Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2507
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: 75348
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1302 original size:1 final size:1
Alignment explanation
Indices: 1296--1382 Score: 129
Period size: 1 Copynumber: 87.0 Consensus size: 1
1286 CCTTCTCTTC
* *
1296 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAACAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
1361 AAAAAAAAGAGAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAA
1383 CCTACTTAAG
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.94, C:0.02, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:2432 original size:55 final size:55
Alignment explanation
Indices: 2347--3302 Score: 1385
Period size: 55 Copynumber: 17.3 Consensus size: 55
2337 TCCGCTTTTT
2347 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
2402 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
2457 AGTCCTCAACGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* *
2512 AGTCCCCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA--TTTTCC
* * *
2568 AGTCCCCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
*** *
2624 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCGCCTTCT
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
2679 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * *
2734 AATCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
*** *
2790 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCGCCTTCT
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
2845 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
2900 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
2955 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
3010 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
3065 AGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
3120 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * * * *
3175 ATTCCCCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * *
3230 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-T
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* *
3285 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
3303 TACAATTTAT
Statistics
Matches: 839, Mismatches: 47, Indels: 30
0.92 0.05 0.03
Matches are distributed among these distances:
54 7 0.01
55 673 0.80
56 157 0.19
57 2 0.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:2590 original size:27 final size:26
Alignment explanation
Indices: 2504--2590 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 26
2494 AAGTTGGTGG
2504 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
* * **
2530 CACCTCTCAAAG-CCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCC-CA-AAG-AGCAGGA
2559 CACCTTTTCAGTCCCCAAAGAGCAGGA
1 CACC-TTTCAGTCCCCAAAGAGCAGGA
2586 CACCT
1 CACCT
2591 CTCAAAGCCC
Statistics
Matches: 45, Mismatches: 8, Indels: 16
0.65 0.12 0.23
Matches are distributed among these distances:
26 11 0.24
27 10 0.22
28 8 0.18
29 10 0.22
30 6 0.13
ACGTcount: A:0.29, C:0.36, G:0.18, T:0.17
Consensus pattern (26 bp):
CACCTTTCAGTCCCCAAAGAGCAGGA
Found at i:2981 original size:26 final size:26
Alignment explanation
Indices: 2896--3036 Score: 70
Period size: 26 Copynumber: 5.2 Consensus size: 26
2886 TGGTGGCATT
2896 TTTCAGTCCTCAAAGAGCAGGACACC
1 TTTCAGTCCTCAAAGAGCAGGACACC
* * * ** **
2922 TTTCAAAGCCCACACAAGTTGGTGG-CATT
1 TTTC--AGTCCTCA-AAG-AGCAGGACACC
2951 TTTCAGTCCTCAAAGAGCAGGACACC
1 TTTCAGTCCTCAAAGAGCAGGACACC
* * * ** **
2977 TTTCAAAGCCCACACAAGTTGGTGG-CATT
1 TTTC--AGTCCTCA-AAG-AGCAGGACACC
3006 TTTCAGTCCTCAAAGAGCAGGACACC
1 TTTCAGTCCTCAAAGAGCAGGACACC
3032 TTTCA
1 TTTCA
3037 AAGCCCACAC
Statistics
Matches: 77, Mismatches: 28, Indels: 20
0.62 0.22 0.16
Matches are distributed among these distances:
25 6 0.08
26 23 0.30
27 12 0.16
28 12 0.16
29 18 0.23
30 6 0.08
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (26 bp):
TTTCAGTCCTCAAAGAGCAGGACACC
Found at i:3059 original size:165 final size:166
Alignment explanation
Indices: 2347--3302 Score: 1534
Period size: 165 Copynumber: 5.8 Consensus size: 166
2337 TCCGCTTTTT
*
2347 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAA
*
2411 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAACGAGCAGGA
65 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGA
2475 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
130 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
