Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2660
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: 81854
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Found at i:1434 original size:79 final size:82
Alignment explanation
Indices: 1323--1507 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
1313 GCTACTCGTT
* * *
1323 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
1386 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
1403 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
1466 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
1483 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1508 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:1507 original size:40 final size:40
Alignment explanation
Indices: 1304--1507 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
1294 CGGAATTTAA
** *
1304 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
1344 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
1384 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
1423 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
1463 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
1503 CCGGA
1 CCGGA
1508 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:9345 original size:79 final size:82
Alignment explanation
Indices: 9234--9418 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
9224 GCTACTCGTT
* * *
9234 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
9297 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
9314 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
9377 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
9394 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
9419 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:9418 original size:40 final size:40
Alignment explanation
Indices: 9215--9418 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
9205 CGGAATTTAA
** *
9215 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
9255 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
9295 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
9334 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
9374 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
9414 CCGGA
1 CCGGA
9419 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 92 0.66
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:15162 original size:43 final size:43
Alignment explanation
Indices: 15115--15198 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
15105 TTAGGGATGT
* * * *
15115 TGGCATCGATATGTGATTA-AGTGTAAGACCTTGTTTGGGACAG
1 TGGCATCAATATGTGAGTACA-TGTAAGACCATGTCTGGGACAG
15158 TGGCATCAATATGTGAGTACATGTAAGACCATGTCTGGGAC
1 TGGCATCAATATGTGAGTACATGTAAGACCATGTCTGGGAC
15199 GTTGGAATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 35 0.97
44 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (43 bp):
TGGCATCAATATGTGAGTACATGTAAGACCATGTCTGGGACAG
Found at i:23103 original size:101 final size:99
Alignment explanation
Indices: 22976--23165 Score: 281
Period size: 101 Copynumber: 1.9 Consensus size: 99
22966 CGGGATATAT
* * * *
22976 ATAGCTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTTTGATCACG
1 ATAGCTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATAA--TTGATCACA
23041 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAG
64 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAG
* * * * *
23077 ATAGTTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATG
1 ATAGCTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATAATTGATCACATG
23142 TGTAGTACTAAGTGCAGGCTACTA
66 TGTAGTACTAAGTGCAGGCTACTA
23166 TGCGTACCAA
Statistics
Matches: 80, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 32 0.40
101 48 0.60
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (99 bp):
ATAGCTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGCGTACCGGATAATTGATCACATG
TGTAGTACTAAGTGCAGGCTACTACGTGTATCAG
Found at i:23111 original size:50 final size:50
Alignment explanation
Indices: 22976--23181 Score: 243
Period size: 50 Copynumber: 4.1 Consensus size: 50
22966 CGGGATATAT
* * * * *
22976 ATAGCTAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTG
1 ATAGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG
* * * * *
23026 ATAACTTTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAG
1 AT-AGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG
* *
23077 ATAGTTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGG
1 ATAGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG
* * * * *
