Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1293
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: 240166
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:211621 original size:21 final size:21
Alignment explanation
Indices: 211596--211650 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
211586 CACTTGCAAC
*
211596 TCATTTCTTTTCTCCTCTAAT
1 TCATTTATTTTCTCCTCTAAT
**
211617 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTCCTCTAAT
* *
211638 TCACTTAATTTCT
1 TCATTTATTTTCT
211651 TTTCAAGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (21 bp):
TCATTTATTTTCTCCTCTAAT
Found at i:211651 original size:21 final size:21
Alignment explanation
Indices: 211611--211654 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
211601 TCTTTTCTCC
* *
211611 TCTAATTCATTTATTTTCTTT
1 TCTAATTCACTTAATTTCTTT
211632 TCTAATTCACTTAATTTCTTT
1 TCTAATTCACTTAATTTCTTT
211653 TC
1 TC
211655 AAGAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.61
Consensus pattern (21 bp):
TCTAATTCACTTAATTTCTTT
Found at i:213248 original size:32 final size:33
Alignment explanation
Indices: 213206--213291 Score: 104
Period size: 35 Copynumber: 2.6 Consensus size: 33
213196 ACTATCTTTC
213206 AAGGCTAAGATAGAAACCTC-CCTATCTTTT-CA
1 AAGGCTAAGATAG-AACCTCTCCTATCTTTTACA
** *
213238 CGGGCTAAGATAGAACCTTTCTTCTATCTTTTACA
1 AAGGCTAAGATAGAACC--TCTCCTATCTTTTACA
213273 AAGGCTAAGATAGAACCTC
1 AAGGCTAAGATAGAACCTC
213292 ACAATCACTT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
31 4 0.09
32 11 0.24
33 4 0.09
34 9 0.20
35 17 0.38
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (33 bp):
AAGGCTAAGATAGAACCTCTCCTATCTTTTACA
Found at i:213811 original size:24 final size:24
Alignment explanation
Indices: 213774--213819 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
213764 ATGAACAGTG
* *
213774 ATGAACAGTAATAAATAGTGATAC
1 ATGAACAATAATAAACAGTGATAC
*
213798 ATGAACAATGATAAACAGTGAT
1 ATGAACAATAATAAACAGTGAT
213820 GTAGCGATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.24
Consensus pattern (24 bp):
ATGAACAATAATAAACAGTGATAC
Found at i:213834 original size:32 final size:32
Alignment explanation
Indices: 213752--213882 Score: 154
Period size: 32 Copynumber: 4.0 Consensus size: 32
213742 ACTATTCACA
* * *
213752 ATGTATCGATATATGAACAGTGATGAACAGTA
1 ATGTAGCGATACATGAACAGTGATGAACAGTG
* * * *
213784 ATAAATAGTGATACATGAACAATGATAAACAGTG
1 AT--GTAGCGATACATGAACAGTGATGAACAGTG
*
213818 ATGTAGCGATACATGAATAGTGATGAACAGTG
1 ATGTAGCGATACATGAACAGTGATGAACAGTG
* *
213850 ATGTATCGATACATGAATAGTGATGAACAGTG
1 ATGTAGCGATACATGAACAGTGATGAACAGTG
213882 A
1 A
213883 AAATGAGATT
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
32 59 0.70
34 25 0.30
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (32 bp):
ATGTAGCGATACATGAACAGTGATGAACAGTG
Found at i:216979 original size:32 final size:33
