Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold295
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: 1524207
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:119333 original size:19 final size:20
Alignment explanation
Indices: 119309--119346 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
119299 ATAATCAAAT
*
119309 CAAATTAATAATC-ACTTGC
1 CAAATTAAGAATCGACTTGC
119328 CAAATTAAGAATCGACTTG
1 CAAATTAAGAATCGACTTG
119347 ATGTTTCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (20 bp):
CAAATTAAGAATCGACTTGC
Found at i:120082 original size:21 final size:21
Alignment explanation
Indices: 120056--120133 Score: 113
Period size: 21 Copynumber: 3.7 Consensus size: 21
120046 AAAAAATTCC
120056 AAATGTATCGATACATTTGTA
1 AAATGTATCGATACATTTGTA
*
120077 AAATGTATCGATACATTTGTG
1 AAATGTATCGATACATTTGTA
* *
120098 GAATGTATCGATACA-TTCTA
1 AAATGTATCGATACATTTGTA
120118 CAAATGTATCGATACA
1 -AAATGTATCGATACA
120134 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (21 bp):
AAATGTATCGATACATTTGTA
Found at i:120193 original size:19 final size:19
Alignment explanation
Indices: 120169--120236 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
120159 AATTCAACAG
120169 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
120188 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
120203 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
120220 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
120237 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:120207 original size:32 final size:32
Alignment explanation
Indices: 120171--120233 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
120161 TTCAACAGTT
*
120171 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
120203 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
120234 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:120208 original size:13 final size:13
Alignment explanation
Indices: 120190--120214 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
120180 ACATAAGTTT
120190 TGTATCGATACAA
1 TGTATCGATACAA
120203 TGTATCGATACA
1 TGTATCGATACA
120215 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:120294 original size:13 final size:13
Alignment explanation
Indices: 120276--120301 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
120266 CATTTTTCTG
120276 TGTATCGATACAT
1 TGTATCGATACAT
120289 TGTATCGATACAT
1 TGTATCGATACAT
120302 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:120298 original size:33 final size:33
Alignment explanation
Indices: 120256--120322 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
120246 GCCAAGGAAA
***
120256 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
120289 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
120322 T
1 T
120323 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:122726 original size:51 final size:51
Alignment explanation
Indices: 122668--123045 Score: 265
Period size: 51 Copynumber: 7.4 Consensus size: 51
122658 TCAATTCTCC
* *
122668 ACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAACCACTAATTTTCT
1 ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCT
* * * *
122719 ATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAA-AATACCAATTTCTT
1 ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTA--ATTTTC-T
* *** * * * * *
122772 CACAATCGGGGATACTCCAACCCCG--GGGATATTCCAACCCCGT--TATTC-
1 -ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACAC-TAATTTTCT
* * * * * * * *
122820 CCGA--GAGGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTT-T
1 ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCT
* * * * *
122868 CATAATCGGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTCC
1 -ACAATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACACTAA-TTTTCT
* *
122921 ACAATCAGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCT
1 ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCT
* * * *
122972 ATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAA-AATACCAATTTCTT
1 ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTA--ATTTTC-T
123025 CACAATCGGGGATACTCCAAC
1 -ACAATCGGGGATACTCCAAC
123046 CTCGTTAATC
Statistics
Matches: 248, Mismatches: 57, Indels: 41
0.72 0.16 0.12
Matches are distributed among these distances:
45 17 0.07
46 1 0.00
47 9 0.04
48 3 0.01
49 1 0.00
50 12 0.05
51 103 0.42
52 55 0.22
53 5 0.02
54 42 0.17
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCT
Found at i:122800 original size:17 final size:17
Alignment explanation
Indices: 122778--122813 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
122768 TCTTCACAAT
122778 CGGGGATACTCCAACCC
1 CGGGGATACTCCAACCC
*
122795 CGGGGATATTCCAACCC
1 CGGGGATACTCCAACCC
122812 CG
1 CG
122814 TTATTCCCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.39, G:0.25, T:0.14
Consensus pattern (17 bp):
CGGGGATACTCCAACCC
Found at i:123099 original size:28 final size:27
Alignment explanation
Indices: 123029--123104 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
123019 TTTCTTCACA
*
123029 ATCGGGGATACTCCAACCTCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
123056 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
123082 TTCGAGGGGATACTCCAACCCCG
1 ATC--GGGGATACTCCAACCCCG
123105 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.09
27 22 0.50
28 18 0.41
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:123237 original size:78 final size:79
Alignment explanation
Indices: 123058--123259 Score: 219
Period size: 78 Copynumber: 2.6 Consensus size: 79
123048 CGTTAATCAT
*
123058 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
* * * *
123123 TGATTTTTCATAAT
66 CGATTTCTCACAAC
* * * * * * ** *
123137 TGGGGATACTCCAACCCAGTTATTTTCGAGGGGATACTCTAA-TCCTGATTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAAT-A
123200 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * * *
123215 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCC
123260 TGTTATTATC
Statistics
Matches: 99, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
77 3 0.03
78 56 0.57
79 40 0.40
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:135643 original size:21 final size:21
Alignment explanation
Indices: 135618--135700 Score: 82
Period size: 21 Copynumber: 3.9 Consensus size: 21
135608 TTCTCTTCAA
135618 AAAAAAAAAAAAGAAAAAAGC
1 AAAAAAAAAAAAGAAAAAAGC
135639 AAAAAAAAAAAAGAAAAGAA-C
1 AAAAAAAAAAAAGAAAA-AAGC
*
135660 AAAACAAAAAACAA-AACAAAG-
1 AAAA-AAAAAA-AAGAAAAAAGC
*
135681 AAAAATAGAGAAAAGAAAAA
1 AAAAA-A-AAAAAAGAAAAA
135701 GAACCTGCTT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
20 1 0.02
21 31 0.60
22 18 0.35
23 2 0.04
ACGTcount: A:0.83, C:0.06, G:0.10, T:0.01
Consensus pattern (21 bp):
AAAAAAAAAAAAGAAAAAAGC
Found at i:135655 original size:26 final size:27
Alignment explanation
Indices: 135616--135684 Score: 90
Period size: 25 Copynumber: 2.6 Consensus size: 27
135606 CCTTCTCTTC
135616 AAAAAAAAAA-AAAAGAA-AAAAGC-AA
1 AAAAAAAAAAGAAAAGAACAAAA-CAAA
135641 AAAAAAAAAAGAAAAGAACAAAACAAA
1 AAAAAAAAAAGAAAAGAACAAAACAAA
135668 AAACAAAACAAAGAAAA
1 AAA-AAAA-AAAGAAAA
135685 ATAGAGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
25 10 0.26
26 8 0.21
27 9 0.23
28 4 0.10
29 8 0.21
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (27 bp):
AAAAAAAAAAGAAAAGAACAAAACAAA
Found at i:135694 original size:26 final size:23
Alignment explanation
Indices: 135616--135700 Score: 80
Period size: 25 Copynumber: 3.5 Consensus size: 23
135606 CCTTCTCTTC
135616 AAAAAAAAAAAAAAGAAAAAAGCAA
1 AAAAAAAAAAAAAAGAAAAAAG--A
*
135641 AAAAAAAAAAGAAAAGAACAAAACA
1 AAAAAAAAAA-AAAAGAA-AAAAGA
* *
135666 AAAAACAAAACAAAGAAAAATAGA
1 AAAAAAAAAAAAAAGAAAAA-AGA
* *
135690 GAAAAGAAAAA
1 AAAAAAAAAAA
135701 GAACCTGCTT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.06
24 16 0.32
25 20 0.40
26 7 0.14
27 4 0.08
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.01
Consensus pattern (23 bp):
AAAAAAAAAAAAAAGAAAAAAGA
Found at i:135700 original size:1 final size:1
Alignment explanation
Indices: 135616--135685 Score: 50
Period size: 1 Copynumber: 70.0 Consensus size: 1
135606 CCTTCTCTTC
* ** * * * * * * *
135616 AAAAAAAAAAAAAAGAAAAAAGCAAAAAAAAAAAAGAAAAGAACAAAACAAAAAACAAAACAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
