Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2536
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: 75259
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Found at i:15626 original size:39 final size:39
Alignment explanation
Indices: 15422--15644 Score: 232
Period size: 40 Copynumber: 5.6 Consensus size: 39
15412 TTGAATGCTG
* * * * * *
15422 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * *
15462 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
*
15502 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* **
15542 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAA
* *
15582 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
15621 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
15645 TGAACGAGGA
Statistics
Matches: 158, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
39 39 0.25
40 109 0.69
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:15664 original size:79 final size:80
Alignment explanation
Indices: 15497--15679 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
15487 GTGCGAGATA
* * *
15497 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
15562 CAGTCGTGCGAGTTG
66 CAGTCGAACGAGGAG
* * * *
15577 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
* *
15641 CATTTGAACGAGGAG
66 CAGTCGAACGAGGAG
* *
15656 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
15680 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CAGTCGAACGAGGAG
Found at i:19428 original size:23 final size:24
Alignment explanation
Indices: 19384--19428 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
19374 ATATGCTCAA
* *
19384 AGAATATTATGTACATATATATCT
1 AGAATATTATGCACATAAATATCT
*
19408 AGAA-ATTATGCACTTAAATAT
1 AGAATATTATGCACATAAATAT
19429 ATATATGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (24 bp):
AGAATATTATGCACATAAATATCT
Found at i:25117 original size:37 final size:37
Alignment explanation
Indices: 25071--25198 Score: 220
Period size: 37 Copynumber: 3.5 Consensus size: 37
25061 ACATAAAGTT
* *
25071 ATCGGGTCTTACCCGGACAAAATCTCCACGCGTAGTC
1 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
*
25108 ATCGAGTCTTACCCGGACATAATCTCCACACGTAGTC
1 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
*
25145 ATCGGGTCTTACCCAGACATAATCTCCACACGTAGTC
1 ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
25182 ATCGGGTCTTACCCGGA
1 ATCGGGTCTTACCCGGA
25199 ATATATTTCC
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 85 1.00
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (37 bp):
ATCGGGTCTTACCCGGACATAATCTCCACACGTAGTC
Found at i:25469 original size:47 final size:47
Alignment explanation
Indices: 25405--25936 Score: 758
Period size: 47 Copynumber: 11.1 Consensus size: 47
25395 ACACGTTTCG
* * * * **
25405 CATTAGCCATTCAGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * *
25452 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
25499 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
25546 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* ** *
25593 CATTGGCCATTCGGCCTTATCACGCATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C--ACATACGCATGTTCACATTCATCA
25644 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
***
25691 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCA
*
25742 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
25789 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
***
25836 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCA
* *
25887 CATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
25934 CAT
1 CAT
25937 AAAATCCTAA
Statistics
Matches: 441, Mismatches: 32, Indels: 24
0.89 0.06 0.05
Matches are distributed among these distances:
47 310 0.70
49 2 0.00
51 129 0.29
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:25674 original size:145 final size:143
Alignment explanation
Indices: 25405--25936 Score: 777
Period size: 145 Copynumber: 3.7 Consensus size: 143
25395 ACACGTTTCG
* * * * *
25405 CATTAGCCATTCAGCCTTACCACATATATTCAT-GTTCACATTCATCACATTGGCCATTCGGCCT
1 CATTGGCCATTCGGCCTTATCACACATATACATGGTTCACATTCATCACATTGGCCATTCGGCCT
