
Alignment explanation
Indices: 72752--72795 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
72742 TATGTCAATA
72752 TTATTAAATATATATAAAATT
1 TTATTAAA-ATAT-TAAAATT
72773 TTA-TAAAATATTAAAATT
1 TTATTAAAATATTAAAATT
*
72791 ATATT
1 TTATT
72796 TTATTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 9 0.43
19 5 0.24
20 4 0.19
21 3 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTATTAAAATATTAAAATT
Found at i:72810 original size:21 final size:23
Alignment explanation
Indices: 72770--72813 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
72760 TATATATAAA
72770 ATTTTATAAAATATTAAAATTAT
1 ATTTTATAAAATATTAAAATTAT
*
72793 ATTTTATTAAA-A-TAAAATTAT
1 ATTTTATAAAATATTAAAATTAT
72814 TATTACTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 1 0.05
23 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTTATAAAATATTAAAATTAT
Found at i:73029 original size:26 final size:26
Alignment explanation
Indices: 72981--73035 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
72971 ATAATCACCT
72981 TATTATAATTTTAAAATAAA-ATATAA
1 TATTATAATTTTAAAATAAATAT-TAA
73007 TATTATATATTTTAATAAT-AATATTAA
1 TATTATA-ATTTTAA-AATAAATATTAA
73034 TA
1 TA
73036 ATAAAAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 7 0.27
27 14 0.54
28 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TATTATAATTTTAAAATAAATATTAA
Found at i:73044 original size:18 final size:18
Alignment explanation
Indices: 72985--73044 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
72975 TCACCTTATT
*
72985 ATAATTTTAA-AATAAAA
1 ATAATATTAATAATAAAA
* *
73002 TATAATATTATATATTTTAATA
1 -ATAATATTA-ATA--ATAAAA
73024 ATAATATTAATAATAAAA
1 ATAATATTAATAATAAAA
73042 ATA
1 ATA
73045 CAATACATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
18 15 0.45
19 1 0.03
20 4 0.12
21 9 0.27
22 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATATTAATAATAAAA
Found at i:73111 original size:11 final size:11
Alignment explanation
Indices: 73095--73134 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
73085 TGAATATTTT
73095 TATTAAAATTA
1 TATTAAAATTA
*
73106 TATTAAAATAA
1 TATTAAAATTA
73117 TATT-AAATTA
1 TATTAAAATTA
73127 TATATAAA
1 TAT-TAAA
73135 TAATAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 8 0.32
11 15 0.60
12 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TATTAAAATTA
Found at i:73126 original size:21 final size:21
Alignment explanation
Indices: 73095--73144 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
73085 TGAATATTTT
73095 TATTAAAATTATAT-TAAAATAA
1 TATT-AAATTATATAT-AAATAA
73117 TATTAAATTATATATAAATAA
1 TATTAAATTATATATAAATAA
*
73138 TAATAAA
1 TATTAAA
73145 ATGTTTTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATTAAATTATATATAAATAA
Found at i:74371 original size:29 final size:29
Alignment explanation
Indices: 74322--74412 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
74312 CAAATTTTAG
* * *
74322 TTAGTGACAAAAATGTGAATTTTGAAAGT
1 TTAGTGACCAAAATATAAATTTTGAAAGT
** *
74351 TTAGTGGTCAAAGTATAAATTTTGGAAAGGT
1 TTAGTGACCAAAATATAAATTTT-GAAA-GT
* * *
74382 TCAGTGACCAAAATATAATTTTTAAAAGT
1 TTAGTGACCAAAATATAAATTTTGAAAGT
74411 TT
1 TT
74413 TAAATTTTGG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
29 20 0.43
30 7 0.15
31 20 0.43
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (29 bp):
TTAGTGACCAAAATATAAATTTTGAAAGT
Found at i:74402 original size:30 final size:29
Alignment explanation
Indices: 74320--74411 Score: 78
Period size: 31 Copynumber: 3.1 Consensus size: 29
74310 CTCAAATTTT
* * *
74320 AGTT-AGTGACAAAAATGTGAATTTTGAA
1 AGTTCAGTGACCAAAATATAAATTTTGAA
* ** *
74348 AGTTTAGTGGTCAAAGTATAAATTTTGGAA
1 AGTTCAGTGACCAAAATATAAATTTT-GAA
* *
74378 AGGTTCAGTGACCAAAATATAATTTTTAAA
1 A-GTTCAGTGACCAAAATATAAATTTTGAA
74408 AGTT
1 AGTT
74412 TTAAATTTTG
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
28 4 0.08
29 18 0.37
30 7 0.14
31 20 0.41
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (29 bp):
AGTTCAGTGACCAAAATATAAATTTTGAA
Found at i:75995 original size:24 final size:24
Alignment explanation
Indices: 75944--75996 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
75934 CATAATTCAA
* *
75944 GTCAAGTAGCAGATCATAATCCAT
1 GTCAAGTAGCAGATCAAAATCCAG
* * *
75968 GTCAAGTATCATATCAAAATCTAG
1 GTCAAGTAGCAGATCAAAATCCAG
75992 GTCAA
1 GTCAA
75997 AAATCAGATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (24 bp):
GTCAAGTAGCAGATCAAAATCCAG
Found at i:76771 original size:29 final size:29
Alignment explanation
Indices: 76709--76884 Score: 180
Period size: 29 Copynumber: 6.2 Consensus size: 29
76699 ACACAATTAT
*
76709 CACCCTTTTAAGAAATATTTACGAAAATAA
1 CACCCTTTTAA-AAATAATTACGAAAATAA
* * *
76739 CACCCTTTTAAAAATAATTATGAATATAT
1 CACCCTTTTAAAAATAATTACGAAAATAA
*
76768 CACCATTTTAAAAATAATTACGAAAATAA
1 CACCCTTTTAAAAATAATTACGAAAATAA
** * *
76797 CACATTTTTAAAAAAAATTACGAAAATAG
1 CACCCTTTTAAAAATAATTACGAAAATAA
* *
76826 CA--CTCTT-AAAA-AATTACAAAAATAA
1 CACCCTTTTAAAAATAATTACGAAAATAA
* * * *
76851 CACCATTTTCAAAATAATTATGAAAATAT
1 CACCCTTTTAAAAATAATTACGAAAATAA
76880 CACCC
1 CACCC
76885 GGTCAACGGT
Statistics
Matches: 120, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
25 14 0.12
26 4 0.03
27 6 0.05
28 4 0.03
29 81 0.68
30 11 0.09
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.30
Consensus pattern (29 bp):
CACCCTTTTAAAAATAATTACGAAAATAA
Found at i:76797 original size:58 final size:57
Alignment explanation
Indices: 76706--76883 Score: 211
Period size: 58 Copynumber: 3.1 Consensus size: 57
76696 TTTACACAAT
* * *
76706 TATCACCCTTTTAAGAAATATTTACGAAAATAACACCCTTTTAAAAATAATTATGAATA
1 TATCA-CCTTTTAA-AAATAATTACGAAAATAACACCATTTTAAAAATAATTATGAAAA
* *
76765 TATCACCATTTTAAAAATAATTACGAAAATAACA-CATTTTTAAAAAAAATTACGAAAA
1 TATCACC-TTTTAAAAATAATTACGAAAATAACACCA-TTTTAAAAATAATTATGAAAA
* * * *
76823 TAGCA-CTCTT-AAAA-AATTACAAAAATAACACCATTTTCAAAATAATTATGAAAA
1 TATCACCTTTTAAAAATAATTACGAAAATAACACCATTTTAAAAATAATTATGAAAA
76877 TATCACC
1 TATCACC
76884 CGGTCAACGG
Statistics
Matches: 103, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
54 37 0.36
55 7 0.07
56 3 0.03
57 2 0.02
58 43 0.42
59 11 0.11
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.30
Consensus pattern (57 bp):
TATCACCTTTTAAAAATAATTACGAAAATAACACCATTTTAAAAATAATTATGAAAA
Found at i:77852 original size:188 final size:186
Alignment explanation
Indices: 77503--77876 Score: 696
Period size: 188 Copynumber: 2.0 Consensus size: 186
77493 TAACATGGTT
* *
77503 TTGCTGACACTTCTAGGGTAAATTCAGGGCTTGGTCCCTGAATTTCATTTATCTCTAAATAGACT
1 TTGCCGACACTTCTAGGGTAAATTCAGGGCTTGGTCCCTAAATTTCATTTATCTCTAAATAGACT
77568 ACAAGTTTTGAGAACTTTTAATTTAGTCCCCAATTCACCAAATTACTTAATTAAATCCTCAATTT
66 ACAAGTTTTGAGAACTTTTAATTTAGTCCCCAATTCACCAAATTACTTAATTAAATCCTCAATTT
77633 CAATTAATATATATTTTTTTCAAAATTTTGGGTTGTTACAATTCTCCCGTTACAAG
131 CAATTAATATATATTTTTTTCAAAATTTTGGGTTGTTACAATTCTCCCGTTACAAG
77689 TTGCCGACACTTCTAGGGTAAATTCAGGGCTTGGTCCCTAAATTTCATTTATCTCTAAAATAGAC
1 TTGCCGACACTTCTAGGGTAAATTCAGGGCTTGGTCCCTAAATTTCATTTATCTCT-AAATAGAC
77754 TACAAGTTTTGAGAACTTTTAATTTAGTCCCCAATTTCACCAAATTACTTAATTAAATCCTCAAA
65 TACAAGTTTTGAGAACTTTTAATTTAGTCCCCAA-TTCACCAAATTACTTAATTAAATCCTC-AA