135681 AAAAA
1 AAAAA
135686 TAGAGAAAAG
Statistics
Matches: 50, Mismatches: 19, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:136749 original size:27 final size:27
Alignment explanation
Indices: 136719--136804 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
136709 TTGGTGGCAT
136719 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
136746 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
136774 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
136801 TTTC
1 TTTC
136805 AAAGCCCACC
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:137182 original size:55 final size:55
Alignment explanation
Indices: 136669--137181 Score: 754
Period size: 55 Copynumber: 9.3 Consensus size: 55
136659 TTCGCTTTTT
*
136669 AGTCCTCAAAGAGTAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
136724 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
136779 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACCCAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
136834 AGTCCTTAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTT--
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA--TTTTCC
*
136889 AGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
**
136944 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA-CCTCTC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTC-C
*
136999 AGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
137054 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * ** * *
137109 AATCTTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-T
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* *
137164 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
137182 TACACTTTAT
Statistics
Matches: 421, Mismatches: 24, Indels: 26
0.89 0.05 0.06
Matches are distributed among these distances:
53 4 0.01
54 8 0.02
55 394 0.94
56 11 0.03
57 4 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:138077 original size:20 final size:20
Alignment explanation
Indices: 138052--138106 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
138042 GCCAAGGAAA
*
138052 TGTATCGATACATTTTTCTG
1 TGTATCGATACATTTATCTG
** *
138072 TGTATCGATACATGGATCTT
1 TGTATCGATACATTTATCTG
138092 TGTATCGATACATTT
1 TGTATCGATACATTT
138107 GGAAATTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTATCTG
Found at i:140512 original size:51 final size:51
Alignment explanation
Indices: 140454--140831 Score: 283
Period size: 51 Copynumber: 7.4 Consensus size: 51
140444 TCAATTCTCC
* *
140454 ACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAACCACTAATTTTCT
1 ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCT
* * * *
140505 ATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAA-AATACCAATTTCTT
1 ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTA--ATTTTC-T
* *** * * * * *
140558 CACAATCGGGGATACTCCAACCCCG--GGGATATTCCAACCCCGTTA-TTTC-
1 -ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACAC-TAATTTTCT
* * * * * * *
140607 -CGA--GAGGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTT-T
1 ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCT
* * * * *
140654 CATAATCGGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTCC
1 -ACAATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAACACTAA-TTTTCT
*
140707 ACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCT
1 ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCT
* * * *
140758 ATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAA-AATACCAATTTCTT
1 ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTA--ATTTTC-T
140811 CACAATCGGGGATACTCCAAC
1 -ACAATCGGGGATACTCCAAC
140832 CCCGTTAATC
Statistics
Matches: 253, Mismatches: 52, Indels: 41
0.73 0.15 0.12
Matches are distributed among these distances:
45 17 0.07
46 2 0.01
47 12 0.05
49 1 0.00
50 9 0.04
51 108 0.43
52 57 0.23
53 5 0.02
54 42 0.17
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCT
Found at i:140586 original size:17 final size:17
Alignment explanation
Indices: 140564--140599 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
140554 TCTTCACAAT
140564 CGGGGATACTCCAACCC
1 CGGGGATACTCCAACCC
*
140581 CGGGGATATTCCAACCC
1 CGGGGATACTCCAACCC
140598 CG
1 CG
140600 TTATTTCCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.39, G:0.25, T:0.14
Consensus pattern (17 bp):
CGGGGATACTCCAACCC
Found at i:140744 original size:103 final size:105
Alignment explanation
Indices: 140612--140835 Score: 294
Period size: 103 Copynumber: 2.2 Consensus size: 105
140602 ATTTCCGAGA
* * *
140612 GGATACTCCAACCCCGACTTTATTTTCAAAATATTGATTTT-TCATAATCGGGGATACTCCAACC
1 GGATACTCCAACCCCGACTTTATTTTCAAAACACTAATTTTCT-ATAATCGGGGATACTCCAACC
* * * *
140676 CCGGTTTTA-TTGC-TAAAACACTAATTT-TTCCACAATCGG
65 CCGATTTTATTTCCAAAAAACACCAATTTCTT-CACAATCGG
* * * *
140715 GGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAACTC
1 GGATACTCCAACCCCGACTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAACCC
*
140780 CGATTTTATTTCCAAAAAATACCAATTTCTTCACAATCGG
66 CGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGG
140820 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
140836 TTAATCATCG
Statistics
Matches: 103, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
103 63 0.61
104 4 0.04
105 34 0.33
106 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (105 bp):
GGATACTCCAACCCCGACTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTCCAACCC
CGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGG
Found at i:140849 original size:27 final size:28
Alignment explanation
Indices: 140815--140890 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
140805 TTTCTTCACA
140815 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
140842 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
140870 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
140891 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:141026 original size:78 final size:79
Alignment explanation
Indices: 140844--141047 Score: 241
Period size: 78 Copynumber: 2.6 Consensus size: 79
140834 CGTTAATCAT
* *
140844 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
* * *
140909 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * ** *
140923 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAATCCC-GATTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAAT-A
140986 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * * *
141001 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
141048 TTATTATCTC
Statistics
Matches: 104, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
77 3 0.03
78 59 0.57
79 42 0.40
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:142835 original size:108 final size:112
Alignment explanation
Indices: 142681--142903 Score: 375
Period size: 108 Copynumber: 2.0 Consensus size: 112
142671 ATGTTAACTA
* *
142681 TTTAACCTTTTTATTGAAAGATAAAAAATCCAACCCAATTCCCTTTCTTTGTGTTGATTTCACAA
1 TTTAACCTTTTTATTGAAAGATAAAAAATCCAACCCAATTCCCTTTCCTTGGGTTGATTTCACAA
*
142746 GTATATATAATCACC-ACTTAAATATTATCTAATTACTCTTTTAATTT
66 GTATATATAAGCACCAAC-TAAATATTATCTAATTACTCTTTTAATTT
142793 TTTAACCTTTTTATTG-AA-A-AAAAAATCCAA-CCAATTCCCTTTCCTTGGGTTGATTTCACAA
1 TTTAACCTTTTTATTGAAAGATAAAAAATCCAACCCAATTCCCTTTCCTTGGGTTGATTTCACAA
142854 GTATATATAAGCACCAACTAAATATTATCTAATTACTCTTTTAATTT
66 GTATATATAAGCACCAACTAAATATTATCTAATTACTCTTTTAATTT
142901 TTT
1 TTT
142904 TACATAAATA
Statistics
Matches: 107, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
108 75 0.70
109 13 0.12
110 1 0.01
111 2 0.02
112 16 0.15
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (112 bp):
TTTAACCTTTTTATTGAAAGATAAAAAATCCAACCCAATTCCCTTTCCTTGGGTTGATTTCACAA
GTATATATAAGCACCAACTAAATATTATCTAATTACTCTTTTAATTT
Found at i:143262 original size:2 final size:2
Alignment explanation
Indices: 143248--143286 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
143238 ACTAAAACTT
143248 TA TA TA -A TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
143287 CCTTTCAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:145631 original size:17 final size:17
Alignment explanation
Indices: 145607--145653 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
145597 TAATTTTTTG
*
145607 GTAT-TATTTATTTGGT
1 GTATATATTTATTTGAT
145623 GTATATATTTAATTTGAT
