Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold257
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: 204476
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:143547 original size:28 final size:28
Alignment explanation
Indices: 143474--143547 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
143464 TCTCACAATC
*
143474 GGGGATACTCCAACCCCATTATTTCAAA
1 GGGGATACTCCAACCCCGTTATTTCAAA
*
143502 GGGGATACTCCAACCCCGTTATTTTAAA
1 GGGGATACTCCAACCCCGTTATTTCAAA
* *
143530 GGGGATACCCCTACCCCG
1 GGGGATACTCCAACCCCG
143548 ACTTTATTAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCAAA
Found at i:143554 original size:107 final size:107
Alignment explanation
Indices: 143293--143560 Score: 263
Period size: 107 Copynumber: 2.5 Consensus size: 107
143283 TAATCGAGGG
* * * * * * * ***
143293 TACTCCAACCCTGTTATTTCCGAA-AGGATACTCCAACCCCGGCTTTA-TATCTAAAATATTGAT
1 TACTCCAACCCCGTTATTT-CTAAGGGGATACCCCAACCCCGACTTTATTA-CCAAAACACCAAT
* * * * **
143356 TTTTCATAATCGGGGGTACTCCAACCCCGTTATGTCATCGGGGA
64 TTCTCACAATCGGGGATACTCCAACCCCATTATGTCAAAGGGGA
* * ** * * *
143400 TACTCCAATCCCGTTATTTCTGAGGGGATACTTCAACCTCGATTTTATTTCCAAAACACCAATTT
1 TACTCCAACCCCGTTATTTCTAAGGGGATACCCCAACCCCGACTTTATTACCAAAACACCAATTT
*
143465 CTCACAATCGGGGATACTCCAACCCCATTATTTCAAAGGGGA
66 CTCACAATCGGGGATACTCCAACCCCATTATGTCAAAGGGGA
*
143507 TACTCCAACCCCGTTATTT-TAAAGGGGATACCCCTACCCCGACTTTATTACCAA
1 TACTCCAACCCCGTTATTTCT-AAGGGGATACCCCAACCCCGACTTTATTACCAA
143561 TTTTCGACAT
Statistics
Matches: 128, Mismatches: 30, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
106 3 0.02
107 124 0.97
108 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (107 bp):
TACTCCAACCCCGTTATTTCTAAGGGGATACCCCAACCCCGACTTTATTACCAAAACACCAATTT
CTCACAATCGGGGATACTCCAACCCCATTATGTCAAAGGGGA
Found at i:150935 original size:20 final size:20
Alignment explanation
Indices: 150910--150974 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
150900 AAAACCCAGA
150910 TGTATCGATACAACATTCCT
1 TGTATCGATACAACATTCCT
150930 TGTATCGAT---ACA----T
1 TGTATCGATACAACATTCCT
*
150943 TGTATCAATACAACATTCCT
1 TGTATCGATACAACATTCCT
150963 TGTATCGATACA
1 TGTATCGATACA
150975 TTGGGTACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
13 9 0.25
16 3 0.08
17 3 0.08
20 21 0.58
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAACATTCCT
Found at i:150954 original size:33 final size:33
Alignment explanation
Indices: 150910--150977 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
150900 AAAACCCAGA
*
150910 TGTATCGATACAACATTCCTTGTATCGATACAT
1 TGTATCAATACAACATTCCTTGTATCGATACAT
150943 TGTATCAATACAACATTCCTTGTATCGATACAT
1 TGTATCAATACAACATTCCTTGTATCGATACAT
150976 TG
1 TG
150978 GGTACTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (33 bp):
TGTATCAATACAACATTCCTTGTATCGATACAT
Found at i:153473 original size:20 final size:20
Alignment explanation
Indices: 153450--153503 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
153440 CACACCCAGA
153450 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
153470 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
153490 TGTATCGATACATT
1 TGTATCGATACATT
153504 GTATCGATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:153507 original size:13 final size:13
Alignment explanation
Indices: 153489--153515 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
153479 ACATTATGCT
153489 TTGTATCGATACA
1 TTGTATCGATACA
153502 TTGTATCGATACA
1 TTGTATCGATACA
153515 T
1 T
153516 GTTAATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:153525 original size:19 final size:19
Alignment explanation
Indices: 153501--153556 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
153491 GTATCGATAC
**
153501 ATTGTATCGATACATGTTA
1 ATTGTATCGATACATGACA
153520 ATTGTATCGATACATGGACA
1 ATTGTATCGATACAT-GACA
*
153540 ATTGTATTGATACATGA
1 ATTGTATCGATACATGA
153557 GATTGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:153544 original size:20 final size:20
Alignment explanation
Indices: 153501--153555 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
153491 GTATCGATAC
**
153501 ATTGTATCGATACAT-GTTA
1 ATTGTATCGATACATGGACA
153520 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
*
153540 ATTGTATTGATACATG
1 ATTGTATCGATACATG
153556 AGATTGGCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:155809 original size:17 final size:18
Alignment explanation
Indices: 155780--155813 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
155770 TTTAATACGT
155780 ATTTTTAATAAAATTAAA
1 ATTTTTAATAAAATTAAA
155798 ATTTTTAA-AAAATTAA
1 ATTTTTAATAAAATTAA
155814 GGCAATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTTTAATAAAATTAAA
Found at i:156169 original size:24 final size:24
Alignment explanation
Indices: 156148--156199 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
156138 AGGGAATATT
156148 AAATTGGAATTATAATTAAATACC
1 AAATTGGAATTATAATTAAATACC
156172 AAATTGGAATTATAATTAAATACC
1 AAATTGGAATTATAATTAAATACC
156196 AAAT
1 AAAT
156200 ATTGACATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.33
Consensus pattern (24 bp):
AAATTGGAATTATAATTAAATACC
Found at i:157768 original size:20 final size:20
Alignment explanation
Indices: 157720--157776 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
157710 AAAAAAAATC
**
157720 CAAATGTATCGATACATTTG
1 CAAATGTATCGATACATTCA
*
157740 TAGAATGTATCGATACATTCA
1 CA-AATGTATCGATACATTCA
157761 CAAATGTATCGATACA
1 CAAATGTATCGATACA
157777 GGGTCCCAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (20 bp):
CAAATGTATCGATACATTCA
Found at i:157836 original size:19 final size:19
Alignment explanation
Indices: 157812--157879 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
157802 AATTCAACGA
157812 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
157831 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
157846 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
