Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold23
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: 3125668
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 362582 characters in sequence are not A, C, G, or T
File 5 of 18
Found at i:598679 original size:41 final size:41
Alignment explanation
Indices: 598620--598713 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
598610 CTGCCAAGAA
*
598620 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
598661 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
598702 ATGTATCGATAC
1 ATGTATCGATAC
598714 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:598695 original size:21 final size:21
Alignment explanation
Indices: 598620--598695 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
598610 CTGCCAAGAA
* *
598620 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
598641 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
598661 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
598682 ATGTATCGATACAT
1 ATGTATCGATACAT
598696 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:599401 original size:53 final size:53
Alignment explanation
Indices: 599321--599427 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
599311 CTCCTTTATC
*
599321 TCCCCTGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
1 TCCCCCGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
599374 TCCCCCGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
1 TCCCCCGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
599427 T
1 T
599428 TATTTGCACT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.36
Consensus pattern (53 bp):
TCCCCCGTTTATTTAAAAAATCTCCCCCTTAATCAAGTGATTCATATCAAAAT
Found at i:601229 original size:13 final size:13
Alignment explanation
Indices: 601211--601236 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
601201 ATAATCACCC
601211 TGTATCGATACAA
1 TGTATCGATACAA
601224 TGTATCGATACAA
1 TGTATCGATACAA
601237 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:603335 original size:15 final size:15
Alignment explanation
Indices: 603315--603345 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
603305 ATTTCGTTTG
*
603315 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
603330 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
603345 G
1 G
603346 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:607518 original size:20 final size:20
Alignment explanation
Indices: 607493--607565 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
607483 CAACTTTTTT
607493 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
607513 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
607534 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
607554 ATGTATCGATAC
1 ATGTATCGATAC
607566 TTTGAATTGT
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:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:607531 original size:41 final size:41
Alignment explanation
Indices: 607472--607565 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
607462 CTGCCAAGAA
*
607472 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
607513 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
607554 ATGTATCGATAC
1 ATGTATCGATAC
607566 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:607547 original size:21 final size:21
Alignment explanation
Indices: 607472--607547 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
607462 CTGCCAAGAA
* *
607472 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
607493 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
607513 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
607534 ATGTATCGATACAT
1 ATGTATCGATACAT
607548 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:609072 original size:13 final size:13
Alignment explanation
Indices: 609054--609078 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
609044 TCTCTATTCA
609054 TGTATCGATACAG
1 TGTATCGATACAG
609067 TGTATCGATACA
1 TGTATCGATACA
609079 TCACTATTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:614872 original size:20 final size:19
Alignment explanation
Indices: 614838--614886 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
614828 CAATGAATCA
*
614838 ATACATTTCATCATGTATCG
1 ATACATTTC-CCATGTATCG
614858 ATACAATTTCCCATGTATCG
1 ATAC-ATTTCCCATGTATCG
614878 ATACATTTC
1 ATACATTTC
614887 ACTTAGGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 17 0.63
21 5 0.19
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (19 bp):
ATACATTTCCCATGTATCG
Found at i:615641 original size:21 final size:21
Alignment explanation
Indices: 615589--615641 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
615579 TTTAAATAAA
*
615589 CTCCCCTTTAATAAAATTTTT
1 CTCCCCTTTGATAAAATTTTT
615610 CTCCACC-TTGAT-AAATTTTT
1 CTCC-CCTTTGATAAAATTTTT
615630 CTTCCCCTTTGA
1 C-TCCCCTTTGA
615642 AAGCTTATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 11 0.39
21 15 0.54
22 2 0.07
ACGTcount: A:0.23, C:0.28, G:0.04, T:0.45
Consensus pattern (21 bp):
CTCCCCTTTGATAAAATTTTT
Found at i:616426 original size:13 final size:13
Alignment explanation
Indices: 616408--616464 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
616398 CATTTTATGG
616408 TGTATCGATACAA
1 TGTATCGATACAA
616421 TGTATCGATACATA
1 TGTATCGATACA-A
*
616435 CTTTGTGTATCGATATAA
1 -----TGTATCGATACAA
616453 TGTATCGATACA
1 TGTATCGATACA
616465 TACTTTGTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 23 0.64
14 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:616445 original size:19 final size:19
Alignment explanation
Indices: 616421--616483 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
616411 ATCGATACAA
616421 TGTATCGATACATACTTTG
1 TGTATCGATACATACTTTG
*
616440 TGTATCGAT--ATA----A
1 TGTATCGATACATACTTTG
616453 TGTATCGATACATACTTTG
1 TGTATCGATACATACTTTG
616472 TGTATCGATACA
1 TGTATCGATACA
616484 AGTTTGGCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 9 0.25
15 3 0.08
17 3 0.08
19 21 0.58
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATACTTTG
Found at i:616448 original size:32 final size:32
Alignment explanation
Indices: 616385--616484 Score: 157
Period size: 32 Copynumber: 3.1 Consensus size: 32
616375 CGTTACAAGC
*
616385 CAATGTATCGATACAT-TTTATGGTGTATCGATA
1 CAATGTATCGATACATACTT-T-GTGTATCGATA
616418 CAATGTATCGATACATACTTTGTGTATCGATA
1 CAATGTATCGATACATACTTTGTGTATCGATA
*
616450 TAATGTATCGATACATACTTTGTGTATCGATA
1 CAATGTATCGATACATACTTTGTGTATCGATA
616482 CAA
1 CAA
616485 GTTTGGCTAC
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 44 0.70
33 17 0.27
34 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (32 bp):
CAATGTATCGATACATACTTTGTGTATCGATA
Found at i:625710 original size:13 final size:13
Alignment explanation
Indices: 625692--625717 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
625682 CTATTTATGA
625692 TGTATCGATACAC
1 TGTATCGATACAC
625705 TGTATCGATACAC
1 TGTATCGATACAC
625718 ACAAATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:625764 original size:24 final size:23
Alignment explanation
Indices: 625731--625775 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
625721 AATATGTATC
*
625731 GATACATGAATAGTGATGAACAGT
1 GATACATGAACAGTG-TGAACAGT
*
625755 GATACGTGAACAGTGTGAACA
1 GATACATGAACAGTGTGAACA
625776 AACAAGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.40, C:0.11, G:0.27, T:0.22
Consensus pattern (23 bp):
GATACATGAACAGTGTGAACAGT
Found at i:625994 original size:23 final size:24
Alignment explanation
Indices: 625949--625995 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
625939 CAAAGAATTG
*
625949 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
625973 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
625996 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:628600 original size:34 final size:35
Alignment explanation
Indices: 628562--628628 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
628552 CCTTACAACA
628562 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
628596 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
628629 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:628754 original size:20 final size:21
Alignment explanation
Indices: 628709--628761 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
628699 TACATATTTG
*
628709 TGTGTATCGATA-CTATGCAA
1 TGTGTATCGATACCTATGAAA
* *
628729 TTTGTATCGATACCT-TTAAA
1 TGTGTATCGATACCTATGAAA
628749 TGTGTATCGATAC
1 TGTGTATCGATAC
628762 TTTTCAGGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (21 bp):
TGTGTATCGATACCTATGAAA
Found at i:628821 original size:21 final size:21
Alignment explanation
Indices: 628795--628835 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
628785 GTCAACCTTG
628795 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
628816 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
628836 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:629359 original size:13 final size:13
Alignment explanation
Indices: 629341--629365 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
629331 CATTTTATGG
629341 TGTATCGATACAA
1 TGTATCGATACAA
629354 TGTATCGATACA
1 TGTATCGATACA
629366 TACTTTGTAT
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:631513 original size:19 final size:19
Alignment explanation
Indices: 631455--631551 Score: 74
Period size: 13 Copynumber: 5.7 Consensus size: 19
631445 TTTCAACGAT
*
631455 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTA
631475 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
631489 -TGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
631507 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
*
631521 -TGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTA
*
631539 TTATATCGATACA
1 TTGTATCGATACA
631552 ATGTATCGCT
Statistics
Matches: 62, Mismatches: 3, Indels: 25
0.69 0.03 0.28
Matches are distributed among these distances:
13 22 0.35
14 1 0.02
16 4 0.06
18 1 0.02
19 22 0.35
20 12 0.19
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:631516 original size:32 final size:32
Alignment explanation
Indices: 631456--631564 Score: 173
Period size: 32 Copynumber: 3.4 Consensus size: 32
631446 TTCAACGATT
*
631456 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTATTGTATCGATACAA
631489 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
* *
631521 TGTATCGATACATAAGTTTTATATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
*
631553 TGTATCGCTACA
1 TGTATCGATACA
631565 AAGCTACTAC
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 59 0.82
33 13 0.18
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:631681 original size:52 final size:52
Alignment explanation
Indices: 631637--631765 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
631627 CACTGATCTT
*
631637 TGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
631689 TGTATCGATACATGCAGGCAAATTTGCCCAGAAGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
631741 TGTATCGATACATGTAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
631766 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:636916 original size:316 final size:315
Alignment explanation
Indices: 636339--636969 Score: 1059
Period size: 316 Copynumber: 2.0 Consensus size: 315
636329 GAGGGTAAAT
* * * * *
636339 AGACCCCATTGGAATGGTACTTTGACACACTTTCAAAGAAAAATTATAAAAAAATCATGAAAAAT
1 AGACACCATTGGAAAGGTACTTTAACACACTTTCAAAGAAAAATTATAAAAAAATAAGGAAAAAT
* *
