Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3027
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: 67396
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1556 original size:39 final size:39
Alignment explanation
Indices: 1460--1641 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 39
1450 TTGAATGCTG
* * *
1460 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTA-TAAT
** *
1499 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATAAT
* *
1539 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-TAAT
* * *
1579 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATAAT
1618 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
1642 GAATGAGTTA
Statistics
Matches: 123, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
38 1 0.01
39 56 0.46
40 58 0.47
41 8 0.07
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATAAT
Found at i:1590 original size:40 final size:40
Alignment explanation
Indices: 1460--1641 Score: 187
Period size: 39 Copynumber: 4.6 Consensus size: 40
1450 TTGAATGCTG
* *
1460 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
** * *
1499 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTA-TAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
*
1539 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* ** *
1579 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TTTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
1618 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
1642 GAATGAGTTA
Statistics
Matches: 122, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
38 1 0.01
39 57 0.47
40 54 0.44
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:1596 original size:79 final size:80
Alignment explanation
Indices: 1460--1638 Score: 224
Period size: 79 Copynumber: 2.3 Consensus size: 80
1450 TTGAATGCTG
* * *
1460 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
1524 TGTGCGAGTTATAAT
66 CGTGCGAGTTATAAA
**
1539 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
*
1600 ATTCGTGCGAGTTTTAAA
63 ATTCGTGCGAGTTATAAA
1618 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
1639 ATTGAATGAG
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
78 2 0.02
79 77 0.88
80 9 0.10
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTATAAA
Found at i:9362 original size:40 final size:40
Alignment explanation
Indices: 9278--9461 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
9268 TTGAATGCTG
* * * *
9278 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
** *
9317 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
9358 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
9398 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
9438 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
9462 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:9415 original size:80 final size:81
Alignment explanation
Indices: 9278--9458 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 81
9268 TTGAATGCTG
* * *
9278 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
9342 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
9358 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
9419 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
9438 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
9459 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:9482 original size:39 final size:38
Alignment explanation
Indices: 9359--9508 Score: 131
Period size: 40 Copynumber: 3.8 Consensus size: 38
9349 GTTATTAATT
* ** * *
9359 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A
** *
9399 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA
*
9438 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA
* *
9478 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG
9509 GAGCTAAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
39 30 0.32
40 63 0.68
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (38 bp):
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Found at i:13247 original size:49 final size:48
Alignment explanation
Indices: 13067--13260 Score: 192
Period size: 49 Copynumber: 3.9 Consensus size: 48
13057 TCTATTGTGA
* * * *
13067 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTTGAAAACTGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTAC---CAGACTGT
* * * *** *
13118 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTTGA-TGGAGA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGACT---GT
* *
13168 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGACTG-T
*
13217 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGA
13261 TAACTTCGGC
Statistics
Matches: 120, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
47 1 0.01
48 2 0.02
49 41 0.34
50 41 0.34
51 35 0.29
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.28
Consensus pattern (48 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGACTGT
Found at i:15329 original size:16 final size:17
Alignment explanation
Indices: 15308--15340 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15298 GTTTACAGTA
15308 CAAACA-AACAAAATTT
1 CAAACATAACAAAATTT
*
15324 CAAACATATCAAAATTT
1 CAAACATAACAAAATTT
15341 GTATAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
CAAACATAACAAAATTT
Found at i:31050 original size:12 final size:12
Alignment explanation
Indices: 31029--31058 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
31019 AATTTGGATG
*
31029 TTATTGTTATTA
1 TTATTTTTATTA
31041 TTATTTTTATTA
1 TTATTTTTATTA
31053 TTATTT
1 TTATTT
31059 CGTAGGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (12 bp):
TTATTTTTATTA
Found at i:33045 original size:28 final size:27
Alignment explanation
Indices: 32975--33090 Score: 135
Period size: 28 Copynumber: 4.3 Consensus size: 27
32965 TGGAGGAAGC
*
32975 GTTCTGGTGGCTCTGCCATAAATATCT
1 GTTCTGGTGGCTCTGCCACAAATATCT
* * *
33002 GTTCTAGTGGCTCTGCCACAAATTTTT
1 GTTCTGGTGGCTCTGCCACAAATATCT
* *
33029 GTTTCTGGTGGCCCTGCCACAATTATCT
1 G-TTCTGGTGGCTCTGCCACAAATATCT
* *
33057 GTATCTGGTGACTCTGTCAC-AATATCT
1 GT-TCTGGTGGCTCTGCCACAAATATCT
33084 GTTCTGG
1 GTTCTGG
33091 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
26 5 0.07
27 33 0.45
28 36 0.49
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (27 bp):
GTTCTGGTGGCTCTGCCACAAATATCT
Found at i:46150 original size:18 final size:17
Alignment explanation
Indices: 46129--46183 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
46119 AAAATTCTTT
46129 TCTCTTATTCTTTTCTCC
1 TCTCTTATTCTTTTCT-C
*
46147 TCTCTTCATCTATTTTCTC
1 TCTCTT-AT-TCTTTTCTC
*
46166 T-TCTTCTTCTTTTC-C
1 TCTCTTATTCTTTTCTC
46181 TCT
1 TCT
46184 ATAGCCGAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 2 0.06
16 7 0.23
17 1 0.03
18 10 0.32
19 4 0.13
20 7 0.23
ACGTcount: A:0.05, C:0.33, G:0.00, T:0.62
Consensus pattern (17 bp):
TCTCTTATTCTTTTCTC
Found at i:47670 original size:20 final size:21
Alignment explanation
Indices: 47627--47672 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
47617 ACTGTTTTGT
47627 TATGGG-CCAACTGTATTGAA
1 TATGGGCCCAACTGTATTGAA
*
47647 -ATGGGCCCAACTGTGTT-AA
1 TATGGGCCCAACTGTATTGAA
47666 TATGGGC
1 TATGGGC
47673 AAGACCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGGGCCCAACTGTATTGAA
Found at i:47792 original size:28 final size:27
Alignment explanation
Indices: 47701--47806 Score: 81
Period size: 28 Copynumber: 3.7 Consensus size: 27
47691 ACTTGTAATA
* * *
47701 GGGCTACGGCCCAAATTGATACTGATAT
1 GGGCTA-GGCCCAGATTAATATTGATAT
*
47729 GGGCTAGGCCCAGTATAATATGATATTG-TAAG
1 GGGCTAGGCCCAG-AT--TA--ATATTGAT-AT
47761 GGGCTATGGCCCAGATTAATATTGATAT
1 GGGCTA-GGCCCAGATTAATATTGATAT
47789 GGGCTAAGGCCCAG-TTAA
1 GGGCT-AGGCCCAGATTAA
47807 CTCTGATTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 19
0.73 0.06 0.22
Matches are distributed among these distances:
27 10 0.16
28 27 0.42
29 2 0.03
30 3 0.05
31 1 0.02
32 14 0.22
33 7 0.11
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.26
Consensus pattern (27 bp):
GGGCTAGGCCCAGATTAATATTGATAT
Found at i:51533 original size:47 final size:47
Alignment explanation
Indices: 51455--51907 Score: 699
Period size: 47 Copynumber: 9.6 Consensus size: 47
51445 CCCTTCGGGA
* * * * * *
51455 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
51502 CCTGTCACATATATACACTTTAACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
51549 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
51596 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
51643 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
51692 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
51739 CTTATCACATATATACACTTTCACATTCATCACATCAGCAATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
51786 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
51835 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
51882 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
51908 CACAATTATC
Statistics
Matches: 372, Mismatches: 30, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
47 284 0.76
49 88 0.24
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:51693 original size:96 final size:94
Alignment explanation
Indices: 51455--51907 Score: 699
Period size: 96 Copynumber: 4.8 Consensus size: 94
51445 CCCTTCGGGA
