Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_878
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: 43226
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3723 original size:25 final size:25
Alignment explanation
Indices: 3695--3750 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
3685 CGTAAAATTT
* *
3695 TATAAAATTGTAACATTATAAAA-TA
1 TATAAAATT-AAAAATTATAAAACTA
* *
3720 TATAGAATTAAAAATTATAAAACTT
1 TATAAAATTAAAAATTATAAAACTA
3745 TATAAA
1 TATAAA
3751 GTCATAAGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (25 bp):
TATAAAATTAAAAATTATAAAACTA
Found at i:3735 original size:7 final size:8
Alignment explanation
Indices: 3694--3741 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
3684 TCGTAAAATT
3694 TTATAAAA
1 TTATAAAA
* *
3702 TTGTAACA
1 TTATAAAA
3710 TTATAAAA
1 TTATAAAA
*
3718 TATATAGAA
1 T-TATAAAA
3727 TTA-AAAA
1 TTATAAAA
3734 TTATAAAA
1 TTATAAAA
3742 CTTTATAAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
7 6 0.19
8 19 0.59
9 7 0.22
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (8 bp):
TTATAAAA
Found at i:4008 original size:15 final size:15
Alignment explanation
Indices: 3946--4010 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
3936 TTTTTTATTT
*
3946 TTTTATAATTTTACA
1 TTTTATAATTTTATA
** *
3961 TTTTTATTTTTTTAGA
1 -TTTTATAATTTTATA
** *
3977 TTTTATAAAATTCTA
1 TTTTATAATTTTATA
3992 TTTTATAATTTTATA
1 TTTTATAATTTTATA
4007 TTTT
1 TTTT
4011 TTATATTTTT
Statistics
Matches: 37, Mismatches: 12, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
15 25 0.68
16 12 0.32
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (15 bp):
TTTTATAATTTTATA
Found at i:4022 original size:10 final size:10
Alignment explanation
Indices: 3931--4073 Score: 54
Period size: 10 Copynumber: 14.7 Consensus size: 10
3921 TTAGGATCAT
*
3931 TATTTTTTTT
1 TATTTTTTTA
3941 TATTTTTTTA
1 TATTTTTTTA
*
3951 TAATTTTACATTTT
1 T-ATTTT---TTTA
3965 TATTTTTTTA
1 TATTTTTTTA
* * *
3975 GATTTTATAA
1 TATTTTTTTA
*
3985 AATTCTATTTTA
1 TATT-T-TTTTA
*
3997 TA--ATTTTA
1 TATTTTTTTA
4005 TA-TTTTTTA
1 TATTTTTTTA
4014 TATTTTTTTA
1 TATTTTTTTA
* * *
4024 -A-ATTATAA
1 TATTTTTTTA
*
4032 TATTTTTCTA
1 TATTTTTTTA
4042 -A---TTTTA
1 TATTTTTTTA
4048 T-TTTTTTTA
1 TATTTTTTTA
*
4057 TATTTTTTTT
1 TATTTTTTTA
4067 TATTTTT
1 TATTTTT
4074 ATAGGCATGG
Statistics
Matches: 97, Mismatches: 21, Indels: 30
0.66 0.14 0.20
Matches are distributed among these distances:
6 4 0.04
8 11 0.11
9 16 0.16
10 47 0.48
11 6 0.06
12 4 0.04
13 5 0.05
14 4 0.04
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.72
Consensus pattern (10 bp):
TATTTTTTTA
Found at i:5723 original size:7 final size:7
Alignment explanation
Indices: 5711--5736 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5701 ATAAATAGTC
5711 GTATTTA
1 GTATTTA
5718 GTATTTA
1 GTATTTA
5725 GTATTTA
1 GTATTTA
5732 GTATT
1 GTATT
5737 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:6376 original size:18 final size:18
Alignment explanation
Indices: 6353--6390 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6343 TGCTAGGTGC
* *
6353 GTATCCTAGCTCTTATAT
1 GTATCCTAACCCTTATAT
6371 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
6389 GT
1 GT
6391 TTCATTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:10473 original size:93 final size:93
Alignment explanation
Indices: 10358--10528 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
10348 GCCCATAAGT
* *
10358 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
10423 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
*
10451 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
10516 CGAGTTCGGATGC
66 CGAGTTCGGATGC
10529 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:10525 original size:46 final size:46
