Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007940.1 Hibiscus syriacus cultivar Beakdansim tig00110356_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: 1348078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:664557 original size:20 final size:21
Alignment explanation
Indices: 664532--664583 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
664522 TTTTCCCAAT
*
664532 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
664552 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
664573 TCGCAATGCGA
1 TCGCAATGCGA
664584 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:664562 original size:41 final size:41
Alignment explanation
Indices: 664517--664726 Score: 117
Period size: 41 Copynumber: 5.1 Consensus size: 41
664507 AATTTCGCGT
**
664517 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCATAATTCGCAATGCGAATAAGTAAATCGCAA
** * * * *
664558 TGCGAATTTGGA-AAATCGCAATGCG-AT-ACTGACTATTGCAA
1 TGCG-ATTTTCATAATTCGCAATGCGAATAAGT-A-AATCGCAA
** * * * * * **
664599 TGTAATTTTCTTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCATAATTCGCAATGCGA-ATAAGTAAATCGCAA
*
664640 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCATAATTCGCAATGCGAATAAGTAAATCGCAA
* * * * *
664681 CGCGA--TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCA-TAATTCGCAATGCGAA-TAAGTAAATCGCAA
664722 TGCGA
1 TGCGA
664727 ATACGTAAAT
Statistics
Matches: 123, Mismatches: 36, Indels: 20
0.69 0.20 0.11
Matches are distributed among these distances:
39 5 0.04
40 27 0.22
41 85 0.69
42 4 0.03
43 1 0.01
44 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (41 bp):
TGCGATTTTCATAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:664658 original size:21 final size:21
Alignment explanation
Indices: 664603--664665 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
664593 TTGCAATGTA
*
664603 ATTTTCTTAATTCGCATTGCG
1 ATTTTCATAATTCGCATTGCG
* * *
664624 ATTTACGT-ATTCGCGTTGCG
1 ATTTTCATAATTCGCATTGCG
*
664644 ATTTTCATAATTCGCAATGCG
1 ATTTTCATAATTCGCATTGCG
664665 A
1 A
664666 ATACGTAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.41
Consensus pattern (21 bp):
ATTTTCATAATTCGCATTGCG
Found at i:664680 original size:20 final size:20
Alignment explanation
Indices: 664655--664748 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
664645 TTTTCATAAT
664655 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
664675 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
664695 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
664716 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
664736 TCGCAATACGAAT
1 TCGCAATGCGAAT
664749 CTGACTATCG
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 45 0.71
21 18 0.29
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:664735 original size:41 final size:41
Alignment explanation
Indices: 664655--664748 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
664645 TTTTCATAAT
* *
664655 TCGCAATGCGAA-TACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
* * *
664695 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
*
664736 TCGCAATACGAAT
1 TCGCAATGCGAAT
664749 CTGACTATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 12 0.26
41 35 0.74
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
Found at i:665361 original size:19 final size:19
Alignment explanation
Indices: 665290--665374 Score: 63
Period size: 19 Copynumber: 4.7 Consensus size: 19
665280 TAGTTTCGAG
665290 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
**
665310 AATGACTATCGCAA--CG-
1 AATGAAAATCGCAACGCGA
* * *
665326 -A-GAGAATCACAAAGCGA
1 AATGAAAATCGCAACGCGA
665343 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
**
665362 AACCAAAATCGCA
1 AATGAAAATCGCA
665375 TTGCGATTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 11
0.70 0.14 0.15
Matches are distributed among these distances:
14 8 0.16
15 1 0.02
16 2 0.04
17 1 0.02
18 2 0.04
19 24 0.48
20 12 0.24
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:665392 original size:19 final size:19
Alignment explanation
Indices: 665370--665461 Score: 97
Period size: 19 Copynumber: 5.1 Consensus size: 19
665360 GAAACCAAAA
*
665370 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
665389 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
665403 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
665422 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
665441 TCCGCGTTGCGA-TTTCATT
1 T-CGCGTTGCGATTTTCATT
665460 TC
1 TC
665462 AACCAAAGAC
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.17
16 3 0.05
17 3 0.05
18 1 0.02
19 33 0.55
20 10 0.17
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:665577 original size:24 final size:26
Alignment explanation
Indices: 665524--665577 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 26
665514 TTATGTTTAT
*
665524 TGTTTTTGGTATATCTTCACTGTGTA
1 TGTTTTTGGTATATCTTAACTGTGTA
665550 -GTTTTTGG-ATATC-TAACT-TGGTA
1 TGTTTTTGGTATATCTTAACTGT-GTA
665573 TGTTT
1 TGTTT
665578 ATTGTTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
22 1 0.04
23 7 0.28
24 9 0.36
25 8 0.32
ACGTcount: A:0.17, C:0.09, G:0.20, T:0.54
Consensus pattern (26 bp):
TGTTTTTGGTATATCTTAACTGTGTA
Found at i:667311 original size:71 final size:70
Alignment explanation
Indices: 667216--667359 Score: 261
Period size: 71 Copynumber: 2.0 Consensus size: 70
667206 TGTCTTTTGG
667216 TTGAAGTAAATTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTT
1 TTGAAGTAAATTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTT
667281 AGTAT
66 AGTAT
* *
667286 TTGAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGT
1 TTGAAGTAAA-TTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGT
667351 TAGTAT
65 TAGTAT
667357 TTG
1 TTG
667360 TCTTTGTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 10 0.14
71 61 0.86
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.41
Consensus pattern (70 bp):
TTGAAGTAAATTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTT
AGTAT
Found at i:669213 original size:14 final size:14
Alignment explanation
Indices: 669194--669229 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
669184 ATTGTTTAAT
669194 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
669208 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
669222 TGATTTGT
1 TGATTTGT
669230 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:669352 original size:19 final size:19
Alignment explanation
Indices: 669336--669382 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
669326 AAAAATGACT
*
669336 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
669355 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
669374 ATCGCAACG
1 ATCGCAACG
669383 ACAAAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:669442 original size:33 final size:33
Alignment explanation
Indices: 669395--669518 Score: 212
Period size: 33 Copynumber: 3.8 Consensus size: 33
669385 AAAATCGCAA
* * *
669395 TGCGATTTTAATTTCGCTTTGCGATTCCCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
669428 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
669461 TGCGATTTTCATTTCGTATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
669494 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT
669519 AGTCATTTCC
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:669451 original size:19 final size:19
Alignment explanation
Indices: 669427--669538 Score: 91
Period size: 19 Copynumber: 6.4 Consensus size: 19
669417 GATTCCCTCG
669427 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
669446 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
669460 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
669479 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
669493 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
669512 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
669532 TTGCGAT
1 TTGCGAT
669539 AGACATTAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
14 12 0.16
16 14 0.19
17 14 0.19
19 25 0.33
20 10 0.13
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:669465 original size:14 final size:14
Alignment explanation
Indices: 669413--669500 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
669403 TAATTTCGCT
*
669413 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