Alignment explanation
Indices: 216920--216983 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
216910 TACAGGCCAA
216920 TGTATCGATACAACTTTATGTGTATCGATACAT
1 TGTATCGATACAACTTTATGTGTATCGATACAT
*
216953 TGTATCGATACGTAC-TT-TGTGTATCGATACA
1 TGTATCGATAC-AACTTTATGTGTATCGATACA
216984 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.48
33 13 0.45
34 2 0.07
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAACTTTATGTGTATCGATACAT
Found at i:219080 original size:21 final size:20
Alignment explanation
Indices: 219059--219113 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
219049 TGGGGACTGC
*
219059 CCGGTTGTGACCTGGGAGTG
1 CCGGTCGTGACCTGGGAGTG
*
219079 CCGGTCGCGACCTGGGAGTG
1 CCGGTCGTGACCTGGGAGTG
*
219099 TCGGTCGTGACCTGG
1 CCGGTCGTGACCTGG
219114 TGGTCCTGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.09, C:0.25, G:0.44, T:0.22
Consensus pattern (20 bp):
CCGGTCGTGACCTGGGAGTG
Found at i:225737 original size:13 final size:13
Alignment explanation
Indices: 225719--225744 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
225709 CAACTTTATG
225719 TGTATCGATACAT
1 TGTATCGATACAT
225732 TGTATCGATACAT
1 TGTATCGATACAT
225745 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:225758 original size:32 final size:33
Alignment explanation
Indices: 225699--225762 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
225689 TACAGGCCAA
225699 TGTATCGATACAACTTTATGTGTATCGATACAT
1 TGTATCGATACAACTTTATGTGTATCGATACAT
225732 TGTATCGATACATAC-TT-TGTGTATCGATACA
1 TGTATCGATACA-ACTTTATGTGTATCGATACA
225763 AGTTTAGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 14 0.47
33 14 0.47
34 2 0.07
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAACTTTATGTGTATCGATACAT
Found at i:227961 original size:145 final size:140
Alignment explanation
Indices: 227683--228550 Score: 419
Period size: 137 Copynumber: 6.2 Consensus size: 140
227673 CTTAAACTCT
* * * * * * * * * *
227683 TTTTAAATCCCACACAAGCTGGTAGCACTTTTTA-CTTTTTAGTCTTCAAAGAGTAAAATG-CTT
1 TTTTAAAGCCAACACAAGTTGGTGGCACCTTTTATCATTTTAATCCTCAAAGAGCAACATGCCTT
* * * *
227746 TTTC-TTCTTAAAGCCCACACAGGCTGGTGGCACCCTTTTTTATCTTTTTTAGTCCTTAAAAAGC
66 TTTCTTTC-CAAAGCCCACACAAGCTGGTGGCACCC--TTTTATC-CTTTTAGTCCTCAAAAAGC
227810 AAGATGCCTTTTTC
127 AAGATGCCTTTTTC
* * ** *
227824 TTTTTAAAGCCAACATAATTTGGTGGCAGTTTTTATC-TTTTCAATCCTTAAAGAGCAGGACAT-
1 -TTTTAAAGCCAACACAAGTTGGTGGCACCTTTTATCATTTT-AATCCTCAAAGAGCA--ACATG
* * * * *
227887 CTTTTCTTTTTTCCAAAGCTCATACAAGCTGGTGGCACCCATTTTATCCTTTTAAGTCCTCACAA
62 CCTTT-TTCTTTCCAAAGCCCACACAAGCTGGTGGCACCC-TTTTATCCTTTT-AGTCCTCAAAA
*
227952 AGCAGGATGCCTTTTTC
124 AGCAAGATGCCTTTTTC
* * *
227969 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTTATCATTTTAGTCCTCAAAGAGCAAGATGCCTT
1 TTTTAAAGCCAACACAAGTTGGTGGCACCTTTTATCATTTTAATCCTCAAAGAGCAACATGCCTT
* * ** * *