* * * * * * * *
51455 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
51520 TTTAACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* *
51549 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
51614 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* *
51643 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
51708 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
51739 CTTATCACATATATACACTTTCACATTCATCACATCAGCAATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* *
51804 ACTTTCACATTCATCACATTGGCCATTCGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
*
51835 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
*
51900 ATTCACAT
66 TTTCACAT
51908 CACAATTATC
Statistics
Matches: 330, Mismatches: 25, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
94 149 0.45
96 181 0.55
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:51711 original size:143 final size:143
Alignment explanation
Indices: 51455--51907 Score: 739
Period size: 143 Copynumber: 3.2 Consensus size: 143
51445 CCCTTCGGGA
* * * * * * * *
51455 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* * * *
51518 ACTTTAACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
*
51583 TCGGCTATTAGGC
131 TCGGCCATTAGGC
51596 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
51661 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
51726 TCGGCCATTAGGC
131 TCGGCCATTAGGC
* *
51739 CTTATCACATATATACACTTTCACATTCATCACATCAGCAATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
51804 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
51869 TCGGCCATTAGGC
131 TCGGCCATTAGGC
* *
51882 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
51908 CACAATTATC
Statistics
Matches: 293, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
141 47 0.16
143 246 0.84
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (143 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:54559 original size:47 final size:47
Alignment explanation
Indices: 54505--54695 Score: 256
Period size: 47 Copynumber: 4.1 Consensus size: 47
54495 TTAGGATTTT
** * *
54505 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
54552 ATGTGATGGATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
54599 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCT
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * *
54646 ATGTGGTGAATATGAACATGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
54693 ATG
1 ATG
54696 CGAAATATGT
Statistics
Matches: 126, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 126 1.00
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:54654 original size:25 final size:25
Alignment explanation
Indices: 54579--54654 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 25
54569 ATGCATATAT
*
54579 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCTATGTG
* * * * *
54604 ATGA-ATGTG-AGCAT-GCATATGT-
1 GTGATAAG-GCCGAATGGCCTATGTG
54626 GTGATAAGGCCGAATGGCCTATGTG
1 GTGATAAGGCCGAATGGCCTATGTG
54651 GTGA
1 GTGA
54655 ATATGAACAT
Statistics
Matches: 35, Mismatches: 11, Indels: 10
0.62 0.20 0.18
Matches are distributed among these distances:
22 4 0.11
23 11 0.31
24 12 0.34
25 8 0.23
ACGTcount: A:0.28, C:0.13, G:0.34, T:0.25
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCTATGTG
Found at i:54829 original size:98 final size:96
Alignment explanation
Indices: 54669--54852 Score: 298
Period size: 98 Copynumber: 1.9 Consensus size: 96
54659 GAACATGTAT
*
54669 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATATGTATGAGATATGTATATGTGGTAAAGCCGA
1 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
54734 ATGGCTAATGTGAAATATGTATGAGATATGC
66 ATGGCTAATGTGAAATATGTATGAGATATGC
* *
54765 ATATGTGGTAAAGCTGAATGG-TCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGC
1 ATATGTGGTAAAGCCGAATGGCT-AATGCG-AA-ATATATATGAGATATGTATATGTGGTAAAGC
*
54829 CGAATGGCTAGTGTGAAATATGTA
63 CGAATGGCTAATGTGAAATATGTA
54853 GGCGATGTGC
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
95 1 0.01
96 25 0.31
97 2 0.02
98 53 0.65
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.30
Consensus pattern (96 bp):
ATATGTGGTAAAGCCGAATGGCTAATGCGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
ATGGCTAATGTGAAATATGTATGAGATATGC
Found at i:54868 original size:50 final size:48
Alignment explanation
Indices: 54668--54852 Score: 291
Period size: 48 Copynumber: 3.8 Consensus size: 48
54658 TGAACATGTA
*
54668 TATATGTGGTAAAGCCGAATGGCTAATGCGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
54716 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* * *
