Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002352.1 Hibiscus syriacus cultivar Beakdansim tig00004797_pilon, whole genome shotgun sequence
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: 2012169
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:481387 original size:19 final size:19
Alignment explanation
Indices: 481363--481404 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
481353 ACGAGATAAT
*
481363 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
481382 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
481401 CGCA
1 CGCA
481405 TTGCAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:481422 original size:19 final size:19
Alignment explanation
Indices: 481400--481584 Score: 147
Period size: 19 Copynumber: 10.1 Consensus size: 19
481390 GAAACAAAAA
* * *
481400 TCGCATTGCAATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
481419 TCGCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
481438 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
481457 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
481477 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
481493 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
481510 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
481524 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
481543 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
481563 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
481583 TC
1 TC
481585 AACCAAAAGA
Statistics
Matches: 134, Mismatches: 19, Indels: 26
0.75 0.11 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 56 0.42
20 49 0.37
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:481461 original size:38 final size:39
Alignment explanation
Indices: 481400--481489 Score: 146
Period size: 39 Copynumber: 2.3 Consensus size: 39
481390 GAAACAAAAA
* *
481400 TCGCATTGCAATTTTTATTTCGC-GTTACGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGCGGTTACGATTTTCATT
*
481438 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGCGGTTACGATTTTCATT
481477 TCGCGTTGCGATT
1 TCGCGTTGCGATT
481490 GTCTGGTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.48
Consensus pattern (39 bp):
TCGCGTTGCGATTTTTATTTCGCGGTTACGATTTTCATT
Found at i:481500 original size:39 final size:39
Alignment explanation
Indices: 481419--481500 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
481409 AATTTTTATT
* **
481419 TCGC-GTTACGATTTTCATTTCGCGTTGCGATTTTTATT
1 TCGCGGTTACGATTTTCATTTCGCGTTGCGATTTCTAGG
*
481457 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTGTCT-GG
1 TCGCGGTTACGATTTTCATTTCGCGTTGCGATT-TCTAGG
481496 TCGCG
1 TCGCG
481501 ATAGTCATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 4 0.11
39 32 0.84
40 2 0.05
ACGTcount: A:0.10, C:0.21, G:0.26, T:0.44
Consensus pattern (39 bp):
TCGCGGTTACGATTTTCATTTCGCGTTGCGATTTCTAGG
Found at i:481509 original size:33 final size:33
Alignment explanation
Indices: 481472--481559 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
481462 GTTGCGATTT
* *
481472 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
481505 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
481538 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
481560 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:481561 original size:20 final size:20
Alignment explanation
Indices: 481527--481584 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
481517 GCGATTCTCT
**
481527 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
481547 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
481567 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
481585 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:483643 original size:42 final size:42
Alignment explanation
Indices: 483583--483705 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
483573 GCCCGAGTCG
* * *
483583 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
483625 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
483667 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
483706 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:483663 original size:21 final size:21
Alignment explanation
Indices: 483639--483705 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
483629 TCATTCCTCG
483639 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
483660 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
483681 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
483702 AGAG
1 AGAG
483706 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:485084 original size:14 final size:14
Alignment explanation
Indices: 485065--485100 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
485055 ATTGTTTAAT
485065 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
* *
485079 TGATTTGTAAATGT
1 TGATTTGTAAAAGG
485093 TGATTTGT
1 TGATTTGT
485101 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:485309 original size:19 final size:19
Alignment explanation
Indices: 485285--485388 Score: 66
Period size: 19 Copynumber: 6.0 Consensus size: 19
485275 TAAATTCACG
485285 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
**
485304 TTGCGA--TTC-CCTCG--
1 TTGCGATTTTCATTTCGCA
485318 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
485337 TTGCGA-----AATTAGCG
1 TTGCGATTTTCATTTCGCA
* * *
485351 TTGCGATTTTCATCTCTCG
1 TTGCGATTTTCATTTCGCA
485370 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
485389 CTGTGATAGT
Statistics
Matches: 61, Mismatches: 14, Indels: 20
0.64 0.15 0.21
Matches are distributed among these distances:
14 17 0.28
16 6 0.10
17 6 0.10
19 32 0.52
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:485353 original size:33 final size:32
Alignment explanation
Indices: 485278--485377 Score: 114
Period size: 33 Copynumber: 3.1 Consensus size: 32
485268 GCAAAATTAA
485278 ATTCA-CGTTGCGATTTTCATTTCGCATTGCG
1 ATTCAGCGTTGCGATTTTCATTTCGCATTGCG
**
485309 ATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
1 ATT-CAGCGTTGCGATTTTCATTTCGCATTGCG
* * *
485342 AAATT-AGCGTTGCGATTTTCATCTCTCGTTGCG
1 --ATTCAGCGTTGCGATTTTCATTTCGCATTGCG
485375 ATT
1 ATT
485378 TTCATTTCGC
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 6 0.10
32 1 0.02
33 49 0.83
35 3 0.05
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (32 bp):
ATTCAGCGTTGCGATTTTCATTTCGCATTGCG
Found at i:487705 original size:12 final size:12
Alignment explanation
Indices: 487688--487712 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
487678 TCTTCGGGGA
487688 CTTTTTCTTCTT
1 CTTTTTCTTCTT
487700 CTTTTTCTTCTT
1 CTTTTTCTTCTT
487712 C
1 C
487713 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:487921 original size:24 final size:24
Alignment explanation
Indices: 487887--487940 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
487877 CTGAAACATC
* *
487887 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
487911 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
487935 ATCAAA
1 ATCAAA
487941 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:489002 original size:20 final size:20
Alignment explanation
Indices: 488977--489014 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
488967 ATTCATTTGA
*
488977 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
488997 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
489015 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:489033 original size:19 final size:19
Alignment explanation
Indices: 489009--489062 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
488999 ATCGCAACGA
489009 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
489028 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
489047 GAAAATCGCATTGCGA
1 GAAAATCGCAATGCGA
489063 TTTTCTCGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.17
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:489076 original size:14 final size:14
Alignment explanation
