Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1854
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: 95222
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:561 original size:19 final size:19
Alignment explanation
Indices: 517--572 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
507 CTGCCAGTTT
**
517 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
*
537 CATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
*
556 CATGTATCGATATAATG
1 CATGTATCGATACAATG
573 TATCGATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:9078 original size:13 final size:13
Alignment explanation
Indices: 9060--9089 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
9050 ACAATTCTTC
9060 ATGTATCGATACA
1 ATGTATCGATACA
9073 ATGTATCGATACA
1 ATGTATCGATACA
9086 ATGT
1 ATGT
9090 GCCATGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:9174 original size:13 final size:12
Alignment explanation
Indices: 9155--9210 Score: 50
Period size: 13 Copynumber: 4.9 Consensus size: 12
9145 TACAATTGTG
9155 CATGTATCGATA
1 CATGTATCGATA
*
9167 CAATGTATTGATA
1 C-ATGTATCGATA
9180 CA---AT-GA-A
1 CATGTATCGATA
9187 CATGTATCGATA
1 CATGTATCGATA
9199 CAATGTATCGAT
1 C-ATGTATCGAT
9211 CCAAAGCATA
Statistics
Matches: 36, Mismatches: 1, Indels: 13
0.72 0.02 0.26
Matches are distributed among these distances:
7 3 0.08
8 2 0.06
9 2 0.06
10 2 0.06
11 2 0.06
12 4 0.11
13 21 0.58
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (12 bp):
CATGTATCGATA
Found at i:10239 original size:20 final size:21
Alignment explanation
Indices: 10191--10248 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
10181 TACATTACTA
*
10191 TGCA-TGTATCAATACATACT
1 TGCATTGTATCAATACATACG
* *
10211 TGAATTGTATCGATACATA-G
1 TGCATTGTATCAATACATACG
*
10231 TGCATTGTATCTATACAT
1 TGCATTGTATCAATACAT
10249 TGAGCCCAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (21 bp):
TGCATTGTATCAATACATACG
Found at i:18748 original size:20 final size:20
Alignment explanation
Indices: 18723--18760 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
18713 ACAAGAATTG
*
18723 AAAAACATCCTTTCTATCCA
1 AAAAACATCCTTCCTATCCA
18743 AAAAACATCCTTCCTATC
1 AAAAACATCCTTCCTATC
18761 TTCGAGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAACATCCTTCCTATCCA
Found at i:20916 original size:166 final size:167
Alignment explanation
Indices: 20627--20958 Score: 386
Period size: 166 Copynumber: 2.0 Consensus size: 167
20617 TGGAATTCCC
*
20627 TCTTTTTTCGAAATACAAAGTTTTCTTCTCCGTAAATTTTTTTAGGAGGATTTTCATAAGTTTAT
1 TCTTTTTTCGAAATACAAAGTTTTCTACTCCGTAAATTTTTTTAGGAGGATTTTCATAAGTTTAT
* * *
20692 AAATTTTAAAATTCATCAAATATTATTAGTTAACTTACAATAAATCAATTTCAAAAAATTCCTT-
66 AAATTTTAAAATTCATCAAATATCATCAGTTAACTTACAATAAATCAATTTCAAAAAATTCATTA
* *
20756 TTATTTCATTAATTTTTC-TTTTTTT-CTTGAAATTTA
131 AT-TTTCATTAATTTTTCATTTTTTTCCTTAAAATTTA
*** * * * *
20792 TCTTATTTTCGAAATACGGGGTTTTCTACTCTGT-AATTATTTTTGGGGGGATTTTTC-TTAGTT
1 TCTT-TTTTCGAAATACAAAGTTTTCTACTCCGTAAATT-TTTTTAGGAGGA-TTTTCATAAGTT
* * * *** * * *
20855 TATAATTTTTAAAATTCATCAAATATCATCATTTAATTTATGGTAAATTAGTTTTAAAAAATTCA
63 TATAAATTTTAAAATTCATCAAATATCATCAGTTAACTTACAATAAATCAATTTCAAAAAATTCA
*
20920 TTAATTTTCATTAGTTTTTCATTTTTTTCCTTAAAATTT
128 TTAATTTTCATTAATTTTTCATTTTTTTCCTTAAAATTT
20959 CCCTATTCTT
Statistics
Matches: 138, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
165 8 0.06
166 108 0.78
167 13 0.09
168 9 0.07
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (167 bp):
TCTTTTTTCGAAATACAAAGTTTTCTACTCCGTAAATTTTTTTAGGAGGATTTTCATAAGTTTAT
AAATTTTAAAATTCATCAAATATCATCAGTTAACTTACAATAAATCAATTTCAAAAAATTCATTA
ATTTTCATTAATTTTTCATTTTTTTCCTTAAAATTTA
Found at i:21610 original size:13 final size:13
Alignment explanation
Indices: 21588--21620 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
21578 AGCTTGGGAG
21588 AAAAAA-AGAGAA
1 AAAAAAGAGAGAA
*
21600 AGAAAAGAGAGAA
1 AAAAAAGAGAGAA
21613 AAAAAAGA
1 AAAAAAGA
21621 AAAATTAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAAGAGAGAA
Found at i:22839 original size:142 final size:142
Alignment explanation
Indices: 22516--23207 Score: 867
Period size: 142 Copynumber: 4.9 Consensus size: 142
22506 TACTTTATCC
* * * *
22516 AATAACAATTATCA-CTTCAATTTTTC-AGATTTTCTAATATTCTTATGGGTATCCGTGAGG-GT
1 AATAAAAATTATTATCTT-AATTTTTCAAGA-TTTCTAATATTCTTATGGTTTTCCGT-AGGAGT
* * * * * *
22578 ATAGAAATTTTCAAAACTTTTCAAATATTTTTGGTTCTCTATTAAAGTACGAAATGAATTTTATT
63 ATAGAAATCTTCAAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTACGAAATGAATTTT-TT
*
22643 CTGGAAATTAAAAATTA
127 -TGAAAATTAAAAATTA
* * *
22660 AAAAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCTTATGATTTTTCGTAGGAGTATA