157863 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
157880 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:157850 original size:32 final size:32
Alignment explanation
Indices: 157814--157876 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
157804 TTCAACGATT
*
157814 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
157846 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
157877 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:157851 original size:13 final size:13
Alignment explanation
Indices: 157833--157857 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
157823 ACATAAGTTT
157833 TGTATCGATACAA
1 TGTATCGATACAA
157846 TGTATCGATACA
1 TGTATCGATACA
157858 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:157937 original size:13 final size:13
Alignment explanation
Indices: 157919--157944 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
157909 CATTTTTCTG
157919 TGTATCGATACAT
1 TGTATCGATACAT
157932 TGTATCGATACAT
1 TGTATCGATACAT
157945 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:157941 original size:33 final size:33
Alignment explanation
Indices: 157899--157965 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
157889 GCCAAGGAAA
***
157899 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
157932 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
157965 T
1 T
157966 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:160448 original size:27 final size:28
Alignment explanation
Indices: 160418--160493 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
160408 AATTTTCACA
160418 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
* *
160445 ATCGAGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
160473 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
160494 ACTTTATCTC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:160655 original size:53 final size:52
Alignment explanation
Indices: 160313--160664 Score: 211
Period size: 51 Copynumber: 6.7 Consensus size: 52
160303 AATTCTCCAC
* * * * *
160313 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTT-CTAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCCAT
*
160364 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTT--CAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACACC-AATTTTCCCAT
* * * * * * * *
160417 AATCGGGGATACTCCAACCCCG--TTAATCATCGAGGATACTCCAA---CCCCGTT
1 AATCGGGGATACTCCAACTCCGATTTTAT-TTCCA--AAACACCAATTTTCCC-AT
* * * * * *** *
160468 ATTTCCGAGGGGATACTCCAACCCCGACTTTATCTCCAAAATATTGATTTT-TCAT
1 A-AT-C--GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCCAT
* * * * * *
160523 AATCGGGGATACTCCAA-TCCCGGTTTTATTGCTAAAACACTAATTTTTCCAC
1 AATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACACCAATTTTCCCAT
* * * * *
160575 AATCGGGGATACTCTAACCCCGGTTTTATTTTCAAAACACCAATTTTCCCTTT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCC-AT
160628 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAA
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAA
160665 AAAATACTAA
Statistics
Matches: 226, Mismatches: 53, Indels: 42
0.70 0.17 0.13
Matches are distributed among these distances:
50 2 0.01
51 71 0.31
52 52 0.23
53 63 0.28
54 10 0.04
55 20 0.09
56 4 0.02
57 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (52 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCCAT
Found at i:160721 original size:28 final size:29
Alignment explanation
Indices: 160685--160761 Score: 104
Period size: 28 Copynumber: 2.7 Consensus size: 29
160675 TTTTTTCATA
* * *
160685 ATCGAGGATACTCCAACCTCGTTA-TTTC
1 ATCGGGGATACTCCAACCCCGTTACTTCC
160713 ATCGGGGATACTCCAACCCCGTTACTTCC
1 ATCGGGGATACTCCAACCCCGTTACTTCC
*
160742 A-AGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
160762 GTTTTATTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 40 0.91
29 4 0.09
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCGTTACTTCC
Found at i:160779 original size:268 final size:262
Alignment explanation
Indices: 160308--160810 Score: 729
Period size: 268 Copynumber: 1.9 Consensus size: 262
160298 TTCTCAATTC
* * * *
160308 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
*
160373 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGGGGATACTCCAACCCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCC
* *
160438 GTTAATCATCGAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATCT
131 GTTAATCATCGAGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGACTTTATCT
* * *
160503 CCAAAATATTGATTTTTCATAATCGGGGATACTCCAATCCCGGTTTTATTGCTAAAACACTAATT
196 CCAAAATATTAATTTCTCATAATCGGAGATACTCCAATCCCGGTTTTATTGCTAAAACACTAATT
160568 TT
261 TT
* * *
160570 TCCACAATCGGGGATACTCTAACCCCGGTTTTATTTTCAAAACACCAATTTTCCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT--CTATAATCGGG
* * * *
160635 GATACTCCAACTCCGATTTTATTTCCAAAAAAAATACTAATTTTTTCATAATCGAGGATACTCCA
64 GATACTCCAACTCCGATTTTATTTCC--AAAAAACACCAA-ATTTTCACAATCGAGGATACTCCA
* * * **
160700 ACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGGTT
126 ACCCCGTTA-ATCATCGAGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGACT
*
160765 TTAT-TCCCAAAATATTAATTTCTCATAATTGGAGATACTCCAATCC
190 TTATCT-CCAAAATATTAATTTCTCATAATCGGAGATACTCCAATCC
160811 TGTTATTTTC
Statistics
Matches: 211, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
262 46 0.22
264 36 0.17
266 10 0.05
267 30 0.14
268 89 0.42
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (262 bp):
TCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAAATTTTCACAATCGAGGATACTCCAACCCC
GTTAATCATCGAGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGACTTTATCT
CCAAAATATTAATTTCTCATAATCGGAGATACTCCAATCCCGGTTTTATTGCTAAAACACTAATT
TT
Found at i:160827 original size:107 final size:109
Alignment explanation
Indices: 160632--160835 Score: 249
Period size: 107 Copynumber: 1.9 Consensus size: 109
