Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 122 of 325
Found at i:39126647 original size:36 final size:35
Alignment explanation
Indices: 39126606--39126675 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 35
39126596 TCTTGCCTCT
*
39126606 CTTTTCTTTTT-ATTTCATTTTCTTTTTCTTCTCTTG
1 CTTTTCTTTTTCATTTC-TTTTCTTTGT-TTCTCTTG
*
39126642 CTTTTCTTTTTCTTTTCTTTTCTTTGTTTCTCTT
1 CTTTTCTTTTTCATTTCTTTTCTTTGTTTCTCTT
39126676 TACAAGAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 7 0.23
36 20 0.65
37 4 0.13
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.74
Consensus pattern (35 bp):
CTTTTCTTTTTCATTTCTTTTCTTTGTTTCTCTTG
Found at i:39126648 original size:20 final size:20
Alignment explanation
Indices: 39126623--39126660 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39126613 TTTTATTTCA
39126623 TTTTCTTTTTCTTCTCTTGC
1 TTTTCTTTTTCTTCTCTTGC
*
39126643 TTTTCTTTTTCTTTTCTT
1 TTTTCTTTTTCTTCTCTT
39126661 TTCTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTCTTTTTCTTCTCTTGC
Found at i:39129380 original size:30 final size:30
Alignment explanation
Indices: 39129346--39129442 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
39129336 TAAACTAAAA
39129346 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
39129376 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
39129406 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
39129435 ATGAGCTA
1 -TGAGCTA
39129443 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 6
0.73 0.19 0.09
Matches are distributed among these distances:
29 3 0.06
30 45 0.88
31 3 0.06
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:39131150 original size:30 final size:31
Alignment explanation
Indices: 39131055--39131152 Score: 94
Period size: 30 Copynumber: 3.2 Consensus size: 31
39131045 TAAACTAAAA
*
39131055 TGAGCTAAGCTTTTAGCTCGTGAGCT-AAAGT
1 TGAGCTAAG-GTTTAGCTCGTGAGCTGAAAGT
* * * * * *
39131086 TGAGCTGAGGCTAAACTCTTAAGCTG-AAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
*
39131116 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
39131146 TGAGCTA
1 TGAGCTA
39131153 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
30 40 0.78
31 11 0.22
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.30
Consensus pattern (31 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTGAAAGT
Found at i:39136957 original size:30 final size:30
Alignment explanation
Indices: 39136886--39136968 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
39136876 CTTTTGTTTC
* *
39136886 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
39136917 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
39136946 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
39136969 GATTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:39136959 original size:12 final size:12
Alignment explanation
Indices: 39136944--39136975 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39136934 TTTTTCAATC
39136944 TCATTTTCTTTT
1 TCATTTTCTTTT
39136956 TCATTTTCTTTT
1 TCATTTTCTTTT
*
39136968 TGATTTTC
1 TCATTTTC
39136976 AAAGGCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.16, G:0.03, T:0.72
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:39137047 original size:5 final size:5
Alignment explanation
Indices: 39137037--39137099 Score: 58
Period size: 5 Copynumber: 12.0 Consensus size: 5
39137027 CTTTTTCCTC
*
39137037 TCTTT TCTTT T-TATT TCGTTT TCTTTT TCTTT T-TCT TCTTT TGCTTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTTT TCTTT TCTTT T-C-TTT
39137085 TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT
39137100 GTTTTCTCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
4 4 0.08
5 29 0.59
6 11 0.22
7 5 0.10
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (5 bp):
TCTTT
Found at i:39137059 original size:6 final size:6
Alignment explanation
Indices: 39137050--39137099 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
39137040 TTTCTTTTTA
*
39137050 TTTCGT TTTCTT TTTCTT TTTCTTCT TTTGCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTC-T-T TTT-CTT TTTCTT TTTCTT TTTCTT
39137099 T
1 T
39137100 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 18 0.46
7 5 0.13
8 5 0.13
9 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:39137083 original size:21 final size:20
Alignment explanation
Indices: 39137039--39137099 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 20
39137029 TTTTCCTCTC
39137039 TTTTCTTTTTATTTCGTTTTCT
1 TTTTCTTTTT-TTTC-TTTTCT
*
39137061 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTTTTCTTTT-CT
39137082 TTTTCTTTTCTTTTCTTT
1 TTTTCTTTT-TTTTCTTT
39137100 GTTTTCTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.11
21 14 0.40
22 17 0.49
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTCTTTTTTTTCTTTTCT
Found at i:39137100 original size:21 final size:21
Alignment explanation
Indices: 39137039--39137110 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
39137029 TTTTCCTCTC
*
39137039 TTTTCTTTTTATTTCGTTTTCT
1 TTTTCTTTTT-TTTCGTTTGCT
* *
39137061 TTTTCTTTTTCTTCTTTTGCT
1 TTTTCTTTTTTTTCGTTTGCT
39137082 TTTTCTTTTCTTTTC-TTTG-T
1 TTTTCTTTT-TTTTCGTTTGCT
39137102 TTTCTCTTT
1 TTT-TCTTT
39137111 ACAAAAATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
20 4 0.09
21 26 0.59
22 14 0.32
ACGTcount: A:0.01, C:0.17, G:0.04, T:0.78
Consensus pattern (21 bp):
TTTTCTTTTTTTTCGTTTGCT
Found at i:39140709 original size:21 final size:22
Alignment explanation
Indices: 39140683--39140726 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
39140673 AAACGAGCTC
39140683 GTTGAGCTAAGTTAAG-TTGAA
1 GTTGAGCTAAGTTAAGCTTGAA
* *
39140704 GTTGAGCTGATTTAAGCTTGAA
1 GTTGAGCTAAGTTAAGCTTGAA
39140726 G
1 G
39140727 GAGTATGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.34
Consensus pattern (22 bp):
GTTGAGCTAAGTTAAGCTTGAA
Found at i:39143354 original size:4 final size:4
Alignment explanation
Indices: 39143341--39143370 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
39143331 ATATTTGAAC
39143341 TAAA -AAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
39143371 TACACCAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:39146262 original size:29 final size:29
Alignment explanation
Indices: 39146201--39146290 Score: 128
Period size: 29 Copynumber: 3.1 Consensus size: 29
39146191 CACATACCTA
* *
39146201 TATATGGCCCACTAGGCCC-AATCATATT
1 TATATGGCCCATTAGGCCCAAATCACATT
*
39146229 TATATGGCCCATTAGGCCCAAATCACGTT
1 TATATGGCCCATTAGGCCCAAATCACATT
* *
39146258 TATATGGCCCATCAGGCCCAATTCACATT
1 TATATGGCCCATTAGGCCCAAATCACATT
39146287 TATA
1 TATA
39146291 GTCAAGCTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
28 18 0.33
29 37 0.67
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
TATATGGCCCATTAGGCCCAAATCACATT
Found at i:39148333 original size:20 final size:21
Alignment explanation
Indices: 39148295--39148343 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
39148285 TGAGCTAGAT
*
39148295 CGAGCTGAATTCTAGCTCAAA
1 CGAGCTGAATTCGAGCTCAAA
*
39148316 CGAGCTGAA-TCGAGCTCAAG
1 CGAGCTGAATTCGAGCTCAAA
*
39148336 TGAGCTGA
1 CGAGCTGA
39148344 TGGGAGCTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
CGAGCTGAATTCGAGCTCAAA