228034 TTTCTTTCTAAAGCCCACACAAGCTAGTGGCA-CCTTTTATCCTTTTAGTCCTCAAAGCGTAGGA
66 TTTCTTTCCAAAGCCCACACAAGCTGGTGGCACCCTTTTATCCTTTTAGTCCTCAAAAAGCAAGA
* *
228098 T--ATCTTTC
131 TGCCTTTTTC
* * * * * * * * ***
228106 ---GAAAGCCTATACAAGCTAGTGGCACCCTTTTTATCCTTTTTAGTCTTCAAAGAGCTGGATGC
1 TTTTAAAGCCAACACAAGTTGGTGGCA-CC-TTTTAT-CATTTTAATCCTCAAAGAGCAACATGC
* * * * *
228168 TTTTTTCTTT--AAGGCCCACACAAGCTGGTAGCA-TCTTCTT-TCCTTTTAGTTCT-AAAAGAG
63 CTTTTTCTTTCCAAAGCCCACACAAGCTGGTGGCACCCTT-TTATCCTTTTAGTCCTCAAAA-AG
* * *
228228 TAAGA--CGTCTTTC
126 CAAGATGCCTTTTTC
* * * * * * * * * * *
228241 ---TAAAGCCCACACAAGCTGGTTGTACCTTTTATCCTTTTAGTCTTTAAAGAG---TAGGAC--
1 TTTTAAAGCCAACACAAGTTGGTGGCACCTTTTATCATTTTAATCCTCAAAGAGCAACATGCCTT
* * * * * * * *
228298 -GTCTTTCTAAAGCTCACATAAGTTGGTGGCACCCCTTTTATCCTTTTTTGTCCACAAAGAGCAA
66 TTTCTTTCCAAAGCCCACACAAGCTGGTGGCA-CCCTTTTATCC-TTTTAGTCCTCAAAAAGCAA
*
228362 GATGCCTTATTC
129 GATGCCTTTTTC
* * * * * * * * *** *
228374 TTTTCAAAGCCCACACGAGCTGGTGGCACTTTTTATCCTTTTAGTCTTCAAAGAACTGGATGTCT
1 TTTT-AAAGCCAACACAAGTTGGTGGCACCTTTTATCATTTTAATCCTCAAAGAGCAACATGCCT
* * * * * *
228439 TTTCTTTTTCTAAAACTCACACAAGCTGGTGGCA-CCTTTTAGCCCTTTT-GTCCTCAAAAAACA
65 TTT-TCTTTCCAAAGCCCACACAAGCTGGTGGCACCCTTTTA-TCCTTTTAGTCCTCAAAAAGCA
* ** *
228502 GGACACATTTTTC
128 AGATGCCTTTTTC
* *
228515 GTTTTAAAGCTC-ACGCAAGTTAGTGGCACCTATTTA
1 -TTTTAAAGC-CAACACAAGTTGGTGGCACCT-TTTA
228551 CTTCAACCTT
Statistics
Matches: 569, Mismatches: 117, Indels: 80
0.74 0.15 0.10
Matches are distributed among these distances:
126 5 0.01
128 18 0.03
129 4 0.01
130 6 0.01
131 13 0.02
132 20 0.04
133 11 0.02
134 24 0.04
135 66 0.12
136 9 0.02
137 81 0.14
139 15 0.03
140 15 0.03
141 40 0.07
142 80 0.14
143 18 0.03
144 74 0.13
145 42 0.07
146 25 0.04
147 3 0.01
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.36
Consensus pattern (140 bp):
TTTTAAAGCCAACACAAGTTGGTGGCACCTTTTATCATTTTAATCCTCAAAGAGCAACATGCCTT
TTTCTTTCCAAAGCCCACACAAGCTGGTGGCACCCTTTTATCCTTTTAGTCCTCAAAAAGCAAGA
TGCCTTTTTC
Found at i:228052 original size:70 final size:70
Alignment explanation
Indices: 227680--228496 Score: 551
Period size: 70 Copynumber: 11.8 Consensus size: 70
227670 AAACTTAAAC
* * * * * * * *
227680 TCTTTTTAAATCCCACACAAGCTGGTAGCACTTTTTA-CTTTTTAGTCTTCAAAGAGTAAAATG-
1 TCTTTCTAAAGCCCACACAAGCTGGTGGCACCTTTTATCCTTTTAGTCCTCAAAGAGCAAGATGC
227743 CTTTT
66 CTTTT
* * * *
227748 TC-TTCTTAAAGCCCACACAGGCTGGTGGCACCCTTTTTTATCTTTTTTAGTCCTTAAAAAGCAA
1 TCTTTC-TAAAGCCCACACAAGCTGGTGGCA-CC--TTTTATC-CTTTTAGTCCTCAAAGAGCAA
227812 GATGCCTTTT
61 GATGCCTTTT
* * * ** ** * * *
227822 TCTTTTTAAAGCCAACATAATTTGGTGGCAGTTTTTAT-CTTTTCAATCCTTAAAGAGCAGGACA
1 TCTTTCTAAAGCCCACACAAGCTGGTGGCACCTTTTATCCTTTT-AGTCCTCAAAGAGCA--AGA
*
227886 T-CTTTTCT
63 TGCCTTT-T
* * * * *
227894 TTTTTCCAAAGCTCATACAAGCTGGTGGCACCCATTTTATCCTTTTAAGTCCTCACAA-AGCAGG
1 TCTTTCTAAAGCCCACACAAGCTGGTGGCA-CC-TTTTATCCTTTT-AGTCCTCA-AAGAGCAAG
