Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1340
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: 186353
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:153990 original size:39 final size:38
Alignment explanation
Indices: 153926--154006 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 38
153916 ACTTTTTCTA
**
153926 TCTTGTTTGACTGTATTGGTTTTAGGACGTAGTCAAAC
1 TCTTGTTTGACTGTATTGGCATTAGGACGTAGTCAAAC
153964 TCTTCGTTTGACTGTATTGGCATTAGGACGTAGTCAAAC
1 TCTT-GTTTGACTGTATTGGCATTAGGACGTAGTCAAAC
154003 TCTT
1 TCTT
154007 TTTCACCTCG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 4 0.10
39 36 0.90
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (38 bp):
TCTTGTTTGACTGTATTGGCATTAGGACGTAGTCAAAC
Found at i:154048 original size:47 final size:47
Alignment explanation
Indices: 153967--154082 Score: 153
Period size: 47 Copynumber: 2.5 Consensus size: 47
153957 GTCAAACTCT
* * * * *
153967 TCGTTTGACTGTATTGGCATTAGGACGTAGTCAAACTCTTTTTCA-CC
1 TCGTTTGACTGTATTGGCGTTAGAACCTACTCAAACT-TTTTCCACCC
154014 TCGTTTGACTGTATTGGCGTTAGAACCTACTCAAACTTTTTCCACCC
1 TCGTTTGACTGTATTGGCGTTAGAACCTACTCAAACTTTTTCCACCC
* *
154061 TCGTTTGACTATATTGGTGTTA
1 TCGTTTGACTGTATTGGCGTTA
154083 AGACTTGGTC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
46 6 0.10
47 55 0.90
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.40
Consensus pattern (47 bp):
TCGTTTGACTGTATTGGCGTTAGAACCTACTCAAACTTTTTCCACCC
Found at i:154048 original size:86 final size:83
Alignment explanation
Indices: 153881--154050 Score: 193
Period size: 86 Copynumber: 2.0 Consensus size: 83
153871 TTCAAGTTTT
* * *
153881 TCTTCGTTTGACTATGAGCATTAGGACCTGATCAAACTTTTTCTATCTTGTTTGACTGTATTGGT
1 TCTTCGTTTGACTATGAGCATTAGGACCTGATCAAACTTTTTCTACCTCGTTTGACTGTATTGGC
* * * *
153946 TTTAGGACGTAGTCAAAC
66 GTTAGAACCTACTCAAAC
*
153964 TCTTCGTTTGACTGTATTG-GCATTAGGACGT-AGTCAAACTCTTTT-TCACCTCGTTTGACTGT
1 TCTTCGTTTGAC--TA-TGAGCATTAGGACCTGA-TCAAACT-TTTTCT-ACCTCGTTTGACTGT
154026 ATTGGCGTTAGAACCTACTCAAAC
60 ATTGGCGTTAGAACCTACTCAAAC
154050 T
1 T
154051 TTTTCCACCC
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
83 12 0.16
84 1 0.01
85 21 0.29
86 39 0.53
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (83 bp):
TCTTCGTTTGACTATGAGCATTAGGACCTGATCAAACTTTTTCTACCTCGTTTGACTGTATTGGC
GTTAGAACCTACTCAAAC
Found at i:154095 original size:47 final size:46
Alignment explanation
Indices: 153967--154123 Score: 145
Period size: 47 Copynumber: 3.3 Consensus size: 46
153957 GTCAAACTCT
* * * * *
153967 TCGTTTGACTGTATTGGCATTAGGACGTAGTCAAACTCTTTTTCACC
1 TCGTTTGACTATATTGGCGTTAAGACCTAGTCAAACT-TTTTCCACC
* *
154014 TCGTTTGACTGTATTGGCGTT-AGAACCTACTCAAACTTTTTCCACCC
1 TCGTTTGACTATATTGGCGTTAAG-ACCTAGTCAAACTTTTTCCA-CC
* * * * * *
154061 TCGTTTGACTATATTGGTGTTAAGACTTGGTCAAACTCTTTCTATCA
1 TCGTTTGACTATATTGGCGTTAAGACCTAGTCAAACTTTTTCCA-CC
154108 TCGTTTTGACTATATT
