Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 101 of 172
Found at i:29143178 original size:116 final size:116
Alignment explanation
Indices: 29143058--29143271 Score: 340
Period size: 116 Copynumber: 1.8 Consensus size: 116
29143048 TTGCAATAGG
* * *
29143058 TATCGATACCACAT-AACATGTATCAATACTTGTGACTTAAATGAAGTATTTTTAAAACACCGAA
1 TATCGATACCACATGAA-AGGTATCAATACATGTAACTTAAATGAAGTATTTTTAAAACACCGAA
29143122 ACTAAAAACAGTATCGGTACCCACCCAAGGGTATCGATACTTTTTGGAAAAA
65 ACTAAAAACAGTATCGGTACCCACCCAAGGGTATCGATACTTTTTGGAAAAA
* * *
29143174 TATCGATACCACATGAAAGGTATCGATACATGTAACTTAAATGAAGTATTTTTAAAACACTGAAG
1 TATCGATACCACATGAAAGGTATCAATACATGTAACTTAAATGAAGTATTTTTAAAACACCGAAA
* *
29143239 CTAAAAATAGTATCGGTACCCAGCCAAGGGTAT
66 CTAAAAACAGTATCGGTACCCACCCAAGGGTAT
29143272 TGATGTAACA
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
116 87 0.98
117 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (116 bp):
TATCGATACCACATGAAAGGTATCAATACATGTAACTTAAATGAAGTATTTTTAAAACACCGAAA
CTAAAAACAGTATCGGTACCCACCCAAGGGTATCGATACTTTTTGGAAAAA
Found at i:29150560 original size:18 final size:18
Alignment explanation
Indices: 29150539--29150603 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
29150529 TTTAATAAAA
29150539 TTAATAAATTTTATTATT
1 TTAATAAATTTTATTATT
* *
29150557 TTAATAAATTATT-TAATA
1 TTAATAAATT-TTATTATT
29150575 TT-AT-AATTTTATT-TT
1 TTAATAAATTTTATTATT
*
29150590 GATAATAAATTTTA
1 -TTAATAAATTTTA
29150604 ACAATAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
15 3 0.08
16 6 0.16
17 4 0.11
18 22 0.59
19 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TTAATAAATTTTATTATT
Found at i:29150565 original size:26 final size:27
Alignment explanation
Indices: 29150521--29150585 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 27
29150511 CATATTTAGT
*
29150521 TATT-TAAATTTAATAAAATTAATAAA
1 TATTATAATTTTAATAAAATTAATAAA
* * * *
29150547 TTTTATTATTTTAAT-AAATTATTTAA
1 TATTATAATTTTAATAAAATTAATAAA
29150573 TATTATAATTTTA
1 TATTATAATTTTA
29150586 TTTTGATAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
26 23 0.74
27 8 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TATTATAATTTTAATAAAATTAATAAA
Found at i:29150584 original size:34 final size:34
Alignment explanation
Indices: 29150545--29150651 Score: 98
Period size: 33 Copynumber: 3.1 Consensus size: 34
29150535 AAAATTAATA
29150545 AATTTTATTATTTTAATAAATTATTTAATATTAT
1 AATTTTATTATTTTAATAAATTATTTAATATTAT
* * *
29150579 AATTTTATT-TTGATAATAAA-T-TTTAACAATAAT
1 AATTTTATTATT-TTAATAAATTATTTAA-TATTAT
*
29150612 AATTTTA-AATTTTAATAATATTTATATTAATA-TAT
1 AATTTTATTATTTTAATAA-A-TTAT-TTAATATTAT
29150647 AATTT
1 AATTT
29150652 ATAAATATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
32 11 0.19
33 17 0.29
34 16 0.28
35 8 0.14
36 2 0.03
37 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (34 bp):
AATTTTATTATTTTAATAAATTATTTAATATTAT
Found at i:29150641 original size:22 final size:22
Alignment explanation
Indices: 29150539--29150641 Score: 60
Period size: 22 Copynumber: 4.9 Consensus size: 22
29150529 TTTAATAAAA
29150539 TTAATAA-ATTT-TATT--ATT
1 TTAATAATATTTATATTAAATT
29150557 TTAATAAATTATTTAATATTATAATT
1 TTAAT-AA-TATTT-ATATTA-AATT
* *
29150583 TT-AT--T-TTGATAATAAATT
1 TTAATAATATTTATATTAAATT
* * * *
