Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold175
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: 1254584
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 4 of 8
Found at i:508475 original size:13 final size:13
Alignment explanation
Indices: 508454--508486 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
508444 CGATCCATGG
*
508454 TACAATGTATCGA
1 TACATTGTATCGA
508467 TACATTGTATCGA
1 TACATTGTATCGA
508480 TACATTG
1 TACATTG
508487 CTTGTAACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:510095 original size:15 final size:15
Alignment explanation
Indices: 510075--510103 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
510065 TTGTGAATTG
510075 TGATTTTTTTTATTT
1 TGATTTTTTTTATTT
510090 TGATTTTTTTTATT
1 TGATTTTTTTTATT
510104 GAATTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (15 bp):
TGATTTTTTTTATTT
Found at i:510109 original size:14 final size:14
Alignment explanation
Indices: 510075--510116 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
510065 TTGTGAATTG
510075 TGATTTTTTTTATTT
1 TGATTTTTTTTA-TT
510090 TGATTTTTTTTA-T
1 TGATTTTTTTTATT
* *
510103 TGAATTTTGTTATT
1 TGATTTTTTTTATT
510117 CTTTTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 11 0.46
14 1 0.04
15 12 0.50
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.74
Consensus pattern (14 bp):
TGATTTTTTTTATT
Found at i:510403 original size:27 final size:27
Alignment explanation
Indices: 510351--510403 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
510341 TAACTGAATC
* *
510351 GATTAAATCAAATTTAATTGATTTTTT
1 GATTAAATCAAATTTAATCGACTTTTT
*
510378 GATTAAAT-AAATCTTGATCGACTTTT
1 GATTAAATCAAAT-TTAATCGACTTTT
510404 ACTTTCCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (27 bp):
GATTAAATCAAATTTAATCGACTTTTT
Found at i:510507 original size:13 final size:13
Alignment explanation
Indices: 510489--510514 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
510479 GTGGGCAAGG
510489 TTTTATTTTTTTA
1 TTTTATTTTTTTA
510502 TTTTATTTTTTTA
1 TTTTATTTTTTTA
510515 ATGTAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:515802 original size:2 final size:2
Alignment explanation
Indices: 515738--515789 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
515728 GATTTATAAC
515738 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
515780 TA TA GA TA TA
1 TA TA TA TA TA
515790 AAACTTTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:519121 original size:2 final size:2
Alignment explanation
Indices: 519114--519144 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
519104 TGCTTTTTAC
519114 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 T
519145 GTATTATTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:522030 original size:16 final size:16
Alignment explanation
Indices: 522006--522065 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
521996 ATGATTGAAT
*
522006 TAATCTTAAACTT-AAA
1 TAATTTTAAA-TTAAAA
522022 TAATTTTAAATTAAAA
1 TAATTTTAAATTAAAA
* ***
522038 TTATTTTAAATTCTCA
1 TAATTTTAAATTAAAA
522054 TAATTTTAAATT
1 TAATTTTAAATT
522066 TTATATTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
15 2 0.05
16 35 0.95
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTTTAAATTAAAA
Found at i:522137 original size:30 final size:30
Alignment explanation
Indices: 522103--522165 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
522093 TTCTATAACT
*
522103 TAACATTATAGTTGTCCCCTAGGCCCTAGC
1 TAACATCATAGTTGTCCCCTAGGCCCTAGC
522133 TAACATCATAGTTGTCCCCTAGGCCCTAGC
1 TAACATCATAGTTGTCCCCTAGGCCCTAGC
522163 TAA
1 TAA
522166 TAATATTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (30 bp):
TAACATCATAGTTGTCCCCTAGGCCCTAGC
Found at i:522515 original size:27 final size:26
Alignment explanation
Indices: 522465--522515 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
522455 GTGTAATATT
*
522465 TATTTTATTTTTTTTATATTTTATCA
1 TATTTTATTTTTTTTATATATTATCA
522491 TATTTTAATTATTTTTT-TATATTAT
1 TATTTT-ATT-TTTTTTATATATTAT
522516 GTTCATGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 6 0.27
27 10 0.45
28 6 0.27
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (26 bp):
TATTTTATTTTTTTTATATATTATCA
Found at i:523629 original size:18 final size:16
Alignment explanation
Indices: 523606--523648 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 16
523596 ATATATATTT
523606 AAATAAATAATTTTCAA
1 AAATAAATAATTTT-AA
*
523623 AACATAAAAAAATTTTAA
1 AA-AT-AAATAATTTTAA
523641 AAATAAAT
1 AAATAAAT
523649 TAAATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 3 0.14
17 4 0.18
18 6 0.27
19 9 0.41
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATAAATAATTTTAA
Found at i:523653 original size:18 final size:18
Alignment explanation
Indices: 523606--523653 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
523596 ATATATATTT
523606 AAATAAAT-AATTTTCAA
1 AAATAAATAAATTTTCAA
*
523623 AACATAAAAAAATTTT-AA
1 AA-ATAAATAAATTTTCAA
523641 AAATAAATTAAAT
1 AAATAAA-TAAAT
523654 ATATTCAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.27
18 13 0.50
19 6 0.23
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAAATAAATTTTCAA
Found at i:524585 original size:2 final size:2
Alignment explanation
Indices: 524563--524615 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
524553 TCAATCTTCA
* *
524563 AT AT -T AT AC AT AT AC 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
524604 AT AT AT AT AT AT
1 AT AT AT AT AT AT
524616 CTGATTTTGG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:525817 original size:6 final size:6
Alignment explanation
Indices: 525806--525831 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
525796 ATATGTAATT
525806 TTTATA TTTATA TTTATA TTTATA TT
1 TTTATA TTTATA TTTATA TTTATA TT
525832 ATTTTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:530183 original size:20 final size:21
Alignment explanation
Indices: 530147--530187 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
530137 AGTATAGATA
530147 TTTTTCAAGCATAAAAATAATG
1 TTTTTCAAG-ATAAAAATAATG
530169 TTTTTCAAG-TAAAAATAAT
1 TTTTTCAAGATAAAAATAAT
530188 CCAAAGTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTTTCAAGATAAAAATAATG
Found at i:530325 original size:33 final size:33
Alignment explanation
Indices: 530283--530348 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
530273 CACACCCAGA
*
530283 TGTATCGATACAT-ATTACTTCGTATCGATACAT
1 TGTATCGATACATCATGACTT-GTATCGATACAT
*
530316 TGTATCGATATATCATGACTTGTATCGATACAT
1 TGTATCGATACATCATGACTTGTATCGATACAT
530349 AAAACTGGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 24 0.80
34 6 0.20
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATCATGACTTGTATCGATACAT
Found at i:530416 original size:14 final size:14
Alignment explanation
Indices: 530397--530427 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
530387 ATTACTGTTC
*
530397 ATCACTGTTCATGT
1 ATCACTATTCATGT
530411 ATCACTATTCATGT
1 ATCACTATTCATGT
530425 ATC
1 ATC
530428 GATACAAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.42
Consensus pattern (14 bp):
ATCACTATTCATGT
Found at i:530962 original size:35 final size:36
Alignment explanation
Indices: 530892--530963 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
530882 CTAAGTGATT
*
530892 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAAGGA
1 GAGAGGTTCTATCTTAGCCTGTGAAAAAGATAAGGA
530928 GAGAGGTTCTATCTTAGCCTGTG-AAAAGATAAGGA
1 GAGAGGTTCTATCTTAGCCTGTGAAAAAGATAAGGA
530963 G
1 G
530964 GTTTCTATCC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 13 0.37
36 22 0.63
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (36 bp):
GAGAGGTTCTATCTTAGCCTGTGAAAAAGATAAGGA
Found at i:530988 original size:30 final size:31
Alignment explanation
Indices: 530894--530988 Score: 86
Period size: 36 Copynumber: 2.9 Consensus size: 31
530884 AAGTGATTGA
* *
530894 GAGGTTCTATCTTAGCCTTTGAAAAAGATAAGGAG
1 GAGGTTCTATCCTAGCCTGTG-AAAAGAT-A--AG
*
530929 AGAGGTTCTATCTTAGCCTGTGAAAAGATAAG
1 -GAGGTTCTATCCTAGCCTGTGAAAAGATAAG
*
530961 GAGGTTTCTATCCTAGTCT-TG-AAAGATA
1 GAGG-TTCTATCCTAGCCTGTGAAAAGATA
530989 GTGTTGTAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
30 7 0.13
31 6 0.11
32 14 0.25
34 1 0.02
35 7 0.13
36 20 0.36
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.31
Consensus pattern (31 bp):
GAGGTTCTATCCTAGCCTGTGAAAAGATAAG
Found at i:534892 original size:28 final size:28
Alignment explanation
Indices: 534856--534955 Score: 132
Period size: 28 Copynumber: 3.6 Consensus size: 28
534846 GAAATAAAAT
*
534856 CGGGATTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCTCGGAAATAA
**
534884 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCTCGGAAATAA
534912 CGGGGTTGGAGTAT--CCTCGATGAAATAA
1 CGGGGTTGGAGTATCCCCTCG--GAAATAA
*
534940 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
534956 TCAATTGTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
26 5 0.08
28 57 0.92
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCGGAAATAA
Found at i:535056 original size:52 final size:53
Alignment explanation
Indices: 534967--535067 Score: 168
Period size: 52 Copynumber: 1.9 Consensus size: 53
534957 CAATTGTGAA
*
534967 AAAATTGGTGTTTTTGGAAATAAAATCGAAGTTGGAGTATCCCCGATTAAAGG
1 AAAATTGGTGTTTTTGAAAATAAAATCGAAGTTGGAGTATCCCCGATTAAAGG
**
535020 AAAATTGGTG-TTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTA
1 AAAATTGGTGTTTTTGAAAATAAAATCGAAGTTGGAGTATCCCCGATTA
535068 TAAACAATTG
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 35 0.78
53 10 0.22
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.31
Consensus pattern (53 bp):
AAAATTGGTGTTTTTGAAAATAAAATCGAAGTTGGAGTATCCCCGATTAAAGG
Found at i:537478 original size:13 final size:13
Alignment explanation
Indices: 537460--537486 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
537450 ATATTCTACA
537460 AATGTATCGATAC
1 AATGTATCGATAC
537473 AATGTATCGATAC
1 AATGTATCGATAC
537486 A
1 A
537487 TTCTACAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:537483 original size:34 final size:34
Alignment explanation
Indices: 537440--537507 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
537430 ACAAAGATCG
*
537440 ATGTATCGATATATTCTACAAATGTATCGATACA
1 ATGTATCGATACATTCTACAAATGTATCGATACA
537474 ATGTATCGATACATTCTACAAATGTATCGATACA
1 ATGTATCGATACATTCTACAAATGTATCGATACA
537508 TTTCCTTGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (34 bp):
ATGTATCGATACATTCTACAAATGTATCGATACA
Found at i:538462 original size:20 final size:20
Alignment explanation
Indices: 538437--538490 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
538427 TTTTAACTAG
* * *
538437 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTAAAAA
538457 ATGTATCGATACATTAAAAA
1 ATGTATCGATACATTAAAAA
538477 ATGTATCGATACAT
1 ATGTATCGATACAT
538491 CTAGTTCTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTAAAAA
Found at i:551264 original size:31 final size:31
Alignment explanation
Indices: 551221--551287 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
551211 TATTGCATTT
*
551221 TTATTTATTAATATAAATATTATTTTAAAAC
1 TTATATATTAATATAAATATTATTTTAAAAC
551252 TTATATATTAATATAAATATTATTTTAAAAC
1 TTATATATTAATATAAATATTATTTTAAAAC
551283 TTATA
1 TTATA
551288 CAAATAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (31 bp):
TTATATATTAATATAAATATTATTTTAAAAC
Found at i:551300 original size:31 final size:31
Alignment explanation
Indices: 551229--551300 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
551219 TTTTATTTAT
* *
551229 TAATATAAATATTATTTTAAAACTTATATAT
1 TAATATAAATATTATTTTAAAACTTATAAAA
551260 TAATATAAATATTATTTTAAAACTTATACAAA
1 TAATATAAATATTATTTTAAAACTTATA-AAA
551292 TAAT-TAAAT
1 TAATATAAAT
551301 TAAACATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 33 0.87
32 5 0.13
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (31 bp):
TAATATAAATATTATTTTAAAACTTATAAAA
Found at i:551515 original size:7 final size:7
Alignment explanation
Indices: 551503--551545 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
551493 TTTATTTCAA
551503 ATTATTT
1 ATTATTT
551510 ATTATTT
1 ATTATTT
551517 ATTATTT
1 ATTATTT
551524 ATTATTT
1 ATTATTT
551531 ATT-TTT
1 ATTATTT
551537 ATT-TTT
1 ATTATTT
551543 ATT
1 ATT
551546 TAATATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 12 0.33
7 24 0.67
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTATTT
Found at i:551565 original size:26 final size:23
Alignment explanation
Indices: 551512--551571 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 23