1 TCG-TTTGACTATATT
154124 CTTGTTAAAC
Statistics
Matches: 92, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
46 7 0.08
47 71 0.77
48 14 0.15
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.41
Consensus pattern (46 bp):
TCGTTTGACTATATTGGCGTTAAGACCTAGTCAAACTTTTTCCACC
Found at i:154157 original size:36 final size:36
Alignment explanation
Indices: 154093--154293 Score: 174
Period size: 35 Copynumber: 5.6 Consensus size: 36
154083 AGACTTGGTC
*
154093 AAACTCTTTCTATCATCGTTTTGACTATATTCTTGTT
1 AAACTCTTTCCATCATCG-TTTGACTATATTCTTGTT
* *
154130 AAACTATTTCCATCATTGTTTGACTATATTCTTGTT
1 AAACTCTTTCCATCATCGTTTGACTATATTCTTGTT
* * * *
154166 AAACTCTTTCTATCATCATTTGACTATATT-TGGTC
1 AAACTCTTTCCATCATCGTTTGACTATATTCTTGTT
* * * * ** ** *
154201 AAACTTTTTCCATTATCATTTAACCGTA-TCTAATC
1 AAACTCTTTCCATCATCGTTTGACTATATTCTTGTT
* * *
154236 AAACTCTTTCTATCATCATTTGACCATA-TCTTGTT
1 AAACTCTTTCCATCATCGTTTGACTATATTCTTGTT
* * *
154271 ATACTGTTTCCATCATCATTTGA
1 AAACTCTTTCCATCATCGTTTGA
154294 TCATATCTGG
Statistics
Matches: 135, Mismatches: 28, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
34 1 0.01
35 75 0.56
36 44 0.33
37 15 0.11
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47
Consensus pattern (36 bp):
AAACTCTTTCCATCATCGTTTGACTATATTCTTGTT
Found at i:154301 original size:70 final size:69
Alignment explanation
Indices: 154091--154301 Score: 226
Period size: 70 Copynumber: 3.0 Consensus size: 69
154081 TAAGACTTGG
* **
154091 TCAAACTCTTTCTATCATCGTTTTGACTATATTCTTGTTAAACTATTTCCATCATTGTTTGACTA
1 TCAAACTCTTTCTATCATC-ATTTGACTATA-TCTTGTTAAACTATTTCCATCATCATTTGAC-A
**
154156 TATTCTTG
63 TA-TCTAA
* * * * * *
154164 TTAAACTCTTTCTATCATCATTTGACTATAT-TTGGTCAAACTTTTTCCATTATCATTTAACCGT
1 TCAAACTCTTTCTATCATCATTTGACTATATCTT-GTTAAACTATTTCCATCATCATTTGA-CAT
154228 ATCTAA
64 ATCTAA
* * *
154234 TCAAACTCTTTCTATCATCATTTGACCATATCTTGTTATACTGTTTCCATCATCATTTGATCATA
1 TCAAACTCTTTCTATCATCATTTGACTATATCTTGTTAAACTATTTCCATCATCATTTGA-CATA
154299 TCT
65 TCT
154302 GGTTAACCTA
Statistics
Matches: 115, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
70 61 0.53
71 25 0.22
72 11 0.10
73 18 0.16
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.47
Consensus pattern (69 bp):
TCAAACTCTTTCTATCATCATTTGACTATATCTTGTTAAACTATTTCCATCATCATTTGACATAT
CTAA
Found at i:154709 original size:33 final size:32
Alignment explanation
Indices: 154646--154713 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
154636 GTAGCCAAAT
** *
154646 TTGTATCGATACACACAGTATGTATTGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
154678 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
154711 TTG
1 TTG
154714 GCTTGTAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:161382 original size:20 final size:22
Alignment explanation
Indices: 161349--161393 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
161339 GCAGCACTCA
* *