Alignment explanation
Indices: 10350--10525 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
10340 TGTAACCCGC
* * *
10350 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
10396 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* * *
10446 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
10489 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
10526 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 64 0.58
47 29 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:17281 original size:40 final size:40
Alignment explanation
Indices: 17224--17468 Score: 266
Period size: 40 Copynumber: 6.1 Consensus size: 40
17214 TCGAATGATG
* * * *
17224 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTATA
* *
17264 TCCGGACTAAGATCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTATA
** *
17304 TCCGGGTTAAG-TCCCGAGGGCATTTGTGCGAGTTACTATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTATA
*
17344 ACCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTATA
*
17384 ACCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTATA
* * * **
17424 ACCGGGCTATG-TCCTGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGACTAAGATCC-GAAGGCATTTGTGCGAGTTA-CTATA
17464 TCCGG
1 TCCGG
17469 TTAAATTTCG
Statistics
Matches: 179, Mismatches: 20, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
39 6 0.03
40 165 0.92
41 8 0.04
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:17357 original size:80 final size:81
Alignment explanation
Indices: 17224--17447 Score: 296
Period size: 80 Copynumber: 2.8 Consensus size: 81
17214 TCGAATGATG
* * * *
17224 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGACTAAGATCCGAAGGCATT
17288 GGTGCGAGTTACTA-AA
65 GGTGCGAGTTACTATAA
* * *
17304 TCCGGGTTAAGTCCCGAGGGCATTTGTGCGAGTTACTATAACCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGACTAAGATCCGAAGGCATTG
17369 GTGCGAGTTACTATAA
66 GTGCGAGTTACTATAA
* * *
17385 -CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATG-TCCTGAAGGCAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAACCGGACTAAGATCC-GAAGGCAT
17447 T
64 T
17448 TGAACGAGTA
Statistics
Matches: 128, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
79 3 0.02
80 115 0.90
81 10 0.08
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGACTAAGATCCGAAGGCATTG
GTGCGAGTTACTATAA
Found at i:17463 original size:120 final size:120
Alignment explanation
Indices: 17237--17456 Score: 309
Period size: 120 Copynumber: 1.8 Consensus size: 120
17227 GGGCTAAGTC
*
17237 CCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTGGTGCGAGTTACTA
1 CCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTGGTGCGAGTTACTA
* * **
17302 AATCCGGGTTAAGTCCCGAGGGCATTTGTGCGAGTTACTATAACCGGACTAAGAT
66 AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTATAACCGGACTAAGAT
* * * *
17357 CCGAAGGCATTTGTGC-GAGTTACTATAACCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 CCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTGGTGCGAGTTACT
* *
17421 ATAA-CCGGGCTATGTCCTGAAGGCATTTGAACGAGT
65 A-AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGT
17457 AGCTATATCC
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
120 78 0.90
121 9 0.10
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (120 bp):
CCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTGGTGCGAGTTACTA
AATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTATAACCGGACTAAGAT
Found at i:19504 original size:13 final size:15
Alignment explanation
Indices: 19464--19508 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
19454 AGAAAAAATT
19464 ATTTT-TGGTATAT-
1 ATTTTATGGTATATG
19477 -TTTTATGGTATATG
1 ATTTTATGGTATATG