77819 TTTCAATTAA-ATATATTTTTTTCAAAATTTTGGGTTGTTACAATTCTCCCGTTACAAG
128 TTTCAATTAATATATATTTTTTTCAAAATTTTGGGTTGTTACAATTCTCCCGTTACAAG
77877 AAATTTCATC
Statistics
Matches: 183, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
186 54 0.30
187 42 0.23
188 75 0.41
189 12 0.07
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (186 bp):
TTGCCGACACTTCTAGGGTAAATTCAGGGCTTGGTCCCTAAATTTCATTTATCTCTAAATAGACT
ACAAGTTTTGAGAACTTTTAATTTAGTCCCCAATTCACCAAATTACTTAATTAAATCCTCAATTT
CAATTAATATATATTTTTTTCAAAATTTTGGGTTGTTACAATTCTCCCGTTACAAG
Found at i:83404 original size:24 final size:24
Alignment explanation
Indices: 83315--83398 Score: 141
Period size: 24 Copynumber: 3.5 Consensus size: 24
83305 TGCAGATCAG
* *
83315 AATCCATGTCATGTATCATATAAA
1 AATCCAGGTCAAGTATCATATAAA
83339 AATCCAGGTCAAGTATCATATAAA
1 AATCCAGGTCAAGTATCATATAAA
*
83363 AATCCAGGTCAAGTATCATATCAA
1 AATCCAGGTCAAGTATCATATAAA
83387 AATCCAGGTCAA
1 AATCCAGGTCAA
83399 AAATCAGATA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 57 1.00
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCATATAAA
Found at i:83410 original size:48 final size:48
Alignment explanation
Indices: 83315--83410 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
83305 TGCAGATCAG
* * ** *
83315 AATCCATGTCATGTATCATATAAAAATCCAGGTCAAGTATCATATAAA
1 AATCCAGGTCAAGTATCATATAAAAATCCAGGTCAAAAATCAGATAAA
*
83363 AATCCAGGTCAAGTATCATATCAAAATCCAGGTCAAAAATCAGATAAA
1 AATCCAGGTCAAGTATCATATAAAAATCCAGGTCAAAAATCAGATAAA
83411 CTATTCATGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (48 bp):
AATCCAGGTCAAGTATCATATAAAAATCCAGGTCAAAAATCAGATAAA
Found at i:84092 original size:26 final size:26
Alignment explanation
Indices: 84037--84111 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 26
84027 AATAACACCC
* * *
84037 TTTTAAAAATAATTATGAATATATCA-
1 TTTTAAAAATAATTACGAA-AAAACAT
84063 TTTTAAAAATAATTACGAAAAAACATTT
1 TTTTAAAAATAATTACGAAAAAACA--T
*
84091 TTTTAAAAAAAATTACGAAAA
1 TTTTAAAAATAATTACGAAAA
84112 TAGAACTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.10
26 18 0.43
28 20 0.48
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (26 bp):
TTTTAAAAATAATTACGAAAAAACAT
Found at i:84121 original size:28 final size:28
Alignment explanation
Indices: 84063--84165 Score: 88
Period size: 28 Copynumber: 3.8 Consensus size: 28
84053 GAATATATCA
* * * **
84063 TTTTAAAAATAATTACGAAAAAACATTT
1 TTTTAAAAAAAATTACGAAAATAGAACT
84091 TTTTAAAAAAAATTACGAAAATAGAACT
1 TTTTAAAAAAAATTACGAAAATAGAACT
* * *
84119 TTTT--AAAAAATTGC-AAAATAG-CCA
1 TTTTAAAAAAAATTACGAAAATAGAACT
* *
84143 TTTCAAAAATAATTACGAAAATA
1 TTTTAAAAAAAATTACGAAAATA
84166 TCACCCGATC
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
24 4 0.07
25 7 0.11
26 17 0.28
27 6 0.10
28 27 0.44
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (28 bp):
TTTTAAAAAAAATTACGAAAATAGAACT
Found at i:84126 original size:26 final size:26
Alignment explanation
Indices: 84096--84165 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
84086 CATTTTTTTA
*
84096 AAAAAAATTACGAAAATAGA-ACTTTT
1 AAAAAAATTACGAAAATAGACA-TTTC
* * *
84122 TAAAAAATTGC-AAAATAGCCATTTC
1 AAAAAAATTACGAAAATAGACATTTC
84147 AAAAATAATTACGAAAATA
1 AAAAA-AATTACGAAAATA
84166 TCACCCGATC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
25 14 0.40
26 15 0.43
27 6 0.17
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (26 bp):
AAAAAAATTACGAAAATAGACATTTC
Found at i:87838 original size:15 final size:13
Alignment explanation
Indices: 87807--87851 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
87797 GATAAAATGT
87807 ATATAT-ATATGA
1 ATATATGATATGA
87819 ATATATGAATATGTA
1 ATATATG-ATATG-A
87834 ATATATGATATGA
1 ATATATGATATGA
*
87847 GTATA
1 ATATA
87852 AATACAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 6 0.21
13 5 0.17
14 10 0.34
15 8 0.28
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (13 bp):
ATATATGATATGA
Found at i:92648 original size:20 final size:20
Alignment explanation
Indices: 92623--92660 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
92613 AAACTTTTGA
* *
92623 AAAGTTTCGAAAGTCTTAAT
1 AAAGTTTCCAAACTCTTAAT
92643 AAAGTTTCCAAACTCTTA
1 AAAGTTTCCAAACTCTTA
92661 CAATGTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (20 bp):
AAAGTTTCCAAACTCTTAAT
Found at i:93236 original size:19 final size:20
Alignment explanation
Indices: 93209--93261 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
93199 ATACATTGGG
*
93209 CTATAAATATGAAAATGA-T
1 CTATGAATATGAAAATGAGT
*
93228 CTATGAATATAAAAATGAGT
1 CTATGAATATGAAAATGAGT
*
93248 -TATGAATCTGAAAA
1 CTATGAATATGAAAA
93262 GAAAGAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 28 0.97
20 1 0.03
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (20 bp):
CTATGAATATGAAAATGAGT
Found at i:104946 original size:21 final size:20
Alignment explanation
Indices: 104913--104951 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
104903 TATCAAGATC
*
104913 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
104934 TTTGTCGATGCCATAAAT
1 TTTGTCGAAGCCATAAAT
104952 TCATGTAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:128875 original size:3 final size:3
Alignment explanation
Indices: 128869--128947 Score: 149
Period size: 3 Copynumber: 26.0 Consensus size: 3
128859 CAACTCCTCC
128869 TCT TCTT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
128915 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
128948 CCTCTTAGTC
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 72 0.96
4 3 0.04
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:130427 original size:9 final size:9
Alignment explanation
Indices: 130413--130438 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
130403 GAGCAGCATC
130413 GACGATTAT
1 GACGATTAT
130422 GACGATTAT
1 GACGATTAT
130431 GACGATTA
1 GACGATTA
130439 AGAACGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (9 bp):
GACGATTAT
Found at i:131211 original size:21 final size:21
Alignment explanation
Indices: 131185--131226 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
131175 GAGATTGATA
131185 CTTTTCATCGAGGGATCGATC
1 CTTTTCATCGAGGGATCGATC
*
131206 CTTTTCATTGAGGGATCGATC
1 CTTTTCATCGAGGGATCGATC
131227 ATTTGGTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (21 bp):
CTTTTCATCGAGGGATCGATC
Found at i:131349 original size:3 final size:3
Alignment explanation
Indices: 131341--131366 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
131331 TGATTTAATT
131341 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
131367 TATTATTATT
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:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:131371 original size:3 final size:3
Alignment explanation
Indices: 131365--131399 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
131355 CATCATCATC
131365 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
131400 CTACTTGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:131557 original size:22 final size:23
Alignment explanation
Indices: 131507--131559 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
131497 ATAGCCAACT
* *
131507 GGCCCAAACAGAAATCTAAACCCG
1 GGCCCAAACAG-AATCCAAACCAG
