Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold402
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: 38330
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:324 original size:117 final size:118
Alignment explanation
Indices: 64--610 Score: 668
Period size: 117 Copynumber: 4.6 Consensus size: 118
54 ATGCTATTGA
* * * * * *
64 TATATCAGGGCTAAAGTCCGCAAGAGCATTCGT-CTCGTGCTATATCCGGGCTCACTCCCGAAGA
1 TATATCA-GGCT-AAGTCCG-AAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCTCGAAGA
* * * * *
128 GCATTCGCGCTA-ATGATATATCCGGGTTAAGTCC-CGAAGAGCATACGTGCTGGTGT
63 GCATTCGTGCTAGA-GTTATATCCGGGCTAAG-CCTCGAAGAGCATTCGTGCTGGAGT
* * * *
184 T-TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGAGTTATAATCCGGGCTAAGTCTC-AAGA
1 TATAT-CAGGCTAAGT-CCGAAGAGCATACGTGCTGGTGTTAT-ATCCGGGCTAAGTCTCGAAGA
247 GCATTCGTGCTAGAGTTATAT-CGGGCTAA-CCTCGAAGAGCATTCGTTGCTGGAGT
63 GCATTCGTGCTAGAGTTATATCCGGGCTAAGCCTCGAAGAGCATTCG-TGCTGGAGT
302 TA-ATCAGGCTAAAGTCCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCTCG-AGAGC
1 TATATCAGGCT-AAGTCCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCTCGAAGAGC
*
365 AATTCGTGCTAGAGTTATATCCGGGCTAAAGTCTCGAAGAGCATTCGTGCTGGAGT
65 -ATTCGTGCTAGAGTTATATCCGGGCT-AAGCCTCGAAGAGCATTCGTGCTGGAGT
* *
421 TATATCAGGGCT-AGTCCCGAAGAGCATACGTGCTGGTGTTATATCTGGGCTAAGT-TCAAAGAG
1 TATATCA-GGCTAAGT-CCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCTCGAAGAG
* *
484 CATTCGTGCTAGAGTTATATCCGGGCTTAGTCTCGAA-AGCATTCGTGCTGGAGT
64 CATTCGTGCTAGAGTTATATCCGGGCTAAGCCTCGAAGAGCATTCGTGCTGGAGT
* * *
538 TATATCAGGCTAAGTCCGAAGAGCATACGTGCTGGAGTTATATCAGGGCTAAGTCCCGAAGAGCA
1 TATATCAGGCTAAGTCCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCTCGAAGAGCA
*
603 TTCATGCT
66 TTCGTGCT
611 GGTGATGTGT
Statistics
Matches: 382, Mismatches: 25, Indels: 43
0.85 0.06 0.10
Matches are distributed among these distances:
116 64 0.17
117 101 0.26
118 53 0.14
119 82 0.21
120 78 0.20
121 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (118 bp):
TATATCAGGCTAAGTCCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCTCGAAGAGCA
TTCGTGCTAGAGTTATATCCGGGCTAAGCCTCGAAGAGCATTCGTGCTGGAGT
Found at i:473 original size:236 final size:237
Alignment explanation
Indices: 64--610 Score: 745
Period size: 236 Copynumber: 2.3 Consensus size: 237
54 ATGCTATTGA
* * * * *
64 TATATCAGGGCTAAAGTCCGCAAGAGCATTCGT-CTCGTGCTATATCCGGGCTCACTCCCGAAGA
1 TATATCA-GGCTAAAGTCCG-AAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGA
* * * *
128 GCATTCGCGCTAATGATATATCCGGGTTAAGTCCCGAAGAGCATACGTGCTGGTGTTTATCCGGG
64 GCATTCGTGCTAATGATATATCCGGGTAAAGTCCCGAAGAGCATACGTGCTGGAGTTTATCAGGG
*
193 CTAAGTCCCGAAGAGCATTCGTGCTAGAGTTATAATCCGGGCTAAGTCTC-AAGAGCATTCGTGC
129 CTAAGTCCCGAAGAGCATACGTGCTAGAGTTATAATCCGGGCTAAGT-TCAAAGAGCATTCGTGC
257 TAGAGTTATAT-CGGGC-TAACCTCGAAGAGCATTCGTTGCTGGAGT
193 TAGAGTTATATCCGGGCTTAACCTCGAA-AGCATTCG-TGCTGGAGT
*
302 TA-ATCAGGCTAAAGTCCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCTCG-AGAGC
1 TATATCAGGCTAAAGTCCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGC
* * *
365 AATTCGTGCTAGA-GTTATATCCGGGCTAAAGTCTCGAAGAGCATTCGTGCTGGAGTTATATCAG
66 -ATTCGTGCTA-ATGATATATCCGGG-TAAAGTCCCGAAGAGCATACGTGCTGGAGTT-TATCAG
* * *
429 GGCT-AGTCCCGAAGAGCATACGTGCTGGTGTTAT-ATCTGGGCTAAGTTCAAAGAGCATTCGTG
127 GGCTAAGTCCCGAAGAGCATACGTGCTAGAGTTATAATCCGGGCTAAGTTCAAAGAGCATTCGTG
**
492 CTAGAGTTATATCCGGGCTTAGTCTCGAAAGCATTCGTGCTGGAGT
192 CTAGAGTTATATCCGGGCTTAACCTCGAAAGCATTCGTGCTGGAGT