551502 AATTATTTAT
*
551512 TATTTATTATTTATTATTTATTTT
1 TATTT-TTATTTATTATTTATTTG
551536 TATTTTTATTTAATATATTTATGTTG
1 TATTTTTATTT-AT-TATTTAT-TTG
*
551562 TATTTATATT
1 TATTTTTATT
551572 ATTCATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 6 0.19
24 7 0.23
25 7 0.23
26 11 0.35
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (23 bp):
TATTTTTATTTATTATTTATTTG
Found at i:551574 original size:20 final size:19
Alignment explanation
Indices: 551509--551574 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
551499 TCAAATTATT
* *
551509 TATTATTTATTATTTATTATT
1 TATTATTTATT-TGTATT-TA
*
551530 TATT-TTTATTTTTATTTA
1 TATTATTTATTTGTATTTA
551548 -ATATATTTATGTTGTATTTA
1 TAT-TATTTAT-TTGTATTTA
551568 TATTATT
1 TATTATT
551575 CATATTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 2 0.05
18 2 0.05
19 11 0.28
20 18 0.46
21 6 0.15
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
TATTATTTATTTGTATTTA
Found at i:551579 original size:26 final size:24
Alignment explanation
Indices: 551516--551580 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 24
551506 ATTTATTATT
* *
551516 TATTATTTATTATTTATTTTTATTTT
1 TATTA-TTA-TATTTATTTGTATTTA
*
551542 TATTTAATATATTTATGTTGTATTTA
1 TA-TTATTATATTTAT-TTGTATTTA
551568 TATTATTCATATT
1 TATTATT-ATATT
551581 ATATATTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
25 11 0.34
26 18 0.56
27 3 0.09
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.68
Consensus pattern (24 bp):
TATTATTATATTTATTTGTATTTA
Found at i:552839 original size:18 final size:21
Alignment explanation
Indices: 552806--552853 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
552796 TTATATTTAT
*
552806 AAATAAAAATTATTG-ATAA-
1 AAATTAAAATTATTGAATAAC
552825 AAATTAAAA-TATTGAATAAC
1 AAATTAAAATTATTGAATAAC
552845 AATATTAAA
1 AA-ATTAAA
552854 TGGATTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 5 0.20
19 12 0.48
20 2 0.08
21 6 0.24
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (21 bp):
AAATTAAAATTATTGAATAAC
Found at i:553349 original size:38 final size:38
Alignment explanation
Indices: 553297--553372 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
553287 AAAAATGAAA
*
553297 CAAAATTATTAACTTTTTCAAAGAGAAATAATTTGACT
1 CAAAATTATGAACTTTTTCAAAGAGAAATAATTTGACT
553335 CAAAATTATGAACTTTTTCAAAGAGAAATAATTTGACT
1 CAAAATTATGAACTTTTTCAAAGAGAAATAATTTGACT
553373 AACTTATAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (38 bp):
CAAAATTATGAACTTTTTCAAAGAGAAATAATTTGACT
Found at i:553806 original size:16 final size:16
Alignment explanation
Indices: 553767--553810 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
553757 TATTTTATTA
*
553767 ATTATTTTTAATTTTT
1 ATTATTTTTAAATTTT
*
553783 A-TAGTTTTAAATTTT
1 ATTATTTTTAAATTTT
553798 ATTATTTTTAAAT
1 ATTATTTTTAAAT
553811 GATATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
ATTATTTTTAAATTTT
Found at i:553932 original size:17 final size:18
Alignment explanation
Indices: 553902--553936 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
553892 CAAATAAAAA
553902 TTTTATTTTATAAATTAT
1 TTTTATTTTATAAATTAT
553920 TTTTATTTT-TAAATTAT
1 TTTTATTTTATAAATTAT
553937 ACATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTATTTTATAAATTAT
Found at i:559234 original size:19 final size:19
Alignment explanation
Indices: 559184--559234 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
559174 TTAAAAATTA
*
559184 TTTTATATAATTATTTAAT
1 TTTTATATAATTAATTAAT
* *
559203 ATTTA-ATTTATTAATTAAT
1 TTTTATA-TAATTAATTAAT
559222 TTTTATATAATTA
1 TTTTATATAATTA
559235 TGTAAATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 1 0.04
19 23 0.92
20 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTATATAATTAATTAAT
Found at i:559266 original size:26 final size:26
Alignment explanation
Indices: 559221--559271 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
559211 TATTAATTAA
*
559221 TTTTTATATAATTATGT-AAATTTAG
1 TTTTTATATAAATATGTAAAATTTAG
559246 TTTTTATATGAAATA-GATAAAATTTA
1 TTTTTATAT-AAATATG-TAAAATTTA
559272 AATAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 10 0.45
26 5 0.23
27 7 0.32
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (26 bp):
TTTTTATATAAATATGTAAAATTTAG
Found at i:559875 original size:21 final size:22
Alignment explanation
Indices: 559849--559892 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
559839 TTTTTAATTG
*
559849 TAATTATG-AAAAAAATAAAAA
1 TAATTAGGAAAAAAAATAAAAA
559870 TAATTAGGATAAAAAAATAAAAA
1 TAATTAGGA-AAAAAAATAAAAA
559893 GTTAGTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
23 13 0.65
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (22 bp):
TAATTAGGAAAAAAAATAAAAA
Found at i:559897 original size:21 final size:20
Alignment explanation
Indices: 559857--559913 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
559847 TGTAATTATG
559857 AAAAAAATAAAAATAATTAGGAT
1 AAAAAAAT-AAAA-AATTA-GAT
* *
559880 AAAAAAATAAAAAGTTAGTT
1 AAAAAAATAAAAAATTAGAT
*
559900 TAAAAAATAAAAAA
1 AAAAAAATAAAAAA
559914 ATTAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 14 0.47
21 4 0.13
22 4 0.13
23 8 0.27
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (20 bp):
AAAAAAATAAAAAATTAGAT
Found at i:559936 original size:24 final size:25
Alignment explanation
Indices: 559878--559948 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
559868 AATAATTAGG
*
559878 ATAAAAAAATAAAAAGTTAGTTTAAAAA
1 ATAAAAAAATTAAAA-TT--TTTAAAAA
*
559906 ATAAAAAAATTAAATTTTTTAAAAA
1 ATAAAAAAATTAAAATTTTTAAAAA
559931 AT-AAAAAATTAAAATTTT
1 ATAAAAAAATTAAAATTTT
559949 GCATAACTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
24 15 0.38
25 10 0.25
27 2 0.05
28 13 0.32
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (25 bp):
ATAAAAAAATTAAAATTTTTAAAAA
Found at i:560020 original size:19 final size:18
Alignment explanation
Indices: 559984--560024 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
559974 AAACCAATTT
**
559984 AAATTGATATAATTAATA
1 AAATTGATATAAAAAATA
560002 CAAATTGATATAAAAAATA
1 -AAATTGATATAAAAAATA
560021 AAAT
1 AAAT
560025 AATAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (18 bp):
AAATTGATATAAAAAATA
Found at i:562219 original size:51 final size:53
Alignment explanation
Indices: 562156--562281 Score: 175
Period size: 51 Copynumber: 2.4 Consensus size: 53
562146 CTCAATTCGC
* * *
562156 CACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAATTTCCT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTCCT
* *
562208 -ATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTTCCT
*
562261 CACAATCGGGGATACTACAAC
1 CACAATCGGGGATACTCCAAC
562282 CCCGTTGATC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
51 32 0.50
53 14 0.22
54 18 0.28
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.30
Consensus pattern (53 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTCCT
Found at i:562442 original size:52 final size:50
Alignment explanation
Indices: 562323--562544 Score: 156
Period size: 52 Copynumber: 4.3 Consensus size: 50
562313 TTATTTCCGA
* * * * *** *
562323 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTTCATAATC
1 GGGGATACTCCAACCCCAATTTTA-TTCTAAAACACCAATTTTTCACAATC
* * ** *
562374 GGGGATATTTCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCAATTTTATT-CTAAAACACCAATTTTT-CACAATC
* * * * ** *
562426 GGGGATACTCCAACCCCAGTTTTATTTTCGAAACACCAATTTTCCTTTAATT
1 GGGGATACTCCAACCCCAATTTTATTCT-AAAACACCAATTTTTC-ACAATC
* * * *
562478 GGGGATACTCCAACTCCAATTTTATTTCCAAAAATACCAATTTTTCACAGTC
1 GGGGATACTCCAACCCCAATTTTA-TT-CTAAAACACCAATTTTTCACAATC
*
562530 GAGGATACTCCAACC
1 GGGGATACTCCAACC
562545 TTGTTATTTC
Statistics
Matches: 133, Mismatches: 32, Indels: 11
0.76 0.18 0.06
Matches are distributed among these distances:
50 2 0.02
51 35 0.26
52 81 0.61
53 15 0.11
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCCAATTTTATTCTAAAACACCAATTTTTCACAATC
Found at i:562564 original size:28 final size:28
Alignment explanation
Indices: 562532--562603 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
562522 TCACAGTCGA
** * **
562532 GGATACTCCAACCTTGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
562560 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
562588 GGATACTCCAACCCCG
1 GGATACTCCAACCCCG
562604 GCTTTATTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:562622 original size:263 final size:263
Alignment explanation
Indices: 562155--562654 Score: 756
Period size: 263 Copynumber: 1.9 Consensus size: 263
562145 TCTCAATTCG
* * *
562155 CCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTCCTATAATCGGGGAT
1 CCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCCTATAATCGGGGAT
* *
562220 ACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTACAACCCC
66 ACTCCAACTCCAATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTACAACCCC
* *
562285 GTTGATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTT
131 GTTGATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTC
* * *
562350 CCAAAATATTGATTTTTCATAATCGGGGATATTTCAACCCCGGTTTTATTGCTAAAACACTAATT
196 CCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
562415 TTT
261 TTT
* * *
562418 CCACAATCGGGGATACTCCAACCCC-AGTTTTATTTTCGAAACACCAATTTTCCTTTAATTGGGG
1 CCACAATCGGGGATACTCCAACCCCGA-TTTTATTTTCAAAACACCAA-TTTCCTATAATCGGGG
* * *
562482 ATACTCCAACTCCAATTTTATTTCC-AAAAATACCAATTT-TTCACAGTCGAGGATACTCCAACC
64 ATACTCCAACTCCAATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTACAACC
** *
562545 TTGTT-ATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCGTTGA--TCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTT
*
562609 ATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
192 ATTCCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG
562655 TTATTTTCGA
Statistics
Matches: 213, Mismatches: 20, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
261 1 0.00
262 25 0.12
263 149 0.70
264 38 0.18
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (263 bp):
CCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCCTATAATCGGGGAT
ACTCCAACTCCAATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTACAACCCC
GTTGATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTC
CCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
TTT
Found at i:562706 original size:79 final size:79
Alignment explanation
Indices: 562557--562761 Score: 241
Period size: 79 Copynumber: 2.6 Consensus size: 79
562547 GTTATTTCAT
* * *
562557 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
562622 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * ** *
562636 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
562700 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * * *
562715 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
562762 TTATTATCTC
Statistics
Matches: 106, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 3 0.03
79 103 0.97
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:576469 original size:13 final size:13
Alignment explanation
Indices: 576451--576475 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
576441 CAAAGATCAG
576451 TGTATCGATACAA
1 TGTATCGATACAA
576464 TGTATCGATACA
1 TGTATCGATACA
576476 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:576553 original size:33 final size:33
Alignment explanation
Indices: 576516--576582 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
576506 AGTAGCTTAA
576516 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
576549 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
576582 A
1 A
576583 AATCGTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:576556 original size:13 final size:13
Alignment explanation
Indices: 576538--576562 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
576528 CAAAAAAATA
576538 TGTATCGATACAT
1 TGTATCGATACAT
576551 TGTATCGATACA
1 TGTATCGATACA
576563 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:578669 original size:1 final size:1
Alignment explanation
Indices: 578663--578756 Score: 53
Period size: 1 Copynumber: 94.0 Consensus size: 1
578653 ACCTTCTCTT
** ** * * * * * *
578663 AAAAAAAAAGCAAAAAAAAGCAAAAAAAAAAAAAAAAACAAAACAAAATACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
578728 GAGAGAAAAAAAAAGAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
578757 TCTGCTTAAG
Statistics
Matches: 65, Mismatches: 28, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.01
Consensus pattern (1 bp):
A
Found at i:578679 original size:9 final size:9
Alignment explanation
Indices: 578664--578756 Score: 62