2512 AGTCCCCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTTCAGTCCCCAA
1 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTCAA
* *
2577 AGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCTCAAAGAGCAGGA
65 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGA
*
2642 CACCTCTTAAAGCCCACACAAGTTGGTGGCGCC-TTC
130 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
2678 TAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAA
1 -AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAA
* *
2743 AGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCTCAAAGAGCAGGA
65 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGA
*
2808 CACCTCTTAAAGCCCACACAAGTTGGTGGCGCC-TTC
130 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
2844 TAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAA
1 -AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAA
*
2909 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTTCAGTCCTCAAAGAGCAGGA
65 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGA
**
2973 CACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTTC
130 CACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
*
3010 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAA
*
3074 AGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
65 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGA
3138 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
130 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * * *
3175 ATTCCCCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCACCTTTCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAA
* * * * *
3240 GAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TACTCCTCAATGAGCAGGA
66 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGA
3303 TACAATTTAT
Statistics
Matches: 745, Mismatches: 36, Indels: 20
0.93 0.04 0.02
Matches are distributed among these distances:
164 6 0.01
165 356 0.48
166 277 0.37
167 106 0.14
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.21
Consensus pattern (166 bp):
AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAA
GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGAC
ACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:3230 original size:29 final size:29
Alignment explanation
Indices: 3083--3230 Score: 71
Period size: 29 Copynumber: 5.3 Consensus size: 29
3073 AAGAACAGGA
*
3083 CACCTTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTTCAAAGCCCACACAAGTGGGTGG
* * * * * * *
3112 CA-TTTTC-CAGTCCTCA-AAGAGCAG-GA
1 CACCTTTCAAAGCCCACACAAGTG-GGTGG
*
3138 CACCTCTT-AAAGCCCACACAAGTTGGTGG
1 CACCT-TTCAAAGCCCACACAAGTGGGTGG
** * * *
3167 CACCTTTC-ATTCCC-CA-AAGAGCAG-GA
1 CACCTTTCAAAGCCCACACAAGTG-GGTGG
*
3193 CACTTTTCAAAGCCCACACAAGTGGGTGG
1 CACCTTTCAAAGCCCACACAAGTGGGTGG
3222 CACCTTTCA
1 CACCTTTCA
3231 GTCCTCAAAG
Statistics
Matches: 78, Mismatches: 29, Indels: 24
0.60 0.22 0.18
Matches are distributed among these distances:
26 17 0.22
27 15 0.19
28 22 0.28
29 24 0.31
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (29 bp):
CACCTTTCAAAGCCCACACAAGTGGGTGG
Found at i:3919 original size:18 final size:18
Alignment explanation
Indices: 3896--3950 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
3886 AGATAAAGTG
3896 TTTGAAAAAAAAAAAAAA
1 TTTGAAAAAAAAAAAAAA
3914 TTTGAAAAAAAAAAAAAA
1 TTTGAAAAAAAAAAAAAA
**
3932 --AAAAAAAAAAAAAAAA
1 TTTGAAAAAAAAAAAAAA
3948 TTT
1 TTT
3951 TAATGTATCG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 14 0.44
18 18 0.56
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (18 bp):
TTTGAAAAAAAAAAAAAA
Found at i:3922 original size:1 final size:1
Alignment explanation
Indices: 3918--3947 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
3908 AAAAAATTTG
3918 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3948 TTTTAATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3976 original size:21 final size:21
Alignment explanation
Indices: 3952--4008 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3942 AAAAAATTTT
3952 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
3973 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
3994 AATGTATCGATACAT
1 AATGTATCGATACAT
4009 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:4088 original size:19 final size:19
Alignment explanation
Indices: 4064--4131 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
4054 AATTCAACAA
4064 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
4083 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