1 GTATATATTT-ATTTGAT
*
145641 -TAAATATTTATTT
1 GTATATATTTATTT
145654 AGACAGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.30
17 13 0.48
18 6 0.22
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (17 bp):
GTATATATTTATTTGAT
Found at i:150289 original size:22 final size:22
Alignment explanation
Indices: 150261--150337 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
150251 TTTCACGTAA
150261 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
* *
150283 CATTTCATGCTTTTCACGTAA----
1 CATTTCATGC-ATGCA--TAATTTT
150304 CATTTCATGCATGCATAATTTT
1 CATTTCATGCATGCATAATTTT
150326 CATTTCATGCAT
1 CATTTCATGCAT
150338 TTCAAAAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
18 3 0.07
20 3 0.07
21 10 0.23
22 22 0.50
23 3 0.07
25 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (22 bp):
CATTTCATGCATGCATAATTTT
Found at i:150289 original size:43 final size:43
Alignment explanation
Indices: 150235--150358 Score: 196
Period size: 43 Copynumber: 2.9 Consensus size: 43
150225 CATTGAATGC
*
150235 ATTTTCATTTCATGTTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
150278 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
* **
150321 ATTTTCATTTCATGCATTTCA-AAAACATTTCATTGCAT
1 ATTTTCATTTCATGCTTTTCACGTAACATTTCA-TGCAT
150359 TGCACTTCAT
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
42 9 0.12
43 67 0.88
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.45
Consensus pattern (43 bp):
ATTTTCATTTCATGCTTTTCACGTAACATTTCATGCATGCATA
Found at i:150309 original size:21 final size:21
Alignment explanation
Indices: 150240--150313 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
150230 AATGCATTTT
*
150240 CATTTCATGTTTTTCACGTAA
1 CATTTCATGCTTTTCACGTAA
* *
150261 CATTTCATGC-ATGCA--TAA
1 CATTTCATGCTTTTCACGTAA
150279 TTTTCATTTCATGCTTTTCACGTAA
1 ----CATTTCATGCTTTTCACGTAA
150304 CATTTCATGC
1 CATTTCATGC
150314 ATGCATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 14
0.68 0.08 0.23
Matches are distributed among these distances:
18 3 0.07
20 3 0.07
21 19 0.46
22 10 0.24
23 3 0.07
25 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (21 bp):
CATTTCATGCTTTTCACGTAA
Found at i:150359 original size:5 final size:5
Alignment explanation
Indices: 150346--150459 Score: 138
Period size: 5 Copynumber: 22.8 Consensus size: 5
150336 ATTTCAAAAA
* * * * * *
150346 CATTT CATTG CATTG CACTT CATTT CATTT CATTG CATTT CATTG CATTG
1 CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT
* * *
150396 CATTT CATTG CATTT CATTT CATTT CATTT CATTT CATTT CATTG CATTG
1 CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT CATTT
*
150446 CATTT CATTA CATT
1 CATTT CATTT CATT
150460 GCTTTCATGC
Statistics
Matches: 96, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 96 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.51
Consensus pattern (5 bp):
CATTT
Found at i:150460 original size:15 final size:15
Alignment explanation
Indices: 150366--150471 Score: 135
Period size: 15 Copynumber: 7.2 Consensus size: 15
150356 CATTGCACTT
150366 CATTTCATTTCATTG
1 CATTTCATTTCATTG
*
150381 CATTTCATTGCATTG
1 CATTTCATTTCATTG
* *
150396 CATTTCATTGCATTT
1 CATTTCATTTCATTG
*
150411 CATTTCATTTCATTT
1 CATTTCATTTCATTG
150426 CATTTCATTTCATTG
1 CATTTCATTTCATTG
* *
150441 CATTGCATTTCATTA
1 CATTTCATTTCATTG
*
150456 CATTGC-TTTCA-TG
1 CATTTCATTTCATTG
150469 CAT
1 CAT
150472 GAAATGGCCG
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
13 4 0.05
14 5 0.06
15 75 0.89
ACGTcount: A:0.21, C:0.21, G:0.08, T:0.51
Consensus pattern (15 bp):
CATTTCATTTCATTG
Found at i:153390 original size:1 final size:1
Alignment explanation
Indices: 153384--153409 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
153374 CTCGATTTGC
153384 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
153410 CGTTGGCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:160409 original size:22 final size:22
Alignment explanation
Indices: 160384--160425 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
160374 TATATTTATT
160384 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
160406 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
160426 ATTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:160779 original size:14 final size:14
Alignment explanation
Indices: 160762--160807 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
160752 TAACTTTTTT
160762 ATATTTTTTAAAAA
1 ATATTTTTTAAAAA
**
160776 ATATTTATTTATTAA
1 ATATTT-TTTAAAAA
160791 ATATTTTTTAAAAA
1 ATATTTTTTAAAAA
160805 ATA
1 ATA
160808 AAATAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTTTTTAAAAA
Found at i:161886 original size:17 final size:18
Alignment explanation
Indices: 161866--161903 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
161856 TATTTAACTT
*
161866 ATATTTAAATTTAAAA-A
1 ATATTTAAATTAAAAATA
161883 ATA-TTAAATTAAAAATA
1 ATATTTAAATTAAAAATA
161900 ATAT
1 ATAT
161904 ATAATATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATTTAAATTAAAAATA
Found at i:161933 original size:21 final size:21
Alignment explanation
Indices: 161877--161954 Score: 65
Period size: 24 Copynumber: 3.7 Consensus size: 21
161867 TATTTAAATT
*
161877 TAAAAAATATTAAATT-AA-A
1 TAAAAAATATTATATTCAATA
* *
161896 -AATAATATATAATATTCAA-A
1 TAA-AAAATATTATATTCAATA
161916 TAAAAAATATTGATATTCAATGTA
1 TAAAAAATATT-ATATTCAA--TA
161940 TAAAAAATATTATAT
1 TAAAAAATATTATAT
161955 AAATTACATT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
18 2 0.04
19 10 0.21
20 9 0.19
21 10 0.21
23 4 0.09
24 12 0.26
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (21 bp):
TAAAAAATATTATATTCAATA
Found at i:164573 original size:24 final size:24
Alignment explanation
Indices: 164546--164599 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
164536 ATTGAAACAA
*
164546 AAAAATGAAAGAAATTAATAAAA-T
1 AAAAATGAAAAAAATTAA-AAAATT
*
164570 AAAAATTAAAAAAATTAAAAAATT
1 AAAAATGAAAAAAATTAAAAAATT
164594 AAAAAT
1 AAAAAT
164600 AATTTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (24 bp):
AAAAATGAAAAAAATTAAAAAATT
Found at i:164577 original size:15 final size:17
Alignment explanation
Indices: 164544--164603 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
164534 ATATTGAAAC
*
164544 AAAAAAATGAAAGAAATT
1 AAAAAAATTAAA-AAATT
*
164562 AATAAAA-T-AAAAATT
1 AAAAAAATTAAAAAATT
164577 AAAAAAATTAAAAAATT
1 AAAAAAATTAAAAAATT
164594 AAAAATAATT
1 AAAAA-AATT
164604 TTAAATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 11 0.31
16 3 0.08
17 12 0.33
18 10 0.28
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAAAAATTAAAAAATT
Found at i:164589 original size:8 final size:8
Alignment explanation
Indices: 164545--164598 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
164535 TATTGAAACA
*
164545 AAAAAATG
1 AAAAAATT
164553 AAAGAAATT
1 AAA-AAATT
164562 AATAAAA-T
1 AA-AAAATT
164570 -AAAAATT
1 AAAAAATT
164577 AAAAAAATT
1 -AAAAAATT
164586 AAAAAATT
1 AAAAAATT
164594 AAAAA
1 AAAAA
164599 TAATTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
6 4 0.10
7 2 0.05
8 17 0.43
9 16 0.40
10 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (8 bp):
AAAAAATT
Found at i:168309 original size:2 final size:2
Alignment explanation
Indices: 168296--168337 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
168286 ATGAACATAC
*
168296 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
168338 TCCTACAATC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:168311 original size:12 final size:12
Alignment explanation
Indices: 168290--168337 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
168280 TTGATTATGA
*
168290 ACATACATATAT
1 ACATATATATAT
168302 ACATATATATAT
1 ACATATATATAT
*
168314 ATATATATATAT
1 ACATATATATAT
*
168326 ATATATATATAT
1 ACATATATATAT
168338 TCCTACAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (12 bp):
ACATATATATAT
Found at i:169567 original size:3 final size:3
Alignment explanation
Indices: 169559--169584 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
169549 TGATTTTCTT
169559 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
169585 ATGTTGTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:170509 original size:17 final size:17
Alignment explanation
Indices: 170489--170523 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