* *
538 TATATCAGGCT-AAGTCCGAAGAGCATACGTGCTGGAGTTATATCAGGGCTAAGTCCCGAAGAGC
1 TATATCAGGCTAAAGTCCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGC
*
602 ATTCATGCT
66 ATTCGTGCT
611 GGTGATGTGT
Statistics
Matches: 276, Mismatches: 23, Indels: 22
0.86 0.07 0.07
Matches are distributed among these distances:
235 18 0.07
236 154 0.56
237 85 0.31
238 19 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (237 bp):
TATATCAGGCTAAAGTCCGAAGAGCATACGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGC
ATTCGTGCTAATGATATATCCGGGTAAAGTCCCGAAGAGCATACGTGCTGGAGTTTATCAGGGCT
AAGTCCCGAAGAGCATACGTGCTAGAGTTATAATCCGGGCTAAGTTCAAAGAGCATTCGTGCTAG
AGTTATATCCGGGCTTAACCTCGAAAGCATTCGTGCTGGAGT
Found at i:611 original size:40 final size:40
Alignment explanation
Indices: 64--612 Score: 592
Period size: 39 Copynumber: 13.9 Consensus size: 40
54 ATGCTATTGA
* * * *
64 TATATCAGGGCTAAAGT-CCGCAAGAGCATTCGT-CTCGTGC
1 TATATCCGGGCT-AAGTCCCG-AAGAGCATTCGTGCTGGAGT
* * * * *
104 TATATCCGGGCTCACTCCCGAAGAGCATTCGCGCT-AATGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGA-GT
* * *
144 TATATCCGGGTTAAGTCCCGAAGAGCATACGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGAGT
*
184 T-TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGAGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGAGT
* *
223 TATAATCCGGGCTAAGTCTC-AAGAGCATTCGTGCTAGAGT
1 TAT-ATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGAGT
263 TATAT-CGGGCTAA--CCTCGAAGAGCATTCGTTGCTGGAGT
1 TATATCCGGGCTAAGTCC-CGAAGAGCATTCG-TGCTGGAGT
* * *
302 TA-AT-CAGGCTAAAGT-CCGAAGAGCATACGTGCTGGTGT
1 TATATCCGGGCT-AAGTCCCGAAGAGCATTCGTGCTGGAGT
* *
340 TATATCCGGGCTAAGTCTCG-AGAGCAATTCGTGCTAGAGT
1 TATATCCGGGCTAAGTCCCGAAGAGC-ATTCGTGCTGGAGT
*
380 TATATCCGGGCTAAAGTCTCGAAGAGCATTCGTGCTGGAGT
1 TATATCCGGGCT-AAGTCCCGAAGAGCATTCGTGCTGGAGT
* * *
421 TATATCAGGGCT-AGTCCCGAAGAGCATACGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGAGT
* * * *
460 TATATCTGGGCTAAGT-TCAAAGAGCATTCGTGCTAGAGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGAGT
* *
499 TATATCCGGGCTTAGTCTCGAA-AGCATTCGTGCTGGAGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGAGT
* *
538 TATAT-CAGGCTAAGT-CCGAAGAGCATACGTGCTGGAGT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGAGT
* *
576 TATATCAGGGCTAAGTCCCGAAGAGCATTCATGCTGG
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGG
613 TGATGTGTAT
Statistics
Matches: 433, Mismatches: 53, Indels: 46
0.81 0.10 0.09
Matches are distributed among these distances:
36 1 0.00
37 5 0.01
38 65 0.15
39 181 0.42
40 129 0.30
41 47 0.11
42 5 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGAGT
Found at i:3142 original size:22 final size:22
Alignment explanation
Indices: 3117--3192 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 22
3107 TAATAATAAG
3117 TAAACACTATTGATCAGAATAT
1 TAAACACTATTGATCAGAATAT
* * *
3139 TAAACATCTCTATCT-ATAATAATAAG
1 TAAACA---CTAT-TGATCAGAAT-AT
3165 TAAACACTATTGATCAGAATAT
1 TAAACACTATTGATCAGAATAT
3187 TAAACA
1 TAAACA
3193 TCTCTATCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
22 14 0.33
23 10 0.24
25 10 0.24
26 8 0.19
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.32
Consensus pattern (22 bp):
TAAACACTATTGATCAGAATAT
Found at i:3161 original size:48 final size:48
Alignment explanation
Indices: 3107--3204 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
3097 TACCGAATGT
3107 TAATAATAAGTAAACACTATTGATCAGAATATTAAACATCTCTATCTA