160622 CCCTTTAATC
* *
160632 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAAAATACTAATTTTTTCATAATCGAGGATACT
1 GGGGATACTCCAACCCCGATTTTATTTCC--AAAAAATACTAATTTTCTCATAATCGAGGATACT
160697 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCAA
64 CCAACCTCGTTATTTCA-CGGGGATACTCCAACCCCGTTACTTCCAA
* * * *
160744 GGGGATACTCCAACCCCGGTTTTA-TTCC-CAAAATATTAA-TTTCTCATAATTG-GAGATACTC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAAATACTAATTTTCTCATAATCGAG-GATACTC
160805 CAATCCT-GTTATTTTCGA-GGGGATACTCCAA
65 CAA-CCTCGTTA-TTTC-ACGGGGATACTCCAA
160836 TCTCGATTTA
Statistics
Matches: 82, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
106 1 0.01
107 38 0.46
108 16 0.20
109 1 0.01
111 4 0.05
112 22 0.27
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (109 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAAAATACTAATTTTCTCATAATCGAGGATACTCC
AACCTCGTTATTTCACGGGGATACTCCAACCCCGTTACTTCCAA
Found at i:163003 original size:22 final size:22
Alignment explanation
Indices: 162959--163045 Score: 70
Period size: 22 Copynumber: 3.9 Consensus size: 22
162949 TTTTGTATGA
* *
162959 TTTTTTCTTTTTGTGTTT-CTT
1 TTTTTTCTTTTTGTTTTTGATT
162980 TTCTTTT-TTTTTGTTTTTGATT
1 TT-TTTTCTTTTTGTTTTTGATT
** *
163002 TTTTTTGGTTTTGGTTTTGATT
1 TTTTTTCTTTTTGTTTTTGATT
* *
163024 TTATTTTTTCTTTTCTTTTTGA
1 TT-TTTTCT-TTTTGTTTTTGA
163046 CATTGCCTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
21 16 0.30
22 23 0.43
23 4 0.08
24 10 0.19
ACGTcount: A:0.05, C:0.06, G:0.11, T:0.78
Consensus pattern (22 bp):
TTTTTTCTTTTTGTTTTTGATT
Found at i:165764 original size:15 final size:15
Alignment explanation
Indices: 165746--165778 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
165736 GAATATTTTG
165746 TATATATATATATGA
1 TATATATATATATGA
*
165761 TATATATATGTATGA
1 TATATATATATATGA
165776 TAT
1 TAT
165779 GAATGTACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (15 bp):
TATATATATATATGA
Found at i:171060 original size:20 final size:20
Alignment explanation
Indices: 171035--171106 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
171025 TTTTACCTAG
171035 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* *** *
171055 ATGTATTGATACATGCATGA
1 ATGTATCGATACATTTTTCA
*
171075 ATGTATCGATAAATTTTTCA
1 ATGTATCGATACATTTTTCA
171095 ATGTATCGATAC
1 ATGTATCGATAC
171107 TTTCTATCTT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:182832 original size:13 final size:13
Alignment explanation
Indices: 182814--182839 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
182804 ACATACTGCT
182814 TTGTATCGATACA
1 TTGTATCGATACA
182827 TTGTATCGATACA
1 TTGTATCGATACA
182840 CGCTCATTGT
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):
TTGTATCGATACA
Found at i:182870 original size:20 final size:19
Alignment explanation
Indices: 182824--182880 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
182814 TTGTATCGAT
*
182824 ACATTGTATCGATACACGC
1 ACATTGTATCGATACATGC
* *
182843 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
182862 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
182881 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:182870 original size:52 final size:52
Alignment explanation
Indices: 182775--182879 Score: 133
Period size: 52 Copynumber: 2.0 Consensus size: 52
182765 AACCCTTGAA
* **
182775 TGTATCGATACACTCTCAGATGTATCGATACATACTGCTTTGTATCGATACAT
1 TGTATCGATACACGCTCAGATGTATCGATACATAC-GAATTGTATCGATACAT
*
182828 TGTATCGATACACGCTCA-TTGTATCGATACATGGAC-AATTGTATCGATACAT
1 TGTATCGATACACGCTCAGATGTATCGATACAT--ACGAATTGTATCGATACAT
182880 GAAACTGGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
52 27 0.59
53 17 0.37
54 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (52 bp):
TGTATCGATACACGCTCAGATGTATCGATACATACGAATTGTATCGATACAT
Found at i:184492 original size:3 final size:3
Alignment explanation
Indices: 184484--184508 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
184474 TGAAGAGGAA
184484 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
184509 GTGACTCGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:191547 original size:13 final size:13
Alignment explanation
Indices: 191529--191555 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
191519 ACATACTGCT
191529 TTGTATTGATACA
1 TTGTATTGATACA
191542 TTGTATTGATACA
1 TTGTATTGATACA
191555 T
1 T
191556 GCTCATTGTA
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:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TTGTATTGATACA
Found at i:192758 original size:186 final size:185
Alignment explanation
Indices: 192525--192879 Score: 416
Period size: 186 Copynumber: 1.9 Consensus size: 185
192515 TTTATTATTA
* *
192525 TTATTTTAAAAATATCATTCTGTACCTTAATGGAATTCTGAAAAGATA-GAAAAAGTTTTAAAAA
1 TTATTTTAAAAATATCATTCTGTACCTTAAAGGAATTCAGAAAAGATATG-AAAAGTTTTAAAAA
* * * ** * *
192589 TTTTTGTACCCCTACGAATGCCCATAGGAATATTGGAAGTTTTTGAAAAATTAGG-ATATTAAAT
65 TTCTTATACCCCTACGAATGCCCATAGGAATATT-AAAAATTCTGAAAAA-TAGGTATAATAAAT
* * *
192653 TTTATT-TAAAAGAATATTTTTTCATTTTTTATTTAATTTATTTAATTTTACTTTGGT
128 TTTATTATAAAAGAATATTTATGCATTGTTTATTTAATTTATTTAATTTTACTTTGGT
* *
192710 TTATTTTCGAAAATATCATT-TCGTACCTTAAAGGAGACTT-AG-AAAGATATGAAAAGTTTTGA
1 TTATTTT-AAAAATATCATTCT-GTACCTTAAAGGA-A-TTCAGAAAAGATATGAAAAGTTTTAA
* * * *
192772 AAATTCTTATACTCTTACGGATGCCCATAGGAATATTAAAAATTCTGAAAAATAGGTATAATAAT
62 AAATTCTTATACCCCTACGAATGCCCATAGGAATATTAAAAATTCTGAAAAATAGGTATAATAAA
*
192837 TTTTATTCAATAAAATAATATTTATGCATTGTTTATTTAATTT
127 TTTTATT--ATAAAAGAATATTTATGCATTGTTTATTTAATTT
192880 TAATATATTT
Statistics
Matches: 142, Mismatches: 19, Indels: 15
0.81 0.11 0.09
Matches are distributed among these distances:
184 4 0.03
185 32 0.23
186 72 0.51
187 3 0.02
188 31 0.22
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42
Consensus pattern (185 bp):
TTATTTTAAAAATATCATTCTGTACCTTAAAGGAATTCAGAAAAGATATGAAAAGTTTTAAAAAT
