Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3534
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: 86058
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Found at i:12329 original size:38 final size:38
Alignment explanation
Indices: 12255--12375 Score: 112
Period size: 37 Copynumber: 3.3 Consensus size: 38
12245 GGACTAAGAT
* * *
12255 CCGAAGGTATTTGTGC--GATATAATTCCGG-TAAGTC
1 CCGAAGGCATTCGTGCGAGATATAATTCGGGTTAAGTC
*
12290 CCGAAGGCCTT-GTGCGAGATACTAATTCGGGTTAAGTCC
1 CCGAAGGCATTCGTGCGAGATA-TAATTCGGGTTAAGT-C
* *
12329 CCGAA--CATTCGTGCGAG-TTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAT-AATTCGGGTTAAGTC
12365 CCGAAGGCATT
1 CCGAAGGCATT
12376 GAATGAGTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
34 4 0.06
35 9 0.13
36 11 0.15
37 25 0.35
38 16 0.23
39 6 0.08
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (38 bp):
CCGAAGGCATTCGTGCGAGATATAATTCGGGTTAAGTC
Found at i:12384 original size:37 final size:38
Alignment explanation
Indices: 12343--12416 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
12333 ACATTCGTGC
*
12343 GAGTTTA-AATCCGGGTTAAGTCCCGAAGGCA-TTGAAT
1 GAGTTTATAA-CCGGGCTAAGTCCCGAAGGCACTTGAAT
*
12380 GAGTTTATAACCGGGCTATGTCCCGAAGGCACTTGAA
1 GAGTTTATAACCGGGCTAAGTCCCGAAGGCACTTGAA
12417 CGAGGAGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (38 bp):
GAGTTTATAACCGGGCTAAGTCCCGAAGGCACTTGAAT
Found at i:20054 original size:40 final size:40
Alignment explanation
Indices: 19970--20153 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
19960 TTGAATGCTG
* * * *
19970 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
20009 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
20050 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
20090 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
20130 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
20154 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 111 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:20107 original size:80 final size:81
Alignment explanation
Indices: 19970--20150 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
19960 TTGAATGCTG
* * *
19970 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
20034 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
20050 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
20111 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
20130 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
20151 ATTGAATGAG
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 4 0.04
80 76 0.85
81 9 0.10
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:20174 original size:39 final size:39
Alignment explanation
Indices: 20038--20200 Score: 141
Period size: 40 Copynumber: 4.1 Consensus size: 39
20028 GGTATTTGTG
* * * **
20038 CGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTTTGTG
1 CGAGTTATAAAATCCGGGTTAAGTCCCGAAGG-CATTGAA
* * **
20078 CGAGATACT-AATTCCGGGTTAAGTCCCGAAGGCATTCGTG
1 CGAGTTA-TAAAATCCGGGTTAAGTCCCGAAGGCATT-GAA
*
20118 CGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
1 CGAGTTATAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
* * * *
20157 TGAGTTAATATAA-CCGGGCTATGTCCCGAAGGCACTTGAA
1 CGAGTT-ATAAAATCCGGGTTAAGTCCCGAAGGCA-TTGAA
20197 CGAG
1 CGAG
20201 GAGCTAAATC
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
39 29 0.28
40 75 0.71
41 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (39 bp):
CGAGTTATAAAATCCGGGTTAAGTCCCGAAGGCATTGAA
Found at i:26026 original size:26 final size:24
Alignment explanation
Indices: 26017--26075 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
26007 TTGAGCTGAT
26017 AAACAGTAAGCTCTATTAAGCTGG
1 AAACAGTAAGCTCTATTAAGCTGG
* *
26041 AAACAGTAAGCTTTATTTAGCT--
1 AAACAGTAAGCTCTATTAAGCTGG
26063 -AACAGTAAGCTCT
1 AAACAGTAAGCTCT
26076 TTTGAATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.38
24 20 0.62
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (24 bp):
AAACAGTAAGCTCTATTAAGCTGG
Found at i:27479 original size:17 final size:17
Alignment explanation
Indices: 27459--27510 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
27449 GTTCGCATAA
*
27459 AATAACAGTTCATGCAT
1 AATAACAGTTCATACAT
*
27476 AATAAAAGTTCATACA-
1 AATAACAGTTCATACAT
*
27492 ATATAACAGTTCATTCAT
1 A-ATAACAGTTCATACAT
27510 A
1 A
27511 CCACATCGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 1 0.03
17 27 0.93
18 1 0.03