*
25469 TATC-TCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATG
66 TATCACCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATG
25533 TTCACATTCATCA
131 TTCACATTCATCA
**
25546 CATTGGCCATTCGGCCTTATCACACATACGCAT-GTTCACATTCATCACATTGGCCATTCGGCCT
1 CATTGGCCATTCGGCCTTATCACACATATACATGGTTCACATTCATCACATTGGCCATTCGGCCT
* *
25610 TATCACGCATATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGC
66 TATCAC-C--ATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGC
25675 ATGTTCACATTCATCA
128 ATGTTCACATTCATCA
*
25691 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATATACAT---GGTTCACATTCATCACATTGGCCATTCGG
* * *
25756 CCTTATCA-CACATACGCATGTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATACGC
63 CCTTATCACCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGC
25820 ATGTTCACATTCATCA
128 ATGTTCACATTCATCA
* *
25836 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCAG
1 CATTGGCCATTCGGCCTTATCACACATATACAT---GGTTCACATTCATCACATTGGCCATTCGG
* * *
25901 CCTTATCA-CACATACGCATGTTCACATCCATCACAT
63 CCTTATCACCATATATGCATGTTCACATTCATCACAT
25937 AAAATCCTAA
Statistics
Matches: 365, Mismatches: 18, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
141 62 0.17
143 1 0.00
145 265 0.73
147 1 0.00
149 36 0.10
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (143 bp):
CATTGGCCATTCGGCCTTATCACACATATACATGGTTCACATTCATCACATTGGCCATTCGGCCT
TATCACCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATG
TTCACATTCATCA
Found at i:25916 original size:98 final size:94
Alignment explanation
Indices: 25405--25936 Score: 758
Period size: 98 Copynumber: 5.5 Consensus size: 94
25395 ACACGTTTCG
* * * * **
25405 CATTAGCCATTCAGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * *
25470 ATCTCATATATGCATGTTCACATTCATCA
66 ATCACACATACGCATGTTCACATTCATCA
25499 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
25564 ATCACACATACGCATGTTCACATTCATCA
66 ATCACACATACGCATGTTCACATTCATCA
* ** *
25593 CATTGGCCATTCGGCCTTATCACGCATATATATACAGGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCA--C--ACATACGCATGTTCACATTCATCACATTGGCCATTCGG
25658 CCTTATCACACATACGCATGTTCACATTCATCA
62 CCTTATCACACATACGCATGTTCACATTCATCA
***
25691 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCACATTGGCCATTCGG
*
25756 CCTTATCACACATACGCATGTTCACATCCATCA
62 CCTTATCACACATACGCATGTTCACATTCATCA
25789 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
***
25854 ATCACACATATATATACGGGTTCACATTCATCA
66 ATCACACATACGCAT----GTTCACATTCATCA
* *
25887 CATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATCCATCACAT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACAT
25937 AAAATCCTAA
Statistics
Matches: 400, Mismatches: 26, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
94 158 0.40
96 2 0.00
98 240 0.60
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (94 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCACACATACGCATGTTCACATTCATCA
Found at i:29859 original size:40 final size:40
Alignment explanation
Indices: 29841--30216 Score: 585
Period size: 40 Copynumber: 9.4 Consensus size: 40
29831 CTTCAGGAAC
* * * **
29841 TAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGGTT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
* * *
29881 TAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
* *
29921 TAGCCCGGATACATCACTAGCACGAATGCTCCTCAGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
* *
29961 TAGCCCGGATATATCACTAGCACGAATGTTCCTCGGGATT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
30001 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
*
30041 TAGCCCAGATATATCACTAGCACGAATGCTCCTCGGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
30081 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
* *
30121 TAGCTCGGATATATCACTAGCACGAATGCTCTTCGGGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
* *
30161 TAGCTCGGATATATCACTAGCACGAATGCTCTTC-GGACT
1 TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
30200 TAG-CCGGATATATCACT
1 TAGCCCGGATATATCACT
30217 CTCAATTCTC
Statistics
Matches: 314, Mismatches: 22, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
