Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold898
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: 65335
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:7089 original size:13 final size:13
Alignment explanation
Indices: 7071--7096 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7061 AGACACAATA
7071 TGTATCGATACAT
1 TGTATCGATACAT
7084 TGTATCGATACAT
1 TGTATCGATACAT
7097 CCCAAAATGT
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:7092 original size:32 final size:33
Alignment explanation
Indices: 7051--7117 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
7041 CCTTAACTGT
* *
7051 TTGTATCGATAGA-CACAATATGTATCGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
* *
7083 TTGTATCGATACATCCCAAAATGTATCTATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
7116 TT
1 TT
7118 AGCTTGTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTATCGATACA
Found at i:9293 original size:58 final size:58
Alignment explanation
Indices: 9219--9438 Score: 182
Period size: 58 Copynumber: 3.8 Consensus size: 58
9209 TAGGGTTAAT
* *
9219 GTATAATTTT-AGAAAATTGAGGAGGCAAAATGTAATTTTAAAAAGTTCAAAGGTCAAA
1 GTATAATTTTGA-AAAATTTAGGAGGCAAAGTGTAATTTTAAAAAGTTCAAAGGTCAAA
* * * * * * *
9277 GCATAATTTTGAAAAATTTA-AAGGTCAAATTGTAATTTTGATAAGTT-AAGGGTCAAT
1 GTATAATTTTGAAAAATTTAGGAGG-CAAAGTGTAATTTTAAAAAGTTCAAAGGTCAAA
* * ** *
9334 GTGTAATTTTGAAAAGTTTAGG-GATTAATGTGTAATTTTAAAAAGTTC-AAGGATCAAA
1 GTATAATTTTGAAAAATTTAGGAG-GCAAAGTGTAATTTTAAAAAGTTCAAAGG-TCAAA
* * * * *
9392 GTGTAATTTTTAAAAGTTTATGGA-TCAATGTGTAATTTTAAAAAGTT
1 GTATAATTTTGAAAAATTTA-GGAGGCAAAGTGTAATTTTAAAAAGTT
9439 TAGGTACTTA
Statistics
Matches: 132, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
57 49 0.37
58 80 0.61
59 3 0.02
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (58 bp):
GTATAATTTTGAAAAATTTAGGAGGCAAAGTGTAATTTTAAAAAGTTCAAAGGTCAAA
Found at i:9439 original size:29 final size:29
Alignment explanation
Indices: 9249--9440 Score: 187
Period size: 29 Copynumber: 6.7 Consensus size: 29
9239 GGAGGCAAAA
* *
9249 TGTAATTTTAAAAAGTTCAAAGG-TCAAAG
1 TGTAATTTTAAAAAGTT-TAAGGATCAATG
**
9278 CATAATTTTGAAAAA-TTTAAAGG-TCAAAT-
1 TGTAATTTT-AAAAAGTTT-AAGGATC-AATG
* * *
9307 TGTAATTTTGATAAG-TTAAGGGTCAATG
1 TGTAATTTTAAAAAGTTTAAGGATCAATG
* * *
9335 TGTAATTTTGAAAAGTTTAGGGATTAATG
1 TGTAATTTTAAAAAGTTTAAGGATCAATG
* *
9364 TGTAATTTTAAAAAGTTCAAGGATCAAAG
1 TGTAATTTTAAAAAGTTTAAGGATCAATG
* *
9393 TGTAATTTTTAAAAGTTTATGGATCAATG
1 TGTAATTTTAAAAAGTTTAAGGATCAATG
9422 TGTAATTTTAAAAAGTTTA
1 TGTAATTTTAAAAAGTTTA
9441 GGTACTTAAT
Statistics
Matches: 134, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
27 7 0.05
28 21 0.16
29 99 0.74
30 7 0.05
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (29 bp):
TGTAATTTTAAAAAGTTTAAGGATCAATG
Found at i:13082 original size:53 final size:53
Alignment explanation
Indices: 13019--13119 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 53
13009 CATGTGCTAC
* * *
13019 TGGGGTGAGTAGACCT-TTGAAGTCTTAATGAGTGACTTAGTGTCACATTCCGT
1 TGGGGCGAGTAGACCTGGTG-AGTCTTAATGAATGACTTAGTGTCACATTCCGT
* *
13072 TGGGGCGAGTAGACCTGGTGTGTCTTAATGAATGACTTGGTGTCACAT
1 TGGGGCGAGTAGACCTGGTGAGTCTTAATGAATGACTTAGTGTCACAT
13120 CGTATTTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 40 0.95
54 2 0.05
ACGTcount: A:0.22, C:0.15, G:0.31, T:0.33
Consensus pattern (53 bp):
TGGGGCGAGTAGACCTGGTGAGTCTTAATGAATGACTTAGTGTCACATTCCGT
Found at i:16947 original size:16 final size:16