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (17 bp):
AATAACAGTTCATACAT
Found at i:28420 original size:29 final size:28
Alignment explanation
Indices: 28359--28452 Score: 100
Period size: 27 Copynumber: 3.2 Consensus size: 28
28349 CTACACGTAT
* *
28359 ATATATTGTATATATAATAAAACCATAGACGC
1 ATATATT-TATATATAACAAAACC---CACGC
*
28391 ATATATTTTATATATAACAAACCCCACGC
1 ATATA-TTTATATATAACAAAACCCACGC
*
28420 ATATA-TTATATATAACAAAACCCACAC
1 ATATATTTATATATAACAAAACCCACGC
28447 ATATAT
1 ATATAT
28453 AGGTATAATG
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
27 25 0.45
29 9 0.16
32 19 0.35
33 2 0.04
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (28 bp):
ATATATTTATATATAACAAAACCCACGC
Found at i:30661 original size:26 final size:26
Alignment explanation
Indices: 30632--30739 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
30622 TGGTACAAAT
30632 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
30658 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
30684 TGATAATGAGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
30710 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
30736 TGAT
1 TGAT
30740 GGGAATTTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:37592 original size:26 final size:26
Alignment explanation
Indices: 37563--37670 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
37553 TGGTACAAAT
37563 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
37589 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
37615 TGATAATGAGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
37641 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
37667 TGAT
1 TGAT
37671 GGGAATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:40351 original size:20 final size:20
Alignment explanation
Indices: 40326--40366 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
40316 GTGTTTGAGA
*
40326 TTGATATGAGATGGTACAAG
1 TTGATACGAGATGGTACAAG
40346 TTGATACGAGATGGTACAAG
1 TTGATACGAGATGGTACAAG
40366 T
1 T
40367 ATGTACATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.29, T:0.29
Consensus pattern (20 bp):
TTGATACGAGATGGTACAAG
Found at i:42895 original size:32 final size:31
Alignment explanation
Indices: 42830--42896 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
42820 ACCTAAAACT
* * *
42830 ATTAATTCTAATTATTTTAATATTTTATTTA
1 ATTAATTCTAATTATTTTAATATATAATCTA
42861 ATTAATTCCTAATTA-TTTAATTATATAATCTA
1 ATTAATT-CTAATTATTTTAA-TATATAATCTA
42893 ATTA
1 ATTA
42897 CGGTTTTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (31 bp):
ATTAATTCTAATTATTTTAATATATAATCTA
Found at i:45269 original size:25 final size:26
Alignment explanation
Indices: 45241--45311 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 26
45231 TAATAAAACT
*
45241 AAAATCTAACCTAAAAA-GAAAAGAG
1 AAAACCTAACCTAAAAATGAAAAGAG
*
45266 AAAACCTAATCTAAAAATGAAAAGAAAAG
1 AAAACCTAACCTAAAAATGAAAAG---AG
45295 AAAACCTAACCCTAAAA
1 AAAACCTAA-CCTAAAA
45312 CTATGGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
25 15 0.39
26 6 0.16
29 11 0.29
30 6 0.16
ACGTcount: A:0.63, C:0.15, G:0.08, T:0.13
Consensus pattern (26 bp):
AAAACCTAACCTAAAAATGAAAAGAG
Found at i:45311 original size:29 final size:31
Alignment explanation
Indices: 45254--45311 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
45244 ATCTAACCTA
*
45254 AAAAGAAAAGAGAAAACCTAATCTAAAAATG
1 AAAAGAAAAGAGAAAACCTAACCTAAAAATG
45285 AAAAG-AAA-AGAAAACCTAACCCTAAAA
1 AAAAGAAAAGAGAAAACCTAA-CCTAAAA
45312 CTATGGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 11 0.44
30 9 0.36
31 5 0.20
ACGTcount: A:0.66, C:0.14, G:0.10, T:0.10
Consensus pattern (31 bp):
AAAAGAAAAGAGAAAACCTAACCTAAAAATG
Found at i:54878 original size:56 final size:56
Alignment explanation
Indices: 54816--54925 Score: 148
Period size: 56 Copynumber: 2.0 Consensus size: 56
54806 GCATTTAAAA
** * * * *
54816 TTTGATTCATGCATTTTGAATATGTTATGTATCGTGCTCAATGTAGCATTCAATAT
1 TTTGATTCAAACATTTTGAATATGTTATATATCATACTCAATGCAGCATTCAATAT
* *
54872 TTTGATTCAAACATTTTGAATATGTTTTATATCATATTCAATGCAGCATTCAAT
1 TTTGATTCAAACATTTTGAATATGTTATATATCATACTCAATGCAGCATTCAAT
54926 GTTTCTGCTA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (56 bp):
TTTGATTCAAACATTTTGAATATGTTATATATCATACTCAATGCAGCATTCAATAT
Found at i:59272 original size:19 final size:19
Alignment explanation
Indices: 59248--59286 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
59238 TTCCCTAAGG