38 13 0.04
39 8 0.03
40 293 0.93
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
TAGCCCGGATATATCACTAGCACGAATGCTCCTCGGGACT
Found at i:33480 original size:48 final size:47
Alignment explanation
Indices: 33428--33565 Score: 155
Period size: 48 Copynumber: 3.0 Consensus size: 47
33418 TCGTATCTTG
*
33428 GGCCATCCGGCCTTATCACACATATGCATGCTCACATTCATCACATTT
1 GGCCATTCGGCCTTAT-ACACATATGCATGCTCACATTCATCACATTT
33476 GGCCATTCGGCCTTATA-ACCAATATGCATGCTCACAATTC-TCACA-TT
1 GGCCATTCGGCCTTATACA-C-ATATGCATGCTCAC-ATTCATCACATTT
*
33523 GGCCATTCGG-CTTAT--ACATAT-TATGCTTCACATTACATCACAT
1 GGCCATTCGGCCTTATACACATATGCATGC-TCACATT-CATCACAT
33566 AAATCAAATC
Statistics
Matches: 81, Mismatches: 2, Indels: 17
0.81 0.02 0.17
Matches are distributed among these distances:
42 7 0.09
43 9 0.11
44 6 0.07
45 1 0.01
46 6 0.07
47 14 0.17
48 34 0.42
49 4 0.05
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (47 bp):
GGCCATTCGGCCTTATACACATATGCATGCTCACATTCATCACATTT
Found at i:38608 original size:39 final size:39
Alignment explanation
Indices: 38526--38908 Score: 263
Period size: 39 Copynumber: 9.9 Consensus size: 39
38516 CCAGCATGAT
* *
38526 TGCTCTTCAGGAAC-TAGCCGGATATAACAC-AGCACGAA
1 TGCTCTTC-GGGACTTAGCCGGATATATCACTAGCACGAA
**
38564 TGCTCTTCGGGGTTTAGCAC-GATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGC-CGGATATATCACTAGCACGAA
* *
38603 TGCTCTT--GAACTTAG-CGGATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCGGATATATCACTAGCACGAA
* *
38639 TGCTCCTCAGGACTTAGCCGGATATATCACTAGCACG-A
1 TGCTCTTCGGGACTTAGCCGGATATATCACTAGCACGAA
* *
38677 TGTTC-TC-GGA-TTACCCGG--ATATCAC-ACGCTACGAA
1 TGCTCTTCGGGACTTAGCCGGATATATCACTA-GC-ACGAA
* *
38712 TGCTCTTCGGGATTGCTAGCCAGATA-ATC-CTAGCACGAA
1 TGCTCTTCGGGACT--TAGCCGGATATATCACTAGCACGAA
*
38751 TGCT-TTCGGGACTTAGCCGGTATACATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCGG-ATATATCACTAGCACGAA
* *
38790 TGCT-TGCTCGAGACTTACCACGGATACTATCACTAAGC-CGAA
1 TGCTCT--TCGGGACTTAGC-CGGATA-TATCACT-AGCACGAA
*
38832 TGC-CTTTC-GGACTTAGCCGG-TAAGATCACTCA-CACCGGAA
1 TGCTC-TTCGGGACTTAGCCGGAT-ATATCACT-AGCA-C-GAA
*
38872 TGCTC-TCGGGACTTTAGCACCCGGATACATCACTAGC
1 TGCTCTTCGGGAC-TTAG---CCGGATATATCACTAGC
38909 TCGATGGCTA
Statistics
Matches: 279, Mismatches: 26, Indels: 74
0.74 0.07 0.20
Matches are distributed among these distances:
32 1 0.00
33 9 0.03
34 3 0.01
35 13 0.05
36 35 0.13
37 16 0.06
38 53 0.19
39 65 0.23
40 25 0.09
41 24 0.09
42 17 0.06
43 5 0.02
44 12 0.04
45 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
TGCTCTTCGGGACTTAGCCGGATATATCACTAGCACGAA
Found at i:38656 original size:75 final size:75
Alignment explanation
Indices: 38556--38908 Score: 239
Period size: 75 Copynumber: 4.6 Consensus size: 75
38546 GATATAACAC
* ** *
38556 AGCACGAATGCTCTTCGGGGTTTAGCAC-GATATATCACTAGCACGAATGCTCTTGAACTTAGCG
1 AGCACGAATGCTCCTCGGGACTTAGC-CGGATATATCACTAGCACGAATGCTCTTGGACTTAGCG
38620 GATACATCACT
65 GATACATCACT
* * * *
38631 AGCACGAATGCTCCTCAGGACTTAGCCGGATATATCACTAGCACG-ATGTTCTCGGA-TTACCCG
1 AGCACGAATGCTCCTCGGGACTTAGCCGGATATATCACTAGCACGAATGCTCTTGGACTTA-GCG
38694 GAT--ATCAC-
65 GATACATCACT
* * *
38702 ACGCTACGAATGCTCTTCGGGATTGCTAGCCAGATA-ATC-CTAGCACGAATGCT-TTCGGGACT
1 A-GC-ACGAATGCTCCTCGGGACT--TAGCCGGATATATCACTAGCACGAATGCTCTT--GGACT
38764 TAGCCGGTATACATCACT
60 TAG-CGG-ATACATCACT
* * *
38782 AGCACGAATGCTTGCTCGAGACTTACCACGGATACTATCACTAAGC-CGAATGC-CTTTCGGACT
1 AGCACGAATGC-TCCTCGGGACTTAGC-CGGATA-TATCACT-AGCACGAATGCTC-TT-GGACT
*
38845 TAGCCGG-TAAGATCACT
60 TAG-CGGAT-ACATCACT
*
38862 CA-CACCGGAATGCT-CTCGGGACTTTAGCACCCGGATACATCACTAGC
1 -AGCA-C-GAATGCTCCTCGGGAC-TTAG---CCGGATATATCACTAGC
38909 TCGATGGCTA
Statistics
Matches: 221, Mismatches: 26, Indels: 56
0.73 0.09 0.18
Matches are distributed among these distances:
71 1 0.00
72 7 0.03
73 28 0.13
74 21 0.10
75 51 0.23
76 6 0.03
77 5 0.02
78 13 0.06
79 15 0.07
80 20 0.09
81 30 0.14
82 17 0.08
83 6 0.03
84 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (75 bp):
AGCACGAATGCTCCTCGGGACTTAGCCGGATATATCACTAGCACGAATGCTCTTGGACTTAGCGG
ATACATCACT
Found at i:49857 original size:29 final size:29