1 AATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCTTATGGTTTTCCGTAGGAGTATA
* * ** * *
22725 AAAATCTTCAAAACTTTTCATATTTTTTCGGCCCTCCATTAAGGTACAAAATGAATTTTTTTTAA
66 GAAATCTTCAAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTACGAAATGAATTTTTTTGAA
22790 AATTAAAAATTA
131 AATTAAAAATTA
* * *
22802 AATAAAAATTATTATCTTAATTTTTCATGATTTCTAATATTCTTATGGTTTTCTGTAAGAGTATA
1 AATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCTTATGGTTTTCCGTAGGAGTATA
* * * * * * *
22867 AAAACCTTCAAAACTTTTCATATCTTTTCGGTTTTGCATTAAGGTACGAATTGAATCTTTTAG-A
66 GAAATCTTCAAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTACGAAATGAATTTTTTTGAA
22931 AATTAAAAATTA
131 AATTAAAAATTA
*
22943 AATAAAAACTATTATCTTAATTTTTTCAAGATTTCTAATATTCTTATGGTTTTCCGTAAGG-GTA
1 AATAAAAATTATTATCTTAA-TTTTTCAAGATTTCTAATATTCTTATGGTTTTCCGT-AGGAGTA
** * * * *
23007 TAGTGATCTTCAAAACTTTCCATATCTTTTGGGTTCTCTATTAAGGTACGAAAT-AA-ATTTTTG
64 TAGAAATCTTCAAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTACGAAATGAATTTTTTTG
*
23070 AAAATTAAAGATTA
129 AAAATTAAAAATTA
* *
23084 AATAAAAATTATTATCTTAATTTTCCAAGATTTCTAATATTCTTATGGTTTTCCATAGGAGTATA
1 AATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCTTATGGTTTTCCGTAGGAGTATA
* * * *
23149 GAAATCTTCAAAACTTTTCGTATCTTTTCAGTTCTCCATTAAGGTGCAAAATGAGATTT
66 GAAATCTTCAAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTACGAAATGA-ATTT
23208 CCGAAATTTA
Statistics
Matches: 472, Mismatches: 66, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
139 3 0.01
140 87 0.18
141 66 0.14
142 207 0.44
143 8 0.02
144 95 0.20
145 6 0.01
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (142 bp):
AATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCTTATGGTTTTCCGTAGGAGTATA
GAAATCTTCAAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTACGAAATGAATTTTTTTGAA
AATTAAAAATTA
Found at i:23132 original size:282 final size:285
Alignment explanation
Indices: 22516--23202 Score: 868
Period size: 282 Copynumber: 2.4 Consensus size: 285
22506 TACTTTATCC
* * * * * *
22516 AATAACAATTATCA-CTTCAATTTTTC-AGATTTTCTAATATTCTTATGGGTATCCGTGAGGGTA
1 AATAAAAATTATTATCTT-AATTTTTCAAGA-TTTCTAATATTCTTATGGTTTTCCGTAAGAGTA
* * * * * *
22579 TAGAAATTTTCAAAACTTTTCAAATATTTTTGGTTCTCTATTAAAGTACGAAATGAATTTTATTC
64 TAGAAATCTTCAAAACTTTTCATATCTTTTCGGTTCTC-ATTAAGGTACGAAATGAATTCTATTC
* *
22644 TGGAAATTAAAAATTAAAAAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCTTATGAT
128 TAGAAATTAAAAATTAAAAAAAAACTATTATCTTAATTTTTCAAGATTTCTAATATTCTTATGAT
* * *
22709 TTTTCGTAGGAGTATAAAAATCTTCAAAACTTTTCATATTTTTTCGGCCCTCCATTAAGGTACAA
193 TTTCCGTAGGAGTATAAAAATCTTCAAAACTTTCCATATCTTTTCGGCCCTCCATTAAGGTACAA
* *
22774 AATGAATTTTTTTTAAAATTAAAAATTA
258 AATGAATATTTTTGAAAATTAAAAATTA
* *
22802 AATAAAAATTATTATCTTAATTTTTCATGATTTCTAATATTCTTATGGTTTTCTGTAAGAGTATA
1 AATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCTTATGGTTTTCCGTAAGAGTATA
* * * *
22867 AAAACCTTCAAAACTTTTCATATCTTTTCGGTTTTGCATTAAGGTACGAATTGAA-TCT-TT-TA
66 GAAATCTTCAAAACTTTTCATATCTTTTCGGTTCT-CATTAAGGTACGAAATGAATTCTATTCTA
* *
22929 GAAATTAAAAATTAAATAAAAACTATTATCTTAATTTTTTCAAGATTTCTAATATTCTTATGGTT
130 GAAATTAAAAATTAAAAAAAAACTATTATCTTAA-TTTTTCAAGATTTCTAATATTCTTATGATT
*** * ** * *
22994 TTCCGTAAGG-GTATAGTGATCTTCAAAACTTTCCATATCTTTTGGGTTCTCTATTAAGGTACGA
194 TTCCGT-AGGAGTATAAAAATCTTCAAAACTTTCCATATCTTTTCGGCCCTCCATTAAGGTACAA
*
23058 AAT-AA-ATTTTTGAAAATTAAAGATTA
258 AATGAATATTTTTGAAAATTAAAAATTA
* * *
23084 AATAAAAATTATTATCTTAATTTTCCAAGATTTCTAATATTCTTATGGTTTTCCATAGGAGTATA
1 AATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCTTATGGTTTTCCGTAAGAGTATA
* * * *
23149 GAAATCTTCAAAACTTTTCGTATCTTTTCAGTTCTCCATTAAGGTGCAAAATGA
66 GAAATCTTCAAAACTTTTCATATCTTTTCGGTTCT-CATTAAGGTACGAAATGA
23203 GATTTCCGAA
Statistics
Matches: 346, Mismatches: 50, Indels: 14
0.84 0.12 0.03
Matches are distributed among these distances:
282 123 0.36
283 35 0.10
284 83 0.24
285 5 0.01
286 94 0.27
287 6 0.02
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (285 bp):
AATAAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCTTATGGTTTTCCGTAAGAGTATA
GAAATCTTCAAAACTTTTCATATCTTTTCGGTTCTCATTAAGGTACGAAATGAATTCTATTCTAG
AAATTAAAAATTAAAAAAAAACTATTATCTTAATTTTTCAAGATTTCTAATATTCTTATGATTTT
CCGTAGGAGTATAAAAATCTTCAAAACTTTCCATATCTTTTCGGCCCTCCATTAAGGTACAAAAT
GAATATTTTTGAAAATTAAAAATTA
Found at i:23647 original size:154 final size:149
Alignment explanation
Indices: 23341--23938 Score: 583
Period size: 154 Copynumber: 3.9 Consensus size: 149
23331 TTTTACATCA
* ** * * * * *
23341 AAGGTATCCCTAAGGGATATTTTTGTAATTTTTTAAAA-TCGAGTCCTTGGTTTTCATTGAGTAT
1 AAGGTATCCCT-AGGGGTATTTTCATAATTTTCTAAAACT-GAGTCCTAGGTTGTCACTG-GTCT
* * * * * *
23405 GCTTTTACGTTGAAGATGGGTGTTTAGGATAGGTTCATCGCATCTATAATCTTTTTTAAGTCTTT