Period size: 9 Copynumber: 9.6 Consensus size: 9
578654 CCTTCTCTTA
578664 AAAAAAAAGC
1 AAAAAAAA-C
578674 AAAAAAAAGC
1 AAAAAAAA-C
*
578684 AAAAAAAAA
1 AAAAAAAAC
578693 AAAAAAAAC
1 AAAAAAAAC
578702 AAAACAAAATAC
1 -AAA-AAAA-AC
* *
578714 AAAACAAAG
1 AAAAAAAAC
578723 AAAAAGAGAGA-
1 AAAAA-A-A-AC
*
578734 AAAAAAAAG
1 AAAAAAAAC
*
578743 AAAAAAAAG
1 AAAAAAAAC
578752 AAAAA
1 AAAAA
578757 TCTGCTTAAG
Statistics
Matches: 71, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
8 1 0.01
9 28 0.39
10 26 0.37
11 13 0.18
12 3 0.04
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.01
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:578679 original size:10 final size:9
Alignment explanation
Indices: 578664--578756 Score: 87
Period size: 10 Copynumber: 9.6 Consensus size: 9
578654 CCTTCTCTTA
578664 AAAAAAAAG
1 AAAAAAAAG
578673 CAAAAAAAAG
1 -AAAAAAAAG
*
578683 CAAAAAAAAA
1 -AAAAAAAAG
*
578693 AAAAAAAAC
1 AAAAAAAAG
*
578702 AAAACAAAAT
1 AAAA-AAAAG
578712 ACAAAACAAAG
1 A-AAAA-AAAG
*
578723 AAAAAGAGAG
1 AAAAA-AAAG
578733 AAAAAAAAAG
1 -AAAAAAAAG
578743 AAAAAAAAG
1 AAAAAAAAG
578752 AAAAA
1 AAAAA
578757 TCTGCTTAAG
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
9 26 0.36
10 34 0.47
11 12 0.17
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.01
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:578680 original size:12 final size:12
Alignment explanation
Indices: 578663--578750 Score: 64
Period size: 12 Copynumber: 7.6 Consensus size: 12
578653 ACCTTCTCTT
578663 AAAAAAAAAGC-
1 AAAAAAAAAGCA
578674 -AAAAAAAAGCA
1 AAAAAAAAAGCA
578685 AAAAAAAAA--A
1 AAAAAAAAAGCA
*
578695 AAAAAACAAAACA
1 AAAAAA-AAAGCA
*
578708 AAATACAAAA-CA
1 AAA-AAAAAAGCA
*
578720 AAGAAAAAGAG-A
1 AA-AAAAAAAGCA
578732 GAAAAAAAAAG-A
1 -AAAAAAAAAGCA
578744 AAAAAAA
1 AAAAAAA
578751 GAAAAATCTG
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
10 17 0.27
11 10 0.16
12 25 0.39
13 10 0.16
14 2 0.03
ACGTcount: A:0.84, C:0.07, G:0.08, T:0.01
Consensus pattern (12 bp):
AAAAAAAAAGCA
Found at i:578689 original size:18 final size:18
Alignment explanation
Indices: 578663--578756 Score: 71
Period size: 21 Copynumber: 4.7 Consensus size: 18
578653 ACCTTCTCTT
578663 AAAAAAAAAGCAAAAAAAAGC
1 AAAAAAAAA--AAAAAAAA-C
578684 AAAAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAAAAC
* *
578702 AAAACAAAATACAAAACAAAG
1 AAAA-AAAA-A-AAAAAAAAC
* *
578723 AAAAAGAGAGAAAAAAAAAG
1 AAAAA-A-AAAAAAAAAAAC
578743 AAAAAAAAGAAAAA
1 AAAAAAAA-AAAAA
578757 TCTGCTTAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
18 6 0.10
19 18 0.29
20 15 0.24
21 22 0.35
22 1 0.02
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.01
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAAAC
Found at i:579806 original size:55 final size:54
Alignment explanation
Indices: 579720--581537 Score: 2104
Period size: 55 Copynumber: 32.4 Consensus size: 54
579710 TCCGTCCGCT
* * *
579720 TTTCAGTCCCCAAAGAGCAGGACACCATTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
579774 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
579829 TTTCCAGTCCTCAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCAC
* *
579884 CTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
579938 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
579993 TTTCCAGTCCTCAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCAC
* * * * *
580048 CTTCAGTACAT-AAAGAGCGGGACACATTTTCTTTTAAAGCGCACACAAGTTGGTGGCAC
1 TTTCAGT-CCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCAC
* * *
580107 CTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCATC-CAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCA-CACAAGTTGGTGGCA-C
* *
580167 TTT-AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* * *
580227 TTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
580281 TTTCCAGTCCTCAAAGAGTAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-C
*
580337 TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* *
580392 TTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
580446 TTTCCAGTCCTCAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCAC
* * * *
580501 CTTCAGTCCACAAAGAGCGGGACACATTTTCTTTTAAAG-CCACACAAGTTGGTGGCAC
1 TTTCAGTCCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCAC
* * *
580559 CTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCATC-CAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCA-CACAAGTTGGTGGCA-C
* *
580619 TTT-AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* * * *
580679 TTTCAGTCCCCAAAGAGCAGGATACCTTTTAAAGCCCACACAAGTTGGTGGCATT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
580734 TTTCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-C
* *
580789 TTTCAGTCCTCAAAGAGCAGGGCGCCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
*
580844 TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* *
580899 TTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
580953 TTTCCAGTCCTCAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCAC
* * * *
581008 CTTCAGTCCACAAAGAGCGGGACACATTTTCTTTTAAAG-CCACACAAGTTGGTGGCAC
1 TTTCAGTCCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCAC
* ** *
581066 CTTCAGTCCTCAAAGAGTGGGACGCCTTTTCTTTTAAAGCCCATC-CAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCA-CACAAGTTGGTGGCA-C
* *
581126 TTT-AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* * * *
581186 TTTCAGTCCCCAAAGAGCAGGATACCTTTTAAAGCCCACACAAGTTGGTGGCATT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
581241 TTTCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-C
* * *
581296 TTTCAGTCCTCAAAGAGCAGGGCGCCTTTCAAAGCCCACATAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* * *
581351 TTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
581405 TTTCCAGTCGTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-C
* *
581461 TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCAC
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
* * *
581515 TTTTTACTCCTCAATGAGCAGGA
1 -TTTCAGTCCTCAAAGAGCAGGA
581538 TACACTTTAT
Statistics
Matches: 1563, Mismatches: 112, Indels: 177
0.84 0.06 0.10
Matches are distributed among these distances:
53 4 0.00
54 133 0.09
55 983 0.63
56 22 0.01
58 99 0.06
59 163 0.10
60 90 0.06
61 54 0.03
64 12 0.01
65 3 0.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (54 bp):
TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
Found at i:580403 original size:29 final size:29
Alignment explanation
Indices: 580316--580403 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 29
580306 CCTCTTAAAG
580316 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
* ** * * ***
580345 CTCA-A-AGAG-CAG-GACGCCTTTCAAAG
1 CCCACACA-AGTTGGTGGCACCTTTCAGTC
580371 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
580400 CCCA
1 CCCA
580404 AAGAGCAGGA
Statistics
Matches: 38, Mismatches: 16, Indels: 10
0.59 0.25 0.16
Matches are distributed among these distances:
26 12 0.32
27 5 0.13
28 5 0.13
29 16 0.42
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.20
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAGTC
Found at i:580429 original size:26 final size:26
Alignment explanation
Indices: 580347--580429 Score: 60
Period size: 26 Copynumber: 3.1 Consensus size: 26
580337 TTTCAGTCCT
*
580347 CAAAGAGCAGGACGCCTTTCAAAGCC
1 CAAAGAGCAGGACACCTTTCAAAGCC
** * ***
580373 CACACA-AGTTGGTGGCACCTTTCAGTCCC
1 CA-A-AGAG-CAG-GACACCTTTCAAAGCC
580402 CAAAGAGCAGGACACCTTTCAAAGCC
1 CAAAGAGCAGGACACCTTTCAAAGCC
580428 CA
1 CA
580430 CACAAGTTGG
Statistics
Matches: 39, Mismatches: 13, Indels: 10
0.63 0.21 0.16
Matches are distributed among these distances:
26 16 0.41
27 5 0.13
28 5 0.13
29 13 0.33
ACGTcount: A:0.31, C:0.33, G:0.20, T:0.16
Consensus pattern (26 bp):
CAAAGAGCAGGACACCTTTCAAAGCC
Found at i:580591 original size:452 final size:449
Alignment explanation
Indices: 579747--581538 Score: 2638
Period size: 452 Copynumber: 4.0 Consensus size: 449
579737 CAGGACACCA
* * *
579747 TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCC
1 TTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACACCTTTTAAAGCC
*
579811 CACACAAGTTGGTGGCATTTTCCAGTCCTCAGAGAGCAGGACACCTCTTAAAGCCCACACAAGTT
65 CACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTT
*
579876 GGTGGCACC-TTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TT
130 GGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCT
*
579939 TTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCC
195 TT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCC
* * * * *
580003 TCAGAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTACATAAAGAGCG
258 CCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCACAAAGAGCA
* *
580067 GGACACATTTTCTTTTAAAGCGCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGC
323 GGACAC-----CTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGC
580132 CTTTTCTTTTAAAGCCCATC-CAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCTTTTT
383 CTTTTCTTTTAAAGCCCA-CACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCTTTTT
580196 CTT
447 CTT
580199 TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCC
1 TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCC
*
580264 ACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACACCTCTTAAAGCCCACACAAGTTG
66 ACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTG
*
580329 GTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
131 GTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * *
580394 TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTC
196 TCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCC
* *
580458 AGAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCACAAAGAGCGGG
260 AAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCACAAAGAGCAGG
*
580522 ACACATTTTCTTTTAAAG-CCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCT
325 ACAC-----CTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCT
580586 TTTCTTTTAAAGCCCATC-CAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCT
385 TTTCTTTTAAAGCCCA-CACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCT
580650 T
449 T
*
580651 TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGATACCTTTTAAAGCCC
1 TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCC
*
580716 ACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTG
66 ACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTG
* *
580781 GTGGCACCTTTCAGTCCTCAAAGAGCAGGGCGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
131 GTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
*
580846 TCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCA
196 TCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCA
** * *
580911 AAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAGAGAGCAGG
261 AAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCACAAAGAGCAGG
* * *
580975 ACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCACAAAGAGCGGGACACATTTTCT
325 ACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCT
* ** * *
581040 TTTAAAG-CCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGTGGGACGCCTTTTCTT
390 TTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTT
* **
581099 TT-AAAGCCCATC-CAAGTTGGTGGCACCTTT-AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTC
1 TTCAAAGCCCA-CACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGA--C---ACCTTTT-
* * * *
581161 AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGATACCTTTTAAAGCCCAC
59 AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCAC
**
581225 ACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGG
123 ACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGG
* * *
581289 TGGCACCTTTCAGTCCTCAAAGAGCAGGGCGCCTTTCAAAGCCCACATAAGTTGGTGGCACCTTT
187 TGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT
* ** **
581354 CAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCGTCAA
252 CAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCACAA
*
581419 AGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGAC
317 AGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCGGGAC
* * * *
581484 GCC-TTTC----AAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAATGAGCAGGAT
381 GCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTTAGTCCTCAAAGAGCAGGAT
581539 ACACTTTATT
Statistics
Matches: 1257, Mismatches: 62, Indels: 44
0.92 0.05 0.03
Matches are distributed among these distances:
446 17 0.01
447 27 0.02
448 60 0.05
449 73 0.06
450 16 0.01
451 7 0.01