23127 ATAATT-GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAA
1 ATAGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG
23176 ATAGTT
1 ATAGTT
23182 TGTCTACATA
Statistics
Matches: 132, Mismatches: 23, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
49 42 0.32
50 50 0.38
51 40 0.30
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
ATAGTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAG
Found at i:29558 original size:28 final size:27
Alignment explanation
Indices: 29503--29587 Score: 109
Period size: 27 Copynumber: 3.1 Consensus size: 27
29493 AGCATGGCTG
* * *
29503 CCAGAACAGATAA-TGTGACATAGTCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
*
29529 CCAGATACAGATATTTGTGGCAGAGCCA
1 CCAGA-ACAGATAATTGTGGCAGAGCCA
*
29557 CCAGAACAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAATTGTGGCAGAGCCA
29584 CCAG
1 CCAG
29588 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
26 5 0.10
27 31 0.61
28 15 0.29
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (27 bp):
CCAGAACAGATAATTGTGGCAGAGCCA
Found at i:29721 original size:27 final size:26
Alignment explanation
Indices: 29691--29741 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
29681 AGTCAAATTA
*
29691 ACCCAAAGGGTATAATGGTCATTTTAC
1 ACCC-AAGGGTATAATGGTAATTTTAC
*
29718 ACCCAGGGGTATAATGGTAATTTT
1 ACCCAAGGGTATAATGGTAATTTT
29742 CCATACTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (26 bp):
ACCCAAGGGTATAATGGTAATTTTAC
Found at i:33703 original size:27 final size:26
Alignment explanation
Indices: 33657--33708 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
33647 GCGAGGCTGC
33657 TAGATATTGTGACGAAGTCACCAGAA
1 TAGATATTGTGACGAAGTCACCAGAA
* *
33683 TAGATATATGTGGCGAGGTCACCAGA
1 TAGATAT-TGTGACGAAGTCACCAGA
33709 TTGCAGCGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (26 bp):
TAGATATTGTGACGAAGTCACCAGAA
Found at i:39084 original size:22 final size:23
Alignment explanation
Indices: 39062--39113 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
39052 ATGTTTTTAC
39062 TTTTATTTTAT-TTTAAGACTACT
1 TTTTATTTT-TCTTTAAGACTACT
39085 TTTTATTTTTCTTTAAG-CTTA-T
1 TTTTATTTTTCTTTAAGAC-TACT
39107 TTTTATT
1 TTTTATT
39114 AGGTTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.21, C:0.08, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTTATTTTTCTTTAAGACTACT
Found at i:45648 original size:43 final size:43
Alignment explanation
Indices: 45528--45648 Score: 127
Period size: 43 Copynumber: 2.8 Consensus size: 43
45518 CATAGGATTT
* * ** *
45528 TCAATATGTGTTTTCATGTAAGACCACATCTAAGACATTGGCA
1 TCAATATGTGATTACATGTAAGACCACATCTGGGACAGTGGCA
* *** *
45571 TCGATATGTGATTA-AGTGTAAGACCTTGTTTGGGACAGTGGCA
1 TCAATATGTGATTACA-TGTAAGACCACATCTGGGACAGTGGCA
*
45614 TCAATATGTGACTACATGTAAGACCACATCTGGGA
1 TCAATATGTGATTACATGTAAGACCACATCTGGGA
45649 TGTTGGCATT
Statistics
Matches: 60, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
42 1 0.02
43 58 0.97
44 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (43 bp):
TCAATATGTGATTACATGTAAGACCACATCTGGGACAGTGGCA
Found at i:50871 original size:47 final size:47
Alignment explanation
Indices: 50820--51187 Score: 558
Period size: 47 Copynumber: 7.7 Consensus size: 47
50810 TTAGGATTCT
* * *
50820 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
50867 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
50916 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
50963 ATGTGATGAATGTGAAAGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* *
51010 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCTG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
51059 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
51106 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
51153 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
51188 TCCCGAAGGG
Statistics
Matches: 297, Mismatches: 19, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
46 1 0.00
47 206 0.69
49 90 0.30
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:50920 original size:96 final size:96
Alignment explanation
Indices: 50820--51187 Score: 552
Period size: 96 Copynumber: 3.9 Consensus size: 96
50810 TTAGGATTCT
* * *
50820 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
50884 GTGTATATATATGTGATAAGGCCTAATGGCCG
65 GTGTATATATATGTGATAAGGCCTAATGGCCG
50916 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA-
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
50980 -GTATATATATGTGATAAGGCCTAATGGCCG
66 TGTATATATATGTGATAAGGCCTAATGGCCG
* *
51010 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATAGCTGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