Alignment explanation
Indices: 49823--49896 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
49813 TAATCAACCG
*
49823 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
49852 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
49881 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
49897 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:54146 original size:39 final size:40
Alignment explanation
Indices: 54101--54268 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
54091 CGGGGTTTAG
* * *
54101 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
54140 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
54180 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
54220 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
54261 CCGGATAT
1 CCGGATAT
54269 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:54251 original size:41 final size:40
Alignment explanation
Indices: 54124--54268 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
54114 CTCGCACAAG
* * * * *
54124 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
54164 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
54204 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
54245 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
54269 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:62129 original size:39 final size:40
Alignment explanation
Indices: 62084--62250 Score: 97
Period size: 40 Copynumber: 4.2 Consensus size: 40
62074 CGGGGTTTAG
* * *
62084 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
62123 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
62163 CCGGATATAGTCGCTAGCACAAATGCCTT--GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
62202 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
62243 CCGGATAT
1 CCGGATAT
62251 CATTCGAGTA
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
38 3 0.03
39 33 0.31
40 56 0.52
41 12 0.11
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:62154 original size:40 final size:40
Alignment explanation
Indices: 62107--62250 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
62097 CTCGCACAAG
* * * * *
62107 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
62147 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
62187 GCCTT--GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
62227 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
62251 CATTCGAGTA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
38 3 0.03
39 18 0.20
40 54 0.60
41 12 0.13
42 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:64750 original size:28 final size:27
Alignment explanation
Indices: 64693--64844 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
64683 TAAATTGTGC
*
64693 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
64720 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
64748 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
64775 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* * *
64803 AGCACTAAGTGTGCAAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
64830 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
64845 GACTTAATAT
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
27 65 0.56
28 52 0.44
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:64757 original size:55 final size:55
Alignment explanation
Indices: 64693--64844 Score: 243
Period size: 55 Copynumber: 2.8 Consensus size: 55
64683 TAAATTGTGC
64693 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* *
64748 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
64803 AGCACTAAGTGTGC-AAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAA-TTGACTATGTAGCACTAAGTGTGCG
64845 GACTTAATAT
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
54 1 0.01
55 89 0.99
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:68653 original size:37 final size:37
Alignment explanation
Indices: 68594--68775 Score: 321
Period size: 37 Copynumber: 4.9 Consensus size: 37
68584 AGCTCAGACG
* *
68594 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