Indices: 489057--489110 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
489047 GAAAATCGCA
489057 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
489071 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
489088 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
489104 TTGCGAT
1 TTGCGAT
489111 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:489089 original size:33 final size:33
Alignment explanation
Indices: 489052--489129 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
489042 GAAATGAAAA
***
489052 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
489085 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
489118 TCGCGTTGCGAT
1 TCGCATTGCGAT
489130 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:489236 original size:14 final size:14
Alignment explanation
Indices: 489217--489253 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
489207 CATCAATTAA
489217 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
489231 ACAAATCATCTTTT
1 ACAAATCAACATTT
489245 ACAAATCAA
1 ACAAATCAA
489254 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:491143 original size:19 final size:19
Alignment explanation
Indices: 491121--491187 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
491111 CGAAACTTAA
491121 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
* *
491140 ATCGCAACACGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
491160 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
491179 ATCGCAACG
1 ATCGCAACG
491188 ATAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:491156 original size:20 final size:19
Alignment explanation
Indices: 491103--491186 Score: 71
Period size: 19 Copynumber: 4.4 Consensus size: 19
491093 TAGTTTACTT
* *
491103 TCGCAACACGAAACTTA-AA
1 TCGCAACACGAAA-TGACTA
*
491122 TCGCAACGCGAAATGACTA
1 TCGCAACACGAAATGACTA
*
491141 TCGCAACACGGAAATGGCTA
1 TCGCAACAC-GAAATGACTA
** **
491161 TCGCAATGCGAAATGAAAA
1 TCGCAACACGAAATGACTA
491180 TCGCAAC
1 TCGCAAC
491187 GATAAAATCG
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
18 2 0.04
19 34 0.65
20 16 0.31
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.15
Consensus pattern (19 bp):
TCGCAACACGAAATGACTA
Found at i:491195 original size:14 final size:14
Alignment explanation
Indices: 491176--491233 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
491166 ATGCGAAATG
491176 AAAATCGCAACGAT
1 AAAATCGCAACGAT
491190 AAAATCGCAACGCGAAAT
1 AAAATCGCAA--CG--AT
* *
491208 GAAATCGCAACGAC
1 AAAATCGCAACGAT
491222 AAAATCGCAACG
1 AAAATCGCAACG
491234 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:491218 original size:32 final size:33
Alignment explanation
Indices: 491160--491238 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
491150 GGAAATGGCT
* *
491160 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
491193 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
491225 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
491239 CACAAATTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:491289 original size:14 final size:14
Alignment explanation
Indices: 491267--491324 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
491257 TTTCATTTCG
491267 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
491281 CGTTACGATTTCATTT
1 CGTTGCGATTT--TGT
491297 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
491313 CGTTGCGATTTT
1 CGTTGCGATTTT
491325 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:491331 original size:33 final size:33
Alignment explanation
Indices: 491250--491340 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
491240 ACAAATTGCA
*
491250 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
491283 TTACGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
491315 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
491341 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:491359 original size:20 final size:21
Alignment explanation
Indices: 491334--491380 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
491324 TCATTTCGCA
491334 TTGCGATAGCCAT-TTCCGTG
1 TTGCGATAGCCATATTCCGTG
* *
491354 TTGCGATAGTCATATTTCGTG
1 TTGCGATAGCCATATTCCGTG
491375 TTGCGA
1 TTGCGA
491381 AAGTAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (21 bp):
TTGCGATAGCCATATTCCGTG
Found at i:491888 original size:18 final size:18
Alignment explanation
Indices: 491862--491906 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
491852 GTCGATCAAA
*
491862 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
491880 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
491898 TGATGGCTC
1 TGATGGCTC
491907 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:493251 original size:20 final size:20
Alignment explanation
Indices: 493226--493268 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
493216 AATAATTTCT
493226 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
493246 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
493266 GAA
1 GAA
493269 TTCGACTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.56, C:0.19, G:0.16, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:493859 original size:41 final size:41
Alignment explanation
Indices: 493736--493873 Score: 134
Period size: 41 Copynumber: 3.4 Consensus size: 41
493726 CGCTTTGAAA
* * * * *
493736 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTTTATTATCGCATTGCGAAAGTAAGT
*** * * *
493777 ATCGCATTGCGA-AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTTTATTATCGCATTGCGAAAGTAAGT
* * * *
493817 ATCTCGTTGCGATTTTTTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTTTATTATCGCATTGCGAAAGTAAGT
493858 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
493874 CCCAATTCGC
Statistics
Matches: 77, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 31 0.40
41 46 0.60
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTTTTATTATCGCATTGCGAAAGTAAGT
Found at i:493862 original size:20 final size:20
Alignment explanation
Indices: 493736--493870 Score: 110
Period size: 20 Copynumber: 6.7 Consensus size: 20
493726 CGCTTTGAAA
*
493736 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
493757 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
*
493777 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
493797 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
493817 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
493838 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
493858 ATCGCATTGCGAT
1 ATCGCATTGCGAT
493871 TTTCCCAATT
Statistics
Matches: 92, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
19 2 0.02
20 66 0.72
21 24 0.26
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:493891 original size:21 final size:21
Alignment explanation
Indices: 493859--493934 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
493849 ATAGTCAGTA
*
493859 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* * **
493880 TCGCGTTTCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
493900 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
493921 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
493935 ACTTATTCGC
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:493903 original size:20 final size:20
Alignment explanation
Indices: 493878--493951 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
493868 GATTTTCCCA
*
493878 ATTCGCGTTTCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
493898 ATTCGCATTGCGATTTTCCCA
1 ATTCGCGTTGCGA-TTTACTT
493919 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
*
493939 ATTCGCATTGCGA
1 ATTCGCGTTGCGA
493952 ATTGGGAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:493904 original size:41 final size:41
Alignment explanation
Indices: 493859--493951 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
493849 ATAGTCAGTA
*
493859 TCGCATTGCGATTTTCCCAATTCGCGTTTCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