452 808 0.64
453 246 0.20
454 3 0.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (449 bp):
TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCC
ACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTG
GTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
TCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCA
AAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCACAAAGAGCAGGA
CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTT
TTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTT
Found at i:580715 original size:507 final size:507
Alignment explanation
Indices: 579719--581514 Score: 2826
Period size: 507 Copynumber: 3.5 Consensus size: 507
579709 CTCCGTCCGC
* *
579719 TTTTCAGTCCCCAAAGAGCAGGACACCAT-TCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGT
1 TTTTCAGTCCCCAAAGAGCAGGACACC-TCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGT
* *
579782 CCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAGAGA
64 CCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGA
*
579846 GCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACAC
128 GCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACAC
579909 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGC
192 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGC
** * * * *
579974 CCACACAAGTTGGTGGCATTTTCCAGTCCTCAGAGAGCAGGACAC-----CTCTTAAAGCCCACA
257 CCACACAAGTTGGTGGCACCTT-CAGTCCACAAAGAGCGGGACACATTTTCTTTTAAAG-CCACA
* * * *
580034 CAAGTTGGTGGCACCTTCAGTACAT-AAAGAGCGGGACACATTTTCTTTTAAAGCGCA-CACAAG
320 CAAGTTGGTGGCACCTTCAGT-CCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCATC-CAAG
* * * *
580097 TTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTT-AAAGCCCATC-CAAGTTGG
383 TTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCA-CACAAGTTGG
* *
580160 TGGCACCTTT-AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGC
447 TGGCACCTTTCAGTCCCCAAAGAGCAGGATAC-----CTTTT-AAAGCCCACACAAGTTGGTGGC
*
580224 AC
506 AT
* * *
580226 CTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTC
1 TTTTCAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTC
*
580290 CTCAAAGAGTAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAG
65 CTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAG
*
580354 CAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCT
129 CAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCT
*
580419 TTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAGAGAGCAGGACACCTCTT-AAAGCC
194 TTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCC
580483 CACACAAGTTGGTGGCACCTTCAGTCCACAAAGAGCGGGACACATTTTCTTTTAAAGCCACACAA
258 CACACAAGTTGGTGGCACCTTCAGTCCACAAAGAGCGGGACACATTTTCTTTTAAAGCCACACAA
580548 GTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCATCCAAGTTGGT
323 GTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCATCCAAGTTGGT
580613 GGCACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
388 GGCACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
580678 CTTTCAGTCCCCAAAGAGCAGGATACCTTTTAAAGCCCACACAAGTTGGTGGCAT
453 CTTTCAGTCCCCAAAGAGCAGGATACCTTTTAAAGCCCACACAAGTTGGTGGCAT
*
580733 TTTTCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
1 TTTTCAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
* *
580798 TCAAAGAGCAGGGCGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCA
66 TCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCA
*
580863 GGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTT
131 GGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTT
*
580928 CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAGAGAGCAGGACACCTCTT-AAAGCCCA
196 CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCA
580992 CACAAGTTGGTGGCACCTTCAGTCCACAAAGAGCGGGACACATTTTCTTTTAAAGCCACACAAGT
260 CACAAGTTGGTGGCACCTTCAGTCCACAAAGAGCGGGACACATTTTCTTTTAAAGCCACACAAGT
*
581057 TGGTGGCACCTTCAGTCCTCAAAGAGTGGGACGCCTTTTCTTTTAAAGCCCATCCAAGTTGGTGG
325 TGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCATCCAAGTTGGTGG
581122 CACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCT
390 CACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCT
581187 TTCAGTCCCCAAAGAGCAGGATACCTTTTAAAGCCCACACAAGTTGGTGGCAT
455 TTCAGTCCCCAAAGAGCAGGATACCTTTTAAAGCCCACACAAGTTGGTGGCAT
*
581240 TTTTCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
1 TTTTCAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
* * * *
581305 TCAAAGAGCAGGGCGCCTTTCAAAGCCCACATAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCA
66 TCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCA
* * **
581370 GGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCGTCAAAGAGCAGGACACCTC
131 GGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACACCT-
* *
581434 TT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCC
194 TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCC
*
581497 CACACGAGTTGGTGGCAC
258 CACACAAGTTGGTGGCAC
581515 TTTTTACTCC
Statistics
Matches: 1223, Mismatches: 44, Indels: 44
0.93 0.03 0.03
Matches are distributed among these distances:
506 10 0.01
507 932 0.76
508 122 0.10
509 2 0.00
510 2 0.00
511 101 0.08
512 35 0.03
513 19 0.02
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (507 bp):
TTTTCAGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCC
TCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCA
GGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTT
CAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCAC
ACAAGTTGGTGGCACCTTCAGTCCACAAAGAGCGGGACACATTTTCTTTTAAAGCCACACAAGTT
GGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCATCCAAGTTGGTGGC
ACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
TCAGTCCCCAAAGAGCAGGATACCTTTTAAAGCCCACACAAGTTGGTGGCAT
Found at i:580817 original size:26 final size:26
Alignment explanation
Indices: 580787--580874 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
580777 GTTGGTGGCA
580787 CCTTTCAGTCCTCAAAGAGCAGGGCG
1 CCTTTCAGTCCTCAAAGAGCAGGGCG
* * * *
580813 CCTTTCAAAGCCCACACAAGTTG--GTGGCA
1 CCTTTC--AGTCCTCA-AAG-AGCAG-GGCG
*
580842 CCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAGTCCTCAAAGAGCAGGGCG
580868 CCTTTCA
1 CCTTTCA
580875 AAGCCCACAC
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
25 1 0.02
26 18 0.39
27 7 0.15
28 7 0.15
29 12 0.26
30 1 0.02
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (26 bp):
CCTTTCAGTCCTCAAAGAGCAGGGCG
Found at i:580910 original size:29 final size:29
Alignment explanation
Indices: 580768--580910 Score: 77
Period size: 29 Copynumber: 5.1 Consensus size: 29
580758 CCTCTTAAAG
580768 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
* ** * ***
580797 CTCA-A-AGAG-CAG-GGCGCCTTTCAAAG
1 CCCACACA-AGTTGGTGGCACCTTTCAGTC
580823 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
* ** * * ***
580852 CTCA-A-AGAG-CAG-GACGCCTTTCAAAG
1 CCCACACA-AGTTGGTGGCACCTTTCAGTC
580878 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
580907 CCCA
1 CCCA
580911 AAGAGCAGGA
Statistics
Matches: 74, Mismatches: 30, Indels: 20
0.60 0.24 0.16
Matches are distributed among these distances:
26 25 0.34
27 10 0.14
28 10 0.14
29 29 0.39
ACGTcount: A:0.25, C:0.33, G:0.22, T:0.20
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAGTC
Found at i:580936 original size:26 final size:26
Alignment explanation
Indices: 580854--580936 Score: 60
Period size: 26 Copynumber: 3.1 Consensus size: 26
580844 TTTCAGTCCT
*
580854 CAAAGAGCAGGACGCCTTTCAAAGCC
1 CAAAGAGCAGGACACCTTTCAAAGCC
** * ***
580880 CACACA-AGTTGGTGGCACCTTTCAGTCCC
1 CA-A-AGAG-CAG-GACACCTTTCAAAGCC
580909 CAAAGAGCAGGACACCTTTCAAAGCC
1 CAAAGAGCAGGACACCTTTCAAAGCC
580935 CA
1 CA
580937 CACAAGTTGG
Statistics
Matches: 39, Mismatches: 13, Indels: 10
0.63 0.21 0.16
Matches are distributed among these distances:
26 16 0.41
27 5 0.13
28 5 0.13
29 13 0.33
ACGTcount: A:0.31, C:0.33, G:0.20, T:0.16
Consensus pattern (26 bp):
CAAAGAGCAGGACACCTTTCAAAGCC
Found at i:581362 original size:29 final size:28
Alignment explanation
Indices: 581275--581362 Score: 65
Period size: 29 Copynumber: 3.1 Consensus size: 28
581265 CCTCTTAAAG
581275 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACA-AAGTTGGTGGCACCTTTCAGTC
* ** * ***
581304 CTCA-AAGAG-CAG-GGCGCCTTTCAAAG
1 CCCACAA-AGTTGGTGGCACCTTTCAGTC
581330 CCCACATAAGTTGGTGGCACCTTTCAGTC
1 CCCACA-AAGTTGGTGGCACCTTTCAGTC
581359 CCCA
1 CCCA
581363 AAGAGCAGGA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 13 0.32
27 5 0.12
28 5 0.12
29 17 0.43
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.22
Consensus pattern (28 bp):
CCCACAAAGTTGGTGGCACCTTTCAGTC
Found at i:582275 original size:21 final size:21
Alignment explanation
Indices: 582249--582305 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
582239 AAAATATCCA
582249 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
582270 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
582291 AATGTATCGATACAT
1 AATGTATCGATACAT
582306 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:582454 original size:13 final size:13
Alignment explanation
Indices: 582436--582461 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
582426 CATTTTTTTG
582436 TGTATCGATACAT
1 TGTATCGATACAT
582449 TGTATCGATACAT
1 TGTATCGATACAT
582462 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:584894 original size:51 final size:53
Alignment explanation
Indices: 584831--584956 Score: 166
Period size: 51 Copynumber: 2.4 Consensus size: 53
584821 CTCAATTCGC
* * *
584831 CACAATCGGGGATATTCCAACTCCGAATTTATTTTC-AAAACACTAATTTCCT
1 CACAATCGGGGATACTCCAACTCCGAATTTATTTCCAAAAACACCAATTTCCT
* * *
584883 -ATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
1 CACAATCGGGGATACTCCAACTCCGAATTTATTTCC-AAAAACACCAATTTCCT
*
584936 CACAATCGGGGATACTACAAC
1 CACAATCGGGGATACTCCAAC
584957 CCCGTTGATC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
51 31 0.49
53 14 0.22
54 18 0.29
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.29
Consensus pattern (53 bp):
CACAATCGGGGATACTCCAACTCCGAATTTATTTCCAAAAACACCAATTTCCT
Found at i:585063 original size:51 final size:52
Alignment explanation
Indices: 584998--585219 Score: 207
Period size: 52 Copynumber: 4.3 Consensus size: 52
584988 TTATTTCCGA
** * * * *
584998 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTT-CATAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCCACAATC
* * * *
585049 GGGGATATTTCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCCACAATC
* * * **
585101 GGGGATACTCCAACCCCGGTTTTATTTTCGAAACACCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCC-ACAATC
* ** * * *
585153 GGGGATACTCCAACTCCAATTTTATTTCCAAAAATACCAATTTTT-CACAGTC
1 GGGGATACTCCAACCCCGGTTTTATTTCC-AAAACACTAATTTTTCCACAATC
*
585205 GAGGATACTCCAACC
1 GGGGATACTCCAACC
585220 TTGTTATTTC
Statistics
Matches: 137, Mismatches: 30, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
51 41 0.30
52 83 0.61
53 9 0.07
54 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCCACAATC
Found at i:585117 original size:52 final size:50
Alignment explanation
Indices: 584831--585219 Score: 178
Period size: 52 Copynumber: 7.4 Consensus size: 50
584821 CTCAATTCGC
* * * * * *
584831 CACAATCGGGGATATTCCAACTCCGAATTTATTTTCAAAACACTAA-TTTC
1 CACAATCGGGGATACTCCAACCCCGATTTTATTCT-AAAACACCAATTTTT
* * *
584881 CTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTA-TT-C-TAAAACACCAATTT-TT
* * ** **
584936 CACAATCGGGGATACTACAACCCCG-TTGATCATCGGGGATACTCCAAC-CCCGTTATTT
1 CACAATCGGGGATACTCCAACCCCGATT--T--T-----ATTCTAAAACACCAATT-TTT
* * * * ***
584994 C-CGA--GGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTA-TTCTAAAACACCAATTTTT
* * * * *
585042 CATAATCGGGGATATTTCAACCCCGGTTTTATTGCTAAAACACTAATTTTT
1 CACAATCGGGGATACTCCAACCCCGATTTTATT-CTAAAACACCAATTTTT
* * * *
585093 CCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCGAAACACCAATTTTC
1 -CACAATCGGGGATACTCCAACCCCGATTTTATTCT-AAAACACCAATTTTT
** * * * *
585145 CTTTAATCGGGGATACTCCAACTCCAATTTTATTTCCAAAAATACCAATTTTT
1 C-ACAATCGGGGATACTCCAACCCCGATTTTA-TT-CTAAAACACCAATTTTT
* *
585198 CACAGTCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
585220 TTGTTATTTC
Statistics
Matches: 251, Mismatches: 60, Indels: 54
0.69 0.16 0.15
Matches are distributed among these distances:
47 1 0.00
48 8 0.03
49 3 0.01
50 3 0.01
51 62 0.25
52 86 0.34
53 26 0.10
54 24 0.10
55 20 0.08
56 1 0.00
57 3 0.01
58 7 0.03
59 4 0.02
60 1 0.00
61 1 0.00
62 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (50 bp):
CACAATCGGGGATACTCCAACCCCGATTTTATTCTAAAACACCAATTTTT
