Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold219
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: 770726
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:316227 original size:19 final size:21
Alignment explanation
Indices: 316189--316227 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
316179 GTAGCCTTGA
*
316189 CCATGCATTTTTTACTATGTT
1 CCATGCATTTTTAACTATGTT
316210 CCATGCA-TTTTAAC-ATGT
1 CCATGCATTTTTAACTATGT
316228 CCAACATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 6 0.35
21 7 0.41
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (21 bp):
CCATGCATTTTTAACTATGTT
Found at i:320543 original size:18 final size:18
Alignment explanation
Indices: 320522--320603 Score: 66
Period size: 18 Copynumber: 4.6 Consensus size: 18
320512 TTTTGAACAA
320522 AAAAAAAGAAAGAAAGAG
1 AAAAAAAGAAAGAAAGAG
*
320540 -AAAAGAG-AAGAAA-AG
1 AAAAAAAGAAAGAAAGAG
320555 ATGAAAAAAGAAAG-AAG-G
1 A--AAAAAAGAAAGAAAGAG
320573 AAAGAAGAAGAAAGAAAGAG
1 AAA-AA-AAGAAAGAAAGAG
* *
320593 AGAAGAAGAAA
1 AAAAAAAGAAA
320604 AGAAGCTTAG
Statistics
Matches: 51, Mismatches: 4, Indels: 18
0.70 0.05 0.25
Matches are distributed among these distances:
15 2 0.04
16 8 0.16
17 8 0.16
18 23 0.45
19 7 0.14
20 3 0.06
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (18 bp):
AAAAAAAGAAAGAAAGAG
Found at i:320575 original size:8 final size:9
Alignment explanation
Indices: 320528--320608 Score: 57
Period size: 8 Copynumber: 9.0 Consensus size: 9
320518 ACAAAAAAAA
320528 AGAAAGAA-
1 AGAAAGAAG
320536 AGAGAA-AAG
1 AGA-AAGAAG
*
320545 AGAAGAAAAG
1 AGAA-AGAAG
320555 ATGAAA-AA-
1 A-GAAAGAAG
320563 AGAAAGAAG
1 AGAAAGAAG
320572 -GAAAGAAG
1 AGAAAGAAG
320580 AAGAAAGAAAG
1 -AGAAAG-AAG
320591 AGAGAAGAAG
1 AGA-AAGAAG
320601 A-AAAGAAG
1 AGAAAGAAG
320609 CTTAGGCCAC
Statistics
Matches: 62, Mismatches: 0, Indels: 22
0.74 0.00 0.26
Matches are distributed among these distances:
7 4 0.06
8 23 0.37
9 9 0.15
10 17 0.27
11 9 0.15
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (9 bp):
AGAAAGAAG
Found at i:320576 original size:22 final size:22
Alignment explanation
Indices: 320545--320604 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
320535 AAGAGAAAAG
*
320545 AGAAGAAAAGATGAAAAAAGAA
1 AGAAGAAAAGAAGAAAAAAGAA
* *
320567 AGAAGGAAAGAAGAAGAAAGAA
1 AGAAGAAAAGAAGAAAAAAGAA
*
320589 AG-AGAGAAGAAGAAAA
1 AGAAGAAAAGAAGAAAA
320605 GAAGCTTAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 11 0.34
22 21 0.66
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (22 bp):
AGAAGAAAAGAAGAAAAAAGAA
Found at i:322838 original size:20 final size:20
Alignment explanation
Indices: 322809--322846 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
322799 TACTGCCAGT
322809 TTCATATATTGATACAATTG
1 TTCATATATTGATACAATTG
*
322829 TTCATGTATTGATACAAT
1 TTCATATATTGATACAAT
322847 AAGCATGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (20 bp):
TTCATATATTGATACAATTG
Found at i:326848 original size:16 final size:16
Alignment explanation
Indices: 326829--326859 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
326819 TTTTTCTATC
326829 AAAAATTTTGAAAGTT
1 AAAAATTTTGAAAGTT
326845 AAAAATTTTGAAAGT
1 AAAAATTTTGAAAGT
326860 CTTTCGTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (16 bp):
AAAAATTTTGAAAGTT
Found at i:329527 original size:15 final size:14
Alignment explanation
Indices: 329505--329536 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
329495 GTTCGATAAT
329505 TTTCTTTTCAACAA
1 TTTCTTTTCAACAA
329519 TTTCATTTTCAACAA
1 TTTC-TTTTCAACAA
329534 TTT
1 TTT
329537 TTGATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTCTTTTCAACAA
Found at i:331171 original size:22 final size:24
Alignment explanation
Indices: 331141--331185 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
331131 TCTCACAATC
*
331141 TCTTCAAGA-ATTATACCCCAAAT
1 TCTTCAAGAGATTATAACCCAAAT
*
331164 TCTT-AAGAGATTGTAACCCAAA
1 TCTTCAAGAGATTATAACCCAAA
331186 GTTGAATGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (24 bp):
TCTTCAAGAGATTATAACCCAAAT
Found at i:331713 original size:13 final size:13
Alignment explanation
Indices: 331695--331721 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
331685 TACAATAAGC
331695 ATGTATCAATACA
1 ATGTATCAATACA
331708 ATGTATCAATACA
1 ATGTATCAATACA
331721 A
1 A
331722 AGCATATGTA
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:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:332059 original size:7 final size:7
Alignment explanation
Indices: 332049--332073 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
332039 ACTAATTCCT
332049 AATTTCA
1 AATTTCA
332056 AATTTCA
1 AATTTCA
332063 AATTTCA
1 AATTTCA
332070 AATT
1 AATT
332074 GTTAGGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTTCA
Found at i:332307 original size:21 final size:21
Alignment explanation
Indices: 332274--332314 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
332264 CTAAGTAAAA
332274 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
332295 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
332315 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:332379 original size:20 final size:19
Alignment explanation
Indices: 332354--332424 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
332344 ACCTTGAAAA
332354 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
332374 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
**
332393 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
332414 GTATCGATACA
1 GTATCGATACA
332425 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:332478 original size:53 final size:53
Alignment explanation
Indices: 332394--332530 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
332384 AGATTGCATA
332394 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
* *
332448 GTATCGATACACACAATATGTATTGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
332501 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
332531 TTGGGAGTAG
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 65 0.82
54 14 0.18
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:332573 original size:10 final size:10
Alignment explanation
Indices: 332554--332648 Score: 55
Period size: 10 Copynumber: 9.1 Consensus size: 10
332544 AATCTCATTT
*
332554 TCACTGTTCA
1 TCACTATTCA
332564 TCACTATTCA
1 TCACTATTCA
*
332574 TCACTGTTCA
1 TCACTATTCA
* * *
332584 TGTATCGATACA
1 T-CA-CTATTCA
332596 TCACTATTCA
1 TCACTATTCA
* *
332606 TAACTGTTCA
1 TCACTATTCA
* * *
332616 TGTATCGATACA
1 T-CA-CTATTCA
332628 TCACTATTCA
1 TCACTATTCA
*
332638 TCACTGTTCA
1 TCACTATTCA
332648 T
1 T
332649 GTATCGATAC
Statistics
Matches: 62, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
10 48 0.77
11 4 0.06
12 10 0.16
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.39
Consensus pattern (10 bp):
TCACTATTCA
Found at i:332603 original size:32 final size:32
Alignment explanation
Indices: 332562--332662 Score: 193
Period size: 32 Copynumber: 3.2 Consensus size: 32
332552 TTTCACTGTT
332562 CATCACTATTCATCACTGTTCATGTATCGATA
1 CATCACTATTCATCACTGTTCATGTATCGATA
*
332594 CATCACTATTCATAACTGTTCATGTATCGATA
1 CATCACTATTCATCACTGTTCATGTATCGATA
332626 CATCACTATTCATCACTGTTCATGTATCGATA
1 CATCACTATTCATCACTGTTCATGTATCGATA
332658 CATCA
1 CATCA
332663 TAAATAGTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.37
Consensus pattern (32 bp):
CATCACTATTCATCACTGTTCATGTATCGATA
Found at i:340300 original size:13 final size:13
Alignment explanation
Indices: 340282--340307 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
340272 ACATAGGTTT
340282 TGTATCGATACAA
1 TGTATCGATACAA
340295 TGTATCGATACAA
1 TGTATCGATACAA
340308 AATTAACCTG
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:340356 original size:20 final size:20
Alignment explanation
Indices: 340331--340408 Score: 102
Period size: 20 Copynumber: 3.8 Consensus size: 20
340321 ACTGCCAAGG
*
340331 AAATGTATCGATACATTAAT
1 AAATGTATCGATACATTATT
* *
340351 AAATGTATCGATAAATTTTTT
1 AAATGTATCGATACA-TTATT
340372 AAATTGTATCGATACATTATT
1 AAA-TGTATCGATACATTATT
*
340393 CAATGTATCGATACAT
1 AAATGTATCGATACAT