493900 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
493941 TCGCATTGCGA
1 TCGCATTGCGA
493952 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:504832 original size:19 final size:19
Alignment explanation
Indices: 504789--504964 Score: 63
Period size: 20 Copynumber: 8.9 Consensus size: 19
504779 AAATGACCAA
**
504789 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACGCGAAAT
*
504808 CAAATTCGCAACGTGAAAT
1 CAAATTCGCAACGCGAAAT
* * **
504827 CCAATTTCGCAACAC-ATGTT
1 -CAAATTCGCAACGCGA-AAT
* *
504847 CCAAAATCGCAACGTGAATAGT
1 -CAAATTCGCAACGCGAA-A-T
* **
504869 TAAA-TCGCAACGATAATAT
1 CAAATTCGCAACGCGAA-AT
*
504888 GTAAA-TCGCAACGCGAATAT
1 -CAAATTCGCAACGCGAA-AT
** *
504908 -GTATATCGCAACGCGTAAGT
1 CAAAT-TCGCAACGCG-AAAT
* *
504928 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACGC-GAAAT
504948 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
504965 TTTTATTTTC
Statistics
Matches: 120, Mismatches: 26, Indels: 22
0.71 0.15 0.13
Matches are distributed among these distances:
18 1 0.01
19 21 0.17
20 88 0.73
21 9 0.08
22 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (19 bp):
CAAATTCGCAACGCGAAAT
Found at i:504921 original size:20 final size:20
Alignment explanation
Indices: 504850--504922 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
504840 ACATGTTCCA
*
504850 AAATCGCAACGTGAATA-GTT
1 AAATCGCAACGCGAATATG-T
**
504870 AAATCGCAACGATAATATGT
1 AAATCGCAACGCGAATATGT
504890 AAATCGCAACGCGAATATGT
1 AAATCGCAACGCGAATATGT
*
504910 ATATCGCAACGCG
1 AAATCGCAACGCG
504923 TAAGTCAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 46 0.98
21 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Found at i:504936 original size:20 final size:19
Alignment explanation
Indices: 504913--504964 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
504903 AATATGTATA
504913 TCGCAACGCGTAAGTCAAAT
1 TCGCAACGCG-AAGTCAAAT
*
504933 TCGCAACACAGAAGTCAAAT
1 TCGCAACGC-GAAGTCAAAT
504953 TCGCAACGCGAA
1 TCGCAACGCGAA
504965 TTTTATTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 25 0.86
21 1 0.03
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAGTCAAAT
Found at i:505112 original size:22 final size:22
Alignment explanation
Indices: 505087--505137 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
505077 TCACTCTCTA
* *
505087 CGGCGACATCCGTCCCCATCTC
1 CGGCGACATCCGTCCACATATC
*
505109 CGGCGAAATCCGTCCACATATC
1 CGGCGACATCCGTCCACATATC
505131 CGGCGAC
1 CGGCGAC
505138 CCCGTCTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.43, G:0.22, T:0.16
Consensus pattern (22 bp):
CGGCGACATCCGTCCACATATC
Found at i:505501 original size:20 final size:20
Alignment explanation
Indices: 505478--505521 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
505468 CTTAAATTCG
*
505478 CAACACGAAAATGAAAATCA
1 CAACACAAAAATGAAAATCA
* *
505498 CAACTCAAAAATGAAAATCG
1 CAACACAAAAATGAAAATCA
505518 CAAC
1 CAAC
505522 GTTGCGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.57, C:0.23, G:0.09, T:0.11
Consensus pattern (20 bp):
CAACACAAAAATGAAAATCA
Found at i:507122 original size:21 final size:21
Alignment explanation
Indices: 507096--507148 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
507086 CTCGACATCC
507096 AGAGCCATCACCTCCACAACG
1 AGAGCCATCACCTCCACAACG
507117 AGAGCCATCACCTCCACAACG
1 AGAGCCATCACCTCCACAACG
*
507138 AGAGTCATCAC
1 AGAGCCATCAC
507149 TATTCCATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.40, G:0.15, T:0.11
Consensus pattern (21 bp):
AGAGCCATCACCTCCACAACG
Found at i:507751 original size:21 final size:21
Alignment explanation
Indices: 507725--507797 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
507715 CACCTGTCAT
507725 CGTTCAAGAGGCCCCTTCCAC
1 CGTTCAAGAGGCCCCTTCCAC
* *
507746 CGTTCAAGAGGCTCCTGT-CAT
1 CGTTCAAGAGGCCCCT-TCCAC
* *
507767 CGTTCAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTTCCAC
*
507788 CATTCAAGAG
1 CGTTCAAGAG
507798 CTCGATTCAC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 42 0.98
22 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.21, T:0.22
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTTCCAC
Found at i:507764 original size:42 final size:42
Alignment explanation
Indices: 507717--507797 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
507707 GCCCGATTCA
* *
507717 CCTGTCATCGTTCAAGAGGCCCCTTCCACCGTTCAAGAGGCT
1 CCTGTCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCT
*
507759 CCTGTCATCGTTCAAGAGGTCCCTCCCACCATTCAAGAG
1 CCTGTCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAG
507798 CTCGATTCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.23
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCT
Found at i:509226 original size:20 final size:20
Alignment explanation
Indices: 509201--509250 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
509191 AATATGCATT
509201 ATGTTGAAGGCAAAAAAGAC
1 ATGTTGAAGGCAAAAAAGAC
509221 ATGTTGAAGGCAAAAAAGAC
1 ATGTTGAAGGCAAAAAAGAC
*
509241 CTGTTGAAGG
1 ATGTTGAAGG
509251 TACACTTTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.44, C:0.10, G:0.28, T:0.18
Consensus pattern (20 bp):
ATGTTGAAGGCAAAAAAGAC
Found at i:509364 original size:20 final size:20
Alignment explanation
Indices: 509277--509365 Score: 106
Period size: 20 Copynumber: 4.5 Consensus size: 20
509267 AAAAGTCAAA
509277 TTCGCGTTGCGATTTTGACT
1 TTCGCGTTGCGATTTTGACT
* * *
509297 TTTGCGTTACGATTTTGATT
1 TTCGCGTTGCGATTTTGACT
* *
509317 TTTGCGTTGCGATTTTAACT
1 TTCGCGTTGCGATTTTGACT
* *
509337 TTCACGTTGCAATTTTGACT
1 TTCGCGTTGCGATTTTGACT
*
509357 TCCGCGTTG
1 TTCGCGTTG
509366 TGAATTCAAG
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.47
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTGACT
Found at i:509587 original size:40 final size:40
Alignment explanation
Indices: 509532--509683 Score: 187
Period size: 40 Copynumber: 3.8 Consensus size: 40
509522 AAATTCGCAA
* * *
509532 TTCGCGTTGCGATTTTTACTTTGGCGTTGCGATTTTTATT
1 TTCGCGTTGCGATTTTGACTTTGGCGTTGCGATTTTGAAT
** *
509572 TTCGCGTTTTGATTTTGACTTTGGCATTGCGATTTTGAAT
1 TTCGCGTTGCGATTTTGACTTTGGCGTTGCGATTTTGAAT
* * *
509612 TTCGCGTTGCGATTTTGACTTTGGTGTTGCGACTTTGACT
1 TTCGCGTTGCGATTTTGACTTTGGCGTTGCGATTTTGAAT
* * * *
509652 TTCGCATTGCGAATTTGATTTTCGCGTTGCGA
1 TTCGCGTTGCGATTTTGACTTTGGCGTTGCGA
509684 AAGTGTACCT
Statistics
Matches: 95, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 95 1.00
ACGTcount: A:0.12, C:0.16, G:0.24, T:0.47
Consensus pattern (40 bp):
TTCGCGTTGCGATTTTGACTTTGGCGTTGCGATTTTGAAT
Found at i:509684 original size:20 final size:20
Alignment explanation
Indices: 509532--509683 Score: 169
Period size: 20 Copynumber: 7.6 Consensus size: 20
509522 AAATTCGCAA
*
509532 TTCGCGTTGCGATTTTTACT
1 TTCGCGTTGCGATTTTGACT
* * *
509552 TTGGCGTTGCGATTTTTATT
1 TTCGCGTTGCGATTTTGACT
**
509572 TTCGCGTTTTGATTTTGACT
1 TTCGCGTTGCGATTTTGACT
* * *
509592 TTGGCATTGCGATTTTGAAT
1 TTCGCGTTGCGATTTTGACT
509612 TTCGCGTTGCGATTTTGACT
1 TTCGCGTTGCGATTTTGACT
* * *
509632 TTGGTGTTGCGACTTTGACT
1 TTCGCGTTGCGATTTTGACT
* * *
509652 TTCGCATTGCGAATTTGATT
1 TTCGCGTTGCGATTTTGACT
509672 TTCGCGTTGCGA
1 TTCGCGTTGCGA
509684 AAGTGTACCT
Statistics
Matches: 108, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 108 1.00
ACGTcount: A:0.12, C:0.16, G:0.24, T:0.47
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTGACT
Found at i:513194 original size:27 final size:27
Alignment explanation
Indices: 513163--513225 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
513153 TGGACATGGA
*
513163 ATGAGTTGTGATTTAGGGATTTAGGTT
1 ATGAGTTGCGATTTAGGGATTTAGGTT
*
513190 ATGAGTTACGATTTAGGGATTTAGGTT
1 ATGAGTTGCGATTTAGGGATTTAGGTT
513217 ATGAGTTGC
1 ATGAGTTGC
513226 TGCTGCTGCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.24, C:0.03, G:0.32, T:0.41
Consensus pattern (27 bp):
ATGAGTTGCGATTTAGGGATTTAGGTT
Found at i:513286 original size:20 final size:20
Alignment explanation
Indices: 513261--513307 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