636404 GGTTTAATATTTTAAAATGATTTTTCAATGTGCAACAGTGGTGCTGCCAGCAAGGAACGAAGGAA
66 GGTTTAATATTTTAAAATGATTTTTCAATGGGCAACAGTGGTGCTACCAGCAAGGAACGAAGGAA
636469 AACAAAGGAGAATTTTGGTTTTCTTAGTGTTTACGGGTCTAAACTCGAGTCATGGACATTCGAAC
131 AACAAAGGAGAATTTTGGTTTTCTTAGTGTTTACGGGTCTAAACTCGAGTCATGGACATTCGAAC
* *
636534 GTCCGTGACCAAAAGGAAAGAGTGGTATGAGCATTACGAACTCATTTACACAATCCTAGAGTAAT
196 GTCCGTGACCAAAAGGAAAGAGTGGTATGAGCATCAAGAACTCATTTACACAATCCTAGAGTAAT
*
636599 TT-GAGATGATGAAACAGCCCGTTGATCATACCACTCAAGTTTTAACACAAAAACA
261 TTAG-GATGATGAAACAACCCGTTGATCATACCACTCAAGTTTTAACACAAAAACA
*
636654 AGACACCATTGGAAAGGTATTTTAACACACTTTCAAAGAAAAATTATAAAAAAAATAAGGAAAAA
1 AGACACCATTGGAAAGGTACTTTAACACACTTTCAAAGAAAAATTAT-AAAAAAATAAGGAAAAA
* * *
636719 TGGTTTAATATTTTAAAATGATTTTTGAGTGGGCAACAGTGGTGCTACCAGCAAGGAACGGAGGA
65 TGGTTTAATATTTTAAAATGATTTTTCAATGGGCAACAGTGGTGCTACCAGCAAGGAACGAAGGA
636784 AAACAAAGGAGAATTTTGGTTTTCTTAGTGTTTACGGGTCTAAACTCGAGTCATGGACATTCGAA
130 AAACAAAGGAGAATTTTGGTTTTCTTAGTGTTTACGGGTCTAAACTCGAGTCATGGACATTCGAA
* * * *
636849 CGTCTGTGACCGAAAGGGAAGAGTGGTATGAGCATCAAGAACTCATTTACACAAT-CTCGGAGTA
195 CGTCCGTGACCAAAAGGAAAGAGTGGTATGAGCATCAAGAACTCATTTACACAATCCT-AGAGTA
636913 ATTTAGGATGATGAAACAACCCGTTGATCATACCACTCAAGTTTTAACACAAAAACA
259 ATTTAGGATGATGAAACAACCCGTTGATCATACCACTCAAGTTTTAACACAAAAACA
636970 GGGTACAATT
Statistics
Matches: 295, Mismatches: 18, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
315 45 0.15
316 249 0.84
317 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (315 bp):
AGACACCATTGGAAAGGTACTTTAACACACTTTCAAAGAAAAATTATAAAAAAATAAGGAAAAAT
GGTTTAATATTTTAAAATGATTTTTCAATGGGCAACAGTGGTGCTACCAGCAAGGAACGAAGGAA
AACAAAGGAGAATTTTGGTTTTCTTAGTGTTTACGGGTCTAAACTCGAGTCATGGACATTCGAAC
GTCCGTGACCAAAAGGAAAGAGTGGTATGAGCATCAAGAACTCATTTACACAATCCTAGAGTAAT
TTAGGATGATGAAACAACCCGTTGATCATACCACTCAAGTTTTAACACAAAAACA
Found at i:637590 original size:9 final size:9
Alignment explanation
Indices: 637576--637611 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
637566 GCATTTCATA
637576 TTTTTTTCTT
1 TTTTTTTC-T
637586 TTTTTTTCT
1 TTTTTTTCT
*
637595 TTTTCTTCT
1 TTTTTTTCT
637604 TTTTTTTC
1 TTTTTTTC
637612 CTTTATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:637591 original size:10 final size:10
Alignment explanation
Indices: 637576--637615 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
637566 GCATTTCATA
637576 TTTTTTTCTT
1 TTTTTTTCTT
637586 TTTTTTTC-T
1 TTTTTTTCTT
*
637595 TTTTCTTCTT
1 TTTTTTTCTT
*
637605 TTTTTTCCTT
1 TTTTTTTCTT
637615 T
1 T
637616 ATTCTTCTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:637599 original size:16 final size:17
Alignment explanation
Indices: 637578--637624 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 17
637568 ATTTCATATT
637578 TTTTTCTT-TTTTTTTC
1 TTTTTCTTCTTTTTTTC
637594 TTTTTCTTCTTTTTTTTCC
1 TTTTTCTTC-TTTTTTT-C
637613 TTTATTCTTCTT
1 TTT-TTCTTCTT
637625 CTTCTTCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 8 0.30
18 7 0.26
19 6 0.22
20 6 0.22
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTCTTCTTTTTTTC
Found at i:637632 original size:20 final size:19
Alignment explanation
Indices: 637593--637634 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
637583 CTTTTTTTTT
* *
637593 CTTTTTCTTCTTTTTTTTC
1 CTTTTTCTTCTTCTTCTTC
637612 CTTTATTCTTCTTCTTCTTC
1 CTTT-TTCTTCTTCTTCTTC
637632 CTT
1 CTT
637635 CATCCCCACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.71
Consensus pattern (19 bp):
CTTTTTCTTCTTCTTCTTC
Found at i:638905 original size:28 final size:28
Alignment explanation
Indices: 638868--639135 Score: 304
Period size: 28 Copynumber: 9.5 Consensus size: 28
638858 ATCAACTTGC
638868 GTGGGCTTTGAAAGGATGCCACTGACTT
1 GTGGGCTTTGAAAGGATGCCACTGACTT
* *
638896 GTGGGCTTTGAAAAGATGCCACTTACTT
1 GTGGGCTTTGAAAGGATGCCACTGACTT
* *
638924 GTGGGCTTTAAAAGGGTGCCACTGACTT
1 GTGGGCTTTGAAAGGATGCCACTGACTT
* * * *
638952 GTGGGCTTTAAAATGATACCACTAACTT
1 GTGGGCTTTGAAAGGATGCCACTGACTT
*
638980 ATGGGCTTTGAAAAGG-TGCCACTGACTT
1 GTGGGCTTTG-AAAGGATGCCACTGACTT
* * * *
639008 GTGGGCTTCGAAAAGGGTTACCACTAACTT
1 GTGGGCTTTG-AAA-GGATGCCACTGACTT
* *
639038 GTGGGTTTTGAAAGGATGCCACTGATTT
1 GTGGGCTTTGAAAGGATGCCACTGACTT
* * *
639066 ATGGGCTTTGAAAAGATGCCACTGATTT
1 GTGGGCTTTGAAAGGATGCCACTGACTT
* * *
639094 ATGGGCTTTGAGAAGGAAGCCACTAACTT
1 GTGGGCTTTGA-AAGGATGCCACTGACTT
639123 GTGGGCTTTGAAA
1 GTGGGCTTTGAAA
639136 AGAATTCGTA
Statistics
Matches: 203, Mismatches: 33, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
28 153 0.75
29 32 0.16
30 18 0.09
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (28 bp):
GTGGGCTTTGAAAGGATGCCACTGACTT
Found at i:639077 original size:86 final size:84
Alignment explanation
Indices: 638868--639135 Score: 349
Period size: 86 Copynumber: 3.2 Consensus size: 84
638858 ATCAACTTGC
* * *
638868 GTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTTACTTGTGGGCTTT
1 GTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTG
* *
638933 AAAAGGGTGCCACTGACTT
66 AAAAGGGTACCACTAACTT
* * * * *
638952 GTGGGCTTTAAAATGATACCACTAACTTATGGGCTTTGAAAAGGTGCCACTGACTTGTGGGCTTC
1 GTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTT-
639017 GAAAAGGGTTACCACTAACTT
65 GAAAAGGG-TACCACTAACTT
* * * *
639038 GTGGGTTTTGAAAGGATGCCACTGATTTATGGGCTTTGAAAAGATGCCACTGATTTATGGGCTTT
1 GTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGC-TT
* *
639103 GAGAA-GGAAGCCACTAACTT
65 GAAAAGGGTA-CCACTAACTT
639123 GTGGGCTTTGAAA
1 GTGGGCTTTGAAA
639136 AGAATTCGTA
Statistics
Matches: 158, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
84 58 0.37
85 31 0.20
86 67 0.42
87 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (84 bp):
GTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTG
AAAAGGGTACCACTAACTT
Found at i:643491 original size:79 final size:79
Alignment explanation
Indices: 643403--643553 Score: 207
Period size: 79 Copynumber: 1.9 Consensus size: 79
643393 TTGTTCATTG
* * * *
643403 TATTTTCGAAGGGATGCTCCAA-CCTCGATTTTATTT-TCAAAACATCGATTTTCTATAATCAGG
1 TATTTTCGAAGGGATACTCCAACCCT-GATTTTATTTCT-AAAACACCGATTCTCCATAATCAGG
643466 GATACTCTAACCCTGT
64 GATACTCTAACCCTGT
* * *
643482 TATTTTCGAAGGGATACTCCAACCCTGATTTTATTTCTAGAACACCGATTCTCCATAGTCGGGGA
1 TATTTTCGAAGGGATACTCCAACCCTGATTTTATTTCTAAAACACCGATTCTCCATAATCAGGGA
643547 TACTCTA
66 TACTCTA
643554 GCCCCATTGT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
79 59 0.94
80 4 0.06
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (79 bp):
TATTTTCGAAGGGATACTCCAACCCTGATTTTATTTCTAAAACACCGATTCTCCATAATCAGGGA
TACTCTAACCCTGT
Found at i:649902 original size:19 final size:20
Alignment explanation
Indices: 649857--649908 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
649847 TTACAAGCCA
*
649857 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATCTTGGG
*
649877 ATGTATCGATACATCTTGTG
1 ATGTATCGATACATCTTGGG
649897 -TGTATCGATACA
1 ATGTATCGATACA
649909 AATAGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATCTTGGG
Found at i:650602 original size:24 final size:24
Alignment explanation
Indices: 650570--650630 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
650560 TTTCCTTATC
650570 TCTCCCCCTTAATTAAAAAAAAAT
1 TCTCCCCCTTAATTAAAAAAAAAT
650594 TCTCCCCCTTAATTAAAAAAAAAT
1 TCTCCCCCTTAATTAAAAAAAAAT
650618 TCTCCCCCTTAAT
1 TCTCCCCCTTAAT
650631 AAAGCAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.31
Consensus pattern (24 bp):
TCTCCCCCTTAATTAAAAAAAAAT
Found at i:665467 original size:13 final size:13
Alignment explanation
Indices: 665449--665474 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
665439 ACATCATTCT
665449 TTGTATCGATACA
1 TTGTATCGATACA
665462 TTGTATCGATACA
1 TTGTATCGATACA
665475 GGGGGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:665927 original size:20 final size:20
Alignment explanation
Indices: 665902--665956 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
665892 CCAGCACCCA
665902 CCAGGTCGCGACCGGCACTC
1 CCAGGTCGCGACCGGCACTC
665922 CCAGGTCGCGACCGGCACTC
1 CCAGGTCGCGACCGGCACTC
* *
665942 CTAGGTCGCAACCGG
1 CCAGGTCGCGACCGG
665957 GCAGCCCCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.16, C:0.42, G:0.31, T:0.11
Consensus pattern (20 bp):
CCAGGTCGCGACCGGCACTC
Found at i:668052 original size:13 final size:13
Alignment explanation
Indices: 668034--668058 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
668024 ACACAAAGTA
668034 TGTATCGATACAT
1 TGTATCGATACAT
668047 TGTATCGATACA
1 TGTATCGATACA
668059 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:668055 original size:32 final size:33
Alignment explanation
Indices: 668014--668081 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
668004 GTAGCCAAAC
*
668014 TTGTATCGATACA-CA-AAGTATGTATCGATACA
1 TTGTATCGATACACCATAA-AATGTATCGATACA
668046 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
668079 TTG
1 TTG
668082 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:671697 original size:52 final size:52
Alignment explanation
Indices: 671549--671677 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
671539 CGAAATATGA
*
671549 AAATTTGCCTGGATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
671601 AAATTTGCCCGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
671653 AAATTTGTCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
671678 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:671790 original size:13 final size:13
Alignment explanation
Indices: 671772--671796 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
671762 ACAAAACTTA
671772 TGTATCGATACAT
1 TGTATCGATACAT
671785 TGTATCGATACA
1 TGTATCGATACA
671797 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:671792 original size:32 final size:33
Alignment explanation
Indices: 671751--671816 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
671741 AGTAGCTTAT
671751 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
671783 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
671816 A
1 A
671817 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:680780 original size:61 final size:61
Alignment explanation
Indices: 680612--681431 Score: 979
Period size: 61 Copynumber: 13.5 Consensus size: 61
680602 AACAAACATT
* * * * * *
680612 TTGGTGGCA-CTTTTCAGTCCTCAAGGAACAGGACGCTTTTTCCTTTTAAAGCCCAAACAAG
1 TTGGTGGCACCTTCT-AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAG
* * ** *
680673 TTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGGACACCTTTTCCTTTCAAAGCCCACACAAG
1 TTGGTGGCAC-CTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAG
* *
680735 TTGGTGGCACCTTCTAGTCCTCAAAGAGAAGGATGCCTTTTCCTTTTCAAGCCCACACAAG
1 TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAG
* * *
680796 TTGGTGGCACTTTCCTAGTCCTCAAAGAGCAAGATGCCTTTTCC-TTTAAAGCCCACACAAT
1 TTGGTGGCACCTT-CTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAG
680857 TTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAG
1 TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAG
** * *
680917 TTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAG
1 TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAG
* * * *
680972 CTGGTGGCACCTTC-AGTTCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAG
1 TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAG
* * * ** *
681032 GTGGTGGCACCTTCCAATCCTCAAAGAATAGGATG-CTTTCTCCTTTTAAAGCCCACACACG
1 TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTT-TCCTTTTAAAGCCCACACAAG
* *
681093 GTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATG-CTTTCTCCTTTTAAAG-CCACACAAG
