Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold516
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: 54616
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:3076 original size:52 final size:52
Alignment explanation
Indices: 2998--3146 Score: 203
Period size: 52 Copynumber: 2.9 Consensus size: 52
2988 CGAAATATGA
2998 AAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCTAGGC
** * * *
3050 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCTAGGC
* *
3102 AAATTTTCCTGCATGTATCAATACA--AAGATTAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTAA-A-TAGTGTATCGATACA
3147 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
51 1 0.01
52 83 0.99
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCTAGGC
Found at i:3153 original size:13 final size:13
Alignment explanation
Indices: 3135--3159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3125 CAAAGATTAG
3135 TGTATCGATACAA
1 TGTATCGATACAA
3148 TGTATCGATACA
1 TGTATCGATACA
3160 CTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3237 original size:33 final size:33
Alignment explanation
Indices: 3200--3266 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3190 AATAGCTTAA
3200 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3233 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3266 A
1 A
3267 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3240 original size:13 final size:13
Alignment explanation
Indices: 3222--3246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3212 CAAAAAAATA
3222 TGTATCGATACAT
1 TGTATCGATACAT
3235 TGTATCGATACA
1 TGTATCGATACA
3247 ACACTTTATG
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:15256 original size:135 final size:135
Alignment explanation
Indices: 15014--15284 Score: 506
Period size: 135 Copynumber: 2.0 Consensus size: 135
15004 TGACACAAAG
15014 CAAGGCACAAACATTTTAGAAGCATGTACATGGCTATTTTGATTAGAAAATCAAAATTTTGAACC
1 CAAGGCACAAACATTTTAGAAGCATGTACATGGCTATTTTGATTAGAAAATCAAAATTTTGAACC
*
15079 TTATTTAATCAAATTTTCAGACCTAAAAATTAAATTTACCCCAAGTTTGTGATGTTCGCTTGATA
66 TTATTTAATCAAATTTCCAGACCTAAAAATTAAATTTACCCCAAGTTTGTGATGTTCGCTTGATA
15144 AAAAT
131 AAAAT
* *
15149 CAAGGCACAAACATTTTAGGAGCATGTGCATGGCTATTTTGATTAGAAAATCAAAATTTTGAACC
1 CAAGGCACAAACATTTTAGAAGCATGTACATGGCTATTTTGATTAGAAAATCAAAATTTTGAACC
*
15214 TTATTTAATCAAATTTCCAGACCTGAAAATTAAATTTACCCCAAGTTTGTGATGTTCGCTTGATA
66 TTATTTAATCAAATTTCCAGACCTAAAAATTAAATTTACCCCAAGTTTGTGATGTTCGCTTGATA
15279 AAAAT
131 AAAAT
15284 C
1 C
15285 TTAAGCTTAT
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
135 132 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (135 bp):
CAAGGCACAAACATTTTAGAAGCATGTACATGGCTATTTTGATTAGAAAATCAAAATTTTGAACC
TTATTTAATCAAATTTCCAGACCTAAAAATTAAATTTACCCCAAGTTTGTGATGTTCGCTTGATA
AAAAT
Found at i:16350 original size:20 final size:20
Alignment explanation
Indices: 16325--16451 Score: 94
Period size: 20 Copynumber: 5.8 Consensus size: 20
16315 TTTTAACTAG
16325 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
16345 ATGTATCGATATATCTGGCTAAAAA
1 ATGTATCGATACAT-T-G---AAAA
16370 GATAGAATGTATCGATACATT-AAAGA
1 -AT-G--T--ATCGATACATTGAAA-A
* * *
16396 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
*
16416 GTGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
16436 ATGTATCGATACATTG
1 ATGTATCGATACATTG
16452 GGGCAAAAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 26
0.71 0.08 0.22
Matches are distributed among these distances:
20 55 0.65
21 3 0.04
22 2 0.02
24 1 0.01
25 9 0.11
26 3 0.04
27 1 0.01
29 1 0.01
30 1 0.01
31 9 0.11
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:16394 original size:24 final size:20
Alignment explanation
Indices: 16373--16450 Score: 99
Period size: 20 Copynumber: 3.9 Consensus size: 20
16363 CTAAAAAGAT
16373 AGAATGTATCGATACATTAA
1 AGAATGTATCGATACATTAA
16393 AGAATGTATCGATACATTCATA
1 AGAATGTATCGATACATT-A-A
*
16415 CG--TGTATCGATACATTGAA
1 AGAATGTATCGATACATT-AA
16434 A-AATGTATCGATACATT
1 AGAATGTATCGATACATT
16451 GGGGCAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.02