59248 TTGAAAAAATAATGATTTT
1 TTGAAAAAATAATGATTTT
59267 TTGAAAAAATAATGATTTT
1 TTGAAAAAATAATGATTTT
59286 T
1 T
59287 CTCTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (19 bp):
TTGAAAAAATAATGATTTT
Found at i:60321 original size:38 final size:38
Alignment explanation
Indices: 60270--60345 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
60260 GTAAAATTGC
*
60270 CATAATTTGAATTTTGGACTAAATTGAATAGAATGTAT
1 CATAATATGAATTTTGGACTAAATTGAATAGAATGTAT
60308 CATAATATGAATTTTGGACTAAATTGAATAGAATGTAT
1 CATAATATGAATTTTGGACTAAATTGAATAGAATGTAT
60346 TTTGAATGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (38 bp):
CATAATATGAATTTTGGACTAAATTGAATAGAATGTAT
Found at i:62149 original size:13 final size:13
Alignment explanation
Indices: 62131--62155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62121 CTCGGCAGGG
62131 ACACGCCCGTGTA
1 ACACGCCCGTGTA
62144 ACACGCCCGTGT
1 ACACGCCCGTGT
62156 GCAATTACTT
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:0.20, C:0.40, G:0.24, T:0.16
Consensus pattern (13 bp):
ACACGCCCGTGTA
Found at i:77431 original size:47 final size:47
Alignment explanation
Indices: 77377--77570 Score: 280
Period size: 47 Copynumber: 4.1 Consensus size: 47
77367 TTAGGATTTT
** * *
77377 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
77424 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGGATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
77471 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
77518 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
77565 ATGTGA
1 ATGTGA
77571 AATATGTATG
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 131 1.00
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:77603 original size:48 final size:48
Alignment explanation
Indices: 77540--77818 Score: 463
Period size: 48 Copynumber: 5.8 Consensus size: 48
77530 TGAACATGCA
77540 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
77588 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* ** *
77636 CATATGTGGTAAAGTTGAATGG-TCAATGTGAAATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTGAAATATGTATGAGATATG
77684 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* *
77732 CATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTGAAATATGTATGAGATATG
*
77780 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
77819 GGCGATGTGC
Statistics
Matches: 214, Mismatches: 13, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
47 2 0.01
48 210 0.98
49 2 0.01
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
Found at i:77867 original size:144 final size:143
Alignment explanation
Indices: 77540--77858 Score: 387
Period size: 144 Copynumber: 2.2 Consensus size: 143
77530 TGAACATGCA
* * * *
77540 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCG
1 TATATGT-GTAAAGCCGAACGACCAATGTGAAATATGTATGAGATATGCATATGTGGTAAAGCCG
* **
77605 AATGGCTAATGTGAAATATGTATGAGATATGCATATGTGGTAAAGTTGAATGGTCAATGTGAAAT
65 AATGGCTAATGTGAAATATATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAAT
*
77670 ATATATGAGATATG
130 ATATAGGAGATATG
* * *
77684 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGCATATGTGGTAAAGCCG
1 TATATGT-GTAAAGCCGAACGACCAATGTGAAATATGTATGAGATATGCATATGTGGTAAAGCCG
* *
77749 AATGG-TCAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGG-CTAGTGTGAA
65 AATGGCT-AATGTGAAATATATATGAGATATGCATATGTGGTAAAGCCGAATGGTC-AATGTGAA
* * *
77812 ATATGTAGGCGATGTGCG
128 ATATATAGGAGATAT--G
**
77830 TATAT-T-T-TGGCCGAACGACCAATGTGAAA
1 TATATGTGTAAAGCCGAACGACCAATGTGAAA
77859 GGTGTGTATT
Statistics
Matches: 156, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
142 17 0.11
143 3 0.02
144 129 0.83
145 1 0.01
146 6 0.04
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (143 bp):
TATATGTGTAAAGCCGAACGACCAATGTGAAATATGTATGAGATATGCATATGTGGTAAAGCCGA
ATGGCTAATGTGAAATATATATGAGATATGCATATGTGGTAAAGCCGAATGGTCAATGTGAAATA
TATAGGAGATATG
Found at i:78017 original size:37 final size:37
Alignment explanation
Indices: 77967--78078 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
77957 AATATATTCC
*
77967 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCT
1 GGGTAAGACCCGATGACTACGTGTGGAGATTTTGTCT
*
78004 GGGTAAGACCCGATGACTACGTGTGGAGATTTTGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTTTGTCT
* *
78041 GGGTAAGACCCGATAACTTCGTGTGGAGATTTTGTCT
1 GGGTAAGACCCGATGACTACGTGTGGAGATTTTGTCT
78078 G
1 G