29150601 TTAACAATAATAATTTTAAATT
1 TTAATAATATTTATATTAAATT
29150623 TTAATAATATTTATATTAA
1 TTAATAATATTTATATTAA
29150642 TATATAATTT
Statistics
Matches: 62, Mismatches: 11, Indels: 20
0.67 0.12 0.22
Matches are distributed among these distances:
18 11 0.18
19 8 0.13
20 2 0.03
21 6 0.10
22 24 0.39
23 4 0.06
25 2 0.03
26 5 0.08
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (22 bp):
TTAATAATATTTATATTAAATT
Found at i:29150643 original size:15 final size:17
Alignment explanation
Indices: 29150623--29150654 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29150613 ATTTTAAATT
29150623 TTAATA-AT-ATTTATA
1 TTAATATATAATTTATA
29150638 TTAATATATAATTTATA
1 TTAATATATAATTTATA
29150655 AATATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 2 0.13
17 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATATATAATTTATA
Found at i:29150659 original size:27 final size:25
Alignment explanation
Indices: 29150628--29150679 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
29150618 AAATTTTAAT
*
29150628 AATATTTATATTAATATATAATTTATA
1 AATATTTA-A-TAATAAATAATTTATA
*
29150655 AATATTTAATAATAAATATTTTATA
1 AATATTTAATAATAAATAATTTATA
29150680 GTACAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 14 0.61
26 1 0.04
27 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AATATTTAATAATAAATAATTTATA
Found at i:29150674 original size:35 final size:33
Alignment explanation
Indices: 29150558--29150674 Score: 103
Period size: 35 Copynumber: 3.3 Consensus size: 33
29150548 TTTATTATTT
*
29150558 TAATAAATTATTTAATATTATAATTTT--ATTTTGA
1 TAATAAA-TA-TTAATA-TATAATTTTAAATTTTAA
* *
29150592 TAATAAATTTTAACAATAATAATTTTAAATTTTAA
1 TAATAAATATTAA-TAT-ATAATTTTAAATTTTAA
*
29150627 TAATATTTATATTAATATATAATTTATAAATATTTAA
1 TAATA--AATATTAATATATAATTT-TAAAT-TTTAA
29150664 TAATAAATATT
1 TAATAAATATT
29150675 TTATAGTACA
Statistics
Matches: 68, Mismatches: 7, Indels: 15
0.76 0.08 0.17
Matches are distributed among these distances:
32 5 0.07
33 10 0.15
34 7 0.10
35 23 0.34
36 7 0.10
37 16 0.24
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (33 bp):
TAATAAATATTAATATATAATTTTAAATTTTAA
Found at i:29152301 original size:20 final size:20
Alignment explanation
Indices: 29152251--29152302 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
29152241 TAGAAGTGAG
*
29152251 GTAGAAGATGAAGAGATCAA
1 GTAGAAAATGAAGAGATCAA
*
29152271 GTA-AAAGATGAAGATATCAA
1 GTAGAAA-ATGAAGAGATCAA
*
29152291 TTAGAAAATGAA
1 GTAGAAAATGAA
29152303 ATAGATGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.54, C:0.04, G:0.23, T:0.19
Consensus pattern (20 bp):
GTAGAAAATGAAGAGATCAA
Found at i:29155219 original size:36 final size:36
Alignment explanation
Indices: 29155170--29155287 Score: 132
Period size: 36 Copynumber: 3.3 Consensus size: 36
29155160 ATTCCAACCA
**
29155170 AAACACATTAGATGCTCATAAGAGCTAATCCATCTG
1 AAACACACCAGATGCTCATAAGAGCTAATCCATCTG
* **
29155206 AAACACACCAGATGCTCATAAGAGCTAATCTATCCA
1 AAACACACCAGATGCTCATAAGAGCTAATCCATCTG
* * *
29155242 AAACACACCA-ATGGCTCCA-AAAAGCTAGTCCAACTG
1 AAACACACCAGAT-GCT-CATAAGAGCTAATCCATCTG
29155278 AAACACACCA
1 AAACACACCA
29155288 AAACAGGGAG
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
35 2 0.03
36 65 0.94
37 2 0.03
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.18
