Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3626
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: 49303
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:2519 original size:22 final size:23
Alignment explanation
Indices: 2487--2532 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
2477 GGAATTCGCA
2487 CACACACAGTGCTC-TAATCATT
1 CACACACAGTGCTCTTAATCATT
* *
2509 CACACATAGTGCTCTTATTCATT
1 CACACACAGTGCTCTTAATCATT
2532 C
1 C
2533 GTTATTACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (23 bp):
CACACACAGTGCTCTTAATCATT
Found at i:2818 original size:39 final size:40
Alignment explanation
Indices: 2709--2930 Score: 243
Period size: 40 Copynumber: 5.6 Consensus size: 40
2699 CCAGCATGAT
* ** * * * *
2709 TGCTCTTCGGGACCTAGCCTAGACATAACACCAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
** * *
2749 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
2789 TGCTCTTC-GAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
2828 TGCTCCTCGGGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
**
2868 TGCTCTTCGGGACTTAGCCCGGATATGGTCACTTAGCAC-AA
1 TGCTCTTCGGGACTTAGCCCGGATA-CATCAC-TAGCACGAA
*
2909 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
2931 CATCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
39 32 0.20
40 112 0.71
41 8 0.05
42 5 0.03
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:2845 original size:79 final size:80
Alignment explanation
Indices: 2741--2892 Score: 225
Period size: 79 Copynumber: 1.9 Consensus size: 80
2731 ACATAACACC
* ** *
2741 AGCACGAATGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAATGCTCTTC-GAACTTAG
1 AGCACGAATGCTCCTCGGGACTTAGCACGGATACATCACTAGCACGAATGCTCTTCGGAACTTAG
2805 CCCGGATACATCACT
66 CCCGGATACATCACT
* * * *
2820 AGCATGAATGCTCCTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAG
1 AGCACGAATGCTCCTCGGGACTTAGCACGGATACATCACTAGCACGAATGCTCTTCGGAACTTAG
2885 CCCGGATA
66 CCCGGATA
2893 TGGTCACTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 49 0.77
80 15 0.23
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (80 bp):
AGCACGAATGCTCCTCGGGACTTAGCACGGATACATCACTAGCACGAATGCTCTTCGGAACTTAG
CCCGGATACATCACT
Found at i:2916 original size:119 final size:120
Alignment explanation
Indices: 2696--2930 Score: 278
Period size: 119 Copynumber: 2.0 Consensus size: 120
2686 CGAATACACG
* * * * *
2696 TCACCAGCATGATTGCTCTTCGGGACCTAGCCTAGACATAACACCAGCACGAATGCTCTTCGGGG
1 TCACCAGCATGAATGCTCCTCGGGACCTAGCCCAGACACAACACCAGCACGAATGCTCTTCGGGA
* *
2761 TTTAGCACGGATATATCACTAGCACGAATGCTCTTC-GAACTTAGCCCGGATACA
66 CTTAGCACGGATATATCACTAGCACGAAAGCTCTTCGGAACTTAGCCCGGATACA
* * * * * * *
2815 TCACTAGCATGAATGCTCCTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGA
1 TCACCAGCATGAATGCTCCTCGGGACCTAGCCCAGACACAACACCAGCACGAATGCTCTTCGGGA
* * *
2880 CTTAGCCCGGATATGGTCACTTAGCAC-AAAGC-CTTCGGGACTTAGCCCGGA
66 CTTAGCACGGATAT-ATCAC-TAGCACGAAAGCTCTTCGGAACTTAGCCCGGA
2931 CATCATTCAA
Statistics
Matches: 96, Mismatches: 17, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
119 69 0.72
120 21 0.22
121 6 0.06
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (120 bp):
TCACCAGCATGAATGCTCCTCGGGACCTAGCCCAGACACAACACCAGCACGAATGCTCTTCGGGA
CTTAGCACGGATATATCACTAGCACGAAAGCTCTTCGGAACTTAGCCCGGATACA
Found at i:2927 original size:80 final size:79
Alignment explanation
Indices: 2750--2930 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 79
2740 CAGCACGAAT
** * *
2750 GCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAATGCTCTTCGAACTTAGCCCGGATACA
1 GCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAACTTAGCCCGGATACA
* *
2815 TCACTAGCATGAAT
66 TCACTAGCATCAAA
* * *
2829 GCTCCTCGGGACTTAGCCCGGATACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATAT
1 GCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTC-GAACTTAGCCCGGATA-
**
2894 GGTCACTTAGCA-CAAA
64 CATCAC-TAGCATCAAA
2910 GC-CTTCGGGACTTAGCCCGGA
1 GCTCTTCGGGACTTAGCCCGGA
2931 CATCATTCAA
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
79 41 0.47
80 33 0.38
81 8 0.09
82 5 0.06
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (79 bp):
GCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGAACTTAGCCCGGATACA
TCACTAGCATCAAA
Found at i:3272 original size:29 final size:29
Alignment explanation
Indices: 3233--3311 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
3223 CTTAATAATC
*
3233 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
3263 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
3292 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
3312 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:3354 original size:43 final size:43
Alignment explanation
Indices: 3293--3395 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
3283 TGCATTTCAA
*
3293 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGCGAACACTTATT
3336 GCCCGCACACTTAGTGCCAATCTCACAACCGCGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGCGAACACTTATT
3379 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
3396 TGAAAACCAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.26, C:0.37, G:0.16, T:0.21
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGCGAACACTTATT
Found at i:5310 original size:36 final size:37
Alignment explanation
Indices: 5238--5315 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 37
5228 TTATTACGAA
* *
5238 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
*
5275 GTCTTACCCGGACAAAATC-CCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
5311 GTCTT
1 GTCTT
5316 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
36 20 0.53
37 18 0.47
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
Found at i:5520 original size:47 final size:47
Alignment explanation
Indices: 5433--5974 Score: 757
Period size: 47 Copynumber: 11.4 Consensus size: 47
5423 CCTTTCGGGA
* * * * * * * *
5433 CTTATCACATTTATGCACTTTCACATCCATTACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5480 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5527 CTTATCACATATATACACTTTCACATTCATCGCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5574 CTTATCACATATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
5621 CTTATCACACATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5668 CTTATCACATATATACACTTTCACATTCATCACGTCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5715 CTTATCACACATATACACTTTCACATTCATCAC-TCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5761 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
5808 CTTATTACATATATACTACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTA-T-CACATATA-TACACTTTCACATTCATCACATCGGCCATTAGGC
5858 CTTATCACATATATACATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
5909 CTTATCACATATACATACACTTTCACATTCAT--CATCGGCCATTAGGC
1 CTTATCACATAT--ATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
5956 CTTATTACATACATACACT
1 CTTATCACATATATACACT
5975 CTTTGGCTGA
Statistics
Matches: 462, Mismatches: 25, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
45 7 0.02
46 46 0.10
47 291 0.63
48 3 0.01
49 31 0.07
50 41 0.09
51 42 0.09
52 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:10115 original size:40 final size:40
Alignment explanation
Indices: 10060--10197 Score: 224
Period size: 40 Copynumber: 3.5 Consensus size: 40
10050 CGGATGATAA
* *
10060 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
10100 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
10140 CCGGGCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
10180 CC-GGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
10198 TACTTGGGTT
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 14 0.15
40 78 0.85
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:18207 original size:40 final size:40
Alignment explanation
Indices: 18154--18329 Score: 259
Period size: 40 Copynumber: 4.4 Consensus size: 40
18144 GATGATAACT
* * *
18154 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
18194 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
18234 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* * *
18274 GGGCTAGGTCCCGAAGGCATTTGTGAGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
18314 -GGCTATA-TCCCGAAGG
1 GGGCTA-AGTCCCGAAGG
18330 TACTTGGGTT
Statistics
Matches: 127, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
39 14 0.11
40 112 0.88
41 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:27391 original size:47 final size:47
Alignment explanation
Indices: 27169--27428 Score: 209
Period size: 47 Copynumber: 5.6 Consensus size: 47
27159 AGTGTGAGCT
* * ** *
27169 AGTGTAAGA-CATGTCTGGGACATGCATCGGC-C-ACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCAGCTCGAGACGAT-A-AGTC
* * * * *
27215 AGTGTAAGACTATGTCTGGGAAATGCATCGGCATTGAGACGA-GAG-C
1 AGTGTAAGACCATGTCTGGGACATGCATCAGC-TCGAGACGATAAGTC
27261 TAGTGTAAGA-CATGTCTGGGACATGCA-CAGCTCGAGACG-TAAGTC
1 -AGTGTAAGACCATGTCTGGGACATGCATCAGCTCGAGACGATAAGTC
* *
27306 AGTGTAAGA-CATGTCTGGGACATGCATCTGCTACGAGATGAT-AGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCAGCT-CGAGACGATAAGTC
* * * * * *
27352 AGTGTAAGACCATATCTGGTACATGGCATCAGCTTGAGA-TATGAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCAGCTCGAGACGATAAGTC
*
27399 AGTGTAAGACCATGTTTGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACAT-GCATC
27429 GACACCTTAC
Statistics
Matches: 178, Mismatches: 23, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
44 35 0.20
45 8 0.04
46 46 0.26
47 78 0.44
48 8 0.04
50 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGCATCAGCTCGAGACGATAAGTC
Found at i:29827 original size:43 final size:43
Alignment explanation
Indices: 29779--29931 Score: 251
Period size: 43 Copynumber: 3.6 Consensus size: 43
29769 TATTCGGATG
*
29779 ATATCCGGGCTAAGTCGCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