4098 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
4115 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
4132 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:4103 original size:13 final size:13
Alignment explanation
Indices: 4085--4109 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4075 ACATAAGTTT
4085 TGTATCGATACAA
1 TGTATCGATACAA
4098 TGTATCGATACA
1 TGTATCGATACA
4110 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4107 original size:32 final size:32
Alignment explanation
Indices: 4066--4128 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
4056 TTCAACAATT
*
4066 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
4098 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
4129 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:4189 original size:13 final size:13
Alignment explanation
Indices: 4171--4196 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4161 CATTTTTCTG
4171 TGTATCGATACAT
1 TGTATCGATACAT
4184 TGTATCGATACAT
1 TGTATCGATACAT
4197 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4193 original size:33 final size:33
Alignment explanation
Indices: 4151--4217 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4141 GCCAAGGAAA
***
4151 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
4184 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
4217 T
1 T
4218 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:6737 original size:52 final size:52
Alignment explanation
Indices: 6664--7045 Score: 261
Period size: 52 Copynumber: 7.3 Consensus size: 52
6654 TTATTTTCGA
*
6664 GGGGATACTCCAACTCCGGTTTTATCGTT-AAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTAT-GTTCAAAACACCAATTTTTCCACAATC
* * **
6716 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATGTTCAAAACACCAATTTTTCC-ACAATC
* *
6768 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATGTT-C-AAAACACCAATTTTTCCACAATC
* * *** * * *** **
6820 GAGGATACTCCAAC-CTCGTTATTTCATCG-GGGATACTCCAACCCCGTT--ACTTTC
1 GGGGATACTCCAACTC-CGGT-TTT-AT-GTTCAAAACACCAA--TTTTTCCACAATC
*
6874 GAGGGGATACTCCAACTCCGGTTTTATCGTT-AAAACACTAATTTTTCCACAATC
1 --GGGGATACTCCAACTCCGGTTTTAT-GTTCAAAACACCAATTTTTCCACAATC
* * **
6928 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATGTTCAAAACACCAATTTTTCC-ACAATC
* *
6980 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATGTT-C-AAAACACCAATTTTTCCACAATC
*
7032 GAGGATACTCCAAC
1 GGGGATACTCCAAC
7046 CTCGTTATTT
Statistics
Matches: 257, Mismatches: 46, Indels: 54
0.72 0.13 0.15
Matches are distributed among these distances:
51 27 0.11
52 147 0.57
53 33 0.13
54 28 0.11
55 5 0.02
56 16 0.06
57 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACTCCGGTTTTATGTTCAAAACACCAATTTTTCCACAATC
Found at i:6817 original size:104 final size:103
Alignment explanation
Indices: 6664--7044 Score: 402
Period size: 104 Copynumber: 3.6 Consensus size: 103
6654 TTATTTTCGA
* * *
6664 GGGGATACTCCAACTCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATC-TTAAAACACCAATTTTTCCACAATCGAGGATACTCCAA
6729 TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
65 TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
*
6768 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATCGAGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATCTT---AAAACACCAATTTTTCCACAATCGAGGATACTCC
* * * * ** * *
6831 AA-CCTCG--TTATTTCATCGGGGATACTCCAA--CCCCGTTACTTTC
63 AATCCTGGTTTTATTT--TC---AAAACGCCAATTTTCCTTTA--ATC
* * *
6874 GAGGGGATACTCCAACTCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCC
1 --GGGGATACTCCAACTCCGATTTTATC-TTAAAACACCAATTTTTCCACAATCGAGGATACTCC
6939 AATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
63 AATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
*
6980 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATCGAGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATCTT---AAAACACCAATTTTTCCACAATCGAGGATACTCC
7043 AA
63 AA
7045 CCTCGTTATT
Statistics
Matches: 226, Mismatches: 28, Indels: 46
0.75 0.09 0.15
Matches are distributed among these distances:
101 6 0.03
102 4 0.02
103 6 0.03
104 91 0.40
105 26 0.12
106 18 0.08
107 13 0.06
108 48 0.21
109 6 0.03
110 2 0.01
111 6 0.03
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (103 bp):
GGGGATACTCCAACTCCGATTTTATCTTAAAACACCAATTTTTCCACAATCGAGGATACTCCAAT
CCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
Found at i:6853 original size:28 final size:30
Alignment explanation