Found at i:39154819 original size:20 final size:20
Alignment explanation
Indices: 39154772--39154819 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
39154762 AGTAAGCTCG
39154772 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
39154792 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
39154812 GTTGAGCT
1 GTTGAGCT
39154820 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:39156099 original size:22 final size:22
Alignment explanation
Indices: 39156069--39156112 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39156059 TTTGGTATTT
39156069 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
39156091 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
39156113 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:39160522 original size:12 final size:12
Alignment explanation
Indices: 39160505--39160531 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39160495 AAACCGTATG
39160505 CAATTTTTTTTT
1 CAATTTTTTTTT
39160517 CAATTTTTTTTT
1 CAATTTTTTTTT
39160529 CAA
1 CAA
39160532 ACTCTTTTTT
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:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:39160872 original size:22 final size:22
Alignment explanation
Indices: 39160842--39160885 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39160832 TTTGGTATTT
39160842 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
39160864 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
39160886 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:39162915 original size:11 final size:12
Alignment explanation
Indices: 39162885--39162916 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
39162875 TTTCACTCTT
39162885 CTCTTTTTCAAA
1 CTCTTTTTCAAA
39162897 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
39162909 TTCTTTTT
1 CTCTTTTT
39162917 TCACTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:39162928 original size:27 final size:27
Alignment explanation
Indices: 39162898--39162959 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
39162888 TTTTTCAAAC
39162898 TCTTTTTCAA-ATTCTTTT-TTCACTTTT
1 TCTTTTTCAATATTCTTTTCTTCA--TTT
*
39162925 TCTTTTTCAATTTTCTTTTCTTCATTT
1 TCTTTTTCAATATTCTTTTCTTCATTT
39162952 TCTTTTTC
1 TCTTTTTC
39162960 TCTCACTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 21 0.66
28 7 0.22
29 4 0.12
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.69
Consensus pattern (27 bp):
TCTTTTTCAATATTCTTTTCTTCATTT
Found at i:39162929 original size:15 final size:13
Alignment explanation
Indices: 39162909--39162958 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 13
39162899 CTTTTTCAAA
39162909 TTCTTTTTTCACTT
1 TTCTTTTTTCA-TT
39162923 TT-TCTTTTTCAATT
1 TTCT-TTTTTC-ATT
39162937 TTCTTTTCTTCATT
1 TTCTTTT-TTCATT
39162951 TTCTTTTT
1 TTCTTTTT
39162959 CTCTCACTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.06
14 25 0.78
15 5 0.16
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (13 bp):
TTCTTTTTTCATT
Found at i:39162930 original size:14 final size:13
Alignment explanation
Indices: 39162898--39162959 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 13
39162888 TTTTTCAAAC
*
39162898 TCTTTTTCAA-AT
1 TCTTTTTCAATTT
*
39162910 TCTTTTTTCACTTTT
1 TC-TTTTTCA-ATTT
39162925 TCTTTTTCAATTT
1 TCTTTTTCAATTT
39162938 TCTTTTCTTC-ATTT
1 TC-TTT-TTCAATTT
39162952 TCTTTTTC
1 TCTTTTTC
39162960 TCTCACTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
12 5 0.12
13 15 0.36
14 16 0.38
15 6 0.14
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.69
Consensus pattern (13 bp):
TCTTTTTCAATTT
Found at i:39162986 original size:18 final size:18
Alignment explanation
Indices: 39162920--39163016 Score: 77
Period size: 18 Copynumber: 5.2 Consensus size: 18
39162910 TCTTTTTTCA
39162920 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTCAA-TTT
* **
39162939 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCAATTT
* ** **
39162959 CTCTCACTTTTTTGATTT
1 CTTTTTCTTTTTCAATTT
*
39162977 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCAATTT
*
39162995 CTTTTTCTTTTTCAATCT
1 CTTTTTCTTTTTCAATTT
39163013 CTTT
1 CTTT
39163017 CTCCTTTTCT
Statistics
Matches: 58, Mismatches: 18, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
18 40 0.69
19 3 0.05
20 7 0.12
21 8 0.14
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTTTTCAATTT
Found at i:39163005 original size:5 final size:6
Alignment explanation
Indices: 39162920--39163007 Score: 52
Period size: 6 Copynumber: 14.2 Consensus size: 6
39162910 TCTTTTTTCA
* * * **
39162920 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * **
39162971 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT C
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT C
39163008 AATCTCTTTC
Statistics
Matches: 59, Mismatches: 19, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
5 1 0.02
6 45 0.76
7 10 0.17
8 3 0.05
ACGTcount: A:0.08, C:0.19, G:0.02, T:0.70
Consensus pattern (6 bp):
CTTTTT
Found at i:39163024 original size:18 final size:18
Alignment explanation
Indices: 39162983--39163025 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
39162973 ATTTCTTTTT
* *
39162983 CTTTTGCAATTTCTTTTTC
1 CTTTT-CAATCTCTTTCTC
*
39163002 TTTTTCAATCTCTTTCTC
1 CTTTTCAATCTCTTTCTC
39163020 CTTTTC
1 CTTTTC
39163026 TCGCTCAATG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.09, C:0.26, G:0.02, T:0.63
Consensus pattern (18 bp):
CTTTTCAATCTCTTTCTC
Found at i:39168214 original size:10 final size:10
Alignment explanation
Indices: 39168199--39168260 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
39168189 ATTGAACCAT
*
39168199 TACCAATTCG
1 TACCAATTCA
*
39168209 TACCAAATACCA
1 TACC-AAT-TCA
*
39168221 TACCATTTCA
1 TACCAATTCA
39168231 TACCAATTCCA
1 TACCAATT-CA
* *
39168242 TACCATTTCG
1 TACCAATTCA
39168252 TACCAATTC
1 TACCAATTC
39168261 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:39168244 original size:21 final size:21
Alignment explanation
Indices: 39168199--39168261 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
39168189 ATTGAACCAT
* *
39168199 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
39168221 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
39168242 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
39168262 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:39168865 original size:20 final size:20
Alignment explanation
Indices: 39168818--39168865 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
39168808 AGTAAGCTCG
39168818 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
39168838 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
39168858 GTTGAGCT
1 GTTGAGCT
39168866 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:39175939 original size:20 final size:20
Alignment explanation
Indices: 39175914--39175954 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39175904 ATGAAAATAC
39175914 AAAAGAAAAAAAATGAGAAA
1 AAAAGAAAAAAAATGAGAAA
** *
39175934 AAAAGAGGAAAAATGATAAA
1 AAAAGAAAAAAAATGAGAAA
39175954 A
1 A
39175955 GAAAATGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAAAAATGAGAAA
Found at i:39175978 original size:33 final size:32