669427 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
669444 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
669460 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
669477 TATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
669493 TTGCGATT
1 TTGCGATT
669501 TTCATTTCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 13 0.22
19 12 0.20
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:669537 original size:20 final size:20
Alignment explanation
Indices: 669491--669584 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
669481 GCGATTCTCT
**
669491 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
669510 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
669530 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
669549 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
669571 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
669585 AATGATTGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:672066 original size:23 final size:23
Alignment explanation
Indices: 672033--672077 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
672023 CTGAAACATC
672033 ATCAAAATCCGAGTATTGACCAT
1 ATCAAAATCCGAGTATTGACCAT
* *
672056 ATCAAAGTCCGGGTATTGACCA
1 ATCAAAATCCGAGTATTGACCA
672078 AGATCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (23 bp):
ATCAAAATCCGAGTATTGACCAT
Found at i:672853 original size:20 final size:20
Alignment explanation
Indices: 672830--672917 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
672820 TGTATTACCT
* *
672830 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
*
672850 CGTTACGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
672870 CGTTGTGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
* *
672890 CGTTGCGAAAGTCAGTATCA
1 CGTTGCGAAAGTCAGAATCG
672910 CGTTGCGA
1 CGTTGCGA
672918 TTTTGTATTA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.25
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:672951 original size:20 final size:20
Alignment explanation
Indices: 672830--672959 Score: 118
Period size: 20 Copynumber: 6.5 Consensus size: 20
672820 TGTATTACCT
*
672830 CGTTGCGATAGTCAGAATCT
1 CGTTGCGATAGTCAGAATCG
* *
672850 CGTTACGAAAGTCAGAATCG
1 CGTTGCGATAGTCAGAATCG
* *
672870 CGTTGTGAAAGTCAGAATCG
1 CGTTGCGATAGTCAGAATCG
* * *
672890 CGTTGCGAAAGTCAGTATCA
1 CGTTGCGATAGTCAGAATCG
* **
672910 CGTTGCGATTTTGT-ATTATCG
1 CGTTGCGA--TAGTCAGAATCG
*
672931 CGTTGCGATAGTCAGTATCG
1 CGTTGCGATAGTCAGAATCG
*
672951 CATTGCGAT
1 CGTTGCGAT
672960 TTTCCAAATT
Statistics
Matches: 92, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
19 3 0.03
20 74 0.80
21 13 0.14
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (20 bp):
CGTTGCGATAGTCAGAATCG
Found at i:672978 original size:41 final size:40
Alignment explanation
Indices: 672887--673040 Score: 107
Period size: 41 Copynumber: 3.8 Consensus size: 40
672877 AAAGTCAGAA
* * * * * *
672887 TCGCGTTGCGAAAGTCAGTATCACGTTGCGATTTTGTATT
1 TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTGAAAT
* *
672927 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 -TCGCATTGCGATAGTCAGTATCGCATTGCGATTTT-GAAAT
* * * * *
672969 TCGCATTGCGAT--TTACTTATTCGCATTGCGAAATTGGAAAA
1 TCGCATTGCGATAGTCA-GTA-TCGCATTGCG-ATTTTGAAAT
*
673010 TCGCATTGCGATAGT-AATAATCGCATTGCGA
1 TCGCATTGCGATAGTCAGT-ATCGCATTGCGA
673041 ATCTGGAAAC
Statistics
Matches: 92, Mismatches: 14, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
39 2 0.02
40 3 0.03
41 79 0.86
42 7 0.08
43 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (40 bp):
TCGCATTGCGATAGTCAGTATCGCATTGCGATTTTGAAAT
Found at i:672992 original size:20 final size:21
Alignment explanation
Indices: 672948--672999 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
672938 ATAGTCAGTA
*
672948 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
672969 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
672989 TCGCATTGCGA
1 TCGCATTGCGA
673000 AATTGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:673015 original size:21 final size:20
Alignment explanation
Indices: 672989--673049 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
672979 ATTTACTTAT
672989 TCGCATTGCGAAATTGGAAAA
1 TCGCATTGCG-AATTGGAAAA
* *
673010 TCGCATTGCG-ATAGTAATAA
1 TCGCATTGCGAATTGGAA-AA
673030 TCGCATTGCGAATCTGGAAA
1 TCGCATTGCGAAT-TGGAAA
673050 CTGATTTGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 5 0.15
20 12 0.36
21 13 0.39
22 3 0.09
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (20 bp):
TCGCATTGCGAATTGGAAAA
Found at i:673041 original size:41 final size:41
Alignment explanation
Indices: 672927--673049 Score: 108
Period size: 41 Copynumber: 3.0 Consensus size: 41
672917 ATTTTGTATT
* * ** **
672927 ATCGCGTTGCGATAGTCAGT-ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATAGT-AATAATCGCATTGCGAAATTGGAAA
* * * *
672968 TTCGCATTGCGAT-TTACTTATTCGCATTGCGAAATTGGAAA
1 ATCGCATTGCGATAGTA-ATAATCGCATTGCGAAATTGGAAA
673009 ATCGCATTGCGATAGTAATAATCGCATTGCG-AATCTGGAAA
1 ATCGCATTGCGATAGTAATAATCGCATTGCGAAAT-TGGAAA
673050 CTGATTTGTG
Statistics
Matches: 65, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
39 1 0.02
40 5 0.08
41 57 0.88
42 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (41 bp):
ATCGCATTGCGATAGTAATAATCGCATTGCGAAATTGGAAA
Found at i:673838 original size:23 final size:23
Alignment explanation
Indices: 673799--673858 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
673789 ACAACGCTAA
*
673799 ATGAACATATAAATGAATATGTTC
1 ATGAACAT-TAAATGAACATGTTC
673823 ATGAACATTAAATGAACATGTTC
1 ATGAACATTAAATGAACATGTTC
* *
673846 GTGAACAATAAAT
1 ATGAACATTAAAT
673859 AAACGAATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 25 0.76
24 8 0.24
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (23 bp):
ATGAACATTAAATGAACATGTTC
Found at i:673904 original size:30 final size:30
Alignment explanation
Indices: 673852--673963 Score: 111
Period size: 30 Copynumber: 3.7 Consensus size: 30
673842 GTTCGTGAAC
* *
673852 AATAAATAAACGAATACAAACACCTTCAAA
1 AATAAATAAACGAACACGAACACCTTCAAA
* * **
673882 AATAAATAAACGAACATGAACACGATATTGAA
1 AATAAATAAACGAACACGAACAC-CT-TCAAA
* * *
673914 AAT--TTAAATGAACATGAACACCTTCAAA
1 AATAAATAAACGAACACGAACACCTTCAAA
673942 AATAAATAAACGAACACGAACA
1 AATAAATAAACGAACACGAACA
673964 TAACCTTATT
Statistics
Matches: 64, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
28 6 0.09
29 1 0.02
30 50 0.78
31 1 0.02
32 6 0.09
ACGTcount: A:0.57, C:0.17, G:0.08, T:0.18
Consensus pattern (30 bp):
AATAAATAAACGAACACGAACACCTTCAAA
Found at i:674145 original size:14 final size:15
Alignment explanation
Indices: 674117--674152 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
674107 TGTTTCTTTG
674117 TTATTTTATAATATT
1 TTATTTTATAATATT
674132 TTATTTTA-AATATT
1 TTATTTTATAATATT
674146 TATATTT
1 T-TATTT
674153 ATTGTATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTTTATAATATT
Found at i:677290 original size:2 final size:2
Alignment explanation
Indices: 677283--677317 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
677273 ATCAAATCGA
677283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
677318 ATTTAGAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:679085 original size:5 final size:5
Alignment explanation
Indices: 679075--679099 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
679065 CAATTCTTTT
679075 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
679100 TTATATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:682803 original size:41 final size:41
Alignment explanation
Indices: 682674--682805 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 41
682664 CTGGTTCTCC
682674 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
1 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
* * *** **
682715 CCATGCAGT--G-G-AATAGAGAGGTCGTTCTCCCCATGCGAGGTCC
1 CCATGCA-TACGAGCCATA-CGA-GT-G--CGAGCCATGCGAGGTGG
682758 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
1 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
682799 CCATGCA
1 CCATGCA
682806 GTGGAATAGA
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 3 0.04
41 27 0.40
42 2 0.03
43 20 0.30
44 3 0.04
45 3 0.04
46 3 0.04
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (41 bp):
CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
Found at i:682820 original size:55 final size:55