*
131531 AGCCCAAACAG-ATCCAAACCAG
1 GGCCCAAACAGAATCCAAACCAG
131553 GGCCCAA
1 GGCCCAA
131560 CTACCAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 15 0.60
24 10 0.40
ACGTcount: A:0.42, C:0.36, G:0.17, T:0.06
Consensus pattern (23 bp):
GGCCCAAACAGAATCCAAACCAG
Found at i:144254 original size:1 final size:1
Alignment explanation
Indices: 144250--144334 Score: 53
Period size: 1 Copynumber: 85.0 Consensus size: 1
144240 AAGAAAAATG
** *** ** * * *
144250 AAAAAAAAAAAAAATGAAAAAAAATGGAAAAAATGAAAAAATAAAAAAAATAAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
144315 GAAAAAAAAATAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAA
144335 GGGGATTAAG
Statistics
Matches: 63, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.08
Consensus pattern (1 bp):
A
Found at i:144264 original size:16 final size:16
Alignment explanation
Indices: 144243--144324 Score: 105
Period size: 16 Copynumber: 5.0 Consensus size: 16
144233 CTGAAGAAAG
144243 AAAAATGAAAAAAAAA
1 AAAAATGAAAAAAAAA
144259 AAAAATGAAAAAAAATGGA
1 AAAAATGAAAAAAAA---A
144278 AAAAATGAAAAAATAAA
1 AAAAATGAAAAAA-AAA
144295 AAAAAT-AAAAAAAAA
1 AAAAATGAAAAAAAAA
*
144310 AAAGA-GAAAAAAAAA
1 AAAAATGAAAAAAAAA
144325 TAAATAAAAA
Statistics
Matches: 60, Mismatches: 1, Indels: 11
0.83 0.01 0.15
Matches are distributed among these distances:
15 16 0.27
16 21 0.35
17 7 0.12
19 14 0.23
20 2 0.03
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (16 bp):
AAAAATGAAAAAAAAA
Found at i:144309 original size:29 final size:29
Alignment explanation
Indices: 144243--144334 Score: 87
Period size: 29 Copynumber: 3.0 Consensus size: 29
144233 CTGAAGAAAG
*
144243 AAAAATGA-AAAAAAAAAAAAATGAAAAAA
1 AAAAAAGAGAAAAAAAAAAAAAT-AAAAAA
*
144272 AATGGAAAAAATGAAAAAATAAAAAAAATAAAAAA
1 AA---AAAAGA-G-AAAAA-AAAAAAAATAAAAAA
*
144307 AAAAAAGAGAAAAAAAAATAAATAAAAA
1 AAAAAAGAGAAAAAAAAAAAAATAAAAA
144335 GGGGATTAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
29 15 0.29
30 5 0.10
31 1 0.02
32 9 0.17
35 13 0.25
36 9 0.17
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.09
Consensus pattern (29 bp):
AAAAAAGAGAAAAAAAAAAAAATAAAAAA
Found at i:145834 original size:135 final size:135
Alignment explanation
Indices: 145586--145956 Score: 482
Period size: 135 Copynumber: 2.7 Consensus size: 135
145576 TAATGTTTAA
* * * *
145586 TTCT-CATATTTGATCTTCCCTGAAGAAGCAGTGGAACAAGTCTGTCTCGA-TCGTATACTCCCT
1 TTCTCCATATTTGATCTTCCCTGAGGAA-CAGTGGAACAAGTCTGCCTCGATTC-AATATTCCCT
* * * *
145649 TACGAACACTGGAATGAATCAACATTTCCAGATCTGATTTTCCTTGAAGAAACAATAG-AACAGA
64 AAAGAACACTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAAGAAACAA-AGAAACAGA
145713 TCCCTTGT
128 TCCCTTGT
* * *
145721 TTTTGCATATTTGATCTTCCCTGAGGAACAGTGGAACAAGTATGCCTCGATTCAATATTCCCTAA
1 TTCTCCATATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTGCCTCGATTCAATATTCCCTAA
*
145786 AGAACACTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAAGAAACAACGAAACAGATCC
66 AGAACACTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAAGAAACAAAGAAACAGATCC
145851 CTTGT
131 CTTGT
* * * * *
145856 TTCTCCAGATTTGATCTTCCATGAGAAACAGTGGAACAAATCTACCTCGATTCAATATTCCCTAA
1 TTCTCCATATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTGCCTCGATTCAATATTCCCTAA
* * *
145921 AGAACAACAT--AATGAATAAACTTTTCTAGATCTGAT
66 AGAAC-AC-TGGAATGAATCAACATTTCCAGATCTGAT
145957 CCACCCTGAA
Statistics
Matches: 209, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
134 1 0.00
135 181 0.87
136 26 0.12
137 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (135 bp):
TTCTCCATATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTGCCTCGATTCAATATTCCCTAA
AGAACACTGGAATGAATCAACATTTCCAGATCTGATTTTCCCTCAAGAAACAAAGAAACAGATCC
CTTGT
Found at i:146190 original size:3 final size:3
Alignment explanation
Indices: 146182--146206 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
146172 GGGTGCTTTT
146182 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
146207 CTAATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:148606 original size:2 final size:2
Alignment explanation
Indices: 148599--148627 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
148589 ATTATATCAT
148599 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 T
148628 TAATGATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:149729 original size:31 final size:31
Alignment explanation
Indices: 149693--149820 Score: 224
Period size: 31 Copynumber: 4.2 Consensus size: 31
149683 TAGCAGATAG
149693 TGATTATAATGTAAGCATTTTAAAAGTTTAA
1 TGATTATAATGTAAGCATTTTAAAAGTTTAA
149724 TGATTATAATGTAAGCATTTTAAAAGTTTAA
1 TGATTATAATGTAAGCATTTTAAAAGTTTAA
149755 TGATTATAATGTAAGCATTTTAAAAGTTTAA
1 TGATTATAATGTAAGCATTTTAAAAGTTTAA
* *
149786 TGATTATATTGTAAG--TTTTAAAAGTTTGA
1 TGATTATAATGTAAGCATTTTAAAAGTTTAA
149815 TGATTA
1 TGATTA
149821 AAGTTAGAAA
Statistics
Matches: 95, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
29 19 0.20
31 76 0.80
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (31 bp):
TGATTATAATGTAAGCATTTTAAAAGTTTAA
Found at i:150741 original size:21 final size:20
Alignment explanation
Indices: 150717--150764 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
150707 TGATATATTG
* *
150717 TAAAGTATTGATCCTTTTTAT
1 TAAAGTATCGATACTTTTT-T
*
150738 TAAAAGGATCGATACTTTTTT
1 T-AAAGTATCGATACTTTTTT
150759 TAAAGT
1 TAAAGT
150765 TATGTAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 4 0.18
21 3 0.14
22 15 0.68
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.46
Consensus pattern (20 bp):
TAAAGTATCGATACTTTTTT
Found at i:151131 original size:23 final size:23
Alignment explanation
Indices: 151096--151168 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
151086 ATACTTTACA
151096 ATATAAGCACTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
* *
151119 ATATAAACGCTACCTATTACATT
1 ATATAAGCACTACCTATTACATT
* *
151142 ATATAAGCACTACTTATTACATC
1 ATATAAGCACTACCTATTACATT
151165 ATAT
1 ATAT
151169 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAGCACTACCTATTACATT
Found at i:151581 original size:476 final size:471
Alignment explanation
Indices: 150673--152329 Score: 2599
Period size: 469 Copynumber: 3.5 Consensus size: 471
150663 ATAATTTACA
** *
150673 ATATAAGCGCTACCTATTACATCATATTTTTACCTGA-TATATTGTAAAGT-ATTGATCCTTTTT
1 ATATAAGCGCTACCTATTACATCATATTTTTACCT-ATTATATTG-AAAGTGA-CCATACTTTTT
*
150736 ATTAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTG-TT
63 ATAAAAAGGATCGATAC-TTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTT
150800 CATGTTTTCCACCTACAATATTAATTTAATAATTTC--TTACACAAAAAATTATTTGATTG-TTT
127 CATG-TTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTT
* *
150862 AATATTTTAT-AAATATTATTTAGAATTTAAATTTAA-AATATTAACCAAAGATAAAAATATAAT
191 GATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATA-AAT
* *
150925 ATATAATATATATG-TTATGTTTTTAA-TTAATAATAATAAATACCGTAACGT-AAAAATAAATC
255 A-ATAATATATATGTTTTTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATC
*
150987 ATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTAACCTTAAATTAATATTTTCCACAGT
319 ATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTAACCTTAAATTAATGTTTTCCACAGT
*