513251 AAACAATTGT
*
513261 GTTGCGAATTCAAAAATCGA
1 GTTGCGAAATCAAAAATCGA
* *
513281 GTTGCGAAATCAAAATTCGT
1 GTTGCGAAATCAAAAATCGA
513301 GTTGCGA
1 GTTGCGA
513308 TTTAGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (20 bp):
GTTGCGAAATCAAAAATCGA
Found at i:513437 original size:20 final size:20
Alignment explanation
Indices: 513381--513450 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
513371 TGACTTCTGT
* *
513381 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACATATTTGC
513401 GTTGCGATTTACATATTAT-C
1 GTTGCGATTTACATATT-TGC
513421 GTTGCGATTTA-ACTATTTGC
1 GTTGCGATTTACA-TATTTGC
*
513441 GTTGCAATTT
1 GTTGCGATTT
513451 TGAAACCTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
19 2 0.05
20 42 0.95
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.43
Consensus pattern (20 bp):
GTTGCGATTTACATATTTGC
Found at i:514092 original size:5 final size:5
Alignment explanation
Indices: 514083--514139 Score: 87
Period size: 5 Copynumber: 11.4 Consensus size: 5
514073 AAATCACAAA
* * *
514083 AGGGA AGGGA AGGGA AGGGG AGGGG AGGGG AGGGG AGGGG AGGGG AGGGG
1 AGGGG AGGGG AGGGG AGGGG AGGGG AGGGG AGGGG AGGGG AGGGG AGGGG
514133 AGGGG AG
1 AGGGG AG
514140 AGCGGGAGAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (5 bp):
AGGGG
Found at i:514952 original size:17 final size:17
Alignment explanation
Indices: 514930--514967 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
514920 TAACATAATA
514930 TAATTTTCTAT-TATCTT
1 TAATTTT-TATATATCTT
*
514947 TAATTTTTATATATTTT
1 TAATTTTTATATATCTT
514964 TAAT
1 TAAT
514968 AAAATTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (17 bp):
TAATTTTTATATATCTT
Found at i:514997 original size:2 final size:2
Alignment explanation
Indices: 514990--515014 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
514980 CAAATAACTT
514990 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
515015 GTTATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:515226 original size:46 final size:46
Alignment explanation
Indices: 515158--515253 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 46
515148 CACTATTTTA
* * *
515158 TTTTATTCACTTACACATGTGTAAATATGTGTTAAATGTTACATTT
1 TTTTATTCACTTACACATGTGTAAACATATGTTAAATGTCACATTT
** * *
515204 TTTTATTCGTTTACACCA-GTGTAAGCATATGTTAAGTGTCACATTT
1 TTTTATTCACTTACA-CATGTGTAAACATATGTTAAATGTCACATTT
515250 TTTT
1 TTTT
515254 GTAGTATAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 40 0.95
47 2 0.05
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (46 bp):
TTTTATTCACTTACACATGTGTAAACATATGTTAAATGTCACATTT
Found at i:517003 original size:31 final size:31
Alignment explanation
Indices: 516968--517135 Score: 176
Period size: 31 Copynumber: 5.4 Consensus size: 31
516958 TTAATAAACA
** * *
516968 TAAGTTTTGGTCACTTATTTTATTATTTGAT
1 TAAGTTTTGGTCACTTACATTATTGTTTTAT
** * *
516999 TAAGTTTTTATCAGTTACGTTATTGTTTTAT
1 TAAGTTTTGGTCACTTACATTATTGTTTTAT
* * *
517030 TGACTGTTGGTCACTTA-AGTTATTGTTTTAT
1 TAAGTTTTGGTCACTTACA-TTATTGTTTTAT
* *
517061 TAAATTTTGGTCACTTACATTATCGTTTTAT
1 TAAGTTTTGGTCACTTACATTATTGTTTTAT
* *
517092 TAAGTTTTGATCACTTACATTATCGTTTTAT
1 TAAGTTTTGGTCACTTACATTATTGTTTTAT
*
517123 TAAGTTTTAGTCA
1 TAAGTTTTGGTCA
517136 ATTGGACGTT
Statistics
Matches: 113, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
31 112 0.99
32 1 0.01
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.54
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACATTATTGTTTTAT
Found at i:518961 original size:29 final size:29
Alignment explanation
Indices: 518897--518995 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
518887 CATTTTACAG
* *
518897 AAATAGCACCCCTTTTTCGAATTAATTACCA
1 AAATAGCA-CCCATTTT-GAATTAATTCCCA
518928 AAATAGCACCCATTTTGAATTAATTCCCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
* * ** * *
518957 TAATAGCACCAAAATCGAATAAATTCCCA
1 AAATAGCACCCATTTTGAATTAATTCCCA
*
518986 GAATAGCACC
1 AAATAGCACC
518996 GGTCAACGGT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 44 0.75
30 7 0.12
31 8 0.14
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.26
Consensus pattern (29 bp):
AAATAGCACCCATTTTGAATTAATTCCCA
Found at i:519018 original size:17 final size:18
Alignment explanation
Indices: 518996--519034 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
518986 GAATAGCACC
*
518996 GGTCAAC-GGTTGGGTCG
1 GGTCAACGGGTCGGGTCG
519013 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
519031 GGTC
1 GGTC
519035 GTGACCGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.10, C:0.21, G:0.49, T:0.21
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:519068 original size:11 final size:10
Alignment explanation
Indices: 519038--519071 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
519028 TCGGGTCGTG
519038 ACCGGTC-AA
1 ACCGGTCAAA
519047 ACCGGTCAAA
1 ACCGGTCAAA
519057 ACCGGTTCAAA
1 ACCGG-TCAAA
519068 ACCG
1 ACCG
519072 ATTAAACCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 7 0.30
10 7 0.30
11 9 0.39
ACGTcount: A:0.35, C:0.32, G:0.21, T:0.12
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:526239 original size:29 final size:30
Alignment explanation
Indices: 526176--526244 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
526166 CATTTTACAG
*
526176 AAATAGCACCCCTTTTCGAATTAATTACCA
1 AAATAGCACCCATTTTCGAATTAATTACCA
*
526206 AAATAGCACCCATTTT-GAATTAATTCCCA
1 AAATAGCACCCATTTTCGAATTAATTACCA
*
526235 TAATAGCACC
1 AAATAGCACC
526245 AAAATCAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.38, C:0.26, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATAGCACCCATTTTCGAATTAATTACCA
Found at i:528075 original size:30 final size:31
Alignment explanation
Indices: 528032--528108 Score: 120
Period size: 30 Copynumber: 2.5 Consensus size: 31
528022 TTCAATGTCA
* *
528032 AAGTGACCAAAACTTAATAAAACGATAACTT
1 AAGTGACCAAAACTTAATAAAACAATAACGT
528063 AAGTGA-CAAAACTTAATAAAACAATAACGT
1 AAGTGACCAAAACTTAATAAAACAATAACGT
*
528093 AAGTGATCAAAACTTA
1 AAGTGACCAAAACTTA
528109 TGTTTTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 28 0.65
31 15 0.35
ACGTcount: A:0.53, C:0.14, G:0.10, T:0.22
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACGT
Found at i:533153 original size:17 final size:17
Alignment explanation
Indices: 533131--533164 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
533121 TAACACCAAA
* *
533131 AGATCATGATCAGATAT
1 AGATCAAGAGCAGATAT
533148 AGATCAAGAGCAGATAT
1 AGATCAAGAGCAGATAT
533165 TGTTGTCATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (17 bp):
AGATCAAGAGCAGATAT
Found at i:533689 original size:2 final size:2
Alignment explanation
Indices: 533682--533708 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
533672 TATCCATGTT
533682 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
533709 CCTGGATCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:534964 original size:22 final size:22
Alignment explanation
Indices: 534936--534980 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
534926 TCGCAAATGA
534936 TAGTCCAGAAAAATTAACACTT
1 TAGTCCAGAAAAATTAACACTT
534958 TAGTCCAGAAAAATTAACACTT
1 TAGTCCAGAAAAATTAACACTT
534980 T
1 T
534981 GGATTTAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (22 bp):
TAGTCCAGAAAAATTAACACTT
Found at i:544631 original size:30 final size:29
Alignment explanation
Indices: 544565--544639 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 29
544555 TCGTTTCCCG
* * * *
544565 ACCGATCTAATTTGGTGGCCACCGAATTA
1 ACCGAACTAATTCGGTGACCACCAAATTA
**
544594 ATTGAACTAATTCGGTGACCAACCAAATTA
1 ACCGAACTAATTCGGTGACC-ACCAAATTA
544624 ACCGAACTAATTCGGT
1 ACCGAACTAATTCGGT
544640 TCAGTCGTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 15 0.41
30 22 0.59
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (29 bp):
ACCGAACTAATTCGGTGACCACCAAATTA
Found at i:546371 original size:21 final size:23
Alignment explanation
Indices: 546344--546406 Score: 78