TCTTATACCCCTACGAATGCCCATAGGAATATTAAAAATTCTGAAAAATAGGTATAATAAATTTT
ATTATAAAAGAATATTTATGCATTGTTTATTTAATTTATTTAATTTTACTTTGGT
Found at i:194541 original size:166 final size:166
Alignment explanation
Indices: 194154--194934 Score: 818
Period size: 166 Copynumber: 4.8 Consensus size: 166
194144 AAATAATTAA
* * * * * * * * **
194154 AATTTTTCAAAACTGATTCAATGTGAATTTAATAACAATATTAGATGAATTTTAAAAATTTTAAA
1 AATTTTTGAAAACTAATTTAATATAAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAAA
* *
194219 CCAAGGAAAAATCCCCCCGAAAACATTTACGGAGTAGAAAACT-TGATTTTTTGAAAATAAAAGG
66 CCAA-GAAAAATCCCCCCGAAAATATTTACGGAGCAGAAAACTCT-ATTTTTTGAAAAT-AAAGG
** *
194283 -ATTTCAAATAAAAAAATGCAAAACTCATGAAAATAAATG
128 AATTTC-AAGGAAAAAATGGAAAACTCATGAAAATAAATG
*
194322 AATTTTTTGAAATC-AATTTAATATAAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAA
1 AA-TTTTTGAAAACTAATTTAATATAAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAA
** * ** **
194386 ACCAAGAAAAATTCCCCTTGAAAACATTTACGGAGCAGAAAACTCTATTTTTCAAAAATAGGGGA
65 ACCAAGAAAAA-TCCCCCCGAAAATATTTACGGAGCAGAAAACTCTATTTTTTGAAAATAAAGGA
* *
194451 ATTTCAA-GAAAAAATGGAAAACTCATGAAAGTGAATG
129 ATTTCAAGGAAAAAATGGAAAACTCATGAAAATAAATG
* * * * * ** *
194488 AATTTTTGAAAATTGATTTAGTATGAATTAAATGATAATATTTGAAAAATTTTAAAAATTAGAAA
1 AATTTTTGAAAACTAATTTAATATAAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAAA
* * * * ** * * * *
194553 CCAACAAAGATGCTCCCGAAAATATTTACAAAGTAGAAAGCTCTATTTTTTGAAAACAAAGAAAT
66 CCAAGAAAAATCCCCCCGAAAATATTTACGGAGCAGAAAACTCTATTTTTTGAAAATAAAGGAAT
*
194618 TTCAAGG-AAAAATTGAAAA---ATG-----AAA-G
131 TTCAAGGAAAAAATGGAAAACTCATGAAAATAAATG
* * * *
194644 AATTTTTGAAAGCTAATATATTATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAAA
1 AATTTTTGAAAACTAATTTAATATAAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAAA
* * * *
194709 CCAAGAAAAATCCCCCCGAAAATATTGACGGAGAAAAAAACTCTGTTTTTTGAAAAT-AAGAGAA
66 CCAAGAAAAATCCCCCCGAAAATATTTACGGAGCAGAAAACTCTATTTTTTGAAAATAAAG-GAA
* * **
194773 ATTAAAGGAAAAAATAAAAAACTCATGAAAATAAATG
130 TTTCAAGGAAAAAATGGAAAACTCATGAAAATAAATG
* * * * * *
194810 AATTTTTGAAAACTGATTTAATATAAATTGAATGATAATATTTGATGAACTTTAATACTTAAAAA
1 AATTTTTGAAAACTAATTTAATATAAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAAA
* *
194875 CCAAGAAAAATCCCCTCGAAAATATTTACGGAGCAGAAAACTCTGTTTTTTGAAAATAAA
66 CCAAGAAAAATCCCCCCGAAAATATTTACGGAGCAGAAAACTCTATTTTTTGAAAATAAA
194935 TAAAATTCTA
Statistics
Matches: 505, Mismatches: 90, Indels: 37
0.80 0.14 0.06
Matches are distributed among these distances:
155 3 0.01
156 110 0.22
157 12 0.02
160 3 0.01
162 3 0.01
165 68 0.13
166 190 0.38
167 13 0.03
168 93 0.18
169 10 0.02
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.30
Consensus pattern (166 bp):
AATTTTTGAAAACTAATTTAATATAAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAAA
CCAAGAAAAATCCCCCCGAAAATATTTACGGAGCAGAAAACTCTATTTTTTGAAAATAAAGGAAT
TTCAAGGAAAAAATGGAAAACTCATGAAAATAAATG
Found at i:194786 original size:322 final size:322
Alignment explanation
Indices: 194312--194930 Score: 823
Period size: 322 Copynumber: 1.9 Consensus size: 322
194302 AAAACTCATG
* *
194312 AAAATAAATGAATTTTTTGAAATCAATTTAATATAAATTAAATAATAATATTTGATGAATTTTAA
1 AAAATAAATGAATTTTTTGAAAGCAATATAATATAAATTAAATAATAATATTTGATGAATTTTAA
** * * *
194377 AAATTAAAAACCAAGAAAAATTCCCCTTGAAAACATTTACGGAGCAGAAAACTCTATTTTTCAAA
66 AAATTAAAAACCAAGAAAAATTCCCCCCGAAAACATTGACGGAGAAAAAAACTCTATTTTTCAAA
* * * * ** * * *
194442 AATAGGGGAATTTCAAGAAAAAATGGAAAACTCATGAAAGTGAATGAATTTTTGAAAATTGATTT
131 AATAAGAGAAATTAAAGAAAAAATAAAAAACTCATGAAAATAAATGAATTTTTGAAAACTGATTT
* * * * * *
194507 AGTATGAATTAAATGATAATATTTGAAAAATTTTAAAAATTAGAAACCAACAAAGATGCTCC-CG
196 AATATAAATTAAATGATAATATTTGAAAAACTTTAAAAATTAAAAACCAACAAAAAT-CCCCTCG
* *
194571 AAAATATTTACAAAGTAGAAAGCTCTATTTTTTGAAAACAAAGAAATTTCAAGGAAAAATTGA
260 AAAATATTTACAAAGCAGAAAACTCTATTTTTTGAAAACAAAGAAATTTCAAGGAAAAATTGA
* *
194634 AAAATGAAA-GAA-TTTTTGAAAGCTAATATATTATGAATTAAATAATAATATTTGATGAATTTT
1 AAAAT-AAATGAATTTTTTGAAAGC-AATATAATATAAATTAAATAATAATATTTGATGAATTTT
* * **
194697 AAAAATTAAAAACCAAGAAAAA-TCCCCCCGAAAATATTGACGGAGAAAAAAACTCTGTTTTTTG
64 AAAAATTAAAAACCAAGAAAAATTCCCCCCGAAAACATTGACGGAGAAAAAAACTCTATTTTTCA
194761 AAAATAAGAGAAATTAAAGGAAAAAATAAAAAACTCATGAAAATAAATGAATTTTTGAAAACTGA
129 AAAATAAGAGAAATTAAA-GAAAAAATAAAAAACTCATGAAAATAAATGAATTTTTGAAAACTGA
* ** * * *
194826 TTTAATATAAATTGAATGATAATATTTGATGAACTTTAATACTTAAAAACCAAGAAAAATCCCCT
193 TTTAATATAAATTAAATGATAATATTTGAAAAACTTTAAAAATTAAAAACCAACAAAAATCCCCT
** *
194891 CGAAAATATTTACGGAGCAGAAAACTCTGTTTTTTGAAAA
258 CGAAAATATTTACAAAGCAGAAAACTCTATTTTTTGAAAA
194931 TAAATAAAAT
Statistics
Matches: 254, Mismatches: 39, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
321 60 0.24
322 191 0.75
323 3 0.01
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (322 bp):
AAAATAAATGAATTTTTTGAAAGCAATATAATATAAATTAAATAATAATATTTGATGAATTTTAA
AAATTAAAAACCAAGAAAAATTCCCCCCGAAAACATTGACGGAGAAAAAAACTCTATTTTTCAAA
AATAAGAGAAATTAAAGAAAAAATAAAAAACTCATGAAAATAAATGAATTTTTGAAAACTGATTT
AATATAAATTAAATGATAATATTTGAAAAACTTTAAAAATTAAAAACCAACAAAAATCCCCTCGA
AAATATTTACAAAGCAGAAAACTCTATTTTTTGAAAACAAAGAAATTTCAAGGAAAAATTGA
Found at i:195017 original size:165 final size:165
Alignment explanation
Indices: 194634--194996 Score: 471
Period size: 166 Copynumber: 2.2 Consensus size: 165
194624 GAAAAATTGA
* * * * * * *
194634 AAAATGAAAGAATTTTTGAAAGCTAATATATTATGAATTAAATAATAATATTTGATGAATTTTAA
1 AAAATAAAAGAATTTTTGAAAACTGATTTAATATAAATTAAATAATAATATTTGATGAACTTTAA
194699 AAATTAAAAACCAAGAAAAATCCCCCCGAAAATATTGACGGAGAAAAAAACTCTGTTTTTTGAAA
66 AAATTAAAAACCAAGAAAAATCCCCCCGAAAATATTGACGGAGAAAAAAACTCTGTTTTTTGAAA
*
194764 ATAAGAGAAATTAAAGGAAAAAATAAAAAACTCATG
131 ATAAGAAAAATTAAA-GAAAAAATAAAAAACTCATG
* * *
194800 AAAATAAATGAATTTTTGAAAACTGATTTAATATAAATTGAATGATAATATTTGATGAACTTTAA
1 AAAATAAAAGAATTTTTGAAAACTGATTTAATATAAATTAAATAATAATATTTGATGAACTTTAA