Consensus pattern (36 bp):
AAACACACCAGATGCTCATAAGAGCTAATCCATCTG
Found at i:29160939 original size:13 final size:13
Alignment explanation
Indices: 29160887--29161071 Score: 65
Period size: 13 Copynumber: 14.2 Consensus size: 13
29160877 CATATCTATC
*
29160887 CATATAAACATTT
1 CATATAATCATTT
*
29160900 CATATAA-CACTT
1 CATATAATCATTT
29160912 CATATAATCGA-TT
1 CATATAATC-ATTT
*
29160925 CATATAATTATTT
1 CATATAATCATTT
* * **
29160938 CATTTAGTTGTTT
1 CATATAATCATTT
* *
29160951 CTGTATAACTGA-TT
1 C-ATATAA-TCATTT
* *
29160965 CATATAACCATTA
1 CATATAATCATTT
*
29160978 CGTAT-ATCTATTT
1 CATATAATC-ATTT
*
29160991 CTATATAATCAATT
1 C-ATATAATCATTT
* *
29161005 CTTATATTCATTT
1 CATATAATCATTT
* *
29161018 CACA-AAACAATTT
1 CATATAATC-ATTT
* * *
29161031 CGTATAACCAATT
1 CATATAATCATTT
*
29161044 CATATAACCATTT
1 CATATAATCATTT
** *
29161057 TGTATAACCATTT
1 CATATAATCATTT
29161070 CA
1 CA
29161072 AAGTATTAAC
Statistics
Matches: 125, Mismatches: 36, Indels: 22
0.68 0.20 0.12
Matches are distributed among these distances:
12 17 0.14
13 87 0.70
14 17 0.14
15 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.42
Consensus pattern (13 bp):
CATATAATCATTT
Found at i:29163411 original size:13 final size:13
Alignment explanation
Indices: 29163393--29163417 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29163383 CTGTTAATAA
29163393 TTTTTTAATTTGT
1 TTTTTTAATTTGT
29163406 TTTTTTAATTTG
1 TTTTTTAATTTG
29163418 GATTTTGACA
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTTTAATTTGT
Found at i:29165299 original size:79 final size:79
Alignment explanation
Indices: 29165210--29165365 Score: 312
Period size: 79 Copynumber: 2.0 Consensus size: 79
29165200 AAATTATAAA
29165210 TATTAAATGAAGTATGTACTGCAATTCAAATTAATATATTTAAAAATTTAACGTTTTAAATAATA
1 TATTAAATGAAGTATGTACTGCAATTCAAATTAATATATTTAAAAATTTAACGTTTTAAATAATA
29165275 ATATTATTAAAATT
66 ATATTATTAAAATT
29165289 TATTAAATGAAGTATGTACTGCAATTCAAATTAATATATTTAAAAATTTAACGTTTTAAATAATA
1 TATTAAATGAAGTATGTACTGCAATTCAAATTAATATATTTAAAAATTTAACGTTTTAAATAATA
29165354 ATATTATTAAAA
66 ATATTATTAAAA
29165366 ATTTTGATAG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.41
Consensus pattern (79 bp):
TATTAAATGAAGTATGTACTGCAATTCAAATTAATATATTTAAAAATTTAACGTTTTAAATAATA
ATATTATTAAAATT
Found at i:29180248 original size:31 final size:31
Alignment explanation
Indices: 29180213--29180271 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
29180203 TTGGTCATTA
29180213 AACTATTCGAAAGTTTTCATTTAAGCCACTG
1 AACTATTCGAAAGTTTTCATTTAAGCCACTG
* *
29180244 AACTATTTGAAAGTTTTTATTTAAGCCA
1 AACTATTCGAAAGTTTTCATTTAAGCCA
29180272 TTGGATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (31 bp):
AACTATTCGAAAGTTTTCATTTAAGCCACTG
Found at i:29182473 original size:6 final size:6
Alignment explanation
Indices: 29182443--29182472 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
29182433 ATAGAAACAA
*
29182443 GAATAT GAATAT GAATAT GAATAT AAATAT
1 GAATAT GAATAT GAATAT GAATAT GAATAT
29182473 ACAAATTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (6 bp):
GAATAT
Found at i:29185474 original size:15 final size:15
Alignment explanation
Indices: 29185451--29185487 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
29185441 TTAAATTTTT