227958 ATGCCTTTT
62 ATGCCTTTT
* *
227967 TCTTT-TAAAGCCCACACAAGTTGGTGGCACCTTTTATCATTTTAGTCCTCAAAGAGCAAGATGC
1 TCTTTCTAAAGCCCACACAAGCTGGTGGCACCTTTTATCCTTTTAGTCCTCAAAGAGCAAGATGC
228031 CTTTT
66 CTTTT
* * *
228036 TCTTTCTAAAGCCCACACAAGCTAGTGGCACCTTTTATCCTTTTAGTCCTCAAAGCG-TAG--G-
1 TCTTTCTAAAGCCCACACAAGCTGGTGGCACCTTTTATCCTTTTAGTCCTCAAAGAGCAAGATGC
* *
228097 --ATA
66 CTTTT
* * * * * **
228100 TCTTTCGAAAGCCTATACAAGCTAGTGGCACCCTTTTTATCCTTTTTAGTCTTCAAAGAGCTGGA
1 TCTTTCTAAAGCCCACACAAGCTGGTGGCA-CC-TTTTATCC-TTTTAGTCCTCAAAGAGCAAGA
*
228165 TGCTTTTT
63 TGCCTTTT
* * * * * *
228173 TC-TT-TAAGGCCCACACAAGCTGGTAGCATCTTCTT-TCCTTTTAGTTCTAAAAGAGTAAGA--
1 TCTTTCTAAAGCCCACACAAGCTGGTGGCACCTT-TTATCCTTTTAGTCCTCAAAGAGCAAGATG
*
228233 -C---G
65 CCTTTT
* * * * * *
228235 TCTTTCTAAAGCCCACACAAGCTGGTTGTACCTTTTATCCTTTTAGTCTTTAAAGAG-TAG--GA
1 TCTTTCTAAAGCCCACACAAGCTGGTGGCACCTTTTATCCTTTTAGTCCTCAAAGAGCAAGATGC
*
228297 C---G
66 CTTTT
* * * * *
228299 TCTTTCTAAAGCTCACATAAGTTGGTGGCACCCCTTTTATCCTTTTTTGTCCACAAAGAGCAAGA
1 TCTTTCTAAAGCCCACACAAGCTGGTGGCA--CCTTTTATCC-TTTTAGTCCTCAAAGAGCAAGA
*
228364 TGCCTTAT
63 TGCCTTTT
* * * * **
228372 TCTTT-TCAAAGCCCACACGAGCTGGTGGCACTTTTTATCCTTTTAGTCTTCAAAGAACTGGATG
1 TCTTTCT-AAAGCCCACACAAGCTGGTGGCACCTTTTATCCTTTTAGTCCTCAAAGAGCAAGATG
*
228436 TCTTTT
65 CCTTTT
* * * *
228442 CTTTTTCTAAAACTCACACAAGCTGGTGGCACCTTTTAGCCCTTTT-GTCCTCAAA
1 -TCTTTCTAAAGCCCACACAAGCTGGTGGCACCTTTTA-TCCTTTTAGTCCTCAAA
228497 AAACAGGACA
Statistics
Matches: 585, Mismatches: 117, Indels: 91
0.74 0.15 0.11
Matches are distributed among these distances:
62 2 0.00
63 6 0.01
64 96 0.16
65 2 0.00
66 18 0.03
67 31 0.05
68 45 0.08
69 39 0.07
70 99 0.17
71 82 0.14
72 56 0.10
73 54 0.09
74 36 0.06
75 17 0.03
76 2 0.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (70 bp):
TCTTTCTAAAGCCCACACAAGCTGGTGGCACCTTTTATCCTTTTAGTCCTCAAAGAGCAAGATGC
CTTTT
Found at i:228257 original size:64 final size:64
Alignment explanation
Indices: 227967--228427 Score: 266
Period size: 64 Copynumber: 6.9 Consensus size: 64
227957 GATGCCTTTT
* * * * * *
227967 TCTTT-TAAAGCCCACACAAGTTGGTGGCACCTTTTATCATTTTAGTCCTCAAAGAGCAAGATGC
1 TCTTTCTAAAGCCCACACAAGCTGGTAGCACCTTTTATCCTTTTAGTCTTAAAAGAGTAAGA---
*
228031 CTTTT
63 C---G
* * * * * * **
228036 TCTTTCTAAAGCCCACACAAGCTAGTGGCACCTTTTATCCTTTTAGTCCTCAAAGCGTAGGATA
1 TCTTTCTAAAGCCCACACAAGCTGGTAGCACCTTTTATCCTTTTAGTCTTAAAAGAGTAAGACG
* * * * * * *
228100 TCTTTCGAAAGCCTATACAAGCTAGTGGCACCCTTTTTATCCTTTTTAGTCTTCAAAGAGCT-GG
1 TCTTTCTAAAGCCCACACAAGCTGGTAGCA-CC-TTTTATCC-TTTTAGTCTTAAAAGAG-TAAG
*
228164 ATGCT
62 A--CG
* * *
228169 TTTTTCTTTAAGGCCCACACAAGCTGGTAGCATCTTCTT-TCCTTTTAGT-TCTAAAAGAGTAAG
1 TCTTTC--TAAAGCCCACACAAGCTGGTAGCACCTT-TTATCCTTTTAGTCT-TAAAAGAGTAAG
228232 ACG
62 ACG
* * * *
228235 TCTTTCTAAAGCCCACACAAGCTGGTTGTACCTTTTATCCTTTTAGTCTTTAAAGAGTAGGACG