1 TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTT-TCCTTTTAAAGCCCACACAAG
** * * * *
681153 TTGGTGGCAGTTTTCTAGTCCTCGAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCATACAAG
1 TTGGTGGCA-CCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAG
*
681215 TTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATG-CTTTCTCCTTTTAAAGCCCACACAAG
1 TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTT-TCCTTTTAAAGCCCACACAAG
* * * * * *
681276 TTGGTGACACTTTTCTAGTCGTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAT
1 TTGGTGGCAC-CTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAG
* ** *
681338 TTGGTGGCACCTTCTAGTTCTCAAAGAGCAGGATG-CTTTCTCCTTGCAAAGCCCATACAAG
1 TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTT-TCCTTTTAAAGCCCACACAAG
* *
681399 TTGGTGGCACCCTCTAGTCC-CTAAGGAGCAGGA
1 TTGGTGGCACCTTCTAGTCCTC-AAAGAGCAGGA
681432 CCCTTTTTAT
Statistics
Matches: 659, Mismatches: 79, Indels: 42
0.84 0.10 0.05
Matches are distributed among these distances:
54 20 0.03
55 28 0.04
56 1 0.00
59 28 0.04
60 88 0.13
61 340 0.52
62 147 0.22
63 7 0.01
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (61 bp):
TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAG
Found at i:680836 original size:123 final size:122
Alignment explanation
Indices: 680612--681408 Score: 1055
Period size: 123 Copynumber: 6.6 Consensus size: 122
680602 AACAAACATT
* * * * *
680612 TTGGTGGCA-CTTTTCAGTCCTCAAGGAACAGGACGCTTTTTCCTTTTAAAGCCCAAACAAGTTG
1 TTGGTGGCACCTTCT-AGTCCTCAAAGAGCAGGATGC-TTTTCCTTTTAAAGCCCACACAAGTTG
* * *
680676 GTGGCACTTTTCTAGTCCTCAAAGAGTAGGACACCTTTTCCTTTCAAAGCCCACACAAG
64 GTGGCACTTTCCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAG
* *
680735 TTGGTGGCACCTTCTAGTCCTCAAAGAGAAGGATGCCTTTTCCTTTTCAAGCCCACACAAGTTGG
1 TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATG-CTTTTCCTTTTAAAGCCCACACAAGTTGG
* * * *
680800 TGGCACTTTCCTAGTCCTCAAAGAGCAAGATGCCTTTTCC-TTTAAAGCCCACACAAT
65 TGGCACTTTCCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAG
680857 TTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGG
1 TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATG-CTTTTCCTTTTAAAGCCCACACAAGTTGG
* *
680921 TGGCATTTTCC-AGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAG
65 TGGCACTTTCCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAG
* * * *
680972 CTGGTGGCACCTTC-AGTTCTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGGTGG
1 TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATG-CTTTTCCTTTTAAAGCCCACACAAGTTGG
* * * * *
681036 TGGCACCTTCC-AATCCTCAAAGAATAGGATG-CTTTCTCCTTTTAAAGCCCACACACG
65 TGGCACTTTCCTAGTCCTCAAAGAGTAGGACGCCTTT-TCCTTTTAAAGCCCACACAAG
* *
681093 GTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCTTTCTCCTTTTAAAG-CCACACAAGTTGG
1 TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCTTT-TCCTTTTAAAGCCCACACAAGTTGG
* * * *
681157 TGGCAGTTTTCTAGTCCTCGAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCATACAAG
65 TGGCACTTTCCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAG
*
681215 TTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCTTTCTCCTTTTAAAGCCCACACAAGTTGG
1 TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCTTT-TCCTTTTAAAGCCCACACAAGTTGG
* * * *
681280 TGACACTTTTCTAGTCGTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAT
65 TGGCACTTTCCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAG
* ** *
681338 TTGGTGGCACCTTCTAGTTCTCAAAGAGCAGGATGCTTTCTCCTTGCAAAGCCCATACAAGTTGG
1 TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCTTT-TCCTTTTAAAGCCCACACAAGTTGG
681403 TGGCAC
65 TGGCAC
681409 CCTCTAGTCC
Statistics
Matches: 601, Mismatches: 59, Indels: 28
0.87 0.09 0.04
Matches are distributed among these distances:
114 1 0.00
115 99 0.16
116 1 0.00
117 1 0.00
118 1 0.00
119 3 0.00
120 20 0.03
121 107 0.18
122 143 0.24
123 220 0.37
124 5 0.01
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (122 bp):
TTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCTTTTCCTTTTAAAGCCCACACAAGTTGGT
GGCACTTTCCTAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAG
Found at i:684946 original size:13 final size:13
Alignment explanation
Indices: 684928--684955 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
684918 ATATAAAGAT
684928 CAATGTATCGATA
1 CAATGTATCGATA
684941 CAATGTATCGATA
1 CAATGTATCGATA
684954 CA
1 CA
684956 TTGAGTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:685015 original size:13 final size:13
Alignment explanation
Indices: 684993--685050 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
684983 GGCAGTAGCT
*
684993 TTGTAGCGATACA
1 TTGTATCGATACA
685006 TTGTATCGATACAATA
1 TTGTATCGATAC---A
685022 CTTATGTATCGATACA
1 --T-TGTATCGATACA
685038 TTGTATCGATACA
1 TTGTATCGATACA
685051 ACACTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:685031 original size:19 final size:19
Alignment explanation
Indices: 685007--685091 Score: 83
Period size: 19 Copynumber: 4.7 Consensus size: 19
684997 AGCGATACAT
685007 TGTATCGATACAATACTTA
1 TGTATCGATACAATACTTA
685026 TGTATCGATAC---A--T-
1 TGTATCGATACAATACTTA
*
685039 TGTATCGATACAACACTTA
1 TGTATCGATACAATACTTA
* *
685058 TGTATCGATACAGTTACTGTT
1 TGTATCGATACA-ATACT-TA
685079 TGTATCGATACAA
1 TGTATCGATACAA
685092 ATTGTTGAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 15
0.74 0.05 0.21
Matches are distributed among these distances:
13 11 0.20
14 1 0.02
16 2 0.04
18 1 0.02
19 23 0.43
20 3 0.06
21 13 0.24
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (19 bp):
TGTATCGATACAATACTTA
Found at i:685040 original size:32 final size:32
Alignment explanation
Indices: 684930--685069 Score: 135
Period size: 32 Copynumber: 4.4 Consensus size: 32
684920 ATAAAGATCA
* * * *
684930 ATGTATCGATACAATGTATCGATACATTGAGTA
1 ATGTATCGATACATTGTATCGATACAAT-ACTT
** * *
684963 ATGTATCGATACA-T-T-TCCTTGGCAGTAGCTT
1 ATGTATCGATACATTGTATCGAT-ACAATA-CTT
*
684994 -TGTAGCGATACATTGTATCGATACAATACTT
1 ATGTATCGATACATTGTATCGATACAATACTT
*
685025 ATGTATCGATACATTGTATCGATACAACACTT
1 ATGTATCGATACATTGTATCGATACAATACTT
685057 ATGTATCGATACA
1 ATGTATCGATACA
685070 GTTACTGTTT
Statistics
Matches: 88, Mismatches: 13, Indels: 13
0.77 0.11 0.11
Matches are distributed among these distances:
30 15 0.17
31 9 0.10
32 48 0.55
33 16 0.18
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
ATGTATCGATACATTGTATCGATACAATACTT
Found at i:685997 original size:49 final size:51
Alignment explanation
Indices: 685928--686478 Score: 230
Period size: 39 Copynumber: 11.8 Consensus size: 51
685918 TGTTAAAGAT
* * * * *
685928 GCCAATATGATCATTCAAGGCCAACGATATCGGACTT-AAG-GATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGATGAAGGC
* * * **
685977 GCCAATGTGCTGATTGAAGGCCAGCGACATTGGTTTTAAAGATGATGAAGGC
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-GATGAAGGC
686029 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-----G-T------
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGATGAAGGC
* * * * * *
686068 GCCAATGTGCTGATTCAAGGCCAGCGACATTAGTCTT-AA-AGA-CAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGATGAAGGC
** *
686116 GCCAATATGCTGATTCAATTCCAGCGATATTGGGCTT-----G-T------
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGATGAAGGC
* * * * *
686155 GCCAATATGCTGATTCAAGGCCAACGACATTGG-TTTTAA-AGAT---GGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGATGAAGGC
*
686201 GCCAATATGCTGATTCAAGGCCAACGATATTGGACTT-----G-T------
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGATGAAGGC
* * *
686240 GCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAA-AGATAAGAAGGGTT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGAT--GAA-GG-C
* * * * * *
686294 GCCAATATGCTGATTCAAGGCCAGCAATATTAGAC-TCAAGAGGTTAAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-GATGAAGGC
* *
686345 GCCAATATGTTGATTCAAGGCCAGTGATATTGGACTTAAAG-G-T------
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGATGAAGGC
* * * * *
686388 GCCAATGTGCTGATTCAAGGCCAACGACATTAGG-CTT-AA-AGATAAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGAGATGAAGGC
* * *
686437 GCCAATATGTTGATTCAAGGCCAACGATATTAGACTTAAAGA
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
686479 CAAGGTGCCA
Statistics
Matches: 393, Mismatches: 56, Indels: 104
0.71 0.10 0.19
Matches are distributed among these distances:
38 2 0.01
39 96 0.24
42 6 0.02
43 33 0.08
44 3 0.01
45 2 0.01
46 33 0.08
47 2 0.01
48 32 0.08
49 60 0.15
50 6 0.02
51 33 0.08
52 46 0.12
53 5 0.01
54 32 0.08
55 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (51 bp):
GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGATGAAGGC
Found at i:686157 original size:87 final size:88
Alignment explanation
Indices: 685975--686329 Score: 466
Period size: 85 Copynumber: 4.0 Consensus size: 88
685965 AAGGATGAAG
* * * *
685975 GTGCCAATGTGCTGATTGAAGGCCAGCGACATTGGTTTTAAAGATGATGAAGGCGCCAATATGCT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAA-A-GA-GAAGGTGCCAATATGCT
686040 GATTCAAGGCCAGCGATATTGGACTT
63 GATTCAAGGCCAGCGATATTGGACTT
* * *
686066 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGTCTT-AAAGACAAGGTGCCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAAGAGAAGGTGCCAATATGCTGAT
** *
686130 TCAATTCCAGCGATATTGGGCTT
66 TCAAGGCCAGCGATATTGGACTT
* * *
686153 GTGCCAATATGCTGATTCAAGGCCAACGACATTGGT-TT-TAA-AGATGGTGCCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAAGAGAAGGTGCCAATATGCTGAT
*
686215 TCAAGGCCAACGATATTGGACTT
66 TCAAGGCCAGCGATATTGGACTT
686238 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAAGATAAGAAGGGTTGCCAATATG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAAG---AGAA-GG-TGCCAATATG
* *
686303 CTGATTCAAGGCCAGCAATATTAGACT
61 CTGATTCAAGGCCAGCGATATTGGACT
686330 CAAGAGGTTA
Statistics
Matches: 232, Mismatches: 24, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
85 73 0.31
86 6 0.03
87 73 0.31
88 2 0.01
89 1 0.00
90 2 0.01
91 39 0.17
92 2 0.01
93 34 0.15
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (88 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAAGAGAAGGTGCCAATATGCTGAT
TCAAGGCCAGCGATATTGGACTT
Found at i:686267 original size:172 final size:180
Alignment explanation
Indices: 685975--686311 Score: 510
Period size: 172 Copynumber: 1.9 Consensus size: 180
685965 AAGGATGAAG
* * *
685975 GTGCCAATGTGCTGATTGAAGGCCAGCGACATTGGTTTTAAAGATGATGAAGGCGCCAATATGCT
1 GTGCCAATATGCTGATTCAAGGCCAACGACATTGGTTTTAAAGATGAT--AGGCGCCAATATGCT
* *
686040 GATTCAAGGCCAGCGATATTGGACTTGTGCCAATGTGCTGATTCAAGGCCAGCGACATTAGTCTT
64 GATTCAAGGCCAACGATATTGGACTTGTGCCAATATGCTGATTCAAGGCCAGCGACATTAGTCTT
686105 -AAAG-ACAA-GG-TGCCAATATGCTGATTCAATTCCAGCGATATTGGGCTT
129 AAAAGAACAAGGGTTGCCAATATGCTGATTCAATTCCAGCGATATTGGGCTT
*
686153 GTGCCAATATGCTGATTCAAGGCCAACGACATTGGTTTT-AA-A-GAT-GGTGCCAATATGCTGA
1 GTGCCAATATGCTGATTCAAGGCCAACGACATTGGTTTTAAAGATGATAGGCGCCAATATGCTGA
*
686214 TTCAAGGCCAACGATATTGGACTTGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAA
66 TTCAAGGCCAACGATATTGGACTTGTGCCAATATGCTGATTCAAGGCCAGCGACATTAGTCTTAA
*
686279 AAGATAAGAAGGGTTGCCAATATGCTGATTCAA
131 AAG--AACAAGGGTTGCCAATATGCTGATTCAA
686312 GGCCAGCAAT
Statistics
Matches: 145, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
172 75 0.52
173 4 0.03
175 3 0.02
176 4 0.03
177 4 0.03
178 55 0.38
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (180 bp):
GTGCCAATATGCTGATTCAAGGCCAACGACATTGGTTTTAAAGATGATAGGCGCCAATATGCTGA
TTCAAGGCCAACGATATTGGACTTGTGCCAATATGCTGATTCAAGGCCAGCGACATTAGTCTTAA