Alignment explanation
Indices: 682760--682870 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
682750 CGAGGTCCCC
682760 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
682815 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
682870 A
1 A
682871 GAGGTCGTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.28, C:0.22, G:0.34, T:0.16
Consensus pattern (55 bp):
ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
Found at i:682926 original size:139 final size:139
Alignment explanation
Indices: 682676--682951 Score: 552
Period size: 139 Copynumber: 2.0 Consensus size: 139
682666 GGTTCTCCCC
682676 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
682741 CTCCCCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCA
66 CTCCCCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCA
682806 GTGGAATAG
131 GTGGAATAG
682815 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
682880 CTCCCCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCA
66 CTCCCCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCA
682945 GTGGAAT
131 GTGGAAT
682952 GGTGGCCATG
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 137 1.00
ACGTcount: A:0.24, C:0.25, G:0.33, T:0.17
Consensus pattern (139 bp):
ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAGAGAGGTCGTT
CTCCCCATGCGAGGTCCCCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCA
GTGGAATAG
Found at i:682942 original size:41 final size:41
Alignment explanation
Indices: 682815--682944 Score: 115
Period size: 41 Copynumber: 3.1 Consensus size: 41
682805 AGTGGAATAG
682815 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
* * *** **
682856 ATGCAGT--G-G-AATAGAGAGGTCGTTCTCCCCATGCGAGGTCCCC
1 ATGCA-TACGAGCCATA-CGA-GT-G--CGAGCCATGCGAGGTGGCC
682899 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
682940 ATGCA
1 ATGCA
682945 GTGGAATGGT
Statistics
Matches: 65, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.05
39 3 0.05
40 3 0.05
41 25 0.38
42 2 0.03
43 20 0.31
44 3 0.05
45 3 0.05
46 3 0.05
ACGTcount: A:0.24, C:0.27, G:0.32, T:0.17
Consensus pattern (41 bp):
ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
Found at i:682957 original size:19 final size:19
Alignment explanation
Indices: 682933--682970 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
682923 AGCCATGCGA
682933 GGTGGCCATGCAGTGGAAT
1 GGTGGCCATGCAGTGGAAT
682952 GGTGGCCATGCAGTGGAAT
1 GGTGGCCATGCAGTGGAAT
682971 AGGAGAGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.42, T:0.21
Consensus pattern (19 bp):
GGTGGCCATGCAGTGGAAT
Found at i:683015 original size:29 final size:29
Alignment explanation
Indices: 682978--683086 Score: 175
Period size: 29 Copynumber: 3.8 Consensus size: 29
682968 AATAGGAGAG
* * *
682978 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTAT
683007 AGGTCGCCATGTAGTCCCGGCGACCTTAT
1 AGGTCGCCATGTAGTCCCGGCGACCTTAT
683036 AGGTCGCCATGTAGTCCCGGCGACCTTAT
1 AGGTCGCCATGTAGTCCCGGCGACCTTAT
683065 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
683087 CCATTCCCAT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
29 74 0.97
30 2 0.03
ACGTcount: A:0.17, C:0.31, G:0.30, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTAT
Found at i:683157 original size:27 final size:23
Alignment explanation
Indices: 683092--683151 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
683082 CGGCGCCATT
*
683092 CCCATCGTCCATTCACATGCAGC
1 CCCATCATCCATTCACATGCAGC
683115 CCCATCATCCATTCACATGCAGC
1 CCCATCATCCATTCACATGCAGC
683138 CCCATCATCCATTC
1 CCCATCATCCATTC
683152 CTTCACGTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.45, G:0.08, T:0.23
Consensus pattern (23 bp):
CCCATCATCCATTCACATGCAGC
Found at i:683290 original size:25 final size:25
Alignment explanation
Indices: 683262--683313 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
683252 TGTACAATTA
*
683262 TTGGTGAAATAATTAAGGCAGTCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
*
683287 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
683312 TT
1 TT
683314 ATAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (25 bp):
TTGGTGAAATAATTAAGGCAGCCGG
Found at i:683384 original size:4 final size:4
Alignment explanation
Indices: 683375--683432 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
683365 ATTGCAGCCG
** **
683375 AGAA AGAA AGAA AGGG AGAA AGGAA AGAA AGAA AGAA AGGG AGAA AGGAA
1 AGAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA A-GAA
*
683425 AGTA AGAA
1 AGAA AGAA
683433 GAATTCGAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:683402 original size:17 final size:16
Alignment explanation
Indices: 683374--683405 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
683364 GATTGCAGCC
683374 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
683390 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
683406 AAAGAAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:683403 original size:25 final size:25
Alignment explanation
Indices: 683375--683432 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
683365 ATTGCAGCCG
683375 AGAAAGAAAGAAAGGGAGAAAGGAA
1 AGAAAGAAAGAAAGGGAGAAAGGAA
683400 AGAAAGAAAGAAAGGGAGAAAGGAA
1 AGAAAGAAAGAAAGGGAGAAAGGAA
*
683425 AGTAAGAA
1 AGAAAGAA
683433 GAATTCGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (25 bp):
AGAAAGAAAGAAAGGGAGAAAGGAA
Found at i:683699 original size:44 final size:46
Alignment explanation
Indices: 683636--683726 Score: 134
Period size: 44 Copynumber: 2.0 Consensus size: 46
683626 GTTATATAGT
683636 TAAAAAATAATTAATTAGTTTGTATT-GTT-AATAGTT-AGTTATA
1 TAAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATA
* *
683679 TAAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
1 TAAAAAA-TAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATA
683726 T
1 T
683727 TTGTTTGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 7 0.17
44 17 0.40
45 3 0.07
46 7 0.17
47 8 0.19
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (46 bp):
TAAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATA
Found at i:686939 original size:26 final size:24
Alignment explanation
Indices: 686881--686939 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
686871 CTAATAAACC
*
686881 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
686905 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
686933 TAATAAT
1 TAATAAT
686940 ATATGATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:687220 original size:16 final size:16
Alignment explanation
Indices: 687199--687254 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
687189 ACAATGTAAA
687199 TTAAACAAAATATTTT
1 TTAAACAAAATATTTT
* *
687215 TTAAACAACACTAAATATT
1 TTAAACAA-A--ATATTTT
*
687234 TTAAACACAATATTTT
1 TTAAACAAAATATTTT
687250 TTAAA
1 TTAAA
687255 ACGGAAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 18 0.56
17 1 0.03
18 1 0.03
19 12 0.38
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAACAAAATATTTT
Found at i:687779 original size:28 final size:30
Alignment explanation
Indices: 687739--687801 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 30
687729 ATTTTTTATA
*
687739 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
*
687769 TAATAT-A-ATATAACTTAAACTTACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
687797 TAATA
1 TAATA
687802 ATTTATACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 24 0.77
29 1 0.03
30 6 0.19
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:687808 original size:28 final size:28
Alignment explanation
Indices: 687743--687808 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
687733 TTTATATAAT
*
687743 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
*
687771 AT-ATAATATAACTTAAACTTACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
687799 ATAATTTATA
1 ATAATATATA
687809 CTAACAAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.35
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:688170 original size:32 final size:32
Alignment explanation
Indices: 688134--688197 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
688124 GGAATCTCTG
688134 AGCTATGAGCTATGATGCAACGCATACATGCA
1 AGCTATGAGCTATGATGCAACGCATACATGCA
*
688166 AGCTATGAGCTATGATGCAACGCATGCATGCA
1 AGCTATGAGCTATGATGCAACGCATACATGCA
688198 GCAGGACCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (32 bp):
AGCTATGAGCTATGATGCAACGCATACATGCA