161349 CCAGGTCGCGACC-GGCA-CCC
1 CCAGGTCACAACCGGGCAGCCC
161369 CCAGGTCACAACCGGGCAGCCC
1 CCAGGTCACAACCGGGCAGCCC
161391 CCA
1 CCA
161394 CACTAGCAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 4 0.19
22 6 0.29
ACGTcount: A:0.20, C:0.49, G:0.27, T:0.04
Consensus pattern (22 bp):
CCAGGTCACAACCGGGCAGCCC
Found at i:163362 original size:20 final size:20
Alignment explanation
Indices: 163331--163387 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
163321 GTCAAAACCC
*
163331 TGAAAAGTATCGATACACAT
1 TGAAATGTATCGATACACAT
* *
163351 TTAAATGTATCGATACAGAT
1 TGAAATGTATCGATACACAT
* *
163371 TGCATTGTATCGATACA
1 TGAAATGTATCGATACA
163388 TGACCAAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (20 bp):
TGAAATGTATCGATACACAT
Found at i:164296 original size:35 final size:35
Alignment explanation
Indices: 164250--164448 Score: 215
Period size: 35 Copynumber: 5.7 Consensus size: 35
164240 CTTTCACCTA
* * *
164250 TTTTCATCATCATTTGACCATATTTGGTCAAGCTC
1 TTTTCATCATCATTTGACTATATCTGGTCAAACTC
* * *
164285 TTTTCATCATCATTTGACCGA-ATATGGTCAAGCTC
1 TTTTCATCATCATTTGA-CTATATCTGGTCAAACTC
** * *
164320 TTTTTGTCATCGTTTGACTATATCAGGTCAAACTC
1 TTTTCATCATCATTTGACTATATCTGGTCAAACTC
* *
164355 TTTTCATCATCCTTTGGCTATATCTGGTCAAACTC
1 TTTTCATCATCATTTGACTATATCTGGTCAAACTC
* *
164390 TTTTCATCATCCTTT-AGCTATATCTGGTCAAACTT
1 TTTTCATCATCATTTGA-CTATATCTGGTCAAACTC
*
164425 TTTTCATCATCGTTT-AGCTATATC
1 TTTTCATCATCATTTGA-CTATATC
164449 GGTTACCACC
Statistics
Matches: 144, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
34 2 0.01
35 140 0.97
36 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.43
Consensus pattern (35 bp):
TTTTCATCATCATTTGACTATATCTGGTCAAACTC
Found at i:164435 original size:105 final size:105
Alignment explanation
Indices: 164250--164448 Score: 251
Period size: 105 Copynumber: 1.9 Consensus size: 105
164240 CTTTCACCTA
* *
164250 TTTTCATCATCATTTGACCATATTTGGTCAAGCTCTTTTCATCATCATTTGACCGAATATGGTCA
1 TTTTCATCATCATTTGACCATATCTGGTCAAACTCTTTTCATCATCATTTGACCGAATATGGTCA
* *
164315 AGCTCTTTTTGTCATCGTTT-GACTATATCAGGTCAAACTC
66 AACTCTTTTTATCATCGTTTAG-CTATATCAGGTCAAACTC
* * * * * * *
164355 TTTTCATCATCCTTTGGCTATATCTGGTCAAACTCTTTTCATCATCCTTT-AGCTATATCTGGTC
1 TTTTCATCATCATTTGACCATATCTGGTCAAACTCTTTTCATCATCATTTGACCGA-ATATGGTC
164419 AAACT-TTTTTCATCATCGTTTAGCTATATC
65 AAACTCTTTTT-ATCATCGTTTAGCTATATC
164449 GGTTACCACC
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
104 8 0.10
105 71 0.89
106 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.43
Consensus pattern (105 bp):
TTTTCATCATCATTTGACCATATCTGGTCAAACTCTTTTCATCATCATTTGACCGAATATGGTCA
AACTCTTTTTATCATCGTTTAGCTATATCAGGTCAAACTC
Found at i:164822 original size:85 final size:84
Alignment explanation
Indices: 164684--165170 Score: 347
Period size: 85 Copynumber: 5.7 Consensus size: 84
164674 CTCGGTTGAC
* * * ** * * *