* * * * * *
194865 TACTTAAAAACCAAGAAAAATCCCCTCGAAAATATTTACGGAGCAGAAAACTCTGTTTTTTGAAA
66 AAATTAAAAACCAAGAAAAATCCCCCCGAAAATATTGACGGAGAAAAAAACTCTGTTTTTTGAAA
* * **
194930 ATAA-ATAAAATTCTAA-AAAAAATCAATGACTCAT-
131 ATAAGA-AAAATT-AAAGAAAAAATAAAAAACTCATG
*
194964 AAAATAAAAGAAATTTTTTAAAACTGATTTAAT
1 AAAATAAAAG-AATTTTTGAAAACTGATTTAAT
194997 GGTGATTAAA
Statistics
Matches: 171, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
164 9 0.05
165 37 0.22
166 123 0.72
167 2 0.01
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (165 bp):
AAAATAAAAGAATTTTTGAAAACTGATTTAATATAAATTAAATAATAATATTTGATGAACTTTAA
AAATTAAAAACCAAGAAAAATCCCCCCGAAAATATTGACGGAGAAAAAAACTCTGTTTTTTGAAA
ATAAGAAAAATTAAAGAAAAAATAAAAAACTCATG
Found at i:196151 original size:84 final size:84
Alignment explanation
Indices: 195937--196264 Score: 352
Period size: 84 Copynumber: 3.9 Consensus size: 84
195927 AAGCTGACAG
* * *
195937 GTAAACAAGGGATGAAAGGTTGACCAAGGCTAAACCGATAAGTCAACAACGGGTAAAAGAGTTTA
1 GTAAGCAAGGGATAAAAGGTTGACCAAGGCTAAACCGATAAGTCAACAAAGGGTAAAAGAGTTTA
* * * *
196002 CTAGAGATTGAGCCGACAA
66 CCAGGGACTGAGCCGATAA
* ** ** * * * * *
196021 GTAA-AAAAAGATAAAAAATTGACTAGGGCTAAACCGATAAGTCAACAAAGGATAAAGGAGTTCA
1 GTAAGCAAGGGATAAAAGGTTGACCAAGGCTAAACCGATAAGTCAACAAAGGGTAAAAGAGTTTA
* *
196085 CCAGGTACTGAGCCAATAA
66 CCAGGGACTGAGCCGATAA
* * * * * *
196104 GTAAGCAAGGGATAAATGGTTAACTAAGGCTGAACCGATAAGTCAACAAAGGGTTAAGGAGTTTA
1 GTAAGCAAGGGATAAAAGGTTGACCAAGGCTAAACCGATAAGTCAACAAAGGGTAAAAGAGTTTA
* * * *
196169 CCAGGGACTAAACTGATAG
66 CCAGGGACTGAGCCGATAA
* * *
196188 GTAAGCAAGGGATAAAAGGTTGACCAAGGCTGAATCGATAAGTCAACAAAAGGTAAAAGAGTTTA
1 GTAAGCAAGGGATAAAAGGTTGACCAAGGCTAAACCGATAAGTCAACAAAGGGTAAAAGAGTTTA
*
196253 CTAGGGACTGAG
66 CCAGGGACTGAG
196265 TTGACAGGCA
Statistics
Matches: 197, Mismatches: 46, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
83 65 0.33
84 132 0.67
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.18
Consensus pattern (84 bp):
GTAAGCAAGGGATAAAAGGTTGACCAAGGCTAAACCGATAAGTCAACAAAGGGTAAAAGAGTTTA
CCAGGGACTGAGCCGATAA
Found at i:196967 original size:44 final size:44
Alignment explanation
Indices: 196524--197778 Score: 319
Period size: 44 Copynumber: 28.8 Consensus size: 44
196514 TGTTAAACAG
* * ** ** *
196524 GAATGAAAA-AAGCTTGACCAGGGTGGTAACCACATGTCAAGCAG
1 GAATGAAAAGAA-TTTGACCAGGGTGGTAACCATACATCAAATAA
* * * * * *
196568 GAATGAAAGGAGTCTGACTAGGATGGTATCCATACATCAAACT-A
1 GAATGAAAAGAATTTGACCAGGGTGGTAACCATACATCAAA-TAA
** * * * ** *
196612 -CTTGAAAAGAGTTTGACCAGGGTGATAAGCATATGTCAAACAA
1 GAATGAAAAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
* ** * * * *
196655 GAAGGAGGCAG-ATTTGACCA-TGTGGTAACCATGCAACAAATCA
1 GAATGA-AAAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
* * * ** **
196698 GAAT-AAGAAGAATCTGACTAGGGTAGTAACCATATGTCAGACCAA
1 GAATGAA-AAGAATTTGACCAGGGTGGTAACCATACATCA-AATAA
* * * * *
196743 -AATGAGAAGAGTTTGACTAGGGTGGTAACCATACATTAAACAA
1 GAATGAAAAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
* * * * **
196786 GAAAGAGATA-AATTTGACCAGGGTGATAACCATACGTCAGACCAA
1 GAATGA-AAAGAATTTGACCAGGGTGGTAACCATACATCA-AATAA
* * * * * * ** *
196831 -AACGAGAAGAGTTTAACTAGAGTGGTAACCATATGTCAAATAG
1 GAATGAAAAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
** **
196874 GAATGAGGTA-AATTTGACCAGGGTGGTAACCATATGTCAAATAA
1 GAATGA-AAAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
* * *
196918 GAATGAAAAGAATTTGACCAGGGTGGTAATCATACATCATAT-C
1 GAATGAAAAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
* * * **
196961 GAAATGAAAAGAGTTTTACCTGGGTGGTAACCATATGTCAAAT-A
1 G-AATGAAAAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
* * * * * *
197005 GAAAG-GAGGCAAATTTGATC---GTGGTAACCACACGTCAAAT-A
1 GAATGAAAAG--AATTTGACCAGGGTGGTAACCATACATCAAATAA
** * * ** *
197046 GAAATGAGGTAG-GTTTAACCAGGGTGGTAACTGTACATCAAATCA
1 G-AATGA-AAAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
* * * *
197091 GAATGAAAAGAATCTGACTAGGGTGGTAACTATA-AGTCAAACTGA
1 GAATGAAAAGAATTTGACCAGGGTGGTAACCATACA-TCAAA-TAA
* * * ** * *
197136 -AATGAAAAGAGTTTGACCAGGTTAGTAGGCATACGTCAAATAG
1 GAATGAAAAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
* * * * * **
197179 GTA-G-AAGGCAAATTTGACCAAGGTGGTAATCGTATGTCAAATCAA
1 GAATGAAAAG--AATTTGACCAGGGTGGTAACCATACATCAAAT-AA
* * ** * **
197224 -AATGAAAAAAATCTGACCAGGGTGGTAACCATATGTTAGACCAA
1 GAATGAAAAGAATTTGACCAGGGTGGTAACCATACATCA-AATAA
* * * * **
197268 -AATTAAAAGAGTTTGGCCTGGGTGGTAACCATATGTCAAAT-A
1 GAATGAAAAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
* * ** * * **
197310 GAA--AAAGATAGATTTAACTGGGGTAGTAACCATACGTCAAATCT
1 GAATGAAA-AGA-ATTTGACCAGGGTGGTAACCATACATCAAATAA
* * * * *
197354 GAATGAATAA-AATCTAACTAGGGTGGTAAACATACGTCAAACTAA
1 GAATGAA-AAGAATTTGACCAGGGTGGTAACCATACATCAAA-TAA
* * ** *
197399 -AATAAAAAGAGTTTGACCA--G-GGT---CATATGTCAAATAG
1 GAATGAAAAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
* ** * * * * * *
197436 GAAAGAGGCAG-ATTTGA-CTGAAGTGGTAATCGTACGTCAAATCA
1 GAATGA-AAAGAATTTGACCAG-GGTGGTAACCATACATCAAATAA
* * * * *
197480 GAATGAAAAGAATCTAACCAGGGTGGTAACCATACGTCAGACTGA
1 GAATGAAAAGAATTTGACCAGGGTGGTAACCATACATCA-AATAA
* * *
197525 -AATGAAAAGCATTTGACTAGGGTGGTAACCATACATTAAATAA
1 GAATGAAAAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
* * ** * * * *
197568 AAAAGAGGCA-AATTTGACTAGGGTAGTAACCGTACGTCAAATCAA
1 GAATGA-AAAGAATTTGACCAGGGTGGTAACCATACATCAAAT-AA
* * * ** *
197613 -AATGAAAAAAATCTAACCAGGGTGGTAACCATATGTCAAACCAA
1 GAATGAAAAGAATTTGACCAGGGTGGTAACCATACATCAAA-TAA
* * ** *
197657 -AAT-AAGAAGCATTTGACTAGGGTGGTAACCATATGTCAAACAA
1 GAATGAA-AAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
*** * * * ** *
197700 GAA-GAGGGCGGATTTGACTAGGGTGGTAAACATATGTCAAATTA
1 GAATGA-AAAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
* * * * *
197744 GAATGAAAAAAATCTAACCAGAGTGGTAACTATAC
1 GAATGAAAAGAATTTGACCAGGGTGGTAACCATAC