63 GCTTTTA---TGAAAATAGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTT
*
23470 TAGGGGTATTGGGCACTTCTAAGTCG
125 TAGGGGTA-TAGGCACTTCTAAGTCG
* * *
23496 AAGGTATCCTCTAGGGGTATTTTTATAATTTTCTAAAATTGAATCCTAGGTTGTCACTGAGTCTG
1 AAGGTATCC-CTAGGGGTATTTTCATAATTTTCTAAAACTGAGTCCTAGGTTGTCACTG-GTCTG
* * * *
23561 CTTTTTACTGAAAATAGGTATTTAAGATAAGTTCATCCTATCTATAATCATTTTTAAGTCCTTTA
64 C-TTTTA-TGAAAATAGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTTA
* * *
23626 GGGGTATCAGACACTTTTAAGTCA
127 GGGGTAT-AGGCACTTCTAAGTCG
* * *
23650 AAGGTATCCCTTAAGGGTATTTTCATAATTTTCCAAAACTGAGTCTTAGGTT-TCACCTGGT-TC
1 AAGGTATCCC-TAGGGGTATTTTCATAATTTTCTAAAACTGAGTCCTAGGTTGTCA-CTGGTCT-
* * * *
23713 GCTTTTATGCCAAATGTGGGTATTTAGGACAGGTTCATCCCATCTATAATCCTTTTTAAGTCTTT
63 GCTTTTATG--AAA-ATAGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTT
*
23778 TAGGGGTATTGTGCACTTCTAAGTCG
125 TAGGGGTATAG-GCACTTCTAAGTCG
* * * * *
23804 AAGGTATCAAACTTTGGGGCATTTTCATAATTTT-TCAAGAACTGAGTCTTAGGTTGTCACCGGT
1 AAGGTATC---CCTAGGGGTATTTTCATAATTTTCT-AA-AACTGAGTCCTAGGTTGTCACTGGT
23868 CTGCTTTTATGATGAATATAGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCC
61 CTGCTTTTATGA--AA-ATAGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCC
23933 TTTAGG
123 TTTAGG
23939 ATCACCGGCC
Statistics
Matches: 373, Mismatches: 50, Indels: 38
0.81 0.11 0.08
Matches are distributed among these distances:
151 2 0.01
152 6 0.02
153 13 0.03
154 183 0.49
155 54 0.14
156 28 0.08
157 83 0.22
158 4 0.01
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.40
Consensus pattern (149 bp):
AAGGTATCCCTAGGGGTATTTTCATAATTTTCTAAAACTGAGTCCTAGGTTGTCACTGGTCTGCT
TTTATGAAAATAGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTTAGGGG
TATAGGCACTTCTAAGTCG
Found at i:23908 original size:157 final size:152
Alignment explanation
Indices: 23404--23938 Score: 612
Period size: 154 Copynumber: 3.5 Consensus size: 152
23394 TCATTGAGTA
* * * * * * * *
23404 TGCTTTTACGTTGAAGATGGGTGTTTAGGATAGGTTCATCGCATCTATAATCTTTTTTAAGTCTT
1 TGCTTTTATGATGAATATAGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCT
*
23469 TTAGGGGTATTGGGCACTTCTAAGTCGAAGGTATCCTCTAGGGGTATTTTTATAA-TTTTCTAAA
66 TTAGGGGTATT-GGCACTTCTAAGTCGAAGGTATCCT-TAGGGGTATTTTCATAATTTTTC-AAA
* * * *
23533 ATTGAATCCTAGGTTGTCACTGAGTC
128 ACTGAGTCTTAGGTTGTCACCG-GTC
* * * * *
23559 TGCTTTT-T-ACTGAAAATAGGTATTTAAGATAAGTTCATCCTATCTATAATCATTTTTAAGTCC
1 TGCTTTTATGA-TGAATATAGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCC
* * * * * *
23622 TTTAGGGGTATCAGACACTTTTAAGTCAAAGGTATCCCTTAAGGGTATTTTCATAATTTTCCAAA
65 TTTAGGGGTAT-TGGCACTTCTAAGTCGAAGGTAT-CCTTAGGGGTATTTTCATAATTTTTCAAA
23687 ACTGAGTCTTAGGTT-TCACCTGGT-
128 ACTGAGTCTTAGGTTGTCACC-GGTC
*** * * * *
23711 TCGCTTTTATGCCAAATGTGGGTATTTAGGACAGGTTCATCCCATCTATAATCCTTTTTAAGTCT
1 T-GCTTTTATGATGAATATAGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCC
* *
23776 TTTAGGGGTATTGTGCACTTCTAAGTCGAAGGTATCAAACTTTGGGGCATTTTCATAATTTTTCA
65 TTTAGGGGTATTG-GCACTTCTAAGTCGAAGGTATC---CTTAGGGGTATTTTCATAATTTTTCA
23841 AGAACTGAGTCTTAGGTTGTCACCGGTC
126 A-AACTGAGTCTTAGGTTGTCACCGGTC
23869 TGCTTTTATGATGAATATAGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCT
1 TGCTTTTATGATGAATATAGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCT
23934 TTAGG
66 TTAGG
23939 ATCACCGGCC
Statistics
Matches: 316, Mismatches: 49, Indels: 28
0.80 0.12 0.07
Matches are distributed among these distances:
152 1 0.00
153 14 0.04
154 177 0.56
155 14 0.04
156 23 0.07
157 81 0.26
158 6 0.02
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (152 bp):
TGCTTTTATGATGAATATAGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCT
TTAGGGGTATTGGCACTTCTAAGTCGAAGGTATCCTTAGGGGTATTTTCATAATTTTTCAAAACT
GAGTCTTAGGTTGTCACCGGTC
Found at i:30937 original size:50 final size:50
Alignment explanation
Indices: 30862--31070 Score: 190
Period size: 50 Copynumber: 4.2 Consensus size: 50
30852 GCCATGTTGA
* * *
30862 AAGTCCACACTAGCTAACACTTGATAAAGAGGTTAAGCCCTATAGAATCT
1 AAGTCCACACTAGCTAGCACTTGATAAGGAGGTTAAGCCCTATAGAGTCT
* * * * *
30912 AAGTCCACACTAGCTAGCATTTGATAAGGAAGCTAA-TCCTATAGAGTCA
1 AAGTCCACACTAGCTAGCACTTGATAAGGAGGTTAAGCCCTATAGAGTCT
* * * ** * * *
30961 AAGTCTATACAAGCT-GACACCTAAATAGGGAGGTTAAGCCCTGTAGACTCT
1 AAGTCCACACTAGCTAG-CA-CTTGATAAGGAGGTTAAGCCCTATAGAGTCT
* * *
31012 AAGCCCACA-TAAGCTAGCACCTGATATGGAGGTTAAGCCCTATAGAGTCT
1 AAGTCCACACT-AGCTAGCACTTGATAAGGAGGTTAAGCCCTATAGAGTCT
*
31062 AAGTGCACA
1 AAGTCCACA
31071 ATGTAGACAC
Statistics
Matches: 121, Mismatches: 33, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
48 1 0.01
49 24 0.20
50 74 0.61
51 21 0.17
52 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (50 bp):