29185451 TATAAAATTTTAAAA
1 TATAAAATTTTAAAA
*
29185466 TATATAATTTTAAAA
1 TATAAAATTTTAAAA
*
29185481 TTTAAAA
1 TATAAAA
29185488 AGCCAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAAAATTTTAAAA
Found at i:29185589 original size:19 final size:20
Alignment explanation
Indices: 29185555--29185599 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
29185545 TACCTTAATA
**
29185555 TTTAAATACCTTTTTAGGTTT
1 TTTAAATA-CTTTTTACATTT
29185576 TTTAAATA-TTTTTACATTT
1 TTTAAATACTTTTTACATTT
29185595 TTTAA
1 TTTAA
29185600 TAGTATTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 14 0.64
21 8 0.36
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTAAATACTTTTTACATTT
Found at i:29194488 original size:21 final size:21
Alignment explanation
Indices: 29194464--29194503 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
29194454 GATTATATTT
29194464 ATATATTT-TAAATATTATAAA
1 ATATATTTAT-AATATTATAAA
29194485 ATATATTTATAATATTATA
1 ATATATTTATAATATTATA
29194504 GATCTGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATATTTATAATATTATAAA
Found at i:29203611 original size:32 final size:30
Alignment explanation
Indices: 29203569--29203635 Score: 98
Period size: 32 Copynumber: 2.2 Consensus size: 30
29203559 AGCAAACAAA
*
29203569 ATAATTAAATATAAATAAATACATATTTATAT
1 ATAATAAAATATAAATAAA-ACA-ATTTATAT
*
29203601 ATAATAAAATATAAATAGAACAATTTATAT
1 ATAATAAAATATAAATAAAACAATTTATAT
29203631 ATAAT
1 ATAAT
29203636 TTGTCAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 13 0.39
31 3 0.09
32 17 0.52
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (30 bp):
ATAATAAAATATAAATAAAACAATTTATAT
Found at i:29208362 original size:26 final size:25
Alignment explanation
Indices: 29208320--29208388 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 25
29208310 CCCGATATAT
29208320 GGCTCTTCGGAGCTTCCCAATTAAA
1 GGCTCTTCGGAGCTTCCCAATTAAA
* * *
29208345 GGCTCTTTGTGAGCTTCCTAATTAAT
1 GGCTCTTCG-GAGCTTCCCAATTAAA
*
29208371 GGCTCTCCGGAGCTTCCC
1 GGCTCTTCGGAGCTTCCC
29208389 GATATGGCTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
25 16 0.43
26 21 0.57
ACGTcount: A:0.17, C:0.29, G:0.22, T:0.32
Consensus pattern (25 bp):
GGCTCTTCGGAGCTTCCCAATTAAA
Found at i:29208443 original size:73 final size:73
Alignment explanation
Indices: 29208356--29208495 Score: 192
Period size: 73 Copynumber: 1.9 Consensus size: 73
29208346 GCTCTTTGTG
* * *
29208356 AGCTTCCTAATTAATGGCTCTCCGGAGCTTCCCGATA-TGGCTCGCTTGAACTTCCTGATATATG
1 AGCTTCCTAATTAATGGCTCTCCAGAGCTACCCGATATTGGCTCGCATGAACTTCCTGA-ATATG
29208420 GCTATCCGA
65 GCTATCCGA
* ** * *
29208429 AGCTTCTTAATTAATGGCTCTTTAGAGCTACCCGTTATTGGCTCGCATGAGCTTCCTGAATATGG
1 AGCTTCCTAATTAATGGCTCTCCAGAGCTACCCGATATTGGCTCGCATGAACTTCCTGAATATGG
29208494 CT
66 CT
29208496 CTTATAAGCT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 39 0.67
74 19 0.33
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (73 bp):
AGCTTCCTAATTAATGGCTCTCCAGAGCTACCCGATATTGGCTCGCATGAACTTCCTGAATATGG
CTATCCGA
Found at i:29208533 original size:25 final size:25
Alignment explanation
Indices: 29208499--29208565 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
29208489 TATGGCTCTT
* * *
29208499 ATAAGCTTCCTGTTATACATCCCGG
1 ATAAGCTTCCCGTTATACAACCCGA
* *
29208524 ATAAACTTCCCGTTATACAACTCGA