Alignment explanation
Indices: 39175914--39175992 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 32
39175904 ATGAAAATAC
* *
39175914 AAAAG-AAAA-AAAATGAGAAAAAAAGAGGAA
1 AAAAGAAAAAGAAAATGAGAAAAAAACAAGAA
* *
39175944 AAATGATAAAAGAAAATGAGAAAAAGACAAGAA
1 AAAAGA-AAAAGAAAATGAGAAAAAAACAAGAA
39175977 AAAAGAAAGAAGAAAA
1 AAAAGAAA-AAGAAAA
39175993 AGGAAAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.10
32 6 0.15
33 30 0.75
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.05
Consensus pattern (32 bp):
AAAAGAAAAAGAAAATGAGAAAAAAACAAGAA
Found at i:39181737 original size:15 final size:15
Alignment explanation
Indices: 39181717--39181764 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
39181707 TCAAAGATGG
39181717 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
39181732 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
39181747 -TTTATGGATATAAA
1 GTTTATGGATATGAA
39181761 GTTT
1 GTTT
39181765 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:39181744 original size:29 final size:29
Alignment explanation
Indices: 39181711--39181770 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
39181701 AAGGATTCAA
* *
39181711 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
39181740 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
39181769 AG
1 AG
39181771 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:39182901 original size:19 final size:19
Alignment explanation
Indices: 39182877--39182916 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39182867 AGCTCCCATG
39182877 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
39182896 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
39182915 TA
1 TA
39182917 TCAACTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:39186534 original size:15 final size:15
Alignment explanation
Indices: 39186514--39186579 Score: 59
Period size: 14 Copynumber: 4.5 Consensus size: 15
39186504 ACGGTATTGT
39186514 AAAAAAAAATA-T-A
1 AAAAAAAAATATTCA
*
39186527 TAAAAAAAA-ATTCGA
1 AAAAAAAAATATTC-A
* *
39186542 AAAAAAAAAAATTTGA
1 AAAAAAAAATA-TTCA
39186558 AAAAAAAAA-ATTCA
1 AAAAAAAAATATTCA
39186572 AAAAAAAA
1 AAAAAAAA
39186580 GTTTGTATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
12 1 0.02
13 9 0.20
14 11 0.25
15 10 0.23
16 11 0.25
17 2 0.05
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (15 bp):
AAAAAAAAATATTCA
Found at i:39186547 original size:16 final size:16
Alignment explanation
Indices: 39186528--39186579 Score: 81
Period size: 15 Copynumber: 3.4 Consensus size: 16
39186518 AAAAATATAT
39186528 AAAAAAAAATTCGAAA
1 AAAAAAAAATTCGAAA
*
39186544 AAAAAAAAATTTG-AA
1 AAAAAAAAATTCGAAA
39186559 AAAAAAAAATTC-AAA
1 AAAAAAAAATTCGAAA
39186574 AAAAAA
1 AAAAAA
39186580 GTTTGTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 21 0.64
16 12 0.36
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (16 bp):
AAAAAAAAATTCGAAA
Found at i:39186638 original size:13 final size:13
Alignment explanation
Indices: 39186620--39186645 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39186610 ATTTAGTATT
39186620 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
39186633 GAAGAAAAAAAAA
1 GAAGAAAAAAAAA
39186646 TTCGGAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAAAA
Found at i:39186685 original size:20 final size:20
Alignment explanation
Indices: 39186661--39186699 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39186651 AATTAAAACA
*
39186661 AAAAAAGAAGAAAAAAAAATC
1 AAAATAGAA-AAAAAAAAATC
*
39186682 AAAATTGAAAAAAAAAAA
1 AAAATAGAAAAAAAAAAA
39186700 GTGATTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (20 bp):
AAAATAGAAAAAAAAAAATC
Found at i:39186697 original size:33 final size:34
Alignment explanation
Indices: 39186617--39186700 Score: 118
Period size: 34 Copynumber: 2.5 Consensus size: 34
39186607 TGTATTTAGT
**
39186617 ATTGAAGAAAAAAAAAGAAGAAAAAAAAATTCGGA
1 ATTGAA-AAAAAAAAAGAAGAAAAAAAAATTCAAA
39186652 ATT-AAAACAAAAAAAGAAGAAAAAAAAA-TCAAA
1 ATTGAAAA-AAAAAAAGAAGAAAAAAAAATTCAAA
39186685 ATTGAAAAAAAAAAAG
1 ATTGAAAAAAAAAAAG
39186701 TGATTGAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
33 16 0.36
34 26 0.58
35 3 0.07
ACGTcount: A:0.74, C:0.04, G:0.12, T:0.11
Consensus pattern (34 bp):
ATTGAAAAAAAAAAAGAAGAAAAAAAAATTCAAA
Found at i:39187611 original size:21 final size:20
Alignment explanation
Indices: 39187586--39187630 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
39187576 AATCTTGAAT
*
39187586 GAAATTGAGAGA-AGAAAAAA
1 GAAAATGAGAGAGAG-AAAAA
*
39187606 GAAAATGAGAGTGAGAAAAA
1 GAAAATGAGAGAGAGAAAAA
39187626 GAAAA
1 GAAAA
39187631 AAGAATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (20 bp):
GAAAATGAGAGAGAGAAAAA
Found at i:39187647 original size:27 final size:27
Alignment explanation
Indices: 39187583--39187648 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
39187573 ACGAATCTTG
* *
39187583 AATGAAATTGAG-AGAAGAAAAAAGAA
1 AATGAGATTGAGAAAAAGAAAAAAGAA
*
39187609 AATGAGAGTGAGAAAAAGAAAAAAGAA
1 AATGAGATTGAGAAAAAGAAAAAAGAA
**
39187636 TTTGAGATTGAGA
1 AATGAGATTGAGA
39187649 TTGATATTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.15
Consensus pattern (27 bp):
AATGAGATTGAGAAAAAGAAAAAAGAA
Found at i:39187657 original size:12 final size:12
Alignment explanation
Indices: 39187637--39187672 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
39187627 AAAAAAGAAT
*
39187637 TTGAGATTGAGA
1 TTGATATTGAGA
*
39187649 TTGATATTGATA
1 TTGATATTGAGA
39187661 TTGATATTGAGA
1 TTGATATTGAGA
39187673 AAAAAATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (12 bp):
TTGATATTGAGA
Found at i:39198840 original size:9 final size:9
Alignment explanation
Indices: 39198826--39198871 Score: 74
Period size: 9 Copynumber: 5.0 Consensus size: 9
39198816 AAATCACTCT
39198826 TTTTTTTTA
1 TTTTTTTTA
*
39198835 TTTTTTTGA
1 TTTTTTTTA
39198844 TTTTTTTTGA
1 TTTTTTTT-A
39198854 TTTTTTTTA
1 TTTTTTTTA
39198863 TTTTTTTTA
1 TTTTTTTTA
39198872 ACTTGTACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 25 0.74
10 9 0.26
ACGTcount: A:0.11, C:0.00, G:0.04, T:0.85
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:39198849 original size:19 final size:19
Alignment explanation
Indices: 39198825--39198870 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
39198815 TAAATCACTC
*
39198825 TTTTTTTTTATTTTTTTGA
1 TTTTTTTTGATTTTTTTGA
*
39198844 TTTTTTTTGATTTTTTTTA
1 TTTTTTTTGATTTTTTTGA
39198863 TTTTTTTT
1 TTTTTTTT
39198871 AACTTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.09, C:0.00, G:0.04, T:0.87
Consensus pattern (19 bp):
TTTTTTTTGATTTTTTTGA
Found at i:39202886 original size:23 final size:22
Alignment explanation
Indices: 39202835--39202886 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
39202825 CCTCGTCTTT
*
39202835 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
39202857 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
39202880 TTCTTTT
1 TTCTTTT
39202887 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:39212396 original size:17 final size:19
Alignment explanation
Indices: 39212357--39212401 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
39212347 AAAAAAGAAA
39212357 AAAAAAGAAGTTTCAGAAGT