AAGTCCACACTAGCTAGCACTTGATAAGGAGGTTAAGCCCTATAGAGTCT
Found at i:32122 original size:165 final size:166
Alignment explanation
Indices: 31951--32302 Score: 364
Period size: 165 Copynumber: 2.1 Consensus size: 166
31941 ATTTCATATA
* * *
31951 AAATTAGTTTTCAAAAATTCAGTCATCTTCATGAGT-TTGCCATAAAATTAGT-TTTCAAA-AAT
1 AAATTAGTTTTGAAAAATTCAGTCATCTTCATAAATGTTG-CAT---ATTAGTCTTTCAAATAAT
*
32013 -A-TTTCAT-ATAAAACTGAATTTTCTTTTCCATAAATATTTTCGA-GAGGATTTTCTTTGGTCT
62 CATTTTCATGA-AAAACCGAATTTT-TTTTCCATAAATATTTT-GAGGAGGATTTTCTTTGGTCT
*
32074 AAAA-TTTTTAAATGTATCTAATA-ATGTCATGGAATTCCCATT
124 AAAATTTTTTAAATGTATCTAATATA-GTCATGGAACTCCCATT
* * * * * * ** * **
32116 AAATTAGTTTTGAAAATTTAATTCATTTTCATAAATGTTGGATTTTTTTCTTTGAAATCCTCATT
1 AAATTAGTTTTGAAAAATTCAGTCATCTTCATAAATGTTGCATATTAGTCTTTCAAATAATCATT
* * * *
32181 TTCTTGAAAAACCGAGTTTTTTTTCCATAAATATTTTTAGGGGGATTTTCTTTGGTCTAAAATTT
66 TTCATGAAAAACCGAATTTTTTTTCCATAAATATTTTGAGGAGGATTTTCTTTGGTCTAAAATTT
*
32246 TTTAAATGTATCTAATATAGTCATTGAACTCCCATT
131 TTTAAATGTATCTAATATAGTCATGGAACTCCCATT
32282 -AATTCAGTTTTGAAAAATTCA
1 AAATT-AGTTTTGAAAAATTCA
32303 ATTTATTTTC
Statistics
Matches: 154, Mismatches: 23, Indels: 19
0.79 0.12 0.10
Matches are distributed among these distances:
162 3 0.02
163 6 0.04
164 2 0.01
165 74 0.48
166 67 0.44
167 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.45
Consensus pattern (166 bp):
AAATTAGTTTTGAAAAATTCAGTCATCTTCATAAATGTTGCATATTAGTCTTTCAAATAATCATT
TTCATGAAAAACCGAATTTTTTTTCCATAAATATTTTGAGGAGGATTTTCTTTGGTCTAAAATTT
TTTAAATGTATCTAATATAGTCATGGAACTCCCATT
Found at i:32329 original size:166 final size:166
Alignment explanation
Indices: 32022--32330 Score: 439
Period size: 166 Copynumber: 1.9 Consensus size: 166
32012 TATTTCATAT
* *
32022 AAAACTGAATTTTCTTTTCCATAAATATTTTCGAGAGGATTTTCTTTGGTCTAAAATTTTTAAAT
1 AAAACCGAATTTTCTTTTCCATAAATATTTTAGAGAGGATTTTCTTTGGTCTAAAATTTTTAAAT
* *
32087 GTATCTAATAATGTCATGGAATTCCCATTAAATTAGTTTTGAAAATTTAATTCATTTTCATAAAT
66 GTATCTAATAATGTCATGGAACTCCCATTAAATTAGTTTTGAAAATTCAATTCATTTTCATAAAT
*
32152 GTTGGATTTTTTTCTTTGAAATCCTCATTTTCTTGA
131 GTTGAATTTTTTTCTTTGAAATCCTCATTTTCTTGA
* *
32188 AAAACCGAGTTTT-TTTTCCATAAATATTTTTAG-GGGGATTTTCTTTGGTCTAAAATTTTTTAA
1 AAAACCGAATTTTCTTTTCCATAAATA-TTTTAGAGAGGATTTTCTTTGGTCTAAAA-TTTTTAA
* *
32251 ATGTATCTAAT-ATAGTCATTGAACTCCCATT-AATTCAGTTTTGAAAAATTCAATTTATTTTC-
64 ATGTATCTAATAAT-GTCATGGAACTCCCATTAAATT-AGTTTTG-AAAATTCAATTCATTTTCA
* *
32313 TGAATTTTGAATTTTTTT
126 TAAATGTTGAATTTTTTT
32331 GTAATTGATT
Statistics
Matches: 127, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
165 40 0.31
166 71 0.56
167 16 0.13
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (166 bp):
AAAACCGAATTTTCTTTTCCATAAATATTTTAGAGAGGATTTTCTTTGGTCTAAAATTTTTAAAT
GTATCTAATAATGTCATGGAACTCCCATTAAATTAGTTTTGAAAATTCAATTCATTTTCATAAAT
GTTGAATTTTTTTCTTTGAAATCCTCATTTTCTTGA
Found at i:34130 original size:148 final size:149
Alignment explanation
Indices: 33877--34151 Score: 344
Period size: 148 Copynumber: 1.9 Consensus size: 149
33867 TTTTTCGTCC
* * * * *
33877 AATAAAAATTATCACCTAAATTTTTGGAATTTCTAATATTCTCATGGGTATCCATGAGGGTATGA
1 AATAAAAATTATCACCTAAATTTTTAGAATTTCCAATATTCTCATAGGCATCCATAAGGGTATGA
* ** *
33942 AAAATTTTTAAAACTTTTCATATCTTTTCGGTTCTCCATTAAGGTATGAAATG-AATTTTTTGGG
66 AAAATTTTCAAAACTTTTCATATCTTTTCAATCCTCCATTAAGGTATGAAATGAAATTTTTTGGG
34006 AAATAAAAAAATTAAATTA
131 AAATAAAAAAATTAAATTA
* *
34025 AATAAAAATTATGATCC-CAATTTCTTAGAATTTCCAATATTC-CTATAGGCATCCATAAGGGTA
1 AATAAAAATTATCA-CCTAAATTT-TTAGAATTTCCAATATTCTC-ATAGGCATCCATAAGGGTA
* * * *
34088 TG-AAAATTTTCAAAACTCTTT-GTGTCTTTTCAATCCTTCATTAAGTTATGAAATGAAATTTTT
63 TGAAAAATTTTCAAAACT-TTTCATATCTTTTCAATCCTCCATTAAGGTATGAAATGAAATTTTT
34151 T
127 T
34152 AGAAAAACAA
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
148 60 0.56
149 47 0.44
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (149 bp):
AATAAAAATTATCACCTAAATTTTTAGAATTTCCAATATTCTCATAGGCATCCATAAGGGTATGA
AAAATTTTCAAAACTTTTCATATCTTTTCAATCCTCCATTAAGGTATGAAATGAAATTTTTTGGG
AAATAAAAAAATTAAATTA
Found at i:34596 original size:155 final size:154
Alignment explanation
Indices: 34384--34717 Score: 361
Period size: 154 Copynumber: 2.2 Consensus size: 154
34374 AAAGTCACCT
* * **
34384 TTTATCATCATTTTTAAGTCCTTTAAGGAAATCAGGCACTTCTACGTCGAAAGTATCCCCTAGAG
1 TTTATAATCATTTTTAAGTCTTTTAAGGAAATCACACACTTCTACGTCGAAAGTATCCCCTAGAG
* * * *
34449 GCATTTTCA-AAATTTTTCAAA-ATCAAGTCTTAAGTTGTCC-TCGGGTTTGCTTTTATGCCAAA
66 GCATTTT-AGAAATTTTT-AAAGCT-AAGTCTTAAGCTG-CCACCGGGTCTGCTTTTATGCCAAA
*
34511 GGTGGGTATTTAGGATAGGTTCACCCCA
127 GATGGGTATTTAGGATAGGTTCACCCCA
* ** * *
34539 TTTATAATCATTTTTAAGTCTTTTAGGGGTATCACACACTTCTACGTCG-AAGATATCCTCTATA