1 ATAAGCTTCCCGTTATACAACCCGA
29208549 ATAAGCTTCCCGTTATA
1 ATAAGCTTCCCGTTATA
29208566 TGGCTCGAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (25 bp):
ATAAGCTTCCCGTTATACAACCCGA
Found at i:29208572 original size:25 final size:25
Alignment explanation
Indices: 29208454--29208573 Score: 73
Period size: 25 Copynumber: 4.9 Consensus size: 25
29208444 GGCTCTTTAG
* * *
29208454 AGCTACCCGTTAT-TGGCTCGCATG
1 AGCTTCCCGTTATATGGCTCGAATA
* * **
29208478 AGCTTCCTG-AATATGGCTCTTATA
1 AGCTTCCCGTTATATGGCTCGAATA
* *** * *
29208502 AGCTTCCTGTTATACATCCCGGATA
1 AGCTTCCCGTTATATGGCTCGAATA
* ***
29208527 AACTTCCCGTTATACAACTCGAATA
1 AGCTTCCCGTTATATGGCTCGAATA
29208552 AGCTTCCCGTTATATGGCTCGA
1 AGCTTCCCGTTATATGGCTCGA
29208574 GAGAGAGCTT
Statistics
Matches: 72, Mismatches: 22, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
23 2 0.03
24 24 0.33
25 46 0.64
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (25 bp):
AGCTTCCCGTTATATGGCTCGAATA
Found at i:29213627 original size:84 final size:84
Alignment explanation
Indices: 29213517--29213771 Score: 257
Period size: 85 Copynumber: 3.0 Consensus size: 84
29213507 AATTATATCA
** * * *
29213517 AAATAAAATC-TGTTAAACGGTGGGAATAAATCTCGAAACATA-ATTATATGA-TTACATCCTTT
1 AAATAAAATCTTGTTAAACGACGGGAATAAATCTCGAAACAGATATTATATAATTTA-ATCC-TA
* *
29213579 TTTTGGAAACAAAAGAATATC
64 ATTTGGAAACAAAAGAAAATC
* * * * * *
29213600 GAATAAAATCTTTTTAGACGACGGGAATAAATC-CTGAAACAGATTTTATTTAATTTTAATTCTA
1 AAATAAAATCTTGTTAAACGACGGGAATAAATCTC-GAAACAGATATTATATAA-TTTAATCCTA
*
29213664 ATTTGGAAACAAAATAAAATC
64 ATTTGGAAACAAAAGAAAATC
* * * * *
29213685 AAATAAAATCTTGTTAAACGGCGAGAATAAATCTCGAAACAGATTTTATTTAATTTAATTCTAAT
1 AAATAAAATCTTGTTAAACGACGGGAATAAATCTCGAAACAGATATTATATAATTTAATCCTAAT
* *
29213750 TTGGAAACAAAAAAAAAAC
66 TTGGAAACAAAAGAAAATC
29213769 AAA
1 AAA
29213772 ACAAAACAAA
Statistics
Matches: 145, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
83 10 0.07
84 57 0.39
85 71 0.49
86 4 0.03
87 3 0.02
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (84 bp):
AAATAAAATCTTGTTAAACGACGGGAATAAATCTCGAAACAGATATTATATAATTTAATCCTAAT
TTGGAAACAAAAGAAAATC
Found at i:29213924 original size:180 final size:177
Alignment explanation
Indices: 29213601--29213928 Score: 423
Period size: 180 Copynumber: 1.8 Consensus size: 177
29213591 AAGAATATCG
* * *
29213601 AATAAAATCTTTTTAGACGACGGGAATAAATCCTGAAACAGATTTTATTTAATTTTAATTCTAAT
1 AATAAAATCTTGTTAAACGACGAGAATAAATCCTGAAACAGATTTTATTTAATTTTAATTCTAAT
*
29213666 TTGGAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGAGAATAAATCTCGAAACAGATTT
66 TTGGAAACAAAATAAAATCAAATAAAATCTCGTTAAACGGCGAGAATAAATCTCGAAACAGATTT
29213731 TATTTAATTTAATTCTAATTTGGAAACAAAAAAAAAACAAAACAAAACAA
131 TA-TT-ATTTAATT-TAATTTGGAAACAAAAAAAAAACAAAACAAAACAA
29213781 AATAAAATCTTGTTAAACGACGAGAATAAATCGC-GAAACAGATTTTATTTAATTTTAATTTCTC
1 AATAAAATCTTGTTAAACGACGAGAATAAATC-CTGAAACAGATTTTATTTAATTTTAA-TTCT-
* * * * * * *
29213845 ATTTTTGGAAATAAAATCAAAATTAGAATAAAATC-CGTTGAACGGTGGGGATAAAT-TCCGAAA
63 A-ATTTGGAAACAAAAT-AAAATCA-AATAAAATCTCGTTAAACGGCGAGAATAAATCT-CGAAA
*
29213908 TAGATTTTA-T-TTTAATTTAAT
124 CAGATTTTATTATTTAATTTAAT
29213929 ACTCGTTTTT
Statistics
Matches: 129, Mismatches: 12, Indels: 15
0.83 0.08 0.10
Matches are distributed among these distances:
179 4 0.03
180 60 0.47
181 5 0.04
182 2 0.02
183 14 0.11
184 35 0.27
185 9 0.07
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (177 bp):
AATAAAATCTTGTTAAACGACGAGAATAAATCCTGAAACAGATTTTATTTAATTTTAATTCTAAT
TTGGAAACAAAATAAAATCAAATAAAATCTCGTTAAACGGCGAGAATAAATCTCGAAACAGATTT
TATTATTTAATTTAATTTGGAAACAAAAAAAAAACAAAACAAAACAA
Found at i:29214063 original size:175 final size:175
Alignment explanation
Indices: 29213622--29214193 Score: 424
Period size: 175 Copynumber: 3.2 Consensus size: 175
29213612 TTTAGACGAC
* * * *
29213622 GGGAATAAATCCTGAAAC-AGATTTTATTTAATTTTAA-TT-CTAATTTGGAAACAAAAT-AAAA
1 GGGAATAAATCC-GAAACGA-ATTTTATTTACTTTTAATTTCCCATTTTGGAAATAAAATCAAAA
* ** * *
29213683 TCA-AATAAAATCTTGTTAAACGGCGAGAATAAATCTC-GAAACAGATTTTATTTA-ATTTAATT
64 TTAGAATAAAATC-CATTGAACGGCGAGAATAAATC-CGGAAACAGATTTTATTTACATTTAATA
* * * * * * *
29213745 CT-AATTTGGAAACAAAAAAAAAACAAAACAAAACAAAATAAAATC-TTGTTAAAC-GA
127 CTCCATTTGG-AA-ATAAATAAAA-ATAATAGAATAAAAT----TCATTG---AACGGA
* * *
29213801 CGAGAATAAATCGCGAAAC-AGATTTTATTTAATTTTAATTTCTCATTTTTGGAAATAAAATCAA
1 -GGGAATAAATC-CGAAACGA-ATTTTATTTACTTTTAATTTCCCA-TTTTGGAAATAAAATCAA
* * * * *
29213865 AATTAGAATAAAATCCGTTGAACGGTGGGGATAAATTCC-GAAATAGATTTTATTTTA-ATTTAA
62 AATTAGAATAAAATCCATTGAACGGCGAGAATAAA-TCCGGAAACAGATTTTA-TTTACATTTAA
** * * *
29213928 TACTCGTTTTTGGAAATAAAATCAAAAT-TTAGAATAAAA-TCATTGAACGGC
125 TACTC-CATTTGGAAAT-AAATAAAAATAATAGAATAAAATTCATTGAACGGA
*
29213979 GGGAATAAATCCTGAAACGAATTTTATTTACCTTTAATTTCCCA-TTTGGAAAT-AAAT-AAAAT
1 GGGAATAAATCC-GAAACGAATTTTATTTACTTTTAATTTCCCATTTTGGAAATAAAATCAAAAT
* * * **
29214041 AATGGAATAAAATCCATTGAACGGCGAGAATAAATCCGGAAACGGATTTTATTTACTTTTAATTT
65 --TAGAATAAAATCCATTGAACGGCGAGAATAAATCCGGAAACAGATTTTATTTACATTTAATAC
* *
29214106 TCCATTTGGAAATAAATAAAAATAATGGAATAAAATTCGTTGAACGGA
128 TCCATTTGGAAATAAATAAAAATAATAGAATAAAATTCATTGAACGGA
* * *
29214154 GGAAATAAATCCCGAAAAGGATTTTATTTACTTTTAATTT
1 GGGAATAAAT-CCGAAACGAATTTTATTTACTTTTAATTT
29214194 GGAAACAAAA
Statistics
Matches: 321, Mismatches: 49, Indels: 49
0.77 0.12 0.12
Matches are distributed among these distances:
173 14 0.04
174 29 0.09
175 98 0.31
176 3 0.01
177 39 0.12
178 2 0.01
179 2 0.01
180 37 0.12
181 3 0.01
182 1 0.00
183 13 0.04
184 41 0.13
185 26 0.08
186 8 0.02
187 5 0.02
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (175 bp):
GGGAATAAATCCGAAACGAATTTTATTTACTTTTAATTTCCCATTTTGGAAATAAAATCAAAATT
AGAATAAAATCCATTGAACGGCGAGAATAAATCCGGAAACAGATTTTATTTACATTTAATACTCC
ATTTGGAAATAAATAAAAATAATAGAATAAAATTCATTGAACGGA
Found at i:29214065 original size:87 final size:87
Alignment explanation
Indices: 29213804--29214193 Score: 382
Period size: 88 Copynumber: 4.4 Consensus size: 87
29213794 TAAACGACGA
* *
29213804 GAATAAATCGCGAAAC-AGATTTTATTTAATTTTAATTTCTCATTTTTGGAAATAAAATCAAAAT
1 GAATAAATC-CGAAACGA-ATTTTATTTACTTTTAATTTCCCA--TTTGGAAATAAAATCAAAAT
* *
29213868 -TAGAATAAAATCCGTTGAACGGTGG
62 ATAGAATAAAATCCATTGAACGGCGG
* * * * ***
29213893 GGATAAATTCCGAAA-TAGATTTTATTTTA-ATTTAATACTCGTTTTTGGAAATAAAATCAAAAT
1 GAATAAA-TCCGAAACGA-ATTTTA-TTTACTTTTAAT-TTCCCATTTGGAAATAAAATCAAAAT
*
29213956 TTAGAATAAAAT-CATTGAACGGCGG
62 ATAGAATAAAATCCATTGAACGGCGG
*
29213981 GAATAAATCCTGAAACGAATTTTATTTACCTTTAATTTCCCATTTGGAAAT-AAAT-AAAATAAT