170479 AATTTATGTA
*
170489 TATATTTATTTTATATT
1 TATATTAATTTTATATT
*
170506 TATATTAATTTTTTATT
1 TATATTAATTTTATATT
170523 T
1 T
170524 TTATATTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATATTAATTTTATATT
Found at i:170532 original size:11 final size:11
Alignment explanation
Indices: 170489--170556 Score: 52
Period size: 11 Copynumber: 6.1 Consensus size: 11
170479 AATTTATGTA
*
170489 TATATTTATTT
1 TATATTTATAT
170500 TATATTTATAT
1 TATATTTATAT
170511 TA-ATTT-T-T
1 TATATTTATAT
*
170519 TATTTTTATAT
1 TATATTTATAT
170530 TATGATTATATAAT
1 TAT-ATT-TAT-AT
*
170544 ATAAATTTATAT
1 -TATATTTATAT
170556 T
1 T
170557 TTCCCTTTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
8 3 0.07
9 4 0.09
10 5 0.11
11 17 0.37
12 4 0.09
13 6 0.13
14 5 0.11
15 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:170886 original size:6 final size:6
Alignment explanation
Indices: 170875--170909 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
170865 CTGATTTCTC
* *
170875 TCAAAA TCAAAA TCAAAA CCAAAA GCAAAA TCAAA
1 TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAA
170910 TCCCTACTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.20, G:0.03, T:0.11
Consensus pattern (6 bp):
TCAAAA
Found at i:171329 original size:48 final size:48
Alignment explanation
Indices: 171276--171391 Score: 214
Period size: 48 Copynumber: 2.4 Consensus size: 48
171266 TGTATTTTTA
171276 AAATTAGAGATTTGATTTTGGCTTTGATTTCATTTTGATTTTTGAGAG
1 AAATTAGAGATTTGATTTTGGCTTTGATTTCATTTTGATTTTTGAGAG
*
171324 AAATTAGAGATTTGATTTTGGCTTTGATTTCATTTTGATTTTTGGGAG
1 AAATTAGAGATTTGATTTTGGCTTTGATTTCATTTTGATTTTTGAGAG
*
171372 AAATTAGAGATTTGGTTTTG
1 AAATTAGAGATTTGATTTTG
171392 ATTTTAATTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.49
Consensus pattern (48 bp):
AAATTAGAGATTTGATTTTGGCTTTGATTTCATTTTGATTTTTGAGAG
Found at i:171973 original size:23 final size:24
Alignment explanation
Indices: 171939--171996 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 24
171929 ACCCTCAGAC
** *
171939 TTAA-AATATATTATATTTATTTT
1 TTAATAATATATTATAAATATATT
*
171962 TTAATAAT-TATTTTAAATATATT
1 TTAATAATATATTATAAATATATT
*
171985 TTAATAAAATAT
1 TTAATAATATAT
171997 CTAATGCTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTAATAATATATTATAAATATATT
Found at i:172358 original size:27 final size:26
Alignment explanation
Indices: 172328--172380 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
172318 TTGATATATA
172328 TATTTTTA-TTGATGTATTTTTATATTT
1 TATTTTTATTTGAT-TATTTTT-TATTT
*
172355 TATTTTTATTTTATTATTTTTTATTT
1 TATTTTTATTTGATTATTTTTTATTT
172381 AAATATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 15 0.62
28 4 0.17
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (26 bp):
TATTTTTATTTGATTATTTTTTATTT
Found at i:172374 original size:26 final size:26
Alignment explanation
Indices: 172301--172380 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 26
172291 TTCGAGCTTA
* * *
172301 TTATTTTTATTTTAGT-GTTGATATAT
1 TTATTTTTATTTTATTATTTTATAT-T
* *
172327 ATATTTTTA-TTGATGTATTTTTATATT
1 TTATTTTTATTTTAT-TA-TTTTATATT
*
172354 TTATTTTTATTTTATTATTTTTTATT
1 TTATTTTTATTTTATTATTTTATATT
172380 T
1 T
172381 AAATATTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
25 3 0.07
26 18 0.43
27 11 0.26
28 10 0.24
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (26 bp):
TTATTTTTATTTTATTATTTTATATT
Found at i:172377 original size:15 final size:15
Alignment explanation
Indices: 172344--172390 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
172334 TATTGATGTA
*
172344 TTTTTATATT-TTA-
1 TTTTTATTTTATTAT
172357 TTTTTATTTTATTAT
1 TTTTTATTTTATTAT
* *
172372 TTTTTATTTAAATAT
1 TTTTTATTTTATTAT
172387 TTTT
1 TTTT
172391 CATATAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 9 0.31
14 3 0.10
15 17 0.59
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTATTTTATTAT
Found at i:172381 original size:14 final size:13
Alignment explanation
Indices: 172298--172381 Score: 57
Period size: 14 Copynumber: 6.2 Consensus size: 13
172288 ATATTCGAGC
172298 TTATTATTTTTA-
1 TTATTATTTTTAT
* *
172310 TT-TTAGTGTTGAT
1 TTATTA-TTTTTAT
*
172323 ATATATATTTTTAT
1 TTAT-TATTTTTAT
*
172337 TGATGTATTTTTAT
1 TTAT-TATTTTTAT
172351 ATT-TTATTTTTATT
1 -TTATTATTTTTA-T
172365 TTATTATTTTTTAT
1 TTATTA-TTTTTAT
172379 TTA
1 TTA
172382 AATATTTTTC
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
11 3 0.05
12 6 0.11
13 11 0.20
14 26 0.47
15 9 0.16
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (13 bp):
TTATTATTTTTAT
Found at i:172502 original size:15 final size:15
Alignment explanation
Indices: 172482--172517 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
172472 CTTTATATAT
172482 AAATATAAA-ATTTTA
1 AAATATAAATA-TTTA
172497 AAATATAAATATTTA
1 AAATATAAATATTTA
172512 AAATAT
1 AAATAT
172518 TTAAACTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATATAAATATTTA
Found at i:172503 original size:23 final size:24
Alignment explanation
Indices: 172476--172540 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
172466 TTATATCTTT
172476 ATATATAA-ATATAAAAT-TTTAAA
1 ATATA-AATATATAAAATATTTAAA
*
172499 ATATAAATATTTAAAATATTTAAA
1 ATATAAATATATAAAATATTTAAA
* * * *
172523 CTTTACATAAATAAAATA
1 ATATAAATATATAAAATA
172541 AATGTAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 2 0.06
23 13 0.38
24 19 0.56
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATAAATATATAAAATATTTAAA
Found at i:175732 original size:8 final size:8
Alignment explanation
Indices: 175719--175782 Score: 58
Period size: 8 Copynumber: 7.6 Consensus size: 8
175709 TTTAAGCTAC
175719 CTTTTTTT
1 CTTTTTTT
175727 CTTTTTTT
1 CTTTTTTT
175735 GCCTTATTTTT
1 --CTT-TTTTT
* *
175746 CCTTCTTT
1 CTTTTTTT
*
175754 CTTTCTTT
1 CTTTTTTT
175762 -TTTTTTT
1 CTTTTTTT
175769 CTTTTCTTT
1 CTTTT-TTT
175778 CTTTT
1 CTTTT
175783 CTTTTCCCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
7 6 0.13
8 23 0.49
9 10 0.21
10 3 0.06
11 5 0.11
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (8 bp):
CTTTTTTT
Found at i:175774 original size:20 final size:20
Alignment explanation
Indices: 175720--175787 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 20
175710 TTAAGCTACC
175720 TTTTTTTCTTTT-TTTGCCTTAT
1 TTTTTTTCTTTTCTTT--CTT-T
*
175742 TTTTCCTTC-TTTCTTTCTTT
1 TTTT-TTTCTTTTCTTTCTTT
175762 TTTTTTTCTTTTCTTTCTTT
1 TTTTTTTCTTTTCTTTCTTT
175782 TCTTTT
1 T-TTTT
175788 CCCTTTTTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 3 0.08
20 17 0.43
21 7 0.17
22 7 0.17
23 6 0.15
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.79
Consensus pattern (20 bp):
TTTTTTTCTTTTCTTTCTTT
Found at i:175806 original size:43 final size:41
Alignment explanation
Indices: 175720--175807 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 41
175710 TTAAGCTACC
*
175720 TTTTTTTCTTTTTTTGCCTTATTTTTCCTTCTTTCTTTCTTT
1 TTTTTTTCTTTTTTT-CCTTATTTTTCCTTCTTTCCTTCTTT
* *
175762 TTTTTTTCTTTTCTTT-CTTTTCTTTTCCCTT-TTTCCTTCATT
1 TTTTTTTCTTTT-TTTCCTTAT-TTTT-CCTTCTTTCCTTCTTT
175804 TTTT
1 TTTT
175808 CCTTTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
41 4 0.10
42 29 0.73
43 7 0.17
ACGTcount: A:0.02, C:0.20, G:0.01, T:0.76
Consensus pattern (41 bp):
TTTTTTTCTTTTTTTCCTTATTTTTCCTTCTTTCCTTCTTT
Found at i:176163 original size:21 final size:21
Alignment explanation
Indices: 176133--176172 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
176123 TTAGAAAGCT
176133 TGTTTTTTTTT-GTTTGCTAG
1 TGTTTTTTTTTGGTTTGCTAG
176153 TGTTTTCTTTTTGGTTTGCT
1 TGTTTT-TTTTTGGTTTGCT
176173 GATTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.03, C:0.07, G:0.20, T:0.70
Consensus pattern (21 bp):
TGTTTTTTTTTGGTTTGCTAG
Found at i:176365 original size:10 final size:10
Alignment explanation
Indices: 176350--176387 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
176340 CAGTCAACTC
176350 TCTTTTTTTA
1 TCTTTTTTTA
*
176360 TCTTTTCTT-
1 TCTTTTTTTA
176369 TCTTTTTTTTA
1 TC-TTTTTTTA
176380 TCTTTTTT
1 TCTTTTTT
176388 GTATTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.83
11 2 0.08
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (10 bp):
TCTTTTTTTA
Found at i:187225 original size:28 final size:28
Alignment explanation
Indices: 187151--187225 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
187141 AATAAAGCCT