51075 AGTG--TATATATGTGATAAGGCCTAATGGCCG
64 AGTGTATATATATGTGATAAGGCCTAATGGCCG
* * * * * * *
51106 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
51171 TGTATA-A-ATGTGATAAG
66 TGTATATATATGTGATAAG
51188 TCCCGAAGGG
Statistics
Matches: 251, Mismatches: 14, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
94 98 0.39
95 2 0.01
96 150 0.60
98 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (96 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATATGTGATAAGGCCTAATGGCCG
Found at i:50996 original size:143 final size:143
Alignment explanation
Indices: 50841--51187 Score: 581
Period size: 143 Copynumber: 2.4 Consensus size: 143
50831 GTGAACATGC
*
50841 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
*
50906 CTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
66 CTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
50971 AATGTGAAAGTAT
131 AATGTGAAAGTAT
50984 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
*
51049 CTAATAGCTGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
66 CTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
51114 AATGTGAAAGTGT
131 AATGTGAAAGTAT
* * * * * * *
51127 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
51188 TCCCGAAGGG
Statistics
Matches: 193, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
141 10 0.05
142 1 0.01
143 182 0.94
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (143 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGC
CTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
AATGTGAAAGTAT
Found at i:57208 original size:43 final size:44
Alignment explanation
Indices: 57159--57273 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 44
57149 ATGTGTTTTC
* * *
57159 GTGTAAGACCACATTTGGGACGTTGGCATCGATATGTGA-TTAA
1 GTGTAAGACCACGTCTGGGACGTTGGCATCAATATGTGAGTTAA
** *
57202 GTGTAAGACCTTGTCTGGGACAG-TGGCATCAATATGTGAGTTCA
1 GTGTAAGACCACGTCTGGGAC-GTTGGCATCAATATGTGAGTTAA
*
57246 -TGTAAGACCACGTCTGGGACATTGGCAT
1 GTGTAAGACCACGTCTGGGACGTTGGCAT
57274 TGTACGATAT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
43 56 0.93
44 4 0.07
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (44 bp):
GTGTAAGACCACGTCTGGGACGTTGGCATCAATATGTGAGTTAA
Found at i:60841 original size:27 final size:27
Alignment explanation
Indices: 60799--61159 Score: 420
Period size: 27 Copynumber: 13.4 Consensus size: 27
60789 AATCTCATAT
* * *
60799 CTGTAGGCTAGCATTACTAAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* *
60826 CTGTAAGGTAGAATTACCGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* *
60853 CTGTAGGGTAGAATTATTAAAATA-CC
1 CTGTAGGGTAGAATTACTGAAATACCC
* *
60879 CTGTAAGGTAGAATTACCGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
*
60906 TTGTAGGGTAGAATTACTGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* * * *
60933 TTATAAGGTAGAATTACCGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
*
60960 CTATAGGGTAGAATTACT-AAATACCTC
1 CTGTAGGGTAGAATTACTGAAATACC-C
* *
60987 CTGTAAGGTAGAATTACCGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* * *
61014 TTGTATGGTAGAATTACTAAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* * *
61041 CTATAAGGTTGAATTACTGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
*
61068 CTGTAGGGTAGAATTACTGAAATGCCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* **
61095 CTCTAGGGTAGAATTACCAAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* * *
61122 TTGTAGGGTAGAAATACTAAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
*
61149 TTGTAGGGTAG
1 CTGTAGGGTAG
61160 GACTATCGAT
Statistics
Matches: 285, Mismatches: 46, Indels: 6
0.85 0.14 0.02
Matches are distributed among these distances:
26 29 0.10
27 249 0.87
28 7 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (27 bp):
CTGTAGGGTAGAATTACTGAAATACCC
Found at i:60959 original size:54 final size:54
Alignment explanation
Indices: 60799--61159 Score: 501
Period size: 54 Copynumber: 6.7 Consensus size: 54
60789 AATCTCATAT
* *
60799 CTGTAGGCTAGCATTACTAAAATACCCCTGTAAGGTAGAATTACCGAAATACCC
1 CTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAGAATTACCGAAATACCC
*
60853 CTGTAGGGTAGAATTATTAAAATA-CCCTGTAAGGTAGAATTACCGAAATACCC
1 CTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAGAATTACCGAAATACCC
* * * *
60906 TTGTAGGGTAGAATTACTGAAATACCCTTATAAGGTAGAATTACCGAAATACCC
1 CTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAGAATTACCGAAATACCC
*
60960 CTATAGGGTAGAATTACT-AAATACCTCCTGTAAGGTAGAATTACCGAAATACCC
1 CTGTAGGGTAGAATTACTAAAATACC-CCTGTAAGGTAGAATTACCGAAATACCC