20 47 0.92
21 1 0.02
22 2 0.04
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTAA
Found at i:20518 original size:27 final size:27
Alignment explanation
Indices: 20466--20520 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
20456 TTTGGTTGAA
* *
20466 AAATGGGGTTGGAGTATCCCCTCGAAG
1 AAATGGGGTTGGAATATCCCCACGAAG
*
20493 AAATGGGGTTGGAATATCCCGACGAAG
1 AAATGGGGTTGGAATATCCCCACGAAG
20520 A
1 A
20521 TAATTTGAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.33, T:0.20
Consensus pattern (27 bp):
AAATGGGGTTGGAATATCCCCACGAAG
Found at i:20720 original size:148 final size:148
Alignment explanation
Indices: 20452--20748 Score: 542
Period size: 148 Copynumber: 2.0 Consensus size: 148
20442 AAAAAATTTT
*
20452 GATTTTTGGTTGAAAAATGGGGTTGGAGTATCCCCTCGAAGAAATGGGGTTGGAATATCCCGACG
1 GATTTTTGGTTGAAAAACGGGGTTGGAGTATCCCCTCGAAGAAATGGGGTTGGAATATCCCGACG
*
20517 AAGATAATTTGAGCAAAATAAAATCTAAATCTTAAGAAGTTTAAGGCGAGGTTGGAGTATCCCCT
66 AAGATAATTTGAGCAAAATAAAATCTAAATCTTAAGAAGTTTAAAGCGAGGTTGGAGTATCCCCT
20582 CGGAAGAATGGGGTTAGA
131 CGGAAGAATGGGGTTAGA
*
20600 GATTTTTGGTTGAAAAACGGGGTTGGAGTATCCCCTCGGAGAAATGGGGTTGGAATATCCCGACG
1 GATTTTTGGTTGAAAAACGGGGTTGGAGTATCCCCTCGAAGAAATGGGGTTGGAATATCCCGACG
*
20665 AAGATAATTTGAGCAAAATAAAAAT-TAAATCTTGAGAAGTTTAAAGCGAGGTTGGAGTATCCCC
66 AAGATAATTTGAGCAAAAT-AAAATCTAAATCTTAAGAAGTTTAAAGCGAGGTTGGAGTATCCCC
20729 TCGGAAGAATGGGGTTAGA
130 TCGGAAGAATGGGGTTAGA
20748 G
1 G
20749 TACCCCCGAT
Statistics
Matches: 144, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 139 0.97
149 5 0.03
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (148 bp):
GATTTTTGGTTGAAAAACGGGGTTGGAGTATCCCCTCGAAGAAATGGGGTTGGAATATCCCGACG
AAGATAATTTGAGCAAAATAAAATCTAAATCTTAAGAAGTTTAAAGCGAGGTTGGAGTATCCCCT
CGGAAGAATGGGGTTAGA
Found at i:22191 original size:21 final size:21
Alignment explanation
Indices: 22165--22220 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
22155 ATGGTAGTTT
22165 TGTATCGATACATTTCAAGCA
1 TGTATCGATACATTTCAAGCA
* ***
22186 TGTATCAATACA-TTCACTTA
1 TGTATCGATACATTTCAAGCA
22206 TGTATCGATACATTT
1 TGTATCGATACATTT
22221 ACTGTTTGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTTCAAGCA
Found at i:22232 original size:21 final size:21
Alignment explanation
Indices: 22185--22238 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
22175 CATTTCAAGC
*
22185 ATGTATCAATACATTCACT-T
1 ATGTATCAATACATTTACTGT
*
22205 ATGTATCGATACATTTACTGT
1 ATGTATCAATACATTTACTGT
*
22226 TTGTATCAATACA
1 ATGTATCAATACA
22239 AATTATAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (21 bp):
ATGTATCAATACATTTACTGT
Found at i:24512 original size:24 final size:24
Alignment explanation
Indices: 24480--24530 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
24470 GTGTTTGTAG
24480 GGTTGATTCTTGTGATTGAGCTAA
1 GGTTGATTCTTGTGATTGAGCTAA
24504 GGTTGATTCTTGTGATTGAGCTAA
1 GGTTGATTCTTGTGATTGAGCTAA
24528 GGT
1 GGT
24531 AAAGGCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.08, G:0.31, T:0.41
Consensus pattern (24 bp):
GGTTGATTCTTGTGATTGAGCTAA
Found at i:25053 original size:26 final size:26
Alignment explanation
Indices: 25004--25113 Score: 139
Period size: 26 Copynumber: 4.2 Consensus size: 26
24994 TATAATGATA
*
25004 GGATTGATAAAGTTTCAACTTTATCTG
1 GGATTAATAAAG-TTCAACTTTATCTG
* * *
25031 GGATTGATAAAATTCAACTTTATCTA
1 GGATTAATAAAGTTCAACTTTATCTG
* *
25057 GGATTAATAAAGTTTAACTTTATCCG
1 GGATTAATAAAGTTCAACTTTATCTG
* *
25083 GGATTAATAAAGTTAAACTTTATTTG
1 GGATTAATAAAGTTCAACTTTATCTG
25109 GGATT
1 GGATT
25114 CTAGATAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
26 62 0.85
27 11 0.15
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (26 bp):
GGATTAATAAAGTTCAACTTTATCTG
Found at i:25113 original size:52 final size:53
Alignment explanation
Indices: 25002--25105 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 53
24992 TTTATAATGA
* * * *
25002 TAGGATTGATAAAGTTTCAACTTTATCTGGGATTGATAAAATTCAACTTTATC
1 TAGGATTAATAAAGTTTCAACTTTATCCGGGATTAATAAAATTAAACTTTATC
*
25055 TAGGATTAATAAAGTTT-AACTTTATCCGGGATTAATAAAGTTAAACTTTAT