1 AAAAAA-AAGTTTCAGAAGT
*
39212377 AAAAAAAA-TTT-AGAATT
1 AAAAAAAAGTTTCAGAAGT
39212394 AAAAAAAA
1 AAAAAAAA
39212402 AAGAAGAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 13 0.54
18 3 0.12
19 2 0.08
20 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.20
Consensus pattern (19 bp):
AAAAAAAAGTTTCAGAAGT
Found at i:39216554 original size:17 final size:19
Alignment explanation
Indices: 39216515--39216559 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
39216505 AAAAAAGAAA
39216515 AAAAAAGAAGTTTCAGAAGT
1 AAAAAA-AAGTTTCAGAAGT
*
39216535 AAAAAAAA-TTT-AGAATT
1 AAAAAAAAGTTTCAGAAGT
39216552 AAAAAAAA
1 AAAAAAAA
39216560 AAGAAGAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 13 0.54
18 3 0.12
19 2 0.08
20 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.20
Consensus pattern (19 bp):
AAAAAAAAGTTTCAGAAGT
Found at i:39223389 original size:21 final size:21
Alignment explanation
Indices: 39223344--39223406 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
39223334 TTTGAACCAT
* *
39223344 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
39223366 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
39223387 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
39223407 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:39225947 original size:5 final size:5
Alignment explanation
Indices: 39225937--39225993 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
39225927 CTCTTGCCTC
*
39225937 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
39225984 TCTTT TCTTT
1 TCTTT TCTTT
39225994 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:39225977 original size:15 final size:14
Alignment explanation
Indices: 39225937--39225993 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
39225927 CTCTTGCCTC
*
39225937 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
39225952 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
39225967 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
39225984 TCTTTTCTTT
1 TCTTTTCTTT
39225994 ATTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:39226003 original size:21 final size:20
Alignment explanation
Indices: 39225935--39226004 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
39225925 GCCTCTTGCC
39225935 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTT-TTT-ATTT
**
39225958 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTT-TTTTTATTT
39225978 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
39225998 TCTCTTT
1 TCTCTTT
39226005 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 3 0.08
20 17 0.44
21 9 0.23
22 7 0.18
23 3 0.08
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:39226972 original size:11 final size:12
Alignment explanation
Indices: 39226910--39226978 Score: 88
Period size: 11 Copynumber: 5.8 Consensus size: 12
39226900 ATAAATCACT
*
39226910 TTTTTTTTTGAA
1 TTTTTTTTCGAA
39226922 TTTTTTTT-GAA
1 TTTTTTTTCGAA
39226933 TTTTTTTTCGAA
1 TTTTTTTTCGAA
39226945 -TTTTTTTCGAA
1 TTTTTTTTCGAA
*
39226956 TCTTTTTTTTCGAT
1 --TTTTTTTTCGAA
39226970 TTTTTTTTC
1 TTTTTTTTC
39226979 AAACTTGTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
11 22 0.42
12 20 0.38
14 10 0.19
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.72
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:39227270 original size:14 final size:14
Alignment explanation
Indices: 39227236--39227283 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
39227226 GTACGAATGG
**
39227236 AATGGTAGGAATGA
1 AATGGTAGGAACAA
*
39227250 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
39227264 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
39227278 ATTGGT
1 AATGGT
39227284 CGGTTTAGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.44, C:0.04, G:0.31, T:0.21
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:39237295 original size:23 final size:22
Alignment explanation
Indices: 39237243--39237295 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
39237233 TCCACATCTT
*
39237243 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
39237265 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
39237288 TTTCTTTT
1 TTTCTTTT
39237296 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39237347 original size:21 final size:22
Alignment explanation
Indices: 39237300--39237348 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
39237290 TCTTTTTCAC
*
39237300 TCTCAATCTCTTTTTGCTCTTT
1 TCTCATTCTCTTTTTGCTCTTT
39237322 T-TCATTCTCTTTTT-CT-TTT
1 TCTCATTCTCTTTTTGCTCTTT
39237341 TCCTCATT
1 T-CTCATT
39237349 TGTTTTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 2 0.08
21 17 0.71
22 1 0.04
ACGTcount: A:0.08, C:0.27, G:0.02, T:0.63
Consensus pattern (22 bp):
TCTCATTCTCTTTTTGCTCTTT
Found at i:39241713 original size:11 final size:12
Alignment explanation
Indices: 39241697--39241729 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
39241687 CGTATCACAA
39241697 TCTCTTTT-TTC
1 TCTCTTTTGTTC
39241708 TCTCTTTTGTTC
1 TCTCTTTTGTTC
39241720 TCT-TTTTGTT
1 TCTCTTTTGTT
39241730 TTTCAAATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.00, C:0.21, G:0.06, T:0.73
Consensus pattern (12 bp):
TCTCTTTTGTTC
Found at i:39242961 original size:20 final size:20
Alignment explanation
Indices: 39242936--39242983 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
39242926 ATTCACGAAT
39242936 ATTTTTTT-GAATTGTTTTGA
1 ATTTTTTTAGAATT-TTTTGA
39242956 ATTTTTTTAGAATTTTTTGA
1 ATTTTTTTAGAATTTTTTGA
39242976 ATTTTTTT
1 ATTTTTTT
39242984 TCAAATACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (20 bp):
ATTTTTTTAGAATTTTTTGA
Found at i:39242983 original size:10 final size:10
Alignment explanation
Indices: 39242936--39242983 Score: 71
Period size: 10 Copynumber: 4.8 Consensus size: 10
39242926 ATTCACGAAT
39242936 ATTTTTTTGA
1 ATTTTTTTGA
*
39242946 ATTGTTTTGA
1 ATTTTTTTGA
39242956 ATTTTTTTAGA
1 ATTTTTTT-GA
39242967 A-TTTTTTGA
1 ATTTTTTTGA
39242976 ATTTTTTT
1 ATTTTTTT
39242984 TCAAATACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 3 0.09
10 28 0.82
11 3 0.09
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (10 bp):
ATTTTTTTGA
Found at i:39248151 original size:18 final size:18
Alignment explanation
Indices: 39248130--39248164 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39248120 TTTTTCTTTT
39248130 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
39248148 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
39248165 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:39249126 original size:12 final size:11
Alignment explanation
Indices: 39249111--39249141 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
39249101 TTTTCATCAA
39249111 TTTTTTTTAAT
1 TTTTTTTTAAT
*
39249122 TTTTTTTTGAT
1 TTTTTTTTAAT
39249133 TTTTTTTTA
1 TTTTTTTTA
39249142 CTCCAATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (11 bp):
TTTTTTTTAAT
Found at i:39252630 original size:18 final size:18
Alignment explanation
Indices: 39252609--39252643 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
39252599 TTTTTCTTTT
39252609 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
39252627 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