164684 CTTTTTATCCGTTGTTTCCCTATCAGCTTAGTCCTGAGTATAT-TCTTTCATCCTTTGTTAACTT
1 CTTTTTATCCTTTGTTTACCTATCAACTTAGTCCCAAGTAAATCT-TTTTATCCTTTGTTGACTT
*
164748 ATCAGTTCAATCTCGATCAA
65 ATCGGTTCAATCTCGATCAA
* *
164768 CTTTTATATCCTTTGTTTACTTATCAACTTAGTCCCAAGTAAATTTTTTTATCCTTTGTTGAC-T
1 CTTTT-TATCCTTTGTTTACCTATCAACTTAGTCCCAAGTAAATCTTTTTATCCTTTGTTGACTT
* * ** *
164832 AACGGTTCAATTTTAATCGA
65 ATCGGTTCAATCTCGATCAA
* * * * ** * * * * *
164852 CTTTCTGATCCTTTATTTACTTGTCCGCTTAGTCTCGAGTAAATCCTTTCTATCCTTTGTAGGCT
1 CTTT-TTATCCTTTGTTTACCTATCAACTTAGTCCCAAGTAAAT-CTTTTTATCCTTTGTTGACT
* * * *
164917 TATCGGTTTAACCCCAATCAA
64 TATCGGTTCAATCTCGATCAA
** * *
164938 CTTTTATATTTTTTGTTTACCTATCAACTTAGTCCTGAA-TAAATCTTTTTATCTTTTGTTGACT
1 CTTTT-TATCCTTTGTTTACCTATCAACTTAGTCC-CAAGTAAATCTTTTTATCCTTTGTTGACT
* *
165002 TGTCGGTTCAATCTCGGTCAA
64 TATCGGTTCAATCTCGATCAA
* * ** * *
165023 CCTTTTTATCCTTTGTTTACTTGTCAACTTAGTCTTAGGTAAATCTTTTTATCTTTTGTTGACTT
1 -CTTTTTATCCTTTGTTTACCTATCAACTTAGTCCCAAGTAAATCTTTTTATCCTTTGTTGACTT
* * * *
165088 GTCGAG-CCAATC-CTGGTGAA
65 ATCG-GTTCAATCTC-GATCAA
* * * * * * *
165108 CTTTGATCTCCTTTGTTTACCTGTTAGCTTAGTCCCAAGT-AATCCTTTTCATCATTTGTTGAC
1 CTTT-TTATCCTTTGTTTACCTATCAACTTAGTCCCAAGTAAAT-CTTTTTATCCTTTGTTGAC
165171 CTAGCTACTT
Statistics
Matches: 317, Mismatches: 73, Indels: 25
0.76 0.18 0.06
Matches are distributed among these distances:
84 64 0.20
85 202 0.64
86 50 0.16
87 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (84 bp):
CTTTTTATCCTTTGTTTACCTATCAACTTAGTCCCAAGTAAATCTTTTTATCCTTTGTTGACTTA
TCGGTTCAATCTCGATCAA
Found at i:164826 original size:43 final size:43
Alignment explanation
Indices: 164685--164827 Score: 119
Period size: 43 Copynumber: 3.3 Consensus size: 43
164675 TCGGTTGACC
* * * * * *
164685 TTTTTATCCGTTGTTTCCCTATCAGCTTAGTCCTGAGTATATT
1 TTTTTATCCTTTGTTTACTTATCAACTTAGTCCCGAGTAAATT
* * * * * * * *
164728 CTTTCATCCTTTGTTAACTTATC-AGTTCAATCTCGA-TCAACT
1 TTTTTATCCTTTGTTTACTTATCAACTT-AGTCCCGAGTAAATT
* *
164770 TTTATATCCTTTGTTTACTTATCAACTTAGTCCCAAGTAAATT
1 TTTTTATCCTTTGTTTACTTATCAACTTAGTCCCGAGTAAATT
164813 TTTTTATCCTTTGTT
1 TTTTTATCCTTTGTT
164828 GACTAACGGT
Statistics
Matches: 72, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
42 29 0.40
43 43 0.60
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.49
Consensus pattern (43 bp):
TTTTTATCCTTTGTTTACTTATCAACTTAGTCCCGAGTAAATT
Found at i:165081 original size:43 final size:41
Alignment explanation
Indices: 164938--165090 Score: 128
Period size: 43 Copynumber: 3.6 Consensus size: 41
164928 CCCCAATCAA
* * * * *
164938 CTTTTATATTTTTTGTTTACCTATCAACTTAGTCCTGAATAAAT
1 CTTTT-TATCTTTTGTTGACTTGTCAACTTAGT-CTG-GTAAAT
** * * *
164982 CTTTTTATCTTTTGTTGACTTGTC-GGTTCAATCTCGGTCAAC
1 CTTTTTATCTTTTGTTGACTTGTCAACTT-AGTCT-GGTAAAT
* *
165024 CTTTTTATCCTTTGTTTACTTGTCAACTTAGTCTTAGGTAAAT
1 CTTTTTATCTTTTGTTGACTTGTCAACTTAGTC-T-GGTAAAT
165067 CTTTTTATCTTTTGTTGACTTGTC