1 TCTTTCTAAAGCCCACACAAGCTGGTAGCACCTTTTATCCTTTTAGTCTTAAAAGAGTAAGACG
* * * * * * *
228299 TCTTTCTAAAGCTCACATAAGTTGGTGGCACCCCTTTTATCCTTTTTTGTC-CACAAAGAGCAAG
1 TCTTTCTAAAGCCCACACAAGCTGGTAGCA--CCTTTTATCC-TTTTAGTCTTA-AAAGAGTAAG
*
228363 ATG
62 ACG
* * * * *
228366 CCTTATTCTTTTCAAAGCCCACACGAGCTGGTGGCACTTTTTATCCTTTTAGTCTTCAAAGA
1 TC-T-TTC---T-AAAGCCCACACAAGCTGGTAGCACCTTTTATCCTTTTAGTCTTAAAAGA
228428 ACTGGATGTC
Statistics
Matches: 314, Mismatches: 53, Indels: 49
0.75 0.13 0.12
Matches are distributed among these distances:
63 2 0.01
64 99 0.32
65 3 0.01
66 24 0.08
67 38 0.12
68 18 0.06
69 18 0.06
70 65 0.21
71 27 0.09
72 1 0.00
73 19 0.06
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (64 bp):
TCTTTCTAAAGCCCACACAAGCTGGTAGCACCTTTTATCCTTTTAGTCTTAAAAGAGTAAGACG
Found at i:228279 original size:199 final size:201
Alignment explanation
Indices: 227896--228419 Score: 610
Period size: 199 Copynumber: 2.6 Consensus size: 201
227886 TCTTTTCTTT
* *
227896 TTTCCAAAGCTCATACAAGCTGGTGGCACCCATTTTATCCTTTTAAGTCCTCACAA-AGCAGGAT
1 TTTCGAAAGCTCATACAAGCTGGTGGCACCCATTTTATCCTTTTTAGTCCTCA-AAGAGCAGGAT
* * *
227960 GCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTATCATTTTAGTCCTCAAAGAGCA
65 GCCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCA-CTTTTATCCTTTTAGTCCTAAAAGAGCA
*
228025 AGATGCCTTTTTCTTTCTAAAGCCCACACAAGCTAGTGGCACCTTTTATCCTTTTAGTCCTCAAA
129 AGA--CC--TGTCTTTCTAAAGCCCACACAAGCTAGTGGCACCTTTTATCCTTTTAGTCCTCAAA
* *
228090 GCGTAGGATATC
190 GAGTAGGACATC
* * * *
228102 TTTCGAAAGC-CTATACAAGCTAGTGGCACCCTTTTTATCCTTTTTAGTCTTCAAAGAGCTGGAT
1 TTTCGAAAGCTC-ATACAAGCTGGTGGCACCCATTTTATCCTTTTTAGTCCTCAAAGAGCAGGAT
* * * * *
228166 GCTTTTTTC-TTTAAGGCCCACACAAGCTGGTAGCATCTTCTT-TCCTTTTAGTTCTAAAAGAGT
65 GCCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCA-CTT-TTATCCTTTTAGTCCTAAAAGAGC
* * * * *
228229 AAGA-C-GTCTTTCTAAAGCCCACACAAGCTGGTTGTACCTTTTATCCTTTTAGTCTTTAAAGAG
128 AAGACCTGTCTTTCTAAAGCCCACACAAGCTAGTGGCACCTTTTATCCTTTTAGTCCTCAAAGAG
*
228292 TAGGACGTC
193 TAGGACATC
* * * * * * * *
228301 TTTCTAAAGCTCACATAAGTTGGTGGCACCCCTTTTATCCTTTTTTGTCCACAAAGAGCAAGATG
1 TTTCGAAAGCTCATACAAGCTGGTGGCACCCATTTTATCCTTTTTAGTCCTCAAAGAGCAGGATG
* *
228366 CCTTATTCTTTTCAAAGCCCACACGAGCTGGTGGCACTTTTTATCCTTTTAGTC
66 CCTTTTTCTTTT-AAAGCCCACACAAGCTGGTGGCAC-TTTTATCCTTTTAGTC
228420 TTCAAAGAAC
Statistics
Matches: 269, Mismatches: 41, Indels: 21
0.81 0.12 0.06
Matches are distributed among these distances:
199 116 0.43
200 7 0.03
201 32 0.12
202 1 0.00
205 50 0.19
206 63 0.23
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (201 bp):
TTTCGAAAGCTCATACAAGCTGGTGGCACCCATTTTATCCTTTTTAGTCCTCAAAGAGCAGGATG
CCTTTTTCTTTTAAAGCCCACACAAGCTGGTGGCACTTTTATCCTTTTAGTCCTAAAAGAGCAAG
ACCTGTCTTTCTAAAGCCCACACAAGCTAGTGGCACCTTTTATCCTTTTAGTCCTCAAAGAGTAG
GACATC
Found at i:229166 original size:50 final size:50