19491 ATTTTATGG-A-ATG
1 ATTTTATGGTATATG
19504 ATTTT
1 ATTTT
19509 GTTAAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.14
13 16 0.55
14 1 0.03
15 8 0.28
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (15 bp):
ATTTTATGGTATATG
Found at i:20651 original size:42 final size:42
Alignment explanation
Indices: 20604--20701 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
20594 ACTGAGTGTA
* * * * *
20604 CGTGTAAGAACATATCTGGGATATGGGATCGATATGAGATTT
1 CGTGTAAGACCATATCTGGGATATAGCATCAATAAGAGATTT
20646 CGTGTAAGACCATATCTGGGATATAGCATCAATAAGAGATTT
1 CGTGTAAGACCATATCTGGGATATAGCATCAATAAGAGATTT
*
20688 CATGTAAGACCATA
1 CGTGTAAGACCATA
20702 ACTGAGTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGGGATATAGCATCAATAAGAGATTT
Found at i:20746 original size:40 final size:40
Alignment explanation
Indices: 20696--20776 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
20686 TTCATGTAAG
*
20696 ACCATAACTGAGTTATTGGCATCTATACGAGATTACGTGT
1 ACCATAACTGAGTTATTGGCATCTATACGAGATAACGTGT
20736 ACCATAACTGAGTTATTGGCATCTATACGAGATAACGTGT
1 ACCATAACTGAGTTATTGGCATCTATACGAGATAACGTGT
20776 A
1 A
20777 AGAACATTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (40 bp):
ACCATAACTGAGTTATTGGCATCTATACGAGATAACGTGT
Found at i:26020 original size:85 final size:85
Alignment explanation
Indices: 25877--26055 Score: 331
Period size: 85 Copynumber: 2.1 Consensus size: 85
25867 GGCCGGCCAT
25877 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATATTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATATTGGGGTAGTGCATTAT
25942 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
*
25962 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATATTGGGGTAGTGCATTAT
*
26027 GTAAGGATTAATAAAGTAAA
66 GTAAGGATTAATAAAATAAA
*
26047 GGGCATGGG
1 GAGCATGGG
26056 CAATAAAATA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 91 1.00
ACGTcount: A:0.37, C:0.08, G:0.28, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATATTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:28280 original size:47 final size:47
Alignment explanation
Indices: 28229--28570 Score: 459
Period size: 47 Copynumber: 7.1 Consensus size: 47
28219 TTAGGATTTT
* *
28229 ATGTGATGGATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
**
28276 ATGTGATGAATGTGAACCCGTATATATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA--C--ATGCATATGTGTGATAAGGCCGAATGGCCA
** *
28327 ATGTGATGAATGTGAACCTGTATATATATATGCGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA-C-----ATGCATATGTGTGATAAGGCCGAATGGCCA
*
28380 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
*
28427 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* *
28474 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
* * * *
28521 ATGTGATGAATGTGAACATGAATATATGTGGTAAGGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
28568 ATG
1 ATG
28571 CGAAACGTGT
Statistics
Matches: 271, Mismatches: 17, Indels: 14
0.90 0.06 0.05
Matches are distributed among these distances:
47 178 0.66
49 1 0.00
50 2 0.01
51 43 0.16
52 1 0.00
53 46 0.17
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
Found at i:28407 original size:23 final size:23
Alignment explanation
Indices: 28380--28454 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
28370 CGAATGGCCA
28380 ATGTGATGAATGTGAACATGCGT
1 ATGTGATGAATGTGAACATGCGT
* * **
28403 ATGTG-TGATAAG-G-CCGAATGGCCA
1 ATGTGATGA-ATGTGAAC--AT-GCGT
28427 ATGTGATGAATGTGAACATGCGT
1 ATGTGATGAATGTGAACATGCGT
28450 ATGTG
1 ATGTG
28455 TGATAAGGCC
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
21 1 0.03
22 4 0.11
23 16 0.43
24 11 0.30
25 4 0.11
26 1 0.03
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.28
Consensus pattern (23 bp):
ATGTGATGAATGTGAACATGCGT