* *** *
187151 GGGTTGGATTATCCCCTCGGAAATAACG
1 GGGTTGGAGTATCCCCGATGAAATAACA
187179 GGGTTGGAGTATCCCCGATGAAATAACA
1 GGGTTGGAGTATCCCCGATGAAATAACA
187207 GGGTTGGAGTATCCCCGAT
1 GGGTTGGAGTATCCCCGAT
187226 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGATGAAATAACA
Found at i:187270 original size:51 final size:51
Alignment explanation
Indices: 187209--187389 Score: 220
Period size: 51 Copynumber: 3.5 Consensus size: 51
187199 AAATAACAGG
* * * * ** *
187209 GTTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGGAATAAAGCCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCGGA
* *
187260 GTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTT-GAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAG-AAATAAAATCGGA
* ** *
187311 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATTGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCGGA
*
187362 GTTGGAGTATCCCCGATTAAGAAAAATT
1 GTTGGAGTATCCCCGATTATGAAAAATT
187390 GATGTCTTGG
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
50 1 0.01
51 112 0.98
52 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCGGA
Found at i:187418 original size:51 final size:50
Alignment explanation
Indices: 187209--187438 Score: 182
Period size: 51 Copynumber: 4.5 Consensus size: 50
187199 AAATAACAGG
* * * *
187209 GTTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGGAATAAAGCCGGG-
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTT-GGAA-AAAACCGGGA
* * * *
187260 GTTGGAGTATCCCCGATTGTGGAAAATT-AGTGTTTTGAAAATAAAATC-GGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGA-TGTTTTG-GAA-AAAACCGGGA
* * * * ***
187311 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATTGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAA-AAACCGGGA
* *
187362 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTCTTGGAAAGGAAACCGGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAA--AAACCGGGA
* *
187414 -TTGGAGTATCCTCGA-GATGAAAAAT
1 GTTGGAGTATCCCCGATTATGAAAAAT
187439 CTAGAAATTT
Statistics
Matches: 147, Mismatches: 25, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
49 1 0.01
50 17 0.12
51 123 0.84
52 6 0.04
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAAAAACCGGGA
Found at i:187418 original size:102 final size:102
Alignment explanation
Indices: 187209--187438 Score: 232
Period size: 102 Copynumber: 2.3 Consensus size: 102
187199 AAATAACAGG
* * * * *
187209 GTTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGGAATAAAGCCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAAAAATGAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCC
** * * * *
187274 GATTGTGGAAAATTAGTGTTTTGAAAATAAAATCGGA
66 GATTAAGAAAAATTAGTGTCTTGAAAAGAAAACCGGA
* ** * **
187311 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATTGGAGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAAAAATGAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCC
* *
187376 GATTAAGAAAAATT-GATGTCTTGGAAAGGAAACCGG-
66 GATTAAGAAAAATTAG-TGTCTTGAAAAGAAAACCGGA
* *
187412 GATTGGAGTATCCTCGA-GATGAAAAAT
1 G-TTGGAGTATCCCCGATTATGAAAAAT
187439 CTAGAAATTT
Statistics
Matches: 104, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
101 10 0.10
102 94 0.90
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.29
Consensus pattern (102 bp):
GTTGGAGTATCCCCGATTATGAAAAATGAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCC
GATTAAGAAAAATTAGTGTCTTGAAAAGAAAACCGGA
Found at i:189834 original size:21 final size:21
Alignment explanation
Indices: 189810--189851 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
189800 GTATCGATAC
189810 AATGTATCGATATATTTCCTT
1 AATGTATCGATATATTTCCTT
189831 AATGTATCGATATATTTCCTT
1 AATGTATCGATATATTTCCTT
189852 GGCAGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.48
Consensus pattern (21 bp):
AATGTATCGATATATTTCCTT
Found at i:198513 original size:28 final size:28
Alignment explanation
Indices: 198480--198553 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
198470 AATAAAGCCT
* ** * *
198480 GGGTTGGATTATCCCCTCGGAAATAACG
1 GGGTTGGAGTATCCCCGAGAAAATAACA
*
198508 GGGTTGGAGTATCCCCGATAAAATAACA
1 GGGTTGGAGTATCCCCGAGAAAATAACA
198536 GGGTTGGAGTATCCCCGA
1 GGGTTGGAGTATCCCCGA
198554 TTGTGAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGAGAAAATAACA
Found at i:198554 original size:28 final size:28
Alignment explanation
Indices: 198500--198554 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
198490 ATCCCCTCGG
*
198500 AAATAACGGGGTTGGAGTATCCCCGATA
1 AAATAACAGGGTTGGAGTATCCCCGATA
198528 AAATAACAGGGTTGGAGTATCCCCGAT
1 AAATAACAGGGTTGGAGTATCCCCGAT
198555 TGTGAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (28 bp):
AAATAACAGGGTTGGAGTATCCCCGATA
Found at i:198599 original size:51 final size:51
Alignment explanation
Indices: 198538--198718 Score: 220
Period size: 51 Copynumber: 3.5 Consensus size: 51
198528 AAATAACAGG
* * * * ** *
198538 GTTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGGAATAAAGCCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCGGA
* *
198589 GTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTT-GAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAG-AAATAAAATCGGA
* ** *
198640 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATTGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCGGA
*
198691 GTTGGAGTATCCCCGATTAAGAAAAATT
1 GTTGGAGTATCCCCGATTATGAAAAATT
198719 GATGTCTTGG
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
50 1 0.01
51 112 0.98
52 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCGGA
Found at i:198747 original size:51 final size:50
Alignment explanation
Indices: 198538--198767 Score: 182
Period size: 51 Copynumber: 4.5 Consensus size: 50
198528 AAATAACAGG
* * * *
198538 GTTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGGAATAAAGCCGGG-
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTT-GGAA-AAAACCGGGA
* * * *
198589 GTTGGAGTATCCCCGATTGTGGAAAATT-AGTGTTTTGAAAATAAAATC-GGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGA-TGTTTTG-GAA-AAAACCGGGA
* * * * ***
198640 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATTGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAA-AAACCGGGA
* *
198691 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTCTTGGAAAGGAAACCGGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAA--AAACCGGGA
* *
198743 -TTGGAGTATCCTCGA-GATGAAAAAT
1 GTTGGAGTATCCCCGATTATGAAAAAT
198768 CTAGAAATTT
Statistics
Matches: 147, Mismatches: 25, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
49 1 0.01
50 17 0.12
51 123 0.84
52 6 0.04
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.29
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTGGAAAAAACCGGGA
Found at i:198747 original size:102 final size:102
Alignment explanation
Indices: 198538--198767 Score: 232
Period size: 102 Copynumber: 2.3 Consensus size: 102
198528 AAATAACAGG
* * * * *
198538 GTTGGAGTATCCCCGATTGTGAAAAATTAATATTTTAGGAATAAAGCCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAAAAATGAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCC
** * * * *
198603 GATTGTGGAAAATTAGTGTTTTGAAAATAAAATCGGA
66 GATTAAGAAAAATTAGTGTCTTGAAAAGAAAACCGGA
* ** * **
198640 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATTGGAGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAAAAATGAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCC
* *
198705 GATTAAGAAAAATT-GATGTCTTGGAAAGGAAACCGG-
66 GATTAAGAAAAATTAG-TGTCTTGAAAAGAAAACCGGA
* *
198741 GATTGGAGTATCCTCGA-GATGAAAAAT
1 G-TTGGAGTATCCCCGATTATGAAAAAT
198768 CTAGAAATTT
Statistics
Matches: 104, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
101 10 0.10
102 94 0.90
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.29
Consensus pattern (102 bp):
GTTGGAGTATCCCCGATTATGAAAAATGAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCC
GATTAAGAAAAATTAGTGTCTTGAAAAGAAAACCGGA
Found at i:204526 original size:35 final size:34
Alignment explanation
Indices: 204478--204610 Score: 144
Period size: 34 Copynumber: 3.9 Consensus size: 34
204468 ACATCCTTTT
*
204478 AAGTCCACAACTCCGTGGTACCTTTTTCTTTCCCA
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTT-CCA
* * **
204513 AAGTCCACGACTCCATGGCACCTTTTTCTTTTTA
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTCCA
* * *