AAGAACAAGGGTTGCCAATATGCTGATTCAATTCCAGCGATATTGGGCTT
Found at i:686426 original size:43 final size:43
Alignment explanation
Indices: 686337--686477 Score: 158
Period size: 43 Copynumber: 3.1 Consensus size: 43
686327 ACTCAAGAGG
**
686337 TTAAAGGTGCCAATATGTTGATTCAAGGCCAGTGATATT-GGAC
1 TTAAAGGTGCCAATATGTTGATTCAAGGCCAACGATATTAGG-C
* * *
686380 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTAGGC
1 TTAAAGGTGCCAATATGTTGATTCAAGGCCAACGATATTAGGC
*
686423 TTAAAGATAAAGGTGCCAATATGTTGATTCAAGGCCAACGATATTAGAC
1 -T-----TAAAGGTGCCAATATGTTGATTCAAGGCCAACGATATTAGGC
686472 TTAAAG
1 TTAAAG
686478 ACAAGGTGCC
Statistics
Matches: 82, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
43 40 0.49
44 3 0.04
48 1 0.01
49 38 0.46
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (43 bp):
TTAAAGGTGCCAATATGTTGATTCAAGGCCAACGATATTAGGC
Found at i:686457 original size:92 final size:94
Alignment explanation
Indices: 686293--686477 Score: 266
Period size: 92 Copynumber: 2.0 Consensus size: 94
686283 TAAGAAGGGT
* * *
686293 TGCCAATATGCTGATTCAAGGCCAGCAATATTAGACTCAAGAGGTTAAAGGTGCCAATATGTTGA
1 TGCCAATATGCTGATTCAAGGCCAACAACATTAGACTCAAGAGGATAAAGGTGCCAATATGTTGA
** *
686358 TTCAAGGCCAGTGATATTGGACTTAAAGG
66 TTCAAGGCCAACGATATTAGACTTAAAGG
* * * *
686387 TGCCAATGTGCTGATTCAAGGCCAACGACATTAGGCTTAA-A-GATAAAGGTGCCAATATGTTGA
1 TGCCAATATGCTGATTCAAGGCCAACAACATTAGACTCAAGAGGATAAAGGTGCCAATATGTTGA
686450 TTCAAGGCCAACGATATTAGACTTAAAG
66 TTCAAGGCCAACGATATTAGACTTAAAG
686478 ACAAGGTGCC
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
92 46 0.57
93 1 0.01
94 34 0.42
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (94 bp):
TGCCAATATGCTGATTCAAGGCCAACAACATTAGACTCAAGAGGATAAAGGTGCCAATATGTTGA
TTCAAGGCCAACGATATTAGACTTAAAGG
Found at i:686657 original size:33 final size:32
Alignment explanation
Indices: 686480--686864 Score: 336
Period size: 34 Copynumber: 12.1 Consensus size: 32
686470 ACTTAAAGAC
* *
686480 AAGGTGCCACGAAGTTGTGGCCTTACAGAA--AA
1 AAGGTGCCACGGAGTTGTGGACTTA-A-AAGGAA
* *
686512 AAGGGATGCCACGGAGATGTGGGCTTAAAAGGAAA
1 AA-GG-TGCCACGGAGTTGTGGACTTAAAAGG-AA
* *
686547 AAGGGATGCCACGGAGGTGTGGGCTTAAAAGAGAA
1 AA-GG-TGCCACGGAGTTGTGGACTTAAAAG-GAA
* *
686582 AAGGGTGCCACGGAGTCGTGGACTTAAAAAGAA
1 AA-GGTGCCACGGAGTTGTGGACTTAAAAGGAA
686615 AAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
686647 CAAGGTGCCACGGAATTGTGGACTTCAAA-G--
1 -AAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
686677 --GGTGCCACGGAGTTGTGGGCTTAAAAGGAAA
1 AAGGTGCCACGGAGTTGTGGACTTAAAAGG-AA
*
686708 AAGAGTGCCACGGAGTTGTGGATTTAAAA-G--
1 AAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
*
686738 --GGTGCCACGAAGTTGTGGACTTAAAAGGAA
1 AAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
686768 CAAGGTGCCACGGAGTTGTGGACTTTAAAA-G--
1 -AAGGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
* * *
686799 --GTTGCCATGGAGTTGTGGGCTTAAAAGGGAA
1 AAGGTGCCACGGAGTTGTGGACTTAAAA-GGAA
* * *
686830 AAGAGTGCCACGGAGTCGTGGACTTAGAAGAAA
1 AAG-GTGCCACGGAGTTGTGGACTTAAAAGGAA
686863 AA
1 AA
686865 AATGCCACTA
Statistics
Matches: 296, Mismatches: 29, Indels: 55
0.78 0.08 0.14
Matches are distributed among these distances:
27 52 0.18
28 20 0.07
29 1 0.00
32 33 0.11
33 62 0.21
34 88 0.30
35 39 0.13
36 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.34, T:0.19
Consensus pattern (32 bp):
AAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:686685 original size:27 final size:27
Alignment explanation
Indices: 686580--686827 Score: 138
Period size: 27 Copynumber: 8.3 Consensus size: 27
686570 CTTAAAAGAG
* *
686580 AAAAGGGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAATTGTGGACTT
*
686607 AAAAAGAAAAGGTGCCACGGAGTTGTGGACTT
1 -AAAAG----GGTGCCACGGAATTGTGGACTT
686639 AAAAGGAACAAGGTGCCACGGAATTGTGGACTT
1 AAAA-G-----GGTGCCACGGAATTGTGGACTT
* * *
686672 CAAAGGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAATTGTGGACTT
* *
686699 AAAAGGAAAAAGAGTGCCACGGAGTTGTGGATTT
1 AAAA-G-----G-GTGCCACGGAATTGTGGACTT
686733 AAAAGGGTGCCAC-GAAGTTGTGGACTT
1 AAAAGGGTGCCACGGAA-TTGTGGACTT
*
686760 AAAAGGAACAAGGTGCCACGGAGTTGTGGACTTT
1 AAAA-G-----GGTGCCACGGAATTGTGGAC-TT
* * * *
686794 AAAAGGTTGCCATGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAATTGTGGACTT
686821 AAAAGGG
1 AAAAGGG
686828 AAAAGAGTGC
Statistics
Matches: 182, Mismatches: 16, Indels: 45
0.75 0.07 0.19
Matches are distributed among these distances:
26 2 0.01
27 51 0.28
28 25 0.14
31 4 0.02
32 23 0.13
33 46 0.25
34 31 0.17
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAATTGTGGACTT
Found at i:686745 original size:61 final size:61
Alignment explanation
Indices: 686545--686854 Score: 399
Period size: 61 Copynumber: 5.0 Consensus size: 61
686535 CTTAAAAGGA
* * * *
686545 AAAAGGGATGCCACGGAGGTGTGGGCTTAAAAGAGAAAAGGGTGCCACGGAGTCGTGGACTTA
1 AAAAGGG-TGCCACGGAGTTGTGGGCTTAAAAG-GAAAAAGGTGCCACGGAGTTGTGGACTTT
* * *
686608 AAAAGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAATTGTGGAC-TT
1 AAAAG----GGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTT
*
686672 CAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGA-TTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAG-GTGCCACGGAGTTGTGGACTTT
* * *
686733 AAAAGGGTGCCACGAAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTT
* * * *
686794 AAAAGGTTGCCATGGAGTTGTGGGCTTAAAAGGGAAAAGAGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAG-GTGCCACGGAGTTGTGGACTT
686855 AGAAGAAAAA
Statistics
Matches: 217, Mismatches: 22, Indels: 17
0.85 0.09 0.07
Matches are distributed among these distances:
60 50 0.23
61 90 0.41
62 20 0.09
63 5 0.02
64 5 0.02
65 22 0.10
66 23 0.11
67 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.35, T:0.20
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGACTTT
Found at i:686932 original size:31 final size:31
Alignment explanation
Indices: 686827--687115 Score: 334
Period size: 31 Copynumber: 9.2 Consensus size: 31
686817 GCTTAAAAGG
* *
686827 GAAAAGAGTGCCACGGAGTCGTGGACTTAGAA
1 GAAAAGA-TGCCACTGAGTCGTGGACTTTGAA
* *
686859 GAAAAAAATGCCACTAAGTCGTGGACTTTG--
1 G-AAAAGATGCCACTGAGTCGTGGACTTTGAA
686889 GAAAGAGATGCCACTGAGTCGTGGACTTTGAA
1 GAAA-AGATGCCACTGAGTCGTGGACTTTGAA
*
686921 GAAAAGATGCCACTGAGTCATGGACTTTGGGGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTT---GAA
* *
686955 -AAAAGACGCCACTGAGTCATGGACTTTGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTTGAA
* *
686985 GAAAAGGATGCCACTAAGTCGTGGACTTAGAA
1 GAAAA-GATGCCACTGAGTCGTGGACTTTGAA
* *
687017 -AATAGATGCTACTGAGTCGTGGACTTTGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTTGAA
* * *
687047 GAAAAGATGCCACTAAGTTGTGGACTTGGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTTGAA
* *
687078 GAAAAGAAGCCACTAAGTCGTGGACTTTGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTTGAA
*
687109 GGAAAGA
1 GAAAAGA
687116 GATTTGAAGA
Statistics
Matches: 222, Mismatches: 25, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
29 3 0.01
30 50 0.23
31 89 0.40
32 46 0.21
33 31 0.14
34 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.29, T:0.21
Consensus pattern (31 bp):
GAAAAGATGCCACTGAGTCGTGGACTTTGAA
Found at i:686989 original size:126 final size:124
Alignment explanation
Indices: 686827--687109 Score: 388
Period size: 126 Copynumber: 2.3 Consensus size: 124
686817 GCTTAAAAGG
* * * * *
686827 GAAAAGAGTGCCACGGAGTCGTGGACTTAGAAGAAAAAAATGCCACTAAGTCGTGGACTTTGGAA
1 GAAAAGA-AGCCACTGAGTCGTGGACTTTGAAGAAAAAAATGCCACTAAGTCGTGGACTTAGAAA
*
686892 AGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCATGGACTTTGGGGAA
65 AGAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTCATGGAC-TT--GGAA
* * **
686955 -AAAAGACGCCACTGAGTCATGGACTTTGAAGAAAAGGATGCCACTAAGTCGTGGACTTAGAAAA
1 GAAAAGAAGCCACTGAGTCGTGGACTTTGAAGAAAAAAATGCCACTAAGTCGTGGACTTAGAAAA
* * **
687019 TAGATGCTACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTTGTGGACTTGGAA
66 GAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTCATGGACTTGGAA
*
687078 GAAAAGAAGCCACTAAGTCGTGGACTTTGAAG
1 GAAAAGAAGCCACTGAGTCGTGGACTTTGAAG
687110 GAAAGAGATT
Statistics
Matches: 138, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
123 4 0.03
124 28 0.20
125 2 0.01
126 98 0.71
127 6 0.04
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.21
Consensus pattern (124 bp):
GAAAAGAAGCCACTGAGTCGTGGACTTTGAAGAAAAAAATGCCACTAAGTCGTGGACTTAGAAAA
GAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTAAGTCATGGACTTGGAA
Found at i:688411 original size:7 final size:7
Alignment explanation
Indices: 688399--688448 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
688389 CATTCGCACT
688399 TTTTTTG
1 TTTTTTG
688406 TTTTTT-
1 TTTTTTG
* *
688412 TTGTGTG
1 TTTTTTG
*
688419 TGTTGTT-
1 T-TTTTTG
688426 TTTTTTG
1 TTTTTTG
688433 TTTTTTG
1 TTTTTTG
688440 TTTTTTG
1 TTTTTTG
688447 TT
1 TT
688449 GTGTTTGTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
6 8 0.24
7 24 0.71
8 2 0.06
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (7 bp):
TTTTTTG
Found at i:688426 original size:18 final size:17
Alignment explanation
Indices: 688403--688453 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
688393 CGCACTTTTT
688403 TTGTTTTTTTTGTGTGTG
1 TTGTTTTTTTTGTGT-TG
*
688421 TTGTTTTTTTTGT-TTT
1 TTGTTTTTTTTGTGTTG
688437 TTGTTTTTTGTTGTGTT
1 TTGTTTTTT-TTGTGTT
688454 TGTACTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 10 0.33
17 5 0.17
18 15 0.50
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (17 bp):
TTGTTTTTTTTGTGTTG
Found at i:694862 original size:10 final size:10
Alignment explanation
Indices: 694847--694917 Score: 70
Period size: 10 Copynumber: 6.9 Consensus size: 10
694837 TCTTTTTTTT
694847 ACTATTCATC
1 ACTATTCATC
694857 ACTATTCATC
1 ACTATTCATC
* *
694867 ACTGTTCATGT
1 ACTATTCAT-C
* *
694878 ATCGATACATC
1 A-CTATTCATC
*
694889 ACTGTTCATC
1 ACTATTCATC
694899 ACTATTCATC
1 ACTATTCATC
*
694909 ACTGTTCAT
1 ACTATTCAT
694918 GTATCGATAC
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
10 41 0.85
11 2 0.04
12 5 0.10
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.39
Consensus pattern (10 bp):
ACTATTCATC
Found at i:694889 original size:22 final size:22
Alignment explanation
Indices: 694863--694939 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 22
694853 CATCACTATT
694863 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
* * *
694885 CATCACTGTTCAT-CA-CTATT
1 CATCACTGTTCATGTATCGATA
694905 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
*
694927 CATCGCTGTTCAT
1 CATCACTGTTCAT
694940 CACTGTACAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 16 0.35
21 2 0.04
22 28 0.61
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:694910 original size:42 final size:42
Alignment explanation
Indices: 694851--694943 Score: 177
Period size: 42 Copynumber: 2.2 Consensus size: 42
694841 TTTTTTACTA
694851 TTCATCACTATTCATCACTGTTCATGTATCGATACATCACTG
1 TTCATCACTATTCATCACTGTTCATGTATCGATACATCACTG
*
694893 TTCATCACTATTCATCACTGTTCATGTATCGATACATCGCTG
1 TTCATCACTATTCATCACTGTTCATGTATCGATACATCACTG
694935 TTCATCACT
1 TTCATCACT
694944 GTACATTGAG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.39
Consensus pattern (42 bp):
TTCATCACTATTCATCACTGTTCATGTATCGATACATCACTG
Found at i:695509 original size:34 final size:35
Alignment explanation
Indices: 695447--695513 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
695437 CTAAGTGATT
695447 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTT-AAAAAGATAGAGA