54764 CATATGTGGTAAAGCTGAATGG-TCAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGATATG
*
54814 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
54853 GGCGATGTGC
Statistics
Matches: 125, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
47 1 0.01
48 79 0.63
49 4 0.03
50 40 0.32
51 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
Found at i:55100 original size:37 final size:37
Alignment explanation
Indices: 54999--55107 Score: 173
Period size: 37 Copynumber: 2.9 Consensus size: 37
54989 GGAAATATAT
* *
54999 TCCGGGTAAGACCCGATGACTACGTGTAGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
55036 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* **
55073 TCCGGGTAAGACCCGATAACTTTGTGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
55108 CATCTGAGCT
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:0.18, G:0.30, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:56739 original size:40 final size:40
Alignment explanation
Indices: 56376--56727 Score: 542
Period size: 40 Copynumber: 8.8 Consensus size: 40
56366 GAGAATTGAG
56376 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
**
56416 AGTGATATATCCGGGCTAAGTTTCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
56456 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
56496 AGTGATATATCCGAGCTAAGTCCCAAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
56536 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
56576 AGTGATATATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* *
56616 AGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* ** *
56656 AGTGATATATCCGTGCTAAACCCCAAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * *
56696 GGTGTTATATCCGGGCTAGGTCCCAAAGAGCA
1 AGTGATATATCCGGGCTAAGTCCCGAAGAGCA
56728 ATCATGCTGG
Statistics
Matches: 282, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 282 1.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:61408 original size:32 final size:34
Alignment explanation
Indices: 61372--61449 Score: 94
Period size: 32 Copynumber: 2.4 Consensus size: 34
61362 AAATTATTCC
61372 GGGTAAGACCCGATGACTAC--G-GGAGATTATGT
1 GGGTAAGACCCGATGACTACGTGTGGA-ATTATGT
*
61404 GGGTAAGACCC-A-GACTACGTGTGGAATTTTGT
1 GGGTAAGACCCGATGACTACGTGTGGAATTATGT
*
61436 CGGTAAGACCCGAT
1 GGGTAAGACCCGAT
61450 AACTTGTGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 6 0.15
31 1 0.03
32 28 0.72
33 4 0.10
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (34 bp):
GGGTAAGACCCGATGACTACGTGTGGAATTATGT
Found at i:64199 original size:59 final size:56
Alignment explanation
Indices: 64058--64293 Score: 275
Period size: 59 Copynumber: 4.1 Consensus size: 56
64048 TTCCTAGATA
* * * * *
64058 GGTCTTACTCGCA-TACACATATCGCAGTCACATATCGATGCCAAC-TATTAATGT
1 GGTCTTACTCGCACCACATATATCGGAATCACATATCGATGCCAACGTATTAACGT
*
64112 -GTCTTACTTCGCACC-CATATATCAGGAATCACATATCGCATGCCAATGTATTAACGTT
1 GGTCTTAC-TCGCACCACATATATC-GGAATCACATATCG-ATGCCAACGTATTAACG-T
*
64170 GGTCTTACTCGTTACCACATATATCGGAATCACATATCGATGCCAACGTAACTTAAAC-T
1 GGTCTTACTCG-CACCACATATATCGGAATCACATATCGATGCCAACGT-A-TT-AACGT
* *
64229 GGTCTTACTCGCAACACATATATCGGAATCACATATTTGATGCCAACGTATTAACGT
1 GGTCTTACTCGCACCACATATATCGGAATCACATA-TCGATGCCAACGTATTAACGT
64286 GGTCTTAC
1 GGTCTTAC
64294 ACATAATCAC
Statistics
Matches: 157, Mismatches: 11, Indels: 25
0.81 0.06 0.13
Matches are distributed among these distances:
53 7 0.04
54 12 0.08
55 12 0.08
56 10 0.06
57 18 0.11
58 36 0.23
59 49 0.31
60 10 0.06
61 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (56 bp):
GGTCTTACTCGCACCACATATATCGGAATCACATATCGATGCCAACGTATTAACGT
Found at i:64274 original size:117 final size:113
Alignment explanation
Indices: 64076--64293 Score: 291
Period size: 117 Copynumber: 1.9 Consensus size: 113
64066 TCGCATACAC
* *
64076 ATATCGCAGTCACATATCGATGCCAACTATTAATGTGTCTTACTTCGCACCCATATATCAGGAAT
1 ATATCGCAATCACATATCGATGCCAACTATTAATGTGTCTTACTTCGCACACATATATCAGGAAT
*
64141 CACATATCGCATGCCAATGTATTAACGTTGGTCTTACTCGTTACCACAT
66 CACATATCGCATGCCAACGTATTAACG-TGGTCTTACTCGTTACCACAT
*
64190 ATATCGGAATCACATATCGATGCCAACGTAACTTAAACTG-GTCTTAC-TCGCAACACATATATC
1 ATATCGCAATCACATATCGATGCCAAC-T-A-TT-AA-TGTGTCTTACTTCGC-ACACATATATC
*
64253 -GGAATCACATATTTG-ATGCCAACGTATTAACGTGGTCTTAC
60 AGGAATCACATA-TCGCATGCCAACGTATTAACGTGGTCTTAC
64294 ACATAATCAC
Statistics
Matches: 92, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
114 25 0.27
115 1 0.01
116 10 0.11
117 33 0.36
118 21 0.23
119 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (113 bp):
ATATCGCAATCACATATCGATGCCAACTATTAATGTGTCTTACTTCGCACACATATATCAGGAAT
CACATATCGCATGCCAACGTATTAACGTGGTCTTACTCGTTACCACAT
Done.