Found at i:585253 original size:28 final size:28
Alignment explanation
Indices: 585207--585278 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
585197 TCACAGTCGA
** * **
585207 GGATACTCCAACCTTGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
585235 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
585263 GGATACTCAAACCCCG
1 GGATACTCCAACCCCG
585279 GCTTTATTCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:585297 original size:263 final size:263
Alignment explanation
Indices: 584830--585329 Score: 754
Period size: 263 Copynumber: 1.9 Consensus size: 263
584820 TCTCAATTCG
* * *
584830 CCACAATCGGGGATATTCCAACTCCGAATTTATTTTCAAAACACTAATTTCCTATAATCGGGGAT
1 CCACAATCGGGGATACTCCAACCCCGAATTTATTTTCAAAACACCAATTTCCTATAATCGGGGAT
* *
584895 ACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTACAACCCC
66 ACTCCAACTCCAATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTACAACCCC
* * *
584960 GTTGATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTT
131 GTTGATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCAAACCCCGACTTTATTC
* * *
585025 CCAAAATATTGATTTTTCATAATCGGGGATATTTCAACCCCGGTTTTATTGCTAAAACACTAATT
196 CCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
585090 TTT
261 TTT
** * *
585093 CCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCGAAACACCAATTTTCCTTTAATCGGGGA
1 CCACAATCGGGGATACTCCAACCCCGAATTTATTTTCAAAACACCAA-TTTCCTATAATCGGGGA
* * * *
585158 TACTCCAACTCCAATTTTATTTCC-AAAAATACCAATTT-TTCACAGTCGAGGATACTCCAACCT
65 TACTCCAACTCCAATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTACAACCC
* *
585221 TGTT-ATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCAAACCCCGGCTTTA
130 CGTTGA--TCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCAAACCCCGACTTTA
*
585285 TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
193 TTCCCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG
585330 TTATTTTCGA
Statistics
Matches: 212, Mismatches: 22, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
261 1 0.00
262 24 0.11
263 148 0.70
264 39 0.18
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (263 bp):
CCACAATCGGGGATACTCCAACCCCGAATTTATTTTCAAAACACCAATTTCCTATAATCGGGGAT
ACTCCAACTCCAATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTACAACCCC
GTTGATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCAAACCCCGACTTTATTC
CCAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
TTT
Found at i:596155 original size:190 final size:190
Alignment explanation
Indices: 595832--596214 Score: 766
Period size: 190 Copynumber: 2.0 Consensus size: 190
595822 CATCAAATAC
595832 CTATGCGAAGCCCCCGCTTTGTCAGGACGATTAGCAAGGTGGCAAGTCTTGCTCTCAGAATACGA
1 CTATGCGAAGCCCCCGCTTTGTCAGGACGATTAGCAAGGTGGCAAGTCTTGCTCTCAGAATACGA
595897 CATTGTGTACGTGAGCCAAAAGGCTATAAAAGGTAGCGCGATAGCGGACTTTTTAGCAAGTCGTG
66 CATTGTGTACGTGAGCCAAAAGGCTATAAAAGGTAGCGCGATAGCGGACTTTTTAGCAAGTCGTG
595962 CGATGGAAGACTATCAGCCCTTAAACTTTGACTTCCCTGATGAAGACCTAATGTGTATAT
131 CGATGGAAGACTATCAGCCCTTAAACTTTGACTTCCCTGATGAAGACCTAATGTGTATAT
596022 CTATGCGAAGCCCCCGCTTTGTCAGGACGATTAGCAAGGTGGCAAGTCTTGCTCTCAGAATACGA
1 CTATGCGAAGCCCCCGCTTTGTCAGGACGATTAGCAAGGTGGCAAGTCTTGCTCTCAGAATACGA
596087 CATTGTGTACGTGAGCCAAAAGGCTATAAAAGGTAGCGCGATAGCGGACTTTTTAGCAAGTCGTG
66 CATTGTGTACGTGAGCCAAAAGGCTATAAAAGGTAGCGCGATAGCGGACTTTTTAGCAAGTCGTG
596152 CGATGGAAGACTATCAGCCCTTAAACTTTGACTTCCCTGATGAAGACCTAATGTGTATAT
131 CGATGGAAGACTATCAGCCCTTAAACTTTGACTTCCCTGATGAAGACCTAATGTGTATAT
596212 CTA
1 CTA
596215 GGGAAGAAGA
Statistics
Matches: 193, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 193 1.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (190 bp):
CTATGCGAAGCCCCCGCTTTGTCAGGACGATTAGCAAGGTGGCAAGTCTTGCTCTCAGAATACGA
CATTGTGTACGTGAGCCAAAAGGCTATAAAAGGTAGCGCGATAGCGGACTTTTTAGCAAGTCGTG
CGATGGAAGACTATCAGCCCTTAAACTTTGACTTCCCTGATGAAGACCTAATGTGTATAT
Found at i:598042 original size:10 final size:10
Alignment explanation
Indices: 598027--598054 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
598017 TCTTCAAAAA
598027 AAAAAAAAGC
1 AAAAAAAAGC
598037 AAAAAAAAGC
1 AAAAAAAAGC
598047 AAAAAAAA
1 AAAAAAAA
598055 AAAAAATCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGC
Found at i:599110 original size:55 final size:54
Alignment explanation
Indices: 599023--599715 Score: 790
Period size: 55 Copynumber: 12.4 Consensus size: 54
599013 CTCCGTCCGC
* *
599023 TTTTCAGTCCCCAAAGAGCAGGACACCATTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
599077 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
599132 TTTTCCAGTCCTCAGAGAGCAGGACACCTCTT-AAAGCTCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
** *
599187 CCTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
599241 TTTTCCAGTCCTTAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
599296 TTTTCCAGTCCTCAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
** * * *
599351 CCTTCAGTCCTTAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCA
** * * * *
599410 CCTTCAGTCCTCAAAGAGCGGGACGCTTTTCTTTTAAAGCCCATC-TAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACAC----CTTTCAAAGCCCA-CACAAGTTGGTGGCA
* * *
599468 CCTTT-AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAG-CCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
599527 CCTTTCAGTCCCCAAAGAGCAGGGACACCTTTTAAAGCCCACAC-AGTTGGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCA-GGACACCTTTCAAAGCCCACACAAGTT-GGTGGCA
599583 TTTTCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACAC-AGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* *
599636 CCTTATCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 --TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
599692 CCTTTCAGTCCCCAAAGAGCAGGA
1 -TTTTCAGTCCTCAAAGAGCAGGA
599716 AAACAAAAAA
Statistics
Matches: 570, Mismatches: 40, Indels: 57
0.85 0.06 0.09
Matches are distributed among these distances:
53 9 0.02
54 94 0.16
55 290 0.51
56 28 0.05
58 49 0.09
59 74 0.13
60 22 0.04
61 3 0.01
64 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (54 bp):
TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:599226 original size:109 final size:107
Alignment explanation
Indices: 599023--599715 Score: 795
Period size: 109 Copynumber: 6.2 Consensus size: 107
599013 CTCCGTCCGC
* * **
599023 TTTTCAGTCCCCAAAGAGCAGGACACCATTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
1 TTTTCAGTCCTCAAAGAGCAGGACACC-TTTAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCC
599088 TCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
64 TCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
599132 TTTTCCAGTCCTCAGAGAGCAGGACACCTCTTAAAGCTCACACAAGTTGGTGGCACCTTCAGTCC
1 TTTT-CAGTCCTCAAAGAGCAGGACACCT-TTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCC
*
599197 TCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGGCA
64 TCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* **
599241 TTTTCCAGTCCTTAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTT-AAAGCCCACACAAGTTGGTGGCACCTT-CAGTC
*
599306 CTCAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
63 CTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
** * *
599351 CCTTCAGTCCTTAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCA
1 TTTTCAGTCCTCAAAGAGCAGGACAC-----C-TTTAAAGCCCACACAAGTTGGTGGCACCTTCA
* * * *
599416 GTCCTCAAAGAGCGGGACGCTTTTCTTTTAAAGCCCATC-TAAGTTGGTGGCA
60 GTCCTCAAAGAGCAGGACAC----CTTTCAAAGCCCA-CACAAGTTGGTGGCA
* * *
599468 CCTTT-AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAG-CCACACAAGTTGGTGGCACCTT
1 -TTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTT-AAAGCCCACACAAGTTGGTGGCACC-T
* *
599531 TCAGTCCCCAAAGAGCAGGGACACCTTTTAAAGCCCACAC-AGTTGGGTGGCA
57 TCAGTCCTCAAAGAGCA-GGACACCTTTCAAAGCCCACACAAGTT-GGTGGCA
599583 TTTTCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACAC-AGTTGGTGGCACCTTATCAGTC
1 TTTTCAGTCCTCAAAGAGCAGGACACCT-TTAAAGCCCACACAAGTTGGTGGCACC-T-TCAGTC
*
599647 CTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
63 CTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
599692 CCTTTCAGTCCCCAAAGAGCAGGA
1 -TTTTCAGTCCTCAAAGAGCAGGA
599716 AAACAAAAAA
Statistics
Matches: 509, Mismatches: 40, Indels: 69
0.82 0.06 0.11
Matches are distributed among these distances:
108 2 0.00
109 174 0.34
110 142 0.28
111 2 0.00
113 20 0.04
114 34 0.07
115 41 0.08
116 2 0.00
117 61 0.12
118 24 0.05
119 6 0.01
123 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (107 bp):
TTTTCAGTCCTCAAAGAGCAGGACACCTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTC
AAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:599296 original size:164 final size:165
Alignment explanation
Indices: 599024--599715 Score: 870
Period size: 164 Copynumber: 4.1 Consensus size: 165
599014 TCCGTCCGCT
*
599024 TTTCAGTCCCCAAAGAGCAGGACACCATTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
1 TTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCT
*
599089 CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAGAGAGCA
65 CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCA
*
599153 GGACACCTCTT-AAAGCTCACACAAGTTGGTGGCACC
129 GGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACC
* *
599189 -TTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGGCATTTTCCAGTCCT
1 TTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCT
* *
599253 TAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAGAGAGCA
65 CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCA
599317 GGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
129 GGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACC
** * * **
599353 -TTCAGTCCTTAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAG
1 TTTCAGTCCCCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCAG
* * * * *
599417 TCCTCAAAGAGCGGGACGCTTTTCTTTTAAAGCCCATC-TAAGTTGGTGGCACCTTT-AGTCCTC
61 TCCTCAAAGAGCAGGACAC----CTTTCAAAGCCCA-CACAAGTTGGTGGCACTTTTCAGTCCTC
** *
599480 AAAGAGCAGGATGCTTTTTCTTTTCAAAG-CCACACAAGTTGGTGGCACC
121 AAAGAGCAGGA--C---ACCTCTTCAAAGCCCACACAAGTTGGTGGCACC
*
599529 TTTCAGTCCCCAAAGAGCAGGGACACCTTTTAAAGCCCACAC-AGTTGGGTGGCATTTTCAGTCC
1 TTTCAGTCCCCAAAGAGCA-GGACACCTTTCAAAGCCCACACAAGTT-GGTGGCATTTTCAGTCC
*
599593 TCAAAGAGCAGGACACCTCTT-AAAGCCCACAC-AGTTGGTGGCACCTTATCAGTCCTCAAAGAG
64 TCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTCAAAGAG
*
599656 CAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGCACC
127 CAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCACC
599694 TTTCAGTCCCCAAAGAGCAGGA
1 TTTCAGTCCCCAAAGAGCAGGA
599716 AAACAAAAAA
Statistics
Matches: 469, Mismatches: 33, Indels: 51
0.85 0.06 0.09
Matches are distributed among these distances:
164 191 0.41
165 41 0.09
168 32 0.07
169 41 0.09
170 20 0.04
171 17 0.04
172 28 0.06
173 50 0.11
176 24 0.05
177 19 0.04
178 6 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (165 bp):
TTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTC
AAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGG
ACACCTCTTCAAAGCCCACACAAGTTGGTGGCACC
Found at i:600663 original size:1 final size:1
Alignment explanation
Indices: 600657--600698 Score: 57
Period size: 1 Copynumber: 42.0 Consensus size: 1
600647 CCTTCTCTTC
** *
600657 AAAAAAAAAAAAAAGCAAAAAAAAGAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
600699 TCTGCTTAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.93, C:0.02, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:601750 original size:55 final size:54
Alignment explanation
Indices: 601664--602971 Score: 1564
Period size: 55 Copynumber: 23.4 Consensus size: 54
601654 TCCGTCCGCT
* * *
601664 TTTCAGTCCCCAAAGAGCAGGACACCATTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
* *
601718 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGACAT
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
601773 TTTCCAGTCCTCAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCAC
* * *
601828 CTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
601882 TTTCCAGTCCT-AAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
601936 TTTCCAGTCCTCAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCAC
* * *
601991 CTTCAGTCCT-AAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC
1 TTTCAGTCCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCAC
* * *
602049 CTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCATC-CAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCA-CACAAGTTGGTGGCA-C
* * *