695483 GAGAGGTTTCTATCTTAGCC-TT-AAAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTAAAAAGATAG
695514 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 9 0.30
36 8 0.27
37 13 0.43
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTAAAAAGATAGAGA
Found at i:697914 original size:45 final size:45
Alignment explanation
Indices: 697850--697940 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
697840 TTATTCTTTC
697850 AAAGCTCTTTTATTCATTCTTTGTACTCAAACTTCCACAAACACT
1 AAAGCTCTTTTATTCATTCTTTGTACTCAAACTTCCACAAACACT
697895 AAAGCTCTTTTATTCATTCTTTGTACTCAAACTTCCACAAACACT
1 AAAGCTCTTTTATTCATTCTTTGTACTCAAACTTCCACAAACACT
697940 A
1 A
697941 GCCTTGTAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.37
Consensus pattern (45 bp):
AAAGCTCTTTTATTCATTCTTTGTACTCAAACTTCCACAAACACT
Found at i:699709 original size:21 final size:22
Alignment explanation
Indices: 699685--699744 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 22
699675 GAATTAGAGG
699685 AGAAAATGAATGAGTTAG-AAA
1 AGAAAATGAATGAGTTAGCAAA
699706 AG-AAA-GAAATGAGTT-GCAAA
1 AGAAAATG-AATGAGTTAGCAAA
699726 ATGAAAATG-ATGAGTTAGC
1 A-GAAAATGAATGAGTTAGC
699745 TAATAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
19 2 0.06
20 15 0.45
21 10 0.30
22 5 0.15
23 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.25, T:0.20
Consensus pattern (22 bp):
AGAAAATGAATGAGTTAGCAAA
Found at i:701886 original size:20 final size:20
Alignment explanation
Indices: 701861--701902 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
701851 TGTTCATAAA
*
701861 TTTGGTTTTATCAATTTAGC
1 TTTGGTTTTATCAACTTAGC
701881 TTTGGTTTTATCAACTTAGC
1 TTTGGTTTTATCAACTTAGC
701901 TT
1 TT
701903 ATAACAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.55
Consensus pattern (20 bp):
TTTGGTTTTATCAACTTAGC
Found at i:701986 original size:30 final size:29
Alignment explanation
Indices: 701952--702036 Score: 118
Period size: 29 Copynumber: 2.9 Consensus size: 29
701942 AGGTGAGAAC
*
701952 GTATTAAGGTGGAGAGTTTGCATAAAATTT
1 GTATTAAGG-GGAGAGCTTGCATAAAATTT
701982 GTATTAAGGGGGAGAGCTTG-ATAAAATTT
1 GTATTAA-GGGGAGAGCTTGCATAAAATTT
*
702011 GTACTAAAGGGGAGAGCTTGCATAAA
1 GTA-TTAAGGGGAGAGCTTGCATAAA
702037 CTTTTGGTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
29 24 0.48
30 24 0.48
31 2 0.04
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (29 bp):
GTATTAAGGGGAGAGCTTGCATAAAATTT
Found at i:703038 original size:24 final size:24
Alignment explanation
Indices: 703002--703065 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
702992 GATAAATTAT
*
703002 TGTTCATAACTGTTCACATATCAC
1 TGTTCATTACTGTTCACATATCAC
* ** *
703026 TGTTCATTGCTGTTCATGTATCAT
1 TGTTCATTACTGTTCACATATCAC
*
703050 TATTCATTACTGTTCA
1 TGTTCATTACTGTTCA
703066 TCGCTGTTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.45
Consensus pattern (24 bp):
TGTTCATTACTGTTCACATATCAC
Found at i:703094 original size:13 final size:13
Alignment explanation
Indices: 703076--703100 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
703066 TCGCTGTTCA
703076 TGTATCGATACAG
1 TGTATCGATACAG
703089 TGTATCGATACA
1 TGTATCGATACA
703101 TTCTAAATAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:703611 original size:32 final size:33
Alignment explanation
Indices: 703561--703652 Score: 82
Period size: 37 Copynumber: 2.7 Consensus size: 33
703551 AAGTGATTGG
* * *
703561 GAGGTTTTATCTTTGCCTTGAAAGATA-GTGTA
1 GAGGTTATACCTTAGCCTTGAAAGATAGGTGTA
*
703593 GAGGTTCTACCTTAGCCTTTGTAAAAGATAGGGGTGTA
1 GAGGTTATACCTTAGCC-TTG--AAAGATA--GGTGTA
703631 -AGGTTATACCTTAGCCTT-AAAG
1 GAGGTTATACCTTAGCCTTGAAAG
703653 GTAAACAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
32 14 0.28
33 7 0.14
35 7 0.14
36 2 0.04
37 15 0.30
38 5 0.10
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (33 bp):
GAGGTTATACCTTAGCCTTGAAAGATAGGTGTA
Found at i:704730 original size:34 final size:34
Alignment explanation
Indices: 704684--705104 Score: 468
Period size: 34 Copynumber: 12.4 Consensus size: 34
704674 CAAATACCCT
* *
704684 TTTAAAGCCCACAATTCCGTGGCACTTTTTTCATC
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTC-TC
* *
704719 TTT-AAGTCCACAACTCCGTGGCACC-----C-G
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTC
*
704746 TTT-AAGCCCACAACTCCGTGGCACCTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTC
* *
704779 TTTAAAGCCCACAACTCCATGGCACCTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTC
*
704813 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTC
704847 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCT-
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTC
** *
704880 TTTAAAGCCCACAACTCTATGGCACTCTTTTTTTCC
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCT-C
704916 TTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCT-
1 -TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCTC
** *
704951 TTTAAAGCCCACAACTTTGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTC
**
704986 TTTTCAAAGCCCACAACTCTATGGCACCTTTTTCT-
1 -TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCTC
*
705021 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTC
* * * * *
705056 TTTTAAGTCCACAATTCCGTGGCATCTTTTTCCC
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTC
705090 TTTCCAAAGCCCACA
1 TTT--AAAGCCCACA
705105 CAAGTCGGTG
Statistics
Matches: 337, Mismatches: 29, Indels: 39
0.83 0.07 0.10
Matches are distributed among these distances:
27 24 0.07
29 1 0.00
32 1 0.00
33 66 0.20
34 153 0.45
35 24 0.07
36 18 0.05
37 30 0.09
38 20 0.06
ACGTcount: A:0.21, C:0.33, G:0.11, T:0.35
Consensus pattern (34 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTC
Found at i:704757 original size:27 final size:27
Alignment explanation
Indices: 704719--704770 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
704709 TTTTTTCATC
*
704719 TTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAGCCCACAACTCCGTGGCACCCG
704746 TTTAAGCCCACAACTCCGTGGCACC
1 TTTAAGCCCACAACTCCGTGGCACC
704771 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (27 bp):
TTTAAGCCCACAACTCCGTGGCACCCG
Found at i:704823 original size:68 final size:69
Alignment explanation
Indices: 704682--705087 Score: 523
Period size: 68 Copynumber: 6.0 Consensus size: 69
704672 TTCAAATACC
* * * *
704682 CTTTTAAAGCCCACAATTCCGTGGCACT-TTTTTCATCTTT-AAGTCCACAACTCCGTGGCACC-
1 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACCT
704744 ----
66 TTTT
* *
704744 CGTTT-AAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTTAAAGCCCACAACTCCATGGCACCT
1 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACCT
704806 TTTT
66 TTTT
704810 CTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTTAAAGCCCACAACTCCGTGGCACC
1 C-TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACC
704873 TTTTT
65 TTTTT
** *
704878 CTTTTAAAGCCCACAACTCTATGGCACTCTTTTTTTCCTTTTCAAAGCCCACAACTCCGTGGCAC
1 CTTTTAAAGCCCACAACTCCGTGGCACTC--TTTTTCCTTTTTAAAGCCCACAACTCCGTGGCAC
704943 CTTTTT
64 CTTTTT
** * **
704949 CTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCTATGGCACC
1 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTTTTAAAGCCCACAACTCCGTGGCACC
705014 TTTTT
65 TTTTT
* * * *
705019 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT-AAGTCCACAATTCCGTGGCATCT
1 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACCT
705083 TTTT
66 TTTT
705087 C
1 C
705088 CCTTTCCAAA
Statistics
Matches: 306, Mismatches: 24, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
60 4 0.01
61 45 0.15
62 4 0.01
66 1 0.00
67 27 0.09
68 85 0.28
69 10 0.03
70 70 0.23
71 60 0.20
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.35
Consensus pattern (69 bp):
CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACCT
TTTT
Found at i:705195 original size:49 final size:49
Alignment explanation
Indices: 705138--705688 Score: 672
Period size: 49 Copynumber: 11.6 Consensus size: 49
705128 GCCTAATATC
* *
705138 GCTGGCCTTGAATCAACATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
* *
705187 GCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATC
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
*
705230 GCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
*
705279 GCTGGCCTTGAATCAGCACATTGGCA-C--CA---TTAAGTCCAATATA
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
* * *
705322 GCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
* * * * * * *
705371 GTTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGCCCAATATA
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
* *
705420 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
* *
705469 GCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
* *
705518 GCTGGCCTTGAATCAGCACATTGGCA-CCTCACCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
* *
705566 GTTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATA
1 GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
* * * *
705609 GCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCA--TCTT-CATCTTTAAGTCCAATGTA
* *
705661 GCTGGCCTTGAATCAGCACGTTGACATC
1 GCTGGCCTTGAATCAGCACATTGGCATC
705689 CTTTTTCTCA
Statistics
Matches: 437, Mismatches: 44, Indels: 41
0.84 0.08 0.08
Matches are distributed among these distances:
43 115 0.26
44 1 0.00
45 2 0.00
46 3 0.01
47 1 0.00
48 46 0.11
49 231 0.53
50 2 0.00
52 36 0.08
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
GCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATGTA
Found at i:705289 original size:92 final size:92
Alignment explanation
Indices: 705132--705679 Score: 783
Period size: 92 Copynumber: 5.8 Consensus size: 92
705122 TTCTAAGCCT
* *
705132 AATATCGCTGGCCTTGAATCAACATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTG
1 AATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTG
705197 AATCAGCACATTGGCACCTTTAAGTCC
66 AATCAGCACATTGGCACCTTTAAGTCC
*
705224 AATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTG
1 AATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTG
*
705289 AATCAGCACATTGGCACCATTAAGTCC
66 AATCAGCACATTGGCACCTTTAAGTCC
* * *
705316 AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGTTGGCCTTG
1 AATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTG
* *
705381 ACTCAGCACATTGGCACCTTCACCATTAAGCCC
66 AATCAGCACATTGGCACC-T-----TTAAGTCC
*
705414 AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTG
1 AATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTG
*
705479 ACTCAGCACATTGGCACCTTCATCTTTAAGTCC
66 AATCAGCACATTGGCA----C--CTTTAAGTCC
* * * * *
705512 AATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTCACCTTTAAGTCCAATGTAGTTGGCCTTG
1 AATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTG
705576 AATCAGCACATTGGCACCTTTAAGTCC
66 AATCAGCACATTGGCACCTTTAAGTCC
* * *
705603 AATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCC
1 AATATAGCTGGCCTTGAATCAGCATATTGGCA--TCTT-CATCTTTAAGTCCAATGTAGCTGGCC
705668 TTGAATCAGCAC
63 TTGAATCAGCAC
705680 GTTGACATCC
Statistics
Matches: 414, Mismatches: 26, Indels: 29
0.88 0.06 0.06
Matches are distributed among these distances:
91 39 0.09
92 168 0.41
93 1 0.00
94 1 0.00
95 35 0.08
97 44 0.11
98 123 0.30
102 1 0.00
103 1 0.00
104 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (92 bp):
AATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTG
AATCAGCACATTGGCACCTTTAAGTCC
Found at i:705728 original size:55 final size:55
Alignment explanation
Indices: 705593--706154 Score: 373
Period size: 67 Copynumber: 9.9 Consensus size: 55
705583 ACATTGGCAC