39252644 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:39256168 original size:52 final size:50
Alignment explanation
Indices: 39256111--39256233 Score: 156
Period size: 50 Copynumber: 2.4 Consensus size: 50
39256101 ATGAACAAAT
* * *
39256111 GAGTTACTTAATGCATGACTTAATTTAATGATACAAACTTTAACTAACATGG
1 GAGTTACATAATGCATGACTTAATTT-ATGATACAAAC-TTAACTAACACGA
* * * *
39256163 GAGTTACATAATGCATGTCATAATTTATGATGCAAACTTAACTTACACGA
1 GAGTTACATAATGCATGACTTAATTTATGATACAAACTTAACTAACACGA
*
39256213 GAATTACATAATGCATGACTT
1 GAGTTACATAATGCATGACTT
39256234 TATTAAATAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
50 28 0.46
51 10 0.16
52 23 0.38
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (50 bp):
GAGTTACATAATGCATGACTTAATTTATGATACAAACTTAACTAACACGA
Found at i:39256306 original size:39 final size:39
Alignment explanation
Indices: 39256250--39256326 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
39256240 ATATAGAACA
*
39256250 CATACTAATGTTATTCAAACTATAACATAATTAAAGACT
1 CATACTAATGATATTCAAACTATAACATAATTAAAGACT
*
39256289 CATACTAATGATGTTCAAACTATAACATAATTAAAGAC
1 CATACTAATGATATTCAAACTATAACATAATTAAAGAC
39256327 ATAAACTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (39 bp):
CATACTAATGATATTCAAACTATAACATAATTAAAGACT
Found at i:39256335 original size:39 final size:39
Alignment explanation
Indices: 39256253--39256335 Score: 123
Period size: 39 Copynumber: 2.1 Consensus size: 39
39256243 TAGAACACAT
* *
39256253 ACTAATGTTATTCAAACTATAACATAATTAAAGACTCAT
1 ACTAATGATATTCAAACTATAACATAATTAAAGACTCAA
*
39256292 ACTAATGATGTTCAAACTATAACATAATTAAAGACAT-AA
1 ACTAATGATATTCAAACTATAACATAATTAAAGAC-TCAA
39256331 ACTAA
1 ACTAA
39256336 AATAACTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 39 0.98
40 1 0.03
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.30
Consensus pattern (39 bp):
ACTAATGATATTCAAACTATAACATAATTAAAGACTCAA
Found at i:39273057 original size:12 final size:12
Alignment explanation
Indices: 39273028--39273061 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39273018 AACTCATTTC
39273028 CTTCTTTCTTCAA
1 CTTCTTT-TTCAA
39273041 CTTCTTTTTCAA
1 CTTCTTTTTCAA
*
39273053 TTTCTTTTT
1 CTTCTTTTT
39273062 GTTTTCACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (12 bp):
CTTCTTTTTCAA
Found at i:39278823 original size:14 final size:14
Alignment explanation
Indices: 39278801--39278848 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
39278791 ACCTAAACCG
* *
39278801 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
39278815 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
39278829 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
39278843 ACCATT
1 ACCATT
39278849 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:39280749 original size:20 final size:20
Alignment explanation
Indices: 39280726--39280773 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
39280716 TCCAGCTCAA
*
39280726 TTTATCTCATTTGAGCTTGT
1 TTTAGCTCATTTGAGCTTGT
** *
39280746 TTTAGCTTGTTTGAGTTTGT
1 TTTAGCTCATTTGAGCTTGT
39280766 TTTAGCTC
1 TTTAGCTC
39280774 GTTCTTTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.56
Consensus pattern (20 bp):
TTTAGCTCATTTGAGCTTGT
Found at i:39280752 original size:10 final size:10
Alignment explanation
Indices: 39280739--39280772 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
39280729 ATCTCATTTG
39280739 AGCTTGTTTT
1 AGCTTGTTTT
*
39280749 AGCTTGTTTG
1 AGCTTGTTTT
*
39280759 AGTTTGTTTT
1 AGCTTGTTTT
39280769 AGCT
1 AGCT
39280773 CGTTCTTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.12, C:0.09, G:0.24, T:0.56
Consensus pattern (10 bp):
AGCTTGTTTT
Found at i:39286100 original size:56 final size:56
Alignment explanation
Indices: 39285995--39286101 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
39285985 ATTAATGCCG
* * * * *
39285995 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGTCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGTCGT
39286051 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
39286102 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGTCGT
Found at i:39286749 original size:20 final size:20
Alignment explanation
Indices: 39286724--39286778 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
39286714 ACGAGTTAAA
* *
39286724 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
39286744 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
39286764 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
39286779 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:39288297 original size:17 final size:15
Alignment explanation
Indices: 39288260--39288298 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
39288250 TATCTCCCAC
39288260 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
39288276 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
39288293 TCATTT
1 TCATTT
39288299 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:39290636 original size:56 final size:56
Alignment explanation
Indices: 39290531--39290637 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
39290521 ATTAATGCCG
* * * * *
39290531 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGCAGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCAGT
39290587 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
39290638 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCAGT
Found at i:39291286 original size:20 final size:20
Alignment explanation
Indices: 39291261--39291315 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
39291251 ACGAGTTAAA
* *
39291261 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
39291281 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
39291301 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
39291316 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:39293201 original size:26 final size:26
Alignment explanation
Indices: 39293171--39293223 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
39293161 AATTGTAGTT
*
39293171 AAATG-ATAGATATATATGCTATTATG
1 AAATGTATAAATATATAT-CTATTATG
* *
39293197 AAATGTATAAATTTATATTTATTATG
1 AAATGTATAAATATATATCTATTATG
39293223 A
1 A
39293224 CCGAATATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (26 bp):
AAATGTATAAATATATATCTATTATG
Found at i:39294089 original size:14 final size:14
Alignment explanation
Indices: 39294070--39294114 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
39294060 AACTCATCTT
*
39294070 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
39294084 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
39294097 AATTTAATTTAATG
1 AGTTTAATTTAATG
39294111 AGTT
1 AGTT
39294115 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:39298900 original size:14 final size:14
Alignment explanation
Indices: 39298881--39298925 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
39298871 AACTCATCTT
*
39298881 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
39298895 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
39298908 AATTTAATTTAATG
1 AGTTTAATTTAATG
39298922 AGTT
1 AGTT
39298926 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:39302169 original size:22 final size:22