Alignment explanation
Indices: 16904--16953 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
16894 AACTCTAAAA
*
16904 TAAATTATAAAAGAATT
1 TAAATT-TAAAACAATT
**
16921 TAAATACAAAACAATT
1 TAAATTTAAAACAATT
*
16937 TAAATTTAAAATAATT
1 TAAATTTAAAACAATT
16953 T
1 T
16954 GACTTTTAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 22 0.81
17 5 0.19
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (16 bp):
TAAATTTAAAACAATT
Found at i:24023 original size:20 final size:19
Alignment explanation
Indices: 23998--24035 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
23988 TAAATTGGTT
*
23998 TTTTTTTTTAATTTAATATA
1 TTTTTTATTAA-TTAATATA
24018 TTTTTTATTAATTAATAT
1 TTTTTTATTAATTAATAT
24036 TTAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTTATTAATTAATATA
Found at i:25151 original size:17 final size:17
Alignment explanation
Indices: 25129--25180 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 17
25119 TATTTAAAAT
25129 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
*
25146 ATTTTA-ATATA-AT-A
1 ATTTTATATTTATATAA
25160 A-TTTATA-TTATATAA
1 ATTTTATATTTATATAA
25175 ATTTTA
1 ATTTTA
25181 ATATAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 6 0.21
14 5 0.17
15 4 0.14
16 8 0.28
17 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:25162 original size:14 final size:14
Alignment explanation
Indices: 25145--25192 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
25135 TATTTATATA
25145 AATTTTAATATAAT
1 AATTTTAATATAAT
*
25159 AATTTATATTAT-AT
1 AATTT-TAATATAAT
25173 AAATTTTAATATAAT
1 -AATTTTAATATAAT
*
25188 TATTT
1 AATTT
25193 ATTCATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATTTTAATATAAT
Found at i:25171 original size:15 final size:15
Alignment explanation
Indices: 25112--25194 Score: 50
Period size: 15 Copynumber: 5.6 Consensus size: 15
25102 AAGTTGTATT
*
25112 ATAATTGTAT-TTAAA
1 ATAATT-TATATTATA
*
25127 ATATTTTATATT-TA
1 ATAATTTATATTATA
*
25141 TATAAATTT-TAATATA
1 -AT-AATTTATATTATA
25157 ATAATTTATATTAT-
1 ATAATTTATATTATA
*
25171 ATAAATTT-TAATATA
1 AT-AATTTATATTATA
*
25186 ATTATTTAT
1 ATAATTTAT
25195 TCATATTATT
Statistics
Matches: 53, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
14 20 0.38
15 27 0.51
16 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (15 bp):
ATAATTTATATTATA
Found at i:25175 original size:29 final size:30
Alignment explanation
Indices: 25126--25194 Score: 113
Period size: 29 Copynumber: 2.3 Consensus size: 30
25116 TTGTATTTAA
*
25126 AATATTTTATATTTATATAAATTTTAATAT
1 AATAATTTATATTTATATAAATTTTAATAT
25156 AATAATTTATA-TTATATAAATTTTAATAT
1 AATAATTTATATTTATATAAATTTTAATAT
*
25185 AATTATTTAT
1 AATAATTTAT
25195 TCATATTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
29 27 0.73
30 10 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
AATAATTTATATTTATATAAATTTTAATAT
Found at i:25184 original size:17 final size:16
Alignment explanation
Indices: 25129--25180 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 16
25119 TATTTAAAAT
25129 ATTTTATATTTATATAA
1 ATTTTATA-TTATATAA
25146 ATTTTA-A-TATA-ATA
1 ATTTTATATTATATA-A
25160 A-TTTATATTATATAA
1 ATTTTATATTATATAA
25175 ATTTTA
1 ATTTTA
25181 ATATAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
13 5 0.17
14 7 0.23
15 6 0.20
16 6 0.20
17 6 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTATATTATATAA
Found at i:25233 original size:17 final size:17
Alignment explanation