Alignment explanation
Indices: 229082--229196 Score: 158
Period size: 50 Copynumber: 2.3 Consensus size: 50
229072 TCTAGAAAGA
* * * ** *
229082 AAATGTATCGATACATTTTTCCTTGTATTGATACATTCTGGGTTTTTGACTC
1 AAATGTATCGAT--ATTTTTCATTATATCGATACATTCTAAGTTTTTGACCC
229134 AAATGTATCGATATTTTTCATTATATCGATACATTCTAAGTTTTTGACCC
1 AAATGTATCGATATTTTTCATTATATCGATACATTCTAAGTTTTTGACCC
229184 AAATGTATCGATA
1 AAATGTATCGATA
229197 CATTCTTCAA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 45 0.79
52 12 0.21
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (50 bp):
AAATGTATCGATATTTTTCATTATATCGATACATTCTAAGTTTTTGACCC
Found at i:231497 original size:94 final size:96
Alignment explanation
Indices: 231394--231583 Score: 294
Period size: 95 Copynumber: 2.0 Consensus size: 96
231384 CTCACAACCT
*
231394 AACCCTCTAAGCGTGGA-CAAGGCTAAACCTAAAAAATATTTTTATTAAATTTTAG-TTTCCTAT
1 AACCCTCTAAGCGTGGACCAAGGCTAAACCAAAAAAATATTTTTATTAAATTTTAGTTTTCCTAT
* * *
231457 TTTCAAATATCACTCATGAATCTTATCAAAA
66 TCTCAAATATCACTCACGAATCTTACCAAAA
* * *
231488 AACCTTCTAAGCTTGGACCAAGGCTGAACCAAAAAAATATTTTTATTAAATTTTAGTTTTCCTAT
1 AACCCTCTAAGCGTGGACCAAGGCTAAACCAAAAAAATATTTTTATTAAATTTTAGTTTTCCTAT
*
231553 TCTCAAATATCACTCACGAATGTTACCAAAA
66 TCTCAAATATCACTCACGAATCTTACCAAAA
231584 GGGGCACACT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 15 0.17
95 36 0.42
96 35 0.41
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (96 bp):
AACCCTCTAAGCGTGGACCAAGGCTAAACCAAAAAAATATTTTTATTAAATTTTAGTTTTCCTAT
TCTCAAATATCACTCACGAATCTTACCAAAA
Found at i:231708 original size:79 final size:80
Alignment explanation
Indices: 231602--231961 Score: 327
Period size: 79 Copynumber: 4.5 Consensus size: 80
231592 CTAACACCCA
* * * * * *
231602 TTTTCACTTCTAAAACACT-AAATTTTTCATCTCCAGGGATAGTCTAATCCCACCATTTTTGAAG
1 TTTTTACTTCCAAAACATTGAAA-TTTTCATCTCGAGGGATACTCTAACCCCACCATTTTTGAAG
*
231666 AGATACTCCAACCCCC
65 AGATACTCCAACCCCG
* * *
231682 TTTTT-CTTCCAAAACATTGAAATTTTCATCTTGA-GGATACTCTAACCCCACCATTTTTGAGGG
1 TTTTTACTTCCAAAACATTGAAATTTTCATCTCGAGGGATACTCTAACCCCACCATTTTTGAAGA
* *
231745 GATACTCTAAACCCG
66 GATACTCCAACCCCG
* * * * * * **
231760 TTTTTACTTTCAAAATATTTAATTTTTCATCTCGA-GGATACTCTAACCCCATCATTTTCGATTA
1 TTTTTACTTCCAAAACATTGAAATTTTCATCTCGAGGGATACTCTAACCCCACCATTTTTGAAGA
***
231824 GATACTCCAACCTTA
66 GATACTCCAACCCCG
* * * * * *
231839 TTTTTATTTCCTAAACATTGAATTTTTTATCTCGAGGGATACTCTAACCCTACCATCTTTGAA-A
1 TTTTTACTTCCAAAACATTGAAATTTTCATCTCGAGGGATACTCTAACCCCACCATTTTTGAAGA
* *
231903 GGATACTTCAACCTCG
66 -GATACTCCAACCCCG
** * * *
231919 TTTTTACTTTTAAAATACTGAAATTTTCAACTC-AGGGGATACT
1 TTTTTACTTCCAAAACATTGAAATTTTCATCTCGA-GGGATACT
231962 TCAACCCTTT
Statistics
Matches: 225, Mismatches: 50, Indels: 10
0.79 0.18 0.04
Matches are distributed among these distances:
78 42 0.19
79 110 0.49
80 73 0.32
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (80 bp):