197779 GTCAGACCGA
Statistics
Matches: 877, Mismatches: 265, Indels: 138
0.69 0.21 0.11
Matches are distributed among these distances:
37 3 0.00
38 18 0.02
39 2 0.00
40 1 0.00
41 34 0.04
42 15 0.02
43 111 0.13
44 655 0.75
45 32 0.04
46 5 0.01
47 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (44 bp):
GAATGAAAAGAATTTGACCAGGGTGGTAACCATACATCAAATAA
Found at i:196967 original size:88 final size:88
Alignment explanation
Indices: 196537--197733 Score: 372
Period size: 88 Copynumber: 13.7 Consensus size: 88
196527 TGAAAAAAGC
* ** * * * * *
196537 TTGACCAGGGTGGTAACCACATGTCAAGCAGGAATGA-AAGGAGTCTGACTAGGATGGTATCCAT
1 TTGACCAGGGTGGTAACCATATGTCAAATAAGAATGAGAA-GAATTTGACTAGGGTGGTAACCAT
*
196601 ACATCAAACTACTTGAAA--A-G--AGT
65 ACATCAAA-TA---GAAATGAGGTAAAT
* * * * * * *
196624 TTGACCAGGGTGATAAGCATATGTCAAACAAGAAGGAGGCAG-ATTTGACCA-TGTGGTAACCAT
1 TTGACCAGGGTGGTAACCATATGTCAAATAAGAATGA-GAAGAATTTGACTAGGGTGGTAACCAT
* * * *
196687 GCAACAAATCAG-AAT-AAGAAGAAT
65 ACATCAAAT-AGAAATGAGGTA-AAT
* * * ** *
196711 CTGACTAGGGTAGTAACCATATGTCAGACCAA-AATGAGAAGAGTTTGACTAGGGTGGTAACCAT
1 TTGACCAGGGTGGTAACCATATGTCA-AATAAGAATGAGAAGAATTTGACTAGGGTGGTAACCAT
* * *
196775 ACATTAAACAAGAAA-GAGATAAAT
65 ACATCAAA-TAGAAATGAGGTAAAT
* * ** * * * *
196799 TTGACCAGGGTGATAACCATACGTCAGACCAA-AACGAGAAGAGTTTAACTAGAGTGGTAACCAT
1 TTGACCAGGGTGGTAACCATATGTCA-AATAAGAATGAGAAGAATTTGACTAGGGTGGTAACCAT
** *
196863 ATGTCAAATAGGAATGAGGTAAAT
65 ACATCAAATAGAAATGAGGTAAAT
* * *
196887 TTGACCAGGGTGGTAACCATATGTCAAATAAGAATGAAAAGAATTTGACCAGGGTGGTAATCATA
1 TTGACCAGGGTGGTAACCATATGTCAAATAAGAATGAGAAGAATTTGACTAGGGTGGTAACCATA
* * *
196952 CATCATATCGAAATGA--AAAGAGT
66 CATCAAATAGAAATGAGGTAA-A-T
* * * * *
196975 TTTACCTGGGTGGTAACCATATGTCAAAT-AGAAAG-GAGGCAAATTTGA-T--CGTGGTAACCA
1 TTGACCAGGGTGGTAACCATATGTCAAATAAGAATGAGAAG--AATTTGACTAGGGTGGTAACCA
* * **
197035 CACGTCAAATAGAAATGAGGTAGGT
64 TACATCAAATAGAAATGAGGTAAAT
* ** ** * * * *
197060 TTAACCAGGGTGGTAACTGTACATCAAATCAGAATGAAAAGAATCTGACTAGGGTGGTAACTATA
1 TTGACCAGGGTGGTAACCATATGTCAAATAAGAATGAGAAGAATTTGACTAGGGTGGTAACCATA
*
197125 -AGTCAAACT-GAAATGA--AAAGAGT
66 CA-TCAAA-TAGAAATGAGGTAA-A-T
* * ** * * * * *
197148 TTGACCAGGTTAGTAGGCATACGTCAAAT-AG-GT-AGAAGGCAAATTTGACCAAGGTGGTAATC
1 TTGACCAGGGTGGTAACCATATGTCAAATAAGAATGAGAA-G--AATTTGACTAGGGTGGTAACC
* ** ***
197210 GTATGTCAAATCA-AAATGAAAAAAAT
63 ATACATCAAAT-AGAAATGAGGTAAAT
* * ** * * * *
197236 CTGACCAGGGTGGTAACCATATGTTAGACCAA-AATTAAAAGAGTTTGGCCT-GGGTGGTAACCA
1 TTGACCAGGGTGGTAACCATATGTCA-AATAAGAATGAGAAGAATTT-GACTAGGGTGGTAACCA
** * * *
197299 TATGTCAAATAGAAA-AAGATAGAT
64 TACATCAAATAGAAATGAGGTAAAT
* ** * * ** * * * *
197323 TTAACTGGGGTAGTAACCATACGTCAAATCTGAATGA-ATAAAATCTAACTAGGGTGGTAAACAT
1 TTGACCAGGGTGGTAACCATATGTCAAATAAGAATGAGA-AGAATTTGACTAGGGTGGTAACCAT
* **
197387 ACGTCAAACTA-AAAT-A-AAAAGAGT
65 ACATCAAA-TAGAAATGAGGTAA-A-T
* * * * * *
197411 TTGACCA--G-GGT---CATATGTCAAATAGGAAAGAGGCAG-ATTTGACT-GAAGTGGTAATCG
1 TTGACCAGGGTGGTAACCATATGTCAAATAAGAATGA-GAAGAATTTGACTAG-GGTGGTAACCA
* **
197468 TACGTCAAATCAG-AATGA-AAAGAAT
64 TACATCAAAT-AGAAATGAGGTA-AAT
* * * * * * *
197493 CTAACCAGGGTGGTAACCATACGTCAGACTGA-AATGAAAAGCATTTGACTAGGGTGGTAACCAT
1 TTGACCAGGGTGGTAACCATATGTCA-AATAAGAATGAGAAGAATTTGACTAGGGTGGTAACCAT
* * * *
197557 ACATTAAATAAAAAAGAGGCAAAT
65 ACATCAAATAGAAATGAGGTAAAT
* * * * * * * * *
197581 TTGACTAGGGTAGTAACCGTACGTCAAATCAA-AATGAAAAAAATCTAACCAGGGTGGTAACCAT
1 TTGACCAGGGTGGTAACCATATGTCAAAT-AAGAATGAGAAGAATTTGACTAGGGTGGTAACCAT
** * *
197645 ATGTCAAACCA-AAAT-AAG-AAGCAT
65 ACATCAAA-TAGAAATGAGGTAA--AT
* * ** * *
197669 TTGACTAGGGTGGTAACCATATGTCAAACAAGAA-GAGGGCGGATTTGACTAGGGTGGTAAACAT
1 TTGACCAGGGTGGTAACCATATGTCAAATAAGAATGA-GAAGAATTTGACTAGGGTGGTAACCAT
197733 A
65 A
197734 TGTCAAATTA
Statistics
Matches: 814, Mismatches: 220, Indels: 151
0.69 0.19 0.13
Matches are distributed among these distances:
81 2 0.00
82 51 0.06
83 8 0.01
84 3 0.00
85 62 0.08
86 41 0.05
87 158 0.19
88 465 0.57
89 15 0.02
90 6 0.01
91 3 0.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.22
Consensus pattern (88 bp):
TTGACCAGGGTGGTAACCATATGTCAAATAAGAATGAGAAGAATTTGACTAGGGTGGTAACCATA
CATCAAATAGAAATGAGGTAAAT
Found at i:197073 original size:173 final size:173
Alignment explanation
Indices: 196852--197195 Score: 424
Period size: 173 Copynumber: 2.0 Consensus size: 173
196842 TTTAACTAGA
* * * * **
196852 GTGGTAACCATATGTCAAATAGGAATGAGGTAAATTTGACCAGGGTGGTAACCATATGTCAAATA
1 GTGGTAACCACACGTCAAATAGAAATGAGGTAAATTTAACCAGGGTGGTAACCATACATCAAATA
* * *
196917 AGAATGAAAAGAATTTGACCAGGGTGGTAA-TCATACA-TCATA-TCGAAATGAAAAGAGTTTTA
66 AGAATGAAAAGAATCTGACCAGGGTGGTAACT-ATA-AGTCAAACT-GAAATGAAAAGAGTTTGA
* * * *
196979 CCTGGGTGGTAACCATATGTCAAATAGAAAGGAGGCAAATTTGATC
128 CCAGGGTAGTAACCATACGTCAAATAGAAAGAAGGCAAATTTGATC
** ** *
197025 GTGGTAACCACACGTCAAATAGAAATGAGGTAGGTTTAACCAGGGTGGTAACTGTACATCAAATC
1 GTGGTAACCACACGTCAAATAGAAATGAGGTAAATTTAACCAGGGTGGTAACCATACATCAAATA
*
197090 AGAATGAAAAGAATCTGACTAGGGTGGTAACTATAAGTCAAACTGAAATGAAAAGAGTTTGACCA
66 AGAATGAAAAGAATCTGACCAGGGTGGTAACTATAAGTCAAACTGAAATGAAAAGAGTTTGACCA
* ** **
197155 GGTTAGTAGGCATACGTCAAATAGGTAGAAGGCAAATTTGA
131 GGGTAGTAACCATACGTCAAATAGAAAGAAGGCAAATTTGA
197196 CCAAGGTGGT
Statistics
Matches: 144, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
172 1 0.01
173 141 0.98
174 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (173 bp):
GTGGTAACCACACGTCAAATAGAAATGAGGTAAATTTAACCAGGGTGGTAACCATACATCAAATA
AGAATGAAAAGAATCTGACCAGGGTGGTAACTATAAGTCAAACTGAAATGAAAAGAGTTTGACCA
GGGTAGTAACCATACGTCAAATAGAAAGAAGGCAAATTTGATC
Found at i:197084 original size:129 final size:130
Alignment explanation
Indices: 196852--197101 Score: 303
Period size: 129 Copynumber: 1.9 Consensus size: 130
196842 TTTAACTAGA
* * * * *
196852 GTGGTAACCATATGTCAAATAGGAATGAGGTAAATTTGACCAGGGTGGTAACCATATGTCAAATA