1 TAGGATTAATAAAGTTTCAACTTTATCCGGGATTAATAAAATTAAACTTTAT
25106 TTGGGATTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 30 0.65
53 16 0.35
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (53 bp):
TAGGATTAATAAAGTTTCAACTTTATCCGGGATTAATAAAATTAAACTTTATC
Found at i:25959 original size:43 final size:43
Alignment explanation
Indices: 25912--25998 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
25902 TAAATTTAAA
25912 TATACTCATTTTGATTGGACACTATGTTATTTATACTATTTAT
1 TATACTCATTTTGATTGGACACTATGTTATTTATACTATTTAT
25955 TATACTCATTTTGATTGGACACTATGTTATTTATACTATTTAT
1 TATACTCATTTTGATTGGACACTATGTTATTTATACTATTTAT
25998 T
1 T
25999 CTAACTTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.52
Consensus pattern (43 bp):
TATACTCATTTTGATTGGACACTATGTTATTTATACTATTTAT
Found at i:26035 original size:19 final size:19
Alignment explanation
Indices: 26011--26064 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
26001 AACTTTAAAG
26011 TTTTTTATTTTTTGATTCAT
1 TTTTTTATTTTTT-ATTCAT
* * *
26031 TTTTTGAATTTTTCTTCAT
1 TTTTTTATTTTTTATTCAT
26050 TATTTTTATTTTTTA
1 T-TTTTTATTTTTTA
26065 AAATTTCTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTTTATTTTTTATTCAT
Found at i:27545 original size:13 final size:13
Alignment explanation
Indices: 27527--27552 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27517 CAATTTTTTG
27527 TGTATCGATACAT
1 TGTATCGATACAT
27540 TGTATCGATACAT
1 TGTATCGATACAT
27553 ACTTTGTGTA
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:27564 original size:32 final size:33
Alignment explanation
Indices: 27507--27570 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
27497 TACAAGCCAA
**
27507 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
27540 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
27571 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:27969 original size:20 final size:20
Alignment explanation
Indices: 27946--28018 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
27936 ACAATTCAAA
27946 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
27966 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
27987 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
28007 GTATCGATACAT
1 GTATCGATACAT
28019 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:27990 original size:21 final size:21
Alignment explanation
Indices: 27964--28039 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
27954 ACATGTTGCA
27964 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
27985 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
28005 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
28026 ATGTATCGATACAT
1 ATGTATCGATACAT
28040 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:27997 original size:41 final size:41
Alignment explanation
Indices: 27946--28039 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
27936 ACAATTCAAA
*
27946 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
27987 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
28028 GTATCGATACAT
1 GTATCGATACAT
28040 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:28096 original size:13 final size:13
Alignment explanation
Indices: 28078--28103 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28068 TACAGCAAGT
28078 ATGTATCGATACA
1 ATGTATCGATACA
28091 ATGTATCGATACA
1 ATGTATCGATACA
28104 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:30352 original size:21 final size:21
Alignment explanation
Indices: 30319--30363 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
30309 TTGCAAGTTG
*
30319 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
30341 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
30361 AAA
1 AAA
30364 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:32187 original size:15 final size:15
Alignment explanation
Indices: 32167--32197 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
32157 TAAAAATGTC
*
32167 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
32182 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
32197 C
1 C
