Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1556
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: 40329
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Found at i:1704 original size:79 final size:81
Alignment explanation
Indices: 1572--1752 Score: 228
Period size: 79 Copynumber: 2.3 Consensus size: 81
1562 AATGATGTCC
*
1572 GGCTAAGTCCCGAAGG-ATTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTG
1 GGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTG
*
1636 CGAGATACTA-ATTCCG
66 CGAGATACTATA-ACCG
* * * **
1652 GGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGT
1 GGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATTTGT
*
1714 GCGAGTTACTATAACCG
65 GCGAGATACTATAACCG
*
1731 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
1753 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
78 1 0.01
79 57 0.65
80 30 0.34
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
GGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTG
CGAGATACTATAACCG
Found at i:1766 original size:40 final size:40
Alignment explanation
Indices: 1572--1752 Score: 210
Period size: 40 Copynumber: 4.5 Consensus size: 40
1562 AATGATGTCC
* * * *
1572 GGCTAAGTCCCGAAGG-ATTTGTGCTAAGTGACCATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCG
* * *
1612 GACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-ACCG
1652 GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCG
*
1691 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
*
1731 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
1753 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 77 0.63
41 11 0.09
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
Found at i:1774 original size:79 final size:79
Alignment explanation
Indices: 1621--1775 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 79
1611 GGACTAAGAT
* **
1621 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
1686 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
1700 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
*
1763 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
1776 ATTCAAAGGT
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
78 2 0.03
79 40 0.60
80 25 0.37
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:9666 original size:40 final size:39
Alignment explanation
Indices: 9583--9766 Score: 210
Period size: 40 Copynumber: 4.6 Consensus size: 39
9573 TTGAATGATG
* * * *
9583 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
9622 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
9662 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
9701 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
9742 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
9767 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
39 45 0.36
40 70 0.56
41 9 0.07
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:9718 original size:79 final size:80
Alignment explanation
Indices: 9583--9766 Score: 214
Period size: 79 Copynumber: 2.3 Consensus size: 80
9573 TTGAATGATG
* * *
9583 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
9647 GTGCGAGATACTA-A
66 GTGCGAGATACTATA
* * * **
9661 TTCCGGGCTAAGCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAA
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAA
*
9724 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
9741 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
9767 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
78 1 0.01
79 67 0.74
80 22 0.24
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTATA
Found at i:9788 original size:79 final size:79
Alignment explanation
Indices: 9635--9789 Score: 199
Period size: 79 Copynumber: 2.0 Consensus size: 79
9625 GGACTAAGAT
* * **
9635 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
9700 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
9714 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
*
9777 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
9790 ATTCCAAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
78 2 0.03
79 39 0.59
80 25 0.38
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:15246 original size:68 final size:66
Alignment explanation
Indices: 15174--15345 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
15164 CATCATGTGT
* * * *
15174 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
15237 TGTAG
62 TGTAG
** * *
15242 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
15307 AG
65 AG
* * * *
15309 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
15346 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:15279 original size:64 final size:64
Alignment explanation
Indices: 15198--15381 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
15188 AGACATTATG
* * *
15198 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
15262 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
15327 AA
63 AA
* * *
15329 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