* * *
705593 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * **
705645 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * *
705700 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCGTC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-C-TTT-T--TC-TC
705765 AT
54 AT
* *
705767 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT-C----T-TCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * **
705816 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * *
705871 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-CTTTT-TC-TCAT
*
705935 CATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT-C----T-TCAT
1 C---TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * **
705987 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
* * * * *
706042 CTTTAGGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT-G-A-C---ATC-C-TTT-T--TC-TC
706107 AT
54 AT
*
706109 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGACA-CCTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACATCCTT
706155 CATCATCTTT
Statistics
Matches: 395, Mismatches: 64, Indels: 96
0.71 0.12 0.17
Matches are distributed among these distances:
49 76 0.19
50 2 0.01
51 1 0.00
52 41 0.10
53 2 0.01
54 8 0.02
55 97 0.25
56 3 0.01
57 3 0.01
58 5 0.01
59 3 0.01
60 1 0.00
61 14 0.04
62 7 0.02
63 8 0.02
64 10 0.03
65 1 0.00
66 7 0.02
67 106 0.27
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (55 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGACATCCTTTTTCTCAT
Found at i:705882 original size:171 final size:171
Alignment explanation
Indices: 705594--706158 Score: 1013
Period size: 171 Copynumber: 3.3 Consensus size: 171
705584 CATTGGCACC
* * *
705594 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA--TCTT-CATCTTTAAGTTCAATG
705659 TAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCA
63 TAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCA
*
705724 TGAATCAACATATTGGCATCTTTATCACTTTTCTCATCGTCATT
128 TGAATCAACATATTGGCATCTTTATCACTTTTCTCATCATCATT
705768 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
705833 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATGA
66 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATGA
705898 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCATT
131 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCATT
705939 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
*
706004 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCGTTGGCCATGA
66 CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATGA
* *
706069 ATCAACATATTGGCATCTTTATCACTTTTCTCATCTTCATC
131 ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCATT
* * *
706110 TTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGACACCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
706159 ATCTTTAAAA
Statistics
Matches: 381, Mismatches: 10, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
171 339 0.89
172 3 0.01
174 39 0.10
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.37
Consensus pattern (171 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAG
CTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCATGA
ATCAACATATTGGCATCTTTATCACTTTTCTCATCATCATT
Found at i:706996 original size:33 final size:33
Alignment explanation
Indices: 706959--707025 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
706949 TTCAATGATT
706959 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
706992 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
707025 T
1 T
707026 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:706997 original size:13 final size:13
Alignment explanation
Indices: 706979--707003 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
706969 CATAAAATGT
706979 TGTATCGATACAA
1 TGTATCGATACAA
706992 TGTATCGATACA
1 TGTATCGATACA
707004 TATTTTTTTG
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:707128 original size:52 final size:50
Alignment explanation
Indices: 707065--707205 Score: 201
Period size: 52 Copynumber: 2.7 Consensus size: 50
707055 CATTACTCAA
*
707065 ATGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAAATTTGCCCAG
* *
707117 ATGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACTAT--TATGTATCGATACATGCAGGCAAATTTGCCCAG
707169 ATGTATCGATACACTATTAAATGTATCGATACATGCA
1 ATGTATCGATACACTATT--ATGTATCGATACATGCA
707206 AACAACTTTT
Statistics
Matches: 80, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
51 2 0.03
52 78 0.98
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (50 bp):
ATGTATCGATACACTATTATGTATCGATACATGCAGGCAAATTTGCCCAG
Found at i:710343 original size:20 final size:20
Alignment explanation
Indices: 710318--710372 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
710308 TTTTCACAAT
*
710318 TTGTATTGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
710338 TTGTATCAATACATTGTTCA
1 TTGTATCGATACATTGTTCA
710358 TTGTATCGATACATT
1 TTGTATCGATACATT
710373 TTGGGTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:712860 original size:79 final size:79
Alignment explanation
Indices: 712728--712968 Score: 225
Period size: 79 Copynumber: 3.1 Consensus size: 79
712718 TTATCTCTTA
** * **
712728 GATACTCCAACCCCGGTTTTATTTCTAAAATATTGATTTCTCACAATCAGGGATACTCCAACCCC
1 GATACTCCAACCCCGGCCTTATTTCTAAAACATCAATTTCTCACAATCAGGGATACTCCAACCCC
**
712793 GTTATTTTCGCGGG
66 GTTATTTTCAAGGG
* * * * *
712807 GATACTCCAACCTCGGCCTTATTTCTAAAGCATCAATTTTTCACAATCGGGGATACTCCAACCCT
1 GATACTCCAACCCCGGCCTTATTTCTAAAACATCAATTTCTCACAATCAGGGATACTCCAACCCC
* *
712872 TTTATTTTTAAGGG
66 GTTATTTTCAAGGG
* *** * * * *
712886 GATGCTCCAACCCCGATATTATTT-TGAAAACACTGATTTTCT-ATAATCAGGGATACTCCAACT
1 GATACTCCAACCCCGGCCTTATTTCT-AAAACA-TCAATTTCTCACAATCAGGGATACTCCAACC
* * *
712949 CTGTTATTTTCGATGG
64 CCGTTATTTTCAAGGG
712965 GATA
1 GATA
712969 TTTCAATCTC
Statistics
Matches: 129, Mismatches: 31, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
78 1 0.01
79 122 0.95
80 6 0.05
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (79 bp):
GATACTCCAACCCCGGCCTTATTTCTAAAACATCAATTTCTCACAATCAGGGATACTCCAACCCC
GTTATTTTCAAGGG
Found at i:713020 original size:158 final size:158
Alignment explanation
Indices: 712732--713021 Score: 352
Period size: 158 Copynumber: 1.8 Consensus size: 158
712722 CTCTTAGATA
* * * *
712732 CTCCAACCCCGGTTTTATTTCTAAAATATTGATTTCTCACAATCAGGGATACTCCAACCCCGTTA
1 CTCCAACCCCGATATTATTTCTAAAACACTGATTTCTCACAATCAGGGATACTCCAACCCCGTTA
* * * *
712797 TTTTCGCGGGGATACTCCAACCTCGGCCTTATTTCTAAAGCATCAATTTTTCACAATCGGGGATA
66 TTTTCGAGGGGATACTCCAACCTCGACCTTATTTCTAAAGCATCAATTTTCCAAAATCGGGGATA
712862 CTCCAACCCTTTTATTTTTAAGGGGATG
131 CTCCAACCCTTTTATTTTTAAGGGGATG
* * *
712890 CTCCAACCCCGATATTATTT-TGAAAACACTGATTT-TCTATAATCAGGGATACTCCAACTCTGT
1 CTCCAACCCCGATATTATTTCT-AAAACACTGATTTCTC-ACAATCAGGGATACTCCAACCCCGT
* * * * ** * * *
712953 TATTTTCGATGGGATATTTCAATCTCGATTTTATTTCTAGAGCA-CTGATTTTCCAAAATTGGGG
64 TATTTTCGAGGGGATACTCCAACCTCGACCTTATTTCTAAAGCATC-AATTTTCCAAAATCGGGG
713017 ATACT
128 ATACT
713022 TCAGCCCCGT
Statistics
Matches: 109, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
157 4 0.04
158 105 0.96
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.36
Consensus pattern (158 bp):
CTCCAACCCCGATATTATTTCTAAAACACTGATTTCTCACAATCAGGGATACTCCAACCCCGTTA
TTTTCGAGGGGATACTCCAACCTCGACCTTATTTCTAAAGCATCAATTTTCCAAAATCGGGGATA
CTCCAACCCTTTTATTTTTAAGGGGATG
Found at i:725140 original size:18 final size:17
Alignment explanation
Indices: 725117--725165 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
725107 AGGCCACCCA
* **
725117 TTTTTCCTTTTTTCTTT
1 TTTTTTCTTTTTAATTT
725134 TTTTTTCTTTTTAATTT
1 TTTTTTCTTTTTAATTT
* *
725151 TTTTTACTATTTAAT
1 TTTTTTCTTTTTAAT
725166 GATCAAAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTCTTTTTAATTT
Found at i:732236 original size:13 final size:13
Alignment explanation
Indices: 732218--732247 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
732208 ACATTTCATC
*
732218 ATGTATCGATACA
1 ATGTATCAATACA
732231 ATGTATCAATACA
1 ATGTATCAATACA
732244 ATGT
1 ATGT
732248 CCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:732337 original size:19 final size:20
Alignment explanation
Indices: 732292--732344 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
732282 CTACCAGTTT
* *
732292 CATGTATCAATACAATTGAG
1 CATGTATCGATACAATAGAG
*
732312 TATGTATCGATACAA-AGAG
1 CATGTATCGATACAATAGAG
732331 CATGTATCGATACA
1 CATGTATCGATACA
732345 TTGTATCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACAATAGAG
Found at i:732357 original size:32 final size:33
Alignment explanation
Indices: 732314--732378 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
732304 CAATTGAGTA
* *
732314 TGTATCGATACAAAG-AGCATGTATCGATACAT
1 TGTATCAATACAAAGCAGAATGTATCGATACAT
*
732346 TGTATCAATACAAAGCATAATGTATCGATACAT
1 TGTATCAATACAAAGCAGAATGTATCGATACAT
732379 CTGGATATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (33 bp):
TGTATCAATACAAAGCAGAATGTATCGATACAT
Found at i:738547 original size:13 final size:13
Alignment explanation
Indices: 738529--738555 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
738519 ACATGCTGCT
738529 TTGTATCGATACA
1 TTGTATCGATACA
738542 TTGTATCGATACA
1 TTGTATCGATACA
738555 T
1 T
738556 GTTCATTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:738552 original size:33 final size:32
Alignment explanation
Indices: 738510--738574 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
738500 CACACCCAGA
* *
738510 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATG-TGCATTGCATCGATACAT
*
738543 TGTATCGATACATGTTCATTGCATCGATACAT
1 TGTATCGATACATGTGCATTGCATCGATACAT
738575 AGACAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATGTGCATTGCATCGATACAT
Found at i:738588 original size:20 final size:19
Alignment explanation
Indices: 738538--738595 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
738528 TTTGTATCGA
738538 TACATTGTATCGATACATG
1 TACATTGTATCGATACATG
* *
738557 TTCATTGCATCGATACATAG
1 TACATTGTATCGATACAT-G
738577 -ACAATTGTATCGATACATG
1 TAC-ATTGTATCGATACATG
738596 AAACTAGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (19 bp):
TACATTGTATCGATACATG
Found at i:738666 original size:33 final size:33
Alignment explanation
Indices: 738624--738690 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
738614 CTATCACTAT
*
738624 TTGTATCGATACATGATA-CAATGTATCGATACA
1 TTGTATCGATACATGA-AGAAATGTATCGATACA
738657 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATGAAGAAATGTATCGATACA
738690 T
1 T
738691 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (33 bp):
TTGTATCGATACATGAAGAAATGTATCGATACA
Found at i:738670 original size:13 final size:13
Alignment explanation
Indices: 738638--738670 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
738628 ATCGATACAT
*
738638 GATACAATGTATC
1 GATACATTGTATC
738651 GATACATTGTATC
1 GATACATTGTATC
738664 GATACAT
1 GATACAT
738671 GAAGAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
GATACATTGTATC
Found at i:747246 original size:20 final size:19
Alignment explanation
Indices: 747223--747274 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
747213 CACACCCAGA
*
747223 TGTATCGATACATGCTGCTT
1 TGTATCGATACATG-TGCAT
*
747243 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTGCAT
*
747262 TGCATCGATACAT
1 TGTATCGATACAT
747275 AGACAATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTGCAT
Found at i:747366 original size:33 final size:33
Alignment explanation