204547 AAGTCCACAACTCCGTGGCACATTTTCCTTT--T
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTCCA
** *
204579 AAGTCCACAACTCTTTGGCACCTTTATCTTTC
1 AAGTCCACAACTCCGTGGCACCTTTTTCTTTC
204611 AGACCAATGT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
32 26 0.32
34 28 0.34
35 28 0.34
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.36
Consensus pattern (34 bp):
AAGTCCACAACTCCGTGGCACCTTTTTCTTTCCA
Found at i:204560 original size:34 final size:33
Alignment explanation
Indices: 204474--204609 Score: 148
Period size: 35 Copynumber: 4.1 Consensus size: 33
204464 CGTGACATCC
*
204474 TTTTAAGTCCACAACTCCGTGGTACCTTTTTCT
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTTCT
** * *
204507 TTCCCAAAGTCCACGACTCCATGGCACCTTTTTCT
1 TT--TTAAGTCCACAACTCCGTGGCACCTTTTTCT
* *
204542 TTTTAAAGTCCACAACTCCGTGGCA-CATTTTCC
1 TTTT-AAGTCCACAACTCCGTGGCACCTTTTTCT
** *
204575 TTTTAAGTCCACAACTCTTTGGCACCTTTATCT
1 TTTTAAGTCCACAACTCCGTGGCACCTTTTTCT
204608 TT
1 TT
204610 CAGACCAATG
Statistics
Matches: 83, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
32 18 0.22
33 19 0.23
34 18 0.22
35 28 0.34
ACGTcount: A:0.21, C:0.30, G:0.11, T:0.38
Consensus pattern (33 bp):
TTTTAAGTCCACAACTCCGTGGCACCTTTTTCT
Found at i:204728 original size:49 final size:49
Alignment explanation
Indices: 204593--204712 Score: 159
Period size: 49 Copynumber: 2.4 Consensus size: 49
204583 CCACAACTCT
* *
204593 TTGGCACCTTTATCTTTCAGACCAATGTCGCTGGCCTTGAATCAATACA
1 TTGGCACCTTTATCTTTCAGACCAATATCGCTGGCCTTAAATCAATACA
* * * * * * *
204642 TTGGCACCTTCATCTTTAAGCCCAACATCGCTGGCCTTAAATTAGTATA
1 TTGGCACCTTTATCTTTCAGACCAATATCGCTGGCCTTAAATCAATACA
204691 TTGGCACCTTTATCTTTCAGAC
1 TTGGCACCTTTATCTTTCAGAC
204713 TAATTTCATT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (49 bp):
TTGGCACCTTTATCTTTCAGACCAATATCGCTGGCCTTAAATCAATACA
Found at i:206214 original size:10 final size:10
Alignment explanation
Indices: 206184--206237 Score: 58
Period size: 10 Copynumber: 5.6 Consensus size: 10
206174 TTTGATTTGT
206184 TAATTTTTT-
1 TAATTTTTTA
**
206193 T-ATTTTAAA
1 TAATTTTTTA
206202 TAATTTTTTA
1 TAATTTTTTA
*
206212 TAATATTTTA
1 TAATTTTTTA
*
206222 AAATTTTTTA
1 TAATTTTTTA
206232 TAATTT
1 TAATTT
206238 AATAATAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
8 5 0.14
9 2 0.06
10 28 0.80
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:206226 original size:20 final size:22
Alignment explanation
Indices: 206193--206235 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
206183 TTAATTTTTT
206193 TATTTTAAATAATTTTTTATAA
1 TATTTTAAATAATTTTTTATAA
206215 TATTTT-AA-AATTTTTTATAA
1 TATTTTAAATAATTTTTTATAA
206235 T
1 T
206236 TTAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTAAATAATTTTTTATAA
Found at i:206262 original size:12 final size:13
Alignment explanation
Indices: 206233--206266 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
206223 AATTTTTTAT
206233 AATTTAATAATAAA
1 AATTTAA-AATAAA
206247 AATTTAAAAT-AA
1 AATTTAAAATAAA
206259 AATTTAAA
1 AATTTAAA
206267 TTAATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
13 3 0.15
14 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATTTAAAATAAA
Found at i:206340 original size:22 final size:22
Alignment explanation
Indices: 206315--206373 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
206305 AATTAAATTA
*
206315 AATTAAATTGAA-TATATTTAAT
1 AATT-AATTGAATTAAATTTAAT
*
206337 AATTAATTTAATTAAATTTAAT
1 AATTAATTGAATTAAATTTAAT
*
206359 AA-TAATTAAATTAAA
1 AATTAATTGAATTAAA
206374 CATTACTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTAATTGAATTAAATTTAAT
Found at i:206353 original size:31 final size:32
Alignment explanation
Indices: 206300--206368 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
206290 AATTTATAAA
206300 TTAAAAATTAAATTAAATTAAATTGAATATAT
1 TTAAAAATTAAATTAAATTAAATTGAATATAT
* * * *
206332 TTAATAATT-AATTTAATTAAATTTAATAATAA
1 TTAAAAATTAAATTAAATTAAATTGAAT-ATAT
206364 TTAAA
1 TTAAA
206369 TTAAACATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 16 0.52
32 15 0.48
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (32 bp):
TTAAAAATTAAATTAAATTAAATTGAATATAT
Found at i:206364 original size:16 final size:15
Alignment explanation
Indices: 206315--206370 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
206305 AATTAAATTA
*
206315 AATTAAATTGAATAT
1 AATTAAATTTAATAT
* * *
206330 ATTTAATAATTAATTT
1 AATTAA-ATTTAATAT
206346 AATTAAATTTAATAAT
1 AATTAAATTTAAT-AT
206362 AATTAAATT
1 AATTAAATT
206371 AAACATTACT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 11 0.34
16 21 0.66
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
AATTAAATTTAATAT
Found at i:206623 original size:43 final size:43
Alignment explanation
Indices: 206565--206651 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
206555 CTTTCTTTTT
* * * *
206565 TCCCTCTTTGTTAAATAATTAAGTTTTATATATTATCTATACA
1 TCCCTATTTGATAAATAATTAAATTTTATACATTATCTATACA
206608 TCCCTATTTGATAAATAATTAAATTTTATACATTATCTATACA
1 TCCCTATTTGATAAATAATTAAATTTTATACATTATCTATACA
206651 T
1 T
206652 TTTGTTCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (43 bp):
TCCCTATTTGATAAATAATTAAATTTTATACATTATCTATACA
Found at i:216366 original size:28 final size:30
Alignment explanation
Indices: 216325--216381 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
216315 ATACAGCGTA
216325 ACTATTACACTTTT-TTTCCCTT-TTTGTG
1 ACTATTACACTTTTCTTTCCCTTCTTTGTG
* *
216353 ACTATTACATTTTTCTTTTCCTTCTTTGT
1 ACTATTACACTTTTCTTTCCCTTCTTTGT
216382 TTAACTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.52
29 7 0.28
30 5 0.20
ACGTcount: A:0.14, C:0.21, G:0.05, T:0.60
Consensus pattern (30 bp):
ACTATTACACTTTTCTTTCCCTTCTTTGTG
Found at i:216965 original size:22 final size:24
Alignment explanation
Indices: 216935--216988 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 24
216925 TTAAATATTT
216935 TAATATATATTTTT-ATATTAAAA
1 TAATATATATTTTTAATATTAAAA
216958 TAAT-TATATTTTTAATATTAAAA
1 TAATATATATTTTTAATATTAAAA
*
216981 TAAAATAT
1 TAATATAT
216989 TTAAATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 9 0.32
23 16 0.57
24 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TAATATATATTTTTAATATTAAAA
Found at i:218110 original size:12 final size:12
Alignment explanation
Indices: 218083--218121 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
218073 TACTAAAGAT
*
218083 TAAATTTAAAAA
1 TAAATTAAAAAA
218095 -AAATTAAAAAA
1 TAAATTAAAAAA
218106 TAAATTAAAAATA
1 TAAATTAAAAA-A
218119 TAA
1 TAA
218122 TATGGGACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 10 0.42
12 10 0.42
13 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAATTAAAAAA
Found at i:218745 original size:13 final size:13
Alignment explanation
Indices: 218727--218752 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
218717 TACATCAAGT
218727 ATGTATCGATACA
1 ATGTATCGATACA
218740 ATGTATCGATACA
1 ATGTATCGATACA
218753 CCAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:218750 original size:32 final size:33
Alignment explanation
Indices: 218709--218772 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
218699 TAGCCAAACT
* **
218709 TGTATCGATACATCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
218741 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
218773 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:223840 original size:13 final size:13
Alignment explanation
Indices: 223822--223847 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
223812 CAATTTTTTG
223822 TGTATCGATACAT
1 TGTATCGATACAT
223835 TGTATCGATACAT
1 TGTATCGATACAT
223848 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:223931 original size:20 final size:21
Alignment explanation
Indices: 223886--223938 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
223876 CTGCCAAGAA
* **
223886 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTGTAAC
223907 ATGTATCGATACAT-TGTAAC
1 ATGTATCGATACATCTGTAAC
223927 ATGTATCGATAC
1 ATGTATCGATAC
223939 TTTGAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (21 bp):
ATGTATCGATACATCTGTAAC
Found at i:226409 original size:13 final size:13
Alignment explanation
Indices: 226391--226416 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
226381 ATAATCACCC
226391 TGTATCGATACAA
1 TGTATCGATACAA
226404 TGTATCGATACAA