151052 GAAAAAAGTATGGACACTTTTATAAAAAGGATAAATACTTTACAATATAAGCACTACCTATTACA
384 -AAAAAAGTATGGA-ACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACA
*
151117 TTATATAAACGCTACCTATTACATT
447 TTATATAAACGATACCTATTACATT
* *
151142 ATATAAGCACTACTTATTACATCATATTTTTACCTATTATATTGAAAGTGACCATACTTTTTATA
1 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGACCATACTTTTTATA
* *
151207 AAAATGATCGATATTTTTTTTAAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTC
66 AAAAGGATCGATA-CTTTTTT-AAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGTGTTTC
*
151272 ATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTG
128 ATG-TTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTG
*
151337 ATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATAG
192 ATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATAA
*
151402 TAATATATATGTTTTTGTTTTTAATTTAATAATAATTTATACCGTAACGTAAAAAATAAATCATT
257 TAATATATATGTTTTTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATT
* *
151467 AGATGCCTATAATTACTAAATTAATATCTTAAAACTAACCTTAAATTAATGTTTTCTACAGTAAA
322 AGACGCCTATAATTACTAAATTAATATCTTAAAACTAACCTTAAATTAATGTTTTCCACAGT-AA
151532 AAAAGTATGGAACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTAT
386 AAAAGTATGGAACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTAT
151597 ATAAACGATACCTATTACATT
451 ATAAACGATACCTATTACATT
* * *
151618 ATATAAGCGCTACTTATTACATCATATTTTTACCTATTATATTGAACGTGTCCATAC-TTTTAT-
1 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGACCATACTTTTTATA
151681 AAAAGGATCGATACTTTTTTAAAG-TATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCAT
66 AAAAGGATCGATACTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGTGTTTCAT
151745 GTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGA-TGTTTTGATA
130 GTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATA
* *
151809 -TTTATAAAATA-TATTTAGAATTTAAATTTAACAATATTAACCAAAGATTAATAATAAATATTT
195 TTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGA-TAATAATAAATAATA
*
151872 ATAAAATATGTTTATT-TTTAATTAATTTAATAATAATATATA-CGTAACGTAAAAAAT-AATCA
259 AT-ATATATGTTT-TTGTTT--TTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCA
* * *
151934 TTAGACGTCTATAATTACTAAATTAATATTTTAAAACTAACCTTAAATTAATGTTTTCCACAGTG
320 TTAGACGCCTATAATTACTAAATTAATATCTTAAAACTAACCTTAAATTAATGTTTTCCACAGTA
* * *
151999 AAAAAGTATGGACCTTTTATAAAAAGGATAGATACTTTACAATATAAACACTACCTATTACA--G
385 AAAAAGTATGGAACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTA
* *
152062 TATAAATGATACCCATTTACATT
450 TATAAACGATACCTA-TTACATT
*
152085 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATA
1 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGACCATACTTTTTATA
* *
152150 AAAAGGATCGATACTTTTTTAAAGTTATGTAATTTATATTTCAATTTTTTTAAAAGTGTTTCATG
66 AAAAGGATCGATACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATG
* *
152215 TTTTCACCTATAATATTAATTTAATAATTTCATTT--ACAAAAAATTATTTGATTGTTTTGATAT
131 TTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATAT
152278 TTTATAAAATATTATTTAGAATTTAAATTTAACAATATT-ACCAAAGATAATA
196 TTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATA
152330 TATTATGCGT
Statistics
Matches: 1115, Mismatches: 47, Indels: 53
0.92 0.04 0.04
Matches are distributed among these distances:
466 13 0.01
467 114 0.10
468 141 0.13
469 248 0.22
470 128 0.11
471 98 0.09
472 4 0.00
473 29 0.03
474 35 0.03
475 47 0.04
476 172 0.15
477 86 0.08
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (471 bp):
ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGACCATACTTTTTATA
AAAAGGATCGATACTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATG
TTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATAT
TTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATAATAAT
ATATATGTTTTTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGAC
GCCTATAATTACTAAATTAATATCTTAAAACTAACCTTAAATTAATGTTTTCCACAGTAAAAAAG
TATGGAACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAA
CGATACCTATTACATT
Found at i:151608 original size:23 final size:23
Alignment explanation
Indices: 151582--151644 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
151572 ATATAAGCAC
151582 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
151605 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
* *
151628 TACTTATTACATCATAT
1 TACCTATTACATTATAT
151645 TTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:154088 original size:191 final size:190
Alignment explanation
Indices: 153735--154116 Score: 714
Period size: 191 Copynumber: 2.0 Consensus size: 190
153725 TTGTTCGTGC
153735 AATTGAAGATGGAATAGTAGAATGCGTATGAACGAGTTGAAAGCAGATTACTTAAGTTCCCATAC
1 AATTGAAGATGGAATAGTAGAATGCGTATGAACGAGTTGAAAGCAGATTACTTAAGTTCCCATAC
153800 GAAGCCCTTCAGATCACAAAACTGGCGACCTTGAAAGCCATGCCGCTGCGATTTTTACCCACGAA
66 GAAGCCCTTCAGATCACAAAACTGGCGACCTTGAAAGCCATGCCGCTGCGATTTTTACCCACGAA
153865 TCTTTTCGTGTGTTCCAAGATGAACTTATAC-GGAGACATTGTACCGGATTGAGGCAAAGA
131 TCTTTTCGTGTGTTCCAAGATGAAC-TATACGGGAGACATTGTACCGGATTGAGGCAAAGA
153925 AATTGAAGATGGAATTAGTAGAATGCGTATGAACGAGTTGAAAGCAGATTACTTAAGTTCCCATA
1 AATTGAAGATGGAA-TAGTAGAATGCGTATGAACGAGTTGAAAGCAGATTACTTAAGTTCCCATA
153990 CGAAGCCCTTCCAGATCACAAAACTGGTCGACCTTGAAAGCCATGCCGCTGCGATTTTTACCCAC
65 CGAAGCCCTT-CAGATCACAAAACTGG-CGACCTTGAAAGCCATGCCGCTGCGATTTTTACCCAC
154055 GAATCTTTTCGTGTGTTCCAAGATGAA-TATACGGGAGACATTGTACCGGATTGAGGCAAAGA
128 GAATCTTTTCGTGTGTTCCAAGATGAACTATACGGGAGACATTGTACCGGATTGAGGCAAAGA
154117 TTAAGTCCTT
Statistics
Matches: 188, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
190 14 0.07
191 65 0.35
192 45 0.24
193 64 0.34
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (190 bp):
AATTGAAGATGGAATAGTAGAATGCGTATGAACGAGTTGAAAGCAGATTACTTAAGTTCCCATAC
GAAGCCCTTCAGATCACAAAACTGGCGACCTTGAAAGCCATGCCGCTGCGATTTTTACCCACGAA
TCTTTTCGTGTGTTCCAAGATGAACTATACGGGAGACATTGTACCGGATTGAGGCAAAGA
Found at i:155407 original size:297 final size:296
Alignment explanation
Indices: 154864--155444 Score: 972
Period size: 297 Copynumber: 2.0 Consensus size: 296
154854 TAAAATTAGC
* *
154864 GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTAT
1 GACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTAT
154929 ACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGTTCCGATGTGTAAATGTCGACACT
66 ACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGTTCCGATGTGTAAATGTCGACACT
*
154994 TTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATTAAAAG
131 TTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAAAATTAAAAG
155059 TGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTATACCGATATATTACAAAA
196 TGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTATACCGATATATTACAAAA
*
155124 TTATCTAGTACATTATAATTCTGGACATAAAGTACT
261 TTATATAGTACATTATAATTCTGGACATAAAGTACT
*
155160 GACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGTTCATAAAACCGGTATATTTA
1 GACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA-TTA
*
155225 TACCGGTTATATTACAAAATTATCTATTACA-T-TAA-TCTGGGTTCCGATGTGTAAATGTCTAC
65 TACCGGTTATATTACAAAATTATCTATTACATTATAATTCT--GTTCCGATGTGTAAATGTCGAC
155287 ACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAAAATTA
128 AC-TTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAAAATT-