Found at i:688268 original size:15 final size:15
Alignment explanation
Indices: 688248--688427 Score: 137
Period size: 15 Copynumber: 11.1 Consensus size: 15
688238 ACCATCCCCT
688248 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
688263 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* * *
688278 CGTCCAATGCACCATCCCCTC
1 C--CCCATG---CATTCCC-A
688299 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
688314 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
688329 CGTCCCATGCATCCCCTC
1 C--CCCATGCATTCCC-A
688347 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
688362 CATCCCATG-TTGATCCCTC
1 C--CCCATGCAT--TCCC-A
688381 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
* *
688396 CCCCATGCATCCCCTC
1 CCCCATGCATTCCC-A
688412 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
688427 C
1 C
688428 GTCCCATGTT
Statistics
Matches: 131, Mismatches: 18, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
15 47 0.36
16 36 0.27
17 29 0.22
18 6 0.05
19 6 0.05
20 6 0.05
21 1 0.01
ACGTcount: A:0.18, C:0.53, G:0.08, T:0.21
Consensus pattern (15 bp):
CCCCATGCATTCCCA
Found at i:688313 original size:51 final size:50
Alignment explanation
Indices: 688236--688362 Score: 215
Period size: 51 Copynumber: 2.6 Consensus size: 50
688226 GCGACCACCG
688236 TGACCATCCCCT-CCCCATGCATTCCCACCCCATGCATTCCCACGTCCAA
1 TGACCATCCCCTCCCCCATGCATTCCCACCCCATGCATTCCCACGTCCAA
*
688285 TGCACCATCCCCTCCCCCATGCATTCCCACCCCATGCATTCCCACGTCCCA
1 TG-ACCATCCCCTCCCCCATGCATTCCCACCCCATGCATTCCCACGTCCAA
688336 TG--CATCCCCTCCCCCATGCATTCCCAC
1 TGACCATCCCCTCCCCCATGCATTCCCAC
688363 ATCCCATGTT
Statistics
Matches: 75, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
48 25 0.33
49 2 0.03
50 10 0.13
51 38 0.51
ACGTcount: A:0.18, C:0.54, G:0.08, T:0.20
Consensus pattern (50 bp):
TGACCATCCCCTCCCCCATGCATTCCCACCCCATGCATTCCCACGTCCAA
Found at i:688391 original size:82 final size:83
Alignment explanation
Indices: 688249--688427 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 83
688239 CCATCCCCTC
* *
688249 CCCATGCATTCCCACCCCATGCATTCCCACGTCCAATGCACCATCCCCTCCCCCATGCATTCCCA
1 CCCATGCATCCCCACCCCATGCATTCCCACATCCAATGCACCATCCCCTCCCCCATGCATTCCCA
688314 CCCCATGCATTCCCACGT
66 CCCCATGCATTCCCACGT
* * ***
688332 CCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATG-TTGAT-CCCTCCCCCATGCATTCCC
1 CCCATGCATCCCC-ACCCCATGCATTCCCACATCCAATGCACCATCCCCTCCCCCATGCATTCCC
* * *
688395 ACCCCATGCATCCCCTC-C
65 ACCCCATGCATTCCCACGT
*
688413 CCCATGCATTCCCAC
1 CCCATGCATCCCCAC
688428 GTCCCATGTT
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
80 1 0.01
81 12 0.14
82 34 0.41
83 14 0.17
84 22 0.27
ACGTcount: A:0.18, C:0.53, G:0.08, T:0.21
Consensus pattern (83 bp):
CCCATGCATCCCCACCCCATGCATTCCCACATCCAATGCACCATCCCCTCCCCCATGCATTCCCA
CCCCATGCATTCCCACGT
Found at i:688411 original size:65 final size:66
Alignment explanation
Indices: 688314--688440 Score: 229
Period size: 65 Copynumber: 1.9 Consensus size: 66
688304 TGCATTCCCA
688314 CCCCATGCATTCCCACGTCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGATCCC
1 CCCCATGCATTCCCACG-CCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGATCCC
688379 TC
65 TC
*
688381 CCCCATGCATTCCCAC-CCCATGCATCCCCTCCCCCATGCATTCCCACGTCCCATGTTGAT
1 CCCCATGCATTCCCACGCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGAT
688441 TGCATGCATC
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 43 0.73
67 16 0.27
ACGTcount: A:0.17, C:0.50, G:0.09, T:0.24
Consensus pattern (66 bp):
CCCCATGCATTCCCACGCCCATGCATCCCCTCCCCCATGCATTCCCACATCCCATGTTGATCCCT
C
Found at i:688561 original size:29 final size:29
Alignment explanation
Indices: 688528--688616 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
688518 TAATACACAC
688528 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
688557 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
688586 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
688615 AG
1 AG
688617 ACCACTGTAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:692256 original size:21 final size:21
Alignment explanation
Indices: 692217--692256 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
692207 TCATTTTCAT
* * *
692217 TGTATTTTATTTTATTTTTTA
1 TGTATTTGATATTAATTTTTA
692238 TGTATTTGATATTAATTTT
1 TGTATTTGATATTAATTTT
692257 AGGGTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (21 bp):
TGTATTTGATATTAATTTTTA
Found at i:697686 original size:22 final size:20
Alignment explanation
Indices: 697643--697686 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
697633 ATCACATGAA
* *
697643 ATTTTATCTAAAATAGATTT
1 ATTTTATATAAAATAGACTT
697663 ATTTATATATAAATATAGACTT
1 ATTT-TATATAAA-ATAGACTT
697685 AT
1 AT
697687 AAACAAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 7 0.35
22 9 0.45
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (20 bp):
ATTTTATATAAAATAGACTT
Found at i:701505 original size:66 final size:66
Alignment explanation
Indices: 701399--701526 Score: 238
Period size: 66 Copynumber: 1.9 Consensus size: 66
701389 TCTAACAGTT
*
701399 TTAATATAAAATATTTTACAATACAAAACTACCTAAAAGTGTTATTTGAATTGAATTTAGATACT
1 TTAATATAAAATATCTTACAATACAAAACTACCTAAAAGTGTTATTTGAATTGAATTTAGATACT
701464 G
66 G
*
701465 TTAATATAAAATATCTTACAATACAAAACTGCCTAAAAGTGTTATTTGAATTGAATTTAGAT
1 TTAATATAAAATATCTTACAATACAAAACTACCTAAAAGTGTTATTTGAATTGAATTTAGAT
701527 TTTAGTATTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (66 bp):
TTAATATAAAATATCTTACAATACAAAACTACCTAAAAGTGTTATTTGAATTGAATTTAGATACT
G
Found at i:701687 original size:2 final size:2
Alignment explanation
Indices: 701682--701720 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
701672 CGAGTGTGTG
701682 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
701721 GATAGATCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:711018 original size:20 final size:20
Alignment explanation
Indices: 710988--711045 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
710978 ACCTTTAAAG
710988 CATGTCAAAAAGACATAAAAA
1 CATGTC-AAAAGACATAAAAA
711009 CATGTCAAAAGACATAAAAA
1 CATGTCAAAAGACATAAAAA
711029 CATGTCAAAAGACATAA
1 CATGTCAAAAGACATAA
711046 TTATTAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 31 0.84
21 6 0.16
ACGTcount: A:0.59, C:0.16, G:0.10, T:0.16
Consensus pattern (20 bp):
CATGTCAAAAGACATAAAAA
Found at i:712810 original size:14 final size:14
Alignment explanation
Indices: 712791--712828 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
712781 GAATAATATT
*
712791 TTATATATTTTACA
1 TTATATATTTTAAA
712805 TTATATA-TTTAAA
1 TTATATATTTTAAA
*
712818 TTAAATATTTT
1 TTATATATTTT
712829 TAATGTCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
TTATATATTTTAAA
Found at i:715576 original size:40 final size:40
Alignment explanation
Indices: 715536--715613 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
715526 ATATGTATTA
715536 TATATCAT--TATAAAATAATATTTA-AATTAAAATTAAAT
1 TATATCATAGTATAAAA-AATATTTATAATTAAAATTAAAT
* * *
715574 TATATCATAGTATTATAAATATTTATAATTAAATTTAAAT
1 TATATCATAGTATAAAAAATATTTATAATTAAAATTAAAT
715614 AAAACTTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 8 0.24
39 8 0.24
40 18 0.53
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (40 bp):
TATATCATAGTATAAAAAATATTTATAATTAAAATTAAAT
Found at i:721116 original size:19 final size:20
Alignment explanation
Indices: 721079--721127 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
721069 ATAACTGTAA
721079 AAATAATATTTTGAAATAAT
1 AAATAATATTTTGAAATAAT
***
721099 -AATAATATTTTTTTATAAT
1 AAATAATATTTTGAAATAAT
721118 AAATAATATT
1 AAATAATATT
721128 ATTTATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AAATAATATTTTGAAATAAT
Found at i:721132 original size:19 final size:19
Alignment explanation
Indices: 721094--721133 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
721084 ATATTTTGAA
*
721094 ATAATAATAATATTTTTTT
1 ATAATAATAATATTTATTT
721113 ATAATAAATAATA-TTATTT
1 ATAAT-AATAATATTTATTT
721132 AT
1 AT
721134 TAAATTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATAATAATAATATTTATTT
Found at i:722998 original size:148 final size:148
Alignment explanation
Indices: 722730--723053 Score: 470
Period size: 148 Copynumber: 2.2 Consensus size: 148
722720 AGAAATTAGT
*
722730 TGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTTATCATTTTTT
1 TGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTTAGCATTTTTT
* ** * * *
722795 GGCCTCCTGTATTATTAATGGCCCATTGTAAAGATTATTAATGACTCATTTTGACATTTTCAGGC
66 GGCATCCTACATTATTAATGACCCATTCTAAAGATTATTAATGACCCATTTTGACATTTTCAGGC
* *
722860 AT-GATGTATTATTAAATA
131 ATAG-TGCATTATTAAAGA
* *
722878 TGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCATTGAAAAGTTGTTGGCATTTTTT
1 TGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTTAGCATTTTTT
* * * *
722943 GGCATCCTACATTATTAATGACCCGTTCTGAAGATTATTAATGGCCCATTTTGACATTTTCGGGC
66 GGCATCCTACATTATTAATGACCCATTCTAAAGATTATTAATGACCCATTTTGACATTTTCAGGC
*
723008 ATAGTGCATTATTAGAGA
131 ATAGTGCATTATTAAAGA
* *
723026 TAACATTTGACTGAAAAGTTGCTGAAGA
1 TGACATTTCACTGAAAAGTTGCTGAAGA
723054 GGAACATAAT
Statistics
Matches: 157, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
148 156 0.99
149 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (148 bp):
TGACATTTCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTTAGCATTTTTT
GGCATCCTACATTATTAATGACCCATTCTAAAGATTATTAATGACCCATTTTGACATTTTCAGGC
ATAGTGCATTATTAAAGA
Found at i:723145 original size:102 final size:102
Alignment explanation
Indices: 722967--723173 Score: 326
Period size: 102 Copynumber: 2.0 Consensus size: 102
722957 TTAATGACCC
*
722967 GTTCTGAAGATTATTAATGGCCCATTTTGACATTTTCGGGCATAGTGCATTATTAGAGATAACAT
1 GTTCTAAAGATTATTAATGGCCCATTTTGACATTTTCGGGCATAGTGCATTATTAGAGATAACAT
* *
723032 TTGACTGAAAAGTTGCTGAAGAGGAACATAATTGGCA
66 TTCACTAAAAAGTTGCTGAAGAGGAACATAATTGGCA
** *
723069 GTTCTAAAGATTATTAATGTTCCGTTTTGACATTTTCGGGCAT-GTTGCATTATTAGAGATAACA
1 GTTCTAAAGATTATTAATGGCCCATTTTGACATTTTCGGGCATAG-TGCATTATTAGAGATAACA
* *
723133 TTTCACTAAAAAGTTGTTGAAGATGAACATAATTGGCA
65 TTTCACTAAAAAGTTGCTGAAGAGGAACATAATTGGCA
723171 GTT
1 GTT
723174 GGGTATGATG
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
101 1 0.01
102 95 0.99
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (102 bp):
GTTCTAAAGATTATTAATGGCCCATTTTGACATTTTCGGGCATAGTGCATTATTAGAGATAACAT
TTCACTAAAAAGTTGCTGAAGAGGAACATAATTGGCA
Found at i:726115 original size:3 final size:3
Alignment explanation
Indices: 726107--726145 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
726097 ATATATTAAA
* * *
726107 AAT AAT AAT AAT AAT ATT AAT ATT AAT ATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
726146 TTAATATAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:726127 original size:12 final size:12
Alignment explanation
Indices: 726107--726151 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
726097 ATATATTAAA
*
726107 AATAATAATAAT
1 AATATTAATAAT
*
726119 AATATTAATATT
1 AATATTAATAAT
726131 AATATTAATAAT
1 AATATTAATAAT
726143 AAT-TTAATA
1 AATATTAATA
726152 TAAAAAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 6 0.20
12 24 0.80
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATTAATAAT
Found at i:728089 original size:2 final size:2
Alignment explanation
Indices: 728084--728110 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
728074 TTTCAGTCTA
728084 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
728111 GTGTGTGTGT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:729269 original size:2 final size:2
Alignment explanation
Indices: 729262--729307 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
729252 AATGATTAAT
729262 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
729304 AG AG
1 AG AG
729308 TTTACTGTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:729448 original size:60 final size:60
Alignment explanation
Indices: 729350--729713 Score: 469
Period size: 60 Copynumber: 6.1 Consensus size: 60
729340 ATACTCTAAG
** *
729350 TTAGAAGGCCCTTCAAAGCCCTCGGCTGCAATAGCTATATTATGTTGATTGCTGCTTTCA
1 TTAGAAGGCATTTCAAAGCCCTCGGCTGCAATAACTATATTATGTTGATTGCTGCTTTCA
* * * * *
729410 TTAGACGACATTTCGAAGCCCTCGACTGCAACAACTATATTATGTTGATTGCTGCTTTCA
1 TTAGAAGGCATTTCAAAGCCCTCGGCTGCAATAACTATATTATGTTGATTGCTGCTTTCA
* * * *
729470 TTAGAAGGCATTTCGAAGCTCTTGTCTGCAATAACTATATTATGTTGATTGCTGCTTTCA
1 TTAGAAGGCATTTCAAAGCCCTCGGCTGCAATAACTATATTATGTTGATTGCTGCTTTCA
* *
729530 TTAGAAGGCATTTCAAAGCCCTCGGCTGCAATAACTATATTATGTTGATTGCTGATTTCG
1 TTAGAAGGCATTTCAAAGCCCTCGGCTGCAATAACTATATTATGTTGATTGCTGCTTTCA
* * * * * **
729590 TTAGAAGGCCTTTCTAAGCCCTTGGCTGCAATAACTATATCATGTTGATTGTTGCTTTTG
1 TTAGAAGGCATTTCAAAGCCCTCGGCTGCAATAACTATATTATGTTGATTGCTGCTTTCA
* * * * * *
729650 TTAGAAGGCATTTCAAAGCCATTGGCTGC-ATCAACTATATCATATTGATTGCTTCTTTCT
1 TTAGAAGGCATTTCAAAGCCCTCGGCTGCAAT-AACTATATTATGTTGATTGCTGCTTTCA
729710 TTAG
1 TTAG
729714 TGATAGTTTC
Statistics
Matches: 268, Mismatches: 35, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
59 2 0.01
60 266 0.99
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (60 bp):
TTAGAAGGCATTTCAAAGCCCTCGGCTGCAATAACTATATTATGTTGATTGCTGCTTTCA
Found at i:730426 original size:2 final size:2
Alignment explanation
Indices: 730421--730461 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
730411 AGTATATATA
*
730421 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
730462 TATGGTAGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.02, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:749635 original size:36 final size:35
Alignment explanation
Indices: 749533--749616 Score: 132
Period size: 35 Copynumber: 2.4 Consensus size: 35
749523 ACCCGCACTT
* * * *
749533 CTCTGGGTTTAAAAGAATACATATAGTCCAAACAG
1 CTCTGGGTTTGAAAGAATATATATAGCCCAAACAA
749568 CTCTGGGTTTGAAAGAATATATATAGCCCAAACAA
1 CTCTGGGTTTGAAAGAATATATATAGCCCAAACAA
749603 CTCTGGGTTTGAAA
1 CTCTGGGTTTGAAA
749617 CCTACTAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (35 bp):
CTCTGGGTTTGAAAGAATATATATAGCCCAAACAA
Found at i:750143 original size:14 final size:14
Alignment explanation
Indices: 750114--750142 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
750104 TAAGTCCGTC
750114 TTAAAATTATTTTT
1 TTAAAATTATTTTT
750128 TTAAAA-TATTTTT
1 TTAAAATTATTTTT
750141 TT
1 TT
750143 TTACTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTAAAATTATTTTT
Found at i:756709 original size:36 final size:36
Alignment explanation
Indices: 756556--756734 Score: 189
Period size: 36 Copynumber: 5.0 Consensus size: 36
756546 CGTTTTGGGA
* *
756556 AAAGCTAAACAAGCTCAACCGCCGGCAGCTCAAAAC
1 AAAGCTAAACAAGCTCAACCTCCGGCAGCTCAGAAC
** * *
756592 AAAGCTAAATTATCTCAACCTCCGGTAGCTCAGAAC
1 AAAGCTAAACAAGCTCAACCTCCGGCAGCTCAGAAC
** * *
756628 AAAGCTAAATTATCTCAACCTCCGGTAGCTCAGAAC
1 AAAGCTAAACAAGCTCAACCTCCGGCAGCTCAGAAC
*
756664 AAAGCTAAACAAGCTCAA-CTGCCGGCATCTCAGAAC
1 AAAGCTAAACAAGCTCAACCT-CCGGCAGCTCAGAAC
* * * * * *
756700 AAAACTAAACAATCTGAACCACCGCCGGCTCAGAA
1 AAAGCTAAACAAGCTCAACCTCCGGCAGCTCAGAA
756735 TCTTGTACTT
Statistics
Matches: 123, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
35 2 0.02
36 120 0.98
37 1 0.01
ACGTcount: A:0.39, C:0.30, G:0.15, T:0.16
Consensus pattern (36 bp):
AAAGCTAAACAAGCTCAACCTCCGGCAGCTCAGAAC
Found at i:757276 original size:6 final size:6
Alignment explanation
Indices: 757261--757295 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
757251 GGAGTACTGT
* *
757261 GAAGAA GAAGAG GAAGAG GAAGAG GAAAAG GAAGA
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGA
757296 AACCGTGCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:757735 original size:38 final size:40
Alignment explanation
Indices: 757657--757751 Score: 97
Period size: 38 Copynumber: 2.4 Consensus size: 40
757647 TTTAAACATT
* **
757657 AAAAACAATTAAAATATATTATAATAATCAATGATGATAAA
1 AAAAACAATTAAAATATATTAAAATAAT-AATGAAAATAAA
* *
757698 AAAAACAATTAAAATATA-TAAAATAAT-TTTAAAATAAA
1 AAAAACAATTAAAATATATTAAAATAATAATGAAAATAAA
*
757736 AAATAA-AATTATAATA
1 AAA-AACAATTAAAATA
757752 AAAGTAATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
38 19 0.40
39 2 0.04
40 8 0.17
41 18 0.38
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.29
Consensus pattern (40 bp):
AAAAACAATTAAAATATATTAAAATAATAATGAAAATAAA
Found at i:757751 original size:18 final size:18
Alignment explanation
Indices: 757693--757754 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
757683 ATCAATGATG
757693 ATAAAAAA-AACAATTAAA
1 ATAAAAAATAA-AATTAAA
**
757711 ATATATAAAATAATTTTAAA
1 ATA-A-AAAATAAAATTAAA
*
757731 ATAAAAAATAAAATTATA
1 ATAAAAAATAAAATTAAA
757749 ATAAAA
1 ATAAAA
757755 GTAATTATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
18 20 0.56
19 2 0.06
20 12 0.33