1 TTTATAATCATTTTTAAGTCTTTTAAGGAAATCACACACTTCTACGTCGAAAG-TATCCCCTAGA
* * * * **
34603 GGCATTTTAGTAATTTTTAAAGCTAAGTTTTAGGCTGCCACCGGGTCTGCTTTTTTGCTGAAGAT
65 GGCATTTTAGAAATTTTTAAAGCTAAGTCTTAAGCTGCCACCGGGTCTGCTTTTATGCCAAAGAT
* * *
34668 GGGTATTTAGGGTAGGTTCATCCCG
130 GGGTATTTAGGATAGGTTCACCCCA
* *
34693 TCTATAATCCTTTTTAAGTCCTTTT
1 TTTATAATCATTTTTAAGT-CTTTT
34718 CAAATGCCTT
Statistics
Matches: 149, Mismatches: 25, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
153 2 0.01
154 75 0.50
155 72 0.48
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (154 bp):
TTTATAATCATTTTTAAGTCTTTTAAGGAAATCACACACTTCTACGTCGAAAGTATCCCCTAGAG
GCATTTTAGAAATTTTTAAAGCTAAGTCTTAAGCTGCCACCGGGTCTGCTTTTATGCCAAAGATG
GGTATTTAGGATAGGTTCACCCCA
Found at i:36265 original size:45 final size:44
Alignment explanation
Indices: 36200--36294 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 44
36190 TTATAGAGTC
** * * *
36200 AAAGTCCATATTAGTTGGCACTTAATAGAGAGGTTAAACCCTAT
1 AAAGTCCATATTAACTGGCACCTAATAAAGAGGTTAAACACTAT
* *
36244 AGAAGTCCGTATTAACTGGCACCTAATAAAGAGGTTAAGCACTAT
1 A-AAGTCCATATTAACTGGCACCTAATAAAGAGGTTAAACACTAT
36289 AAAGTC
1 AAAGTC
36295 AAAAGTCTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 6 0.14
45 37 0.86
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (44 bp):
AAAGTCCATATTAACTGGCACCTAATAAAGAGGTTAAACACTAT
Found at i:36385 original size:50 final size:50
Alignment explanation
Indices: 35916--36385 Score: 209
Period size: 50 Copynumber: 9.5 Consensus size: 50
35906 ACAATAATTA
* * * * ** * **
35916 GCACCTAATAAGGAGGTTAAGCTCTATAAAGTTTAAGTCCACACAAATTG
1 GCACTTAATAGGGAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGCTG
* * * * * * *
35966 GCATCTT-ATAGGGAGCTTAAGCCTTATAGAGTCTATGTCCATACAAGCTA
1 GCA-CTTAATAGGGAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGCTG
* * * * * * * *
36016 GCACCTAATAGGAAAGTTAAGCCTTGTAGAGTCTAAGTCCGCACAAGCTG
1 GCACTTAATAGGGAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGCTG
* * * * ** * * ***
36066 GCTCCTGATAGAGAGGTTAAGCATTGTAGAGTAAAAAGTCCATGTTAGCTG
1 GCACTTAATAGGGAGGTTAAGCCCTATAGAGT-CAAAGTCCACACTAGCTG
* * ** * * *
36117 GCACCTT-ATAAGAACATTAAGTCCTATATAGTCAAAGTCCACACTAGTTG
1 GCA-CTTAATAGGGAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGCTG
* * * * * * * *
36167 GCA-TCTGATAAGGAAGTTAAGTCTTATAGAGTCAAAGTCCATATTAGTTG
1 GCACT-TAATAGGGAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGCTG
* * ** * *
36217 GCACTTAATAGAGAGGTTAAACCCTAT--AG---AAGTCCGTATTAACTG
1 GCACTTAATAGGGAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGCTG
* ** * * * *
36262 GCACCTAATAAAGAGGTTAAGCACTATAAAGTCAAAAGTCTACACTAGCTA
1 GCACTTAATAGGGAGGTTAAGCCCTATAGAGTC-AAAGTCCACACTAGCTG
** * * * * *
36313 GCACTTGTTAGGAAGGTAAAGCCCTATGGAGTCTAAGTCCACACTAGTTG
1 GCACTTAATAGGGAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGCTG
36363 GCACTTAATAGGGAGGTTAAGCC
1 GCACTTAATAGGGAGGTTAAGCC
36386 TTACAAATAA
Statistics
Matches: 311, Mismatches: 96, Indels: 26
0.72 0.22 0.06
Matches are distributed among these distances:
45 36 0.12
47 2 0.01
48 3 0.01
49 3 0.01
50 201 0.65
51 64 0.21
52 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (50 bp):
GCACTTAATAGGGAGGTTAAGCCCTATAGAGTCAAAGTCCACACTAGCTG
Found at i:36474 original size:48 final size:50
Alignment explanation
Indices: 36374--36483 Score: 145
Period size: 48 Copynumber: 2.2 Consensus size: 50
36364 CACTTAATAG
*
36374 GGAGGTTAAG-CCTTACAAATAAAAAGTCCAATTTAGTTAGCACTTGGGAA
1 GGAGGTTAAGCCCTTA-AAATAAAAAGTCCAATTAAGTTAGCACTTGGGAA
* * * *
36424 GGAGGTTAAGCCCTT-AGATAGAAAGTCCAATTAATTTA-CACTTGGTAA
1 GGAGGTTAAGCCCTTAAAATAAAAAGTCCAATTAAGTTAGCACTTGGGAA
36472 GGAGGTTAAGCC
1 GGAGGTTAAGCC
36484 TTATAAGGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 21 0.39
49 19 0.35
50 10 0.19
51 4 0.07
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (50 bp):
GGAGGTTAAGCCCTTAAAATAAAAAGTCCAATTAAGTTAGCACTTGGGAA
Found at i:42805 original size:78 final size:78
Alignment explanation
Indices: 42723--42871 Score: 203
Period size: 78 Copynumber: 1.9 Consensus size: 78
42713 AAACCAAACT
* * *
42723 TTTAAGATTATTTTAGTATTTTTGCATTAAA-ATCAAGCATTT-AGCATTAGTTTTGCATTTTTA
1 TTTAAGATCATTTTAGTATTTTTGCATTAAACCT-AAGCATTTAAG-ATTAGTTTTGCACTTTTA
*
42786 TCTCAAAATCGAACA
64 TATCAAAATCGAACA
* * *
42801 TTTAAGGTCATTTTAGTATTTTTGCATTAAACCTAATCCTTTAAGATTAGTTTTGCACTTTTATA
1 TTTAAGATCATTTTAGTATTTTTGCATTAAACCTAAGCATTTAAGATTAGTTTTGCACTTTTATA
42866 TCAAAA
66 TCAAAA
42872 CCAAGCCTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 59 0.95
79 3 0.05
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (78 bp):
TTTAAGATCATTTTAGTATTTTTGCATTAAACCTAAGCATTTAAGATTAGTTTTGCACTTTTATA
TCAAAATCGAACA