1 GTGGTAACCATATGTCAAATAGAAAGGAGGCAAATTTGACC--GGTGGTAACCACACGTCAAATA
* *
196917 AGAATGAAAAGAATTTGACCAGGGTGGTAATCATACATCATATC-GAAATGAAAAGAGTTTTACC
64 AGAATGAAAAGAATTTAACCAGGGTGGTAATCATACATCAAATCAG-AATGAAAAGAGTTTTACC
196981 TGG
128 TGG
*
196984 GTGGTAACCATATGTCAAATAGAAAGGAGGCAAATTTGATC-GTGGTAACCACACGTCAAAT-AG
1 GTGGTAACCATATGTCAAATAGAAAGGAGGCAAATTTGACCGGTGGTAACCACACGTCAAATAAG
** * *
197047 AAATGAGGTAG-GTTTAACCAGGGTGGTAA-CTGTACATCAAATCAGAATGAAAAGA
66 -AATGA-AAAGAATTTAACCAGGGTGGTAATC-ATACATCAAATCAGAATGAAAAGA
197102 ATCTGACTAG
Statistics
Matches: 102, Mismatches: 12, Indels: 11
0.82 0.10 0.09
Matches are distributed among these distances:
128 3 0.03
129 59 0.58
130 3 0.03
132 37 0.36
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (130 bp):
GTGGTAACCATATGTCAAATAGAAAGGAGGCAAATTTGACCGGTGGTAACCACACGTCAAATAAG
AATGAAAAGAATTTAACCAGGGTGGTAATCATACATCAAATCAGAATGAAAAGAGTTTTACCTGG
Found at i:197228 original size:132 final size:131
Alignment explanation
Indices: 196614--197862 Score: 802
Period size: 132 Copynumber: 9.5 Consensus size: 131
196604 TCAAACTACT
* * * ** * *
196614 TGAAAAGAGTTTGACCAGGGTGATAAGCATATGTCAAACAAGAAGGAGGCAGATTTGACCA-TGT
1 TGAAAAGAGTTTGACCAGGGTGGTAACCATATGTCAAA-TAGAAAAAGGCAGATTTGACTAGGGT
* * ** * * * * * *
196678 GGTAACCATGCAACAAATCAGAAT-AAGAAGAATCTGACTAGGGTAGTAACCATATGTCAGACCA
65 GGTAACCGTACGTCAAATCAGAATGAA-AAAAATCTAACCAGGGTGGTAACCATACGTCAAACCA
196742 AAA
129 AAA
* * ** * * * ** * *
196745 TGAGAAGAGTTTGACTAGGGTGGTAACCATACATTAAACAAGAAAGAGATAAATTTGACCAGGGT
1 TGAAAAGAGTTTGACCAGGGTGGTAACCATATGTCAAA-TAGAAAAAGGCAGATTTGACTAGGGT
* * * * * * * * * * * * * *
196810 GATAACCATACGTCAGACCAAAACGAGAAGAGTTTAACTAGAGTGGTAACCATATGTCAAA-TAG
65 GGTAACCGTACGTCAAATCAGAATGAAAAAAATCTAACCAGGGTGGTAACCATACGTCAAACCA-
*
196874 GAA
129 AAA
* * *
196877 TGAGGTAA-A-TTTGACCAGGGTGGTAACCATATGTCAAATAAGAATGAAAAG-A-ATTTGACCA
1 TGA--AAAGAGTTTGACCAGGGTGGTAACCATATGTCAAAT-AGAA--AAAGGCAGATTTGACTA
* * * * * * * * * *
196938 GGGTGGTAATCATACATCATATC-GAAATGAAAAGAGTTTTACCTGGGTGGTAACCATATGTCAA
61 GGGTGGTAACCGTACGTCAAATCAG-AATGAAAAAAATCTAACCAGGGTGGTAACCATACGTCAA
*
197002 A-TAGAAA
125 ACCA-AAA
* * * * * * * * * *
197009 GGAGGCAA-A-TTTGATC---GTGGTAACCACACGTCAAATAGAAATGAGGTAGGTTTAACCAGG
1 TGA--AAAGAGTTTGACCAGGGTGGTAACCATATGTCAAATAGAAA-AAGGCAGATTTGACTAGG
* * * * * * * *
197069 GTGGTAACTGTACATCAAATCAGAATGAAAAGAATCTGACTAGGGTGGTAACTATAAGTCAAACT
63 GTGGTAACCGTACGTCAAATCAGAATGAAAAAAATCTAACCAGGGTGGTAACCATACGTCAAACC
*
197134 GAAA
128 AAAA
* * ** * * * * * *
197138 TGAAAAGAGTTTGACCAGGTTAGTAGGCATACGTCAAATAGGTAGAAGGCAAATTTGACCAAGGT
1 TGAAAAGAGTTTGACCAGGGTGGTAACCATATGTCAAATA-GAAAAAGGCAGATTTGACTAGGGT
* * * * * * *
197203 GGTAATCGTATGTCAAATCAAAATGAAAAAAATCTGACCAGGGTGGTAACCATATGTTAGACCAA
65 GGTAACCGTACGTCAAATCAGAATGAAAAAAATCTAACCAGGGTGGTAACCATACGTCAAACCAA
197268 AA
130 AA
* * * ** * * *
197270 TTAAAAGAGTTTGGCCTGGGTGGTAACCATATGTCAAATAGAAAAAGATAGATTTAACTGGGGTA
1 TGAAAAGAGTTTGACCAGGGTGGTAACCATATGTCAAATAGAAAAAGGCAGATTTGACTAGGGTG
* * * * * *
197335 GTAACCATACGTCAAATCTGAATGAATAAAATCTAACTAGGGTGGTAAACATACGTCAAACTAAA
66 GTAACCGTACGTCAAATCAGAATGAAAAAAATCTAACCAGGGTGGTAACCATACGTCAAACCAAA
197400 A
131 A
* * *
197401 TAAAAAGAGTTTGACCA--G-GGT---CATATGTCAAATAGGAAAGAGGCAGATTTGACT-GAAG
1 TGAAAAGAGTTTGACCAGGGTGGTAACCATATGTCAAATA-GAAAAAGGCAGATTTGACTAG-GG
* * * **
197459 TGGTAATCGTACGTCAAATCAGAATGAAAAGAATCTAACCAGGGTGGTAACCATACGTCAGACTG
64 TGGTAACCGTACGTCAAATCAGAATGAAAAAAATCTAACCAGGGTGGTAACCATACGTCAAACCA
197524 AAA
129 AAA
* ** * * *
197527 TGAAAAGCA-TTTGACTAGGGTGGTAACCATACATTAAATAAAAAAGAGGCAAATTTGACTAGGG
1 TGAAAAG-AGTTTGACCAGGGTGGTAACCATATGTCAAATAGAAAA-AGGCAGATTTGACTAGGG
* * *
197591 TAGTAACCGTACGTCAAATCAAAATGAAAAAAATCTAACCAGGGTGGTAACCATATGTCAAACCA
64 TGGTAACCGTACGTCAAATCAGAATGAAAAAAATCTAACCAGGGTGGTAACCATACGTCAAACCA
197656 AAA
129 AAA
* * * * *
197659 T-AAGAAGCA-TTTGACTAGGGTGGTAACCATATGTCAAACAAGAAGAGGGCGGATTTGACTAGG
1 TGAA-AAG-AGTTTGACCAGGGTGGTAACCATATGTCAAA-TAGAAAAAGGCAGATTTGACTAGG
* * * * * * *
197722 GTGGTAAACATATGTCAAATTAGAATGAAAAAAATCTAACCAGAGTGGTAACTATACGTCAGACC
63 GTGGTAACCGTACGTCAAATCAGAATGAAAAAAATCTAACCAGGGTGGTAACCATACGTCAAACC
*
197787 GAAA
128 AAAA
* * * * * * * *
197791 CGAAAA-ATGTTTAACTAGGGTGGTAACCATGTGTCGAACAGGAAAGAGGCATATTTGACTAGGG
1 TGAAAAGA-GTTTGACCAGGGTGGTAACCATATGTCAAATA-GAAAAAGGCAGATTTGACTAGGG
197855 TGGTAACC
64 TGGTAACC
197863 ACATGTTAAA
Statistics
Matches: 883, Mismatches: 198, Indels: 73
0.77 0.17 0.06
Matches are distributed among these distances:
125 14 0.02
126 88 0.10
127 5 0.01
128 10 0.01
129 92 0.10
130 3 0.00
131 139 0.16
132 516 0.58
133 12 0.01
134 4 0.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.22
Consensus pattern (131 bp):
TGAAAAGAGTTTGACCAGGGTGGTAACCATATGTCAAATAGAAAAAGGCAGATTTGACTAGGGTG
GTAACCGTACGTCAAATCAGAATGAAAAAAATCTAACCAGGGTGGTAACCATACGTCAAACCAAA
A
Found at i:197935 original size:44 final size:43
Alignment explanation
Indices: 196714--197950 Score: 320
Period size: 44 Copynumber: 28.3 Consensus size: 43
196704 GAAGAATCTG
* * * * * * * *
196714 ACTAGGGTAGTAACCATATGTCAGACCAAAATGAGAAGAGTTTG
1 ACTAGGGTGGTAACCATACGTCA-AACAGAATGAAAAAAATTTA
* * * * * *
196758 ACTAGGGTGGTAACCATACATTAAACAAGAAAGAGATAAATTTG
1 ACTAGGGTGGTAACCATACGTCAAAC-AGAATGAAAAAAATTTA
* * * * * * * *
196802 ACCAGGGTGATAACCATACGTCAGACCAAAACGAGAAGAGTTTA
1 ACTAGGGTGGTAACCATACGTCA-AACAGAATGAAAAAAATTTA
* * * *** *
196846 ACTAGAGTGGTAACCATATGTCAAATAGGAATGAGGTAAATTTG
1 ACTAGGGTGGTAACCATACGTCAAACA-GAATGAAAAAAATTTA
* * * * *
196890 ACCAGGGTGGTAACCATATGTCAAATAAGAATGAAAAGAATTTG
1 ACTAGGGTGGTAACCATACGTCAAA-CAGAATGAAAAAAATTTA
* * * * **
196934 ACCAGGGTGGTAATCATACATCATATC-GAAATGAAAAGAGTTTTA
1 ACTAGGGTGGTAACCATACGTCA-AACAG-AATGAAAA-AAATTTA
* * * * *** *
196979 CCT-GGGTGGTAACCATATGTCAAATAGAAAGGAGGCAAATTTG
1 ACTAGGGTGGTAACCATACGTCAAACAG-AATGAAAAAAATTTA
* * * *** **
197022 A-T--CGTGGTAACCACACGTCAAATAGAAATGAGGTAGGTTTA