29822 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
*
29865 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGC---TAG-TGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTG-CT
29905 ATATCCGGGCTAAGTCCCGAAGGCATT
1 ATATCCGGGCTAAGTCCCGAAGGCATT
29932 CATGCTAGCG
Statistics
Matches: 106, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
39 2 0.02
40 31 0.29
43 73 0.69
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.26
Consensus pattern (43 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
Found at i:31372 original size:40 final size:40
Alignment explanation
Indices: 31302--31479 Score: 270
Period size: 40 Copynumber: 4.5 Consensus size: 40
31292 AACCCAAGTA
* *
31302 CCTTCGGGATTTAG-CCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
31341 CCTTCGGTACCTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
31381 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
31421 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
31461 CCTTCGGGACTGAGCCCGG
1 CCTTCGGGACTTAGCCCGG
31480 TTATCATCCG
Statistics
Matches: 128, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
39 12 0.09
40 116 0.91
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:35876 original size:40 final size:40
Alignment explanation
Indices: 35832--36020 Score: 360
Period size: 40 Copynumber: 4.7 Consensus size: 40
35822 GCTACTAGCT
35832 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
35872 CAAATGCCTTCGGGACTTAGGCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
35912 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
35952 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
35992 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
36021 CAATCCGAAT
Statistics
Matches: 145, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 145 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:35945 original size:80 final size:80
Alignment explanation
Indices: 35809--36020 Score: 365
Period size: 80 Copynumber: 2.7 Consensus size: 80
35799 CCTTCGGAGT
* *
35809 TTAG-CCGGATATAGCT-ACTAGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
35872 CAAATGCCTTCGGGAC
65 CAAATGCCTTCGGGAC
* *
35888 TTAGGCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
35953 AAATGCCTTCGGGAC
66 AAATGCCTTCGGGAC
35968 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
36021 CAATCCGAAT
Statistics
Matches: 126, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
79 5 0.04
80 121 0.96
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (80 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
AAATGCCTTCGGGAC
Found at i:39373 original size:40 final size:40
Alignment explanation
Indices: 39325--39487 Score: 231
Period size: 40 Copynumber: 4.1 Consensus size: 40
39315 GGGATTTAAA
* *
39325 CGGATATAGCT-ACTCGCTCGAATGCCTTCGGGACATAGCC
1 CGGATATAG-TAACTCGCACGAATGCCTTCGGGACTTAGCC
39365 CGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGCC
1 CGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGCC
39405 CGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGCC
1 CGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGCC
* * * * *
39445 CGGGA-CTAGTCACTAGCGCAAATGCCTTCGGGACTTAGCC
1 C-GGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGCC
39485 CGG
1 CGG
39488 TTATCATCCA
Statistics
Matches: 114, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
39 3 0.03
40 108 0.95
41 3 0.03
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.21
Consensus pattern (40 bp):
CGGATATAGTAACTCGCACGAATGCCTTCGGGACTTAGCC
Found at i:39561 original size:13 final size:13
Alignment explanation
Indices: 39541--39575 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
39531 ATTTATATTC
39541 CATTTAAATACAT
1 CATTTAAATACAT
39554 -AGTTTAAATACAT
1 CA-TTTAAATACAT
39567 CATTTAAAT
1 CATTTAAAT
39576 TGTCAAAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.05
13 18 0.90
14 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (13 bp):
CATTTAAATACAT
Found at i:46558 original size:38 final size:40
Alignment explanation
Indices: 46449--46659 Score: 305
Period size: 38 Copynumber: 5.5 Consensus size: 40
46439 AAACCAAGTA
* * *
46449 CCTTC-GGATTTAG-CCGGATATAGCT-ACTAGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
46487 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
46527 CCTTCGGGACTTAG-CCGG-TATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
46565 CCTTCGGGACTTAGCCCGG-T-TAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
46603 CCTTC-GGACTTAGCCCGGATATAGT-ACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
46641 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
46660 TTATCATCCG
Statistics
Matches: 160, Mismatches: 6, Indels: 13
0.89 0.03 0.07
Matches are distributed among these distances:
37 13 0.08
38 79 0.49
39 34 0.21
40 34 0.21
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Done.