Alignment explanation
Indices: 39302141--39302184 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39302131 TTTTGAACCA
39302141 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
39302163 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
39302185 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:39303200 original size:18 final size:19
Alignment explanation
Indices: 39303157--39303202 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
39303147 CGAGAGAAGC
*
39303157 GAAAAAG-AGAAAGAATGT
1 GAAAAAGAAAAAAGAATGT
* *
39303175 GAACAAGAAAAAAGAGTG-
1 GAAAAAGAAAAAAGAATGT
39303193 GAAAAAGAAA
1 GAAAAAGAAA
39303203 TTGAGATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.65, C:0.02, G:0.26, T:0.07
Consensus pattern (19 bp):
GAAAAAGAAAAAAGAATGT
Found at i:39308562 original size:13 final size:12
Alignment explanation
Indices: 39308532--39308587 Score: 53
Period size: 12 Copynumber: 4.7 Consensus size: 12
39308522 AATGTGAAAC
*
39308532 AAAAAGAAATTG
1 AAAAAGAAGTTG
39308544 AAAAAGAAGTTG
1 AAAAAGAAGTTG
*
39308556 AAGAAAGAAG-AG
1 AA-AAAGAAGTTG
*
39308568 AAAATG-AGTTAG
1 AAAAAGAAGTT-G
39308580 AAAAAGAA
1 AAAAAGAA
39308588 ACAAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 22 0.63
13 8 0.23
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.12
Consensus pattern (12 bp):
AAAAAGAAGTTG
Found at i:39320658 original size:18 final size:18
Alignment explanation
Indices: 39320637--39320696 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
39320627 GACCTCACTC
39320637 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** *
39320655 TCTTTTTCAATCTCTTTT
1 TCTTTTTTGATTTCTTTT
39320673 TCTTTTCTTTTGATTTCTTTT
1 TC--TT-TTTTGATTTCTTTT
39320694 TCT
1 TCT
39320697 CGCTCGCACT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 17 0.52
19 1 0.03
20 2 0.06
21 13 0.39
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:39336518 original size:20 final size:20
Alignment explanation
Indices: 39336493--39336547 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
39336483 TGTGGTTCAA
*
39336493 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
39336513 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
39336533 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
39336548 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:39343264 original size:20 final size:19
Alignment explanation
Indices: 39343241--39343306 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
39343231 AAGCTCAAAC
39343241 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
39343261 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
39343281 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
39343301 GAGCTA
1 GAGCTA
39343307 GGAAAAACTA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:39343268 original size:30 final size:30
Alignment explanation
Indices: 39343232--39343306 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
39343222 ACTTAAGCCA
39343232 AGCTCAAACGAGCTAAAGTAAGCTAAAT-TG
1 AGCTCAAACGAGCTAAAGTAAGCT-AATGTG
* *
39343262 AGCTCAAACGAGCTAAATTAAGCTCATGTG
1 AGCTCAAACGAGCTAAAGTAAGCTAATGTG
39343292 AGCT-AAATCGAGCTA
1 AGCTCAAA-CGAGCTA
39343307 GGAAAAACTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 5 0.12
30 36 0.88
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (30 bp):
AGCTCAAACGAGCTAAAGTAAGCTAATGTG
Found at i:39344395 original size:30 final size:31
Alignment explanation
Indices: 39344361--39344457 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
39344351 AGCTCACTCC
*
39344361 TAGCTC-ACTTTCAACTTACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
* * * *
39344391 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
* * *
39344421 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTTACGAGCTAAACCT
39344451 TAGCTCA
1 TAGCTCA
39344458 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 48 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTTACGAGCTAAACCT
Found at i:39352864 original size:27 final size:27
Alignment explanation
Indices: 39352830--39353006 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39352820 TAAATTGTAC
39352830 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
39352857 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
39352883 ATGCACTAAGTGTGCGAATTGAC-ATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
39352910 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
39352938 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39352965 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
39352992 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39353007 GACTCAATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
26 18 0.14
27 93 0.72
28 18 0.14
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:39352943 original size:81 final size:80
Alignment explanation
Indices: 39352831--39352985 Score: 231
Period size: 81 Copynumber: 1.9 Consensus size: 80
39352821 AAATTGTACA
* *
39352831 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
39352895 TGCGAATTGACATGCG
65 TGCGAATTGACATGCG
** *
39352911 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
39352976 TGCGAGTTGA
65 TGCGAATTGA
39352986 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
80 15 0.22
81 51 0.76
82 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (80 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACATGCG
Found at i:39363166 original size:11 final size:10
Alignment explanation
Indices: 39363150--39363188 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
39363140 TGTAGATTCA
39363150 AAAAAAAATCG
1 AAAAAAAAT-G
39363161 AAAAAAAATG
1 AAAAAAAATG
*
39363171 AAAAAAATTG
1 AAAAAAAATG
39363181 AAAAAAAA
1 AAAAAAAA
39363189 ATTGCATACG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.10
Consensus pattern (10 bp):
AAAAAAAATG
Found at i:39363176 original size:20 final size:20
Alignment explanation
Indices: 39363151--39363188 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39363141 GTAGATTCAA
39363151 AAAAAAATCGAAAAAAAATG
1 AAAAAAATCGAAAAAAAATG
*
39363171 AAAAAAATTGAAAAAAAA
1 AAAAAAATCGAAAAAAAA
39363189 ATTGCATACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.11
Consensus pattern (20 bp):
AAAAAAATCGAAAAAAAATG
Found at i:39363192 original size:12 final size:11
Alignment explanation
Indices: 39363150--39363188 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
39363140 TGTAGATTCA
*
39363150 AAAAAAAATCG
1 AAAAAAAATTG
39363161 AAAAAAAA-TG
1 AAAAAAAATTG
39363171 -AAAAAAATTG
1 AAAAAAAATTG
39363181 AAAAAAAA
1 AAAAAAAA
39363189 ATTGCATACG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 7 0.28
10 3 0.12
11 15 0.60
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.10
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:39372426 original size:12 final size:12
Alignment explanation
Indices: 39372410--39372447 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
39372400 TTTTTGCTCG
39372410 ATTTTTTTTTCA
1 ATTTTTTTTTCA
* *
39372422 CTTTTTTTTTGA
1 ATTTTTTTTTCA
39372434 ATTTTTTTTTCA
1 ATTTTTTTTTCA
39372446 AT
1 AT
39372448 CAAAAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.74