1 TAATAATAAGTAAACACTATTGATCAGAATATTAAACATCTCTATCTA
3155 TAATAATAAGTAAACACTATTGATCAGAATATTAAACATCTCTATCTA
1 TAATAATAAGTAAACACTATTGATCAGAATATTAAACATCTCTATCTA
3203 TA
1 TA
3205 CTTATTTAGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (48 bp):
TAATAATAAGTAAACACTATTGATCAGAATATTAAACATCTCTATCTA
Found at i:3185 original size:23 final size:23
Alignment explanation
Indices: 3111--3185 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 23
3101 GAATGTTAAT
3111 AATAAGTAAACACTATTGATCAG
1 AATAAGTAAACACTATTGATCAG
* * *
3134 AAT-ATTAAACATCTCTATCT-ATAAT
1 AATAAGTAAACA---CTAT-TGATCAG
3159 AATAAGTAAACACTATTGATCAG
1 AATAAGTAAACACTATTGATCAG
3182 AATA
1 AATA
3186 TTAAACATCT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
22 8 0.20
23 14 0.35
25 10 0.25
26 8 0.20
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (23 bp):
AATAAGTAAACACTATTGATCAG
Found at i:3185 original size:26 final size:26
Alignment explanation
Indices: 3108--3185 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
3098 ACCGAATGTT
3108 AATAATAAGTAAACACTATTGATCAG
1 AATAATAAGTAAACACTATTGATCAG
* *
3134 AAT-AT---TAAACATCT-CT-ATCTAT
1 AATAATAAGTAAACA-CTATTGATC-AG
3156 AATAATAAGTAAACACTATTGATCAG
1 AATAATAAGTAAACACTATTGATCAG
3182 AATA
1 AATA
3186 TTAAACATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 16
0.67 0.07 0.27
Matches are distributed among these distances:
21 3 0.08
22 11 0.28
23 4 0.10
25 4 0.10
26 15 0.38
27 3 0.08
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.31
Consensus pattern (26 bp):
AATAATAAGTAAACACTATTGATCAG
Found at i:4330 original size:47 final size:47
Alignment explanation
Indices: 4258--4666 Score: 559
Period size: 47 Copynumber: 8.6 Consensus size: 47
4248 ATACATGAGC
* * *
4258 TAAGGCCCGAATGGCAAATGTGATGAATGTGAACATGCATTTGTGTGC
1 TAAGG-CCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
* ** *
4306 TAAGGCCAAATGGAAAATGTGATGAATGTGAACATGCAT-TGTTGTGG
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATG-TGTGA
* *
4353 TAAGACCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
* * *
4400 TAAGGCCGAATGGCCAACGTGATGAATATGAACATGCATATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
* * *
4447 TAAGGCCGAATGGCCAATGTGATGAATATGAACATGTATATCTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
4494 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
* * * *
4541 TAAGGCCGAATGACCAATGTGAAGAATATGAACATGCATATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
* * **
4588 TAAGGCACGAATGACCAATGTGATTAAATGTGAACATGCATACATGTGA
1 TAAGGC-CGAATGGCCAATGTGA-TGAATGTGAACATGCATATGTGTGA
*
4637 TAAGGCAGAATGGCCAATGTGATGAATGTG
1 TAAGGCCGAATGGCCAATGTGATGAATGTG
4667 GATGTGTATA
Statistics
Matches: 326, Mismatches: 31, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
46 2 0.01
47 260 0.80
48 37 0.11
49 27 0.08
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.26
Consensus pattern (47 bp):
TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGTGA
Found at i:4729 original size:46 final size:46
Alignment explanation
Indices: 4676--4766 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
4666 GGATGTGTAT
* * *
4676 ATATGTGGGAAAGCCGAATGGTTAATGCGAAATGCGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATACGTATGAGATGG
* * * *
4722 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATACGTATGAGATG
4767 TGTATATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.32, T:0.26