1 GAATAAATCC-GAAACGAATTTTATTTACTTTTAATTTCCCATTTGGAAATAAAATCAAAAT-AT
* *
29214044 GGAATAAAATCCATTGAACGGCGA
64 AGAATAAAATCCATTGAACGGCGG
* * *
29214068 GAATAAATCCGGAAACGGATTTTATTTACTTTTAATTTTCCATTTGGAAAT-AAATAAAAATAAT
1 GAATAAATCC-GAAACGAATTTTATTTACTTTTAATTTCCCATTTGGAAATAAAATCAAAAT-AT
* * * *
29214132 GGAATAAAATTCGTTGAACGGAGG
64 AGAATAAAATCCATTGAACGGCGG
* * *
29214156 AAATAAATCCCGAAAAGGATTTTATTTACTTTTAATTT
1 GAATAAAT-CCGAAACGAATTTTATTTACTTTTAATTT
29214194 GGAAACAAAA
Statistics
Matches: 261, Mismatches: 28, Indels: 25
0.83 0.09 0.08
Matches are distributed among these distances:
85 5 0.02
86 14 0.05
87 81 0.31
88 114 0.44
89 39 0.15
90 8 0.03
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (87 bp):
GAATAAATCCGAAACGAATTTTATTTACTTTTAATTTCCCATTTGGAAATAAAATCAAAATATAG
AATAAAATCCATTGAACGGCGG
Found at i:29219450 original size:21 final size:21
Alignment explanation
Indices: 29219421--29219460 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29219411 ATAAGTAGCT
29219421 TTGTAATGGTTGAAATATGAC
1 TTGTAATGGTTGAAATATGAC
* *
29219442 TTGTTATGGTTGAATTATG
1 TTGTAATGGTTGAAATATG
29219461 GTAGATAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.25, T:0.45
Consensus pattern (21 bp):
TTGTAATGGTTGAAATATGAC
Found at i:29225648 original size:31 final size:31
Alignment explanation
Indices: 29225613--29225714 Score: 114
Period size: 31 Copynumber: 3.3 Consensus size: 31
29225603 GGTTGTAATA
* *
29225613 GTAAATTAGTGAGCTGTTTAGAGTTGTGATC
1 GTAAATTAGTGAGCTATTTAGAGTTGCGATC
* *
29225644 GTAAATCAGTGAGCTATTTGGAGTTGCGATC
1 GTAAATTAGTGAGCTATTTAGAGTTGCGATC
* *** * *
29225675 GTAAATAAACAAGCTTTTTGGAGTTGCGATC
1 GTAAATTAGTGAGCTATTTAGAGTTGCGATC
29225706 GTAAATTAG
1 GTAAATTAG
29225715 CTAACTTAGA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.34
Consensus pattern (31 bp):
GTAAATTAGTGAGCTATTTAGAGTTGCGATC
Found at i:29225793 original size:94 final size:93
Alignment explanation
Indices: 29225666--29225962 Score: 387
Period size: 94 Copynumber: 3.2 Consensus size: 93
29225656 GCTATTTGGA
* * * *
29225666 GTTGCGATCGTAAATAAACAAGCTTTTTGGAGTTGCGATCGTAAATTAGCTAACTTAGAAGAAAT
1 GTTGTGATCGTAAATCAACAAGCTATTTGGAGTTGCGATCGTAAATCA-CTAACTTAGAAGAAAT
*
29225731 TGTTCATGATTGTAAATCAATAAATTTAG
65 TGTTCATGATTGTAAATCAATGAATTTAG
* *
29225760 GTTGTGATCGTAAATCAGCAAGCTATTTAGAGTTGCGATCGTAAATCAACTAACTTAGAAGAAAT
1 GTTGTGATCGTAAATCAACAAGCTATTTGGAGTTGCGATCGTAAATC-ACTAACTTAGAAGAAAT
* *
29225825 TGTTCATGATTGTAAATCAGTGAACTTAG
65 TGTTCATGATTGTAAATCAATGAATTTAG
* * * * * *
29225854 GTTGTGATCGTAAATCAATAAGTTGTTTGGAGTTGCAATCGAAAATCAATCAACTTAGAAGAAAT
1 GTTGTGATCGTAAATCAACAAGCTATTTGGAGTTGCGATCGTAAATCACT-AACTTAGAAGAAAT
* * * *
29225919 TTTTCATGATCGTAAATAAATGCATTTAG
65 TGTTCATGATTGTAAATCAATGAATTTAG
*
29225948 GTTGTGGTCGTAAAT
1 GTTGTGATCGTAAAT
29225963 TAGCGAGCCT
Statistics
Matches: 177, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
93 2 0.01
94 174 0.98
95 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (93 bp):
GTTGTGATCGTAAATCAACAAGCTATTTGGAGTTGCGATCGTAAATCACTAACTTAGAAGAAATT
GTTCATGATTGTAAATCAATGAATTTAG
Found at i:29225803 original size:31 final size:31
Alignment explanation
Indices: 29225624--29225807 Score: 110
Period size: 31 Copynumber: 5.9 Consensus size: 31
29225614 TAAATTAGTG
* * **