Found at i:44020 original size:43 final size:43
Alignment explanation
Indices: 43959--44057 Score: 171
Period size: 43 Copynumber: 2.3 Consensus size: 43
43949 TACTTTTCAT
*
43959 AATGTATCGATACATGCATTTTAAATTTATAACCGTTGGGCAC
1 AATGTATCGATACATGCATTTGAAATTTATAACCGTTGGGCAC
*
44002 AATGTATCGATACATGCATTTGAAATTTATAGCCGTTGGGCAC
1 AATGTATCGATACATGCATTTGAAATTTATAACCGTTGGGCAC
*
44045 AATGTACCGATAC
1 AATGTATCGATAC
44058 TTTTCACTAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (43 bp):
AATGTATCGATACATGCATTTGAAATTTATAACCGTTGGGCAC
Found at i:48182 original size:21 final size:21
Alignment explanation
Indices: 48158--48204 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
48148 TTTGATGCTG
48158 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
48178 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
48199 ATTTTG
1 ATTTTG
48205 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:48343 original size:13 final size:13
Alignment explanation
Indices: 48325--48363 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
48315 ATAATCACCC
*
48325 TGTATCGATACAG
1 TGTATCGATACAA
48338 TGTATCGATACAA
1 TGTATCGATACAA
48351 TGTATCGATACAA
1 TGTATCGATACAA
48364 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:48374 original size:20 final size:20
Alignment explanation
Indices: 48349--48427 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
48339 GTATCGATAC
48349 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
48369 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
48394 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
48414 CATGTATCGATACA
1 AATGTATCGATACA
48428 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:50462 original size:15 final size:15
Alignment explanation
Indices: 50442--50472 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
50432 ATTTCGTTTG
*
50442 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
50457 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
50472 G
1 G
50473 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:52296 original size:21 final size:21
Alignment explanation
Indices: 52267--52311 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
52257 AAGTTTTCAT
*
52267 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
52287 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
52309 TTT
1 TTT
52312 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:54547 original size:13 final size:13
Alignment explanation
Indices: 54529--54554 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54519 CAATTTTTTG
54529 TGTATCGATACAT
1 TGTATCGATACAT
54542 TGTATCGATACAT
1 TGTATCGATACAT
54555 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:55015 original size:20 final size:20
Alignment explanation
Indices: 54990--55041 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
54980 TACAAGCAAT
*
54990 GTATCGATACAATCTATCAA
1 GTATCGATACAATCTACCAA
* * *
55010 GTATCGATACATTGTACCAT
1 GTATCGATACAATCTACCAA
55030 GTATCGATACAA
1 GTATCGATACAA
55042 ACATTGGTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
GTATCGATACAATCTACCAA
Found at i:55704 original size:21 final size:22
Alignment explanation
Indices: 55660--55736 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
55650 AGTTATCATT
* *
55660 TTTCTCCCCCTCAATTAAAGAA
1 TTTCTCCCCCTTAATCAAAGAA
*
55682 TTTCTCCCCTTTAATCAAA-AA
1 TTTCTCCCCCTTAATCAAAGAA
*
55703 TTTCTCCCCCTTAATCAAAGCA
1 TTTCTCCCCCTTAATCAAAGAA
55725 TTTCTCCCCCTT
1 TTTCTCCCCCTT
55737 TGTCAAATCT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
21 20 0.41
22 29 0.59
ACGTcount: A:0.26, C:0.35, G:0.03, T:0.36
Consensus pattern (22 bp):
TTTCTCCCCCTTAATCAAAGAA
Found at i:57640 original size:13 final size:13
Alignment explanation
Indices: 57622--57650 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
57612 AAATAGTACC
57622 CAATGTATCGATA
1 CAATGTATCGATA
57635 CAATGTATCGATA
1 CAATGTATCGATA
57648 CAA
1 CAA
57651 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:62392 original size:13 final size:13
Alignment explanation
Indices: 62374--62398 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62364 CATATTTCTT
62374 TGTATCGATACAC
1 TGTATCGATACAC
62387 TGTATCGATACA
1 TGTATCGATACA
62399 TGATCTTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:64956 original size:10 final size:10
Alignment explanation
Indices: 64937--64967 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
64927 GTATCGATAC
64937 ATGAACAGTG
1 ATGAACAGTG
*
64947 ATGAATAGTG
1 ATGAACAGTG
64957 ATGAACAGTG
1 ATGAACAGTG
64967 A
1 A
64968 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:65055 original size:53 final size:53
Alignment explanation