1 TGTATCGATACAA
226417 AGAAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:228519 original size:15 final size:15
Alignment explanation
Indices: 228499--228529 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
228489 ATTTCGTTTG
*
228499 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
228514 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
228529 G
1 G
228530 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:230282 original size:21 final size:21
Alignment explanation
Indices: 230253--230297 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
230243 AAGTTTTCAT
*
230253 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
230273 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
230295 TTT
1 TTT
230298 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:232533 original size:13 final size:13
Alignment explanation
Indices: 232515--232540 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
232505 CAATTTTTTG
232515 TGTATCGATACAT
1 TGTATCGATACAT
232528 TGTATCGATACAT
1 TGTATCGATACAT
232541 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:236649 original size:39 final size:39
Alignment explanation
Indices: 236606--236706 Score: 89
Period size: 39 Copynumber: 2.6 Consensus size: 39
236596 ATTAAGGGGG
*
236606 AAATTTTTTTTTTAAAGGGGAGAATGCATGAATTTGCGA
1 AAATTTTTTTTTTAAAGGGGAGAATGCACGAATTTGCGA
*** * * * **
236645 AAATTACCTTATTAAAGGGAAGAATGTACGAATTTGTTA
1 AAATTTTTTTTTTAAAGGGGAGAATGCACGAATTTGCGA
*
236684 AAATTATTTTGTTT-AA-GGGAGAA
1 AAATT-TTTTTTTTAAAGGGGAGAA
236707 AGAAAAGAAA
Statistics
Matches: 46, Mismatches: 15, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
38 6 0.13
39 37 0.80
40 3 0.07
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.37
Consensus pattern (39 bp):
AAATTTTTTTTTTAAAGGGGAGAATGCACGAATTTGCGA
Found at i:237353 original size:13 final size:13
Alignment explanation
Indices: 237335--237360 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
237325 TACATCAAGT
237335 ATGTATCGATACA
1 ATGTATCGATACA
237348 ATGTATCGATACA
1 ATGTATCGATACA
237361 CCAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:237358 original size:32 final size:33
Alignment explanation
Indices: 237317--237380 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
237307 TAGCCAAACT
* **
237317 TGTATCGATACATCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
237349 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
237381 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:238837 original size:27 final size:28
Alignment explanation
Indices: 238791--238844 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
238781 TTCGGTTCAA
* *
238791 AAATATTAATAATTGATTAAATTAATTT
1 AAATAATAATAATCGATTAAATTAATTT
238819 AAATAATAA-AATCGATTAAATTAATT
1 AAATAATAATAATCGATTAAATTAATT
238845 AATAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (28 bp):
AAATAATAATAATCGATTAAATTAATTT
Found at i:239275 original size:11 final size:11
Alignment explanation
Indices: 239251--239290 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
239241 AAAATAATTT
239251 AATTGATAAAAA
1 AATT-ATAAAAA
*
239263 AATTATTAAAA
1 AATTATAAAAA
239274 AATT-TAAAAA
1 AATTATAAAAA
239284 AATTATA
1 AATTATA
239291 TTATTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.36
11 12 0.48
12 4 0.16
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
AATTATAAAAA
Found at i:239277 original size:28 final size:28
Alignment explanation
Indices: 239223--239280 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
239213 AATCGGATTG
*
239223 AATTGATAAATTAAATTAAAAATAATTT
1 AATTGATAAATAAAATTAAAAATAATTT
239251 AATTGATAAA-AAAATTATTAAAA-AATTT
1 AATTGATAAATAAAATTA--AAAATAATTT
239279 AA
1 AA
239281 AAAAATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 6 0.22
28 17 0.63
29 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (28 bp):
AATTGATAAATAAAATTAAAAATAATTT
Found at i:239332 original size:20 final size:21
Alignment explanation
Indices: 239292--239337 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
239282 AAAATTATAT
**
239292 TATTTTTATATTTTTTAAAAA
1 TATTTTTATATTTAATAAAAA
239313 TATTTTTATATTTAAT-AAAA
1 TATTTTTATATTTAATAAAAA
239333 TATTT
1 TATTT
239338 AAATTATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTTATATTTAATAAAAA
Found at i:240192 original size:2 final size:2
Alignment explanation
Indices: 240180--240217 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
240170 TTTTTACTAT
*
240180 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
240218 AAACAAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:240514 original size:3 final size:3
Alignment explanation
Indices: 240506--240531 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
240496 AGTTTAATTG
240506 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
240532 TCTCTGTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:248259 original size:19 final size:19
Alignment explanation
Indices: 248235--248277 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
248225 TTTTAAATAT
* * *
248235 TTAAAAATAATAATTTATA
1 TTAAAAATAAAAAATTAAA
248254 TTAAAAATAAAAAATTAAA
1 TTAAAAATAAAAAATTAAA
248273 TTAAA
1 TTAAA
248278 TTTACAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAAAAATAAAAAATTAAA
Found at i:248502 original size:15 final size:15
Alignment explanation
Indices: 248484--248534 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
248474 TTAAAAGTTA
248484 TTTATTTATATAAAT
1 TTTATTTATATAAAT
*
248499 TTTA-TTATATTAATAA
1 TTTATTTATA-TAA-AT
*
248515 TTTATATAATATAAAT
1 TTTAT-TTATATAAAT
248531 TTTA
1 TTTA
248535 ATATATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 5 0.17
15 7 0.24
16 10 0.34
17 3 0.10
18 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTATTTATATAAAT
Found at i:248506 original size:14 final size:14
Alignment explanation
Indices: 248484--248540 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
248474 TTAAAAGTTA
248484 TTTATTTATATAAAT
1 TTTA-TTATATAAAT
248499 TTTATTATATTAATAAT
1 TTTATTATA-T-A-AAT
*
248516 TTATATAATATAAAT
1 TT-TATTATATAAAT
*
248531 TTTAATATAT
1 TTTATTATAT
248541 TTATATATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
14 11 0.31
15 10 0.29
16 2 0.06
17 6 0.17
18 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTATTATATAAAT
Found at i:248545 original size:18 final size:18
Alignment explanation
Indices: 248492--248584 Score: 59
Period size: 18 Copynumber: 5.2 Consensus size: 18
248482 TATTTATTTA
*
248492 TATAAATTTTATTATATT
1 TATAAATTTTAATATATT
* *
248510 AAT-AA-TTT-ATATA-A
1 TATAAATTTTAATATATT
248524 TATAAATTTTAATATATT
1 TATAAATTTTAATATATT
* ** *
248542 TATATATTCAAATTATATC
1 TATAAATTTTAA-TATATT
*
248561 TATAATTATTTTTATATATT
1 TATAA--ATTTTAATATATT
248581 TATA
1 TATA
248585 TTATGTAATT
Statistics
Matches: 54, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
14 2 0.04
15 6 0.11
16 6 0.11
17 7 0.13
18 11 0.20
19 9 0.17
20 9 0.17
21 4 0.07
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TATAAATTTTAATATATT
Found at i:248827 original size:16 final size:16
Alignment explanation
Indices: 248788--248818 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
248778 AAAAATTTTA
*
248788 ATATATATTTATGTGC
1 ATATATATTTATATGC
248804 ATATATATTTATATG
1 ATATATATTTATATG
248819 TATGTATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (16 bp):
ATATATATTTATATGC
Found at i:248938 original size:16 final size:17
Alignment explanation
Indices: 248914--248946 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
248904 ACTTTATGAT
248914 TTAATAATTAAAAAATA
1 TTAATAATTAAAAAATA
*
248931 TTAA-AATTAATAAATA
1 TTAATAATTAAAAAATA
248947 AATTTGAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAATAATTAAAAAATA
Found at i:249965 original size:20 final size:20
Alignment explanation
Indices: 249936--249986 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
249926 AAGTAACAAG
* *
249936 ATAAATAATATGAATATAAT
1 ATAAAAAATACGAATATAAT
249956 ATAAAAAATACGAATATAAT
1 ATAAAAAATACGAATATAAT
249976 ATAAAAAATAC
1 ATAAAAAATAC
249987 ATATAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (20 bp):
ATAAAAAATACGAATATAAT
Found at i:249990 original size:18 final size:19
Alignment explanation
Indices: 249948--249997 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