Indices: 6817--6889 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 30
6807 ATTTTTCACA
* *
6817 ATCGAGGATACTCCAACCTCGTTA-TTTC-
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
6845 ATCGGGGATACTCCAACCCCGTTACTTTCG
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
6875 A--GGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
6890 TCCGGTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 36 0.88
29 4 0.10
30 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (30 bp):
ATCGGGGATACTCCAACCCCGTTACTTTCG
Found at i:6931 original size:212 final size:212
Alignment explanation
Indices: 6549--7112 Score: 1004
Period size: 212 Copynumber: 2.6 Consensus size: 212
6539 AATTCTCCAC
* * *
6549 AATCGAGGATATTCCAACTCCGATTTTATTTCCAAAAAAAATACCAATTTCTTCACAATCGGGGA
1 AATCGGGGATACTCCAACTCCGATTTTATTTCC---AAAAATACCAATTT-TTCACAATCGAGGA
* * *
6614 TACTCCAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAAC
62 TACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAAC
6678 TCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTT
127 TCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTT
6743 TCAAAACGCCAATTTTCCTTT
192 TCAAAACGCCAATTTTCCTTT
6764 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
6829 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
66 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
6894 GTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAA
131 GTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAA
6959 AACGCCAATTTTCCTTT
196 AACGCCAATTTTCCTTT
6976 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
* *
7041 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCG
66 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
*
7106 GCTTTAT
131 GTTTTAT
7113 TCCCAAAATA
Statistics
Matches: 339, Mismatches: 9, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
211 28 0.08
212 280 0.83
215 31 0.09
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (212 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
GTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAA
AACGCCAATTTTCCTTT
Found at i:7065 original size:28 final size:28
Alignment explanation
Indices: 7029--7105 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
7019 ATTTTTCACA
* * *
7029 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
7057 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
7085 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
7106 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:9788 original size:27 final size:27
Alignment explanation
Indices: 9714--9802 Score: 109
Period size: 27 Copynumber: 3.5 Consensus size: 27
9704 ATTAATCTCC
9714 TTATAACAATTG---TTTCTTTATATT
1 TTATAACAATTGTTATTTCTTTATATT
* * *
9738 TTATAA-AA--ATTATTCCTTTGTATT
1 TTATAACAATTGTTATTTCTTTATATT
9762 TTATAACAATTGTTATTTCTTTATATT
1 TTATAACAATTGTTATTTCTTTATATT
9789 TTATAACAATTGTT
1 TTATAACAATTGTT
9803 TTTTTATATT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
23 2 0.04
24 22 0.42
25 2 0.04
27 27 0.51
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.56
Consensus pattern (27 bp):
TTATAACAATTGTTATTTCTTTATATT
Found at i:9819 original size:24 final size:24
Alignment explanation
Indices: 9714--9812 Score: 126
Period size: 24 Copynumber: 4.0 Consensus size: 24
9704 ATTAATCTCC
9714 TTATAACAATTGTTTCTTTATATT
1 TTATAACAATTGTTTCTTTATATT
* * * *
9738 TTATAAAAATTATTCCTTTGTATT
1 TTATAACAATTGTTTCTTTATATT
9762 TTATAACAATTGTTATTTCTTTATATT
1 TTATAACAATTG---TTTCTTTATATT
*
9789 TTATAACAATTGTTTTTTTATATT
1 TTATAACAATTGTTTCTTTATATT
9813 ATGTAACTTG
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
24 41 0.65
27 22 0.35
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (24 bp):
TTATAACAATTGTTTCTTTATATT
Found at i:15147 original size:15 final size:16
Alignment explanation
Indices: 15129--15159 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
15119 AAATATAGCA
15129 ACTGAAAA-ATAATTT
1 ACTGAAAATATAATTT
15144 ACTGAAAATATAATTT
1 ACTGAAAATATAATTT
15160 TTTATGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (16 bp):
ACTGAAAATATAATTT
Found at i:18220 original size:20 final size:21
Alignment explanation
Indices: 18181--18220 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
18171 AAATCTTCAC
**
18181 TTTTCTTTTTTTTTTTAATTT
1 TTTTCTTTTTTTTTACAATTT
18202 TTTTC-TTTTTTTTACAATT
1 TTTTCTTTTTTTTTACAATT
18221 GTCATGCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTCTTTTTTTTTACAATTT
Found at i:24464 original size:323 final size:323