21 2 0.06
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
ATAAAAAATAAAATTAAA
Found at i:762880 original size:21 final size:21
Alignment explanation
Indices: 762841--762880 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
762831 GGGTACTAGT
*
762841 TATTTGTTTGAGATTTATTGG
1 TATTTGTTTGAGATCTATTGG
762862 TATTTGTTTGTA-ATCTATT
1 TATTTGTTTG-AGATCTATT
762881 TACGTATGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.20, C:0.03, G:0.17, T:0.60
Consensus pattern (21 bp):
TATTTGTTTGAGATCTATTGG
Found at i:781470 original size:36 final size:36
Alignment explanation
Indices: 781413--781487 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
781403 ACTAAACCCG
*
781413 TCCCCGTCCCCGTTTAACATAAA-GAGTTTTTCCCTA
1 TCCCCGTCCCCGTTTAACATAAACG-GTTTTTCCCCA
* *
781449 TCCCTGTCCCCGTTTAGCATAAACGGTTTTTCCCCA
1 TCCCCGTCCCCGTTTAACATAAACGGTTTTTCCCCA
781485 TCC
1 TCC
781488 TCGTTTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
36 34 0.97
37 1 0.03
ACGTcount: A:0.19, C:0.36, G:0.12, T:0.33
Consensus pattern (36 bp):
TCCCCGTCCCCGTTTAACATAAACGGTTTTTCCCCA
Found at i:783897 original size:17 final size:17
Alignment explanation
Indices: 783875--783909 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
783865 CCCGACCCGA
*
783875 CCGACCCGATCGTTGAC
1 CCGACCCGACCGTTGAC
783892 CCGACCCGACCGTTGAC
1 CCGACCCGACCGTTGAC
783909 C
1 C
783910 GTTAACTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.14
Consensus pattern (17 bp):
CCGACCCGACCGTTGAC
Found at i:787302 original size:15 final size:15
Alignment explanation
Indices: 787279--787319 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
787269 ATGACCACGT
*
787279 GCCGAGCCGAGCCGA
1 GCCGTGCCGAGCCGA
* *
787294 GCCGTGCCGTGCCGT
1 GCCGTGCCGAGCCGA
787309 GCCGTGCCGAG
1 GCCGTGCCGAG
787320 ACGAACGACG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.10, C:0.39, G:0.41, T:0.10
Consensus pattern (15 bp):
GCCGTGCCGAGCCGA
Found at i:792534 original size:21 final size:22
Alignment explanation
Indices: 792486--792534 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
792476 ATAATAAGAT
792486 AAACATTTTAAAAAATTTAATG
1 AAACATTTTAAAAAATTTAATG
*
792508 -ACCATTTTAAAAAA-TTAATG
1 AAACATTTTAAAAAATTTAATG
792528 AAACATT
1 AAACATT
792535 AAGGACTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (22 bp):
AAACATTTTAAAAAATTTAATG
Found at i:792768 original size:2 final size:2
Alignment explanation
Indices: 792761--792791 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
792751 ATAATAAATA
792761 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
792792 AACAAGTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:796777 original size:16 final size:15
Alignment explanation
Indices: 796748--796789 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
796738 CGATTTTTCG
796748 TTATAATT-TTTTTA
1 TTATAATTATTTTTA
796762 TTATAATTATTGTTTA
1 TTATAATTATT-TTTA
*
796778 TTATGATTATTT
1 TTATAATTATTT
796790 GAAAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 8 0.32
15 3 0.12
16 14 0.56
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (15 bp):
TTATAATTATTTTTA
Found at i:800128 original size:35 final size:34
Alignment explanation
Indices: 800043--800129 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
800033 AATATAATTT
*
800043 TAAATACAACAAACTTACAATAAGAATTAAATAG
1 TAAATACAACAAAATTACAATAAGAATTAAATAG
* * *
800077 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATAG
800115 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
800130 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATAG
Found at i:802427 original size:17 final size:18
Alignment explanation
Indices: 802407--802447 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
802397 AAATTATATT
802407 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
802424 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
802442 ATTAAA
1 AGTAAA
802448 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:806590 original size:23 final size:23
Alignment explanation
Indices: 806562--806610 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
806552 TATGTTGAAC
*
806562 CTTTTAAACTAATAGTTGAAATA
1 CTTTTAAACCAATAGTTGAAATA
806585 CTTTTAAACCAATAGTTGAAATA
1 CTTTTAAACCAATAGTTGAAATA
806608 CTT
1 CTT
806611 AAATGTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (23 bp):
CTTTTAAACCAATAGTTGAAATA
Found at i:808000 original size:16 final size:16
Alignment explanation
Indices: 807981--808014 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
807971 CAATATACGA
807981 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
807997 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
808013 AT
1 AT
808015 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:808089 original size:16 final size:18
Alignment explanation
Indices: 808057--808090 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
808047 TATTAATGTA
808057 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
808075 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
808091 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:808761 original size:130 final size:130
Alignment explanation
Indices: 808557--808804 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
808547 AATTTTCTTC
* * *
808557 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAATACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
808622 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAACATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAACATATATAAA
* * *
808687 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
808752 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
808805 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAACATATATAAA
Found at i:809262 original size:35 final size:35
Alignment explanation
Indices: 809201--809276 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
809191 AATTGAATTT
* * *
809201 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGAAAATTAGGGTTTAGAATGA
*
809236 AATTGAATTACTTTGAAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGAAAATTAGGGTTTAGAATGA
809271 AATTGA
1 AATTGA
809277 GGACTATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGAAAATTAGGGTTTAGAATGA
Found at i:811600 original size:31 final size:31
Alignment explanation
Indices: 811562--811651 Score: 144
Period size: 31 Copynumber: 2.9 Consensus size: 31
811552 CAAATTTTTT
*
811562 TTGTTCATGTTCGTTCATTAAAGAATATAGC
1 TTGTTCATGTTCGTTCATTAAAGAATATAGA
*
811593 TTGTTCATGTTCGTTCATTAAGGAATATAGA
1 TTGTTCATGTTCGTTCATTAAAGAATATAGA
*
811624 TTGTTCATGTTCGTTCATTTAAATAATA
1 TTGTTCATGTTCGTTCA-TTAAAGAATA
811652 AACGAACACG
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
31 46 0.85
32 8 0.15
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (31 bp):
TTGTTCATGTTCGTTCATTAAAGAATATAGA
Found at i:811671 original size:14 final size:14
Alignment explanation
Indices: 811652--811691 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
811642 TTAAATAATA
*
811652 AACGAACACGAACG
1 AACGAACACAAACG
*
811666 AACGAACATAAACG
1 AACGAACACAAACG
811680 AAC-AACACAAAC
1 AACGAACACAAAC
811692 ACAAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.57, C:0.28, G:0.12, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:812525 original size:36 final size:36
Alignment explanation
Indices: 812457--812525 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
812447 GGGACGATGA
** *
812457 AAAATCGTTTATGATAAACGGGGACGGTGATGGAAG
1 AAAATCGTTTATGATAAACGGCAACGGAGATGGAAG
*
812493 AAAATCGTTTATGCTAAACGGCAACGGAGATGG
1 AAAATCGTTTATGATAAACGGCAACGGAGATGG
812526 GTTTGATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (36 bp):
AAAATCGTTTATGATAAACGGCAACGGAGATGGAAG
Found at i:812604 original size:2 final size:2
Alignment explanation
Indices: 812597--812681 Score: 53
Period size: 2 Copynumber: 47.0 Consensus size: 2
812587 TTAAAATAAT
*
812597 TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A TA AA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
812634 AA T- TA -A AA AA TA TA TA TA -A TA TT TA TA TA TT TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
812672 TA TA TA TA TA
1 TA TA TA TA TA
812682 CCCGGCCCGA
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
1 9 0.14
2 57 0.86
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:812662 original size:13 final size:13