Period size: 21 Copynumber: 2.9 Consensus size: 23
546334 TGATGCATGG
546344 GGTATCGATACCTATAT-GAACA
1 GGTATCGATACCTATATGGAACA
**
546366 -GTATCGATACC-ATATGGAGGA
1 GGTATCGATACCTATATGGAACA
*
546387 GGTATCGATACCTATGTGGA
1 GGTATCGATACCTATATGGA
546407 GAGTAACAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 4 0.11
21 14 0.40
22 11 0.31
23 6 0.17
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (23 bp):
GGTATCGATACCTATATGGAACA
Found at i:547351 original size:18 final size:18
Alignment explanation
Indices: 547328--547362 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
547318 GTTCTTAAGG
*
547328 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
547346 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
547363 AATTCTACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:550605 original size:21 final size:23
Alignment explanation
Indices: 550554--550607 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
550544 TGTATGAACA
*
550554 GTATCGAT-TCTATATGGAGGAG
1 GTATCGATACCTATATGGAGGAG
* *
550576 GTATGGATACCTATATGGA-G-T
1 GTATCGATACCTATATGGAGGAG
550597 GTATCGATACC
1 GTATCGATACC
550608 AGGGATCATC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 10 0.37
22 8 0.30
23 9 0.33
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (23 bp):
GTATCGATACCTATATGGAGGAG
Found at i:551163 original size:12 final size:12
Alignment explanation
Indices: 551146--551174 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
551136 AAGTGATAAG
551146 AGATATGAGGAA
1 AGATATGAGGAA
551158 AGATATGAGGAA
1 AGATATGAGGAA
551170 A-ATAT
1 AGATAT
551175 ATATGTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.52, C:0.00, G:0.28, T:0.21
Consensus pattern (12 bp):
AGATATGAGGAA
Found at i:551539 original size:18 final size:18
Alignment explanation
Indices: 551516--551568 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
551506 ATTCTTAAGG
551516 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
** *
551534 AGTGGTTATTCGAGACAT
1 AGTGGTCCTTCGGGACAT
*
551552 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTCGGGACA
551569 AATTCTACGC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:552494 original size:20 final size:20
Alignment explanation
Indices: 552466--552504 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
552456 ATACTTGACC
* *
552466 CTAGGGTATTGATACTACTA
1 CTAGAGTATTAATACTACTA
552486 CTAGAGTATTAATACTACT
1 CTAGAGTATTAATACTACT
552505 CTCTTGGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (20 bp):
CTAGAGTATTAATACTACTA
Found at i:560344 original size:23 final size:23
Alignment explanation
Indices: 560318--560362 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
560308 CACCACAGCT
*
560318 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
560341 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
560363 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:560600 original size:149 final size:149
Alignment explanation
Indices: 560341--560644 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
560331 CGAAGTGCCC
* * *
560341 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAATGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
560406 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
560471 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
560490 CGTAGAATTGCACCGTAATGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAATGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
560555 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
*
560620 CATATGTCTCGAAGAACCG
131 CATATGTCCCGAAGAACCG
560639 CGTAGA
1 CGTAGA
560645 CCCTCGACTC
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAATGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:561649 original size:18 final size:18
Alignment explanation
Indices: 561628--561662 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
561618 TCCCCTCTAG
561628 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
561646 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
561663 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:562268 original size:21 final size:21
Alignment explanation
Indices: 562244--562288 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
562234 TGTTGTTCGT
* *
562244 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
562265 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
562286 TTG
1 TTG
562289 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:565374 original size:23 final size:23
Alignment explanation
Indices: 565348--565392 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
565338 CACCACAGCT
*
565348 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
565371 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
565393 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:565630 original size:149 final size:149
Alignment explanation
Indices: 565371--565674 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
565361 CGAAGTGCCC
* *
565371 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
565436 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
565501 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
565520 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
* *
565585 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCTAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
*
565650 CATATGTCTCGAAGAACCG
131 CATATGTCCCGAAGAACCG
565669 CGTAGA
1 CGTAGA
565675 CCCTCGACTC
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:566681 original size:18 final size:18
Alignment explanation
Indices: 566660--566694 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
566650 TCCCCTCTAA
566660 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
566678 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
566695 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:567300 original size:21 final size:21
Alignment explanation
Indices: 567276--567320 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
567266 TGTTGTTCGT
* *
567276 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
567297 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
567318 TTG
1 TTG
567321 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:569229 original size:6 final size:6
Alignment explanation
Indices: 569218--569242 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
569208 ATATACCCTA
569218 AATTAT AATTAT AATTAT AATTAT A
1 AATTAT AATTAT AATTAT AATTAT A
569243 TATATAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:569287 original size:19 final size:19
Alignment explanation
Indices: 569244--569308 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
569234 ATAATTATAT
* *
569244 ATATAACATTATATTTTAATA
1 ATATAACAATAAATTTT--TA
*
569265 ATATAAGAATAAATTTTTA
1 ATATAACAATAAATTTTTA
* *
569284 ATATAACATTAACTTTTTA
1 ATATAACAATAAATTTTTA
569303 TATATA
1 -ATATA
569309 TAAGAGGTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 18 0.49
20 5 0.14
21 14 0.38
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATAACAATAAATTTTTA
Found at i:572282 original size:90 final size:90
Alignment explanation
Indices: 572119--572296 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
572109 TAATCCCGAA
* * * * * *
572119 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCTCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
572184 TAGGGTAACTTGAATATAAAAGGAT
66 TAGGGTAACTTGAATATAAAAGGAT
572209 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
**
572274 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGAATATAAAAGG
572297 GTATGTTAGG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGAATATAAAAGGAT
Found at i:577356 original size:89 final size:89
Alignment explanation
Indices: 577205--577384 Score: 252
Period size: 89 Copynumber: 2.0 Consensus size: 89
577195 CAATCTCCAC
* * * **
577205 TATTTAATCAATGTTAAATCGAGATATATTATTTTTCTCGTACTTGTTAACGTATTACATCAGTG