* * * * *
155352 AAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTAT-TTATACCGGTTTATTA
191 AAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTATACCGATATATTA
* *
155416 TAAAATTATATATTACATTATAATTCTGG
256 CAAAATTATATAGTACATTATAATTCTGG
155445 GTTCCGATGT
Statistics
Matches: 267, Mismatches: 13, Indels: 9
0.92 0.04 0.03
Matches are distributed among these distances:
294 3 0.01
295 3 0.01
296 82 0.31
297 133 0.50
298 46 0.17
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (296 bp):
GACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTAT
ACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGTTCCGATGTGTAAATGTCGACACT
TTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAAAATTAAAAG
TGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTATACCGATATATTACAAAA
TTATATAGTACATTATAATTCTGGACATAAAGTACT
Found at i:155917 original size:181 final size:183
Alignment explanation
Indices: 155141--156229 Score: 1752
Period size: 180 Copynumber: 6.0 Consensus size: 183
155131 GTACATTATA
* *
155141 ATTCTGGACATAAAGTACTGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGTT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
155206 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACA-T-TAA-TCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
*
155268 CCGATGTGTAAATGTCTACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
155321 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
155386 CATAAAACCGG--TATTTATACCGGTT-TATTATAAAATTATATATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
*
155448 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATTGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
155501 ATT-T-GACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* * *
155564 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTACTAAATTATAATTCTAGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
155629 CCGATGTGTAAATGTCGACACTTTTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACAC---TTTTTGACAAGGTATCGACACATTTTTCTTCC
*
155685 ATTCTGGACATAAAGTACCAACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
155750 CAT-AAA-TGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTTTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
*
155813 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCT
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
155866 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
155931 CATAAAACCGGTATA-TTATA-CGGTTATATTACAAAATTA--TATTACATTATAA-TCATGGGT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTC-TGGGT
155991 TCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
130 TCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
* *
156045 ATTCTGGACATAAAG----GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCACT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* * * *
156106 CATAAAACCAGTATATTTATACCGATTATATTACAAAATTATCTATTATATTATAATTATGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
* * * *
156171 CCAATGTTTTTTCAA--TCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCC
131 CCGATG---TGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
156225 ATTCT
1 ATTCT
156230 TTTTCAATCG
Statistics
Matches: 854, Mismatches: 33, Indels: 44
0.92 0.04 0.05
Matches are distributed among these distances:
175 59 0.07
176 5 0.01
177 38 0.04
178 86 0.10
179 113 0.13
180 194 0.23
181 169 0.20
182 12 0.01
183 6 0.01
184 107 0.13
185 4 0.00
186 61 0.07
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (183 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
Found at i:156254 original size:50 final size:51
Alignment explanation
Indices: 156178--156279 Score: 197
Period size: 50 Copynumber: 2.0 Consensus size: 51
156168 GTTCCAATGT
156178 TTTTTCAATCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCCATTC
1 TTTTTCAATCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCCATTC
156229 TTTTTCAATCGAC-CTTTTTGAAAAGGTATCGACACATTTTTCTTCCATTC
1 TTTTTCAATCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCCATTC
156279 T
1 T
156280 GGACATAAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 38 0.75
51 13 0.25
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.44
Consensus pattern (51 bp):
TTTTTCAATCGACACTTTTTGAAAAGGTATCGACACATTTTTCTTCCATTC
Found at i:157513 original size:3 final size:3
Alignment explanation
Indices: 157505--157563 Score: 55
Period size: 3 Copynumber: 19.7 Consensus size: 3
157495 ACTTGTTTGG
* * * * *
157505 ATC ATC ATC ATC ATC GTC ATC ATC ATC GTC GTC ATC TTC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* *
157553 TTC ATC TTC AT
1 ATC ATC ATC AT
157564 TGACCGCTTG
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.22, C:0.32, G:0.07, T:0.39
Consensus pattern (3 bp):
ATC
Found at i:157526 original size:15 final size:15
Alignment explanation
Indices: 157506--157558 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
157496 CTTGTTTGGA
157506 TCATCATCATCATCG
1 TCATCATCATCATCG
*
157521 TCATCATCATCGTCG
1 TCATCATCATCATCG
157536 TCATC-T--TCATCG
1 TCATCATCATCATCG
*
157548 TCATCTTCATC
1 TCATCATCATC
157559 TTCATTGACC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 10 0.30
13 1 0.03
14 1 0.03
15 21 0.64
ACGTcount: A:0.21, C:0.34, G:0.08, T:0.38
Consensus pattern (15 bp):
TCATCATCATCATCG
Found at i:159340 original size:200 final size:200
Alignment explanation
Indices: 158997--159760 Score: 1271
Period size: 200 Copynumber: 3.8 Consensus size: 200
158987 AACATTAAAC
* * * *
158997 AGTGTCGATACA-TATTATATACCAATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTG
1 AGTGTCGATACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* * *
159061 AAAAATTACCTAATACATTATACTTTTCGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
65 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
* *
159126 GGATCAACACTTTATGGTTGTACCCTGTTTGCCATTCATTCTGGACCAAAAATAACGACACAAAC
130 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATAACGACACAAAC
*
159191 TACAAA
195 TAAAAA
*
159197 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
159262 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* * *
159327 GATCGACACTTTATTGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAA-AATCGACAAAAAC
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATAA-CGACACAAAC
*
159391 TATAAA
195 TAAAAA
* *
159397 AGTGTCAATACATTATTTAGACCTATTCTCTCATAAAACTGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
159462 AAAATTATCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
159527 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATAACGACACAAACT
159592 AAAAA
196 AAAAA
*
159597 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* * *
159662 AAAATTACTTATTACATTATACTTTTGGGTTTCGATATTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
159727 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
159761 ATTGTAAATT
Statistics
Matches: 529, Mismatches: 32, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
199 2 0.00
200 522 0.99
201 5 0.01
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (200 bp):
AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATAACGACACAAACT
AAAAA
Found at i:160005 original size:18 final size:18
Alignment explanation
Indices: 159982--160042 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
159972 TCTCATTCAT
*
159982 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
160000 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
160019 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
160038 AATTA
1 AATTA
160043 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:160018 original size:19 final size:19
Alignment explanation
Indices: 159994--160042 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
159984 TTATATTCAC
159994 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
160013 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
160032 ATACAAAATTA
1 ATACAAAATTA
160043 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:161870 original size:33 final size:33
Alignment explanation
Indices: 161833--161898 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
161823 CATCTTAATA
*
161833 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
161866 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
161899 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:161957 original size:21 final size:21
Alignment explanation
Indices: 161932--161996 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
161922 CCCCTTATGC
* *
161932 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
161953 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
161974 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
161995 CT
1 CT
161997 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:163503 original size:20 final size:19
Alignment explanation
Indices: 163457--163503 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
163447 TCCGGTAACG
*
163457 TTTTACCGGTTTTATCATT
1 TTTTACCAGTTTTATCATT
*
163476 TTGGTACCAGTTTTATCATAT
1 TT-TTACCAGTTTTATCAT-T
163497 TTTTACC
1 TTTTACC
163504 TAGTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCAGTTTTATCATT
Found at i:163717 original size:181 final size:181
Alignment explanation
Indices: 163304--163715 Score: 583
Period size: 181 Copynumber: 2.3 Consensus size: 181
163294 TTTTTTACAT
* * *
163304 GTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACA
1 GTTTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACA
* *
163369 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAGCATCGA
66 TTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAGCACCGA
* * * ***
163434 CACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGGTACCA
131 CACTTTAAATATATCCGGTAACGCTTTACCAGTTTTATCATTTCAATACCA
163485 GTTTTATCATATTTTTACCTAG-TATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACAC
1 GTTTTATCATATTTTTACCT-GTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACAC
* ** * * * *
163549 TTTATAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTTTTGATCCTTATATTAAAGTACC
65 ATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-TAAAGCACC
* * *
163614 GACACTTTAAATGTATCCGGTAGCGCTTTACCAGTTTTATCATTTCAATACCG
129 GACACTTTAAATATATCCGGTAACGCTTTACCAGTTTTATCATTTCAATACCA
* * *
163667 GTTTTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
1 GTTTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
163716 AATTTGGATC
Statistics
Matches: 204, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
181 108 0.53
182 96 0.47
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (181 bp):
GTTTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACA
TTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATAAAGCACCGA
CACTTTAAATATATCCGGTAACGCTTTACCAGTTTTATCATTTCAATACCA
Found at i:164683 original size:31 final size:30
Alignment explanation
Indices: 164637--164714 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 30
164627 ATAATGGTGG
*
164637 AGTGACCATTTGTTACAAATCGATAACGTT
1 AGTGACCATTTGTTACAAATAGATAACGTT
* *
164667 AGTGATCATTTTGTTACAAATAGATAATGTT
1 AGTGACCA-TTTGTTACAAATAGATAACGTT
* *
164698 AGTAACTAATTTGTTAC
1 AGTGAC-CATTTGTTAC
164715 TTTTGAAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 7 0.17
31 32 0.80
32 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (30 bp):
AGTGACCATTTGTTACAAATAGATAACGTT
Found at i:166439 original size:20 final size:20
Alignment explanation
Indices: 166414--166459 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
166404 AAATACCATG
166414 TTAATTAGATTTTGGAACAA
1 TTAATTAGATTTTGGAACAA
166434 TTAATTAGATTTTGGAACAA
1 TTAATTAGATTTTGGAACAA
166454 TTAATT
1 TTAATT
166460 TGGGATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.43
Consensus pattern (20 bp):
TTAATTAGATTTTGGAACAA
Found at i:168265 original size:20 final size:21
Alignment explanation
Indices: 168228--168267 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
168218 AGCCGTTGGG
**
168228 GCCTGATGGTATTGATACTAT
1 GCCTGATGGTATCAATACTAT
168249 GCCT-ATGGTATCAATACTA
1 GCCTGATGGTATCAATACTA
168268 CTATACAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (21 bp):
GCCTGATGGTATCAATACTAT
Found at i:171597 original size:119 final size:121
Alignment explanation
Indices: 171424--171650 Score: 327
Period size: 119 Copynumber: 1.9 Consensus size: 121
171414 AGTTAGCATA
* *
171424 GTCTGAACCATAATAATGTGGATTATATCCCGGATCTGGTCACCACAAGGTCGAATCAAATAATT
1 GTCTGAACCATAATAATGTGGATCATATCCCGGATCGGGTCACCACAAGGTCGAATCAAATAATT
* * * *
171489 TAAACAAAT-TA-ACAAAATAAAATAAAA-TAAATAAAAAAGTTGGTGGTTAACAGG
66 CAAACAAATATATA-AAAATAAAAGAAAAGAAAAGAAAAAAGTTGGTGGTTAACAGG
**
171543 GTCTGAACCATAATAATGTGGATCATA-CCTCGGATCGGGTCACCACAAGGTCGAATTGAATAAT
1 GTCTGAACCATAATAATGTGGATCATATCC-CGGATCGGGTCACCACAAGGTCGAATCAAATAAT
*
171607 TCAAATAAATATATAAAAATAAAAGAAAAGAAAAGAAAAAAGTT
65 TCAAACAAATATATAAAAATAAAAGAAAAGAAAAGAAAAAAGTT
171651 AGTGTTTTTA
Statistics
Matches: 95, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
118 2 0.02
119 65 0.68
120 15 0.16
121 13 0.14
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (121 bp):
GTCTGAACCATAATAATGTGGATCATATCCCGGATCGGGTCACCACAAGGTCGAATCAAATAATT
CAAACAAATATATAAAAATAAAAGAAAAGAAAAGAAAAAAGTTGGTGGTTAACAGG
Found at i:173013 original size:97 final size:97
Alignment explanation
Indices: 172827--173135 Score: 415
Period size: 97 Copynumber: 3.2 Consensus size: 97
172817 GAATTGTTTT
* * * * *
172827 GCATTTAACTTGCATTAATGGCACCTTTATGCAAAAAAATGCAACATTTGTCATCTAACTTGCAT
1 GCATTTAACTTGCATTAGTGGCACCTTTCTGC-CATAAATGCACCATTTGTCATCTAACTTGCAT
*
172892 TAGTGACACCTTTCTGCC-AAAATGCGTCGTTAG
65 TAGTGGCACCTTTCTGCCAAAAATGC-TCGTTAG
*
172925 GCATTTAACTTGCATTAGTGGCACCTTTCTGCCATAAATGCACCATTTGTCATCTAAC-TGCATC
1 GCATTTAACTTGCATTAGTGGCACCTTTCTGCCATAAATGCACCATTTGTCATCTAACTTGCATT
*
172989 AGTGGCACCTTTCTGCCAAAAATGCACTGTTAG
66 AGTGGCACCTTTCTGCCAAAAATGCTC-GTTAG
* * *
173022 GCATTTAACTTGCATTAGTGACACCTTTCTGCCATAAATGCACCATTTGTTATCTTACTTGCATT
1 GCATTTAACTTGCATTAGTGGCACCTTTCTGCCATAAATGCACCATTTGTCATCTAACTTGCATT
* * * * *
173087 AGTGGTACCTTTCTTCCATAAATGCATCATTTG
66 AGTGGCACCTTTCTGCCAAAAATGC-TCGTTAG
*
173120 TCATTTAACTTGCATT
1 GCATTTAACTTGCATT
173136 TTAGAGCAGT
Statistics
Matches: 188, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
96 22 0.12
97 90 0.48
98 75 0.40