Alignment explanation
Indices: 812592--812679 Score: 66
Period size: 13 Copynumber: 7.2 Consensus size: 13
812582 AATATTTAAA
812592 ATAAT-TATATAT
1 ATAATATATATAT
812604 AT-ATATATATAT
1 ATAATATATATAT
812616 ATAATAT-TA-AT
1 ATAATATATATAT
*
812627 A-AAT-TA-AAAT
1 ATAATATATATAT
* *
812637 -TAAAAAATATAT
1 ATAATATATATAT
812649 ATAATATTTATATAT
1 ATAATA--TATATAT
*
812664 TTAATATATATAT
1 ATAATATATATAT
812677 ATA
1 ATA
812680 TACCCGGCCC
Statistics
Matches: 59, Mismatches: 7, Indels: 19
0.69 0.08 0.22
Matches are distributed among these distances:
9 2 0.03
10 7 0.12
11 6 0.10
12 16 0.27
13 17 0.29
15 11 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:812663 original size:15 final size:15
Alignment explanation
Indices: 812643--812681 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
812633 AAATTAAAAA
*
812643 ATATATATAATATTT
1 ATATATATAATATAT
*
812658 ATATATTTAATATAT
1 ATATATATAATATAT
812673 ATATATATA
1 ATATATATA
812682 CCCGGCCCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATATATAATATAT
Found at i:813143 original size:2 final size:2
Alignment explanation
Indices: 813136--813165 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
813126 TTCTTTAATT
813136 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
813166 TGGTTGAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:816091 original size:20 final size:20
Alignment explanation
Indices: 816066--816131 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
816056 GTTGCAACTT
816066 AAAATTTGGTTTCTATATGA
1 AAAATTTGGTTTCTATATGA
** * *
816086 AAAATTAAGTTTCAACCTA-AA
1 AAAATTTGGTTTCTA--TATGA
* *
816107 AAAATCTGGTTTGTATATGA
1 AAAATTTGGTTTCTATATGA
816127 AAAAT
1 AAAAT
816132 CGGTTGCAAC
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
19 2 0.06
20 18 0.55
21 11 0.33
22 2 0.06
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (20 bp):
AAAATTTGGTTTCTATATGA
Found at i:820029 original size:17 final size:17
Alignment explanation
Indices: 820007--820039 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
819997 TATGCAAGAG
820007 TTTAATTTAAAACAAAA
1 TTTAATTTAAAACAAAA
820024 TTTAATTTAAAACAAA
1 TTTAATTTAAAACAAA
820040 GTTCTAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
TTTAATTTAAAACAAAA
Found at i:822882 original size:30 final size:30
Alignment explanation
Indices: 822841--822945 Score: 192
Period size: 30 Copynumber: 3.5 Consensus size: 30
822831 ATTAAAAAAA
*
822841 GACCAAAATGGAAATTCTCTATATGTTAAG
1 GACCAAAATGGAAATTATCTATATGTTAAG
*
822871 GACCGAAATGGAAATTATCTATATGTTAAG
1 GACCAAAATGGAAATTATCTATATGTTAAG
822901 GACCAAAATGGAAATTATCTATATGTTAAG
1 GACCAAAATGGAAATTATCTATATGTTAAG
822931 GACCAAAATGGAAAT
1 GACCAAAATGGAAAT
822946 GATAAGAATT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (30 bp):
GACCAAAATGGAAATTATCTATATGTTAAG
Found at i:828569 original size:17 final size:17
Alignment explanation
Indices: 828543--828577 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
828533 TATTCCCAGA
828543 TCCATGCCCATTCACAT
1 TCCATGCCCATTCACAT
* *
828560 TCCATTCCCATTCCCAT
1 TCCATGCCCATTCACAT
828577 T
1 T
828578 GTTGGCATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.43, G:0.03, T:0.34
Consensus pattern (17 bp):
TCCATGCCCATTCACAT
Found at i:832598 original size:31 final size:30
Alignment explanation
Indices: 832554--832619 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
832544 CAAAAAACAT
**
832554 AAGATATAGTCACTTTTGTTTTTATTTAATC
1 AAGATATAGTCAC-TTTCATTTTATTTAATC
*
832585 AAGATAT-GATCACTTTCATTTTATTTAATT
1 AAGATATAG-TCACTTTCATTTTATTTAATC
832615 AAGAT
1 AAGAT
832620 GTGGTCACCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (30 bp):
AAGATATAGTCACTTTCATTTTATTTAATC
Found at i:833416 original size:23 final size:23
Alignment explanation
Indices: 833349--833399 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 23
833339 TATAATTATA
833349 TATTAACTTA--AAATA--TTA-
1 TATTAACTTATTAAATATTTTAC
833367 TATTAACTTATTAAATATTTTAC
1 TATTAACTTATTAAATATTTTAC
833390 TATTAACTTA
1 TATTAACTTA
833400 ATTTAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.36
20 5 0.18
22 3 0.11
23 10 0.36
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTAACTTATTAAATATTTTAC
Found at i:835289 original size:28 final size:27
Alignment explanation
Indices: 835234--835289 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
835224 ATTAGGTAAA
*
835234 TTATTTGTATAATCATTAATCGTTTCT
1 TTATTTGTATAATCATTAATCATTTCT
*
835261 TTATTTGTATAATCATTTAATTATTTCT
1 TTATTTGTATAATCA-TTAATCATTTCT
835289 T
1 T
835290 CTTTTCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.59
Consensus pattern (27 bp):
TTATTTGTATAATCATTAATCATTTCT
Found at i:837631 original size:22 final size:21
Alignment explanation
Indices: 837591--837631 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
837581 ATTAATAAGA
*
837591 TTGATATAATTATATATTTGG
1 TTGATATAATTATACATTTGG
*
837612 TTGATATTATTTATACATTT
1 TTGATA-TAATTATACATTT
837632 TATTATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (21 bp):
TTGATATAATTATACATTTGG
Found at i:839509 original size:13 final size:15
Alignment explanation
Indices: 839478--839510 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
839468 CTTCTTCATC
839478 TTTCCCATTGGATGT
1 TTTCCCATTGGATGT
839493 TTTCCCA-TGGA-GT
1 TTTCCCATTGGATGT
839506 TTTCC
1 TTTCC
839511 GGTAAGCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 4 0.22
15 7 0.39
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.45
Consensus pattern (15 bp):
TTTCCCATTGGATGT
Found at i:840801 original size:2 final size:2
Alignment explanation
Indices: 840794--840840 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
840784 TCAAACAATA
840794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
840836 AT AT A
1 AT AT A
840841 GTACTATTCG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:845368 original size:33 final size:33
Alignment explanation
Indices: 845326--845402 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
845316 GAGTGGTAAG
*
845326 CGTTGCTGTCGGTTTGGTTTTTTGTGGGTCCTA
1 CGTTGCTGTCGGTTTGGTTTTTGGTGGGTCCTA
845359 CGTTGCTGTCGGTTTGGTTTTTGGTGGGTCCTA
1 CGTTGCTGTCGGTTTGGTTTTTGGTGGGTCCTA
845392 CGTTGCTGTCG
1 CGTTGCTGTCG
845403 TGGAGTAGGC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.03, C:0.17, G:0.35, T:0.45
Consensus pattern (33 bp):
CGTTGCTGTCGGTTTGGTTTTTGGTGGGTCCTA
Found at i:845698 original size:22 final size:22
Alignment explanation
Indices: 845673--845739 Score: 54
Period size: 20 Copynumber: 3.2 Consensus size: 22
845663 TTTTGTTACA
845673 CAATTTATTACTTTTTAAATTT
1 CAATTTATTACTTTTTAAATTT
* * *
845695 CAA-TCA-GAATTTTT---TTT
1 CAATTTATTACTTTTTAAATTT
845712 AACAATTTATTACTTTTTAAATTT
1 --CAATTTATTACTTTTTAAATTT
845736 CAAT
1 CAAT
845740 CAGAAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 14
0.62 0.12 0.27
Matches are distributed among these distances:
17 3 0.09
19 3 0.09
20 8 0.25
21 8 0.25
22 7 0.22
24 3 0.09
ACGTcount: A:0.34, C:0.10, G:0.01, T:0.54
Consensus pattern (22 bp):
CAATTTATTACTTTTTAAATTT
Found at i:845719 original size:41 final size:42
Alignment explanation
Indices: 845663--845744 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 42
845653 GGGGTGACCA
845663 TTTTGTTACACAATTTATTACTTTTTAAATTTCAATCAGAAT
1 TTTTGTTACACAATTTATTACTTTTTAAATTTCAATCAGAAT
*
845705 TTTTTTTA-ACAATTTATTACTTTTTAAATTTCAATCAGAA
1 TTTTGTTACACAATTTATTACTTTTTAAATTTCAATCAGAA
845745 AAAAAAATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 32 0.82
42 7 0.18
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (42 bp):
TTTTGTTACACAATTTATTACTTTTTAAATTTCAATCAGAAT
Found at i:852223 original size:15 final size:15
Alignment explanation
Indices: 852203--852237 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
852193 TTAAAAAATA
*
852203 TATTTAATATTTATT
1 TATTTAATATATATT
*
852218 TATTTATTATATATT
1 TATTTAATATATATT
852233 TATTT
1 TATTT
852238 TATTAGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTAATATATATT
Found at i:852754 original size:21 final size:21
Alignment explanation
Indices: 852728--852768 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
852718 GATTTAAAAA
852728 TACTTTTAATTTATGGTAAAT
1 TACTTTTAATTTATGGTAAAT
852749 TACTTTTAATTTATGGTAAA
1 TACTTTTAATTTATGGTAAA
852769 ATATAAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (21 bp):
TACTTTTAATTTATGGTAAAT