TTTTTACTTCCAAAACATTGAAATTTTCATCTCGAGGGATACTCTAACCCCACCATTTTTGAAGA
GATACTCCAACCCCG
Found at i:231946 original size:159 final size:156
Alignment explanation
Indices: 231592--231961 Score: 391
Period size: 159 Copynumber: 2.3 Consensus size: 156
231582 AAGGGGCACA
* * * * * * *
231592 CTAACACCCATTTTCACTTCTAAAACACTAAATTTTTCATCTCCAGGGATAGTCTAATCCCACCA
1 CTAA-ACCCGTTTTTACTTTTAAAATACTAAA-TTTTCATCTCGA-GGATACTCTAACCCCACCA
* * *
231657 TTTTTGAAGAGATACTCCAACCCCCTTTTTCTTCCAAAACATTGAAATTTTCATCTTGAGGATAC
63 TTTTCGAAGAGATACTCCAACCCCATTTTTCTTCCAAAACATTGAAATTTTCATCTCGAGGATAC
* **
231722 TCTAACCCCACCATTTTTGAGGGGATACT
128 TCTAACCCCACCATCTTTGAAAGGATACT
* * * *
231751 CTAAACCCGTTTTTACTTTCAAAATATTTAATTTTTCATCTCGAGGATACTCTAACCCCATCATT
1 CTAAACCCGTTTTTACTTTTAAAATA-CTAAATTTTCATCTCGAGGATACTCTAACCCCACCATT
** ** * * * *
231816 TTCGATTAGATACTCCAACCTTATTTTTATTTCCTAAACATTGAATTTTTTATCTCGAGGGATAC
65 TTCGAAGAGATACTCCAACCCCATTTTT-CTTCCAAAACATTGAAATTTTCATCTCGA-GGATAC
*
231881 TCTAACCCTACCATCTTTGAAAGGATACT
128 TCTAACCCCACCATCTTTGAAAGGATACT
* * *
231910 -TCAACCTCGTTTTTACTTTTAAAATACTGAAATTTTCAACTCAGGGGATACT
1 CTAAACC-CGTTTTTACTTTTAAAATACT-AAATTTTCATCTC-GAGGATACT
231962 TCAACCCTTT
Statistics
Matches: 173, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
157 40 0.23
158 58 0.34
159 67 0.39
160 8 0.05
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (156 bp):
CTAAACCCGTTTTTACTTTTAAAATACTAAATTTTCATCTCGAGGATACTCTAACCCCACCATTT
TCGAAGAGATACTCCAACCCCATTTTTCTTCCAAAACATTGAAATTTTCATCTCGAGGATACTCT
AACCCCACCATCTTTGAAAGGATACT
Found at i:232011 original size:53 final size:53
Alignment explanation
Indices: 231903--232022 Score: 138
Period size: 53 Copynumber: 2.3 Consensus size: 53
231893 ATCTTTGAAA
*
231903 GGATACTTCAA-CCTCGTTTTTACTTTTAAAATACTGAAATTTTCAACTCAGG
1 GGATACTTCAACCCTCGTTTTTACTTTTAAAACACTGAAATTTTCAACTCAGG
* * * * *
231955 GGATACTTCAACCCT-TTTTTTATTTTCTAAAACATTGAAGTTTTCATCTCTA-G
1 GGATACTTCAACCCTCGTTTTTACTTT-TAAAACACTGAAATTTTCAACTC-AGG
*
232008 GGATACCTCAACCCT
1 GGATACTTCAACCCT
232023 ACTATCTTCG
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
52 20 0.34
53 37 0.64
54 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (53 bp):
GGATACTTCAACCCTCGTTTTTACTTTTAAAACACTGAAATTTTCAACTCAGG
Found at i:232066 original size:133 final size:130
Alignment explanation
Indices: 231824--232175 Score: 367
Period size: 133 Copynumber: 2.7 Consensus size: 130
231814 TTTTCGATTA
* *
231824 GATACTCCAA-CCTTATTTTTATTTCCT-AAACATTGAATTTTTTATCTCGAGGGATACTCTAAC
1 GATACTCCAACCCTT-TTTTTATTTTCTAAAACATTGAA--TTTTATCTCTAGGGATACTCTAAC
* * * * * * **
231887 CCTACCATCTTTGAAAGGATACTTCAACCTCGTTTTTACTTTTAAAATACTGAAATTTTCAACTC
63 CCTACTATCTTTG-AGGGATACTCCAACCTCATTTTTACTTCTAAAACACAAAAATTTTCAACTC
*
231952 AGGG
127 AAGG
*
231956 GATACTTCAACCCTTTTTTTATTTTCTAAAACATTGAAGTTTTCATCTCTAGGGATAC-CTCAAC