15382 CGAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 33 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:18682 original size:68 final size:68
Alignment explanation
Indices: 18607--18758 Score: 168
Period size: 67 Copynumber: 2.2 Consensus size: 68
18597 CATCATGTGT
* * * *
18607 ACAAGAGAGCTACGAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTACGAGACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
18670 TGTAG
64 TGTAG
* * * *
18675 ACAAGAGACCTACG-G-GATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCAT
1 ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCAT
18738 GTAG
65 GTAG
*
18742 ACAAAAGAGCTACGAGA
1 ACAAGAGAGCTACGAGA
18759 TAAACTGGCT
Statistics
Matches: 69, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
64 24 0.35
65 3 0.04
66 3 0.04
67 25 0.36
68 14 0.20
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (68 bp):
ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATG
TAG
Found at i:23172 original size:13 final size:13
Alignment explanation
Indices: 23156--23191 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
23146 ATGATTTTGT
23156 GAAAATTTCGTTC
1 GAAAATTTCGTTC
23169 GAAAATTTCGTTC
1 GAAAATTTCGTTC
23182 GAAAATTTCG
1 GAAAATTTCG
23192 ACGTTTGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (13 bp):
GAAAATTTCGTTC
Found at i:24393 original size:50 final size:50
Alignment explanation
Indices: 24273--24505 Score: 260
Period size: 50 Copynumber: 4.7 Consensus size: 50
24263 TCTATTGTGA
* * * * * *
24273 GGTCACGTGTGTGGTACTAAGTGTAGGCTACTACG-TGTACCTGATTATT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGATGTACCGGATAATT
*
24322 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGA-GTACC-GATAACTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGATGTACCGGATAA-TT
* * * * **
24371 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTAT-ATGTATCAGATGGTT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGATGTACCGGATAATT
* *
24421 AGGTCACATGTGTAGTACTAAGTACAGGCTACTA-CATGTACCGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGATGTACCGGATAATT
*
24471 GGTCACATGTGTAGTACTAAGTGCAAGCTACTATG
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATG
24506 CGTTCCTGAT
Statistics
Matches: 154, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
48 4 0.03
49 69 0.45
50 78 0.51
51 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (50 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGATGTACCGGATAATT
Found at i:24491 original size:99 final size:99
Alignment explanation
Indices: 24273--24504 Score: 290
Period size: 99 Copynumber: 2.3 Consensus size: 99
24263 TCTATTGTGA
* * ** * * *
24273 GGTCACGTGTGTGGTACTAAGTGTAGGCTACTACGTGTACCTGATTATTGGTCGCATGTGTAGTA
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATATGTACCAGATGATTGGTCACATGTGTAGTA
* *
24338 CTAAGTGCAGGCTACTATGAGTACCGATAACTTC
66 CTAAGTACAGGCTACTATCAGTACCGATAACTTC
* * *
24372 GATCACGTGTGTAGTACTAAGTGCAGGCTACTATATGTATCAGATGGTTAGGTCACATGTGTAGT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATATGTACCAGATGATT-GGTCACATGTGTAGT
24437 ACTAAGTACAGGCTACTA-CATGTACCGGATAA-TT-
65 ACTAAGTACAGGCTACTATCA-GTACC-GATAACTTC
* *
24471 GGTCACATGTGTAGTACTAAGTGCAAGCTACTAT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTAT
24505 GCGTTCCTGA
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
99 72 0.63
100 38 0.33
101 5 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (99 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATATGTACCAGATGATTGGTCACATGTGTAGTA
CTAAGTACAGGCTACTATCAGTACCGATAACTTC
Found at i:27525 original size:39 final size:38
Alignment explanation
Indices: 27496--27710 Score: 250
Period size: 39 Copynumber: 5.5 Consensus size: 38
27486 GCTACTCATT
* *
27496 CAAATGCCTTCGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGACTTAACCCGGTT-TAGTAACTCGCA
*
27535 CAAATGCCTTCGGACTTAACCCGATTTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAACCCGGTTTAGTAACTCGCA
*
27573 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGTA
1 CAAATGCCTTC-GGACTTAACCCGG-TTTAGTAACTCGCA
* * * *
27613 CAAATGCCTTCGGATCTTAGTCCAGATTTAGTAACTCGTA
1 CAAATGCCTTCGGA-CTTA-ACCCGGTTTAGTAACTCGCA
* * ** *
27653 CAAATGCCTTCGGGCTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGACTTAACCCG-GTTTAGTAACTCGCA
27692 CAAATGCCTTCGGATCTTA
1 CAAATGCCTTCGGA-CTTA
27711 GTCCGGATAT
Statistics
Matches: 155, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
38 26 0.17
39 67 0.43
40 59 0.38
41 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (38 bp):
CAAATGCCTTCGGACTTAACCCGGTTTAGTAACTCGCA
Found at i:27616 original size:40 final size:39
Alignment explanation
Indices: 27496--27757 Score: 305
Period size: 40 Copynumber: 6.6 Consensus size: 39
27486 GCTACTCATT
*
27496 CAAATGCCTTCGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATT-TAGTAACTCGCA
*
27535 CAAATGCCTTCGGACTTAACCC-GATTTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* *
27573 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGTA
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGTAACTCGCA
* * *
27613 CAAATGCCTTCGGATCTTAGTCCAGATTTAGTAACTCGTA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * *
27653 CAAATGCCTTCGGGCTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
27692 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
27733 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTC-GGACTTAGCCCGGA
27758 CATCATTCAA
Statistics
Matches: 193, Mismatches: 23, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
38 24 0.12
39 68 0.35
40 90 0.47
41 11 0.06
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:27713 original size:79 final size:79
Alignment explanation
Indices: 27496--27755 Score: 323
Period size: 79 Copynumber: 3.3 Consensus size: 79
27486 GCTACTCATT
* * * *
27496 CAAATGCCTTC-GGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGA-CTTA-ACCCG
1 CAAATGCCTTCGGGACTTAGCCCGATT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCAG
27558 ATTTAGTAACTCGCA
65 ATTTAGTAACTCGCA
* *
27573 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGTACAAATGCCTTCGGATCTTAGTCCAG
1 CAAATGCCTTCGGGACTTAGCCC-GATTTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCAG
*
27638 ATTTAGTAACTCGTA
65 ATTTAGTAACTCGCA
* * *
27653 CAAATGCCTTCGGG-CTTAGCCCGAAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCG-ATTTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCAG
* * * *
27717 ATATGGTCACTTAGCA
65 ATTTAGTAAC-TCGCA
27733 CAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCG
27756 GACATCATTC
Statistics
Matches: 159, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
77 11 0.07
78 35 0.22
79 66 0.42
80 47 0.30
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGATTTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCAGA
TTTAGTAACTCGCA
Found at i:27751 original size:119 final size:118
Alignment explanation
Indices: 27496--27744 Score: 299
Period size: 119 Copynumber: 2.1 Consensus size: 118
27486 GCTACTCATT
* * *
27496 CAAATGCCTTCGGA-CATAG-CCCGGTTATAGTAACTCGCACAAATGCCTTCGGACTTAACCCGA
1 CAAATGCCTTCGGATCTTAGTCCAGATT-TAGTAACTCGCACAAATGCCTTCGGACTTAACCCGA
* * * *
27559 TTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGTA
65 ATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA
* * *
27613 CAAATGCCTTCGGATCTTAGTCCAGATTTAGTAACTCGTACAAATGCCTTCGGGCTTAGCCCGAA
1 CAAATGCCTTCGGATCTTAGTCCAGATTTAGTAACTCGCACAAATGCCTTCGGACTTAACCCG-A
* ** * *
27678 ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
65 ATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCA
27733 CAAA-GCCTTCGG
1 CAAATGCCTTCGG
27745 GACTTAGCCC
Statistics
Matches: 112, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
117 14 0.12
118 39 0.35
119 52 0.46
120 7 0.06
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (118 bp):
CAAATGCCTTCGGATCTTAGTCCAGATTTAGTAACTCGCACAAATGCCTTCGGACTTAACCCGAA
TTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA
Found at i:33147 original size:28 final size:28
Alignment explanation
Indices: 33082--33231 Score: 212
Period size: 28 Copynumber: 5.4 Consensus size: 28
33072 GAGATTGGCG
* * * *
33082 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
33111 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
33139 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
33167 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
33195 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
33222 CTGAGTGTGC
1 CTAAGTGTGC
33232 AGACTTAATA
Statistics
Matches: 112, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 23 0.21
28 74 0.66
29 15 0.13
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:36490 original size:26 final size:28
Alignment explanation
Indices: 36416--36530 Score: 166
Period size: 28 Copynumber: 4.2 Consensus size: 28
36406 AGTCCGCACC
*
36416 AGTGTCTATATAATC-AACTCGCACACTT
1 AGTG-CTACATAATCAAACTCGCACACTT
*
36444 AGTGCTATATAATCAAACTCGCACACTT
1 AGTGCTACATAATCAAACTCGCACACTT
*
36472 AGT-C-ACATAATCAAGCTCGCACACTT
1 AGTGCTACATAATCAAACTCGCACACTT
36498 AGTGCTACATAATCAAACTCGC-CACTT
1 AGTGCTACATAATCAAACTCGCACACTT
36525 AGTGCT
1 AGTGCT
36531 GTAAATTTTT
Statistics
Matches: 81, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
26 23 0.28
27 23 0.28
28 35 0.43
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (28 bp):
AGTGCTACATAATCAAACTCGCACACTT
Found at i:36499 original size:54 final size:52
Alignment explanation
Indices: 36425--36527 Score: 179
Period size: 54 Copynumber: 1.9 Consensus size: 52
36415 CAGTGTCTAT
*
36425 ATAATCAACTCGCACACTTAGTGCTATATAATCAAACTCGCACACTTAGTCAC
1 ATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGC-CACTTAGTCAC
36478 ATAATCAAGCTCGCACACTTAGTGCTACATAATCAAACTCGCCACTTAGT
1 ATAATCAA-CTCGCACACTTAGTGCTACATAATCAAACTCGCCACTTAGT
36528 GCTGTAAATT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
53 16 0.33
54 32 0.67
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.26
Consensus pattern (52 bp):
ATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCCACTTAGTCAC
Done.