340409 GTAGGCAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 27 0.54
21 12 0.24
22 11 0.22
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (20 bp):
AAATGTATCGATACATTATT
Found at i:354294 original size:5 final size:5
Alignment explanation
Indices: 354280--354333 Score: 50
Period size: 4 Copynumber: 12.0 Consensus size: 5
354270 AAAAATAAAT
354280 AAAAC AAAAAC AAAAC -AAAC -AAA- AAAAC AAAAC -AAAC -AAA- AAAAC
1 AAAAC -AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
354325 AAAA- AAAAC
1 AAAAC AAAAC
354334 GACAAAAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
4 24 0.56
5 14 0.33
6 5 0.12
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:354332 original size:12 final size:12
Alignment explanation
Indices: 354267--354343 Score: 66
Period size: 12 Copynumber: 6.3 Consensus size: 12
354257 CTTCGAATAT
*
354267 AAAAAAAATAAA
1 AAAAAAAACAAA
* *
354279 TAAAACAAA-AAC
1 -AAAAAAAACAAA
*
354291 AAAACAAACAAA
1 AAAAAAAACAAA
354303 AAAACAAAACAAA
1 AAAA-AAAACAAA
*
354316 CAAAAAAACAAA
1 AAAAAAAACAAA
**
354328 AAAAACGACAAA
1 AAAAAAAACAAA
354340 AAAA
1 AAAA
354344 GGGGTTCGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
11 8 0.15
12 29 0.54
13 17 0.31
ACGTcount: A:0.83, C:0.13, G:0.01, T:0.03
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:354333 original size:9 final size:9
Alignment explanation
Indices: 354285--354343 Score: 68
Period size: 9 Copynumber: 6.6 Consensus size: 9
354275 TAAATAAAAC
354285 AAAAACAAA
1 AAAAACAAA
*
354294 ACAAAC-AA
1 AAAAACAAA
354302 AAAAACAAA
1 AAAAACAAA
*
354311 ACAAAC-AA
1 AAAAACAAA
354319 AAAAACAAA
1 AAAAACAAA
354328 AAAAACGACAA
1 AAAAAC-A-AA
354339 AAAAA
1 AAAAA
354344 GGGGTTCGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
8 14 0.33
9 20 0.48
10 1 0.02
11 7 0.17
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (9 bp):
AAAAACAAA
Found at i:354340 original size:17 final size:17
Alignment explanation
Indices: 354285--354333 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
354275 TAAATAAAAC
354285 AAAAACAAAACAAACAA
1 AAAAACAAAACAAACAA
354302 AAAAACAAAACAAACAA
1 AAAAACAAAACAAACAA
*
354319 AAAAACAAAAAAAAC
1 AAAAACAAAACAAAC
354334 GACAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAACAAAACAAACAA
Found at i:355305 original size:28 final size:27
Alignment explanation
Indices: 355253--355327 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
355243 ATCTTCAATG
* * *
355253 GAATCAAGAAAAGTGCTGATCCCCAAAA
1 GAATCAAGAAAATTGC-AATTCCCAAAA
* *
355281 GAATCATGACAAATTGCAATTCCCAATA
1 GAATCAAGA-AAATTGCAATTCCCAAAA
*
355309 GAATCAAGAAACTTGCAAT
1 GAATCAAGAAAATTGCAAT
355328 AGCTTTGGTC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
27 9 0.23
28 24 0.62
29 6 0.15
ACGTcount: A:0.45, C:0.20, G:0.15, T:0.20
Consensus pattern (27 bp):
GAATCAAGAAAATTGCAATTCCCAAAA
Found at i:355895 original size:27 final size:27
Alignment explanation
Indices: 355830--355888 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
355820 GGCATCCTTT
*
355830 CTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
355857 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
355884 TTTTT
1 CTTTT
355889 CTTTCCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.22, C:0.32, G:0.14, T:0.32
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:355921 original size:29 final size:29
Alignment explanation
Indices: 355888--355974 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
355878 GGCACCTTTT
*
355888 TCTTTCCAAAAGCCCACGACTCTGTGGCA
1 TCTTTCCTAAAGCCCACGACTCTGTGGCA
*
355917 TCTTTCCTAAAGCCCATGACT-TCGTGGCA
1 TCTTTCCTAAAGCCCACGACTCT-GTGGCA
* * *
355946 T-TCTTCCTAAAGTCCACAACTCCGTGGCA
1 TCT-TTCCTAAAGCCCACGACTCTGTGGCA
355975 CCCTTTTAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.04
29 47 0.96
ACGTcount: A:0.23, C:0.33, G:0.16, T:0.28
Consensus pattern (29 bp):
TCTTTCCTAAAGCCCACGACTCTGTGGCA
Found at i:356008 original size:27 final size:27
Alignment explanation
Indices: 355955--356067 Score: 100
Period size: 27 Copynumber: 3.9 Consensus size: 27
355945 ATTCTTCCTA
* * *
355955 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCATAACTCCATGGCACCTTTTT
*
355982 AAGTCCATAACTCCATGGCACATTTTTCTTTTCA
1 AAGTCCATAACTCCATGGCAC------CTTTT-T
* * *
356016 AAGCCCATAACTTCGTGGCACCTTTTT
1 AAGTCCATAACTCCATGGCACCTTTTT
356043 AAGTCCATAACTCCATGGCACCTTT
1 AAGTCCATAACTCCATGGCACCTTT
356068 CTCCTTCTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
27 41 0.60
28 5 0.07
33 4 0.06
34 18 0.26
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.32
Consensus pattern (27 bp):
AAGTCCATAACTCCATGGCACCTTTTT
Found at i:356080 original size:61 final size:60
Alignment explanation
Indices: 355833--356085 Score: 203
Period size: 61 Copynumber: 4.2 Consensus size: 60
355823 ATCCTTTCTT
* * ** * *
355833 TAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTCC
1 TAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCATGGCA-CATTTTCCTT-C
* * * * * * * *
355895 AAAAGCCCACGACTCTGTGGCA-TCTTTCCTAAAGCCCATGACTTCGTGG--CA--TT-CTTCC
1 TAAAGCCCACAACTCCGTGGCACCCTTT--T-AAGTCCATAACTCCATGGCACATTTTCCTT-C
* * *
355953 TAAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCATGGCACATTTTTCTTT
1 TAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCATGGCACATTTTCCTTC
* * * *
356013 TCAAAGCCCATAACTTCGTGGCACCTTTTTAAGTCCATAACTCCATGGCACCTTTCTCCTTC
1 T-AAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCATGGCACATTT-TCCTTC
356075 TAAAGCCCACA
1 TAAAGCCCACA
356086 TAAGTCGGTG
Statistics
Matches: 150, Mismatches: 30, Indels: 23
0.74 0.15 0.11
Matches are distributed among these distances:
56 14 0.09
57 1 0.01
58 24 0.16
59 6 0.04
60 3 0.02
61 65 0.43
62 23 0.15
63 1 0.01
64 13 0.09
ACGTcount: A:0.24, C:0.33, G:0.13, T:0.30
Consensus pattern (60 bp):
TAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCATGGCACATTTTCCTTC
Found at i:356139 original size:63 final size:63
Alignment explanation
Indices: 356072--356193 Score: 158
Period size: 63 Copynumber: 1.9 Consensus size: 63
356062 ACCTTTCTCC
* **
356072 TTCTAAAGCCCACATAAGTCGGTGGCAACC-TCTTCTAAAA-CCCACACAAGTCAGTGGCAACCA
1 TTCTAAAGCCCACACAAGTCAATGGCAACCTTC-T-TAAAAGCCCACACAAGTCAGTGGCAACCA
* * *
356135 TTCTAAAGCTCACACAAGTCAATGGTAACCTTCTTAAAAGCCCACACAAGTCGGTGGCA
1 TTCTAAAGCCCACACAAGTCAATGGCAACCTTCTTAAAAGCCCACACAAGTCAGTGGCA
356194 TCTCTTCCTA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
62 5 0.10
63 44 0.86
64 2 0.04
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (63 bp):
TTCTAAAGCCCACACAAGTCAATGGCAACCTTCTTAAAAGCCCACACAAGTCAGTGGCAACCA
Found at i:356149 original size:31 final size:30
Alignment explanation
Indices: 356070--356193 Score: 140
Period size: 32 Copynumber: 4.0 Consensus size: 30
356060 GCACCTTTCT
* *
356070 CCTTCTAAAGCCCACATAAGTCGGTGGCAA
1 CCTTCTAAAGCCCACACAAGTCAGTGGCAA
*
356100 CCTCTTCTAAAACCCACACAAGTCAGTGGCAA
1 -C-CTTCTAAAGCCCACACAAGTCAGTGGCAA
* * *
356132 CCATTCTAAAGCTCACACAAGTCAATGGTAA
1 CC-TTCTAAAGCCCACACAAGTCAGTGGCAA
*
356163 CCTTCTTAAAAGCCCACACAAGTCGGTGGCA
1 CCTTC-T-AAAGCCCACACAAGTCAGTGGCA
356194 TCTCTTCCTA
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
30 4 0.05
31 29 0.37
32 45 0.58
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (30 bp):
CCTTCTAAAGCCCACACAAGTCAGTGGCAA
Found at i:356361 original size:52 final size:52
Alignment explanation
Indices: 356266--356772 Score: 205
Period size: 52 Copynumber: 9.6 Consensus size: 52
356256 CTTTCAAGTG
* * ** *
356266 CCTTGAATCAGCACATTGGCACCTTTTTCTTTCATAAGTCCAATATCGCTAA
1 CCTTGAATCAGCATATTGGCACCTTTATCACTCATAAGCCCAATATCGCTAA
* * * *
356318 CCTTGAATCAACATATTGGCATCTTTATCACTCTTAAGCCCAATATCGCTGA
1 CCTTGAATCAGCATATTGGCACCTTTATCACTCATAAGCCCAATATCGCTAA
* * *** * * **
356370 CCTTGAATCAGCATATTGGCACATTTCTCATTCTTCTCATCTTTAAGTATAATGTCACTGG
1 CCTTGAATCAGCATATTGGCAC-CTT-T-A-TC-ACTCA----TAAGCCCAATATCGCTAA
* * * ** * * * *
356431 CCTTGAATCAGCACATTGGCACTTTTTTCTTTCTTAAGTCCAATATCACTAG
1 CCTTGAATCAGCATATTGGCACCTTTATCACTCATAAGCCCAATATCGCTAA
* * ** * * * **
356483 CCTTGAATCAGCATATTGGCACATTTTTCTTTCTTAGGTCCAATATCGCTGG
1 CCTTGAATCAGCATATTGGCACCTTTATCACTCATAAGCCCAATATCGCTAA
* *** * * * *
356535 CCTTGAATCAGCATATTGGTACCTTGGCCA-TCTTTAAGTCCAATGTCGCTAG