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:39372426 original size:24 final size:24
Alignment explanation
Indices: 39372399--39372445 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
39372389 TCTTTTCTTT
39372399 TTTTTTGCTCG-ATTTTTTTTTCAC
1 TTTTTT-CTCGAATTTTTTTTTCAC
* *
39372423 TTTTTTTTTGAATTTTTTTTTCA
1 TTTTTTCTCGAATTTTTTTTTCA
39372446 ATCAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.72
Consensus pattern (24 bp):
TTTTTTCTCGAATTTTTTTTTCAC
Found at i:39373985 original size:20 final size:20
Alignment explanation
Indices: 39373960--39374003 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
39373950 GGGTTAAGAT
*
39373960 TGAGTTGAATTGAGCTTGAG
1 TGAGTTGAATTGAGCTCGAG
*
39373980 TGAGTTGACTTGAGCTCGAG
1 TGAGTTGAATTGAGCTCGAG
39374000 TGAG
1 TGAG
39374004 CTGGAAACGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.36, T:0.32
Consensus pattern (20 bp):
TGAGTTGAATTGAGCTCGAG
Found at i:39374300 original size:27 final size:27
Alignment explanation
Indices: 39374270--39374321 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
39374260 ACAAGTGAGG
39374270 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
39374297 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
39374322 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:39379520 original size:17 final size:18
Alignment explanation
Indices: 39379494--39379535 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
39379484 CAAATGAGAG
*
39379494 AAAA-AGAAAA-TAGGGA
1 AAAAGAGAAAATTAAGGA
39379510 AAAAGAGAAAATTAAGGA
1 AAAAGAGAAAATTAAGGA
39379528 AAAAGAGA
1 AAAAGAGA
39379536 GAGAAAAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.17
17 6 0.26
18 13 0.57
ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07
Consensus pattern (18 bp):
AAAAGAGAAAATTAAGGA
Found at i:39386518 original size:22 final size:22
Alignment explanation
Indices: 39386488--39386531 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39386478 TTTGGTATTT
39386488 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
39386510 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
39386532 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:39388843 original size:21 final size:22
Alignment explanation
Indices: 39388797--39388843 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
39388787 CATTTTTCTT
*
39388797 TTCTTTTTCACTCTCTCTCAAT
1 TTCTTTTTCACTCTCTCTCAAA
* *
39388819 TTCTTTTTCAGT-TCTTTCAAA
1 TTCTTTTTCACTCTCTCTCAAA
39388840 TTCT
1 TTCT
39388844 CCAAAGATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.15, C:0.26, G:0.02, T:0.57
Consensus pattern (22 bp):
TTCTTTTTCACTCTCTCTCAAA
Found at i:39400742 original size:14 final size:14
Alignment explanation
Indices: 39400720--39400764 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
39400710 TTGAAGAAGC
39400720 AACTCATTAAATTA
1 AACTCATTAAATTA
*
39400734 AATTCATTAAA-TA
1 AACTCATTAAATTA
*
39400747 AACTCATTTAATTA
1 AACTCATTAAATTA
39400761 AACT
1 AACT
39400765 AAGATGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:39400808 original size:42 final size:42
Alignment explanation
Indices: 39400747--39400852 Score: 194
Period size: 42 Copynumber: 2.5 Consensus size: 42
39400737 TCATTAAATA
39400747 AACTCATTTAATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTT-ATTAAACTAAGATGAGTTGTATTAATGACCAGC
39400790 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
1 AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
*
39400832 AACTAATTTATTAAACTAAGA
1 AACTCATTTATTAAACTAAGA
39400853 GGCTTAAATG
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
42 53 0.85
43 9 0.15
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (42 bp):
AACTCATTTATTAAACTAAGATGAGTTGTATTAATGACCAGC
Found at i:39405113 original size:11 final size:10
Alignment explanation
Indices: 39405097--39405155 Score: 66
Period size: 11 Copynumber: 5.7 Consensus size: 10
39405087 CATAAATCAC
39405097 TTTTTTTTCAA
1 TTTTTTTT-AA
*
39405108 TTTTTTTTTA
1 TTTTTTTTAA
39405118 TTTTTTTTAAA
1 TTTTTTTT-AA
*
39405129 TTTTTTTCGAA
1 TTTTTTT-TAA
39405140 TTTTTTTT-A
1 TTTTTTTTAA
39405149 TTTTTTT
1 TTTTTTT
39405156 AACTTGTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
9 8 0.19
10 9 0.21
11 25 0.60
ACGTcount: A:0.15, C:0.03, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:39407698 original size:24 final size:23
Alignment explanation
Indices: 39407670--39407726 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
39407660 ATACCATTTC
**
39407670 ATACCATTTCGTACCAATTCCCAA
1 ATACCATTTCGTACCAA-AACCAA
***
39407694 ATACCAAAACGTACCAAAACCAA
1 ATACCATTTCGTACCAAAACCAA
39407717 ATACCATTTC
1 ATACCATTTC
39407727 TTAATTATCC
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.42, C:0.32, G:0.04, T:0.23
Consensus pattern (23 bp):
ATACCATTTCGTACCAAAACCAA
Found at i:39409422 original size:20 final size:20
Alignment explanation
Indices: 39409399--39409452 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
39409389 AGCTCCGTCC
39409399 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** * *
39409419 AGCTCGTTTTAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
*
39409439 AGCTCAACTGAGCT
1 AGCTCAACTCAGCT
39409453 TACTTTCAGC
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.33
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:39409710 original size:15 final size:15
Alignment explanation
Indices: 39409690--39409725 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
39409680 TAGTTATATT
39409690 TTAATTAATTTTGTG
1 TTAATTAATTTTGTG
39409705 TTAATTAATTTTGTG
1 TTAATTAATTTTGTG
39409720 TTAATT
1 TTAATT
39409726 CATGAAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (15 bp):
TTAATTAATTTTGTG
Found at i:39413948 original size:13 final size:12
Alignment explanation
Indices: 39413914--39413982 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 12
39413904 AAAACAATGG
39413914 TCAATTTTTTTT
1 TCAATTTTTTTT
39413926 TCAAGGTTTTTTTT
1 TCAA--TTTTTTTT
39413940 TCTAA--TTTTTT
1 TC-AATTTTTTTT
*
39413951 TC-A-CTTTTTT
1 TCAATTTTTTTT
*
39413961 TGAA--TTTTTT
1 TCAATTTTTTTT
39413971 TCAATTTTTTTT
1 TCAATTTTTTTT
39413983 AAACTTACTT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
9 1 0.02
10 16 0.33
11 9 0.19
12 10 0.21
14 10 0.21
15 2 0.04
ACGTcount: A:0.16, C:0.09, G:0.04, T:0.71
Consensus pattern (12 bp):
TCAATTTTTTTT
Found at i:39413968 original size:9 final size:10
Alignment explanation
Indices: 39413934--39413981 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
39413924 TTTCAAGGTT
39413934 TTTTTTTCTAA
1 TTTTTTTC-AA
*
39413945 TTTTTTTCAC
1 TTTTTTTCAA
*
39413955 TTTTTTTGAA
1 TTTTTTTCAA
39413965 TTTTTTTCAA
1 TTTTTTTCAA
39413975 TTTTTTT
1 TTTTTTT
39413982 TAAACTTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
10 25 0.76
11 8 0.24
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (10 bp):
TTTTTTTCAA
Found at i:39433970 original size:29 final size:29
Alignment explanation
Indices: 39433904--39433960 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
39433894 GATTCAAAGA
* *
39433904 TGGGTTTGTGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
39433933 TGGGTTTATGGATATAAAGCTTT-TGTAG
1 TGGGTTTATGGATATAAAG-TTTATGTAG