Found at i:28632 original size:45 final size:46
Alignment explanation
Indices: 28544--28633 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 46
28534 GAACATGAAT
* * * *
28544 ATATGTGGTAAGGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
* * *
28590 ATATGTGGTAAAG-CAAATGGCTAATGTGAGATATGTACGAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATG
28634 TGTATATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
45 25 0.68
46 12 0.32
ACGTcount: A:0.33, C:0.09, G:0.32, T:0.26
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAACATGTACGAGATGG
Found at i:28925 original size:37 final size:37
Alignment explanation
Indices: 28783--28924 Score: 239
Period size: 37 Copynumber: 3.8 Consensus size: 37
28773 AATATATTCT
28783 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
28820 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
* *
28857 GGGTAAGACCCGATGACTACGCGTGGAGATTTTGTCC
1 GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
* * *
28894 GGGTAAGACCCGATAACTTCATGTGGAGATT
1 GGGTAAGACCCGATGACTACGTGTGGAGATT
28925 TCGTCTGAGC
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 99 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
GGGTAAGACCCGATGACTACGTGTGGAGATTATGTCC
Found at i:30460 original size:42 final size:42
Alignment explanation
Indices: 30387--30492 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 42
30377 TTAGGGTTAC
* *
30387 AGAG-ATTACGTGTAAGGCCATATATGGGATATGGCATCGATA
1 AGAGAATT-CGTGTAAGACCATATATGCGATATGGCATCGATA
* *
30429 TGAGAATTCGTGTAAGACCATATCTGCGATATGGCATCGATA
1 AGAGAATTCGTGTAAGACCATATATGCGATATGGCATCGATA
* *
30471 AGAGATTTCATGTAAGACCATA
1 AGAGAATTCGTGTAAGACCATA
30493 GCTGGCATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
42 53 0.95
43 3 0.05
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (42 bp):
AGAGAATTCGTGTAAGACCATATATGCGATATGGCATCGATA
Found at i:30527 original size:43 final size:41
Alignment explanation
Indices: 30414--30535 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 41
30404 CCATATATGG
* * *
30414 GATATGGCATCGATATGAGAATTCGTGTAAGACCATATCTGC
1 GATATCGCATCGATATGAG-ATTCATGTAAGACCATAGCTGC
* *
30456 GATATGGCATCGATAAGAGATTTCATGTAAGACCATAGCTG-
1 GATATCGCATCGATATGAGA-TTCATGTAAGACCATAGCTGC
* * *
30497 GCATATTCGTATTGATATGAGATTACATGTAAGGCCATA
1 G-ATA-TCGCATCGATATGAGATT-CATGTAAGACCATA
30536 TCTGATATAT
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.03
42 41 0.60
43 25 0.37
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (41 bp):
GATATCGCATCGATATGAGATTCATGTAAGACCATAGCTGC
Found at i:33485 original size:39 final size:40
Alignment explanation
Indices: 33328--33496 Score: 243
Period size: 40 Copynumber: 4.2 Consensus size: 40
33318 GCTACTCGTT
* *
33328 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
33368 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
33408 CCAATGCCTTCAGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
33448 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
33487 CAAATGCCTT
1 CAAATGCCTT
33497 TGGATCTTAG
Statistics
Matches: 119, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
39 31 0.26
40 86 0.72
41 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:33536 original size:79 final size:79
Alignment explanation
Indices: 33328--33552 Score: 229
Period size: 80 Copynumber: 2.8 Consensus size: 79
33318 GCTACTCGTT
* * * ** * *
33328 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCAGGACTTAACCCGAATATAGTAACTAGCACAAA-GCCTTCGGGACTTAGCCCGG
*
33393 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
* * * * *
33408 CCAATGCCTTCAGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCAGGACTTAACCCGAATATAGTAACTAGCA-CAAAGCCTTCGGGACTTAGCCCGG
*