* * * * *
61014 TTGTATGGTAGAATTACTAAAATACCCCTATAAGGTTGAATTACTGAAATACCC
1 CTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAGAATTACCGAAATACCC
* * * * *
61068 CTGTAGGGTAGAATTACTGAAATGCCCCTCTAGGGTAGAATTACCAAAATACCC
1 CTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAGAATTACCGAAATACCC
* * * *
61122 TTGTAGGGTAGAAATACTAAAATACCCTTGTAGGGTAG
1 CTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAG
61160 GACTATCGAT
Statistics
Matches: 271, Mismatches: 33, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
53 57 0.21
54 207 0.76
55 7 0.03
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (54 bp):
CTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAGAATTACCGAAATACCC
Found at i:61851 original size:27 final size:26
Alignment explanation
Indices: 61807--61858 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
61797 CTCACTGTAA
*
61807 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
61834 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
61859 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:68640 original size:27 final size:27
Alignment explanation
Indices: 68598--68883 Score: 322
Period size: 27 Copynumber: 10.6 Consensus size: 27
68588 AATCTCATAT
* * *
68598 CTGTAGGCTAGCATTACTAAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* * *
68625 CTGTAAGGTAGAATTACCGAACTACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* * *
68652 TTGTAGGGTAGAATTACTAAAATTCCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* *
68679 CTATAAGGG-AGAATTACCGAAATACCC
1 CTGT-AGGGTAGAATTACTGAAATACCC
68706 CTGTAGGGTAGAATTACTGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* * *
68733 TTGTAGAGTAGAATTACTGAAATAACC
1 CTGTAGGGTAGAATTACTGAAATACCC
* * **
68760 CTATAAGGTAGAATTACCAAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
*
68787 CTATAGGGTAGAATTACTGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* *
68814 CTGTAGGGGAGAATTACCGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* * * *
68841 TTTTAGGGTAGAAATACTAAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
*
68868 CTGTAGGGTAGGATTA
1 CTGTAGGGTAGAATTA
68884 TCGATTTACC
Statistics
Matches: 212, Mismatches: 45, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
26 4 0.02
27 204 0.96
28 4 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
CTGTAGGGTAGAATTACTGAAATACCC
Found at i:68745 original size:81 final size:81
Alignment explanation
Indices: 68610--68883 Score: 361
Period size: 81 Copynumber: 3.4 Consensus size: 81
68600 GTAGGCTAGC
* * * * *
68610 ATTACTAAAATACCCCTGTAAGGTAGAATTACCGAACTACCCTTGTAGGGTAGAATTACTAAAAT
1 ATTACCAAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTTGTAGGGTAGAATTACTGAAAT
*
68675 TCCCCTATAAGGGAGA
66 TACCCTATAAGGGAGA
* *
68691 ATTACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTTGTAGAGTAGAATTACTGAAAT
1 ATTACCAAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTTGTAGGGTAGAATTACTGAAAT
* *
68756 AACCCTATAAGGTAGA
66 TACCCTATAAGGGAGA
* * * *
68772 ATTACCAAAATACCCCTATAGGGTAGAATTACTGAAATACCCCTGTAGGGGAGAATTACCGAAA-
1 ATTACCAAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTTGTAGGGTAGAATTACTGAAAT
* *
68836 TACCCTTTTAGGGTAGA
66 TACCCTATAAGGG-AGA
* * *
68853 AATACTAAAATACCCCTGTAGGGTAGGATTA
1 ATTACCAAAATACCCCTGTAGGGTAGAATTA
68884 TCGATTTACC
Statistics
Matches: 168, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
80 9 0.05
81 159 0.95
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (81 bp):
ATTACCAAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTTGTAGGGTAGAATTACTGAAAT
TACCCTATAAGGGAGA
Found at i:70626 original size:29 final size:29
Alignment explanation
Indices: 70593--70666 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
70583 GTTATGAGAT
* *
70593 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA
* *
70622 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGACTTGAAAGTACA
70651 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
70667 CGGTTAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGACTTGAAAGTACA
Found at i:78726 original size:29 final size:29
Alignment explanation
Indices: 78693--78766 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
78683 GTTGTGAGAT
* *
78693 TGGCACTAGGTGTGCGAACTTGAAA-TGCA
1 TGGCACTAAGTGTGCG-ACTTGAAAGTACA
* *
78722 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGACTTGAAAGTACA
78751 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
78767 CGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.15
29 34 0.85
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGACTTGAAAGTACA
Done.