1 CCTTGAATCAGCATATTGGCACCTTTATCACTC-ATAAGCCCAATATCGCTAA
* * ** * **
356587 CCTTGAATTAGCATATTAGCACCTTCT-TCTTTC-TGAAGTCCAATATCGCTGG
1 CCTTGAATCAGCATATTGGCACCTT-TATCACTCAT-AAGCCCAATATCGCTAA
* * * * * * * * * **
356639 CCTTGAATCAGCATATTAGCGCCTTTCTCA-TCTTTGAGTCCAATGTTGTTGG
1 CCTTGAATCAGCATATTGGCACCTTTATCACTC-ATAAGCCCAATATCGCTAA
* * * * * * **
356691 CCTTGAATCAGCACATTAGCACTTTTGTCA-TCTTTAAACCCAATATCGCTGG
1 CCTTGAATCAGCATATTGGCACCTTTATCACTC-ATAAGCCCAATATCGCTAA
* *
356743 CCTTGAATCAGCATATTAGCACTTTTATCA
1 CCTTGAATCAGCATATTGGCACCTTTATCA
356773 TTCTTCTCAT
Statistics
Matches: 370, Mismatches: 69, Indels: 32
0.79 0.15 0.07
Matches are distributed among these distances:
51 6 0.02
52 310 0.84
53 5 0.01
54 1 0.00
55 1 0.00
56 5 0.01
57 5 0.01
59 1 0.00
60 3 0.01
61 33 0.09
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (52 bp):
CCTTGAATCAGCATATTGGCACCTTTATCACTCATAAGCCCAATATCGCTAA
Found at i:356449 original size:61 final size:55
Alignment explanation
Indices: 356265--356655 Score: 230
Period size: 52 Copynumber: 7.3 Consensus size: 55
356255 TCTTTCAAGT
* * * * *
356265 GCCTTGAATCAGCACATTGGCAC-CTTT-TTC-TTTCATAAGTCCAATATCGCTA
1 GCCTTGAATCAGCATATTGGCACATTTTCTTCTTTTCTTAAGTACAATATCACTA
* * * ** *
356317 ACCTTGAATCAACATATTGGCATC-TTTATC-AC---TCTTAAGCCCAATATCGCT-
1 GCCTTGAATCAGCATATTGGCA-CATTT-TCTTCTTTTCTTAAGTACAATATCACTA
* * *
356368 GACCTTGAATCAGCATATTGGCACATTTCTCATTCTTCTCATCTTTAAGTATAATGTCACTG
1 G-CCTTGAATCAGCATATTGGCACATTT-TC-TTCTT-T--TC-TTAAGTACAATATCACTA
* *
356430 GCCTTGAATCAGCACATTGGCAC-TTTT-TTC-TTTCTTAAGTCCAATATCACTA
1 GCCTTGAATCAGCATATTGGCACATTTTCTTCTTTTCTTAAGTACAATATCACTA
* * * *
356482 GCCTTGAATCAGCATATTGGCACA-TTT-TTC-TTTCTTAGGTCCAATATCGCTG
1 GCCTTGAATCAGCATATTGGCACATTTTCTTCTTTTCTTAAGTACAATATCACTA
* * ** * * * * *
356534 GCCTTGAATCAGCATATTGGTACCTTGGC--CATCT-TTAAGTCCAATGTCGCTA
1 GCCTTGAATCAGCATATTGGCACATTTTCTTCTTTTCTTAAGTACAATATCACTA
* * * * * * *
356586 GCCTTGAATTAGCATATTAGCAC--CTTCTTC-TTTCTGAAGTCCAATATCGCTG
1 GCCTTGAATCAGCATATTGGCACATTTTCTTCTTTTCTTAAGTACAATATCACTA
356638 GCCTTGAATCAGCATATT
1 GCCTTGAATCAGCATATT
356656 AGCGCCTTTC
Statistics
Matches: 273, Mismatches: 44, Indels: 44
0.76 0.12 0.12
Matches are distributed among these distances:
50 1 0.00
51 3 0.01
52 213 0.78
53 8 0.03
54 3 0.01
55 1 0.00
56 1 0.00
57 3 0.01
59 1 0.00
60 5 0.02
61 33 0.12
62 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (55 bp):
GCCTTGAATCAGCATATTGGCACATTTTCTTCTTTTCTTAAGTACAATATCACTA
Found at i:356541 original size:165 final size:156
Alignment explanation
Indices: 356265--356655 Score: 469
Period size: 165 Copynumber: 2.4 Consensus size: 156
356255 TCTTTCAAGT
* * *
356265 GCCTTGAATCAGCACATTGGCACCTTTTTCTTTCATAAGTCCAATATCGCTAACCTTGAATCAAC
1 GCCTTGAATCAGCACATTGGCACCTTTTTCTTTCTTAAGTCCAATATCGCTAGCCTTGAATCAGC
356330 ATATTGGCATCTTTATCACTCTTAAGCCCAATATCGCTGACCTTGAATCAGCATATTGGCACATT
66 ATATTGGCATCTTTATCACTCTTAAGCCCAATATCGCTGACCTTGAATCAGCATATTGG-----T
* ** * *
356395 TCTCATTCTTCTCATCTTTAAGTATAATGTCACTG
126 AC-C-TT-GGC-CATCTTTAAGTACAATGTCACTA
* *
356430 GCCTTGAATCAGCACATTGGCACTTTTTTCTTTCTTAAGTCCAATATCACTAGCCTTGAATCAGC
1 GCCTTGAATCAGCACATTGGCACCTTTTTCTTTCTTAAGTCCAATATCGCTAGCCTTGAATCAGC
* ** * * *
356495 ATATTGGCA-CATTTTTCTTTCTTAGGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTACCT
66 ATATTGGCATC-TTTATCACTCTTAAGCCCAATATCGCTGACCTTGAATCAGCATATTGGTACCT
* *
356559 TGGCCATCTTTAAGTCCAATGTCGCTA
130 TGGCCATCTTTAAGTACAATGTCACTA
* * * * * *
356586 GCCTTGAATTAGCATATTAGCACCTTCTTCTTTCTGAAGTCCAATATCGCTGGCCTTGAATCAGC
1 GCCTTGAATCAGCACATTGGCACCTTTTTCTTTCTTAAGTCCAATATCGCTAGCCTTGAATCAGC
356651 ATATT
66 ATATT
356656 AGCGCCTTTC
Statistics
Matches: 199, Mismatches: 26, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
156 81 0.41
157 1 0.01
158 2 0.01
159 1 0.01
160 2 0.01
164 1 0.01
165 111 0.56
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (156 bp):
GCCTTGAATCAGCACATTGGCACCTTTTTCTTTCTTAAGTCCAATATCGCTAGCCTTGAATCAGC
ATATTGGCATCTTTATCACTCTTAAGCCCAATATCGCTGACCTTGAATCAGCATATTGGTACCTT
GGCCATCTTTAAGTACAATGTCACTA
Found at i:356617 original size:104 final size:103
Alignment explanation
Indices: 356427--356764 Score: 367
Period size: 104 Copynumber: 3.3 Consensus size: 103
356417 TATAATGTCA
* * * ** * * *
356427 CTGGCCTTGAATCAGCACATTGGCACTTTTTTC-TTTCTTAAGTCCAATATCACTAGCCTTGAAT
1 CTGGCCTTGAATCAGCATATTAGCACCTTGCTCATCT-TTAAGTCCAATGTCGCTAGCCTTGAAT
* * *
356491 CAGCATATTGGCACATTTTTCTTTCTTAGGTCCAATATCG
65 CAGCATATTAGCAC-CTTTTCTTTCTTAAGTCCAATATCG
* *
356531 CTGGCCTTGAATCAGCATATTGGTACCTTGGC-CATCTTTAAGTCCAATGTCGCTAGCCTTGAAT
1 CTGGCCTTGAATCAGCATATTAGCACCTT-GCTCATCTTTAAGTCCAATGTCGCTAGCCTTGAAT
* *
356595 TAGCATATTAGCACCTTCTTCTTTCTGAAGTCCAATATCG
65 CAGCATATTAGCACCTT-TTCTTTCTTAAGTCCAATATCG
* * * * * *
356635 CTGGCCTTGAATCAGCATATTAGCGCCTTTCTCATCTTTGAGTCCAATGTTGTTGGCCTTGAATC
1 CTGGCCTTGAATCAGCATATTAGCACCTTGCTCATCTTTAAGTCCAATGTCGCTAGCCTTGAATC
* * * **
356700 AGCACATTAGCA-CTTTTGTCATCTTTAAACCCAATATCG
66 AGCATATTAGCACCTTTTCT-TTC-TTAAGTCCAATATCG
356739 CTGGCCTTGAATCAGCATATTAGCAC
1 CTGGCCTTGAATCAGCATATTAGCAC
356765 TTTTATCATT
Statistics
Matches: 199, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
102 3 0.02
103 8 0.04
104 186 0.93
105 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (103 bp):
CTGGCCTTGAATCAGCATATTAGCACCTTGCTCATCTTTAAGTCCAATGTCGCTAGCCTTGAATC
AGCATATTAGCACCTTTTCTTTCTTAAGTCCAATATCG
Found at i:356642 original size:156 final size:153
Alignment explanation
Indices: 356407--356768 Score: 395
Period size: 156 Copynumber: 2.3 Consensus size: 153
356397 TCATTCTTCT
** * * *
356407 CATCTTTAAGTATAATGTCACTGGCCTTGAATCAGCACATTGGCACTTTTTTCTTTCTTAAGTCC
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTTTTCTTTC-TAAGTCC
* * *
356472 AATATCACTAGCCTTGAATCAGCATATTGGCACATTTTTCTTTCTTAGGTCCAATATCGCTGGCC
65 AATATCGCTAGCCTTGAATCAGCATATTGGCAC-TTTATC-ATCTTAGGTCCAATATCGCTGGCC
*
356537 TTGAATCAGCATATTGGTACCTTGGC
128 TTGAATCAGCATATTGGTACCTTTGC
* * * *
356563 CATCTTTAAGTCCAATGTCGCTAGCCTTGAATTAGCATATTAGCACCTTCTTCTTTCTGAAGTCC
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTTTTCTTTCT-AAGTCC
* * * * * *
356628 AATATCGCTGGCCTTGAATCAGCATATTAGCGC-CTTTCTCATCTTTGAGTCCAATGTTGTTGGC
65 AATATCGCTAGCCTTGAATCAGCATATT-G-GCACTTTATCATCTTAG-GTCCAATATCGCTGGC
* * * * *
356692 CTTGAATCAGCACATTAGCACTTTTGT
127 CTTGAATCAGCATATTGGTACCTTTGC
** * *
356719 CATCTTTAAACCCAATATCGCTGGCCTTGAATCAGCATATTAGCA-CTTTT
1 CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTTT
356769 ATCATTCTTC
Statistics
Matches: 173, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
155 10 0.06
156 159 0.92
157 2 0.01
158 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (153 bp):
CATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTTTTCTTTCTAAGTCCA
ATATCGCTAGCCTTGAATCAGCATATTGGCACTTTATCATCTTAGGTCCAATATCGCTGGCCTTG
AATCAGCATATTGGTACCTTTGC
Found at i:356797 original size:61 final size:61
Alignment explanation
Indices: 356718--356848 Score: 183
Period size: 61 Copynumber: 2.1 Consensus size: 61
356708 AGCACTTTTG
** * *
356718 TCATCTTTAAACCCAATATCGCTGGCCTTGAATCAGCATATT-AGCACTTTTATCATTCTTC
1 TCATCTTTAAACCCAATATCGCTGGCAATGAATCAGCATATTGA-CACCTCTATCATTCTTC
* * *
356779 TCATCTTTAAGCCTAATATCGCTGGCAATGAATCAGCATATTGACACCTCTATCATTTTTC
1 TCATCTTTAAACCCAATATCGCTGGCAATGAATCAGCATATTGACACCTCTATCATTCTTC
356840 TCATCTTTA
1 TCATCTTTA
356849 TCATCCTTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 61 0.98
62 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (61 bp):
TCATCTTTAAACCCAATATCGCTGGCAATGAATCAGCATATTGACACCTCTATCATTCTTC
Found at i:365077 original size:20 final size:21
Alignment explanation
Indices: 365052--365107 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
365042 CCTATGATTT
365052 AAAAAAGAAAAAAAAAACC-A
1 AAAAAAGAAAAAAAAAACCAA
** *
365072 AAAAAATTAATAAAAAACCAA
1 AAAAAAGAAAAAAAAAACCAA
365093 AAAATAAGAAAAAAA
1 AAAA-AAGAAAAAAA
365108 CTCAGATGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 16 0.57
21 5 0.18
22 7 0.25
ACGTcount: A:0.82, C:0.07, G:0.04, T:0.07
Consensus pattern (21 bp):
AAAAAAGAAAAAAAAAACCAA
Found at i:366482 original size:24 final size:24