33472 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* ** * *
33487 CAAATGCCTT-TGGATCTTAGTCCGAATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCAGGA-CTTAACCCGAATATAGTAAC-TAGCACAAAGCCTTCGGGACTTAGCCCG
33551 GA
64 GA
33553 CATCATTCGA
Statistics
Matches: 121, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
78 3 0.02
79 57 0.47
80 58 0.48
81 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCAGGACTTAACCCGAATATAGTAACTAGCACAAAGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:33536 original size:119 final size:120
Alignment explanation
Indices: 33330--33552 Score: 265
Period size: 119 Copynumber: 1.9 Consensus size: 120
33320 TACTCGTTCA
* *
33330 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAAT
* * *
33395 TTAGTAACTCGCACCAATGCCTTCAGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTAGCACCAAAGCCTTCAGGACTTAACCCGGATTTAGTAACTCGCACC
* * * **
33450 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTT-TGGATCTTAGTCCGA
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGA
* * * *
33512 ATATGGTCACTTAGCA-CAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAAC-TAGCACCAAAGCCTTCAGGACTTAACCCGGA
33553 CATCATTCGA
Statistics
Matches: 86, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
118 4 0.05
119 66 0.77
120 16 0.19
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGAAT
ATAGTAACTAGCACCAAAGCCTTCAGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:40037 original size:1 final size:1
Alignment explanation
Indices: 40031--40091 Score: 104
Period size: 1 Copynumber: 61.0 Consensus size: 1
40021 ATAATCACAT
* *
40031 AAAAAAAAAAAAAAAAATAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
40092 TAGTATACAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.97, C:0.00, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:41375 original size:41 final size:40
Alignment explanation
Indices: 41277--41500 Score: 174
Period size: 40 Copynumber: 5.6 Consensus size: 40
41267 ATCCGTGTCA
* * * * *
41277 AATGCCTTCGGGACCATAGCCCGTGTTATAGTAACTCGTACA
1 AATGCCTTCGGGA-CTTAACCCG-GATATAGTAACTCGCACC
*
41319 AATG-C-TCGGGACTTAACCCGGATATAGTAACTCCCACC
1 AATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCACC
*
41357 GAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
1 -AATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCACC
* * *
41398 AATGCCTTCGGG-C-TATACCCAGA-ATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTA-ACCCGGATA-TAGTAACTCGCACC
** * * *
41437 AATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-C
1 AATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TCGCACC
* * *
41477 AAAGCCTTCAGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41501 CATCATTCGA
Statistics
Matches: 149, Mismatches: 22, Indels: 24
0.76 0.11 0.12
Matches are distributed among these distances:
38 18 0.12
39 39 0.26
40 46 0.31
41 42 0.28
42 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATATAGTAACTCGCACC
Found at i:41434 original size:39 final size:40
Alignment explanation
Indices: 41305--41447 Score: 152
Period size: 39 Copynumber: 3.6 Consensus size: 40
41295 GCCCGTGTTA
* * *
41305 TAGTAACTCGTACAAATG-C-TCGGGACTTAACCC-GGAT
1 TAGTAACTCGCACCAATGCCTTCGGGACTTAACCCAGAAT
* * *
41342 ATAGTAACTCCCACCGAATGCCTTCGGGACTTAACCCGGATT
1 -TAGTAACTCGCACC-AATGCCTTCGGGACTTAACCCAGAAT
41384 TAGTAACTCGCACCAATGCCTTCGGG-C-TATACCCAGAAT
1 TAGTAACTCGCACCAATGCCTTCGGGACTTA-ACCCAGAAT
* *
41423 TAGTATCTCGCACAAATGCCTTCGG
1 TAGTAACTCGCACCAATGCCTTCGG
41448 ATCTTAGTCC
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
38 13 0.14
39 35 0.39
40 13 0.14
41 27 0.30
42 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
TAGTAACTCGCACCAATGCCTTCGGGACTTAACCCAGAAT
Done.