602109 TTT-AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCTACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* * *
602169 TTTCAGTCCCCAAAGAGCAGGACACCTTTTAAA-CCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
602222 TTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-C
*
602278 TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* *
602333 TTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
602387 TTTCCAGTCCTCAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCAC
* * * *
602442 CTTCAGTCCACAAAGAGCGGGACACATTTTCTTTTAAAG-CCACACAAGTTGGTGGCAC
1 TTTCAGTCCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * *
602500 CTTCAGTCCTTAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCATC-CAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCA-CACAAGTTGGTGGCA-C
* *
602560 TTT-AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* * *
602620 TTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
602674 TTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-C
*
602730 TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* * *
602785 TTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
602839 TTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-C
*
602895 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACGAGTTGGTGGCAC
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
* * *
602949 TTTTTACTCCTCAATGAGCAGGA
1 -TTTCAGTCCTCAAAGAGCAGGA
602972 TACACTTTAT
Statistics
Matches: 1118, Mismatches: 70, Indels: 131
0.85 0.05 0.10
Matches are distributed among these distances:
53 18 0.02
54 193 0.17
55 605 0.54
56 19 0.02
57 2 0.00
58 83 0.07
59 93 0.08
60 59 0.05
61 36 0.03
64 8 0.01
65 2 0.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (54 bp):
TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
Found at i:602344 original size:29 final size:29
Alignment explanation
Indices: 602257--602344 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 29
602247 CCTCTTAAAG
602257 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
* ** * * ***
602286 CTCA-A-AGAG-CAG-GACGCCTTTCAAAG
1 CCCACACA-AGTTGGTGGCACCTTTCAGTC
602312 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
602341 CCCA
1 CCCA
602345 AAGAGCAGGA
Statistics
Matches: 38, Mismatches: 16, Indels: 10
0.59 0.25 0.16
Matches are distributed among these distances:
26 12 0.32
27 5 0.13
28 5 0.13
29 16 0.42
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.20
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAGTC
Found at i:602370 original size:26 final size:26
Alignment explanation
Indices: 602288--602370 Score: 60
Period size: 26 Copynumber: 3.1 Consensus size: 26
602278 TTTCAGTCCT
*
602288 CAAAGAGCAGGACGCCTTTCAAAGCC
1 CAAAGAGCAGGACACCTTTCAAAGCC
** * ***
602314 CACACA-AGTTGGTGGCACCTTTCAGTCCC
1 CA-A-AGAG-CAG-GACACCTTTCAAAGCC
602343 CAAAGAGCAGGACACCTTTCAAAGCC
1 CAAAGAGCAGGACACCTTTCAAAGCC
602369 CA
1 CA
602371 CACAAGTTGG
Statistics
Matches: 39, Mismatches: 13, Indels: 10
0.63 0.21 0.16
Matches are distributed among these distances:
26 16 0.41
27 5 0.13
28 5 0.13
29 13 0.33
ACGTcount: A:0.31, C:0.33, G:0.20, T:0.16
Consensus pattern (26 bp):
CAAAGAGCAGGACACCTTTCAAAGCC
Found at i:602532 original size:451 final size:452
Alignment explanation
Indices: 601691--602948 Score: 2241
Period size: 451 Copynumber: 2.8 Consensus size: 452
601681 CAGGACACCA
* * *
601691 TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCC
1 TTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACACCTTTTAAAGCC
* *
601755 CACACAAGTTGGTGACATTTTCCAGTCCTCAGAGAGCAGGACACCTCTTAAAGCCCACACAAGTT
65 CACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTT
* * *
601820 GGTGGCACC-TTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGATGGCA-TT
130 GGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCT
*
601883 TTCCAGT-CCTAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
195 TT-CAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
*
601947 CAGAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTAAAGAGCGGGA
259 CAGAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCCAAAGAGCGGGA
602012 CACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTT
324 CACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTT
602077 TTCTTTTAAAGCCCATCCAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTT
389 TTCTTTTAAAGCCCATCCAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTT
*
602141 TTCAAAGCCTACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAA-CCC
1 TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCC
602205 ACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTG
66 ACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTG
602270 GTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
131 GTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
602335 TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
196 TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
602400 GAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCACAAAGAGCGGGAC
261 GAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCC-CAAAGAGCGGGAC
*
602465 ACATTTTCTTTTAAAG-CCACACAAGTTGGTGGCACCTTCAGTCCTTAAAGAGCGGGACGCCTTT
325 ACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTT
602529 TCTTTTAAAGCCCATCCAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTT
390 TCTTTTAAAGCCCATCCAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTT
602592 TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCC
1 TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCC
602657 ACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTG
66 ACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTG
602722 GTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
131 GTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
*
602787 TCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
196 TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
* *
602852 AAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
261 GAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCC-CAAAGAGCGGGA
* *
602917 CAC-----CTTTCAAAGCCCACACGAGTTGGTGGCAC
324 CACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCAC
602949 TTTTTACTCC
Statistics
Matches: 781, Mismatches: 19, Indels: 17
0.96 0.02 0.02
Matches are distributed among these distances:
448 8 0.01
449 92 0.12
450 107 0.14
451 285 0.36
452 267 0.34
453 22 0.03
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.23
Consensus pattern (452 bp):
TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCC
ACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTG
GTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT
TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
GAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCCAAAGAGCGGGACA
CATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTT
CTTTTAAAGCCCATCCAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGATGCTTTTTCTT
Found at i:602796 original size:29 final size:29
Alignment explanation
Indices: 602709--602796 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 29
602699 CCTCTTAAAG
602709 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
* ** * * ***
602738 CTCA-A-AGAG-CAG-GACGCCTTTCAAAG
1 CCCACACA-AGTTGGTGGCACCTTTCAGTC
602764 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
602793 CCCA
1 CCCA
602797 AAGAGCAGGA
Statistics
Matches: 38, Mismatches: 16, Indels: 10
0.59 0.25 0.16
Matches are distributed among these distances:
26 12 0.32
27 5 0.13
28 5 0.13
29 16 0.42
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.20
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAGTC
Found at i:603710 original size:21 final size:21
Alignment explanation
Indices: 603684--603740 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
603674 AAATTATCCA
603684 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
603705 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
603726 AATGTATCGATACAT
1 AATGTATCGATACAT
603741 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:603820 original size:19 final size:19
Alignment explanation
Indices: 603796--603863 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
603786 AATTCAACAA
603796 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
603815 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
603830 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
603847 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
603864 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:603835 original size:13 final size:13
Alignment explanation
Indices: 603817--603841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
603807 ACATAAGTTT
603817 TGTATCGATACAA
1 TGTATCGATACAA
603830 TGTATCGATACA
1 TGTATCGATACA
603842 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:603839 original size:32 final size:32
Alignment explanation
Indices: 603798--603860 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
603788 TTCAACAATT
*
603798 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
603830 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
603861 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:603909 original size:21 final size:20
Alignment explanation
Indices: 603883--603938 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
603873 GCCAAGGAAA
*
603883 TGTATCGATACATTTTTCTAG
1 TGTATCGATACATTTATCT-G
** *
603904 TGTATCGATACATGGATCTT
1 TGTATCGATACATTTATCTG
603924 TGTATCGATACATTT
1 TGTATCGATACATTT
603939 GAAATTTTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTATCTG
Found at i:606347 original size:51 final size:51
Alignment explanation
Indices: 606287--606648 Score: 221
Period size: 52 Copynumber: 6.9 Consensus size: 51
606277 AATTCACCAC
* * * *
606287 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTCCTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCCTAT
* * *
606338 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC--AAAACACCAATTTCCT-AT
* * * ** * * **
606392 AATCGGGGATACTACAACCCCG--TTGATCATCGGGGATACTCCAA-CCCCGTTAT
1 AATCGGGGATACTCCAACCCCGATTTTAT-TTC--CAAAACACCAATTTCC--TAT
** * * *** *
606445 TTTCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAATATTGATTT-TTCAT
1 AATC--GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCCT-AT
* * * * * *
606498 AATCGGGGATATTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCC-AC
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAA--TTTCCTAT
* * * *
606550 AATCGGGGATACTCCAACCCCGGTTTTATTTTCGAAACACCAATTTTCCTTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAA-TTTCCTAT
* * *
606602 AATCGGGGATACTCCAACTCCAATTTTATTTCCAAAAATACCAATTT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTT
606649 TTCACAGTTG
Statistics
Matches: 233, Mismatches: 59, Indels: 37
0.71 0.18 0.11
Matches are distributed among these distances:
51 68 0.29
52 76 0.33
53 41 0.18
54 25 0.11
55 17 0.07
56 2 0.01
57 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTCCTAT
Found at i:606460 original size:28 final size:27
Alignment explanation
Indices: 606393--606468 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
606383 TTTCTTCACA
*
606393 ATCGGGGATACTACAACCCCGTTGATC
1 ATCGGGGATACTCCAACCCCGTTGATC
*
606420 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTGATC
*
606446 TTCGAGGGGATACTCCAACCCCG
1 ATC--GGGGATACTCCAACCCCG
606469 ACTTTATTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.09
27 22 0.50
28 18 0.41
ACGTcount: A:0.24, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTGATC
Found at i:606706 original size:28 final size:28
Alignment explanation
Indices: 606662--606731 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
606652 ACAGTTGAGG
** * **
606662 ATACTCCAACCTTGTTATTTCATCGGGA
1 ATACTCCAACCCCGTTACTTCAGAGGGA
* *
606690 ATACTCCAACCCCGTTACTTCCGAGGGG
1 ATACTCCAACCCCGTTACTTCAGAGGGA
606718 ATACTCCAACCCCG
1 ATACTCCAACCCCG
606732 GCTTTATTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (28 bp):
ATACTCCAACCCCGTTACTTCAGAGGGA
Found at i:606750 original size:263 final size:263
Alignment explanation
Indices: 606283--606782 Score: 745
Period size: 263 Copynumber: 1.9 Consensus size: 263
606273 TCTCAATTCA
* * *
606283 CCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTCCTATAATCGGGGAT
1 CCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCCTATAATCGGGGAT
* *
606348 ACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTACAACCCC
66 ACTCCAACTCCAATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTACAACCCC
* * * *