Alignment explanation
Indices: 366422--366499 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 24
366412 GCTGTATTTG
*
366422 TGTTAAAG-CCACATTAGCTGGCACA
1 TGTTAAAGCCCACATTAGATGG--CA
* * *
366447 TAAGTTCAAGCCCACATTAGTTGTCA
1 T--GTTAAAGCCCACATTAGATGGCA
*
366473 TGTTAAAGCCCATATTAGATGGCA
1 TGTTAAAGCCCACATTAGATGGCA
366497 TGT
1 TGT
366500 GAATCATAGC
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
24 22 0.51
25 1 0.02
26 3 0.07
27 6 0.14
28 11 0.26
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (24 bp):
TGTTAAAGCCCACATTAGATGGCA
Found at i:366840 original size:28 final size:28
Alignment explanation
Indices: 366809--366880 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
366799 GCATGAATCG
* *
366809 AAGCTCATATTAGTTGGCACATGAGTTA
1 AAGCTCATATTAGTTGGCACATAAGTCA
* * * *
366837 AAGCCCATACTAGCTGGCACTTAAGTCA
1 AAGCTCATATTAGTTGGCACATAAGTCA
*
366865 AAGCTCACATTAGTTG
1 AAGCTCATATTAGTTG
366881 ATAGCTACAT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (28 bp):
AAGCTCATATTAGTTGGCACATAAGTCA
Found at i:367971 original size:4 final size:4
Alignment explanation
Indices: 367962--367987 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
367952 GGAAAAAAAG
367962 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
367988 GAAAATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:371341 original size:2 final size:2
Alignment explanation
Indices: 371334--371371 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
371324 TAACATGAAC
371334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
371372 GTATGAATGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:376890 original size:11 final size:10
Alignment explanation
Indices: 376870--376992 Score: 60
Period size: 10 Copynumber: 12.5 Consensus size: 10
376860 TATAAGATAT
*
376870 TAATATAATA
1 TAATAAAATA
376880 TAAGTAAAATA
1 TAA-TAAAATA
*
376891 -ATTAAAATA
1 TAATAAAATA
*
376900 TAATAAAGTA
1 TAATAAAATA
376910 -AA-AAAATA
1 TAATAAAATA
*
376918 TTATAAAATA
1 TAATAAAATA
*
376928 -ATTTAAATATA
1 TA-ATAAA-ATA
*
376939 TAATATAATA
1 TAATAAAATA
* **
376949 AAAT-TTATA
1 TAATAAAATA
376958 TAATAAAA-A
1 TAATAAAATA
*
376967 TTATTAAAATA
1 -TAATAAAATA
* *
376978 TCATAATATA
1 TAATAAAATA
376988 TAATA
1 TAATA
376993 TTTTAAATAT
Statistics
Matches: 83, Mismatches: 20, Indels: 20
0.67 0.16 0.16
Matches are distributed among these distances:
8 5 0.06
9 18 0.22
10 46 0.55
11 13 0.16
12 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.36
Consensus pattern (10 bp):
TAATAAAATA
Found at i:376895 original size:23 final size:23
Alignment explanation
Indices: 376868--376948 Score: 69
Period size: 23 Copynumber: 3.5 Consensus size: 23
376858 ATTATAAGAT
376868 ATTAATATAATATAAGTAAAATA
1 ATTAATATAATATAAGTAAAATA
376891 ATTAAAATATAATA-AAGTAAAA-A
1 ATT--AATATAATATAAGTAAAATA
* * * * *
376914 AATATTATAAAATAATTTAAAT-
1 ATTAATATAATATAAGTAAAATA
376936 ATATAATATAATA
1 AT-TAATATAATA
376949 AAATTTATAT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
21 7 0.16
22 7 0.16
23 14 0.31
24 8 0.18
25 9 0.20
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
ATTAATATAATATAAGTAAAATA
Found at i:376930 original size:37 final size:37
Alignment explanation
Indices: 376871--376992 Score: 111
Period size: 39 Copynumber: 3.1 Consensus size: 37
376861 ATAAGATATT
376871 AATATAATATAAGTAAAATAATTAAAATATAATAAAGTAA
1 AATA-AATATAA-TAAAATAATTAAAATATAATAAA-TAA
*
376911 AA-AAATATTATAAAATAATTTAAATATATAATATAATAA
1 AATAAATATAATAAAATAA-TTAAA-ATATAATA-AATAA
** * * *
376950 AATTTATATAATAAAAATTATTAAAATATCATAATATAT
1 AATAAATATAAT-AAAATAATTAAAATATAATAA-ATAA
376989 AATA
1 AATA
376993 TTTTAAATAT
Statistics
Matches: 68, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
37 8 0.12
38 12 0.18
39 27 0.40
40 15 0.22
41 6 0.09
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (37 bp):
AATAAATATAATAAAATAATTAAAATATAATAAATAA
Found at i:376940 original size:18 final size:18
Alignment explanation
Indices: 376884--377020 Score: 75
Period size: 18 Copynumber: 7.3 Consensus size: 18
376874 ATAATATAAG
376884 TAAAATAATTAAAATATAA
1 TAAAATAATTAAAATAT-A
* *
376903 TAAAGTAA-AAAAATATTA
1 TAAAATAATTAAAATA-TA
*
376921 TAAAATAATTTAAATATA
1 TAAAATAATTAAAATATA
* *
376939 TAATATAATAAAATTTATATAA
1 TAAAATAATTAAA---ATAT-A
*
376961 TAAAAATTATTAAAATATCA
1 T-AAAATAATTAAAATAT-A
* * *
376981 TAATAT-A-TAATAT-TT
1 TAAAATAATTAAAATATA
*
376996 TAAATATAATTATAATATA
1 TAAA-ATAATTAAAATATA
377015 TAAAAT
1 TAAAAT
377021 TATATGAATA
Statistics
Matches: 88, Mismatches: 19, Indels: 23
0.68 0.15 0.18
Matches are distributed among these distances:
15 3 0.03
16 3 0.03
17 6 0.07
18 33 0.38
19 22 0.25
20 6 0.07
21 4 0.05
22 2 0.02
23 9 0.10
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.38
Consensus pattern (18 bp):
TAAAATAATTAAAATATA
Found at i:376953 original size:23 final size:24
Alignment explanation
Indices: 376919--377017 Score: 74
Period size: 23 Copynumber: 4.5 Consensus size: 24
376909 AAAAAAATAT
376919 TATAA-AATAATTTAAATATATAA
1 TATAATAATAATTTAAATATATAA
376942 TATAATAA-AA-TT---TATATAA
1 TATAATAATAATTTAAATATATAA
* *
376961 TA-AA-AATTATTAAAATATCATAA
1 TATAATAATAATTTAAATAT-ATAA
* *
376984 TAT-ATAATATTTTAAATATA-AT
1 TATAATAATAATTTAAATATATAA
377006 TATAATATATAA
1 TATAATA-ATAA
377018 AATTATATGA
Statistics
Matches: 58, Mismatches: 7, Indels: 21
0.67 0.08 0.24
Matches are distributed among these distances:
17 2 0.03
18 3 0.05
19 10 0.17
22 9 0.16
23 18 0.31
24 16 0.28
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (24 bp):
TATAATAATAATTTAAATATATAA
Found at i:377020 original size:20 final size:21
Alignment explanation
Indices: 376980--377020 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
376970 TTAAAATATC
* *
376980 ATAATATATAATATTTTAAAT
1 ATAATATATAATATATAAAAT
377001 ATAAT-TATAATATATAAAAT
1 ATAATATATAATATATAAAAT
377021 TATATGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATATATAATATATAAAAT
Found at i:377023 original size:15 final size:15
Alignment explanation
Indices: 376932--377024 Score: 53
Period size: 14 Copynumber: 6.5 Consensus size: 15
376922 AAAATAATTT
376932 AAATATATAATATAATA
1 AAAT-TATAATAT-ATA
376949 AAATT-T-ATATAATA
1 AAATTATAATAT-ATA
376963 AAA--AT--TAT-TA
1 AAATTATAATATATA
376973 AAATATCATAATATATA
1 AAAT-T-ATAATATATA
* *
376990 ATATTTTAA-ATAT-
1 AAATTATAATATATA
377003 -AATTATAATATATA
1 AAATTATAATATATA
377017 AAATTATA
1 AAATTATA
377025 TGAATATCAT
Statistics
Matches: 61, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
10 5 0.08
12 9 0.15
13 5 0.08
14 17 0.28
15 11 0.18
16 5 0.08
17 9 0.15
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTATAATATATA
Found at i:377740 original size:23 final size:25
Alignment explanation
Indices: 377714--377761 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
377704 AATAATATTT
377714 TATTAA-AATTT-TTAATAAAATAA
1 TATTAATAATTTATTAATAAAATAA
377737 TATTAATTAATTTATTAATAAAATA
1 TATTAA-TAATTTATTAATAAAATA
377762 TTTAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.27
25 5 0.23
26 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TATTAATAATTTATTAATAAAATAA
Found at i:377772 original size:23 final size:25
Alignment explanation
Indices: 377714--377773 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 25
377704 AATAATATTT
377714 TATTAAA-ATTT-TTAATAAAATAA
1 TATTAAATATTTATTAATAAAATAA
*
377737 TATTAATTAATTTATTAATAAAAT-A
1 TATTAAAT-ATTTATTAATAAAATAA
377762 T-TTAAATATTTA
1 TATTAAATATTTA
377774 AATATTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 11 0.34
24 5 0.16
25 6 0.19
26 10 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TATTAAATATTTATTAATAAAATAA
Found at i:379217 original size:18 final size:19
Alignment explanation
Indices: 379182--379230 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
379172 TAATTATACA
*
379182 AAATATATAAAATTAAATT
1 AAATATATAAAATCAAATT
*
379201 AAAT-TATAATATCAAA-T
1 AAATATATAAAATCAAATT
379218 -AATAATATAAAAT
1 AAAT-ATATAAAAT
379231 ATCCTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 3 0.12
17 1 0.04
18 17 0.68
19 4 0.16
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATATATAAAATCAAATT
Found at i:379295 original size:26 final size:25
Alignment explanation
Indices: 379239--379299 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
379229 ATATCCTTAT
* *
379239 TTTTTAAAAAATTTTATATCATATA
1 TTTTAAAAAAATTTTATATCATTTA
*
379264 TTTTAAAAATAATTTTAT-TTATTTA
1 TTTTAAAAA-AATTTTATATCATTTA
379289 TTCTTAAAAAA
1 TT-TTAAAAAA
379300 CCAACCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 16 0.52
26 15 0.48
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTTAAAAAAATTTTATATCATTTA
Found at i:380532 original size:13 final size:13
Alignment explanation
Indices: 380514--380607 Score: 70
Period size: 13 Copynumber: 7.2 Consensus size: 13
380504 GATGATTTTT
380514 TATTATATTTATA
1 TATTATATTTATA
380527 TATTATATTTTATTA
1 TATTATA-TTTA-TA
*
380542 TATATAAATATTATA
1 TAT-TATAT-TTATA
* *
380557 TATT-TATATAAA
1 TATTATATTTATA
*
380569 TTTTATATTT-TA
1 TATTATATTTATA
*
380581 -A-TATATTAATA
1 TATTATATTTATA
*
380592 TATTATAATTATA
1 TATTATATTTATA
380605 TAT
1 TAT
380608 ATAATTTTTG
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
10 6 0.10
11 2 0.03
12 8 0.13
13 24 0.39
14 5 0.08
15 11 0.18
16 6 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTATATTTATA
Found at i:380540 original size:23 final size:23
Alignment explanation
Indices: 380511--380598 Score: 87
Period size: 23 Copynumber: 4.0 Consensus size: 23
380501 TATGATGATT
380511 TTTTATTATATTTATATATTATA
1 TTTTATTATATTTATATATTATA
* *
380534 TTTTATTATATATAAATATTATA
1 TTTTATTATATTTATATATTATA
*
380557 TATTTA-TATA---A-ATTTTATA
1 T-TTTATTATATTTATATATTATA
* *
380576 TTTTAATATATTAATATATTATA
1 TTTTATTATATTTATATATTATA
380599 ATTATATATA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
18 4 0.07
19 12 0.22
20 1 0.02
22 1 0.02
23 33 0.60
24 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTATTATATTTATATATTATA
Found at i:380595 original size:42 final size:43
Alignment explanation
Indices: 380515--380615 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 43
380505 ATGATTTTTT
* * *
380515 ATTATATTTAT-ATATTATATTTTATTATATATAAATATTATA
1 ATTATATATATAATTTTATATTTTAATATATATAAATATTATA
380557 TATT-TATATA-AATTTTATATTTTAATATAT-TAATATATTATA
1 -ATTATATATATAATTTTATATTTTAATATATATAA-ATATTATA
380599 ATTATATATATAATTTT
1 ATTATATATATAATTTT
380616 TGCCTATGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
41 6 0.12
42 36 0.71
43 9 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (43 bp):
ATTATATATATAATTTTATATTTTAATATATATAAATATTATA
Found at i:385766 original size:2 final size:2
Alignment explanation
Indices: 385759--385788 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
385749 CAAGAATTAA
385759 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
385789 CGCGTGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:387241 original size:21 final size:22
Alignment explanation
Indices: 387191--387241 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
387181 GTTGGAATGG
*
387191 AAGAGA-AAAAAGAAAGTCAGA
1 AAGAGAGAAAAAGAAAGTAAGA
*
387212 AAGTA-AGAAAAA-CAAGTAAGA
1 AAG-AGAGAAAAAGAAAGTAAGA
387233 AAGAGAGAA
1 AAGAGAGAA
387242 CGTTGCTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.04
21 18 0.72
22 6 0.24
ACGTcount: A:0.67, C:0.04, G:0.24, T:0.06
Consensus pattern (22 bp):
AAGAGAGAAAAAGAAAGTAAGA
Found at i:387360 original size:2 final size:2
Alignment explanation
Indices: 387348--387384 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
387338 GCTCCCAAAC
387348 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
387385 TGAACTTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:388764 original size:6 final size:6
Alignment explanation
Indices: 388755--388800 Score: 56
Period size: 6 Copynumber: 7.2 Consensus size: 6
388745 TGCATTTGTT
*
388755 TTTTAA TTTTAA GTTTTAA TTTTAA TTTTAAA TTATATA TTTTAA T
1 TTTTAA TTTTAA -TTTTAA TTTTAA TTTT-AA TTTTA-A TTTTAA T
388801 ATTGGTTCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 19 0.54
7 16 0.46
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (6 bp):
TTTTAA
Found at i:388771 original size:13 final size:12
Alignment explanation
Indices: 388755--388800 Score: 56
Period size: 13 Copynumber: 3.6 Consensus size: 12
388745 TGCATTTGTT
388755 TTTTAATTTTAA
1 TTTTAATTTTAA
388767 GTTTTAATTTTAA
1 -TTTTAATTTTAA
*
388780 TTTTAAATTATATA
1 TTTT-AATTTTA-A
388794 TTTTAAT
1 TTTTAAT
388801 ATTGGTTCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 4 0.13
13 21 0.70
14 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (12 bp):
TTTTAATTTTAA
Found at i:388777 original size:19 final size:20
Alignment explanation
Indices: 388755--388800 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
388745 TGCATTTGTT
* *
388755 TTTTAATTTTAAGTTTTA-A
1 TTTTAATTTTAAATTATATA
388774 TTTTAATTTTAAATTATATA
1 TTTTAATTTTAAATTATATA
388794 TTTTAAT
1 TTTTAAT
388801 ATTGGTTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTAATTTTAAATTATATA
Found at i:389145 original size:16 final size:16
Alignment explanation
Indices: 389124--389161 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
389114 CTCTAAAAAA
389124 TATATTTTAAATTTTT
1 TATATTTTAAATTTTT
389140 TATA-TTTAAATTTTT
1 TATATTTTAAATTTTT
389155 T-TATTTT
1 TATATTTT
389162 TATTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 15 0.71
16 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATATTTTAAATTTTT
Found at i:389163 original size:16 final size:15
Alignment explanation
Indices: 389128--389163 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
389118 AAAAAATATA
389128 TTTTAAATTTTTTAT
1 TTTTAAATTTTTTAT
*
389143 ATTTAAATTTTTTTAT
1 TTTTAAA-TTTTTTAT
389159 TTTTA
1 TTTTA
389164 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTAAATTTTTTAT
Found at i:390464 original size:13 final size:14
Alignment explanation
Indices: 390448--390493 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
390438 TATATTTAAT
390448 TTTTAAAAA-TATA
1 TTTTAAAAATTATA
390461 TTTTAAAAATTATA
1 TTTTAAAAATTATA
*
390475 TTTTAATAATTAATA
1 TTTTAAAAATT-ATA
390490 TTTT
1 TTTT
390494 TATCAAGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 9 0.30
14 14 0.47
15 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTTAAAAATTATA
Found at i:395019 original size:21 final size:20
Alignment explanation
Indices: 394968--395033 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
394958 TTTGGTTATT
*
394968 AAAAGTTGCATTCTTTCATCC
1 AAAAATTGCATTCTTTCAT-C
*
394989 AAAAAATGCATTCTTTCATC
1 AAAAATTGCATTCTTTCATC
*
395009 AAACTATTGCA-TCATTTCATC
1 AAA-AATTGCATTC-TTTCATC
395030 AAAA
1 AAAA
395034 TACATATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.16
21 32 0.84
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (20 bp):
AAAAATTGCATTCTTTCATC
Found at i:398852 original size:58 final size:58
Alignment explanation
Indices: 398734--398864 Score: 142
Period size: 58 Copynumber: 2.3 Consensus size: 58
398724 TTTTTTTGTA
* * * *
398734 AATTT-TCATGATTTAGGACCATTTATGCATTCTCATGTATTTTAGAGTCATTCTATT
1 AATTTGTCATGATTTAGAACCATTTATGCATTCTCATGCATTTCAGAGTCATTCTAGT
* * *
398791 AATTTGTCATGATTTAGAACCGTTTATGCAATT-TCATGCATTTCATGGGT-ATTTTAGT
1 AATTTGTCATGATTTAGAACCATTTATGC-ATTCTCATGCATTTCA-GAGTCATTCTAGT
* *
398849 AATTTGCCATGCTTTA
1 AATTTGTCATGATTTA
398865 AGGATTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
57 5 0.08
58 51 0.82
59 6 0.10
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.46
Consensus pattern (58 bp):
AATTTGTCATGATTTAGAACCATTTATGCATTCTCATGCATTTCAGAGTCATTCTAGT
Found at i:399030 original size:29 final size:30
Alignment explanation
Indices: 398982--399073 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 30
398972 TTATGTATGT
*
398982 TAGA-GTCATCTTA-GTTATTTTTCATGATC
1 TAGAGGTCAT-TTACGTAATTTTTCATGATC
*
399011 TAGAGGT-TTTTACGTAA-TTTT-ATGAATGC
1 TAGAGGTCATTTACGTAATTTTTCATG-AT-C
* * *
399040 T-GAGGTCATTTAGGTCATTTTTCATAATC
1 TAGAGGTCATTTACGTAATTTTTCATGATC
399069 TAGAG
1 TAGAG
399074 ACTTTCATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
27 3 0.06
28 14 0.29
29 19 0.39
30 11 0.22
31 2 0.04
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (30 bp):
TAGAGGTCATTTACGTAATTTTTCATGATC