Indices: 747324--747390 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
747314 CTATCACTAT
*
747324 TTGTATCGATACATGATA-CAATGTATCGATACA
1 TTGTATCGATACATGA-AGAAATGTATCGATACA
747357 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATGAAGAAATGTATCGATACA
747390 T
1 T
747391 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (33 bp):
TTGTATCGATACATGAAGAAATGTATCGATACA
Found at i:747370 original size:13 final size:13
Alignment explanation
Indices: 747338--747370 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
747328 ATCGATACAT
*
747338 GATACAATGTATC
1 GATACATTGTATC
747351 GATACATTGTATC
1 GATACATTGTATC
747364 GATACAT
1 GATACAT
747371 GAAGAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
GATACATTGTATC
Found at i:750161 original size:81 final size:81
Alignment explanation
Indices: 749988--750244 Score: 358
Period size: 81 Copynumber: 3.2 Consensus size: 81
749978 AAAAGGAACG
* * * * * * *
749988 GGGTTGGAGTATCCCCTTGAAGATTGTGGGGTTGGAGTAACCCGA-AGATGGAAAATTTGAT-TT
1 GGGTTGGAGTATCCCCCTGAAAATGGTGGGGTTGGAGTATCCCCATAGATGGAAAGTTGGATATT
*
750051 TTTGGAAGTAAAGACG
66 TTTGGAAGTAAAGACA
750067 GGGTTGGAGTATCCCCCTGAAAATGGTGGGGTTGGAGTATCCCCATAGATGGAAAGTTGGATATT
1 GGGTTGGAGTATCCCCCTGAAAATGGTGGGGTTGGAGTATCCCCATAGATGGAAAGTTGGATATT
750132 TTTGGAAGTAAAGACA
66 TTTGGAAGTAAAGACA
* * * * * *
750148 GGGTTAGAGTAT-CCTCTCAAAAAAGGTGGGATTAGAGTATCCCCATAGATGGAAAGTTGGATAT
1 GGGTTGGAGTATCCCCCT-GAAAATGGTGGGGTTGGAGTATCCCCATAGATGGAAAGTTGGATAT
750212 TTTTGGAAGTAAAGACA
65 TTTTGGAAGTAAAGACA
750229 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
750245 GATAATGAAA
Statistics
Matches: 158, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
79 40 0.25
80 18 0.11
81 98 0.62
82 2 0.01
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.28
Consensus pattern (81 bp):
GGGTTGGAGTATCCCCCTGAAAATGGTGGGGTTGGAGTATCCCCATAGATGGAAAGTTGGATATT
TTTGGAAGTAAAGACA
Found at i:750287 original size:52 final size:53
Alignment explanation
Indices: 750182--750293 Score: 165
Period size: 53 Copynumber: 2.1 Consensus size: 53
750172 GGTGGGATTA
* *
750182 GAGTATCCCCATAGATGGAAAGTTGGATATTTTTGGAAGTAAAGACAGGGTTG
1 GAGTATCCCCATAGATGAAAAATTGGATATTTTTGGAAGTAAAGACAGGGTTG
* *
750235 GAGTATCCCCGATA-ATGAAAAATTGGGTATTTTT-GAAGTAAAGACTGGGTTG
1 GAGTATCCCC-ATAGATGAAAAATTGGATATTTTTGGAAGTAAAGACAGGGTTG
750287 GAGTATC
1 GAGTATC
750294 TCCTCAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
52 24 0.44
53 27 0.50
54 3 0.06
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.29
Consensus pattern (53 bp):
GAGTATCCCCATAGATGAAAAATTGGATATTTTTGGAAGTAAAGACAGGGTTG
Found at i:750344 original size:133 final size:133
Alignment explanation
Indices: 750095--750372 Score: 332
Period size: 133 Copynumber: 2.1 Consensus size: 133
750085 GAAAATGGTG
* *
750095 GGGTTGGAGTATCCCCATAGATGGAAAGTTGGATATTTTTGGAAGTAAAGACAGGGTTAGAGTAT
1 GGGTTGGAGTATCCCCATAGATGAAAAATTGGATATTTTTGGAAGTAAAGACAGGGTTAGAGTAT
* * * * *
750160 CCTCTCAAAAAAGGTGGGATTAGAGTATCCCCATAGATGGAAAGTTGGATATTTTTGGAAGTAAA
66 CCTCTCAAAAAAGGTGGGATTAGAGCATCCCAATAGATGAAAAGTTGGATA-TTTTGAAAATAAA
*
750225 GACA
130 AACA
* * *
750229 GGGTTGGAGTATCCCCGATA-ATGAAAAATTGGGTATTTTT-GAAGTAAAGACTGGGTTGGAGTA
1 GGGTTGGAGTATCCCC-ATAGATGAAAAATTGGATATTTTTGGAAGTAAAGACAGGGTTAGAGTA
* * * * *
750292 T-CTCCTCAAAAATGGTAGGG-TTAGAGCATCCTTAAT-GGTGAAAATTTTGATATTTTGAAAAT
65 TCCT-CTCAAAAAAGGT-GGGATTAGAGCATCC-CAATAGATGAAAAGTTGGATATTTTGAAAAT
750354 AAAAACA
127 AAAAACA
750361 GGGTTGGAGTAT
1 GGGTTGGAGTAT
750373 TCCCTCAGAA
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
132 28 0.23
133 55 0.44
134 38 0.31
135 3 0.02
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.29
Consensus pattern (133 bp):
GGGTTGGAGTATCCCCATAGATGAAAAATTGGATATTTTTGGAAGTAAAGACAGGGTTAGAGTAT
CCTCTCAAAAAAGGTGGGATTAGAGCATCCCAATAGATGAAAAGTTGGATATTTTGAAAATAAAA
ACA
Found at i:758380 original size:15 final size:15
Alignment explanation
Indices: 758360--758396 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
758350 AAAAAGTCAA
758360 AAAAAAAACAAAAAC
1 AAAAAAAACAAAAAC
* *
758375 AAAAAAAACACACAC
1 AAAAAAAACAAAAAC
758390 AAAAAAA
1 AAAAAAA
758397 GTACAAAGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAACAAAAAC
Found at i:759638 original size:31 final size:30
Alignment explanation
Indices: 759586--759644 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
759576 ATCTCTCTTC
*
759586 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
1 TCAAAGTCCACAACTCAGTGGCA-CTTTTCT
*
759617 TCAAAGTCCATAACTTC-GTGGCACTTTT
1 TCAAAGTCCACAAC-TCAGTGGCACTTTT
759645 TTTTTCCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 5 0.20
31 18 0.72
32 2 0.08
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (30 bp):
TCAAAGTCCACAACTCAGTGGCACTTTTCT
Found at i:759681 original size:27 final size:27
Alignment explanation
Indices: 759651--759742 Score: 76
Period size: 27 Copynumber: 3.2 Consensus size: 27
759641 TTTTTTTTTC
* *
759651 CTTTTAAGCCCACAACTTCGTGGCATT
1 CTTTTAAGCCCACAACTACGTGGCAAT
* *
759678 CTTTTCCTTTTAAGTCCACAACTACGTGGCAAC
1 C---T--TT-TAAGCCCACAACTACGTGGCAAT
* *
759711 CTTTTAAGCCCACAACTCCGTGGCACT
1 CTTTTAAGCCCACAACTACGTGGCAAT
759738 CTTTT
1 CTTTT
759743 TTTTTTTAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
27 25 0.49
28 2 0.04
30 2 0.04
32 2 0.04
33 20 0.39
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.34
Consensus pattern (27 bp):
CTTTTAAGCCCACAACTACGTGGCAAT
Found at i:759755 original size:34 final size:35
Alignment explanation
Indices: 759711--759941 Score: 229
Period size: 34 Copynumber: 6.9 Consensus size: 35
759701 ACGTGGCAAC
759711 CTTTTAAGCCCACAACTCCGTGGCACTCTTTTTTT
1 CTTTTAAGCCCACAACTCCGTGGCACTCTTTTTTT
759746 -TTTTAAGCCCACAACTCCGTGGCACT-TTTTTTT
1 CTTTTAAGCCCACAACTCCGTGGCACTCTTTTTTT
* * * *
759779 CCTTTTAAGCCCACAACTACGTAGCATTC-TTTTTC
1 -CTTTTAAGCCCACAACTCCGTGGCACTCTTTTTTT
* *
759814 CTTTTAAGTCCACAACTCCATGGCAC-C-------
1 CTTTTAAGCCCACAACTCCGTGGCACTCTTTTTTT
* *
759841 CTTTTAAGCCCACTACTTCGTGGCACT-TTTTTTT
1 CTTTTAAGCCCACAACTCCGTGGCACTCTTTTTTT
*
759875 CCTTTTAAGCCCATAACTCCGTGGCA-T-TTTTTTT
1 -CTTTTAAGCCCACAACTCCGTGGCACTCTTTTTTT
* * *
759909 CCTTTTAAGTCCACAACTCTGTGGCACCCTTTT
1 -CTTTTAAGCCCACAACTCCGTGGCACTCTTTT
759942 AAGTCCACAA
Statistics
Matches: 162, Mismatches: 20, Indels: 27
0.78 0.10 0.13
Matches are distributed among these distances:
27 22 0.14
33 8 0.05
34 78 0.48
35 50 0.31
36 4 0.02
ACGTcount: A:0.19, C:0.30, G:0.11, T:0.39
Consensus pattern (35 bp):
CTTTTAAGCCCACAACTCCGTGGCACTCTTTTTTT
Found at i:759811 original size:96 final size:95
Alignment explanation
Indices: 759628--759804 Score: 266
Period size: 96 Copynumber: 1.8 Consensus size: 95
759618 CAAAGTCCAT
* * * *
759628 AACTTCGTGGCACTTTTTTTTTCCTTTTAAGCCCACAACTTCGTGGCATTCTTTTCCTTTTAAGT
1 AACTCCGTGGCACTCTTTTTTT-CTTTTAAGCCCACAACTCCGTGGCATTCTTTTCCTTTTAAGC
*
759693 CCACAACTACGTGGCAACCTTTTAAGCCCAC
65 CCACAACTACGTAGCAACCTTTTAAGCCCAC
*
759724 AACTCCGTGGCACTCTTTTTTT-TTTTAAGCCCACAACTCCGTGGCACTTTTTTTTCCTTTTAAG
1 AACTCCGTGGCACTCTTTTTTTCTTTTAAGCCCACAACTCCGTGGCA--TTCTTTTCCTTTTAAG
759788 CCCACAACTACGTAGCA
64 CCCACAACTACGTAGCA
759805 TTCTTTTTCC
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
94 23 0.32
96 50 0.68
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.37
Consensus pattern (95 bp):
AACTCCGTGGCACTCTTTTTTTCTTTTAAGCCCACAACTCCGTGGCATTCTTTTCCTTTTAAGCC
CACAACTACGTAGCAACCTTTTAAGCCCAC
Found at i:759821 original size:69 final size:69
Alignment explanation
Indices: 759710--760017 Score: 262
Period size: 69 Copynumber: 4.7 Consensus size: 69
759700 TACGTGGCAA
* * **
759710 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTTTTTTTAAGCCCACAACTCCGTGGCACTTTT
1 CCTTTTAAGCCCACAACTACGTGGCATTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTTTT
759775 TTTT
66 TTTT
* * *
759779 CCTTTTAAGCCCACAACTACGTAGCATTCTTTTTCCTTTTAAGTCCACAACTCCATGGCAC----
1 CCTTTTAAGCCCACAACTACGTGGCATTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTTTT
759840 ----
66 TTTT
* * * *
759840 CCTTTTAAGCCCACTACTTCGTGGCACTTTTTTTTCCTTTTAAGCCCATAACTCCGTGGCA-TTT
1 CCTTTTAAGCCCACAACTACGTGGCA-TTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTTT
759904 TTTTT
65 TTTTT
* * *
759909 CCTTTTAAGTCCACAACT-CTGTGGCA--C-----CCTTTTAAGTCCACAACTTCC-TGGCGC--
1 CCTTTTAAGCCCACAACTAC-GTGGCATTCTTTTTCCTTTTAAGCCCACAAC-TCCGTGGCACTT
* *
759963 CTTATT
64 TTTTTT
* * * *
759969 CCTTTTAAGTCCACAACTCCATGGCA-TCTTTCTCCTTTTAAGCCCACAA
1 CCTTTTAAGCCCACAACTACGTGGCATTCTTTTTCCTTTTAAGCCCACAA
760018 GTTAGTGGCA
Statistics
Matches: 196, Mismatches: 24, Indels: 41
0.75 0.09 0.16
Matches are distributed among these distances:
60 27 0.14
61 44 0.22
62 33 0.17
66 15 0.08
68 1 0.01
69 76 0.39
ACGTcount: A:0.20, C:0.31, G:0.11, T:0.37
Consensus pattern (69 bp):
CCTTTTAAGCCCACAACTACGTGGCATTCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACTTTT
TTTT
Found at i:759844 original size:61 final size:62
Alignment explanation
Indices: 759779--759900 Score: 174
Period size: 62 Copynumber: 2.0 Consensus size: 62
759769 ACTTTTTTTT
*
759779 CCTTTTAAGCCCACAACTACGTAGCA-TTCTTTTTCCTTTTAAGTCCACAACTCCATGGCAC
1 CCTTTTAAGCCCACAACTACGTAGCACTTCTTTTTCCTTTTAAGCCCACAACTCCATGGCAC
* * * * * *
759840 CCTTTTAAGCCCACTACTTCGTGGCACTTTTTTTTCCTTTTAAGCCCATAACTCCGTGGCA
1 CCTTTTAAGCCCACAACTACGTAGCACTTCTTTTTCCTTTTAAGCCCACAACTCCATGGCA
759901 TTTTTTTTCC
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
61 23 0.43
62 30 0.57
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.35
Consensus pattern (62 bp):
CCTTTTAAGCCCACAACTACGTAGCACTTCTTTTTCCTTTTAAGCCCACAACTCCATGGCAC
Found at i:759847 original size:96 final size:96
Alignment explanation
Indices: 759746--760058 Score: 375
Period size: 96 Copynumber: 3.3 Consensus size: 96
759736 CTCTTTTTTT
* *
759746 TTTTAAGCCCACAACTCCGTGGCACTTTTTTTTCCTTTTAAGCCCACAACTACGTAGCATTCTTT
1 TTTTAAGCCCACAACTCCGTGGCACTTTTTTTTCCTTTTAAGCCCACAACTCCGTGGCATTCTTT
*
759811 TTCCTTTTAAGTCCACAACTCCATGGCACCC
66 TTCCTTTTAAGTCCACAACTCTATGGCACCC
* * * *
759842 TTTTAAGCCCACTACTTCGTGGCACTTTTTTTTCCTTTTAAGCCCATAACTCCGTGGCATTTTTT
1 TTTTAAGCCCACAACTCCGTGGCACTTTTTTTTCCTTTTAAGCCCACAACTCCGTGGCATTCTTT
*
759907 TTCCTTTTAAGTCCACAACTCTGTGGCACCC
66 TTCCTTTTAAGTCCACAACTCTATGGCACCC
* * * * * *
759938 TTTTAAGTCCACAACTTCC-TGGCGC--CTTATTCCTTTTAAGTCCACAACTCCATGGCA-TCTT
1 TTTTAAGCCCACAAC-TCCGTGGCACTTTTTTTTCCTTTTAAGCCCACAACTCCGTGGCATTCTT
* * *
759999 TCTCCTTTTAAGCCCACAAGT-TAGTGGCACCC
65 TTTCCTTTTAAGTCCACAACTCTA-TGGCACCC
* *
760031 TTTTCAAAAGCCCACAAGTCGGTGGCAC
1 TTTT---AAGCCCACAACTCCGTGGCAC
760059 CCTTTTCAAA
Statistics
Matches: 185, Mismatches: 26, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
92 1 0.01
93 33 0.18
94 27 0.15
95 2 0.01
96 120 0.65
97 2 0.01
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.35
Consensus pattern (96 bp):
TTTTAAGCCCACAACTCCGTGGCACTTTTTTTTCCTTTTAAGCCCACAACTCCGTGGCATTCTTT
TTCCTTTTAAGTCCACAACTCTATGGCACCC
Found at i:759941 original size:130 final size:130
Alignment explanation
Indices: 759624--759934 Score: 461
Period size: 130 Copynumber: 2.4 Consensus size: 130
759614 TCTTCAAAGT
*
759624 CCATAACTTCGTGGCACTTTTTTTTTCCTTTTAAGCCCACAACT-TCGTGGCATTC-TTTTCCTT
1 CCATAACTCCGTGGCAC-TTTTTTTTCCTTTTAAGCCCACAACTCT-GTGGCATTCTTTTTCCTT
*
759687 TTAAGTCCACAACTACGTGGCAACCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTTTTTTTAA
64 TTAAGTCCACAACTACATGGCAACCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTTTTTTTAA
759752 GC
129 GC
* *
759754 CCACAACTCCGTGGCACTTTTTTTTCCTTTTAAGCCCACAACTAC-GTAGCATTCTTTTTCCTTT
1 CCATAACTCCGTGGCACTTTTTTTTCCTTTTAAGCCCACAACT-CTGTGGCATTCTTTTTCCTTT
* * * *
759818 TAAGTCCACAACTCCATGGCACCCTTTTAAGCCCACTACTTCGTGGCACT-TTTTTTTCCTTTTA
65 TAAGTCCACAACTACATGGCAACCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTTT--TTTTA
759882 AGC
128 AGC
*
759885 CCATAACTCCGTGGCA-TTTTTTTTCCTTTTAAGTCCACAACTCTGTGGCA
1 CCATAACTCCGTGGCACTTTTTTTTCCTTTTAAGCCCACAACTCTGTGGCA
759935 CCCTTTTAAG
Statistics
Matches: 164, Mismatches: 11, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
129 42 0.26
130 99 0.60
131 23 0.14
ACGTcount: A:0.20, C:0.30, G:0.12, T:0.39
Consensus pattern (130 bp):
CCATAACTCCGTGGCACTTTTTTTTCCTTTTAAGCCCACAACTCTGTGGCATTCTTTTTCCTTTT
AAGTCCACAACTACATGGCAACCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTTTTTTTAAGC
Found at i:760079 original size:29 final size:30
Alignment explanation
Indices: 760008--760132 Score: 136
Period size: 29 Copynumber: 4.3 Consensus size: 30
759998 TTCTCCTTTT
*
760008 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
*
760038 AAGCCCACAAGTCGGTGGCACCCTTTTC-A
1 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
*
760067 AAGCCC-CTAAGTCAGTGGCAACC-TTT-AA
1 AAGCCCAC-AAGTCAGTGGCACCCTTTTCAA
* **
760095 AAGCACACAAGTTGGT-GCAACCC-TTTCAA
1 AAGCCCACAAGTCAGTGGC-ACCCTTTTCAA
760124 AAGCCCACA
1 AAGCCCACA
760133 CAAGTTGGTG
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
27 2 0.02
28 22 0.27
29 31 0.38
30 26 0.32
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (30 bp):
AAGCCCACAAGTCAGTGGCACCCTTTTCAA
Found at i:760105 original size:57 final size:59
Alignment explanation
Indices: 760008--760132 Score: 152
Period size: 57 Copynumber: 2.2 Consensus size: 59
759998 TTCTCCTTTT
* * *
760008 AAGCCCACAAGTTAGTGGCACCCTTTTCAAAAGCCCACAAGTCGGTGGC-ACCCTTTTC-A
1 AAGCCCACAAGTCAGTGGCAACCTTTTCAAAAGCACACAAGTCGGT-GCAACCC-TTTCAA
*
760067 AAGCCC-CTAAGTCAGTGGCAACC-TTT-AAAAGCACACAAGTTGGTGCAACCCTTTCAA
1 AAGCCCAC-AAGTCAGTGGCAACCTTTTCAAAAGCACACAAGTCGGTGCAACCCTTTCAA
760124 AAGCCCACA
1 AAGCCCACA
760133 CAAGTTGGTG
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
56 6 0.10
57 28 0.48
58 5 0.09
59 19 0.33
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (59 bp):
AAGCCCACAAGTCAGTGGCAACCTTTTCAAAAGCACACAAGTCGGTGCAACCCTTTCAA
Found at i:760268 original size:39 final size:39
Alignment explanation
Indices: 760213--760445 Score: 180
Period size: 39 Copynumber: 5.5 Consensus size: 39
760203 AAGACTAATG
* *
760213 TCGCTGGCCTTTAATCAGCACATTAGCACAAGTCCAATA
1 TCGCTGGCCTTGAATCAGCACATTGGCACAAGTCCAATA
* * *
760252 TCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCA------C---AAGTCCAATA
* * *
760300 TCACTGGTCTTGAATCAGCACATTGGCACAAGCCCAATA
1 TCGCTGGCCTTGAATCAGCACATTGGCACAAGTCCAATA
* * *
760339 TCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCTTTAA-TACCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCA------C---AAGT-CCAATA
*
760387 TCGTTGGCCTTGAATCAGCACATTGGCACAAGTCCAATA
1 TCGCTGGCCTTGAATCAGCACATTGGCACAAGTCCAATA
760426 TCGCTGGCCTTGAATCAGCA
1 TCGCTGGCCTTGAATCAGCA
760446 TATTAGCGCC
Statistics
Matches: 153, Mismatches: 21, Indels: 40
0.71 0.10 0.19
Matches are distributed among these distances:
39 83 0.54
40 1 0.01
42 2 0.01
45 2 0.01
48 65 0.42
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (39 bp):
TCGCTGGCCTTGAATCAGCACATTGGCACAAGTCCAATA
Found at i:760301 original size:87 final size:87
Alignment explanation
Indices: 760155--760606 Score: 553
Period size: 87 Copynumber: 5.0 Consensus size: 87
760145 GTCTTCTTCT
* * *
760155 AAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTGTCTCTAAGACTAATGTCGCTGG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGG
*
760220 CCTTTAATCAGCACATTAGCAC
66 CCTTGAATCAGCACATTAGCAC
*
760242 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCACTGG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGG
* *
760307 TCTTGAATCAGCACATTGGCAC
66 CCTTGAATCAGCACATTAGCAC
* * * *
760329 AAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCTTTAATACCAATGTCGTTGG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGG
*
760394 CCTTGAATCAGCACATTGGCAC
66 CCTTGAATCAGCACATTAGCAC
* * *
760416 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCGCCTTTGTCATCTTTAAGTCCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTG---TCTTTAAGACCAATGTCG
* *
760481 CTGGCCTTGAATCAGTACATTGGCACCTTCATC
62 CTGGCCTTGAATCAGCACATT---A---GCA-C
* * **
760514 TTTAAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCGCTTTCATCATCTTTAAGACCAATG
1 ---AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC---C-TTGTCTTTAAGACCAATG
760579 TCGCTGGCCTTGAATCAGCACATTAGCA
59 TCGCTGGCCTTGAATCAGCACATTAGCA
760607 TCTTCAACTT
Statistics
Matches: 317, Mismatches: 31, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
87 197 0.62
88 3 0.01
91 35 0.11
95 2 0.01
97 2 0.01
98 2 0.01
101 74 0.23
104 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (87 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGG
CCTTGAATCAGCACATTAGCAC
Found at i:760531 original size:49 final size:49
Alignment explanation
Indices: 760416--760751 Score: 289
Period size: 52 Copynumber: 6.7 Consensus size: 49
760406 ACATTGGCAC
* * * *
760416 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCGCCTTTGTCATCTTT
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTT
*
760468 AAGTCCAATGTCGCTGGCCTTGAATCAGTACATTGGCACCTTCATCTTT
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
* * * * *
760517 AAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCGCTTTCATCATCTTT
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC---CTTCATCTTT
* * * *
760569 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTAGCATCTTCAACTTT
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
** * * * * * * * *
760618 AAGTCTGATATCGTTGACCTTGAATTAGCATATTGGCATCTTTAATATTCCT
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTCATCTT--T
* ** * *
760670 AAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTGGCA--TTCTTCTTC
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
* * *
760717 AAGTCTAATGTTGCTGGCCATGAATCAGCACATTG
1 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
760752 TCATTCTTCA
Statistics
Matches: 224, Mismatches: 54, Indels: 17
0.76 0.18 0.06
Matches are distributed among these distances:
47 29 0.13
49 84 0.38
50 6 0.03
52 105 0.47
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (49 bp):
AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTT
Found at i:760591 original size:101 final size:99
Alignment explanation
Indices: 760416--760751 Score: 372
Period size: 101 Copynumber: 3.4 Consensus size: 99
760406 ACATTGGCAC
* * *
760416 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCGCCTTTGTCATCTTTAAGTCCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCG-CTTTATCATCTTTAAGACCAATGTCG
*
760481 CTGGCCTTGAATCAGTACATTGGCACCTTCATCTTT
65 CTGGCCTTGAATCAGCACATTGGCA-CTTCATCTTT
*
760517 AAGTCCAATATCGCTGGCTTTGAATCAGCATATTGGCGCTTTCATCATCTTTAAGACCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCTTT-ATCATCTTTAAGACCAATGTCG
* *
760582 CTGGCCTTGAATCAGCACATTAGCATCTTCAACTTT
65 CTGGCCTTGAATCAGCACATTGGCA-CTTCATCTTT
** * * * * * *
760618 AAGTCTGATATCGTTGACCTTGAATTAGCATATTGGCATCTTTAAT-AT-TCCTAAGCCCAATGT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-GCTTT-ATCATCT-TTAAGACCAATGT
** * *
760681 CGCTGGCCTTGTCTCAGCACATTGGCA-TTCTTCTTC
63 CGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTT
* * * * *
760717 AAGTCTAATGTTGCTGGCCATGAATCAGCACATTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
760752 TCATTCTTCA
Statistics
Matches: 200, Mismatches: 32, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
99 33 0.17
100 5 0.03
101 156 0.78
102 6 0.03
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (99 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCTTTATCATCTTTAAGACCAATGTCGC
TGGCCTTGAATCAGCACATTGGCACTTCATCTTT
Found at i:761338 original size:18 final size:18
Alignment explanation
Indices: 761306--761352 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
761296 GGAGACGAAT
*
761306 TCATGAC-TATTAGATTA
1 TCATGACTTTTTAGATTA
761323 TCATGACTTTTTAGATTA
1 TCATGACTTTTTAGATTA
761341 TCATGACTTTTT
1 TCATGACTTTTT
761353 GTTAAGCTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.49
Consensus pattern (18 bp):
TCATGACTTTTTAGATTA
Found at i:761617 original size:20 final size:20
Alignment explanation
Indices: 761592--761693 Score: 98
Period size: 20 Copynumber: 4.8 Consensus size: 20
761582 ACTGCCAAGG
761592 CAATGTATCGATACATTATT
1 CAATGTATCGATACATTATT
761612 CAATGTATCGATACATTGTATCGAT
1 CAATGTATCGATACA-T-TAT---T
* *
761637 ACATTGTATCGATATATTGA-T
1 -CAATGTATCGATACATT-ATT
**
761658 CTTTGTATCGATACATTATT
1 CAATGTATCGATACATTATT
761678 CAATGTATCGATACAT
1 CAATGTATCGATACAT
761694 GCAGGCAAGT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
19 1 0.01
20 45 0.66
21 2 0.03
22 3 0.04
24 1 0.01
25 3 0.04
26 13 0.19
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
CAATGTATCGATACATTATT
Found at i:761633 original size:13 final size:13
Alignment explanation
Indices: 761615--761655 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
761605 CATTATTCAA
761615 TGTATCGATACAT
1 TGTATCGATACAT
761628 TGTATCGATACAT
1 TGTATCGATACAT
*
761641 TGTATCGATATAT
1 TGTATCGATACAT
761654 TG
1 TG
761656 ATCTTTGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:766607 original size:51 final size:51
Alignment explanation
Indices: 766531--766648 Score: 184
Period size: 51 Copynumber: 2.3 Consensus size: 51
766521 AATAGTCAGC
* *
766531 ATGTATCGATACATTTAGGTCAAAACCCAGAATGTATCGATACAATGAATA
1 ATGTATCGATACATTTAGGTCAAAACCCAAAATGTATCGATACAATGAAAA
*
766582 ATGTATCGATACATTT-GGTTCAAAACCCAAAATGTATCGATGCAATGAAAA
1 ATGTATCGATACATTTAGG-TCAAAACCCAAAATGTATCGATACAATGAAAA
*
766633 ATGTATTGATACATTT
1 ATGTATCGATACATTT
766649 TCTTTTCAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 2 0.03
51 60 0.97
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (51 bp):
ATGTATCGATACATTTAGGTCAAAACCCAAAATGTATCGATACAATGAAAA
Found at i:767068 original size:18 final size:18
Alignment explanation
Indices: 767038--767084 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
767028 GGGGACAAAT
767038 TCATGAC-TTTTAGATTA
1 TCATGACTTTTTAGATTA
767055 TCATGACTTTTTAGATTA
1 TCATGACTTTTTAGATTA
767073 TCATGACTTTTT
1 TCATGACTTTTT
767085 GTTAAGCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 7 0.24
18 22 0.76
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.51
Consensus pattern (18 bp):
TCATGACTTTTTAGATTA
Found at i:767350 original size:20 final size:20
Alignment explanation
Indices: 767325--767379 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
767315 CTGCCAAGGA
767325 AATGTATCGATACATT-ATTC
1 AATGTATCGATACATTGA-TC
767345 AATGTATCGATACATTGATC
1 AATGTATCGATACATTGATC
**
767365 TTTGTATCGATACAT
1 AATGTATCGATACAT
767380 CTAGGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTGATC
Found at i:781989 original size:22 final size:22
Alignment explanation
Indices: 781946--781990 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
781936 CCAAAAGTCT
**
781946 ATTAAAAAAATAAACTTAAGGA
1 ATTAAAAAAATAAAAATAAGGA
781968 ATTAAAAGAAATAAAAAT-AGGA
1 ATTAAAA-AAATAAAAATAAGGA
781990 A
1 A
781991 CTTTAATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.20
Consensus pattern (22 bp):
ATTAAAAAAATAAAAATAAGGA
Done.