1 CTTTTTATCTTTTGTTGACTTGTC
165091 GAGCCAATCC
Statistics
Matches: 85, Mismatches: 20, Indels: 9
0.75 0.18 0.08
Matches are distributed among these distances:
42 32 0.38
43 48 0.56
44 5 0.06
ACGTcount: A:0.19, C:0.18, G:0.12, T:0.52
Consensus pattern (41 bp):
CTTTTTATCTTTTGTTGACTTGTCAACTTAGTCTGGTAAAT
Found at i:165154 original size:255 final size:255
Alignment explanation
Indices: 164695--165155 Score: 549
Period size: 255 Copynumber: 1.8 Consensus size: 255
164685 TTTTTATCCG
* * * *
164695 TTGTTTCCCTATCAGCTTAGTCCTGAGTATATTCTTTCATCCTTTGTTAACTTATCAGTTCAATC
1 TTGTTTACCTATCAACTTAGTCCTGAATAAATTCTTTCATCCTTTGTTAACTTATCAGTTCAATC
*
164760 TCGATCAACTTTTATATCCTTTGTTTACTTATCAACTTAGTCCCAAGTAAATTTTTTTATCCTTT
66 TCGATCAACTTTTATATCCTTTGTTTACTTATCAACTTAGTCCCAAGTAAATCTTTTTATCCTTT
* ** * * * *
164825 GTTGACTAACGGTTCAATTTTAATCGACTTTCTGATCCTTTATTTACTTGTCCGCTTAGTCTCGA
131 GTTGACTAACGGTCCAATCCTAATCGACTTTCTGATCCTTTATTTACCTGTCAGCTTAGTCCCAA
164890 GTAAATCCTTTCTATCCTTTGTAGGCTTATCGGTTTAACCCCAATCAACTTTTATATTTT
196 GTAAATCCTTTCTATCCTTTGTAGGCTTATCGGTTTAACCCCAATCAACTTTTATATTTT
* * * * *
164950 TTGTTTACCTATCAACTTAGTCCTGAATAAA-TCTTTTTATCTTTTGTTGACTTGTCGGTTCAAT
1 TTGTTTACCTATCAACTTAGTCCTGAATAAATTC-TTTCATCCTTTGTTAACTTATCAGTTCAAT
* * ** * *
165014 CTCGGTCAACCTTTT-TATCCTTTGTTTACTTGTCAACTTAGTCTTAGGTAAATCTTTTTATCTT
65 CTCGATCAA-CTTTTATATCCTTTGTTTACTTATCAACTTAGTCCCAAGTAAATCTTTTTATCCT
** ** * *
165078 TTGTTGACTTGTCGAG-CCAATCCTGGT-GAAC-TT-TGATCTCCTTTGTTTACCTGTTAGCTTA
129 TTGTTGAC-TAACG-GTCCAATCCTAATCG-ACTTTCTGA--TCCTTTATTTACCTGTCAGCTTA
165139 GTCCCAAGT-AATCCTTT
189 GTCCCAAGTAAATCCTTT
165156 TCATCATTTG
Statistics
Matches: 170, Mismatches: 29, Indels: 14
0.80 0.14 0.07
Matches are distributed among these distances:
254 5 0.03
255 122 0.72
256 42 0.25
257 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (255 bp):
TTGTTTACCTATCAACTTAGTCCTGAATAAATTCTTTCATCCTTTGTTAACTTATCAGTTCAATC
TCGATCAACTTTTATATCCTTTGTTTACTTATCAACTTAGTCCCAAGTAAATCTTTTTATCCTTT
GTTGACTAACGGTCCAATCCTAATCGACTTTCTGATCCTTTATTTACCTGTCAGCTTAGTCCCAA
GTAAATCCTTTCTATCCTTTGTAGGCTTATCGGTTTAACCCCAATCAACTTTTATATTTT
Found at i:165308 original size:66 final size:65
Alignment explanation
Indices: 165186--165339 Score: 168
Period size: 66 Copynumber: 2.3 Consensus size: 65
165176 TACTTTGTCC
* * * * *
165186 TAGTCAACTTCTGTTCGATTTTGGTTTCACCCTGGTCACCCTTTTCCTGACGTGATGGTTTT-GC
1 TAGTCAACTTCTTTTCGACTTAGGTTTCACCCTGGTCACCATTTT-CTGACATGAT-GTTTTCGC
165250 CT
64 CT
* * *
165252 TGGTCAACTTCTTTTCGACTTAGGTTTACACCCTTGTCATCATTTGT-TGACATGATGTTTTCGC
1 TAGTCAACTTCTTTTCGACTTAGGTTT-CACCCTGGTCACCATTT-TCTGACATGATGTTTTCGC
165316 CT
64 CT
* *
165318 TAGTCAACTTATTTTAGACTTA
1 TAGTCAACTTCTTTTCGACTTA
165340 AGATTAGCTC
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
65 5 0.07
66 54 0.73
67 14 0.19
68 1 0.01
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.44