606413 GTTGATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTT
131 GTTGATCATCGGGAATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTC
* * *
606478 CCAAAATATTGATTTTTCATAATCGGGGATATTCCAACCCCGGTTTTATTGCTAAAACACTAATT
196 CCAAAATATTGATTTCTCATAATCAGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
606543 TTT
261 TTT
* * *
606546 CCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCGAAACACCAATTTTCCTTTAATCGGGGA
1 CCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAA-TTTCCTATAATCGGGGA
* * * * *
606611 TACTCCAACTCCAATTTTATTTCC-AAAAATACCAATTT-TTCACAGTTGAGGATACTCCAACCT
65 TACTCCAACTCCAATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTACAACCC
* *
606674 TGTT-ATTTCATCGGGAATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTA
130 CGTTGA--TCATCGGGAATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTA
*
606738 TTCCCAAAATATTGATTTCTCATAATTAGGGATACTCCAACCCCG
193 TTCCCAAAATATTGATTTCTCATAATCAGGGATACTCCAACCCCG
606783 TTATTTTCGA
Statistics
Matches: 211, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
261 1 0.00
262 23 0.11
263 148 0.70
264 39 0.18
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (263 bp):
CCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTCCTATAATCGGGGAT
ACTCCAACTCCAATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTACAACCCC
GTTGATCATCGGGAATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATTC
CCAAAATATTGATTTCTCATAATCAGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATT
TTT
Found at i:606834 original size:79 final size:79
Alignment explanation
Indices: 606690--606889 Score: 222
Period size: 79 Copynumber: 2.5 Consensus size: 79
606680 TTCATCGGGA
* * * *
606690 ATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATT
1 ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATATCGATT
* **
606755 TCTCATAATTAGGG
66 TCTCACAACCAGGG
* * * ** *
606769 ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTC-TAATCATCGAT
1 ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-ATCGAT
*
606833 TTCTCACAACCGGGG
65 TTCTCACAACCAGGG
* * * *
606848 ATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
606890 TTATTATCTC
Statistics
Matches: 101, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
78 3 0.03
79 98 0.97
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.29
Consensus pattern (79 bp):
ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATATCGATT
TCTCACAACCAGGG
Found at i:609545 original size:21 final size:21
Alignment explanation
Indices: 609504--609547 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
609494 CTCCCCTTTA
* *
609504 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
609525 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
609546 TC
1 TC
609548 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:611367 original size:13 final size:13
Alignment explanation
Indices: 611349--611374 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
611339 ATAATCACCC
611349 TGTATCGATACAA
1 TGTATCGATACAA
611362 TGTATCGATACAA
1 TGTATCGATACAA
611375 AGAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:613150 original size:15 final size:15
Alignment explanation
Indices: 613130--613160 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
613120 ATTTCGTTTG
*
613130 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
613145 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
613160 G
1 G
613161 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:614993 original size:21 final size:21
Alignment explanation
Indices: 614964--615008 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
614954 AAGTTTTCAT
*
614964 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
614984 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
615006 TTT
1 TTT
615009 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:617245 original size:13 final size:13
Alignment explanation
Indices: 617227--617252 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
617217 CAATTTTTTG
617227 TGTATCGATACAT
1 TGTATCGATACAT
617240 TGTATCGATACAT
1 TGTATCGATACAT
617253 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:619852 original size:20 final size:19
Alignment explanation
Indices: 619827--619899 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
619817 CTGCCAGTTT
**
619827 CATGTATCGATACAACTGTC
1 CATGTATCGATACAA-TGAA
*
619847 CATGTATCAATACAATGAA
1 CATGTATCGATACAATGAA
* *
619866 CATGTATTGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
619887 -ATGTATCGATACA
1 CATGTATCGATACA
619900 TCTGGGTGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 16 0.36
20 27 0.61
21 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:619878 original size:19 final size:20
Alignment explanation
Indices: 619827--619880 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
619817 CTGCCAGTTT
**
619827 CATGTATCGATACAACTGTC
1 CATGTATCGATACAACTGAA
*
619847 CATGTATCAATACAA-TGAA
1 CATGTATCGATACAACTGAA
*
619866 CATGTATTGATACAA
1 CATGTATCGATACAA
619881 AGCATAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAACTGAA
Found at i:627519 original size:19 final size:21
Alignment explanation
Indices: 627495--627547 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
627485 CTGCCAGTTT
*
627495 CATGTATCGATACAATG-A-A
1 CATGTATCGATACAAAGCATA
627514 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAAAGCATA
627535 -ATGTATCGATACA
1 CATGTATCGATACA
627548 TTTGGGTGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 16 0.52
20 14 0.45
21 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (21 bp):
CATGTATCGATACAAAGCATA
Found at i:628411 original size:21 final size:20
Alignment explanation
Indices: 628385--628451 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 20
628375 AAACTTCAAA
628385 AAAAAAGTCAAAAGCAAAAGC
1 AAAAAAGTCAAAAGCAAAA-C
*
628406 ATAAAAA-CCAAAA-CAAAAC
1 A-AAAAAGTCAAAAGCAAAAC
*
628425 AAAGAAAGTGCAAACGCAAAATC
1 AAA-AAAGT-CAAAAGCAAAA-C
628448 AAAA
1 AAAA
628452 GGGGGAGCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
18 2 0.05
19 5 0.14
20 5 0.14
21 10 0.27
22 11 0.30
23 4 0.11
ACGTcount: A:0.67, C:0.16, G:0.10, T:0.06
Consensus pattern (20 bp):
AAAAAAGTCAAAAGCAAAAC
Found at i:629909 original size:28 final size:28
Alignment explanation
Indices: 629877--630091 Score: 127
Period size: 27 Copynumber: 7.7 Consensus size: 28
629867 CAAACTTTTT
*
629877 CTTTTAAAGTCCATAACTCCATGGCAACC
1 CTTTTAAAGTCCACAACTCCATGGCAA-C
* *
629906 TTTTCTTTTAAAGTCCACAACTCCGTGGCATC
1 ----CTTTTAAAGTCCACAACTCCATGGCAAC
* *
629938 CTTTT-AAGTCTACAACTCCATGGCACC
1 CTTTTAAAGTCCACAACTCCATGGCAAC
* * ** *
629965 CTTTT-AAGTCTATAACTCTGTGGCACC
1 CTTTTAAAGTCCACAACTCCATGGCAAC
*
629992 CTTTTAAAGTCCACAACTTCATGGC-AC
1 CTTTTAAAGTCCACAACTCCATGGCAAC
* * * **** *
630019 C-CTAAAAGTCCATAACTTTGCGGC-AT
1 CTTTTAAAGTCCACAACTCCATGGCAAC
* * *
630045 CTTTTTAAGTCCACAACTTCGTGGC-AC
1 CTTTTAAAGTCCACAACTCCATGGCAAC
*
630072 CTTTTTAAAGTCCACCACTC
1 C-TTTTAAAGTCCACAACTC
630092 TGTGACACCT
Statistics
Matches: 147, Mismatches: 32, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
26 19 0.13
27 69 0.47
28 34 0.23
32 1 0.01
33 24 0.16
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (28 bp):
CTTTTAAAGTCCACAACTCCATGGCAAC
Found at i:629915 original size:33 final size:33
Alignment explanation
Indices: 629839--629942 Score: 136
Period size: 33 Copynumber: 3.1 Consensus size: 33
629829 TTTAGTGGCA
** *
629839 TTTCTTTTCAAAGAACATAACTCCATGGCAAACTT
1 TTTCTTTT-AAAGTCCATAACTCCATGGC-AACCT
629874 TTTCTTTTAAAGTCCATAACTCCATGGCAACCT
1 TTTCTTTTAAAGTCCATAACTCCATGGCAACCT
* * *
629907 TTTCTTTTAAAGTCCACAACTCCGTGGCATCCT
1 TTTCTTTTAAAGTCCATAACTCCATGGCAACCT
629940 TTT
1 TTT
629943 AAGTCTACAA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 37 0.59
34 18 0.29
35 8 0.13
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.38
Consensus pattern (33 bp):
TTTCTTTTAAAGTCCATAACTCCATGGCAACCT
Found at i:629952 original size:27 final size:26
Alignment explanation
Indices: 629910--630104 Score: 147
Period size: 27 Copynumber: 7.2 Consensus size: 26
629900 GCAACCTTTT
629910 CTTTTAAAGTCCACAACTCCGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCA-C
* *
629938 CTTTTAAGTCTACAACTCCATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-C
* * *
629965 CTTTTAAGTCTATAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-C
* *
629992 CTTTTAAAGTCCACAACTTCATGGCAC
1 CTTTT-AAGTCCACAACTCCGTGGCAC
* ** * ** *
630019 CCTAAAAGTCCATAACTTTGCGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCA-C
* *
630046 TTTTTAAGTCCACAACTTCGTGGCAC
1 CTTTTAAGTCCACAACTCCGTGGCAC
* * *
630072 CTTTTTAAAGTCCACCACTCTGTGACAC
1 C-TTTT-AAGTCCACAACTCCGTGGCAC
630100 CTTTT
1 CTTTT
630105 TAAAGCCCAC
Statistics
Matches: 133, Mismatches: 30, Indels: 9
0.77 0.17 0.05
Matches are distributed among these distances:
26 17 0.13
27 78 0.59
28 38 0.29
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.32
Consensus pattern (26 bp):
CTTTTAAGTCCACAACTCCGTGGCAC
Found at i:630159 original size:86 final size:84
Alignment explanation
Indices: 630055--630770 Score: 642
Period size: 86 Copynumber: 8.4 Consensus size: 84
630045 CTTTTTAAGT
* * * * * * *
630055 CCACAACTTCGTGGCACCTTTTTAAAGTCCACCACTCTGTGACA-CCTTTTTAAAGCCCACAAGT
1 CCACAAGTTAGTGGCACCTTTTCAAAGCCCACAACT-TGTGGCACCCTTTTCAAAGCCCACAAGT
*
630119 CAGTGGTAACCCTTTTCAAAGC
65 CAGTGG-CA-CCTTTTCAAAGC
* * * * * * *
630141 CCACAAGTTACTGGCACCTTCTCAAAGCCCACAAGTTAGTGACA-TCTTTTTAAAACCCACAAGT
1 CCACAAGTTAGTGGCACCTTTTCAAAGCCCACAACTT-GTGGCACCCTTTTCAAAGCCCACAAGT
630205 CAGTGGCAACCCTTTTCAAAGC
65 CAGTGGC-A-CCTTTTCAAAGC
* * *
630227 CCACAAGTTAGTGGCACCTTTTCAAAGCCCATAAGTCTGTGGCATCC-TTTCAAAG-CCACAAGT
1 CCACAAGTTAGTGGCACCTTTTCAAAGCCCACAACT-TGTGGCACCCTTTTCAAAGCCCACAAGT
*
630290 CAGTGGCACTTTTTCAAAGC
65 CAGTGGCACCTTTTCAAAGC
* * * * *
630310 CCACAAGTCAATGGCATCTTTTTAAAGCCCACAAGTTAGTGGCACCCTTTT-AAAGCCCACAAGT
1 CCACAAGTTAGTGGCACCTTTTCAAAGCCCACAACTT-GTGGCACCCTTTTCAAAGCCCACAAGT
* * *
630374 TAGTGGCACCTTCTCAAAAC
65 CAGTGGCACCTTTTCAAAGC
** *
630394 CCACAAGTTAGTGGCATTTTTTCAAAGCCCACAAGCTAGTGGCAACCCTTTTCAAAGCCCACAAG
1 CCACAAGTTAGTGGCACCTTTTCAAAGCCCACAA-CTTGTGGC-ACCCTTTTCAAAGCCCACAAG
* * *
630459 TCAATGGCACCTTCTCAAAAC
64 TCAGTGGCACCTTTTCAAAGC
* * *
630480 CCACAAGTTATTGGCATCTTTTCAAAGCCCACAAGCTAGTGGCAACCCTTTTCAAAGCCCACAAG
1 CCACAAGTTAGTGGCACCTTTTCAAAGCCCACAA-CTTGTGGC-ACCCTTTTCAAAGCCCACAAG
**
630545 TCAGTGGCACCTTCCCAAAGC
64 TCAGTGGCACCTTTTCAAAGC
* * * ** *
630566 TCACAAGTTTGTGGCATCC-TTTCAAAGCCCACAAGTCAATGGCA-CTTTTTCAAAGCCCACAAG
1 CCACAAGTTAGTGGCA-CCTTTTCAAAGCCCACAACT-TGTGGCACCCTTTTCAAAGCCCACAAG
* * *
630629 TTAGTGGCATCTTTTTAAAGC
64 TCAGTGGCACCTTTTCAAAGC
* * * * * * *
630650 CCACAAGTCAGTAGCACCCTTTT-AAAACCCACAAGTAAGTGGTA-TCTTTTCAAAGCCCACAAG
1 CCACAAGTTAGTGGCA-CCTTTTCAAAGCCCACAACT-TGTGGCACCCTTTTCAAAGCCCACAAG
* *
630713 TAAGTGACATCC-TTTCAAAGCC
64 TCAGTGGCA-CCTTTTCAAAG-C
* * *
630735 CGCATAAGTTAGTGGCAACTTTCTTTAAAGCCCACA
1 C-CACAAGTTAGTGGC-ACCTT-TTCAAAGCCCACA
630771 CAAGTTAGTG
Statistics
Matches: 537, Mismatches: 74, Indels: 36
0.83 0.11 0.06
Matches are distributed among these distances:
82 1 0.00
83 54 0.10
84 159 0.30
85 33 0.06
86 275 0.51
87 6 0.01
88 9 0.02
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (84 bp):
CCACAAGTTAGTGGCACCTTTTCAAAGCCCACAACTTGTGGCACCCTTTTCAAAGCCCACAAGTC
AGTGGCACCTTTTCAAAGC
Found at i:630169 original size:28 final size:28
Alignment explanation
Indices: 630055--630783 Score: 700
Period size: 28 Copynumber: 25.6 Consensus size: 28
630045 CTTTTTAAGT
* * * *
630055 CCACAACTTCGTGGCACCTTTTTAAAGT
1 CCACAAGTTAGTGGCACCTTTTCAAAGC
* * * *
630083 CCACCACTCT-GTGACACCTTTTTAAAGC
1 CCACAAGT-TAGTGGCACCTTTTCAAAGC
* *
630111 CCACAAGTCAGTGGTAACCCTTTTCAAAGC
1 CCACAAGTTAGTGG-CA-CCTTTTCAAAGC
* *
630141 CCACAAGTTACTGGCACCTTCTCAAAGC
1 CCACAAGTTAGTGGCACCTTTTCAAAGC
* * * *
630169 CCACAAGTTAGTGACATCTTTTTAAAAC
1 CCACAAGTTAGTGGCACCTTTTCAAAGC
*
630197 CCACAAGTCAGTGGCAACCCTTTTCAAAGC
1 CCACAAGTTAGTGGC-A-CCTTTTCAAAGC
630227 CCACAAGTTAGTGGCACCTTTTCAAAGC
1 CCACAAGTTAGTGGCACCTTTTCAAAGC
*
630255 CCATAAGTCT-GTGGCATCC-TTTCAAAG-
1 CCACAAGT-TAGTGGCA-CCTTTTCAAAGC
* *
630282 CCACAAGTCAGTGGCACTTTTTCAAAGC
1 CCACAAGTTAGTGGCACCTTTTCAAAGC
* * * *
630310 CCACAAGTCAATGGCATCTTTTTAAAGC
1 CCACAAGTTAGTGGCACCTTTTCAAAGC
630338 CCACAAGTTAGTGGCACCCTTTT-AAAGC
1 CCACAAGTTAGTGGCA-CCTTTTCAAAGC
* *
630366 CCACAAGTTAGTGGCACCTTCTCAAAAC
1 CCACAAGTTAGTGGCACCTTTTCAAAGC
**
630394 CCACAAGTTAGTGGCATTTTTTCAAAGC