32198 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:34297 original size:13 final size:13
Alignment explanation
Indices: 34279--34316 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
34269 CATTTTTATT
34279 TGTATCGATACAA
1 TGTATCGATACAA
*
34292 TGTATCGATACAC
1 TGTATCGATACAA
34305 TGTATCGATACA
1 TGTATCGATACA
34317 GGGTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:36749 original size:20 final size:20
Alignment explanation
Indices: 36726--36798 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
36716 ACAATTCAAA
36726 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
36746 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
36767 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
36787 GTATCGATACAT
1 GTATCGATACAT
36799 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:36770 original size:21 final size:21
Alignment explanation
Indices: 36744--36819 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
36734 ACATGTTGCA
36744 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
36765 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
36785 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
36806 ATGTATCGATACAT
1 ATGTATCGATACAT
36820 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:36777 original size:41 final size:41
Alignment explanation
Indices: 36726--36819 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
36716 ACAATTCAAA
*
36726 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
36767 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
36808 GTATCGATACAT
1 GTATCGATACAT
36820 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:36876 original size:13 final size:13
Alignment explanation
Indices: 36858--36883 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36848 TACAGCAAGT
36858 ATGTATCGATACA
1 ATGTATCGATACA
36871 ATGTATCGATACA
1 ATGTATCGATACA
36884 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:38217 original size:18 final size:18
Alignment explanation
Indices: 38194--38232 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
38184 AATCAAAATA
38194 ATTTTAACAAATTCGTAC
1 ATTTTAACAAATTCGTAC
*
38212 ATTTTAACGAATTCGTAC
1 ATTTTAACAAATTCGTAC
38230 ATT
1 ATT
38233 CTCCCCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (18 bp):
ATTTTAACAAATTCGTAC
Found at i:40127 original size:13 final size:13
Alignment explanation
Indices: 40109--40133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40099 ATAATCCCCC
40109 TGTATCGATACAG
1 TGTATCGATACAG
40122 TGTATCGATACA
1 TGTATCGATACA
40134 AAGAAAAATG
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:42236 original size:15 final size:15
Alignment explanation
Indices: 42200--42237 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
42190 TTCATTAATT
* *
42200 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
42215 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
42230 TCATTTTG
1 TCATTTTG
42238 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:46000 original size:32 final size:30
Alignment explanation
Indices: 45964--46022 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
45954 GAAATCAAAT
45964 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
45996 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
46023 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:46352 original size:19 final size:18
Alignment explanation
Indices: 46282--46352 Score: 53
Period size: 19 Copynumber: 4.0 Consensus size: 18
46272 TACAAGCCAA
*
46282 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA--TTTGG
46302 TGTATCGATAC-A-TT-G
1 TGTATCGATACAATTTGG
*
46317 T-T-TCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
46334 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
46353 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 7 0.16
14 1 0.02
15 3 0.07
16 4 0.09
17 2 0.05
18 2 0.05
19 13 0.30
20 11 0.26
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:46422 original size:20 final size:20
Alignment explanation
Indices: 46376--46452 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