Indices: 25199--25236 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
25189 ATTTATTCAT
*
25199 ATTA-TTTTAAATTTTA
1 ATTATTTTTAAATTATA
*
25215 ATTATTTTTATATTATA
1 ATTATTTTTAAATTATA
25232 ATTAT
1 ATTAT
25237 GTAACGGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTATTTTTAAATTATA
Found at i:25420 original size:10 final size:11
Alignment explanation
Indices: 25377--25421 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
25367 GTTAACAAAT
25377 ATTTTATTATA
1 ATTTTATTATA
* *
25388 TTTTTATAATA
1 ATTTTATTATA
25399 ATTTTATT-TA
1 ATTTTATTATA
25409 ATTTT-TTATA
1 ATTTTATTATA
25419 ATT
1 ATT
25422 ACTTTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 2 0.07
10 12 0.41
11 15 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTATTATA
Found at i:25603 original size:3 final size:3
Alignment explanation
Indices: 25586--25650 Score: 53
Period size: 3 Copynumber: 21.3 Consensus size: 3
25576 ATATAAAAAT
* * * *
25586 ATA A-A ATA TTA ATA ATA ACA ATA TTA ATA ATA ATTA ATA ATA AGAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA A-TA
25632 ATA A-A ATA ATA ATTA ATA A
1 ATA ATA ATA ATA A-TA ATA A
25651 AAAATTGACT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
2 4 0.08
3 37 0.76
4 8 0.16
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:25603 original size:22 final size:22
Alignment explanation
Indices: 25578--25653 Score: 82
Period size: 22 Copynumber: 3.3 Consensus size: 22
25568 TTTTTAACAT
25578 ATAAAAATATAAAATATTAATA
1 ATAAAAATATAAAATATTAATA
*
25600 ATAACAATATTAATAATAATTAATA
1 ATAAAAATA-TAA-AAT-ATTAATA
* *
25625 ATAAGAA-ATAAAATAATAATTA
1 ATAAAAATATAAAATATTAA-TA
25647 ATAAAAA
1 ATAAAAA
25654 ATTGACTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.09
22 19 0.41
23 6 0.13
24 4 0.09
25 13 0.28
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (22 bp):
ATAAAAATATAAAATATTAATA
Found at i:25608 original size:15 final size:14
Alignment explanation
Indices: 25586--25652 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 14
25576 ATATAAAAAT
25586 ATAAAATATTAATA
1 ATAAAATATTAATA
25600 ATAACAATATTAATA
1 ATAA-AATATTAATA
* *
25615 ATAATTAATAATAAGAA
1 ATAA--AATATTAA-TA
*
25632 ATAAAATAATAATTA
1 ATAAAATATTAA-TA
25647 ATAAAA
1 ATAAAA
25653 AATTGACTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.09
15 29 0.64
16 7 0.16
17 5 0.11
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (14 bp):
ATAAAATATTAATA
Found at i:25639 original size:25 final size:24
Alignment explanation
Indices: 25578--25654 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 24
25568 TTTTTAACAT
25578 ATAAAAATATAA-AAT-ATTAATA
1 ATAAAAATATAATAATAATTAATA
*
25600 ATAACAATATTAATAATAATTAATA
1 ATAAAAATA-TAATAATAATTAATA
*
25625 ATAAGAAATAAAATAATAATTAATA
1 ATAA-AAATATAATAATAATTAATA
25650 A-AAAA
1 ATAAAA
25655 TTGACTAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
22 8 0.17
23 5 0.10
24 5 0.10
25 26 0.54
26 4 0.08
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (24 bp):
ATAAAAATATAATAATAATTAATA
Found at i:29232 original size:43 final size:41
Alignment explanation
Indices: 29162--29320 Score: 151
Period size: 43 Copynumber: 3.7 Consensus size: 41
29152 ATTTACCGTA
* * *
29162 TAAACGTCGCGAAATATTAAAATTTAGTGGCATTTTAAGCGTG
1 TAAA-GTCGCTAAAT-TTCAAATTTAGTGGCATTTTAAGTGTG
*
29205 TAAATGTTGCTAAATTTCAAATTTTAGTGGCATTTTAAGTGTGG
1 TAAA-GTCGCTAAATTTCAAA-TTTAGTGGCATTTTAAGTGT-G
* * * * *
29249 GAAAGCCACTAAATTTCAAAATTTAGTGGCCTTTT--GTGTA