1 ACTAGGGTGGTAACCATACGTCAAACAG-AATGAAAAAAATTTA
* ** * * * *
197063 ACCAGGGTGGTAACTGTACATCAAATCAGAATGAAAAGAATCTG
1 ACTAGGGTGGTAACCATACGTCAAA-CAGAATGAAAAAAATTTA
* * * * * *
197107 ACTAGGGTGGTAACTATAAGTCAAACTGAAATGAAAAGAGTTTG
1 ACTAGGGTGGTAACCATACGTCAAACAG-AATGAAAAAAATTTA
* * * ** * * ** *
197151 ACCAGGTTAGTAGGCATACGTCAAATAG-GTAGAAGGCAAATTTG
1 ACTAGGGTGGTAACCATACGTCAAACAGAAT-GAA-AAAAATTTA
* * * * * * * *
197195 ACCAAGGTGGTAATCGTATGTCAAATCAAAATGAAAAAAATCTG
1 ACTAGGGTGGTAACCATACGTCAAA-CAGAATGAAAAAAATTTA
* * * * * * * * *
197239 ACCAGGGTGGTAACCATATGTTAGACCAAAATTAAAAGAGTTTGG
1 ACTAGGGTGGTAACCATACGTCA-AACAGAATGAAAAAAATTT-A
* * * *
197284 CCT-GGGTGGTAACCATATGTCAAATAGAA--AAAGATAGATTTA
1 ACTAGGGTGGTAACCATACGTCAAACAGAATGAAA-A-AAATTTA
* * * * *
197326 ACTGGGGTAGTAACCATACGTCAAATCTGAATGAATAAAATCTA
1 ACTAGGGTGGTAACCATACGTCAAA-CAGAATGAAAAAAATTTA
* * * *
197370 ACTAGGGTGGTAAACATACGTCAAACTAAAAT-AAAAAGAGTTTG
1 ACTAGGGTGGTAACCATACGTCAAAC-AGAATGAAAAA-AATTTA
* * * * *** * *
197414 ACCA--G-GGT---CATATGTCAAATAGGAAAGAGGCAGATTTG
1 ACTAGGGTGGTAACCATACGTCAAACA-GAATGAAAAAAATTTA
* * * * *
197452 ACT-GAAGTGGTAATCGTACGTCAAATCAGAATGAAAAGAATCTA
1 ACTAG-GGTGGTAACCATACGTCAAA-CAGAATGAAAAAAATTTA
* * * ** *
197496 ACCAGGGTGGTAACCATACGTCAGACTGAAATGAAAAGCATTTG
1 ACTAGGGTGGTAACCATACGTCAAACAG-AATGAAAAAAATTTA
* * * * * *** *
197540 ACTAGGGTGGTAACCATACATTAAATAAAAAAGAGGCAAATTTG
1 ACTAGGGTGGTAACCATACGTCAAA-CAGAATGAAAAAAATTTA
* * * *
197584 ACTAGGGTAGTAACCGTACGTCAAATCAAAATGAAAAAAATCTA
1 ACTAGGGTGGTAACCATACGTCAAA-CAGAATGAAAAAAATTTA
* * * ** *
197628 ACCAGGGTGGTAACCATATGTCAAACCAAAAT-AAGAAGCATTTG
1 ACTAGGGTGGTAACCATACGTCAAA-CAGAATGAA-AAAAATTTA
* ***** *
197672 ACTAGGGTGGTAACCATATGTCAAACAAGAA-GAGGGCGGATTTG
1 ACTAGGGTGGTAACCATACGTCAAAC-AGAATGA-AAAAAATTTA
* * * *
197716 ACTAGGGTGGTAAACATATGTCAAATTAGAATGAAAAAAATCTA
1 ACTAGGGTGGTAACCATACGTCAAA-CAGAATGAAAAAAATTTA
* * * * * * **
197760 ACCAGAGTGGTAACTATACGTCAGACCGAAACGAAAAATGTTTA
1 ACTAGGGTGGTAACCATACGTCAAACAG-AATGAAAAAAATTTA
** * * *** * *
197804 ACTAGGGTGGTAACCATGTGTCGAACAGGAAAGAGGCATATTTG
1 ACTAGGGTGGTAACCATACGTCAAACA-GAATGAAAAAAATTTA
* * * *
197848 ACTAGGGTGGTAACCACATGTTAAACAGGAA--AAAAGCAGATTTA
1 ACTAGGGTGGTAACCATACGTCAAACA-GAATGAAAA--AAATTTA
* *
197892 ACTAGGGTGGTAACCGTACATCAAATCAGAATGAAAAAAATTTA
1 ACTAGGGTGGTAACCATACGTCAAA-CAGAATGAAAAAAATTTA
**
197936 ACCGGGGTGGTAACC
1 ACTAGGGTGGTAACC
197951 GTCAGACCAA
Statistics
Matches: 860, Mismatches: 280, Indels: 106
0.69 0.22 0.09
Matches are distributed among these distances:
37 1 0.00
38 18 0.02
39 2 0.00
40 1 0.00
41 41 0.05
42 7 0.01
43 52 0.06
44 706 0.82
45 25 0.03
46 7 0.01
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23
Consensus pattern (43 bp):
ACTAGGGTGGTAACCATACGTCAAACAGAATGAAAAAAATTTA
Found at i:198139 original size:22 final size:22
Alignment explanation
Indices: 198114--198158 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
198104 TGAGTAAGGC
198114 TGTAGTAATCCATCATTTAAGA
1 TGTAGTAATCCATCATTTAAGA
198136 TGTAGTAATCCATCATTTAAGA
1 TGTAGTAATCCATCATTTAAGA
198158 T
1 T
198159 TTCTAAGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
TGTAGTAATCCATCATTTAAGA
Found at i:198336 original size:3 final size:3
Alignment explanation
Indices: 198328--198357 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
198318 TATTCATTTA
198328 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
198358 GTGATTTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:199254 original size:75 final size:76
Alignment explanation
Indices: 199175--199318 Score: 184
Period size: 76 Copynumber: 1.9 Consensus size: 76
199165 AGATGCTGAC
** * * *
199175 GAAGATAATCATGATGGGGAATATGTGG-TTCTATAATTTCCATTAAAAG-TCAAAACAAACTAA
1 GAAGATAATCACAATGGGAAATATGTGGTTTCTAAAATTTCCATCAAAAGCTCAAAA-AAACTAA
199238 CAAGAGGCCGAA
65 CAAGAGGCCGAA
* * * *
199250 GAAGATGATCACAATGGGAAATATGTGGTTTCTAAAATTTTCATCAAAAGCTGAAAAAAATTAAC
1 GAAGATAATCACAATGGGAAATATGTGGTTTCTAAAATTTCCATCAAAAGCTCAAAAAAACTAAC
199315 AAGA
66 AAGA
199319 ATGATGATGT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
75 24 0.41
76 29 0.50
77 5 0.09
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (76 bp):
GAAGATAATCACAATGGGAAATATGTGGTTTCTAAAATTTCCATCAAAAGCTCAAAAAAACTAAC
AAGAGGCCGAA
Found at i:203226 original size:20 final size:19
Alignment explanation
Indices: 203180--203236 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
203170 TTGTATCGAT
* *
203180 ACATTGTATGGATACATGT
1 ACATTGTATCGATACATGG
*
203199 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
203218 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
203237 AGGTTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:203302 original size:13 final size:13
Alignment explanation
Indices: 203281--203311 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
203271 CGATACATGG
*
203281 TACAATGTATCGA
1 TACATTGTATCGA
203294 TACATTGTATCGA
1 TACATTGTATCGA
203307 TACAT
1 TACAT
203312 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:203323 original size:33 final size:33
Alignment explanation
Indices: 203265--203333 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
203255 CTACCACTGT
*
203265 TTGTATCGATACATGGTACAATGTATCGATACA
1 TTGTATCGATACATGATACAATGTATCGATACA
* *
203298 TTGTATCGATACATGATGA-ATTGTATCGATGCA
1 TTGTATCGATACATGAT-ACAATGTATCGATACA
203331 TTG
1 TTG
203334 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATACAATGTATCGATACA
Found at i:203437 original size:10 final size:11
Alignment explanation
Indices: 203422--203450 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
203412 GAAAGCATTA
203422 AAACAAGCAC-
1 AAACAAGCACT
203432 AAACAAGCACT
1 AAACAAGCACT
203443 AAACAAGC
1 AAACAAGC
203451 TTGTAACGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.59, C:0.28, G:0.10, T:0.03
Consensus pattern (11 bp):
AAACAAGCACT
Done.