Alignment explanation
Indices: 23876--24519 Score: 1074
Period size: 323 Copynumber: 2.0 Consensus size: 323
23866 GCTTGGTAGA
* ** *
23876 TGTCGTAACGTGCGCTCGACCCCGGTGATAGGGCAAATGAGGCACGCTCGACTTAATATCCCTCG
1 TGTCGTAACGTGCACTCGACCCCGACGATAGGGCAAAGGAGGCACGCTCGACTTAATATCCCTCG
*
23941 TGATTGGGGATTTCTATGGCATGATAGGAAGTGTGTTGATTAAAAGGGGAAGATCAGCAGATGAA
66 TGATTGGGGATTGCTATGGCATGATAGGAAGTGTGTTGATTAAAAGGGGAAGATCAGCAGATGAA
* *
24006 TCGCCCATCTAATTGATCTTCAATGGTCACTACGAAGTGACCGAGATTTTGGAGTCGCCACCGAT
131 TCGCCCATCTAATTGATCTTCAATGGTCACTACGAAGTGACCAAAATTTTGGAGTCGCCACCGAT
*
24071 CATTTCGGGCTAGGCATGATCGGATGCGTATTGAAACCTATGTCTTGAGTTACAAAACTCAAAAC
196 CATTTCGGGCTAGGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACAAAACTCAAAAC
* * * *
24136 ATCGATCTCGAGGTTTG-TGTACTTTAGAGATTCATCGGTTGGGTTCGGGAGTTGGTTACGCGC
261 ATCGATCCCGAGGTCTGCT-TACCTTAGAGATTCACCGGTTGGGTTCGGGAGTTGGTTACGCGC
*
24199 TGTCGTAACGTGCATTCGACCCCGACGATAGGGCAAAGGAGGCACGCTCGACTTAATATCCCTCG
1 TGTCGTAACGTGCACTCGACCCCGACGATAGGGCAAAGGAGGCACGCTCGACTTAATATCCCTCG
* * *
24264 TGATTGGGGATTGCTATGGCATGATGGGAAGTGTGTTGATTAAAGGGGGAAGATCAGTAGATGAA
66 TGATTGGGGATTGCTATGGCATGATAGGAAGTGTGTTGATTAAAAGGGGAAGATCAGCAGATGAA
* *
24329 TCGTCCATCTAATTGATCTTCAATGGTCACTACGAAGTGACCAAAATTTTGGAGTCGCCACTGAT
131 TCGCCCATCTAATTGATCTTCAATGGTCACTACGAAGTGACCAAAATTTTGGAGTCGCCACCGAT
* *
24394 CATTTCGGGCTAGGCATGATCGGATGCCTATTGAGACCTATGTCTTGAGTTACGAAACTCAAAAC
196 CATTTCGGGCTAGGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACAAAACTCAAAAC
* *
24459 ATCGATCCCGTGGTCTGCTTACCTTAGAGATTCGCCGGTTGGGTTCGGGAGTTGGTTACGC
261 ATCGATCCCGAGGTCTGCTTACCTTAGAGATTCACCGGTTGGGTTCGGGAGTTGGTTACGC
24520 ACAAAGAGGT
Statistics
Matches: 298, Mismatches: 22, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
323 297 1.00
324 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (323 bp):
TGTCGTAACGTGCACTCGACCCCGACGATAGGGCAAAGGAGGCACGCTCGACTTAATATCCCTCG
TGATTGGGGATTGCTATGGCATGATAGGAAGTGTGTTGATTAAAAGGGGAAGATCAGCAGATGAA
TCGCCCATCTAATTGATCTTCAATGGTCACTACGAAGTGACCAAAATTTTGGAGTCGCCACCGAT
CATTTCGGGCTAGGCATGATCGGATGCCTATTGAAACCTATGTCTTGAGTTACAAAACTCAAAAC
ATCGATCCCGAGGTCTGCTTACCTTAGAGATTCACCGGTTGGGTTCGGGAGTTGGTTACGCGC
Found at i:26441 original size:13 final size:13
Alignment explanation
Indices: 26423--26447 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26413 CAAAGATCAG
26423 TGTATCGATACAA
1 TGTATCGATACAA
26436 TGTATCGATACA
1 TGTATCGATACA
26448 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:34542 original size:52 final size:52
Alignment explanation
Indices: 34464--34579 Score: 171
Period size: 52 Copynumber: 2.2 Consensus size: 52
34454 TCATTGATAT
*
34464 TGATGATGCCATGATGGCGATCAGAGTCAAAGTGA-CTTGGCGTCACTAATAA
1 TGATGATGCCATGATGGCAATCAGAGTCAAAGTGATC-TGGCGTCACTAATAA
* * * *
34516 TGATGATGCCATGGTGGCAATTAGAGTCAGAGTGATCTGGTGTCACTAATAA
1 TGATGATGCCATGATGGCAATCAGAGTCAAAGTGATCTGGCGTCACTAATAA
34568 TGATGATGCCAT
1 TGATGATGCCAT
34580 AGCGAATATC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
52 57 0.98
53 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (52 bp):
TGATGATGCCATGATGGCAATCAGAGTCAAAGTGATCTGGCGTCACTAATAA
Found at i:34594 original size:52 final size:54
Alignment explanation
Indices: 34483--34597 Score: 150
Period size: 52 Copynumber: 2.2 Consensus size: 54
34473 CATGATGGCG
* *
34483 ATCAGAGTCAAAGTGACTTGGCGTCACTAATAATGATGATGCCATGGTGGCAAT
1 ATCAGAGTCAAAGTGACTTGGCGTCACTAATAATGATGATGCCATAGTCGCAAT
* *
34537 -T-AGAGTCAGAGTGA-TCTGGTGTCACTAATAATGATGATGCCATAG-CG-AAT
1 ATCAGAGTCAAAGTGACT-TGGCGTCACTAATAATGATGATGCCATAGTCGCAAT
34587 ATCAGAGTCAA
1 ATCAGAGTCAA
34598 TAAGGAAAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
50 3 0.06
51 3 0.06
52 46 0.87
53 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (54 bp):
ATCAGAGTCAAAGTGACTTGGCGTCACTAATAATGATGATGCCATAGTCGCAAT
Found at i:36812 original size:22 final size:21
Alignment explanation
Indices: 36786--36840 Score: 69
Period size: 19 Copynumber: 2.7 Consensus size: 21
36776 ATTCAACAAT
36786 TTGTATCGATACAAACAAGTAA
1 TTGTATCGATACAAACAAGT-A
* *
36808 TTGTATCGATAC--ATAAGTG
1 TTGTATCGATACAAACAAGTA
36827 TTGTATCGATACAA
1 TTGTATCGATACAA
36841 TGTATCGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 12 0.41
20 5 0.17
22 12 0.41
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (21 bp):
TTGTATCGATACAAACAAGTA
Found at i:36832 original size:19 final size:19
Alignment explanation
Indices: 36808--36871 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