78079 AGCTAAAGGT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (37 bp):
GGGTAAGACCCGATGACTACGTGTGGAGATTTTGTCT
Found at i:79384 original size:15 final size:15
Alignment explanation
Indices: 79364--79392 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
79354 GGCTAAGTCC
79364 CGAAGAGCATTCGTA
1 CGAAGAGCATTCGTA
79379 CGAAGAGCATTCGT
1 CGAAGAGCATTCGT
79393 GCTAGTGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21
Consensus pattern (15 bp):
CGAAGAGCATTCGTA
Found at i:79434 original size:40 final size:40
Alignment explanation
Indices: 79379--79736 Score: 558
Period size: 40 Copynumber: 9.2 Consensus size: 40
79369 AGCATTCGTA
79379 CGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCC
1 CGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCC
*
79419 CGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTCC
1 CGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCC
*
79459 TGAAGAGCATTCGTGCTAGTGA--TATCCGGGCTAAGT-C
1 CGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCC
*
79496 CGAAGAGCATTCGTGCTAGTGATGTATCC-GACTAAGTCC
1 CGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCC
*
79535 C-AAGAGCATTCGTGCTAGTGATATATCC-GGCTAAGTCC
1 CGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCC
*
79573 CGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTCC
1 CGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCC
*
79613 C-AAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTCC
1 CGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCC
79652 CGAAGAGCATTCGTGCTAGTGATGTATCC-GGCTAA-T-C
1 CGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCC
* * *
79689 CGAAGAGCATTCGTGCT-GTGTTATATCCGGGCTAGGTCC
1 CGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCC
79728 CGAAGAGCA
1 CGAAGAGCA
79737 ATCATGCTGG
Statistics
Matches: 296, Mismatches: 13, Indels: 19
0.90 0.04 0.06
Matches are distributed among these distances:
36 9 0.03
37 45 0.15
38 58 0.20
39 87 0.29
40 97 0.33
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCC
Found at i:79516 original size:77 final size:77
Alignment explanation
Indices: 79379--79736 Score: 557
Period size: 77 Copynumber: 4.6 Consensus size: 77
79369 AGCATTCGTA
79379 CGAAGAGCATTCGTGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
1 CGAAGAGCATTCGTGCTAGTGA--TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
79444 ATCCGGACTAAGTC
64 ATCCGGACTAAGTC
79458 CTGAAGAGCATTCGTGCTAGTGATATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTAGTGATGTA
1 C-GAAGAGCATTCGTGCTAGTGATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTA
79522 TCC-GACTAAGTC
65 TCCGGACTAAGTC
*
79534 CCAAGAGCATTCGTGCTAGTGATATATCC-GGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
1 CGAAGAGCATTCGTGCTAGTG--ATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
79598 ATCCGGACTAAGTC
64 ATCCGGACTAAGTC
* *
79612 CCAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
1 CGAAGAGCATTCGTGCTAGTGA--TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
79677 ATCCGG-CTAA-TC
64 ATCCGGACTAAGTC
*
79689 CGAAGAGCATTCGTGCT-GTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 CGAAGAGCATTCGTGCTAGTG--ATATCCGGGCTAAGTCCCGAAGAGCA
79737 ATCATGCTGG
Statistics
Matches: 264, Mismatches: 5, Indels: 23
0.90 0.02 0.08
Matches are distributed among these distances:
75 19 0.07
76 45 0.17
77 84 0.32
78 54 0.20
79 41 0.16
80 21 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (77 bp):
CGAAGAGCATTCGTGCTAGTGATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTAT
CCGGACTAAGTC
Found at i:80881 original size:13 final size:13
Alignment explanation
Indices: 80863--80892 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
80853 TATATGTGTT
80863 TGAAATGCATTTG
1 TGAAATGCATTTG
80876 TGAAATGCATTTG
1 TGAAATGCATTTG
80889 TGAA
1 TGAA
80893 TTAAATTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (13 bp):
TGAAATGCATTTG
Found at i:83830 original size:47 final size:47
Alignment explanation
Indices: 83776--83969 Score: 271
Period size: 47 Copynumber: 4.1 Consensus size: 47
83766 TTAGGATTTT
** * *
83776 ATGTGATGAATATGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
83823 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * **
83870 ATGTGATGAATGTGAGCATGCATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
83917 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
83964 ATGTGA
1 ATGTGA
83970 AATATGTATG
Statistics