Found at i:401952 original size:26 final size:26
Alignment explanation
Indices: 401907--401964 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
401897 AAATTTAATT
401907 ATAAATTATAAAAATCTTAATATTTGA
1 ATAAATTATAAAAATCTTAA-ATTTGA
401934 ATAAA-TATAAAAAAT-TTAAATTT-A
1 ATAAATTAT-AAAAATCTTAAATTTGA
*
401958 TTAAATT
1 ATAAATT
401965 TTTAACTCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
24 5 0.18
25 5 0.18
26 7 0.25
27 11 0.39
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
ATAAATTATAAAAATCTTAAATTTGA
Found at i:413912 original size:24 final size:27
Alignment explanation
Indices: 413839--413909 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
413829 AAACAAGCCT
* *
413839 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
413867 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
413894 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
413910 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:415381 original size:21 final size:22
Alignment explanation
Indices: 415343--415388 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
415333 ATCTGTTGAA
* **
415343 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
415364 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
415386 ACT
1 ACT
415389 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:417870 original size:20 final size:20
Alignment explanation
Indices: 417837--417881 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
417827 AGAATTGAAT
* *
417837 AGGGATACAAGAGAGGGATG
1 AGGGATACAAGAGAAGGAGG
**
417857 AGGGATACTTGAGAAGGAGG
1 AGGGATACAAGAGAAGGAGG
417877 AGGGA
1 AGGGA
417882 GCCTCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.04, G:0.47, T:0.11
Consensus pattern (20 bp):
AGGGATACAAGAGAAGGAGG
Found at i:418025 original size:27 final size:28
Alignment explanation
Indices: 417962--418027 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
417952 AGCCTCCATA
** *
417962 TTTGACAAATACAAAGAAAATTATTATT
1 TTTGACAAATACAAAGAAAACCATCATT
*
417990 TTTGACAAATACAAA-ATAACCATCATT
1 TTTGACAAATACAAAGAAAACCATCATT
418017 TTTGACAAATA
1 TTTGACAAATA
418028 AATAGGTGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 19 0.56
28 15 0.44
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (28 bp):
TTTGACAAATACAAAGAAAACCATCATT
Found at i:418930 original size:13 final size:14
Alignment explanation
Indices: 418905--418964 Score: 75
Period size: 14 Copynumber: 4.1 Consensus size: 14
418895 TTTTAATTTG
418905 ATTTAATTTAAAAA
1 ATTTAATTTAAAAA
*
418919 ATTTAATTAAAAAA
1 ATTTAATTTAAAAA
*
418933 ATTAAAATTTAAAAAA
1 ATT-TAATTT-AAAAA
418949 ATTTAAATTTAAAAA
1 ATTT-AATTTAAAAA
418964 A
1 A
418965 GTTTTGAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
14 16 0.41
15 10 0.26
16 13 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTTAATTTAAAAA
Found at i:418949 original size:17 final size:16
Alignment explanation
Indices: 418909--418964 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
418899 AATTTGATTT
*
418909 AATTT-AAAAAATT-T
1 AATTTAAAAAAATTAA
418923 AA-TTAAAAAAATTAA
1 AATTTAAAAAAATTAA
*
418938 AATTTAAAAAAATTTA
1 AATTTAAAAAAATTAA
418954 AATTTAAAAAA
1 AATTTAAAAAA
418965 GTTTTGAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
13 2 0.05
14 10 0.27
15 2 0.05
16 23 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATTTAAAAAAATTAA
Found at i:419106 original size:19 final size:19
Alignment explanation
Indices: 419059--419126 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
419049 TAAAAGATCG
* *
419059 AAAAAATA-ATAAATTATA
1 AAAAAATATTTAATTTATA
* * *
419077 AATATATATTTTATTTA-A
1 AAAAAATATTTAATTTATA
419095 AATAAAATATTTAATTTATA
1 AA-AAAATATTTAATTTATA
*
419115 AAAATATATTTA
1 AAAAAATATTTA
419127 TAACTATTAT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
18 9 0.24
19 26 0.68
20 3 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAAAATATTTAATTTATA
Found at i:419155 original size:17 final size:17
Alignment explanation
Indices: 419117--419158 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
419107 AATTTATAAA
*
419117 AATATATTTATAACTAT
1 AATATATTTATAACAAT
* *
419134 TATATATTTATATCAAT
1 AATATATTTATAACAAT
419151 AATATATT
1 AATATATT
419159 ATTAAATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATATTTATAACAAT
Found at i:420271 original size:15 final size:15
Alignment explanation
Indices: 420249--420285 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
420239 TTAATCGCTG
*
420249 TAAT-ATTATTTTTT
1 TAATAATTATATTTT
420263 TAATAATTATATTTT
1 TAATAATTATATTTT
420278 TAATAATT
1 TAATAATT
420286 GCATTTCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATAATTATATTTT
Found at i:422187 original size:14 final size:14
Alignment explanation
Indices: 422168--422203 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
422158 TGTATTGTAT
422168 TGATACAACACTTA
1 TGATACAACACTTA
422182 TGATACAACACTTA
1 TGATACAACACTTA
422196 TGATACAA
1 TGATACAA
422204 TGTATTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.28
Consensus pattern (14 bp):
TGATACAACACTTA
Found at i:422252 original size:19 final size:19
Alignment explanation
Indices: 422228--422283 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
422218 ACATTAACAT
422228 TTATGTATCGATACAATAC
1 TTATGTATCGATACAATAC
* *
422247 TTATGTATCAATACATTTAC
1 TTATGTATCGATACA-ATAC
*
422267 TGTTTGTATCGATACAA
1 T-TATGTATCGATACAA
422284 ATTGTTGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 14 0.47
20 4 0.13
21 12 0.40
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (19 bp):
TTATGTATCGATACAATAC
Found at i:422932 original size:16 final size:16
Alignment explanation
Indices: 422907--422952 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
422897 AGATTAGATC
*
422907 AAAATTTAAAATTTAA
1 AAAATTTAAAATTAAA
* *
422923 AAAATATAAAAATAAA
1 AAAATTTAAAATTAAA
422939 AAAATTTAAAATTA
1 AAAATTTAAAATTA
422953 TTTTATAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTTAAAATTAAA
Found at i:423072 original size:20 final size:21
Alignment explanation
Indices: 423035--423073 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
423025 AACTAAGCTT
*
423035 GTCACATTAGCAAAATCAATG
1 GTCACATTAACAAAATCAATG
423056 GTCACATTAAC-AAATCAA
1 GTCACATTAACAAAATCAA
423074 CATTTATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (21 bp):
GTCACATTAACAAAATCAATG
Found at i:425464 original size:22 final size:22
Alignment explanation
Indices: 425401--425473 Score: 58
Period size: 24 Copynumber: 3.1 Consensus size: 22
425391 ATATAAAATT
*
425401 ATATAATAATTTTTTATATATTGT-
1 ATATAAT-ATTTTTTA-AT-TTTTA
*
425425 ATTTAATATTATTTTTAATTTTTA
1 ATATAATA-T-TTTTTAATTTTTA
* *
425449 ATATAATATTTTTTAAGTTTAA
1 ATATAATATTTTTTAATTTTTA
425471 ATA
1 ATA
425474 AAAGCTAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 14 0.34
23 5 0.12
24 16 0.39
25 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (22 bp):
ATATAATATTTTTTAATTTTTA
Found at i:425763 original size:2 final size:2
Alignment explanation
Indices: 425756--425786 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
425746 AAACTCATGA
425756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
425787 ACTTTTCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:425886 original size:22 final size:23
Alignment explanation
Indices: 425861--425909 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
425851 TTTTTCTTTA
425861 TTTTA-TTTATTT-TTATAAGATTT
1 TTTTAGTTTATTTATTAT-A-ATTT
425884 TTTTAGTTTATTTATTATAATTT
1 TTTTAGTTTATTTATTATAATTT
425907 TTT
1 TTT
425910 AAACAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 12 0.50
24 8 0.33
25 4 0.17
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (23 bp):
TTTTAGTTTATTTATTATAATTT
Found at i:428641 original size:21 final size:21
Alignment explanation
Indices: 428617--428656 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
428607 TAAGTTTTGT
428617 AAATAAAATTTATA-ATAATTA
1 AAAT-AAATTTATATATAATTA
*
428638 AAATTAATTTATATATAAT
1 AAATAAATTTATATATAAT
428657 GCTACTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATAAATTTATATATAATTA
Found at i:428868 original size:26 final size:26
Alignment explanation