39433961 GTTTGGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.23, C:0.02, G:0.32, T:0.44
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:39434423 original size:20 final size:20
Alignment explanation
Indices: 39434377--39434423 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
39434367 AGCTCGTTTC
*
39434377 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
39434397 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
39434417 CAGCTCA
1 CAGCTCA
39434424 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:39441597 original size:56 final size:55
Alignment explanation
Indices: 39441481--39441598 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
39441471 TGCATGCTTT
* * * *
39441481 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
39441535 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
39441591 CATTAAAT
1 CATTAAAT
39441599 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:39442247 original size:20 final size:20
Alignment explanation
Indices: 39442222--39442276 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
39442212 ACGAGTTAAA
*
39442222 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTTGAATGAGCTAAC
*
39442242 TTGAGCATGAATGAGCTAAC
1 TTGAGCTTGAATGAGCTAAC
*
39442262 TTGAGCTCGAATGAG
1 TTGAGCTTGAATGAG
39442277 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (20 bp):
TTGAGCTTGAATGAGCTAAC
Found at i:39443192 original size:16 final size:15
Alignment explanation
Indices: 39443166--39443195 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39443156 TTTCAATCCA
39443166 TCATCCCAATCAAAG
1 TCATCCCAATCAAAG
39443181 TCATCACCAATCAAA
1 TCATC-CCAATCAAA
39443196 AATTGATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
TCATCCCAATCAAAG
Found at i:39443704 original size:15 final size:16
Alignment explanation
Indices: 39443684--39443721 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
39443674 TATCTCACAC
39443684 TCATTTCTTTTTC-TT
1 TCATTTCTTTTTCATT
39443699 TCATTTCTTTTTCATTT
1 TCATTTCTTTTTCA-TT
39443716 TCATTT
1 TCATTT
39443722 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 13 0.62
17 8 0.38
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.71
Consensus pattern (16 bp):
TCATTTCTTTTTCATT
Found at i:39446455 original size:23 final size:22
Alignment explanation
Indices: 39446403--39446455 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
39446393 TCCACGTCTT
*
39446403 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
39446425 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
39446448 TTTCTTTT
1 TTTCTTTT
39446456 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39449385 original size:20 final size:20
Alignment explanation
Indices: 39449360--39449414 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
39449350 ACGAGTTAAA
* *
39449360 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
39449380 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
39449400 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
39449415 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:39457340 original size:11 final size:10
Alignment explanation
Indices: 39457315--39457375 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
39457305 ACCAATAAAA
39457315 TAAA-TGAGC
1 TAAATTGAGC
*
39457324 TGAATTGTAGC
1 TAAATTG-AGC
39457335 TAAATTGAGC
1 TAAATTGAGC
**
39457345 TCGATTGAGC
1 TAAATTGAGC
39457355 TGAAA-TGAGC
1 T-AAATTGAGC
*
39457365 TCAATTGAGC
1 TAAATTGAGC
39457375 T
1 T
39457376 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:39457376 original size:20 final size:20
Alignment explanation
Indices: 39457316--39457376 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
39457306 CCAATAAAAT
*
39457316 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
39457336 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
39457357 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
39457377 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:39459462 original size:17 final size:18
Alignment explanation
Indices: 39459442--39459475 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39459432 CTTTTTTTTT
39459442 TCAATTT-TTTCTCAATC
1 TCAATTTCTTTCTCAATC
*
39459459 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTCTCAAT
39459476 TTTCTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.56
Consensus pattern (18 bp):
TCAATTTCTTTCTCAATC
Found at i:39459472 original size:6 final size:6
Alignment explanation
Indices: 39459463--39459567 Score: 52
Period size: 6 Copynumber: 17.2 Consensus size: 6
39459453 TCAATCTCAA
* * * ** **
39459463 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTAT TTTGAT
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCT-T TTTCTT
* ** * *
39459515 TT-CTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
39459561 TTTCTT T
1 TTTCTT T
39459568 CAATTTCTTT
Statistics
Matches: 69, Mismatches: 25, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
5 7 0.10
6 49 0.71
7 10 0.14
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:39459580 original size:6 final size:6
Alignment explanation
Indices: 39459514--39459567 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
39459504 ACTATTTTGA
* ** * *
39459514 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
39459561 TTTCTT T
1 TTTCTT T
39459568 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:39465356 original size:21 final size:21
Alignment explanation
Indices: 39465330--39465370 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39465320 TTAACTCGAT
39465330 TTTTTTGTC-ACTTTTTTTTTC
1 TTTTTTGTCGA-TTTTTTTTTC
*
39465351 TTTTTTTTCGATTTTTTTTT
1 TTTTTTGTCGATTTTTTTTT
39465371 GAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.80
Consensus pattern (21 bp):
TTTTTTGTCGATTTTTTTTTC
Found at i:39465366 original size:12 final size:12
Alignment explanation
Indices: 39465325--39465381 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
39465315 TTTTTTTAAC
*
39465325 TCGATTTTTTTG
1 TCGATTTTTTTT
39465337 TC-ACTTTTTTTT
1 TCGA-TTTTTTTT
39465349 TC---TTTTTTT
1 TCGATTTTTTTT
39465358 TCGATTTTTTTT
1 TCGATTTTTTTT
39465370 T-GAATTTTTTTT
1 TCG-ATTTTTTTT
39465382 GAATTTCTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
9 9 0.23
11 2 0.05
12 28 0.72
ACGTcount: A:0.09, C:0.09, G:0.07, T:0.75
Consensus pattern (12 bp):
TCGATTTTTTTT
Found at i:39465382 original size:11 final size:11
Alignment explanation
Indices: 39465351--39465387 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
39465341 TTTTTTTTTC
*
39465351 TTTTTTTTCGAT
1 TTTTTTTT-GAA
39465363 TTTTTTTTGAA
1 TTTTTTTTGAA
39465374 TTTTTTTTGAA
1 TTTTTTTTGAA
39465385 TTT
1 TTT
39465388 CTTCTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:39466767 original size:11 final size:10
Alignment explanation
Indices: 39466742--39466802 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
39466732 ACCAATAAAA
39466742 TAAA-TGAGC
1 TAAATTGAGC
*
39466751 TGAATTGTAGC
1 TAAATTG-AGC
39466762 TAAATTGAGC
1 TAAATTGAGC
**
39466772 TCGATTGAGC
1 TAAATTGAGC
39466782 TGAAA-TGAGC
1 T-AAATTGAGC
*
39466792 TCAATTGAGC
1 TAAATTGAGC
39466802 T
1 T
39466803 GGTCAGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Done.