1 TATTTAATCAATGTTAAATCGAGATATATTACTTTTCTCATACTTGTTAACGAATTACATCAGCA
* *
577270 ATATTGTTTGTGGATATGCTTTTA
66 ACATTGTTTGTGGATATGATTTTA
** * * *
577294 TATTTAATCAATGTTATCTCGAGATATATTACTTTTCTCATCCTTGTTAATGAATTGCATCAGCA
1 TATTTAATCAATGTTAAATCGAGATATATTACTTTTCTCATACTTGTTAACGAATTACATCAGCA
577359 ACATTGTTTGTGGATATGATTTTA
66 ACATTGTTTGTGGATATGATTTTA
577383 TA
1 TA
577385 CGTTGTGTCC
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
89 79 1.00
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (89 bp):
TATTTAATCAATGTTAAATCGAGATATATTACTTTTCTCATACTTGTTAACGAATTACATCAGCA
ACATTGTTTGTGGATATGATTTTA
Found at i:577739 original size:25 final size:25
Alignment explanation
Indices: 577682--577739 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 25
577672 GAACCGAGTA
*
577682 AAACGGTTCGGTTCGGTTTGGCTTT
1 AAACGGTTCGGTTCGGTTCGGCTTT
577707 AAACGGTTCGGTTTTCGGTTCGG-TTT
1 AAACGGTTCGG--TTCGGTTCGGCTTT
577733 AAA-GGTT
1 AAACGGTT
577740 TCATTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 15 0.50
26 6 0.20
27 9 0.30
ACGTcount: A:0.16, C:0.14, G:0.31, T:0.40
Consensus pattern (25 bp):
AAACGGTTCGGTTCGGTTCGGCTTT
Found at i:577902 original size:17 final size:14
Alignment explanation
Indices: 577865--577908 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 14
577855 AAAAACCGAT
577865 AAACCGAACCGAAA
1 AAACCGAACCGAAA
*
577879 AACCCGAACCGTTAAAA
1 AAACCGAACCG---AAA
577896 AAACCGAACCGAA
1 AAACCGAACCGAA
577909 CCGAAAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 12 0.48
17 13 0.52
ACGTcount: A:0.52, C:0.30, G:0.14, T:0.05
Consensus pattern (14 bp):
AAACCGAACCGAAA
Found at i:579464 original size:22 final size:22
Alignment explanation
Indices: 579438--579493 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
579428 TAAACAAGCT
**
579438 TATAAATGAACTTATTCATGAA
1 TATAAATGAACAGATTCATGAA
579460 TATAAATGAACAGATTCATGAA
1 TATAAATGAACAGATTCATGAA
*
579482 TATAAACGAACA
1 TATAAATGAACA
579494 AGTCGATGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (22 bp):
TATAAATGAACAGATTCATGAA
Found at i:584572 original size:28 final size:26
Alignment explanation
Indices: 584541--584593 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 26
584531 ATAGTATTTA
*
584541 TTTTTAATTTTTTTATAAATATTTTAAC
1 TTTTCAATTTTTTT-TAAA-ATTTTAAC
584569 TTTTCAATTTTTTTTAAAATTTTAA
1 TTTTCAATTTTTTTTAAAATTTTAA
584594 TAATTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 7 0.29
27 4 0.17
28 13 0.54
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTTCAATTTTTTTTAAAATTTTAAC
Found at i:585042 original size:21 final size:21
Alignment explanation
Indices: 585018--585065 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
585008 TCGTTATGTT
*
585018 AATATTATAAATCGTCACATC
1 AATATTATAAATCATCACATC
* * *
585039 AATATTATTAATCATCACGTT
1 AATATTATAAATCATCACATC
585060 AATATT
1 AATATT
585066 GTTACAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.40
Consensus pattern (21 bp):
AATATTATAAATCATCACATC
Found at i:588797 original size:42 final size:42
Alignment explanation
Indices: 588733--588847 Score: 185
Period size: 42 Copynumber: 2.7 Consensus size: 42
588723 TTTCCCCGAA
* * *
588733 TTCCCGTGTTTGTTTCAAGTAATTTGTTTTCCGAAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAACGTT
* *
588775 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAACGTT
588817 TTCCCGTGTTTGTTTCACGTAATTCGTTTTC
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTC
588848 TGGAATGTAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.17, C:0.18, G:0.17, T:0.48
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAACGTT
Found at i:589058 original size:12 final size:12
Alignment explanation
Indices: 589037--589069 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
589027 ATATTAATTA
589037 TTAA-AATATTT
1 TTAATAATATTT
*
589048 TTATTAATATTT
1 TTAATAATATTT
589060 TTAATAATAT
1 TTAATAATAT
589070 AATATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 3 0.16
12 16 0.84
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTAATAATATTT
Found at i:589082 original size:22 final size:23
Alignment explanation
Indices: 589049--589092 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
589039 AAAATATTTT
589049 TATTAATATTTTTAATAATATAA
1 TATTAATATTTTTAATAATATAA
*
589072 TATT-ATATTTTTAATATTATA
1 TATTAATATTTTTAATAATATA
589093 TAAAATAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTAATATTTTTAATAATATAA
Found at i:589632 original size:20 final size:20
Alignment explanation
Indices: 589534--589623 Score: 162
Period size: 20 Copynumber: 4.5 Consensus size: 20
589524 TTTCCAGATG
589534 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
589554 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
589574 TTTTCCAGAAATGTAATTTA
1 TTTTCCAGAAATGTAATTCA
*
589594 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
589614 TTTTCCAGAA
1 TTTTCCAGAA
589624 TTCAAATTCC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:589642 original size:15 final size:15
Alignment explanation
Indices: 589606--589687 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
589596 TTACAGAAAT
**
589606 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
589621 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
589635 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
589650 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
*
589665 GTAATTCAAATTTCA
1 GTAATTCAAATTCCA
589680 GTAATTCA
1 GTAATTCA
589688 TTTTCTGGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
14 12 0.20
15 47 0.80
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:589658 original size:30 final size:30
Alignment explanation
Indices: 589606--589687 Score: 132
Period size: 30 Copynumber: 2.8 Consensus size: 30
589596 TTACAGAAAT
589606 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
589635 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
589665 GTAATTCAAATTT-CAGTAATTCA
1 GTAATTC-ATTTTCCAGTAATTCA
589688 TTTTCTGGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
29 16 0.32
30 30 0.60
31 4 0.08
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:589682 original size:45 final size:44
Alignment explanation
Indices: 589606--589692 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 44
589596 TTACAGAAAT
**
589606 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
*
589650 GTAATTCAAATTCCAGTAATTCAAATTTCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
589693 TGGAAAACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.41
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:590304 original size:23 final size:24
Alignment explanation
Indices: 590278--590322 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
590268 AAATTTACAA
590278 TTAAT-AAAATATTTAA-TATCATT
1 TTAATCAAAATA-TTAATTATCATT
590301 TTAATCAAAATATTAATTATCA
1 TTAATCAAAATATTAATTATCA
590323 AAATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (24 bp):
TTAATCAAAATATTAATTATCATT
Found at i:590371 original size:22 final size:23
Alignment explanation
Indices: 590341--590387 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
590331 AAAATATATT
590341 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
590364 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
590386 TA
1 TA
590388 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:590547 original size:27 final size:27
Alignment explanation
Indices: 590467--590552 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
590457 AATAAAATTT
* *
590467 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
590494 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
590521 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
590550 ATA
1 ATA
590553 ATCTAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 19 0.41
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:590736 original size:20 final size:20
Alignment explanation
Indices: 590707--590746 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