99 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.36
Consensus pattern (97 bp):
GCATTTAACTTGCATTAGTGGCACCTTTCTGCCATAAATGCACCATTTGTCATCTAACTTGCATT
AGTGGCACCTTTCTGCCAAAAATGCTCGTTAG
Found at i:173054 original size:49 final size:47
Alignment explanation
Indices: 172824--173135 Score: 308
Period size: 49 Copynumber: 6.4 Consensus size: 47
172814 AATGAATTGT
* * *
172824 TTTG-CATTTAACTTGCATTAATGGCACCTTTATGCAAAAAAATGCAAC
1 TTTGTCATTTAACTTGCATTAGTGGCACCTTTCTGC-CAAAAATGC-AC
* * *
172872 ATTTGTCATCTAACTTGCATTAGTGACACCTTTCTGCC-AAAATGCGTC
1 -TTTGTCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGC-AC
* * *
172920 GTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCCATAAATGCACC
1 -TTTGTCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCA-C
* *
172969 ATTTGTCATCTAAC-TGCATCAGTGGCACCTTTCTGCCAAAAATGCAC
1 -TTTGTCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCAC
* * *
173016 TGTTAGGCATTTAACTTGCATTAGTGACACCTTTCTGCCATAAATGCACC
1 T-TT-GTCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCA-C
* * * *
173066 ATTTGTTATCTT-ACTTGCATTAGTGGTACCTTTCTTCCATAAATGCATC
1 -TTTGTCAT-TTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCA-C
173115 ATTTGTCATTTAACTTGCATT
1 -TTTGTCATTTAACTTGCATT
173136 TTAGAGCAGT
Statistics
Matches: 221, Mismatches: 32, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
46 1 0.00
47 3 0.01
48 81 0.37
49 103 0.47
50 32 0.14
51 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (47 bp):
TTTGTCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCAC
Found at i:178799 original size:49 final size:48
Alignment explanation
Indices: 178740--179081 Score: 319
Period size: 49 Copynumber: 7.0 Consensus size: 48
178730 TTAAACCATG
* * * * *
178740 AGTGGCACCTTTTATACCTAAATGAACTGTTTTGCATTTAACTTGCATT
1 AGTGGCACC-TTTCTGCCAAAATGCACCGTTTTGCATTTAACTTGCATT
* * * * * *
178789 AGTGGAACCTTTATGCAAAAAATGCACCATTTTTCATCTAACTTGCATT
1 AGTGGCACCTTTCTGC-CAAAATGCACCGTTTTGCATTTAACTTGCATT
* * **
178838 AGTTGCACCTTTCTGCCAAAATGCGCCGTTAGGCATTTAACTTGCATT
1 AGTGGCACCTTTCTGCCAAAATGCACCGTTTTGCATTTAACTTGCATT
* * ** *
178886 AGTGGCACCTTTCTGCCAAAAATACAGCGTTAGGCCTTTAACTTGCATT
1 AGTGGCACCTTTCTGCC-AAAATGCACCGTTTTGCATTTAACTTGCATT
** * *
178935 AGTGGCACCTTTCTGCCATAAATGCACTATTTTTCATCTAACTTGCATT
1 AGTGGCACCTTTCTGCCA-AAATGCACCGTTTTGCATTTAACTTGCATT
* * * * *
178984 AGTGGCACCTTTCTACCATAAATACACC-ATTTGTCATCTAACTTGCAAT
1 AGTGGCACCTTTCTGCCA-AAATGCACCGTTTTG-CATTTAACTTGCATT
* *
179033 AGTGGCACCTCTCTGCCAAAAATGCACCG-TTAGACATTTAACTTGCATT
1 AGTGGCACCTTTCTGCC-AAAATGCACCGTTTTG-CATTTAACTTGCATT
179082 TTATAGTTGT
Statistics
Matches: 241, Mismatches: 46, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
48 51 0.21
49 189 0.78
50 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (48 bp):
AGTGGCACCTTTCTGCCAAAATGCACCGTTTTGCATTTAACTTGCATT
Found at i:178994 original size:98 final size:98
Alignment explanation
Indices: 178740--179081 Score: 384
Period size: 98 Copynumber: 3.5 Consensus size: 98
178730 TTAAACCATG
* * * * *
178740 AGTGGCACCTTTTATACC-TAAATGAACTGTTTTGCATTTAACTTGCATTAGTGGAACCTTTATG
1 AGTGGCACC-TTTCTGCCATAAATGCACTGTTTTGCATTTAACTTGCATTAGTGGCACCTTTCTG
* * *
178804 CAAAAAATGCACCATTTTTCATCTAACTTGCATT
65 CCAAAAATACACCATTTGTCATCTAACTTGCATT
* * * **
178838 AGTTGCACCTTTCTGCCA-AAATGCGCCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGC
1 AGTGGCACCTTTCTGCCATAAATGCACTGTTTTGCATTTAACTTGCATTAGTGGCACCTTTCTGC
* * * * * *
178902 CAAAAATACAGCGTTAGGCCTTTAACTTGCATT
66 CAAAAATACACCATTTGTCATCTAACTTGCATT
* * * *
178935 AGTGGCACCTTTCTGCCATAAATGCACTATTTTTCATCTAACTTGCATTAGTGGCACCTTTCTAC
1 AGTGGCACCTTTCTGCCATAAATGCACTGTTTTGCATTTAACTTGCATTAGTGGCACCTTTCTGC
* *
179000 CATAAATACACCATTTGTCATCTAACTTGCAAT
66 CAAAAATACACCATTTGTCATCTAACTTGCATT
* * * *
179033 AGTGGCACCTCTCTGCCAAAAATGCACCG-TTAGACATTTAACTTGCATT
1 AGTGGCACCTTTCTGCCATAAATGCACTGTTTTG-CATTTAACTTGCATT
179082 TTATAGTTGT
Statistics
Matches: 198, Mismatches: 43, Indels: 6
0.80 0.17 0.02
Matches are distributed among these distances:
97 88 0.44
98 110 0.56
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (98 bp):
AGTGGCACCTTTCTGCCATAAATGCACTGTTTTGCATTTAACTTGCATTAGTGGCACCTTTCTGC
CAAAAATACACCATTTGTCATCTAACTTGCATT
Found at i:179514 original size:16 final size:16
Alignment explanation
Indices: 179491--179524 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
179481 CCTTTTATTC
179491 ATTTAATCC-TTCAAA
1 ATTTAATCCTTTCAAA
179506 ATTTAAATCCTTTCAAA
1 ATTT-AATCCTTTCAAA
179523 AT
1 AT
179525 AGTCACTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 5 0.29
17 8 0.47
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTTAATCCTTTCAAA
Found at i:181465 original size:138 final size:138
Alignment explanation
Indices: 181152--181716 Score: 618
Period size: 138 Copynumber: 4.1 Consensus size: 138
181142 TGGAGATGAT
* * * * * *
181152 TTTGGAGACAACAAGATTCCTACGTGATGAGGAAGTTTGGTTATTTGAGGATGACGCTGCTCCTA
1 TTTGGAGACAACAAGGTTCCTACATGATGAGGAAGTCTGATTATCTGAGGATGATGCTGCTCCTA
* * * * * *
181217 CA-TGTTGAGGAGATCTAGTCGATGGACGATATTGTTCATATGTAAAGAGGATGTCTAGCCATCT
66 CACT-TTGAGGAGATCTGGTCGATGGACGACATTGTTC-TATGTGATGAGGACGTCTAGCCGTCT
181281 TTAGGGATAA
129 TTAGGGATAA
* ** *
181291 TTTGGAGACAGCACA-GTTCCTATGTGATGAGGAAGTCTGATTGTCTGAGGATGACT-CTGCTCC
1 TTTGGAGACAACA-AGGTTCCTACATGATGAGGAAGTCTGATTATCTGAGGATGA-TGCTGCTCC
* * *
181354 TACACATTGAGGAGATCTGGTCGGTGGACGACATTGTTCTACGTGATGAGGACGTCTAGCCGTCT
64 TACACTTTGAGGAGATCTGGTCGATGGACGACATTGTTCTATGTGATGAGGACGTCTAGCCGTCT
*
181419 TTACGGATAA
129 TTAGGGATAA
* * ** *
181429 ATTGGAGACAACAAGGTTTCTACATGATGAGGAAGTCTGATTGCCTGAAGATG-TGCTGCTCCTA
1 TTTGGAGACAACAAGGTTCCTACATGATGAGGAAGTCTGATTATCTGAGGATGATGCTGCTCCTA
* * * * * * * *
181493 CGCTTTGAGGAGATCTGGTTGGTGGACGACATTATTTCTATATTATGAGGACATCTAGCTGTCTT
66 CACTTTGAGGAGATCTGGTCGATGGACGACATT-GTTCTATGTGATGAGGACGTCTAGCCGTCTT
181558 TAGGGATAA
130 TAGGGATAA
* * * * * * *
181567 TTTGGAGACAGCATGGTTCCTACATGATGAGGAAGTATGGTTATTTAAGGATGATGTTGCTCCTA
1 TTTGGAGACAACAAGGTTCCTACATGATGAGGAAGTCTGATTATCTGAGGATGATGCTGCTCCTA
* * *
181632 CGCTTTGAGGAGATCTGGTCGATGGACGACATT-TTCCTTTGTGATGAGGACGTCTAACCGTCTT
66 CACTTTGAGGAGATCTGGTCGATGGACGACATTGTT-CTATGTGATGAGGACGTCTAGCCGTCTT
* *
181696 TAAGAATAA
130 TAGGGATAA
* *
181705 TCTAGAGACAAC
1 TTTGGAGACAAC
181717 GATCTCAAGT
Statistics
Matches: 358, Mismatches: 60, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
136 1 0.00
137 42 0.12
138 187 0.52
139 127 0.35
140 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (138 bp):
TTTGGAGACAACAAGGTTCCTACATGATGAGGAAGTCTGATTATCTGAGGATGATGCTGCTCCTA
CACTTTGAGGAGATCTGGTCGATGGACGACATTGTTCTATGTGATGAGGACGTCTAGCCGTCTTT
AGGGATAA
Found at i:181759 original size:36 final size:34
Alignment explanation
Indices: 181736--181810 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 34
181726 TGACGTTAAT
*
181736 TTTGTTTCAAGAGAAACTGTCTCAAACGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTC-AA-GTGACAAAA
181772 TTTGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGT--GACAAAA
181808 TTT
1 TTT
181811 TCTTAAAGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
34 1 0.03
35 2 0.06
36 33 0.92