36798 AAACAAGTAA
36808 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
36827 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
36841 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
36859 TTGTATCGATACA
1 TTGTATCGATACA
36872 ATGTATCACT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 24 0.62
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:36846 original size:13 final size:13
Alignment explanation
Indices: 36828--36852 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36818 ACATAAGTGT
36828 TGTATCGATACAA
1 TGTATCGATACAA
36841 TGTATCGATACA
1 TGTATCGATACA
36853 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:36850 original size:32 final size:32
Alignment explanation
Indices: 36809--36878 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
36799 AACAAGTAAT
36809 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
36841 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
36873 TGTATC
1 TGTATC
36879 ACTACGAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:47506 original size:13 final size:13
Alignment explanation
Indices: 47488--47513 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47478 CAATTTTTTG
47488 TGTATCGATACAT
1 TGTATCGATACAT
47501 TGTATCGATACAT
1 TGTATCGATACAT
47514 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:47599 original size:20 final size:20
Alignment explanation
Indices: 47574--47646 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
47564 ATCTTTTTTT
47574 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
47594 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
47615 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
47635 ATGTATCGATAC
1 ATGTATCGATAC
47647 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:47625 original size:41 final size:42
Alignment explanation
Indices: 47552--47646 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
47542 CTGCCAAGAA
*
47552 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
47594 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
47635 ATGTATCGATAC
1 ATGTATCGATAC
47647 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:48284 original size:16 final size:16
Alignment explanation
Indices: 48253--48298 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
48243 CTCTCCTTTG
48253 TCTCCCCCGTTTAAAAAA
1 TCTCCCCC--TTAAAAAA
48271 TCTCCCCCTTAAAAAA
1 TCTCCCCCTTAAAAAA
48287 TCTCCCCCTTAA
1 TCTCCCCCTTAA
48299 TCAAGTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 20 0.71
18 8 0.29
ACGTcount: A:0.30, C:0.39, G:0.02, T:0.28
Consensus pattern (16 bp):
TCTCCCCCTTAAAAAA
Found at i:50122 original size:13 final size:13
Alignment explanation
Indices: 50104--50142 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
50094 ATAATCACCC
*
50104 TGTATCGATACAG
1 TGTATCGATACAA
50117 TGTATCGATACAA
1 TGTATCGATACAA
50130 TGTATCGATACAA
1 TGTATCGATACAA
50143 CAAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:50153 original size:20 final size:20
Alignment explanation
Indices: 50128--50206 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
50118 GTATCGATAC
50128 AATGTATCGATACAACAAAA
1 AATGTATCGATACAACAAAA
* *
50148 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACA-ACAA----AA
*
50173 GATGTATCGATAC-ACAAAA
1 AATGTATCGATACAACAAAA
50192 ACATGTATCGATACA
1 A-ATGTATCGATACA
50207 TTTTGGACAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.02
20 26 0.57
21 3 0.07
23 3 0.07
25 13 0.28
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAACAAAA
Found at i:52254 original size:15 final size:15
Alignment explanation
Indices: 52218--52255 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
52208 TACATCAATT
* *
52218 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
52233 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
52248 TCATTTTG
1 TCATTTTG
52256 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:56337 original size:13 final size:13
Alignment explanation
Indices: 56319--56344 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56309 CAATTTTTTG
56319 TGTATCGATACAT
1 TGTATCGATACAT
56332 TGTATCGATACAT
1 TGTATCGATACAT
56345 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:56430 original size:20 final size:20
Alignment explanation
Indices: 56405--56477 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
56395 ATCTTTTTTT
56405 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
56425 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