590697 TAATAAAATT
590707 ATAAAAAAA-TATATTTAATA
1 ATAAAAAAATTAT-TTTAATA
*
590727 ATAAATAAATTATTTTAATA
1 ATAAAAAAATTATTTTAATA
590747 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAAAAATTATTTTAATA
Found at i:591542 original size:21 final size:20
Alignment explanation
Indices: 591516--591578 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 20
591506 GCACTTATTG
*
591516 AAATAATTATTAAATTAGTAT
1 AAATAATTATTAAATTA-TAA
*
591537 AAATAATTTTTGAAATATTATAA
1 AAATAATTATT--AA-ATTATAA
591560 AAATAATTATTAAACTTAT
1 AAATAATTATTAAA-TTAT
591579 TAAATTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
20 1 0.03
21 16 0.46
23 14 0.40
24 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (20 bp):
AAATAATTATTAAATTATAA
Found at i:591596 original size:31 final size:31
Alignment explanation
Indices: 591555--591615 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
591545 TTTGAAATAT
591555 TATAAAAATAATTATT-AAACTTATTAAATTA
1 TATAAAAATAATT-TTAAAACTTATTAAATTA
* *
591586 TATATAAATAATTTTAAAATTTATTAAATT
1 TATAAAAATAATTTTAAAACTTATTAAATT
591616 TTGTTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (31 bp):
TATAAAAATAATTTTAAAACTTATTAAATTA
Found at i:601300 original size:125 final size:125
Alignment explanation
Indices: 601078--601330 Score: 364
Period size: 125 Copynumber: 2.0 Consensus size: 125
601068 AATACCCACA
* * **
601078 TTGGGGCACGATTGAACCCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
1 TTGGGGCACGACTGAACCCACATCATGATGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
* * * * *
601143 TGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATGAGATAATG
66 TGAGCCTTACAATTTGAGATGATGAGGCATTTTGAAGGCCCGTACCAGAATAAAATAATG
* * **
601203 TTGGGGCGCGACTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAAGGCATTGAGAA
1 TTGGGGCACGACTGAACCCACATCATGATGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
*
601268 TGAGCCTTATAATTTGAGAT-ATTGAGGCATTTTGAAGGCCCGTACCAGAATAAAATAATG
66 TGAGCCTTACAATTTGAGATGA-TGAGGCATTTTGAAGGCCCGTACCAGAATAAAATAATG
601328 TTG
1 TTG
601331 CGACATTAGT
Statistics
Matches: 113, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
124 1 0.01
125 112 0.99
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (125 bp):
TTGGGGCACGACTGAACCCACATCATGATGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
TGAGCCTTACAATTTGAGATGATGAGGCATTTTGAAGGCCCGTACCAGAATAAAATAATG
Found at i:602670 original size:36 final size:36
Alignment explanation
Indices: 602505--602702 Score: 238
Period size: 36 Copynumber: 5.5 Consensus size: 36
602495 GATTGGAGAA
*
602505 AAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
*
602541 AAACCATCTGAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* * *
602577 AATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* * * *
602613 AAACCATCATAAGTCTTCACCAGAGAGTAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
* * *
602649 AAAGCATCTTAAGTCTTCACC--AAAAGTAGTGAAGC
1 AAACCATCTTAAGCCTTCACCGGAGAA-TAGTGAAGC
* *
602684 AGATCCATTTTAAGCCTTC
1 A-AACCATCTTAAGCCTTC
602703 TCAGAAGAGT
Statistics
Matches: 141, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
34 2 0.01
35 10 0.07
36 129 0.91
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (36 bp):
AAACCATCTTAAGCCTTCACCGGAGAATAGTGAAGC
Found at i:602699 original size:108 final size:107
Alignment explanation
Indices: 602505--602702 Score: 263
Period size: 108 Copynumber: 1.8 Consensus size: 107
602495 GATTGGAGAA
* * *
602505 AAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATA
1 AAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACC-GAAAATA
602570 GTGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGC
65 GTGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGC
* * * * *
602613 AAACCATCATAAGTCTTCACCAGAGAGTAGTGAAGCAAAGCATCTTAAGTCTTCACC-AAAAGTA
1 AAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACCGAAAA-TA
* * *
602677 GTGAAGCAGATCCATTTTAAGCCTTC
65 GTGAAGCA-ATCAATCTGAAGCCTTC
602703 TCAGAAGAGT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
106 3 0.04
107 10 0.13
108 64 0.83
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (107 bp):
AAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACCATCTGAAGCCTTCACCGAAAATAG
TGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGAAGC
Found at i:606730 original size:15 final size:15
Alignment explanation
Indices: 606710--606792 Score: 105
Period size: 15 Copynumber: 5.5 Consensus size: 15
606700 TTCCAGAAAA
606710 TGAATTACTGGAATT
1 TGAATTACTGGAATT
606725 TGAATTACTGGAATT
1 TGAATTACTGGAATT
* **
606740 TGAATTACTGAAAAAA
1 TGAATTACTG-GAATT
606756 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
606771 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
606785 TGAATTAC
1 TGAATTAC
606793 ATTTTTGTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
14 12 0.21
15 34 0.59
16 12 0.21
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:606763 original size:31 final size:29
Alignment explanation
Indices: 606725--606792 Score: 109
Period size: 31 Copynumber: 2.3 Consensus size: 29
606715 TACTGGAATT
606725 TGAATTACTGGAATTTGAATTACTGAAAAAA
1 TGAATTACTGGAATTTGAATT-CTG-AAAAA
*
606756 TGAATTACTGGAATTTGAATTCTGGAAAA
1 TGAATTACTGGAATTTGAATTCTGAAAAA
606785 TGAATTAC
1 TGAATTAC
606793 ATTTTTGTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 12 0.33
30 3 0.08
31 21 0.58
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (29 bp):
TGAATTACTGGAATTTGAATTCTGAAAAA
Found at i:606770 original size:46 final size:45
Alignment explanation
Indices: 606706--606792 Score: 147
Period size: 46 Copynumber: 1.9 Consensus size: 45
606696 GATTTTCCAG
**
606706 AAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTGAA
1 AAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTGAA
606752 AAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 AAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
606793 ATTTTTGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 14 0.36
46 25 0.64
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (45 bp):
AAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTGAA
Found at i:606804 original size:20 final size:20
Alignment explanation
Indices: 606775--606844 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
606765 GGAATTTGAA
606775 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
* *
606795 TTTTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
606815 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
606835 TTCTAGAAAA
1 TTCTGGAAAA
606845 CATCTGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:607066 original size:28 final size:27
Alignment explanation
Indices: 607011--607075 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
607001 TTTACTAAAA
*
607011 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAATATTAT
607039 TCATTATTAAATATATAAAAAA-ATTTAT
1 T-ATTATTAAATATATAAAAAATA-TTAT
607067 TATATATTA
1 TAT-TATTA
607076 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.09
28 24 0.73
29 6 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAATATTAT
Found at i:607101 original size:31 final size:32
Alignment explanation
Indices: 607011--607108 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 32
607001 TTTACTAAAA
*
607011 TATTATTGAAATATAT--AAATA-ATATTAT-T
1 TATTATT-AAATATATAAAAAAATATATTATAT
* *
607040 CATTATTAAATATATAAAAAAATTTATTATA-
1 TATTATTAAATATATAAAAAAATATATTATAT
*
607071 TATTATTAAA-ATA-AAAATATAATATCTTATAT
1 TATTATTAAATATATAAAA-A-AATATATTATAT
607103 TATTAT
1 TATTAT
607109 AATATAATTG
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 8 0.14
29 10 0.18
30 8 0.14
31 24 0.43
32 6 0.11
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (32 bp):
TATTATTAAATATATAAAAAAATATATTATAT
Found at i:607153 original size:22 final size:23
Alignment explanation
Indices: 607128--607171 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
607118 GATTATTTTA