Indices: 428839--428895 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
428829 GAATCTTATA
* *
428839 ATTAATCTTAATAATGTGATTTGATT
1 ATTAATCGTAATAATGTGATTTAATT
* * * *
428865 ATTACTCGTGATAATTTTATTTAATT
1 ATTAATCGTAATAATGTGATTTAATT
428891 ATTAA
1 ATTAA
428896 AATTAATTTA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (26 bp):
ATTAATCGTAATAATGTGATTTAATT
Found at i:428923 original size:15 final size:15
Alignment explanation
Indices: 428887--428929 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
428877 AATTTTATTT
*
428887 AATTATTAA-AATTA
1 AATTATTAATAATAA
*
428901 ATTTATTAATAATAA
1 AATTATTAATAATAA
428916 AATTATTAATAATA
1 AATTATTAATAATA
428930 GGATTTTGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTATTAATAATAA
Found at i:430660 original size:75 final size:76
Alignment explanation
Indices: 430581--430731 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
430571 GTTGCCCTAT
430581 CCTTTTTATC-AAAAAAATAAAAAAATTTGCAGCTGCGTTGATATTTTTTAATTGTTATGGAATT
1 CCTTTTTATCAAAAAAAATAAAAAAATTTGCAGCTGCGTTGATATTTTTTAATTGTTATGGAATT
430645 AAAATTATTTA
66 AAAATTATTTA
430656 CCTTTTTATCAAAAAAAATAAAAAAATTTGCAGCTGCGTTGATATTTTTTAATTGTTATGGAATT
1 CCTTTTTATCAAAAAAAATAAAAAAATTTGCAGCTGCGTTGATATTTTTTAATTGTTATGGAATT
430721 AAAATTATTTA
66 AAAATTATTTA
430732 TAGAAAAGAT
Statistics
Matches: 75, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
75 10 0.13
76 65 0.87
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (76 bp):
CCTTTTTATCAAAAAAAATAAAAAAATTTGCAGCTGCGTTGATATTTTTTAATTGTTATGGAATT
AAAATTATTTA
Found at i:431015 original size:13 final size:13
Alignment explanation
Indices: 430999--431023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
430989 TTAATTTTAA
430999 ATTTTTTTAATTT
1 ATTTTTTTAATTT
431012 ATTTTTTTAATT
1 ATTTTTTTAATT
431024 CAATATCTCT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTTTTAATTT
Found at i:431129 original size:9 final size:9
Alignment explanation
Indices: 431117--431150 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
431107 AACATTATAT
431117 AATTTCTTC
1 AATTTCTTC
431126 AATTTCTTC
1 AATTTCTTC
*
431135 ACTTTCTTC
1 AATTTCTTC
431144 AAATTTC
1 -AATTTC
431151 AAATTTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 17 0.77
10 5 0.23
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (9 bp):
AATTTCTTC
Found at i:435832 original size:9 final size:9
Alignment explanation
Indices: 435806--435886 Score: 53
Period size: 9 Copynumber: 8.9 Consensus size: 9
435796 AAAATTATTG
435806 TTTTAT-TA
1 TTTTATATA
435814 TTTTGA-ATA
1 TTTT-ATATA
435823 TTTTATATA
1 TTTTATATA
*
435832 TTACTTTTATA
1 TT--TTATATA
435843 TTTTAATATA
1 TTTT-ATATA
*
435853 TATTA-AGTA
1 TTTTATA-TA
*
435862 TATTA-ATA
1 TTTTATATA
*
435870 TTATATATA
1 TTTTATATA
435879 TTTTATAT
1 TTTTATAT
435887 GCATATTATA
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
8 11 0.19
9 33 0.56
10 7 0.12
11 8 0.14
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.60
Consensus pattern (9 bp):
TTTTATATA
Found at i:437212 original size:16 final size:16
Alignment explanation
Indices: 437176--437215 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
437166 ACTTAAAATC
*
437176 AAAATGATTCGAACTT
1 AAAATGATTCGAACCT
437192 AAAATGATTCGAAACCT
1 AAAATGATTCG-AACCT
437209 -AAATGAT
1 AAAATGAT
437216 ATGAAATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (16 bp):
AAAATGATTCGAACCT
Found at i:437333 original size:16 final size:16
Alignment explanation
Indices: 437308--437338 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
437298 GGCCTAATCA
437308 AAAATAACTTAAAACC
1 AAAATAACTTAAAACC
*
437324 AAAATGACTTAAAAC
1 AAAATAACTTAAAAC
437339 AGAAGCAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.16, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAATAACTTAAAACC
Found at i:437812 original size:13 final size:13
Alignment explanation
Indices: 437794--437818 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
437784 AGAAGAGAAG
437794 AGAAAAAAAAAAA
1 AGAAAAAAAAAAA
437807 AGAAAAAAAAAA
1 AGAAAAAAAAAA
437819 TTTTTATGTA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAA
Found at i:437879 original size:10 final size:10
Alignment explanation
Indices: 437866--437911 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
437856 TTTAAAATAT
437866 TATAAATTTA
1 TATAAATTTA
*
437876 TATAAATTTT
1 TATAAATTTA
*
437886 TAT-AATTAA
1 TATAAATTTA
437895 TAGTAAATTT-
1 TA-TAAATTTA
437905 TATAAAT
1 TATAAAT
437912 ATTTTAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
9 11 0.37
10 15 0.50
11 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (10 bp):
TATAAATTTA
Found at i:437888 original size:20 final size:20
Alignment explanation
Indices: 437860--437911 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
437850 TTTATGTTTA
* *
437860 AAATATTATAAATTTATA-T
1 AAATTTTATAAATTAATAGT
437879 AAATTTT-TATAATTAATAGT
1 AAATTTTATA-AATTAATAGT
437899 AAATTTTATAAAT
1 AAATTTTATAAAT
437912 ATTTTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.07
19 13 0.46
20 11 0.39
21 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AAATTTTATAAATTAATAGT
Found at i:438733 original size:18 final size:19
Alignment explanation
Indices: 438712--438749 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
438702 TAATTTAATG
438712 ATTAAAAATATTT-TAAAA
1 ATTAAAAATATTTATAAAA
*
438730 ATTAAATATATTTATAAAA
1 ATTAAAAATATTTATAAAA
438749 A
1 A
438750 ATCATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTAAAAATATTTATAAAA
Found at i:441660 original size:10 final size:10
Alignment explanation
Indices: 441637--441698 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 10
441627 TATAAAAAAA
*
441637 TTTATTTAGAT
1 TTTATTTA-TT
441648 TTTATTTATT
1 TTTATTTATT
*
441658 TTTAAGTTATT
1 TTT-ATTTATT
* * *
441669 TTAAAATTAAT
1 TT-TATTTATT
441680 TTTATTTATT
1 TTTATTTATT
441690 TTTATTTAT
1 TTTATTTAT
441699 GATCAAATTA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
10 18 0.44
11 23 0.56
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (10 bp):
TTTATTTATT
Found at i:442017 original size:19 final size:20
Alignment explanation
Indices: 441985--442030 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
441975 GACTTAACAA
441985 TTTTTATATATTTTTT-TAT
1 TTTTTATATATTTTTTGTAT
* *
442004 TTTTTTTATCTTTTTTGTAT
1 TTTTTATATATTTTTTGTAT
*
442024 TATTTAT
1 TTTTTAT
442031 GATGGTGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTTATATATTTTTTGTAT
Found at i:442958 original size:2 final size:2
Alignment explanation
Indices: 442953--442982 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
442943 CCCCCCCCCC
*
442953 CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
442983 TTGTGTGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:449303 original size:20 final size:20
Alignment explanation
Indices: 449257--449310 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
449247 GTTAGAAGCA
*
449257 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCACC
* *
449277 ATTTATCGATACAGTGT-ACC
1 ATGTATCGATACAAT-TCACC
449297 ATGTATCGATACAA
1 ATGTATCGATACAA
449311 ATAGTGGTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:449367 original size:20 final size:20
Alignment explanation
Indices: 449339--449393 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
449329 CTGCCAGTTT
**
449339 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
449359 CATGAATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
449378 CATGTATCGATACAAT
1 CATGTATCGATACAAT
449394 ATATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:458089 original size:20 final size:20
Alignment explanation
Indices: 458064--458117 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
458054 GTTAGAAGCA
* *
458064 ATGTATCAATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
*
458084 ATGTATTGATACAATGTACC
1 ATGTATCGATACAATGTACC
458104 ATGTATCGATACAA
1 ATGTATCGATACAA
458118 ACAGTGGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:458580 original size:19 final size:19
Alignment explanation
Indices: 458556--458619 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
458546 CAAACAGAAA
458556 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