46366 TTCCCAATGA
***
46376 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGAAT
46397 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
46417 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
**
46437 TGTGTATCGATACATT
1 CATGTATCGATACATT
46453 TAAGGGTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.04
20 30 0.64
21 15 0.32
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:48975 original size:79 final size:79
Alignment explanation
Indices: 48837--49040 Score: 239
Period size: 79 Copynumber: 2.6 Consensus size: 79
48827 GAGATAATAA
* * * ** * *
48837 CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGA
1 CGGGGTTGGAGTATACCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAAT-A
*
48902 -TTAGGGAATAAAAT
65 TTTAGGGAATAAAAC
* * * *
48916 CGGGATTGGAGTATTCCCTCGGAAATAACGGGGTTGGAGTATCCCTAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATACCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
* *
48981 TTTGGGAATAAAGC
66 TTAGGGAATAAAAC
* **
48995 CGGGGTTGAAGTATACCCTCGGAGGTAACGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATACCCTCGGAAATAACGGGGTTGGAGTATCCCC
49041 GATGAAATAA
Statistics
Matches: 105, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 1 0.01
79 104 0.99
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATACCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
TTAGGGAATAAAAC
Found at i:49116 original size:52 final size:51
Alignment explanation
Indices: 49058--49188 Score: 156
Period size: 52 Copynumber: 2.5 Consensus size: 51
49048 TAACGAGGTT
*
49058 GGAGTATCCTCGA-TAGTGAAAAATTGGTGTTTTTGGAAATAAAATCAGAGTC
1 GGAGTATCCTCGATTA-TGAAAAATTGGTG-TTTTGAAAATAAAATCAGAGTC
* * * * * *
49110 GGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGGGGTT
1 GGAGTATCCTCGATT-ATGAAAAATTGGTGTTTTGAAAATAAAATCAGAGTC
*
49162 GGAGTATCCTCGATTATGAACAATTGG
1 GGAGTATCCTCGATTATGAAAAATTGG
49189 GAAACTTAAC
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
51 9 0.14
52 44 0.67
53 12 0.18
54 1 0.02
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
GGAGTATCCTCGATTATGAAAAATTGGTGTTTTGAAAATAAAATCAGAGTC
Found at i:51558 original size:13 final size:13
Alignment explanation
Indices: 51540--51565 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51530 ACAAAGATCG
51540 ATGTATCGATACA
1 ATGTATCGATACA
51553 ATGTATCGATACA
1 ATGTATCGATACA
51566 TTTCCTTAAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:51576 original size:21 final size:21
Alignment explanation
Indices: 51552--51593 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
51542 GTATCGATAC
51552 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
51573 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
51594 GGCAGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:51640 original size:19 final size:19
Alignment explanation
Indices: 51618--51735 Score: 80
Period size: 19 Copynumber: 6.7 Consensus size: 19
51608 ACCGATACAT
*
51618 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTAA
51637 TGTATCGAT-----A-TAA
1 TGTATCGATACAAAACTAA
*
51650 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTAA
51669 TGTATCGAT-----A-TAA
1 TGTATCGATACAAAACTAA
* *
51682 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTAA
**
51701 TGTATCGATACATTTACTGAA
1 TGTATCGATACA-AAACT-AA
51722 TGTATCGATACAAA
1 TGTATCGATACAAA
51736 TTATTGAAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 27
0.68 0.08 0.24
Matches are distributed among these distances:
13 22 0.29
14 2 0.03
18 2 0.03
19 34 0.45
20 3 0.04
21 13 0.17
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTAA
Found at i:51654 original size:32 final size:32
Alignment explanation
Indices: 51618--51710 Score: 177
Period size: 32 Copynumber: 2.9 Consensus size: 32
51608 ACCGATACAT
51618 TGTATCGATACAAAACTTATGTATCGATATAA
1 TGTATCGATACAAAACTTATGTATCGATATAA
51650 TGTATCGATACAAAACTTATGTATCGATATAA
1 TGTATCGATACAAAACTTATGTATCGATATAA
*
51682 TGTATCGATACAACACTTATGTATCGATA
1 TGTATCGATACAAAACTTATGTATCGATA
51711 CATTTACTGA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATATAA
Done.