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (34 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGTGACAAAA
Found at i:181915 original size:65 final size:65
Alignment explanation
Indices: 181774--181972 Score: 245
Period size: 65 Copynumber: 3.0 Consensus size: 65
181764 AGACAAAATT
* * * * *
181774 TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTTTCTTAAAGGGAAATAATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTAT-TTCAAGAGAAACAATCTCAAAGGTTT
181839 A
65 A
* * * *
181840 TGTTTCAAGAGAAATTGTCCCAAGCGAGACAAAATTGTTTCAAGAGAAACAATCTCAAAGGCTTA
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTATTTCAAGAGAAACAATCTCAAAGGTTTA
** * * *
181905 TGTTTCAAGAGAAACAATCTCAAGCAAGAAAAAACTTTATTTCGAGAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAA--TTATTTCAAGAGAAACAATCTCAAAGGTT
181970 TA
64 TA
181972 T
1 T
181973 CAATTTTGTT
Statistics
Matches: 114, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
65 51 0.45
66 34 0.30
67 29 0.25
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTATTTCAAGAGAAACAATCTCAAAGGTTTA
Found at i:182307 original size:35 final size:35
Alignment explanation
Indices: 182268--182387 Score: 107
Period size: 36 Copynumber: 3.4 Consensus size: 35
182258 AGGAAGACTG
*
182268 TCTCAAGTGAGACGAATTTTTTTTAAGAAAAACTA
1 TCTCAAGTGAGACAAATTTTTTTTAAGAAAAACTA
** *
182303 TCTCAAGCAAGACAAAATTTGTTTTTAAG-AAAACAA
1 TCTCAAGTGAGAC-AAATTT-TTTTTAAGAAAAACTA
* * * * *
182339 TCCCAAGTGACATAAATTTTGTTTCAAGAAAAACTG
1 TCTCAAGTGAGACAAATTTT-TTTTAAGAAAAACTA
* *
182375 TCTCTAGAGAGAC
1 TCTCAAGTGAGAC
182388 GACACTTTGT
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
34 1 0.02
35 23 0.36
36 32 0.50
37 8 0.12
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (35 bp):
TCTCAAGTGAGACAAATTTTTTTTAAGAAAAACTA
Found at i:183947 original size:44 final size:44
Alignment explanation
Indices: 183893--184028 Score: 146
Period size: 45 Copynumber: 3.0 Consensus size: 44
183883 TCTCGTATTC
* * * *
183893 CTAGAAGATATGAGTCTTAAAAAATGCCCCAATATTTATCATTT
1 CTAGATGATATGGGCCTTAAAAAATGCCCCAACATTTATCATTT
* *
183937 CTAGATGATATGGGCCTTCAAAAATGCCCTAAACATTTATCATTT
1 CTAGATGATATGGGCCTTAAAAAATGCCC-CAACATTTATCATTT
* * * * * *
183982 ATGGATGATGTGGGCCTTCAAAAAATGACCCAACACTTATTATTT
1 CTAGATGATATGGGCCTT-AAAAAATGCCCCAACATTTATCATTT
184027 CT
1 CT
184029 GGCTCCAGCA
Statistics
Matches: 75, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
44 25 0.33
45 41 0.55
46 9 0.12
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (44 bp):
CTAGATGATATGGGCCTTAAAAAATGCCCCAACATTTATCATTT
Found at i:185003 original size:15 final size:15
Alignment explanation
Indices: 184983--185034 Score: 65
Period size: 14 Copynumber: 3.5 Consensus size: 15
184973 TATTTCTTCT
184983 TTTTTTCTCTTTGCC
1 TTTTTTCTCTTTGCC
184998 -TTTTT-TCTTTG-C
1 TTTTTTCTCTTTGCC
185010 TTCTTTTCTCTTTGCTC
1 TT-TTTTCTCTTTGC-C
185027 TTTTTTCT
1 TTTTTTCT
185035 TTTCTTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 1 0.03
13 7 0.22
14 9 0.28
15 6 0.19
16 6 0.19
17 3 0.09
ACGTcount: A:0.00, C:0.23, G:0.06, T:0.71
Consensus pattern (15 bp):
TTTTTTCTCTTTGCC
Found at i:185021 original size:7 final size:7
Alignment explanation
Indices: 184985--185054 Score: 54
Period size: 7 Copynumber: 9.9 Consensus size: 7
184975 TTTCTTCTTT
184985 TTTTCTC
1 TTTTCTC
*
184992 TTTGC-C
1 TTTTCTC
*
184998 TTTTTTC
1 TTTTCTC
*
185005 TTTGCTTC
1 TTTTC-TC
185013 TTTTCTC
1 TTTTCTC
*
185020 TTTGCTC
1 TTTTCTC
*
185027 TTTTTTC
1 TTTTCTC
185034 TTTTCT-
1 TTTTCTC
185040 TTTTCCTTC
1 TTTT-C-TC
185049 TTTTCT
1 TTTTCT
185055 TTGATTTGAT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
6 8 0.17
7 28 0.58
8 8 0.17
9 4 0.08
ACGTcount: A:0.00, C:0.24, G:0.04, T:0.71
Consensus pattern (7 bp):
TTTTCTC
Found at i:185034 original size:21 final size:20
Alignment explanation
Indices: 185010--185056 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
185000 TTTTCTTTGC
185010 TTCTTTTCTCTTTGCTCTT-TT
1 TTCTTTTCT-TTTGC-CTTCTT
*
185031 TTCTTTTCTTTTTCCTTCTT
1 TTCTTTTCTTTTGCCTTCTT
185051 TTCTTT
1 TTCTTT
185057 GATTTGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 3 0.12
20 12 0.50
21 9 0.38
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.74
Consensus pattern (20 bp):
TTCTTTTCTTTTGCCTTCTT
Found at i:185051 original size:29 final size:26
Alignment explanation
Indices: 184975--185044 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 26
184965 ATTTTATTTA
184975 TTTCTTCTT-TTTTTCTCTTTGCCTTT
1 TTTCTT-TTCTTTTTCTCTTTGCCTTT
*
185001 TTTCTTTGCTTCTTTTCTCTTTGCTCTTT
1 TTTCTTTTC-T-TTTTCTCTTTGC-CTTT
185030 TTTCTTTTCTTTTTC
1 TTTCTTTTCTTTTTC
185045 CTTCTTTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 1 0.03
26 6 0.16
27 6 0.16
28 13 0.34
29 12 0.32
ACGTcount: A:0.00, C:0.23, G:0.04, T:0.73
Consensus pattern (26 bp):
TTTCTTTTCTTTTTCTCTTTGCCTTT
Found at i:187581 original size:12 final size:12
Alignment explanation
Indices: 187566--187592 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
187556 AGGAAAATGA
187566 AAAAAACTTGAC
1 AAAAAACTTGAC
187578 AAAAAACTTGAC
1 AAAAAACTTGAC
187590 AAA
1 AAA
187593 GCTGAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.63, C:0.15, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAAAACTTGAC
Found at i:188916 original size:16 final size:16
Alignment explanation
Indices: 188890--188948 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
188880 TAGTTAGTAA
* *
188890 TTAGCATTTAGAAATG
1 TTAGCAGTTAGAAAAG
188906 TTAGCTA-TTAGAAAAG
1 TTAGC-AGTTAGAAAAG
*
188922 TTAACAGTTAGAAAAG
1 TTAGCAGTTAGAAAAG
*
188938 TTAGCGGTTAG
1 TTAGCAGTTAG
188949 CATAGTCCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 1 0.03
16 35 0.95
17 1 0.03
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (16 bp):
TTAGCAGTTAGAAAAG
Found at i:197189 original size:17 final size:18
Alignment explanation
Indices: 197167--197208 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
197157 CTTTCAATTA
197167 TTTATTTAATTATT-TCT
1 TTTATTTAATTATTATCT
*
197184 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
197202 TTTATTT
1 TTTATTT
197209 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:197267 original size:15 final size:16
Alignment explanation
Indices: 197249--197304 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 16
197239 TCTTTACTAC
197249 TATTAT-TTATTATTT
1 TATTATATTATTATTT
**
197264 TATTATATT-TCCTTT
1 TATTATATTATTATTT
197279 TATT-TATTATTATTT
1 TATTATATTATTATTT
*
197294 TATTTTATTAT
1 TATTATATTAT
197305 ACATTTTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
14 4 0.12
15 22 0.65
16 8 0.24
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTATATTATTATTT
Found at i:197299 original size:20 final size:20
Alignment explanation
Indices: 197249--197302 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
197239 TCTTTACTAC
*
197249 TATTA-TTTATTAT-TTTAT
1 TATTATTTTATTTTATTTAT
**
197267 TA-TATTTCCTTTTATTTAT
1 TATTATTTTATTTTATTTAT
197286 TATTATTTTATTTTATT
1 TATTATTTTATTTTATT
197303 ATACATTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 2 0.07
18 7 0.25
19 7 0.25
20 12 0.43
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTATTTTATTTTATTTAT
Done.