Matches: 130, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 130 1.00
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:83876 original size:22 final size:22
Alignment explanation
Indices: 83805--83876 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
83795 GTATATATGA
83805 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
83827 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
83852 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
83874 GAT
1 GAT
83877 GAATGTGAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 9 0.24
25 8 0.22
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:83877 original size:94 final size:94
Alignment explanation
Indices: 83776--84017 Score: 281
Period size: 94 Copynumber: 2.6 Consensus size: 94
83766 TTAGGATTTT
* *
83776 ATGTGATGAATATGAATGTGTATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATATGAATGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATATGAACA
*
83841 TGCATATATGTGATAAGGCCGAATGGCCA
66 TGCATATATGTGATAAAGCCGAATGGCCA
* *** * ** *
83870 ATGTGATGAATGTGAGCATGCATATGCGTGATAAGGCCGAATGGCCAATGTGGTGAATATGAACA
1 ATGTGATGAATATGAATGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATATGAACA
* *
83935 TGCATATATGTGGTAAAGCCGAATGGCTA
66 TGCATATATGTGATAAAGCCGAATGGCCA
* * * * *
83964 ATGTGA--AATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGA
1 ATGTGATGAATATGAATGTG-TA--TATATGTGATAAGGCCGAATGGCCAATGTGA
84018 AATATGTATG
Statistics
Matches: 119, Mismatches: 26, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
92 6 0.05
93 1 0.01
94 87 0.73
95 25 0.21
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.27
Consensus pattern (94 bp):
ATGTGATGAATATGAATGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATATGAACA
TGCATATATGTGATAAAGCCGAATGGCCA
Found at i:84097 original size:98 final size:96
Alignment explanation
Indices: 83940--84123 Score: 307
Period size: 98 Copynumber: 1.9 Consensus size: 96
83930 GAACATGCAT
*
83940 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
1 ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
84005 ATGGCTAATGTGAAATATGTATGAGATATGC
66 ATGGCTAATGTGAAATATGTATGAGATATGC
*
84036 ATATGTGGTAAAGCTGAATGG-TCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGC
1 ATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATATATGAGATATGTATATGTGGTAAAGC
*
84100 CGAATGGCTAGTGTGAAATATGTA
63 CGAATGGCTAATGTGAAATATGTA
84124 GGCGATGTGC
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
95 1 0.01
96 26 0.32
97 2 0.02
98 53 0.65
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.31
Consensus pattern (96 bp):
ATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
ATGGCTAATGTGAAATATGTATGAGATATGC
Found at i:84139 original size:50 final size:48
Alignment explanation
Indices: 83939--84123 Score: 300
Period size: 48 Copynumber: 3.8 Consensus size: 48
83929 TGAACATGCA
83939 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
83987 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* * *
84035 CATATGTGGTAAAGCTGAATGG-TCAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGATATG
*
84085 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
84124 GGCGATGTGC
Statistics
Matches: 126, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
47 1 0.01
48 80 0.63
49 4 0.03
50 40 0.32
51 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.31
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
Found at i:84377 original size:37 final size:37
Alignment explanation
Indices: 84269--84377 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
84259 GGAAATATAT
* * *
84269 TCCGAGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
*
84306 TCCGGGTAAGACCCGATTACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
*
84343 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTT
1 TCCGGGTAAGACCCGATAACTACGTGTGGAGATTT
84378 CGTCTGAGCT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATAACTACGTGTGGAGATTTTG
Found at i:85400 original size:31 final size:31
Alignment explanation
Indices: 85362--85423 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
85352 CAGATCCGAT
*
85362 GATTGTTTTCTATTCCGAGGTAGAATTTATG
1 GATTGTTTGCTATTCCGAGGTAGAATTTATG
* *
85393 GATTGTTTGCTGTTCTGAGGTAGAATTTATG
1 GATTGTTTGCTATTCCGAGGTAGAATTTATG
85424 TACCGAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.21, C:0.08, G:0.26, T:0.45
Consensus pattern (31 bp):
GATTGTTTGCTATTCCGAGGTAGAATTTATG
Done.