56446 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
56466 ATGTATCGATAC
1 ATGTATCGATAC
56478 TTTGAGTTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:56456 original size:41 final size:42
Alignment explanation
Indices: 56383--56477 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
56373 CTGCCAAGAA
*
56383 ATGTATCGATACATCTTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
56425 ATGTATCGATACATC-TTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
56466 ATGTATCGATAC
1 ATGTATCGATAC
56478 TTTGAGTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 37 0.71
42 15 0.29
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (42 bp):
ATGTATCGATACATCTTTTTTCATGTATCGATACATTGCAAC
Found at i:59528 original size:21 final size:21
Alignment explanation
Indices: 59485--59528 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
59475 TAATATTTAT
**
59485 AATTTTTTATTATCAAATTAA
1 AATTTTTTATTATCAAAAAAA
59506 AATTTTTT-TTATACAAAAAAA
1 AATTTTTTATTAT-CAAAAAAA
59527 AA
1 AA
59529 AAATCAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTTTTTATTATCAAAAAAA
Found at i:63083 original size:27 final size:27
Alignment explanation
Indices: 63045--63103 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
63035 CCCCACTACT
63045 CATTTTTAGTTTTCTTAATTATTAAAG
1 CATTTTTAGTTTTCTTAATTATTAAAG
63072 CATTTTTAGTTTTCTTAATTATTAAAG
1 CATTTTTAGTTTTCTTAATTATTAAAG
63099 CATTT
1 CATTT
63104 AAGCAAGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.29, C:0.08, G:0.07, T:0.56
Consensus pattern (27 bp):
CATTTTTAGTTTTCTTAATTATTAAAG
Found at i:63382 original size:2 final size:2
Alignment explanation
Indices: 63375--63401 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
63365 ATCATCAATA
63375 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
63402 GGATATGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64793 original size:23 final size:22
Alignment explanation
Indices: 64769--64812 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
64759 CGGATTATGT
* *
64769 TTTTTATACGTATTAAATCTTG
1 TTTTGATACGTATTAAACCTTG
*
64791 TTTTGCTACGTATTAAACCTTG
1 TTTTGATACGTATTAAACCTTG
64813 GTTTAGTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (22 bp):
TTTTGATACGTATTAAACCTTG
Found at i:65346 original size:3 final size:3
Alignment explanation
Indices: 65334--65363 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
65324 CAACAACAAC
*
65334 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
65364 GCCACCTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:65664 original size:4 final size:4
Alignment explanation
Indices: 65657--65697 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
65647 ATATATATAT
* *
65657 ATAG ATAG ATAA ATAA ATAG ATAG ATAG ATAG ATAG ATAG A
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
65698 GAGAGTAGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (4 bp):
ATAG
Found at i:69678 original size:20 final size:20
Alignment explanation
Indices: 69653--69780 Score: 85
Period size: 20 Copynumber: 5.8 Consensus size: 20
69643 AAGTAACTAG
69653 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
69673 ATGTATCGATACATCTAGGTAAAAAAATAGA
1 ATGTATCGATACAT-T--G------AA-A-A
69704 ATGTATCGATACATTGAAAAA
1 ATGTATCGATACATTG-AAAA
* * * * *
69725 ATATATCGATACAATCATAC
1 ATGTATCGATACATTGAAAA
*
69745 ATATATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
69765 ATGGTATCGATACATT
1 AT-GTATCGATACATT
69781 TGGGTAAAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
20 34 0.40
21 27 0.31
22 1 0.01
23 4 0.05
28 1 0.01
29 2 0.02
30 2 0.02
31 15 0.17
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:69731 original size:21 final size:20
Alignment explanation
Indices: 69707--69780 Score: 85
Period size: 21 Copynumber: 3.6 Consensus size: 20
69697 AAATAGAATG
69707 TATCGATACATTGAAAAAATA
1 TATCGATACATTG-AAAAATA
* * * *
69728 TATCGATACAATCATACATA
1 TATCGATACATTGAAAAATA
*
69748 TATCGATACATTGAAAAATGG
1 TATCGATACATTGAAAAAT-A
69769 TATCGATACATT
1 TATCGATACATT
69781 TGGGTAAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
20 20 0.47
21 23 0.53
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.31
Consensus pattern (20 bp):
TATCGATACATTGAAAAATA
Found at i:71693 original size:33 final size:34
Alignment explanation
Indices: 71656--71737 Score: 89
Period size: 33 Copynumber: 2.4 Consensus size: 34
71646 CTCGGTTCAA
* *
71656 GTTCTCTCAGGTT-TAGGTATTTTTCGGGTTC-GG
1 GTTCTCTCAGGTTCGAGCT-TTTTTCGGGTTCAGG