Indices: 64991--65127 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
64981 CTACTACCAA
64991 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
65044 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
65097 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
65128 TATGCAATCT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:65160 original size:20 final size:20
Alignment explanation
Indices: 65097--65167 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
65087 GCCAATGTCC
**
65097 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
65117 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
65137 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
65157 TGTATCGATAC
1 TGTATCGATAC
65168 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:65233 original size:21 final size:21
Alignment explanation
Indices: 65207--65247 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
65197 GTCAACCTTG
65207 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
65228 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
65248 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:72012 original size:28 final size:27
Alignment explanation
Indices: 71970--72055 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 27
71960 ATTGTTTTGG
**
71970 AAACAAAAAGGGGGAGAGATATTTTTT
1 AAACAAAAAAAGGGAGAGATATTTTTT
*** * *
71997 AAATTTGAAAAAGGGAAAGAT-TGTTTTGG
1 AAA-CAAAAAAAGGGAGAGATAT-TTTT-T
72026 AAACAAAAAAAGGGAGAGATATTTTTT
1 AAACAAAAAAAGGGAGAGATATTTTTT
72053 AAA
1 AAA
72056 AGGAAAACAT
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
27 7 0.16
28 32 0.74
29 4 0.09
ACGTcount: A:0.48, C:0.02, G:0.23, T:0.27
Consensus pattern (27 bp):
AAACAAAAAAAGGGAGAGATATTTTTT
Found at i:72014 original size:56 final size:56
Alignment explanation
Indices: 71940--72055 Score: 196
Period size: 56 Copynumber: 2.1 Consensus size: 56
71930 TTTTTTGAAA
**
71940 TAAATTTGAAAAAAGGAAAAATTGTTTTGGAAACAAAAAGGGGGAGAGATATTTTT
1 TAAATTTGAAAAAAGGAAAAATTGTTTTGGAAACAAAAAAAGGGAGAGATATTTTT
* *
71996 TAAATTTGAAAAAGGGAAAGATTGTTTTGGAAACAAAAAAAGGGAGAGATATTTTT
1 TAAATTTGAAAAAAGGAAAAATTGTTTTGGAAACAAAAAAAGGGAGAGATATTTTT
72052 TAAA
1 TAAA
72056 AGGAAAACAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.28
Consensus pattern (56 bp):
TAAATTTGAAAAAAGGAAAAATTGTTTTGGAAACAAAAAAAGGGAGAGATATTTTT
Found at i:72072 original size:45 final size:45
Alignment explanation
Indices: 72020--72107 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
72010 GGAAAGATTG
72020 TTTTGGAAACAAAAAAAGGG-AGAGATATTTTTTAAAAGGAAAACA
1 TTTTGGAAAC-AAAAAAGGGAAGAGATATTTTTTAAAAGGAAAACA
* *
72065 TTTTGGAAACAAAGAGGGGAAGAGATATTTTTTAAAAGGAAAA
1 TTTTGGAAACAAAAAAGGGAAGAGATATTTTTTAAAAGGAAAA
72108 TTTTTGTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 7 0.17
45 33 0.82
ACGTcount: A:0.49, C:0.03, G:0.23, T:0.25
Consensus pattern (45 bp):
TTTTGGAAACAAAAAAGGGAAGAGATATTTTTTAAAAGGAAAACA
Found at i:72792 original size:13 final size:13
Alignment explanation
Indices: 72774--72798 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
72764 CATATTGCTT
72774 TGTATCGATACAC
1 TGTATCGATACAC
72787 TGTATCGATACA
1 TGTATCGATACA
72799 TGATCTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:72816 original size:32 final size:33
Alignment explanation
Indices: 72755--72817 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
72745 AAGCCCAGAA
*
72755 GTATCGATACATATTGCTTTGTATCGATACACT
1 GTATCGATACATATTGCTTGGTATCGATACACT
72788 GTATCGATACATGA-T-CTTGGTATCGATACA
1 GTATCGATACAT-ATTGCTTGGTATCGATACA
72818 TAGCGAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.50
33 13 0.46
34 1 0.04
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (33 bp):
GTATCGATACATATTGCTTGGTATCGATACACT
Found at i:76052 original size:20 final size:20
Alignment explanation
Indices: 76004--76062 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
75994 AAAAGCCCAA
76004 AATGTATCGATACAATTGTAAG
1 AATGTATCGATAC-ATT-TAAG
* **
76026 CATGTATCGATACATTTACT
1 AATGTATCGATACATTTAAG
76046 AATGTATCGATACATTT
1 AATGTATCGATACATTT
76063 TCTTGGGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 18 0.55
21 3 0.09
22 12 0.36
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (20 bp):
AATGTATCGATACATTTAAG
Found at i:76109 original size:20 final size:20
Alignment explanation
Indices: 76084--76139 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
76074 TGCAGGGTAG
76084 TTATGTATCGATACATTCAC
1 TTATGTATCGATACATTCAC
* *
76104 TTATGTATCGATTCATTTAC
1 TTATGTATCGATACATTCAC
* *
76124 TGTTTATATCGATACA
1 T-TATGTATCGATACA
76140 AATTGTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (20 bp):
TTATGTATCGATACATTCAC
Found at i:78133 original size:19 final size:20