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGCGAAATACGTATGAGATGG
Found at i:6281 original size:18 final size:18
Alignment explanation
Indices: 6258--6293 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
6248 ACATGATCAG
6258 ATGTTTATATGTTGTCAT
1 ATGTTTATATGTTGTCAT
*
6276 ATGTTTATATTTTGTCAT
1 ATGTTTATATGTTGTCAT
6294 GGATGTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.06, G:0.14, T:0.58
Consensus pattern (18 bp):
ATGTTTATATGTTGTCAT
Found at i:6396 original size:8 final size:8
Alignment explanation
Indices: 6383--6408 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
6373 ACATGTGGAA
6383 TTATGATG
1 TTATGATG
6391 TTATGATG
1 TTATGATG
6399 TTATGATG
1 TTATGATG
6407 TT
1 TT
6409 GCATTGCTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (8 bp):
TTATGATG
Found at i:6877 original size:15 final size:15
Alignment explanation
Indices: 6857--6886 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6847 GCTAAGTGAT
6857 AACATGGTGATTGAA
1 AACATGGTGATTGAA
*
6872 AACATGGTGTTTGAA
1 AACATGGTGATTGAA
6887 GCATGAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.30
Consensus pattern (15 bp):
AACATGGTGATTGAA
Found at i:9127 original size:40 final size:40
Alignment explanation
Indices: 9053--9275 Score: 333
Period size: 40 Copynumber: 5.6 Consensus size: 40
9043 AACCCGAGTA
* *
9053 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
*
9092 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
9132 CCTTCGGGACTTAGCCCGAATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
9172 CCTTCGGGACTTAGCCCGGATATTGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
9212 CCTTCGAGACTTAACCCGGATATAGTCACTAGCACAAAGTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAA-TG
*
9253 CCTTCGGGTCTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
9276 CATCCGAATA
Statistics
Matches: 166, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 13 0.08
40 130 0.78
41 23 0.14
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:9817 original size:13 final size:13
Alignment explanation
Indices: 9799--9825 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9789 TTATTATTTC
9799 TAACACAAAATGT
1 TAACACAAAATGT
9812 TAACACAAAATGT
1 TAACACAAAATGT
9825 T
1 T
9826 TATAATATGC
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:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (13 bp):
TAACACAAAATGT
Found at i:16393 original size:40 final size:40
Alignment explanation
Indices: 16319--16541 Score: 315
Period size: 40 Copynumber: 5.6 Consensus size: 40
16309 AACCCAAGTA
* * *
16319 CCTTCGGGATTTAG-CCGGATAT-AGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATC-ACTAGCACAAATG
16358 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
*
16398 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
* ** *
16438 CCTTCGGGACTTAGCCCAGATATCGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
*
16478 CCTTCGGGACTTAACCCGGATATAATCACTAGCACAAAGTG
1 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAA-TG
* *
16519 CCTTCGGGTCTTAGCCCAGATAT
1 CCTTCGGGACTTAGCCCGGATAT
16542 CATCCGAATA
Statistics
Matches: 166, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 13 0.08
40 129 0.78
41 24 0.14
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
Found at i:25673 original size:27 final size:27
Alignment explanation
Indices: 25641--25695 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
25631 TTCCTTTGGT