Found at i:854353 original size:67 final size:67
Alignment explanation
Indices: 854245--854379 Score: 270
Period size: 67 Copynumber: 2.0 Consensus size: 67
854235 ACAAGAGCGG
854245 GTTCGTGGGGAAGACGGGTTATTGAGGATATCAACAGCAACCTTGTTGTCCGGCTCGATTTCAAT
1 GTTCGTGGGGAAGACGGGTTATTGAGGATATCAACAGCAACCTTGTTGTCCGGCTCGATTTCAAT
854310 CA
66 CA
854312 GTTCGTGGGGAAGACGGGTTATTGAGGATATCAACAGCAACCTTGTTGTCCGGCTCGATTTCAAT
1 GTTCGTGGGGAAGACGGGTTATTGAGGATATCAACAGCAACCTTGTTGTCCGGCTCGATTTCAAT
854377 CA
66 CA
854379 G
1 G
854380 ATTGAAACCA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (67 bp):
GTTCGTGGGGAAGACGGGTTATTGAGGATATCAACAGCAACCTTGTTGTCCGGCTCGATTTCAAT
CA
Found at i:859800 original size:22 final size:21
Alignment explanation
Indices: 859775--859818 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
859765 GGTGTAATCT
* *
859775 AATATGTTATTTCACAAATAAA
1 AATATATTAATTC-CAAATAAA
*
859797 AATATATTAATTCCCAATAAA
1 AATATATTAATTCCAAATAAA
859818 A
1 A
859819 TGTCAGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (21 bp):
AATATATTAATTCCAAATAAA
Found at i:861427 original size:19 final size:19
Alignment explanation
Indices: 861403--861439 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
861393 ATGCTTCAAA
861403 CATTCACATAATATATGCG
1 CATTCACATAATATATGCG
861422 CATTCACATAATATATGC
1 CATTCACATAATATATGC
861440 ATTGCATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (19 bp):
CATTCACATAATATATGCG
Found at i:862113 original size:28 final size:29
Alignment explanation
Indices: 862068--862135 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
862058 AAAACTAAAA
* *
862068 AATTATGAAAT-TATAAAAACAGGGG-CTT
1 AATTAT-AAATATAAAAAAACAGGGGTCCT
**
862096 AATTATAAATATAAAAAATTAGGGGTCCT
1 AATTATAAATATAAAAAAACAGGGGTCCT
862125 AATTATAAATA
1 AATTATAAATA
862136 CAAACAGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 4 0.12
28 17 0.50
29 13 0.38
ACGTcount: A:0.50, C:0.06, G:0.13, T:0.31
Consensus pattern (29 bp):
AATTATAAATATAAAAAAACAGGGGTCCT
Found at i:862113 original size:108 final size:113
Alignment explanation
Indices: 861895--862117 Score: 314
Period size: 108 Copynumber: 2.0 Consensus size: 113
861885 AAAAACATGA
* *
861895 TTAAATTTAATTCAAAATTAAATGAGTTAATAAGAGAAATGGAAAAGGAGGGTCAAAACTAAACA
1 TTAAATTTAATTCAAAATT--ATGAGATAATAAGAGAAATGGAAAAAGAGGGTCAAAACTAAACA
**
861960 TTTTATGAAATTATAAAAACTAGGGCCCTAATTATAAATATAAAAATTAG
64 AATTATGAAATTATAAAAACTAGGGCCCTAATTATAAATATAAAAATTAG
*
862010 TTAAATTTAATTCAAAA-T-TGA-ATAATAAGATAAAT-GAAAAAGAGGGTCAAAACTAAA-AAA
1 TTAAATTTAATTCAAAATTATGAGATAATAAGAGAAATGGAAAAAGAGGGTCAAAACTAAACAAA
* *
862070 TTATGAAATTATAAAAAC-AGGGGCTTAATTATAAATATAAAAAATTAG
66 TTATGAAATTATAAAAACTAGGGCCCTAATTATAAATAT-AAAAATTAG
862118 GGGTCCTAAT
Statistics
Matches: 100, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
107 18 0.18
108 28 0.28
109 21 0.21
110 12 0.12
111 3 0.03
114 1 0.01
115 17 0.17
ACGTcount: A:0.53, C:0.06, G:0.13, T:0.28
Consensus pattern (113 bp):
TTAAATTTAATTCAAAATTATGAGATAATAAGAGAAATGGAAAAAGAGGGTCAAAACTAAACAAA
TTATGAAATTATAAAAACTAGGGCCCTAATTATAAATATAAAAATTAG
Found at i:864870 original size:26 final size:26
Alignment explanation
Indices: 864842--864892 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
864832 TTAGAGAAAA
* *
864842 AAAATAAATT-ATTAATATAAAATAT
1 AAAAGAAATTAATTAATAAAAAATAT
*
864867 AAAAGAATTTAATTAATAAAAAATAT
1 AAAAGAAATTAATTAATAAAAAATAT
864893 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
AAAAGAAATTAATTAATAAAAAATAT
Found at i:871756 original size:112 final size:112
Alignment explanation
Indices: 871508--871849 Score: 524
Period size: 112 Copynumber: 3.0 Consensus size: 112
871498 ATTACAAAAA
*
871508 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAA-T-
* *
871573 AATTAAAACGTTAAAATGTTAAAATGTTATCGTATCAGCAAAGTGTCGATATAT
64 --TT-AAA--TTAAAATGTTAAAATGTTAACGTATCAGCAAAGTGTCGAGATAT
*
871627 TTGATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTT
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTT
* *
871692 AAATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AAATTAAAATGTTAAAATGTTAACGTATCAGCAAAGTGTCGAGATAT
* * *
871739 TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAAATATTACTGATAATTTAAA-TT
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTT
*
871803 AAATTAAAATGTTAAAATGTTAACGTATCAGCAAAGTGTAGAGATAT
66 AAATTAAAATGTTAAAATGTTAACGTATCAGCAAAGTGTCGAGATAT
871850 ATGATTTCCA
Statistics
Matches: 211, Mismatches: 12, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
111 46 0.22
112 99 0.47
114 3 0.01
115 2 0.01
118 1 0.00
119 60 0.28
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.37
Consensus pattern (112 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTT
AAATTAAAATGTTAAAATGTTAACGTATCAGCAAAGTGTCGAGATAT
Found at i:872014 original size:19 final size:20
Alignment explanation
Indices: 871975--872016 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
871965 CTTAAAAAGA
*
871975 TAGAGTATTTGAGAGAAATT
1 TAGAGAATTTGAGAGAAATT
871995 TAGAGAATTTGAGA-AAATT
1 TAGAGAATTTGAGAGAAATT
872014 TAG
1 TAG
872017 TGTGATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (20 bp):
TAGAGAATTTGAGAGAAATT
Found at i:873626 original size:68 final size:68
Alignment explanation
Indices: 873517--873719 Score: 316
Period size: 68 Copynumber: 3.0 Consensus size: 68
873507 CATCATAATC
* * *
873517 ATAATTAATCAAATTAAAAAATTAAAACGTAATATATATCATTATCACATGAATAGTTATATAAC
1 ATAATTAATCAAATTTAAAAATTAAAACGTAATATTTATCATAATCACATGAATAGTTATATAAC
873582 TAG
66 TAG
* *
873585 ATAATTAATCAAATTTAAAAATTAAATCGTATTATTTATCATAATCACATGAATAGTTATATAAC
1 ATAATTAATCAAATTTAAAAATTAAAACGTAATATTTATCATAATCACATGAATAGTTATATAAC
*
873650 TGG
66 TAG
* * * *
873653 ATTATTAATCAAATTTAAAAATTAAAACGTAATGTTTATCATAACCACTTGAATAGTTATATAAC
1 ATAATTAATCAAATTTAAAAATTAAAACGTAATATTTATCATAATCACATGAATAGTTATATAAC
873718 TA
66 TA
873720 AATACATAAT
Statistics
Matches: 122, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 122 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (68 bp):
ATAATTAATCAAATTTAAAAATTAAAACGTAATATTTATCATAATCACATGAATAGTTATATAAC
TAG
Found at i:875541 original size:97 final size:97
Alignment explanation
Indices: 875370--875561 Score: 253
Period size: 97 Copynumber: 2.0 Consensus size: 97
875360 ATGGGTGCTA
* * * * ** *
875370 TAGACAGCATAGGATCTGTGTCCTGATCGCAATCTTCAGAGATGAAAGATGAAACCGGGTGGTTC
1 TAGACAGCATAGAATCTGTGTCCTAATCACAATATTCAGAGACCAAAGATGAAACAGGGTGGTTC
* *
875435 TACTGCTAGAGTACTCTCAGAAA-ATCTTACTC
66 TACTCCTAGAGTACTATCA-AAAGATCTTACTC
* *
875467 TAGACAGCATAGAATCTGTGTCCTAATCACAATATTC-GAAGACCAAATATGGAACAGGGTGGTT
1 TAGACAGCATAGAATCTGTGTCCTAATCACAATATTCAG-AGACCAAAGATGAAACAGGGTGGTT
875531 CTACTCCTAGAGTACTATCAAAAGATCTTAC
65 CTACTCCTAGAGTACTATCAAAAGATCTTAC
875562 ATTATACTCT
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
96 4 0.05
97 78 0.95
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (97 bp):
TAGACAGCATAGAATCTGTGTCCTAATCACAATATTCAGAGACCAAAGATGAAACAGGGTGGTTC
TACTCCTAGAGTACTATCAAAAGATCTTACTC
Found at i:887260 original size:19 final size:20
Alignment explanation
Indices: 887183--887273 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 20
887173 AACGCGATTT
*
887183 TGAAAAATGTGTTACGATAG
1 TGAAAAATGTGTTGCGATAG
* *
887203 T-TAAAATGTGTTGCGAGAG
1 TGAAAAATGTGTTGCGATAG
887222 TTTGAAAAACGTGTTGTTGCGATAG
1 --TGAAAAA--TG-TGTTGCGATAG
887247 TGAAAAA-GTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
887266 TGAAAAAT
1 TGAAAAAT
887274 CCAAAATAAG
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
19 33 0.56
20 2 0.03
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.03
25 10 0.17
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.31
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:887260 original size:44 final size:41
Alignment explanation
Indices: 887181--887262 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 41
887171 GCAACGCGAT
* *
887181 TTTGAAAAATGTGTTACGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTACGATAGTGAAAAAGTGTTGCGAGAG
*
887222 TTTGAAAAACGTGTTGTTGCGATAGTGAAAAAGTGTTGCGA
1 TTTGAAAAA--TG-TGTTACGATAGTGAAAAAGTGTTGCGA
887263 TAGTGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 9 0.26
43 2 0.06
44 24 0.69
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (41 bp):
TTTGAAAAATGTGTTACGATAGTGAAAAAGTGTTGCGAGAG
Done.