458575 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
458589 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
458607 TTGTATCGATACA
1 TTGTATCGATACA
458620 ATGTATCGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
19 24 0.62
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:458594 original size:13 final size:13
Alignment explanation
Indices: 458576--458600 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
458566 ACATAAGTGT
458576 TGTATCGATACAA
1 TGTATCGATACAA
458589 TGTATCGATACA
1 TGTATCGATACA
458601 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:458598 original size:32 final size:32
Alignment explanation
Indices: 458557--458627 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
458547 AAACAGAAAT
458557 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
458589 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
458621 TGTATCG
1 TGTATCG
458628 CTACGAAGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:463342 original size:24 final size:22
Alignment explanation
Indices: 463315--463370 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 22
463305 ATAGCTCTCT
463315 CTTAATAAAATTTTTCTTCTCCCC
1 CTTAATAAAA-TTTT-TTCTCCCC
*
463339 CTTAATTAAA-TTTTTCTCCCC
1 CTTAATAAAATTTTTTCTCCCC
463360 CTTAATAAAAT
1 CTTAATAAAAT
463371 GTTTGATGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 17 0.59
22 3 0.10
24 9 0.31
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (22 bp):
CTTAATAAAATTTTTTCTCCCC
Found at i:464862 original size:20 final size:20
Alignment explanation
Indices: 464839--464911 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
464829 ACAATTCAAA
464839 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
464859 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
464880 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
464900 GTATCGATACAT
1 GTATCGATACAT
464912 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:464883 original size:21 final size:21
Alignment explanation
Indices: 464857--464932 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
464847 ACATGTTGCA
464857 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
464878 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
464898 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
464919 ATGTATCGATACAT
1 ATGTATCGATACAT
464933 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:464890 original size:41 final size:41
Alignment explanation
Indices: 464839--464932 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
464829 ACAATTCAAA
*
464839 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
464880 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
464921 GTATCGATACAT
1 GTATCGATACAT
464933 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:464989 original size:13 final size:13
Alignment explanation
Indices: 464971--464996 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
464961 TACAGCAAGT
464971 ATGTATCGATACA
1 ATGTATCGATACA
464984 ATGTATCGATACA
1 ATGTATCGATACA
464997 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:467917 original size:15 final size:15
Alignment explanation
Indices: 467897--467927 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
467887 TAAAAATGTC
*
467897 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
467912 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
467927 C
1 C
467928 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:470015 original size:20 final size:21
Alignment explanation
Indices: 469937--470014 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
469927 ATGTCCAAAA
*
469937 TGTATCGATACATGTTTTTG-
1 TGTATCGATACATCTTTTTGT
** *
469957 TGTATCGATACATCTGGAAATTCT
1 TGTATCGATACATCT---TTTTGT
469981 ATGTATCGATACAT-TTTTTGT
1 -TGTATCGATACATCTTTTTGT
470002 TGTATCGATACAT
1 TGTATCGATACAT
470015 TGTATCGATA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 27 0.59
21 3 0.07
23 2 0.04
24 1 0.02
25 13 0.28
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATCTTTTTGT
Found at i:470019 original size:13 final size:13
Alignment explanation
Indices: 470001--470039 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
469991 ACATTTTTTG
470001 TTGTATCGATACA
1 TTGTATCGATACA
470014 TTGTATCGATACA
1 TTGTATCGATACA
*
470027 CTGTATCGATACA
1 TTGTATCGATACA
470040 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:471642 original size:114 final size:114
Alignment explanation
Indices: 471442--471672 Score: 462
Period size: 114 Copynumber: 2.0 Consensus size: 114
471432 ATGGAAGAAG
471442 ATGTGCCTCCTCTCGAAGAGTCCACCCGACAATCGACGCGTGATTTAGTTAAATCTCTATCACGA
1 ATGTGCCTCCTCTCGAAGAGTCCACCCGACAATCGACGCGTGATTTAGTTAAATCTCTATCACGA
471507 ACGATGCTTGAGCAGTTCGAACTACTCAAACAGCAACTTGACTCGATGA
66 ACGATGCTTGAGCAGTTCGAACTACTCAAACAGCAACTTGACTCGATGA
471556 ATGTGCCTCCTCTCGAAGAGTCCACCCGACAATCGACGCGTGATTTAGTTAAATCTCTATCACGA
1 ATGTGCCTCCTCTCGAAGAGTCCACCCGACAATCGACGCGTGATTTAGTTAAATCTCTATCACGA
471621 ACGATGCTTGAGCAGTTCGAACTACTCAAACAGCAACTTGACTCGATGA
66 ACGATGCTTGAGCAGTTCGAACTACTCAAACAGCAACTTGACTCGATGA
471670 ATG
1 ATG
471673 CTCGTATCAC
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 117 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (114 bp):
ATGTGCCTCCTCTCGAAGAGTCCACCCGACAATCGACGCGTGATTTAGTTAAATCTCTATCACGA
ACGATGCTTGAGCAGTTCGAACTACTCAAACAGCAACTTGACTCGATGA
Found at i:472655 original size:20 final size:20
Alignment explanation
Indices: 472632--472704 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
472622 ACAATTCAAA
472632 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
472652 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
472673 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
472693 GTATCGATACAT
1 GTATCGATACAT
472705 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:472676 original size:21 final size:21
Alignment explanation
Indices: 472650--472725 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
472640 ACATGTTGCA
472650 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
472671 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
472691 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
472712 ATGTATCGATACAT
1 ATGTATCGATACAT
472726 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:472683 original size:41 final size:41
Alignment explanation
Indices: 472632--472725 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
472622 ACAATTCAAA
*
472632 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
472673 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
472714 GTATCGATACAT
1 GTATCGATACAT
472726 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:472782 original size:13 final size:13
Alignment explanation
Indices: 472764--472789 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
472754 TACAGCAAGT
472764 ATGTATCGATACA
1 ATGTATCGATACA
472777 ATGTATCGATACA
1 ATGTATCGATACA
472790 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:474720 original size:19 final size:19
Alignment explanation
Indices: 474696--474763 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
474686 AATTCAACAA
474696 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
474715 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
474730 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
474747 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
474764 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:474735 original size:13 final size:13
Alignment explanation
Indices: 474717--474741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
474707 ACATAAGTTT
474717 TGTATCGATACAA
1 TGTATCGATACAA
474730 TGTATCGATACA
1 TGTATCGATACA
474742 TAAGTATTGT
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:474739 original size:32 final size:32
Alignment explanation
Indices: 474698--474760 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
474688 TTCAACAATT
*
474698 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
474730 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
474761 TAATTAGCTA
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:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Done.