1 TAAAGTCGCTAAATTTC-AAATTTAGTGGCATTTTAAGTGTG
29289 TAAACGTCGCTAAATTTCAACATTTAGTGGCA
1 TAAA-GTCGCTAAATTTCAA-ATTTAGTGGCA
29321 CTTATCTATA
Statistics
Matches: 96, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
40 5 0.05
41 25 0.26
42 5 0.05
43 54 0.56
44 7 0.07
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36
Consensus pattern (41 bp):
TAAAGTCGCTAAATTTCAAATTTAGTGGCATTTTAAGTGTG
Found at i:34014 original size:250 final size:251
Alignment explanation
Indices: 33567--34068 Score: 907
Period size: 250 Copynumber: 2.0 Consensus size: 251
33557 GCTTCATTTG
* *
33567 GATCATCTTCTTCGTCTTCATCCTCATCACTTTGATTATCAAAATCATCACCTTCATACACCTCC
1 GATCATCTTCTTCGTCTTCATCCTCATCACTCTAATTATCAAAATCATCACCTTCATACACCTCC
*
33632 CATAACTGCTTTAACTCTTAAATAAGAGGTTGAGTATAAATGTCAATATCATTCCCTGGACCTTT
66 CATAACTGCTTTAACTCTTAAATAAGAGGTTAAGTATAAATGTCAATATCATTCCCTGGACCTTT
*
33697 CTCTTTGGGAATAATCATAAACAAGATAAAGAAAGATTGTTTCATTCAAATCCATGAGGGCAAAT
131 CTCTCTGGGAATAATCATAAACAAGATAAAGAAAGATTGTTTCATTCAAATCCATGAGGGCAAAT
33762 TATAAAG-ATTAAGATAATTGTCCAAATACTATAAAAAGTACTTATCATTTTAAAT
196 TATAAAGAATTAAGATAATTGTCCAAATACTATAAAAAGTACTTATCATTTTAAAT
33817 GATCATCTTCTTCGTCTTCATCCTCATCACTCTAATTATCAAAATCATCACCTTCATACACCTCC
1 GATCATCTTCTTCGTCTTCATCCTCATCACTCTAATTATCAAAATCATCACCTTCATACACCTCC
*
33882 CATAACTGCTTTAACTCTTCAATAAGAGGTTAAGTATAAATGTCAATATCATTCCCTGGACCTTT
66 CATAACTGCTTTAACTCTTAAATAAGAGGTTAAGTATAAATGTCAATATCATTCCCTGGACCTTT
* *
33947 CTCTCTGGGAATAATCATAAACAAGATAAAGAAAGATTGTTTCATTCAAATCCATGGGGGGAAAT
131 CTCTCTGGGAATAATCATAAACAAGATAAAGAAAGATTGTTTCATTCAAATCCATGAGGGCAAAT
* * *
34012 TATAAAGAATTAAGATAATTGTCCAAGTACTATAAGAAGTATTTATCATTTTAAAT
196 TATAAAGAATTAAGATAATTGTCCAAATACTATAAAAAGTACTTATCATTTTAAAT
34068 G
1 G
34069 GATTAAAACC
Statistics
Matches: 241, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
250 195 0.81
251 46 0.19
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (251 bp):
GATCATCTTCTTCGTCTTCATCCTCATCACTCTAATTATCAAAATCATCACCTTCATACACCTCC
CATAACTGCTTTAACTCTTAAATAAGAGGTTAAGTATAAATGTCAATATCATTCCCTGGACCTTT
CTCTCTGGGAATAATCATAAACAAGATAAAGAAAGATTGTTTCATTCAAATCCATGAGGGCAAAT
TATAAAGAATTAAGATAATTGTCCAAATACTATAAAAAGTACTTATCATTTTAAAT
Found at i:35603 original size:25 final size:27
Alignment explanation
Indices: 35570--35628 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
35560 ATAAATCATT
*
35570 TATTAAATT-TTAAATTAAT-TAAAAA
1 TATTTAATTATTAAATTAATATAAAAA
* *
35595 TATTTAATTATTTACTTAATATAAAAA
1 TATTTAATTATTAAATTAATATAAAAA
35622 T-TTTAAT
1 TATTTAAT
35629 CGTTACATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 8 0.28
26 14 0.48
27 7 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
TATTTAATTATTAAATTAATATAAAAA
Found at i:41123 original size:35 final size:35
Alignment explanation
Indices: 41046--41140 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 35
41036 AAACATTTCG
** *
41046 ACATGTCAACCTACTCCTCATCAACTAGATAATTC
1 ACATGTCAACCTACTCCTTGTCAACTAGATAATAC
* * * *
41081 ACGTGTCAACTTGCTCCTTGTCAACTAGATACTAC
1 ACATGTCAACCTACTCCTTGTCAACTAGATAATAC
* *
41116 ATATGTCAACCTATTCCTTGTCAAC
1 ACATGTCAACCTACTCCTTGTCAAC
41141 CATGCAGCTT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.32
Consensus pattern (35 bp):
ACATGTCAACCTACTCCTTGTCAACTAGATAATAC
Found at i:42265 original size:21 final size:21
Alignment explanation
Indices: 42239--42293 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
42229 GTTACAAGCA
*
42239 ATGTATCGATACAATT-TCCC