249938 AAATAATATG
249948 AATATAATATAAAAAATAC
1 AATATAATATAAAAAATAC
249967 GAATATAATATAAAAAATAC
1 -AATATAATATAAAAAATAC
*
249987 -ATATAAAATAA
1 AATATAATATAA
249998 CATATAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 10 0.34
20 19 0.66
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (19 bp):
AATATAATATAAAAAATAC
Found at i:249996 original size:20 final size:20
Alignment explanation
Indices: 249936--249996 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
249926 AAGTAACAAG
* * *
249936 ATAAATAATATGAATATAAT
1 ATAAAAAATACGAATAAAAT
*
249956 ATAAAAAATACGAATATAAT
1 ATAAAAAATACGAATAAAAT
249976 ATAAAAAATAC-ATATAAAAT
1 ATAAAAAATACGA-ATAAAAT
249996 A
1 A
249997 ACATATAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.03
20 36 0.97
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (20 bp):
ATAAAAAATACGAATAAAAT
Found at i:254812 original size:24 final size:24
Alignment explanation
Indices: 254785--254851 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
254775 TTTATTTTGA
254785 TTTTAGATTTTTTATTTACTGATT
1 TTTTAGATTTTTTATTTACTGATT
* * *
254809 TTTTA-TTTTTTTGATTCATTGATT
1 TTTTAGATTTTTT-ATTTACTGATT
*
254833 TTTTTGAATTTTTTTATTT
1 TTTTAG-A-TTTTTTATTT
254852 TTCATTATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
23 6 0.18
24 18 0.55
26 3 0.09
27 6 0.18
ACGTcount: A:0.18, C:0.03, G:0.07, T:0.72
Consensus pattern (24 bp):
TTTTAGATTTTTTATTTACTGATT
Found at i:256534 original size:2 final size:2
Alignment explanation
Indices: 256527--256567 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
256517 TATCAAAAAC
256527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
256568 GTTGATTGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:258266 original size:27 final size:27
Alignment explanation
Indices: 258226--258295 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
258216 ATATATTGAC
*
258226 AATAAATATAAATTATAATTAAATT-ATA
1 AATAAAAAT-AATTA-AATTAAATTCATA
* *
258254 AATAAAAATAATTAATTTACATTCATA
1 AATAAAAATAATTAAATTAAATTCATA
*
258281 AATAAAGATAATTAA
1 AATAAAAATAATTAA
258296 TTCAACTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 7 0.19
27 22 0.59
28 8 0.22
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (27 bp):
AATAAAAATAATTAAATTAAATTCATA
Found at i:259675 original size:27 final size:27
Alignment explanation
Indices: 259639--259702 Score: 101
Period size: 27 Copynumber: 2.3 Consensus size: 27
259629 ACACGATTAA
259639 TTAATCATGTCATAAATGTGAAATTATG
1 TTAAT-ATGTCATAAATGTGAAATTATG
* *
259667 TTAATATGTCATAAATGTGTAATTGTG
1 TTAATATGTCATAAATGTGAAATTATG
259694 TTAATATGT
1 TTAATATGT
259703 ATCCGTTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.44
Consensus pattern (27 bp):
TTAATATGTCATAAATGTGAAATTATG
Found at i:259923 original size:13 final size:13
Alignment explanation
Indices: 259907--259931 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
259897 CAATTTCAAT
259907 ATTATATAATAGC
1 ATTATATAATAGC
259920 ATTATATAATAG
1 ATTATATAATAG
259932 AAAAGTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
ATTATATAATAGC
Found at i:260265 original size:13 final size:15
Alignment explanation
Indices: 260228--260260 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
260218 AAGTTTATAA
260228 ATATT-AATATATTC
1 ATATTAAATATATTC
260242 ATATTAAATATATTC
1 ATATTAAATATATTC
260257 ATAT
1 ATAT
260261 CATATCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATTAAATATATTC
Found at i:263495 original size:19 final size:20
Alignment explanation
Indices: 263452--263495 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
263442 TTTTAACTAT
263452 TAAATTTTATTTGATTTTGA
1 TAAATTTTATTTGATTTTGA
*
263472 TAAATGTTT-TTTTATTTT-A
1 TAAAT-TTTATTTGATTTTGA
263491 TAAAT
1 TAAAT
263496 AGGTAGCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 6 0.27
20 13 0.59
21 3 0.14
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (20 bp):
TAAATTTTATTTGATTTTGA
Found at i:268445 original size:13 final size:13
Alignment explanation
Indices: 268429--268455 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
268419 ATAAAATAAC
268429 AATAAAATTTATA
1 AATAAAATTTATA
268442 AATAAAATTTATA
1 AATAAAATTTATA
268455 A
1 A
268456 TTCCATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATAAAATTTATA
Found at i:268640 original size:24 final size:23
Alignment explanation
Indices: 268612--268678 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
268602 CTATAATTTT
268612 ATTTAAAATATTTAATATATATA
1 ATTTAAAATATTTAATATATATA
* *
268635 ATTTTAATATATTAATAATTTATATA
1 A-TTTAAAATATT--TAATATATATA
*
268661 ATAT-AAAT-TTTAATATAT
1 ATTTAAAATATTTAATATAT
268679 TTATTATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
21 7 0.19
23 3 0.08
24 13 0.36
25 2 0.06
26 11 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTAAAATATTTAATATATATA
Found at i:268652 original size:17 final size:16
Alignment explanation
Indices: 268622--268679 Score: 68
Period size: 15 Copynumber: 3.7 Consensus size: 16
268612 ATTTAAAATA
268622 TTTAATATA-TATAAT
1 TTTAATATATTATAAT
268637 TTTAATATATTAATAA-
1 TTTAATATATT-ATAAT
*
268653 TTT-ATATAATATAAAT
1 TTTAATATATTAT-AAT
268669 TTTAATATATT
1 TTTAATATATT
268680 TATTATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 2 0.06
15 17 0.47
16 7 0.19
17 10 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAATATATTATAAT
Found at i:268681 original size:9 final size:9
Alignment explanation
Indices: 268611--268681 Score: 50
Period size: 9 Copynumber: 8.7 Consensus size: 9
268601 ACTATAATTT
*
268611 TATTTAAAA
1 TATTTAATA
268620 TATTTAATA
1 TATTTAATA
*
268629 TATAT-A-A
1 TATTTAATA
268636 T-TTTAATA
1 TATTTAATA
268644 TA-TTAATA
1 TATTTAATA
268652 -ATTT-ATA
1 TATTTAATA
*
268659 TAATATAA-A
1 T-ATTTAATA
268668 T-TTTAATA
1 TATTTAATA
268676 TATTTA
1 TATTTA
268682 TTATTAATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
6 2 0.04
7 11 0.23
8 13 0.27
9 21 0.44
10 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
TATTTAATA
Found at i:273687 original size:111 final size:111
Alignment explanation
Indices: 273556--273756 Score: 321
Period size: 111 Copynumber: 1.8 Consensus size: 111
273546 TCACAAATTT
* * * * *
273556 TTACTCGTCAATTTTTTTTTGCAAAATGCATCCCAAAATTCATAATTTTGTCTTTATTATTATTA
1 TTACTCGTCAAATTGTTTTTGCAAAATGCATCCAAAAATTCAAAATTTTGTCTTTACTATTATTA
273621 TAAATTAATATTTTAAGTAAGATATAAAGCTCATTCTTTACTAAAC
66 TAAATTAATATTTTAAGTAAGATATAAAGCTCATTCTTTACTAAAC
* * * *
273667 TTACTTGTCAAATTGTTTTTGTAAAATGTATCCAAAAATTTAAAATTTTGTCTTTACTATTATTA
1 TTACTCGTCAAATTGTTTTTGCAAAATGCATCCAAAAATTCAAAATTTTGTCTTTACTATTATTA
273732 TAAATTAATATTTTAAGTAAGATAT
66 TAAATTAATATTTTAAGTAAGATAT
273757 GAAATTTAAG
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
111 81 1.00
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.46
Consensus pattern (111 bp):
TTACTCGTCAAATTGTTTTTGCAAAATGCATCCAAAAATTCAAAATTTTGTCTTTACTATTATTA
TAAATTAATATTTTAAGTAAGATATAAAGCTCATTCTTTACTAAAC
Found at i:274122 original size:153 final size:154
Alignment explanation
Indices: 273964--274276 Score: 472
Period size: 154 Copynumber: 2.0 Consensus size: 154
273954 TCTTTCAGAT
* * *
273964 TTTTTTTTATTTTCAAAATAC-GA-AGTTTTCTA-TTCCGTAAATTT-TTCGATAGGATTTTTCT
1 TTTTTTCTATTATCAAAATACAGAGA-TTTT-TACTT-CGTAAATTTCTCCGATAGGATTTTTCT
*
274025 AAGTTTATAATTTTCAAAATTCTTCAAATATTATTGTTTAATTCATATTAAATCAGTTTTGAAAA
63 AAGTTTATAATTTTCAAAATTCTTCAAATATTATTGTTTAACTCATATTAAATCAGTTTTGAAAA
*
274090 AATCAATTTATTTTATGAGTTTTAGGA
128 AATCAATTTATTTTATGAGTTTTAGAA
* * * *
274117 TTTTTTCTATTATCAAGATACAGAGATTTTTACTTCGTAAATTTCTCCGGTATGATTTTTCTAGG
1 TTTTTTCTATTATCAAAATACAGAGATTTTTACTTCGTAAATTTCTCCGATAGGATTTTTCTAAG
*
274182 TTTATAATTTTCAAAATTCTTCAAATATTATTGTTTAACTCATATTAAATCAGTTTTGAAAAATT
66 TTTATAATTTTCAAAATTCTTCAAATATTATTGTTTAACTCATATTAAATCAGTTTTGAAAAAAT
*
274247 TAATTTATTTTATGAGTTTTAGAA
131 CAATTTATTTTATGAGTTTTAGAA
274271 TTTTTT
1 TTTTTT
274277 GATACCAAGA
Statistics
Matches: 145, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
153 29 0.20
154 115 0.79
155 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (154 bp):
TTTTTTCTATTATCAAAATACAGAGATTTTTACTTCGTAAATTTCTCCGATAGGATTTTTCTAAG
TTTATAATTTTCAAAATTCTTCAAATATTATTGTTTAACTCATATTAAATCAGTTTTGAAAAAAT
CAATTTATTTTATGAGTTTTAGAA
Done.