68631 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
68668 TAATCTCCACACGTAGTCATCGGGTCTTA-CCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
68704 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACG
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
68741 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
68776 ATATATTTCC
Statistics
Matches: 139, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
36 35 0.25
37 104 0.75
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:68721 original size:73 final size:73
Alignment explanation
Indices: 68590--68771 Score: 321
Period size: 73 Copynumber: 2.5 Consensus size: 73
68580 CTTTAGCTCA
* *
68590 GACGAAATCTCCACACGAAGTTATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGG
1 GACGAAATCTCCACACGTAGTCATCGGGTCTTA-CCGGACAAAATCTCCACACGTAGTCATCGGG
68655 TCTTACCCG
65 TCTTACCCG
68664 GAC-ATAATCTCCACACGTAGTCATCGGGTCTTACCGGACAAAATCTCCACACGTAGTCATCGGG
1 GACGA-AATCTCCACACGTAGTCATCGGGTCTTACCGGACAAAATCTCCACACGTAGTCATCGGG
68728 TCTTACCCG
65 TCTTACCCG
68737 GACGAAATCTCCACACGTAGTCATCGGGTCTTACC
1 GACGAAATCTCCACACGTAGTCATCGGGTCTTACC
68772 CGGAATATAT
Statistics
Matches: 104, Mismatches: 2, Indels: 5
0.94 0.02 0.05
Matches are distributed among these distances:
73 74 0.71
74 30 0.29
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (73 bp):
GACGAAATCTCCACACGTAGTCATCGGGTCTTACCGGACAAAATCTCCACACGTAGTCATCGGGT
CTTACCCG
Found at i:68977 original size:48 final size:48
Alignment explanation
Indices: 68922--69056 Score: 216
Period size: 48 Copynumber: 2.8 Consensus size: 48
68912 GCACATCGCC
68922 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATACCTCA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATACCTCA
* * *
68970 TACATATTTCGCACTAGCCATTCGGCTTTACCACATATACATATCTCG
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATACCTCA
* * *
69018 TACATATTTCACATTAGCCATTCGGCCTTATCACATATA
1 TACATATTTCACACTAGCCATTCGGCTTTACCACATATA
69057 TGCATGTTCA
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 80 1.00
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (48 bp):
TACATATTTCACACTAGCCATTCGGCTTTACCACATATACATACCTCA
Found at i:69091 original size:47 final size:47
Alignment explanation
Indices: 69026--69219 Score: 325
Period size: 47 Copynumber: 4.1 Consensus size: 47
69016 CGTACATATT
* * * *
69026 TCACATTAGCCATTCGGCCTTATCACATATATGCATGTTCATATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
*
69073 TCATATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
69120 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
* *
69167 TCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCA
1 TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
69214 TCACAT
1 TCACAT
69220 AAAATCCTAA
Statistics
Matches: 139, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 139 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (47 bp):
TCACATTGGCCATTCGGCCTTATCACACATATGCATGCTCACATTCA
Found at i:69123 original size:25 final size:25
Alignment explanation
Indices: 69094--69171 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 25
69084 ATTCGGCCTT
69094 ATCACACATATGCATGCTCACATTC
1 ATCACACATATGCATGCTCACATTC
* *
69119 AT--CACAT-TGGCCAT--TCGGCCTT-
1 ATCACACATAT-G-CATGCTC-ACATTC
69141 ATCACACATATGCATGCTCACATTC
1 ATCACACATATGCATGCTCACATTC
69166 ATCACA
1 ATCACA
69172 TTGGCCATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 5 0.12
23 12 0.30
24 12 0.30
25 11 0.28
ACGTcount: A:0.29, C:0.32, G:0.10, T:0.28
Consensus pattern (25 bp):
ATCACACATATGCATGCTCACATTC
Found at i:69146 original size:22 final size:22
Alignment explanation
Indices: 69119--69194 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
69109 GCTCACATTC
69119 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* *
69141 ATCACACATAT-G-CATGCTC-ACATT
1 AT--CACAT-TGGCCAT--TCGGCCTT
69165 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
69188 ATCACAT
1 ATCACAT
69195 ATATGCATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 12 0.29
23 12 0.29
24 12 0.29
25 5 0.12
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Done.