* *
71689 GTTCTTTCGGGTTCGAGCTTTTTTCGGGTTCAGG
1 GTTCTCTCAGGTTCGAGCTTTTTTCGGGTTCAGG
71723 GCTT-TCTCAGGTTCG
1 G-TTCTCTCAGGTTCG
71738 GGTTGTCTCG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
33 23 0.57
34 15 0.38
35 2 0.05
ACGTcount: A:0.07, C:0.18, G:0.30, T:0.44
Consensus pattern (34 bp):
GTTCTCTCAGGTTCGAGCTTTTTTCGGGTTCAGG
Found at i:71698 original size:16 final size:15
Alignment explanation
Indices: 71675--71771 Score: 68
Period size: 16 Copynumber: 6.1 Consensus size: 15
71665 GGTTTAGGTA
71675 TTTTTCGGGTTCGGG
1 TTTTTCGGGTTCGGG
*
71690 TTCTTTCGGGTTCGAGCT
1 TT-TTTCGGGTTCG-G-G
71708 TTTTTCGGGTTCAGGG
1 TTTTTCGGGTTC-GGG
* *
71724 CTTTCTCAGGTTCGGG
1 -TTTTTCGGGTTCGGG
* * *
71740 TTGTCTCGGTTTAGGG
1 TT-TTTCGGGTTCGGG
* *
71756 TATTTCGAGTTCGGG
1 TTTTTCGGGTTCGGG
71771 T
1 T
71772 AATTTCGAGT
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
15 14 0.22
16 25 0.39
17 22 0.34
18 3 0.05
ACGTcount: A:0.06, C:0.16, G:0.34, T:0.43
Consensus pattern (15 bp):
TTTTTCGGGTTCGGG
Found at i:71715 original size:17 final size:16
Alignment explanation
Indices: 71675--71719 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
71665 GGTTTAGGTA
*
71675 TTTTTCGGGTTCGGGT
1 TTTTTCGGGTTCGGCT
*
71691 TCTTTCGGGTTCGAGCT
1 TTTTTCGGGTTCG-GCT
71708 TTTTTCGGGTTC
1 TTTTTCGGGTTC
71720 AGGGCTTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.02, C:0.18, G:0.31, T:0.49
Consensus pattern (16 bp):
TTTTTCGGGTTCGGCT
Found at i:71778 original size:16 final size:15
Alignment explanation
Indices: 71753--71782 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
71743 TCTCGGTTTA
71753 GGGTATTTCGAGTTC
1 GGGTATTTCGAGTTC
71768 GGGTAATTTCGAGTT
1 GGGT-ATTTCGAGTT
71783 TAGGTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.17, C:0.10, G:0.33, T:0.40
Consensus pattern (15 bp):
GGGTATTTCGAGTTC
Found at i:72021 original size:15 final size:14
Alignment explanation
Indices: 72001--72054 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
71991 ATAACACTAG
72001 AAAAGAAAAGAAAAA
1 AAAAGAAAA-AAAAA
* *
72016 AAAAGAAAAACAAC
1 AAAAGAAAAAAAAA
* *
72030 AAAAGCAAAACAAA
1 AAAAGAAAAAAAAA
*
72044 AAAACAAAAAA
1 AAAAGAAAAAA
72055 CCAAAAAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 23 0.72
15 9 0.28
ACGTcount: A:0.83, C:0.09, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAA
Found at i:73702 original size:15 final size:14
Alignment explanation
Indices: 73677--73727 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
73667 ACAAGACGGC
73677 ACAACAAAAACAAAA
1 ACAA-AAAAACAAAA
73692 ACACAAAAAACAACAA
1 ACA-AAAAAACAA-AA
*
73708 AGAAAAAAA-AAAA
1 ACAAAAAAACAAAA
73721 A-AAAAAA
1 ACAAAAAA
73728 GAAGAAAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
12 6 0.18
13 3 0.09
14 2 0.06
15 17 0.52
16 5 0.15
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (14 bp):
ACAAAAAAACAAAA
Found at i:73715 original size:24 final size:24
Alignment explanation
Indices: 73677--73726 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
73667 ACAAGACGGC
* *
73677 ACAACAAAAACAAAAACACAAAAA
1 ACAACAAAAACAAAAAAAAAAAAA
*
73701 ACAACAAAGAAAAAAAAAAAAAAAA
1 ACAACAAA-AACAAAAAAAAAAAAA
73726 A
1 A
73727 AGAAGAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (24 bp):
ACAACAAAAACAAAAAAAAAAAAA
Found at i:73725 original size:26 final size:28
Alignment explanation
Indices: 73682--73737 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 28
73672 ACGGCACAAC
*
73682 AAAAACAAAAACACAAAAAACAACAAAG
1 AAAAACAAAAACAAAAAAAACAACAAAG
* *
73710 AAAAA-AAAAA-AAAAAAAAGAAGAAAG
1 AAAAACAAAAACAAAAAAAACAACAAAG
73736 AA
1 AA
73738 CAAGAACAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 15 0.60
27 5 0.20
28 5 0.20
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (28 bp):
AAAAACAAAAACAAAAAAAACAACAAAG
Found at i:73740 original size:57 final size:59
Alignment explanation
Indices: 73635--73745 Score: 129
Period size: 57 Copynumber: 1.9 Consensus size: 59
73625 CACACCCAAA
* * * **
73635 ACAAAAAACAACAACAACAAAAAAAACAAACAACAAGACGGCACAACAAAAACAAAAAC
1 ACAAAAAACAACAACAACAAAAAAAACAAAAAAAAAGAAGAAACAACAAAAACAAAAAC
* *
73694 ACAAAAAACAACAA-AGA-AAAAAAAA-AAAAAAAAAGAAGAAAGAACAAGAACA
1 ACAAAAAACAACAACA-ACAAAAAAAACAAAAAAAAAGAAGAAACAACAAAAACA
73746 GACCCCCACA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
57 20 0.45
58 9 0.20
59 15 0.34
ACGTcount: A:0.76, C:0.17, G:0.07, T:0.00
Consensus pattern (59 bp):
ACAAAAAACAACAACAACAAAAAAAACAAAAAAAAAGAAGAAACAACAAAAACAAAAAC
Done.