Consensus pattern (65 bp):
TAGTCAACTTCTTTTCGACTTAGGTTTCACCCTGGTCACCATTTTCTGACATGATGTTTTCGCCT
Found at i:170150 original size:168 final size:165
Alignment explanation
Indices: 169956--170344 Score: 471
Period size: 168 Copynumber: 2.3 Consensus size: 165
169946 TTTCATTGAC
* * *** *
169956 TTAAAACTTTTAAAATTCATCAAATATTATCATTTGACTCACATTAAATTTGTTTTGAAAAATTC
1 TTAAAATTTTTAAAATTCATCAAATATTATCATTTGACTCAAATTAAATCAATTTTAAAAAATTC
* * * *
170021 ATTTATTTTCATGAGTTTTAAATTTTTTCTTTGAAATT-TTTCTATTTTTTAAAAAACTC-AGTT
66 ATTCATTTTCATGAGTTTTAAATTTTTTATTTGAAATTCTCT-TA-TTTTCAAAAAA-TCGAG-T
170084 TTTCTATTCTATAAACT-TTTTCA-AGAAAATTTTCATCAAT
127 TTTCTATTCTATAAA-TATTTTCAGAG-AAATTTT-ATCAAT
* *
170124 TTTAAATTTTTAAAATTCATCAAATATTATCATTTGATTCAAATTAAATCAATTTTAAAAAATTC
1 TTAAAATTTTTAAAATTCATCAAATATTATCATTTGACTCAAATTAAATCAATTTTAAAAAATTC
*
170189 ATTCATTTTCATGAGTTTTTAATTTTTTATTTGAAATTCTCTTATTTTCAAAAAATCGAGTTTTC
66 ATTCATTTTCATGAGTTTTAAATTTTTTATTTGAAATTCTCTTATTTTCAAAAAATCGAGTTTTC
* * * *
170254 TATTCTATTAATATTTTCAGAGAGATTTTTTCAGT
131 TATTCTATAAATATTTTCAGAGAAATTTTATCAAT
* * * ** **
170289 TTAAAATTTTTAAAATTCATCTAATATTGTTATTAAACTCTCATTAAATCAATTTT
1 TTAAAATTTTTAAAATTCATCAAATATTATCATTTGACTCAAATTAAATCAATTTT
170345 GCAAAACTCA
Statistics
Matches: 191, Mismatches: 26, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
165 52 0.27
166 29 0.15
167 14 0.07
168 94 0.49
169 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (165 bp):
TTAAAATTTTTAAAATTCATCAAATATTATCATTTGACTCAAATTAAATCAATTTTAAAAAATTC
ATTCATTTTCATGAGTTTTAAATTTTTTATTTGAAATTCTCTTATTTTCAAAAAATCGAGTTTTC
TATTCTATAAATATTTTCAGAGAAATTTTATCAAT
Found at i:171230 original size:13 final size:13
Alignment explanation
Indices: 171212--171237 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
171202 AAATTTTTTG
171212 TGTATCGATACAT
1 TGTATCGATACAT
171225 TGTATCGATACAT
1 TGTATCGATACAT
171238 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:171977 original size:21 final size:21
Alignment explanation
Indices: 171936--171979 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
171926 CTCTCCTTTA
* *
171936 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
171957 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
171978 TC
1 TC
171980 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:173802 original size:13 final size:13
Alignment explanation
Indices: 173784--173809 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
173774 ATAATCACCC
173784 TGTATCGATACAA
1 TGTATCGATACAA
173797 TGTATCGATACAA
1 TGTATCGATACAA
173810 AGAAAAATGT
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):
TGTATCGATACAA
Found at i:175901 original size:15 final size:15
Alignment explanation
Indices: 175881--175911 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
175871 ATTTCGTTTG
*
175881 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