25641 TGAATTGAAATGCCTTTTGATGCTATG
1 TGAATTGAAATGCCTTTTGATGCTATG
25668 TGAATTGAAATGCCTTTTGATGCTATG
1 TGAATTGAAATGCCTTTTGATGCTATG
25695 T
1 T
25696 ATTAGCGCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (27 bp):
TGAATTGAAATGCCTTTTGATGCTATG
Found at i:28806 original size:40 final size:40
Alignment explanation
Indices: 28769--28992 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
28759 GCTACTCGTT
*
28769 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
28809 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
28849 CAAATGCCTTCGGGACTTA-ACCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
28888 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
28927 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28968 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28993 CATCATTCGA
Statistics
Matches: 162, Mismatches: 16, Indels: 12
0.85 0.08 0.06
Matches are distributed among these distances:
38 6 0.04
39 59 0.36
40 84 0.52
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:30185 original size:56 final size:56
Alignment explanation
Indices: 30118--30237 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
30108 TATTAGTTTA
30118 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
30174 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
30230 TTGCCCAT
1 TTGCCCAT
30238 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:36796 original size:40 final size:40
Alignment explanation
Indices: 36664--36915 Score: 271
Period size: 38 Copynumber: 6.6 Consensus size: 40
36654 GCTACTCGTT
*
36664 CAAATGCCTTC-GGACATAGCCCGG-TTATAGTAACTC-CA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
36702 -AAATGCCTTCGGGACATAGCCC---TTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
36738 C-AA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
36776 CAAATGCCTTCGGGACTTAACCC-GA-TTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
36814 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
36853 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
36894 CAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAGCCC
36916 AGACATCATT
Statistics
Matches: 186, Mismatches: 14, Indels: 26
0.82 0.06 0.12
Matches are distributed among these distances:
35 25 0.13
36 6 0.03
37 17 0.09
38 56 0.30
39 26 0.14
40 45 0.24
41 11 0.06
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:36851 original size:77 final size:75
Alignment explanation
Indices: 36666--36865 Score: 264
Period size: 77 Copynumber: 2.7 Consensus size: 75
36656 TACTCGTTCA
* * * *
36666 AATGCCTTCGGACATAGCCCGG-TTATAGTAACTC-CA-AAATGCCTTCGGGACATAGCCCTTTA
1 AATGCCTTCGGGCTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACATAACCCATTA
36728 GTAACTCGCAC
65 GTAACTCGCAC
* *
36739 AA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGATT
1 AATGCCTTCGGG-CTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACATAACCC-ATT
36803 AGTAACTCGCACC
64 AGTAACTCGCA-C
* *
36816 AATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGG
1 AATGCCTTCGGGCTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGG
36866 ATCTTAGTCC
Statistics
Matches: 111, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
72 8 0.07
73 19 0.17
74 4 0.04
75 20 0.18
76 13 0.12
77 38 0.34
78 9 0.08
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (75 bp):
AATGCCTTCGGGCTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACATAACCCATTAG
TAACTCGCAC
Done.