1 GATACTCCAACCCTTTTTTTATTTTCTAAAACATTGAA-TTTT-ATCTCTAGGGATACTCT-AAC
* *
232020 CCTACTATCTTCGAGGGAATACTCCAATCCT-ATTTTTACTTCTAAAACACAAAAATTTTCATCT
63 CCTACTATCTTTGAGGG-ATACTCCAA-CCTCATTTTTACTTCTAAAACACAAAAATTTTCAACT
232084 CAAGG
126 CAAGG
* * * * * * *
232089 GATACTCCAACCATGTTTTTA-CTTCTACAGCACTGAATTTTA-C-ATAGGAGATACTCTAACCC
1 GATACTCCAACCCTTTTTTTATTTTCTAAAACATTGAATTTTATCTCTAGG-GATACTCTAACCC
232151 TACTATCTTTGAGGGGATACTCCAA
65 TACTATCTTTGA-GGGATACTCCAA
232176 ACCCAATTTT
Statistics
Matches: 187, Mismatches: 24, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
128 4 0.02
129 31 0.17
130 6 0.03
131 4 0.02
132 41 0.22
133 98 0.52
134 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (130 bp):
GATACTCCAACCCTTTTTTTATTTTCTAAAACATTGAATTTTATCTCTAGGGATACTCTAACCCT
ACTATCTTTGAGGGATACTCCAACCTCATTTTTACTTCTAAAACACAAAAATTTTCAACTCAAGG
Found at i:233284 original size:13 final size:13
Alignment explanation
Indices: 233266--233292 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
233256 ACATTATGCT
233266 TTGTATCGATACA
1 TTGTATCGATACA
233279 TTGTATCGATACA
1 TTGTATCGATACA
233292 T
1 T
233293 GTTAATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:233302 original size:19 final size:19
Alignment explanation
Indices: 233278--233333 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
233268 GTATCGATAC
**
233278 ATTGTATCGATACATGTTA
1 ATTGTATCGATACATGACA
233297 ATTGTATCGATACATGGACA
1 ATTGTATCGATACAT-GACA
233317 ATTGTATCGATACATGA
1 ATTGTATCGATACATGA
233334 GATTGGTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
ATTGTATCGATACATGACA
Found at i:233321 original size:20 final size:20
Alignment explanation
Indices: 233278--233332 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
233268 GTATCGATAC
**
233278 ATTGTATCGATACAT-GTTA
1 ATTGTATCGATACATGGACA
233297 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
233317 ATTGTATCGATACATG
1 ATTGTATCGATACATG
233333 AGATTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:233407 original size:13 final size:13
Alignment explanation
Indices: 233385--233416 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
233375 TCGATACATT
*
233385 ATACAATGTATCG
1 ATACATTGTATCG
233398 ATACATTGTATCG
1 ATACATTGTATCG
233411 ATACAT
1 ATACAT
233417 AGCTTGTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (13 bp):
ATACATTGTATCG
Found at i:239761 original size:22 final size:20
Alignment explanation
Indices: 239736--239782 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 20
239726 AAATTTCCAC
239736 AAAT-TTTCACTTTTTCACTTCA
1 AAATCTTTCA-TTTTTCA--TCA
*
239758 AAATCTTTTATTTTTCATCA
1 AAATCTTTCATTTTTCATCA
239778 AAATC
1 AAATC
239783 ATCAACAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 8 0.35
22 11 0.48
23 4 0.17
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATCTTTCATTTTTCATCA
Done.