1 CCACAAGTTAGTGGCACCTTTTCAAAGC
*
630422 CCACAAGCTAGTGGCAACCCTTTTCAAAGC
1 CCACAAGTTAGTGGC-A-CCTTTTCAAAGC
* * * *
630452 CCACAAGTCAATGGCACCTTCTCAAAAC
1 CCACAAGTTAGTGGCACCTTTTCAAAGC
* *
630480 CCACAAGTTATTGGCATCTTTTCAAAGC
1 CCACAAGTTAGTGGCACCTTTTCAAAGC
*
630508 CCACAAGCTAGTGGCAACCCTTTTCAAAGC
1 CCACAAGTTAGTGGC-A-CCTTTTCAAAGC
* **
630538 CCACAAGTCAGTGGCACCTTCCCAAAGC
1 CCACAAGTTAGTGGCACCTTTTCAAAGC
* *
630566 TCACAAGTTTGTGGCATCC-TTTCAAAGC
1 CCACAAGTTAGTGGCA-CCTTTTCAAAGC
* * *
630594 CCACAAGTCAATGGCACTTTTTCAAAGC
1 CCACAAGTTAGTGGCACCTTTTCAAAGC
* *
630622 CCACAAGTTAGTGGCATCTTTTTAAAGC
1 CCACAAGTTAGTGGCACCTTTTCAAAGC
* * *
630650 CCACAAGTCAGTAGCACCCTTTT-AAAAC
1 CCACAAGTTAGTGGCA-CCTTTTCAAAGC
* * *
630678 CCACAAGTAAGTGGTATCTTTTCAAAGC
1 CCACAAGTTAGTGGCACCTTTTCAAAGC
* *
630706 CCACAAGTAAGTGACATCC-TTTCAAAGCC
1 CCACAAGTTAGTGGCA-CCTTTTCAAAG-C
* * *
630735 CGCATAAGTTAGTGGCAACTTTCTTTAAAGCC
1 C-CACAAGTTAGTGGC-ACCTT-TTCAAAG-C
630767 CACACAAGTTAGTGGCA
1 C-CACAAGTTAGTGGCA
630784 ACCCTTCTAA
Statistics
Matches: 578, Mismatches: 96, Indels: 51
0.80 0.13 0.07
Matches are distributed among these distances:
26 1 0.00
27 32 0.06
28 389 0.67
29 27 0.05
30 104 0.18
31 3 0.01
32 22 0.04
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (28 bp):
CCACAAGTTAGTGGCACCTTTTCAAAGC
Found at i:630765 original size:32 final size:33
Alignment explanation
Indices: 630724--630785 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
630714 AAGTGACATC
* *
630724 CTTTCAAAGCCCGCATAAGTTAGTGGCAACTTT
1 CTTTCAAAGCCCACACAAGTTAGTGGCAACTTT
630757 CTTT-AAAGCCCACACAAGTTAGTGGCAAC
1 CTTTCAAAGCCCACACAAGTTAGTGGCAAC
630786 CCTTCTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 23 0.85
33 4 0.15
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (33 bp):
CTTTCAAAGCCCACACAAGTTAGTGGCAACTTT
Found at i:632428 original size:2 final size:2
Alignment explanation
Indices: 632416--632453 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
632406 TGTTTTATTG
*
632416 AT AT GT 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
632454 TGAAAATCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:634648 original size:63 final size:63
Alignment explanation
Indices: 634542--634664 Score: 185
Period size: 63 Copynumber: 2.0 Consensus size: 63
634532 GGTCTTCCCC
* * *
634542 TTTTCAACACATATCTTTTACCATGTCATAGAAATCCCTAATCACAAGGGATATTAAGTCAGT
1 TTTTCAACACATACCTCTTACCATGCCATAGAAATCCCTAATCACAAGGGATATTAAGTCAGT
**
634605 TTTTCAACACATACCTCTTACCATGCCATAGAAATTCCC-AATCATGAGGGATATTAAGTC
1 TTTTCAACACATACCTCTTACCATGCCATAGAAA-TCCCTAATCACAAGGGATATTAAGTC
634665 GGGCGTGCCT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 50 0.93
64 4 0.07
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (63 bp):
TTTTCAACACATACCTCTTACCATGCCATAGAAATCCCTAATCACAAGGGATATTAAGTCAGT
Found at i:635629 original size:13 final size:13
Alignment explanation
Indices: 635611--635635 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
635601 ATATTGCTTA
635611 GTATCGATACATT
1 GTATCGATACATT
635624 GTATCGATACAT
1 GTATCGATACAT
635636 ATTCTTGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:635652 original size:32 final size:33
Alignment explanation
Indices: 635590--635653 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
635580 CACACCTAGA
*
635590 TGTATGGATACATATTGCTTAGTATCGATACAT
1 TGTATCGATACATATTGCTTAGTATCGATACAT
*
635623 TGTATCGATACATATT-CTTGGTATCGATACA
1 TGTATCGATACATATTGCTTAGTATCGATACA
635654 CACTAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATATTGCTTAGTATCGATACAT
Found at i:635764 original size:20 final size:21
Alignment explanation
Indices: 635710--635768 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
635700 TCATTATCGA
*
635710 TGCATTGTATCGATACATACT
1 TGCATTGTATCGATACATACG
* *
635731 TGAATTATATCGATACATA-G
1 TGCATTGTATCGATACATACG
*
635751 TGCATTGCATCGATACAT
1 TGCATTGTATCGATACAT
635769 TGAGCCCAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (21 bp):
TGCATTGTATCGATACATACG
Found at i:636797 original size:19 final size:21
Alignment explanation
Indices: 636749--636801 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
636739 AATTTCTACA
636749 ATTTGTATCGATATAAATAGT
1 ATTTGTATCGATATAAATAGT
** *
636770 AAATGTATCGATATATA-AGT
1 ATTTGTATCGATATAAATAGT
636790 -TTTGTATCGATA
1 ATTTGTATCGATA
636802 CAATGTATCG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 10 0.37
20 3 0.11
21 14 0.52
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.42
Consensus pattern (21 bp):
ATTTGTATCGATATAAATAGT
Found at i:640896 original size:3 final size:3
Alignment explanation
Indices: 640888--640930 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
640878 TCAACCATCA
*
640888 ATG ATG ATG AAG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
640931 AGTTGACTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:648015 original size:13 final size:13
Alignment explanation
Indices: 647997--648021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
647987 ATATTACTTA
647997 GTATCGATACATT
1 GTATCGATACATT
648010 GTATCGATACAT
1 GTATCGATACAT
648022 GTTCTTGGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:648038 original size:32 final size:33
Alignment explanation
Indices: 647976--648039 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
647966 CACACCTAGA
647976 TGTATCGATACATATTACTTAGTATCGATACAT
1 TGTATCGATACATATTACTTAGTATCGATACAT
* *
648009 TGTATCGATACATGTT-CTTGGTATCGATACA
1 TGTATCGATACATATTACTTAGTATCGATACA
648040 CACTAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATATTACTTAGTATCGATACAT
Found at i:648107 original size:13 final size:13
Alignment explanation
Indices: 648089--648113 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
648079 AACTCACTTA
648089 GTATCGATACATT
1 GTATCGATACATT
648102 GTATCGATACAT
1 GTATCGATACAT
648114 ACTTGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:648151 original size:20 final size:21
Alignment explanation
Indices: 648098--648154 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
648088 AGTATCGATA
*
648098 CATTGTATCGATACATACTTG
1 CATTGTATCGATACATACGTG
* * *
648119 AATTGTGTTGATACATA-GTG
1 CATTGTATCGATACATACGTG
648139 CATTGTATCGATACAT
1 CATTGTATCGATACAT
648155 TGAGCCTAAC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (21 bp):
CATTGTATCGATACATACGTG
Found at i:649548 original size:717 final size:711
Alignment explanation
Indices: 648172--649603 Score: 2029
Period size: 717 Copynumber: 2.0 Consensus size: 711
648162 AACGGCTATA
* ** * *
648172 AATTTCAAATGCATATATCGATAGGTTAAGAATTGTATCGATACATAGGAGCGTGTTTGTGTAGA
1 AATTTCAAATACATATATCGATACATTAAGAATTGTATCGATACATAGGAGCATATTTGTGTAGA
* *
648237 AACAAGTGTGAAACAAGTCAATAACGGCTAGCAACATCATCATTCCACTACCAACGGCTAAATCA
66 AACAAGTGTGAAACAAGTAAATAACGGCTAGCAACATCATCATTCCACTACCAACGGCGAAATCA
* * * *
648302 ATATTCTAGCATATAAATATGAGTTCCCAACAGCTGAAGAACAACAAGAATCAATAAGAAAGAGT
131 ACATTCTAGCATATAAATATGAGTTCCCAACAGCTGAAGAACAACAAGAACCAACAAGAAACAGT
* *
648367 GAGAATCAACAAGCAATCAAAGTTTTATCATTTCTACATTTCAAAAAGCTTTTCATTGTGTTATT
196 AAGAATC-ACAAGCAATCAAAGTTTTATCATTTCTACATTTCAAAAAGCTTTTCATTGTATTATT
* *
648432 CTTTGAAAGCTCATTTGTATTCTTTTGTGCTTATACTTTCACAAACACTAACCTACTTAGAGGTA
260 CTTTGAAAGCTCATTTGTATTCTCTTGTGCTTATACTTTCACAAACACTAACCTACTTAGAGGCA
* * * * * * * *
648497 TTTTAAGTTTCTTAAATTTCTTTGTGTTGTAAAAATTTGTATTCAACCTTGGGGTACAATCTCTT
325 GTTCAAGTTTCTAAAATTCCTTTGTATTGTAAAAAGTTATATTCAACCTTGGGGTACAATCTCTC
* *
648562 AAGAATTTGGAGTATATTCTTGAAGAGATTGAGAGGTTCTTATCTTAGCCTTGAAAAGATAAGTG
390 AAGAATTTGGAGTATATTCTTGAAGAGATTAAGAGGTTCTTATCTTAGCCTTCAAAAGATAAGTG
* * * *
648627 TTGTAAGGTTATACCTTTGCCTTAAAAGTAAACAATTTGAGTAGTGAATCGTGGTATACACTCGA
455 TTGTAAGATTATACCTTTGCCTTAAAAGTAAACAATTCGAGTAGTAAATCATGGTATACACTCGA
* *
648692 TAAGGAAGTGTCGAGGAGAGAGAACATAGGTGTCGTGTTTGAACCGAACCTCTATAAACACTTAT
520 TAAGGAACTGTCGAGGAGAGAGAACATAGGTGCCGTGTTTGAACCGAACCTCTATAAACACTTAT
* * *
648757 GTCAAGCTTTCTTTTTTCCCTACTCTTTTTATCTTCGAATTATTTTTGAATTAATTCTTTCAAAA
585 GTCAAGCTTTCTCTTTTCCCAACTCTTTTTATCTTCGAATTATTTTTGAATCAATTCTTTCAAAA
*
648822 CCCTCATTTTTCGATAAGAACCAATGCAC-CCCCCTCTTGGTTCATTCAATCCTTGAGCTTAC
650 CCCTCA-TTTTCGATAAGAACCAATGCACTCCCCCTCTTGGTTCATTCAATCCTTAAGCTTAC
* ** *
648884 AATTTCAAATACATGTATCGATACATTATTAATTGTATCGATACATTGGAGCATATTTGTGTAGA
1 AATTTCAAATACATATATCGATACATTAAGAATTGTATCGATACATAGGAGCATATTTGTGTAGA
* *
648949 AACAAGCT-TGAAACAAGTAAATAACGGCTAGTAACATTATCATTCCACTACCAACGG-GAATAT
66 AACAAG-TGTGAAACAAGTAAATAACGGCTAGCAACATCATCATTCCACTACCAACGGCGAA-AT
* * * * *
649012 CAACATTGTAGCTTATAAATATGAG-TCTCCAATAGCTTAATAACAACAAGAACCAACAAGAAAC
129 CAACATTCTAGCATATAAATATGAGTTC-CCAACAGCTGAAGAACAACAAGAACCAACAAGAAAC
* *
649076 A-TCAAGAAATC-CAAGCAATCAAAGTTTTATTATTTTTACATTTCAAAAAGCTTTTATTTCATT
193 AGT-AAG-AATCACAAGCAATCAAAGTTTTATCATTTCTACATTTCAAAAAGC---T-TTTCATT
* *
649139 GTTATTATTCTTTGAAAGCTCATTTGTATTTCTCTTGTGCTTATATTTTCACAAACA-TCAGCCT
252 G-TATTATTCTTTGAAAGCTCATTTGTA-TTCTCTTGTGCTTATACTTTCACAAACACT-AACCT
* * *
649203 ACTTAGAGGCAGTTCGAGTTTGTAAAATTCCTTTGTATTGTAAAAGGTTATATTCAACCTTGGGG
314 ACTTAGAGGCAGTTCAAGTTTCTAAAATTCCTTTGTATTGTAAAAAGTTATATTCAACCTTGGGG
* *
649268 TACAATCTCTCAAGGATTTGG-GATATAATTCTTGGAGAGATTAAGAGGTTCTTATCTTAGCCTT
379 TACAATCTCTCAAGAATTTGGAG-TAT-ATTCTTGAAGAGATTAAGAGGTTCTTATCTTAGCCTT
* * *
649332 CAAAAGATAAGTGTTGTAAGATTATACTTTTGCCTTAAAGGTAAACAATTCGAGTAGTAAATTAT
442 CAAAAGATAAGTGTTGTAAGATTATACCTTTGCCTTAAAAGTAAACAATTCGAGTAGTAAATCAT
* * *
649397 GGTATACACTCGATAAGGAACTGTC-AGGAGAGAGGACGTAGGTGCCGTGTTTGGACCGAACCTC
507 GGTATACACTCGATAAGGAACTGTCGAGGAGAGAGAACATAGGTGCCGTGTTTGAACCGAACCTC
* * *
649461 TATAAACACTTGTGTCAAGCTTTCTCTTTTCCCAATTCTTTTTATCTTCG-ATTCGTTTTTGAAT
572 TATAAACACTTATGTCAAGCTTTCTCTTTTCCCAACTCTTTTTATCTTCGAATT-ATTTTTGAAT
* ** *
649525 CAATTTTTTCAAAACTTTCATTTTCGATAAGAACCAATTCACTCCCCCTCTTGGTTCATTCAATC
636 CAATTCTTTCAAAACCCTCATTTTCGATAAGAACCAATGCACTCCCCCTCTTGGTTCATTCAATC
649590 CTTAAGCTTAC
701 CTTAAGCTTAC
649601 AAT
1 AAT
649604 CTTATTTAAG
Statistics
Matches: 636, Mismatches: 68, Indels: 27
0.87 0.09 0.04
Matches are distributed among these distances:
711 43 0.07
712 165 0.26
713 5 0.01
714 1 0.00
715 8 0.01
716 51 0.08
717 247 0.39
718 116 0.18
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (711 bp):
AATTTCAAATACATATATCGATACATTAAGAATTGTATCGATACATAGGAGCATATTTGTGTAGA
AACAAGTGTGAAACAAGTAAATAACGGCTAGCAACATCATCATTCCACTACCAACGGCGAAATCA
ACATTCTAGCATATAAATATGAGTTCCCAACAGCTGAAGAACAACAAGAACCAACAAGAAACAGT
AAGAATCACAAGCAATCAAAGTTTTATCATTTCTACATTTCAAAAAGCTTTTCATTGTATTATTC
TTTGAAAGCTCATTTGTATTCTCTTGTGCTTATACTTTCACAAACACTAACCTACTTAGAGGCAG
TTCAAGTTTCTAAAATTCCTTTGTATTGTAAAAAGTTATATTCAACCTTGGGGTACAATCTCTCA
AGAATTTGGAGTATATTCTTGAAGAGATTAAGAGGTTCTTATCTTAGCCTTCAAAAGATAAGTGT
TGTAAGATTATACCTTTGCCTTAAAAGTAAACAATTCGAGTAGTAAATCATGGTATACACTCGAT
AAGGAACTGTCGAGGAGAGAGAACATAGGTGCCGTGTTTGAACCGAACCTCTATAAACACTTATG
TCAAGCTTTCTCTTTTCCCAACTCTTTTTATCTTCGAATTATTTTTGAATCAATTCTTTCAAAAC
CCTCATTTTCGATAAGAACCAATGCACTCCCCCTCTTGGTTCATTCAATCCTTAAGCTTAC
Found at i:650217 original size:25 final size:25
Alignment explanation
Indices: 650189--650250 Score: 99
Period size: 24 Copynumber: 2.5 Consensus size: 25
650179 CGGGTTTTAG
650189 AATAAATTTTTATTATTTTTGGTAA
1 AATAAATTTTTATTATTTTTGGTAA
650214 AAT-AATTTTTATTATTTTTGGTAA
1 AATAAATTTTTATTATTTTTGGTAA
*
650238 AATCAAAATTTTA
1 AAT-AAATTTTTA
650251 AAAAATCGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 24 0.71
25 3 0.09
26 7 0.21
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (25 bp):
AATAAATTTTTATTATTTTTGGTAA
Found at i:652802 original size:37 final size:36
Alignment explanation
Indices: 652760--652849 Score: 103
Period size: 37 Copynumber: 2.5 Consensus size: 36
652750 TCACATCAAA
** * *
652760 ATTAATTTTTAATTTTTAATTGTA-ATTTAAATAAATT
1 ATTAATTTTTAAACTTTAATT-TATATTCAAAT-AATC
*
652797 TTTAATTTTTAAACTTTAATTTATATTCAAATAATC
1 ATTAATTTTTAAACTTTAATTTATATTCAAATAATC
652833 ATTAATTTTTAAA-TTTA
1 ATTAATTTTTAAACTTTA
652850 TGCTTTAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.09
36 17 0.37
37 25 0.54
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (36 bp):
ATTAATTTTTAAACTTTAATTTATATTCAAATAATC
Found at i:653465 original size:6 final size:6
Alignment explanation
Indices: 653454--653478 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
653444 GAGGAAGGTA
653454 AGCCAT AGCCAT AGCCAT AGCCAT A
1 AGCCAT AGCCAT AGCCAT AGCCAT A
653479 CCACCCAAAA
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:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
AGCCAT
Done.