607128 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
607150 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
607172 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:607176 original size:22 final size:22
Alignment explanation
Indices: 607132--607188 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
607122 ATTTTATATA
* *
607132 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
607153 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
607175 ATATTTTAAATATT
1 ATATTATAAATATT
607189 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:607187 original size:52 final size:51
Alignment explanation
Indices: 607068--607188 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 51
607058 AAAATTTATT
**
607068 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
607119 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
607173 ATATATTTTAAATATT
1 ATATATTTTAAATATT
607189 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.33
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:607425 original size:42 final size:42
Alignment explanation
Indices: 607378--607497 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
607368 ATGAATTACA
* *
607378 TTCCGGAAAATGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAAAGAATTACGTGAAACAAACACGGGAAAACATT
607420 TTCCGGAAAAAGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAAAGAATTACGTGAAACAAACACGGGAAAACATT
*
607462 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAAAGAATTACGTGAAACAAACACGGGAA
607498 TTCGGGGAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAAAGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:612094 original size:4 final size:4
Alignment explanation
Indices: 612087--612147 Score: 95
Period size: 4 Copynumber: 15.2 Consensus size: 4
612077 TGTTTCACTT
* * *
612087 ATAG ATAG ATAG ATAG ATAG ACAG ATAG ACAG ATAG ACAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
612135 ATAG ATAG ATAG A
1 ATAG ATAG ATAG A
612148 AAGTAACCGC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.51, C:0.05, G:0.25, T:0.20
Consensus pattern (4 bp):
ATAG
Found at i:612222 original size:32 final size:34
Alignment explanation
Indices: 612164--612285 Score: 132
Period size: 32 Copynumber: 3.6 Consensus size: 34
612154 CCGCTAACTT
*
612164 TTCTAAC-TTTTATTTTTTATTTTTTATACTAACA
1 TTCTAACTTTTTA-TTTTTATTGTTTATACTAACA
612198 TTCTAAC-TTTTA-TTTTATTGTTTATACTAACA
1 TTCTAACTTTTTATTTTTATTGTTTATACTAACA
612230 TAT-TAACTTTTTTATTTTTATTGTTCT-TACTAAC-
1 T-TCTAAC-TTTTTATTTTTATTGTT-TATACTAACA
*
612264 TTACTAACATTTTA-TTTTATTG
1 TT-CTAACTTTTTATTTTTATTG
612286 CACAAACTAA
Statistics
Matches: 79, Mismatches: 2, Indels: 15
0.82 0.02 0.16
Matches are distributed among these distances:
32 24 0.30
33 10 0.13
34 23 0.29
35 21 0.27
36 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.02, T:0.60
Consensus pattern (34 bp):
TTCTAACTTTTTATTTTTATTGTTTATACTAACA
Found at i:613005 original size:14 final size:14
Alignment explanation
Indices: 612988--613014 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
612978 GACATTCGTT
612988 TATGTTCATTTATA
1 TATGTTCATTTATA
613002 TATGTTCATTTAT
1 TATGTTCATTTAT
613015 GTTTAGCCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (14 bp):
TATGTTCATTTATA
Found at i:613325 original size:10 final size:10
Alignment explanation
Indices: 613310--613387 Score: 66
Period size: 10 Copynumber: 7.2 Consensus size: 10
613300 TATATTTTCA
613310 TTTATGTTCG
1 TTTATGTTCG
**
613320 TTTATGTTTA
1 TTTATGTTCG
613330 TTTATTGTGTTCG
1 TTTA---TGTTCG
613343 TTTATGTTCG
1 TTTATGTTCG
*
613353 TTTACGTTCG
1 TTTATGTTCG
613363 TTTATTGTTTTCG
1 TTTA-TG--TTCG
*
613376 TTTATATTCG
1 TTTATGTTCG
613386 TT
1 TT
613388 AACATCCATT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
10 37 0.67
11 1 0.02
12 1 0.02
13 16 0.29
ACGTcount: A:0.12, C:0.09, G:0.17, T:0.63
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:613347 original size:33 final size:33
Alignment explanation
Indices: 613310--613387 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
613300 TATATTTTCA
* *
613310 TTTATGTTCGTTTATGTTTATTTATTGTGTTCG
1 TTTATGTTCGTTTACGTTCATTTATTGTGTTCG
* *
613343 TTTATGTTCGTTTACGTTCGTTTATTGTTTTCG
1 TTTATGTTCGTTTACGTTCATTTATTGTGTTCG
*
613376 TTTATATTCGTT
1 TTTATGTTCGTT
613388 AACATCCATT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.12, C:0.09, G:0.17, T:0.63
Consensus pattern (33 bp):
TTTATGTTCGTTTACGTTCATTTATTGTGTTCG
Found at i:615256 original size:89 final size:87
Alignment explanation
Indices: 615101--615272 Score: 238
Period size: 89 Copynumber: 2.0 Consensus size: 87
615091 ATTCTACAAT
* * * * * *
615101 GGTTTAGGAGCATGTAGTTCAAATTTGATAAAAACGGACTTAAAATAAATGATAGATTAAAGAAA
1 GGTTTAAGAGCATGTAGTTAAAATTTGAAAAAAACGGACGTAAAATAAAGGATAAATTAAAGAAA
615166 TAAAGAAATTATAAAAAATGAG
66 TAAAGAAATTATAAAAAATGAG
*
615188 GGTTTAAGAGCATGTTGTTAAAATTTGGTAAAAAAACAGG-CGTAAAATAAAGGATAAATTAAAG
1 GGTTTAAGAGCATGTAGTTAAAATTT-G-AAAAAAAC-GGACGTAAAATAAAGGATAAATTAAAG
*
615252 AAATATAGAAATTATAAAAAA
63 AAATAAAGAAATTATAAAAAA
615273 ATTGAGGAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
87 23 0.31
88 1 0.01
89 48 0.65
90 2 0.03
ACGTcount: A:0.52, C:0.04, G:0.18, T:0.26
Consensus pattern (87 bp):
GGTTTAAGAGCATGTAGTTAAAATTTGAAAAAAACGGACGTAAAATAAAGGATAAATTAAAGAAA
TAAAGAAATTATAAAAAATGAG
Found at i:616600 original size:30 final size:27
Alignment explanation
Indices: 616536--616600 Score: 67
Period size: 30 Copynumber: 2.3 Consensus size: 27
616526 ATAAACACTC
616536 AAAATATTATTATTTTATATATTTAATA
1 AAAATA-TATTATTTTATATATTTAATA
** *
616564 TTAATATATTATTTTAGTTTCATTTTAATA
1 AAAATATATTATTTTA-TAT-A-TTTAATA
616594 AAAATAT
1 AAAATAT
616601 TAATTATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 10 0.34
28 6 0.21
29 1 0.03
30 12 0.41
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
AAAATATATTATTTTATATATTTAATA
Found at i:616814 original size:20 final size:19
Alignment explanation
Indices: 616765--616883 Score: 66
Period size: 19 Copynumber: 6.1 Consensus size: 19
616755 TTTAATAGTT
*
616765 TAATAATATTATTATATTAA
1 TAAT-ATATTAATATATTAA
*
616785 TAAGTA-ATTAATATACTTGA
1 TAA-TATATTAATATA-TTAA
* *
616805 TAATATATTATTTTATTTTAA
1 TAATATATTA--ATATATTAA
*
616826 TAA-ATATTTAATATAATAA
1 TAATATA-TTAATATATTAA
* * *
616845 TAATATTTTTAT-TTTTAA
1 TAATATATTAATATATTAA
*
616863 TAACATA-TAATTATATTAA
1 TAATATATTAA-TATATTAA
616882 TA
1 TA
616884 TTTTTATTTT
Statistics
Matches: 74, Mismatches: 16, Indels: 19
0.68 0.15 0.17
Matches are distributed among these distances:
17 2 0.03
18 10 0.14
19 30 0.41
20 19 0.26
21 10 0.14
22 3 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
TAATATATTAATATATTAA
Found at i:616857 original size:41 final size:41
Alignment explanation
Indices: 616771--616859 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 41
616761 AGTTTAATAA
* * *
616771 TATTATTATATTAATAAGTAATTAATATACTTGATAATATAT
1 TATT-TTATATTAATAAATAATTAATATACATAATAATATAT
* * *
616813 TATTTTATTTTAATAAATATTTAATATA-ATAATAATATTTT
1 TATTTTATATTAATAAATAATTAATATACATAATAATA-TAT
616854 TATTTT
1 TATTTT
616860 TAATAACATA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
40 7 0.17
41 29 0.73
42 4 0.10
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (41 bp):
TATTTTATATTAATAAATAATTAATATACATAATAATATAT
Found at i:616883 original size:40 final size:37
Alignment explanation
Indices: 616815--616895 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 37
616805 TAATATATTA
616815 TTTTA-TTTTAATAAATATTTAATATAATAATAATAT
1 TTTTATTTTTAATAAATATTTAATATAATAATAATAT
*
616851 TTTTATTTTTAATAACATA--TAAT-T-ATATTAATAT
1 TTTTATTTTTAATAA-ATATTTAATATAATAATAATAT
616885 TTTTATTTTTA
1 TTTTATTTTTA
616896 TTTAAAATTG
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
34 20 0.48
35 1 0.02
36 9 0.21
37 9 0.21
38 3 0.07
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (37 bp):
TTTTATTTTTAATAAATATTTAATATAATAATAATAT
Done.