175896 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
175911 G
1 G
175912 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:178399 original size:13 final size:13
Alignment explanation
Indices: 178381--178406 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
178371 AATTTTTTTG
178381 TGTATCGATACAT
1 TGTATCGATACAT
178394 TGTATCGATACAT
1 TGTATCGATACAT
178407 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:180808 original size:21 final size:21
Alignment explanation
Indices: 180784--180830 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
180774 TTTGATGCTG
180784 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
180804 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
180825 ATTTTG
1 ATTTTG
180831 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:180968 original size:11 final size:12
Alignment explanation
Indices: 180951--180986 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
180941 ATAATCACCC
180951 TGTATCGATACA
1 TGTATCGATACA
180963 -GTATCGATACAA
1 TGTATCGATAC-A
180975 TGTATCGATACA
1 TGTATCGATACA
180987 AAGAAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 10 0.45
12 2 0.09
13 10 0.45
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:180981 original size:13 final size:13
Alignment explanation
Indices: 180951--180987 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
180941 ATAATCACCC
180951 TGTATCGATAC-A
1 TGTATCGATACAA
180963 -GTATCGATACAA
1 TGTATCGATACAA
180975 TGTATCGATACAA
1 TGTATCGATACAA
180988 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 12 0.52
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:180998 original size:20 final size:20
Alignment explanation
Indices: 180973--181051 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
180963 GTATCGATAC
180973 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
180993 AATGTATCGATACATAGAATTTCTA
1 AATGTATCGATACAAAGAA-----A
* *
181018 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
181038 CATGTATCGATACA
1 AATGTATCGATACA
181052 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:0.14, G:0.15, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:183082 original size:15 final size:15
Alignment explanation
Indices: 183062--183092 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
183052 ATTTCGTTTG
*
183062 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
183077 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
183092 G
1 G
183093 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:184925 original size:21 final size:21
Alignment explanation
Indices: 184896--184940 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
184886 AAGTTTTCAT
*
184896 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
184916 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
184938 TTT
1 TTT
184941 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
Done.