1 ATGTATCGATACAATTGTACC
42259 TATGTATCGATAC-ATTGTACC
1 -ATGTATCGATACAATTGTACC
42280 ATGTATCGATACAA
1 ATGTATCGATACAA
42294 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACAATTGTACC
Found at i:42285 original size:20 final size:20
Alignment explanation
Indices: 42239--42292 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
42229 GTTACAAGCA
*
42239 ATGTATCGATACAATTTCCCT
1 ATGTATCGATAC-ATTTACCT
42260 ATGTATCGATACATTGTACC-
1 ATGTATCGATACATT-TACCT
42280 ATGTATCGATACA
1 ATGTATCGATACA
42293 AATAGTGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTTACCT
Found at i:42366 original size:19 final size:19
Alignment explanation
Indices: 42322--42377 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
42312 CTGCCAATCT
*
42322 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
*
42342 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAC
42361 CATGTATCGATACAATG
1 CATGTATCGATACAATG
42378 TATCAATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:46846 original size:13 final size:13
Alignment explanation
Indices: 46828--46853 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46818 TACACCAAGT
46828 ATGTATCGATACA
1 ATGTATCGATACA
46841 ATGTATCGATACA
1 ATGTATCGATACA
46854 CCAAAAAATT
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:46872 original size:34 final size:32
Alignment explanation
Indices: 46810--46874 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
46800 TAGCCAAACT
**
46810 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
46842 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
46875 TTGGCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:49079 original size:19 final size:19
Alignment explanation
Indices: 49055--49120 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
49045 TTTCAACGAT
*
49055 TTGTATAGATACATAAGTG
1 TTGTATCGATACATAAGTG
49074 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
49088 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
49106 TTGTATCGATACATA
1 TTGTATCGATACATA
49121 TGAAGCTACT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 25 0.62
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:49092 original size:32 final size:32
Alignment explanation
Indices: 49056--49118 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
49046 TTCAACGATT
49056 TGTATAGATACATAAGTGTTGTATCGATACAA
1 TGTATAGATACATAAGTGTTGTATCGATACAA
*
49088 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATAGATACATAAGTGTTGTATCGATACA
49119 TATGAAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATAGATACATAAGTGTTGTATCGATACAA
Found at i:49093 original size:13 final size:13
Alignment explanation
Indices: 49075--49099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49065 ACATAAGTGT
49075 TGTATCGATACAA
1 TGTATCGATACAA
49088 TGTATCGATACA
1 TGTATCGATACA
49100 TAAGTGTTGT
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:49180 original size:13 final size:13
Alignment explanation
Indices: 49162--49186 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49152 ATTACTCAAA
49162 TGTATCGATACAT
1 TGTATCGATACAT
49175 TGTATCGATACA
1 TGTATCGATACA
49187 CTGATCTTTG
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:49253 original size:48 final size:51
Alignment explanation
Indices: 49195--49319 Score: 184
Period size: 52 Copynumber: 2.5 Consensus size: 51
49185 CACTGATCTT
*
49195 TGTATCGATACATGCAGGCAAATTTGCCC-A-G-ATCTATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAATGTATCGATACACTATGAAA
* *
49243 TGTATCGATACATACAAGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCA-ATGTATCGATACACTATGAAA
*
49295 TGTATCGATACTTGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
49320 TCATATTTCG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
48 27 0.40
50 1 0.01
51 1 0.01
52 38 0.57
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (51 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAATGTATCGATACACTATGAAA
Found at i:55975 original size:20 final size:20
Alignment explanation
Indices: 55950--56009 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
55940 CTGCCAATCT
55950 CATGTATCGATACAATTATC
1 CATGTATCGATACAATTATC
* * *
55970 CATGTATCGATATAATGA-G
1 CATGTATCGATACAATTATC
55989 CATGTATCGATACAATGTATC
1 CATGTATCGATACAAT-TATC
56010 GATACAAAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTATC
Found at i:55994 original size:19 final size:20
Alignment explanation
Indices: 55950--56005 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
55940 CTGCCAATCT
*
55950 CATGTATCGATACAATTATC
1 CATGTATCGATACAATGATC
* *
55970 CATGTATCGATATAATGA-G
1 CATGTATCGATACAATGATC
55989 CATGTATCGATACAATG
1 CATGTATCGATACAATG
56006 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATGATC
Found at i:56008 original size:13 final size:13
Alignment explanation
Indices: 55990--56016 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55980 TATAATGAGC
55990 ATGTATCGATACA
1 ATGTATCGATACA
56003 ATGTATCGATACA
1 ATGTATCGATACA
56016 A
1 A
56017 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:61302 original size:53 final size:53
Alignment explanation
Indices: 61221--61431 Score: 235
Period size: 53 Copynumber: 4.0 Consensus size: 53
61211 ATCATAATGG
* *
61221 CTTGGTGACACTTAGTGAGACAACGCCTTGGTGGCGATCATGGAGAATAGTGA
1 CTTGGTGTCACTTAGTGAGACAACGCCTTGGTGGCGATCAGGGAGAATAGTGA
* * * * * **
61274 TTTGGTGTCACTCAGTGAGACAATGCCTTAGTGGCGATCA-GAATCATAGTGA
1 CTTGGTGTCACTTAGTGAGACAACGCCTTGGTGGCGATCAGGGAGAATAGTGA
* * * * *
61326 CTTAGTGTCACTTAGGGAGACAATGCCTTGGTGGTGATCAGGGAAAATAGTGA
1 CTTGGTGTCACTTAGTGAGACAACGCCTTGGTGGCGATCAGGGAGAATAGTGA
* * * * * *
61379 CATGTTGTCACTTAGTGAGACAACACCTTGATGGCGAACAGGGAGAATGGTGA
1 CTTGGTGTCACTTAGTGAGACAACGCCTTGGTGGCGATCAGGGAGAATAGTGA
61432 AAAATACTAA
Statistics
Matches: 129, Mismatches: 28, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
52 43 0.33
53 86 0.67
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (53 bp):
CTTGGTGTCACTTAGTGAGACAACGCCTTGGTGGCGATCAGGGAGAATAGTGA
Found at i:61365 original size:105 final size:105
Alignment explanation
Indices: 61211--61401 Score: 265
Period size: 105 Copynumber: 1.8 Consensus size: 105
61201 AACGGTCAAG
* * * * * **
61211 ATCATAATGGCTTGGTGACACTTAGTGAGACAACGCCTTGGTGGCGATCATGGAGAATAGTGATT
1 ATCATAATGACTTAGTGACACTTAGGGAGACAACGCCTTGGTGGCGATCAGGGAAAATAGTGACA
61276 TGGTGTCACTCAGTGAGACAATGCCTTAGTGGCGATCAGA
66 TGGTGTCACTCAGTGAGACAATGCCTTAGTGGCGATCAGA
* * * *
61316 ATCATAGTGACTTAGTGTCACTTAGGGAGACAATGCCTTGGTGGTGATCAGGGAAAATAGTGACA
1 ATCATAATGACTTAGTGACACTTAGGGAGACAACGCCTTGGTGGCGATCAGGGAAAATAGTGACA
* *
61381 TGTTGTCACTTAGTGAGACAA
66 TGGTGTCACTCAGTGAGACAA
61402 CACCTTGATG
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
105 73 1.00
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (105 bp):
ATCATAATGACTTAGTGACACTTAGGGAGACAACGCCTTGGTGGCGATCAGGGAAAATAGTGACA
TGGTGTCACTCAGTGAGACAATGCCTTAGTGGCGATCAGA
Done.