Alignment explanation
Indices: 78089--78142 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
78079 CTGCCAGTTT
* **
78089 CATGTATTGATACAATTGTG
1 CATGTATCGATACAATTGAA
78109 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
78128 CATGTATCGATACAA
1 CATGTATCGATACAA
78143 AACATAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:78761 original size:30 final size:30
Alignment explanation
Indices: 78714--78863 Score: 189
Period size: 30 Copynumber: 5.0 Consensus size: 30
78704 ATTAAGGCTT
78714 TCGTTT-AAAAA-TTTCTCCCCCTTGATAA
1 TCGTTTAAAAAATTTTCTCCCCCTTGATAA
78742 TCGTTTAAAAAATTTTCTCCCCCTTGATAA
1 TCGTTTAAAAAATTTTCTCCCCCTTGATAA
*
78772 TCGTTTTAAAAAAATTTTCT-ACCCTTGATAAA
1 TCG-TTT-AAAAAATTTTCTCCCCCTTGAT-AA
*** * *
78804 AAATTTAAAAGATTTTCTCCCCCTTGAGAA
1 TCGTTTAAAAAATTTTCTCCCCCTTGATAA
*
78834 TCGTTTAAAAAATTTTCTCCTCCTTGATAA
1 TCGTTTAAAAAATTTTCTCCCCCTTGATAA
78864 AAAATTTATT
Statistics
Matches: 103, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
28 6 0.06
29 5 0.05
30 57 0.55
31 21 0.20
32 14 0.14
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (30 bp):
TCGTTTAAAAAATTTTCTCCCCCTTGATAA
Found at i:78820 original size:62 final size:61
Alignment explanation
Indices: 78745--78871 Score: 202
Period size: 62 Copynumber: 2.1 Consensus size: 61
78735 TTGATAATCG
*
78745 TTTAAAAAATTTTCTCCCCCTTGATAATCGTTTTAAAAAAATTTTCTAC-CCTTGATAAAAAA
1 TTTAAAAAATTTTCTCCCCCTTGAGAATCG-TTT-AAAAAATTTTCTACTCCTTGATAAAAAA
* *
78807 TTTAAAAGATTTTCTCCCCCTTGAGAATCGTTTAAAAAATTTTCTCCTCCTTGATAAAAAA
1 TTTAAAAAATTTTCTCCCCCTTGAGAATCGTTTAAAAAATTTTCTACTCCTTGATAAAAAA
78868 TTTA
1 TTTA
78872 TTTTCAAACA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
60 13 0.21
61 20 0.33
62 28 0.46
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (61 bp):
TTTAAAAAATTTTCTCCCCCTTGAGAATCGTTTAAAAAATTTTCTACTCCTTGATAAAAAA
Found at i:80896 original size:23 final size:23
Alignment explanation
Indices: 80869--80915 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
80859 TTCAAAAATA
*
80869 TGGCACAAATTAATATCAAATCT
1 TGGCAAAAATTAATATCAAATCT
*
80892 TGGCAAAAATTAATATCGAATCT
1 TGGCAAAAATTAATATCAAATCT
80915 T
1 T
80916 ACCCTATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.32
Consensus pattern (23 bp):
TGGCAAAAATTAATATCAAATCT
Found at i:86942 original size:13 final size:13
Alignment explanation
Indices: 86924--86948 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
86914 CAATTCATCA
86924 TGTATCGATACAT
1 TGTATCGATACAT
86937 TGTATCGATACA
1 TGTATCGATACA
86949 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:86959 original size:33 final size:32
Alignment explanation
Indices: 86904--86968 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
86894 TTTGAAGTAA
*
86904 TGTATCGATACAATTCATCATGTATCGATACAT
1 TGTATCGATACAATTCA-CATGTATCAATACAT
86937 TGTATCGATACAATGTGC-CATGTATCAATACA
1 TGTATCGATACAAT-T-CACATGTATCAATACA
86969 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (32 bp):
TGTATCGATACAATTCACATGTATCAATACAT
Found at i:87714 original size:19 final size:17
Alignment explanation
Indices: 87690--87741 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 17
87680 CGATACACTA
87690 TATCGATACATGATCTTGG
1 TATCGATACATGA-CTT-G
87709 TATCGATACACAATGACTTG
1 TATCGAT--AC-ATGACTTG
87729 TATCGATACATGA
1 TATCGATACATGA
87742 AACTGGCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.13
18 2 0.07
19 7 0.23
20 8 0.27
21 5 0.17
22 4 0.13
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (17 bp):
TATCGATACATGACTTG
Found at i:87717 original size:32 final size:33
Alignment explanation
Indices: 87657--87719 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
87647 GGCCCAGAAG
*
87657 TATCGATACATATTGCTTTGTATCGATACACTA
1 TATCGATACATATTGCTTGGTATCGATACACTA
87690 TATCGATACATGA-T-CTTGGTATCGATACAC
1 TATCGATACAT-ATTGCTTGGTATCGATACAC
87720 AATGACTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.54
33 12 0.43
34 1 0.04
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (33 bp):
TATCGATACATATTGCTTGGTATCGATACACTA
Found at i:92140 original size:38 final size:41
Alignment explanation
Indices: 92098--92188 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
92088 TTATAACAAA
**
92098 AAGGGAGAGAG-AT-T-ATTGTTTATTGGT-AAGAACGTATT
1 AAGGGAGAGAGTATGTAATTGTTTAAAGGTGAA-AACGTATT
*
92136 AAGGGAGAGAGTTTGTAATTGTTTAAAGGTGAAAACGTATT
1 AAGGGAGAGAGTATGTAATTGTTTAAAGGTGAAAACGTATT
*
92177 AAGGGGGAGAGT
1 AAGGGAGAGAGT
92189 TTGCATAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
38 11 0.24
39 1 0.02
40 1 0.02
41 30 0.67
42 2 0.04
ACGTcount: A:0.35, C:0.02, G:0.33, T:0.30
Consensus pattern (41 bp):
AAGGGAGAGAGTATGTAATTGTTTAAAGGTGAAAACGTATT
Done.