29225624 AGCTGTTTAGAGTTGTGATCGTAAATCAGTG
1 AGCTATTTAGAGTTGCGATCGTAAATCAGCA
* * *
29225655 AGCTATTTGGAGTTGCGATCGTAAATAAACA
1 AGCTATTTAGAGTTGCGATCGTAAATCAGCA
* * *
29225686 AGCTTTTTGGAGTTGCGATCGTAAATTAGCTA
1 AGCTATTTAGAGTTGCGATCGTAAATCAGC-A
** * * **
29225718 A-CT-TAGAAGAAATTGTTCATGATTGTAAATCAATA
1 AGCTAT-TTAG-AGTTG--C--GATCGTAAATCAGCA
*
29225753 A---ATTTAG-GTTGTGATCGTAAATCAGCA
1 AGCTATTTAGAGTTGCGATCGTAAATCAGCA
29225780 AGCTATTTAGAGTTGCGATCGTAAATCA
1 AGCTATTTAGAGTTGCGATCGTAAATCA
29225808 ACTAACTTAG
Statistics
Matches: 115, Mismatches: 26, Indels: 24
0.70 0.16 0.15
Matches are distributed among these distances:
27 13 0.11
30 7 0.06
31 73 0.63
32 6 0.05
33 2 0.02
34 2 0.02
35 2 0.02
36 10 0.09
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (31 bp):
AGCTATTTAGAGTTGCGATCGTAAATCAGCA
Found at i:29226140 original size:103 final size:102
Alignment explanation
Indices: 29225957--29226167 Score: 278
Period size: 103 Copynumber: 2.1 Consensus size: 102
29225947 GGTTGTGGTC
* * * * * * * *
29225957 GTAAATTAGCGAGCCTTAATAATATCAGTCGTGATCATAAATTAGCGAGTTGTTTAGAGTTGTGA
1 GTAAATCAGCGAGCCTTAATAATATCAGCCATAATCATAAATCAGCGAGCTATTTAGAGTTGCGA
*
29226022 TCGTAAATTAACTAACTCAGAAAAAAATATTCATGATA
66 TCGTAAATCAACTAACTCAG-AAAAAATATTCATGATA
* *
29226060 GTAAATCAGCGAGCCTTAATAATATCAGCCATAATCTTAAATCATCGAGCTATTTAGAGTTGCGA
1 GTAAATCAGCGAGCCTTAATAATATCAGCCATAATCATAAATCAGCGAGCTATTTAGAGTTGCGA
* * * *
29226125 TTGTAAATCATCTAACTCAGAAAAAATGTTCATGATG
66 TCGTAAATCAACTAACTCAGAAAAAATATTCATGATA
29226162 GTAAAT
1 GTAAAT
29226168 TAATAAACTT
Statistics
Matches: 93, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
102 21 0.23
103 72 0.77
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (102 bp):
GTAAATCAGCGAGCCTTAATAATATCAGCCATAATCATAAATCAGCGAGCTATTTAGAGTTGCGA
TCGTAAATCAACTAACTCAGAAAAAATATTCATGATA
Found at i:29231180 original size:18 final size:18
Alignment explanation
Indices: 29231157--29231191 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29231147 TGAAAAAGTT
29231157 AGAAAAATTTATTAATTA
1 AGAAAAATTTATTAATTA
29231175 AGAAAAATTTATTAATT
1 AGAAAAATTTATTAATT
29231192 GATAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AGAAAAATTTATTAATTA
Found at i:29231749 original size:8 final size:8
Alignment explanation
Indices: 29231726--29231766 Score: 64
Period size: 8 Copynumber: 5.0 Consensus size: 8
29231716 AATAAATAAG
29231726 TATTATAT
1 TATTATAT
29231734 TAATTATAT
1 T-ATTATAT
*
29231743 TATTATAA
1 TATTATAT
29231751 TATTATAT
1 TATTATAT
29231759 TATTATAT
1 TATTATAT
29231767 ATGTAAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTATAT
Found at i:29232570 original size:13 final size:14
Alignment explanation
Indices: 29232552--29232584 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
29232542 AATTAAAGTG
29232552 GAATATATAT-TAT
1 GAATATATATGTAT
29232565 GAATATATATGTAT
1 GAATATATATGTAT
*
29232579 AAATAT
1 GAATAT
29232585 GAAATTGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (14 bp):
GAATATATATGTAT
Found at i:29232741 original size:25 final size:25
Alignment explanation
Indices: 29232712--29232795 Score: 132
Period size: 25 Copynumber: 3.4 Consensus size: 25
29232702 TTAGCGCGCG
*
29232712 CTCTGATTATTAGCACGTTGGTGCT
1 CTCTGATTATTAGCACGTTAGTGCT
*
29232737 CTCTGATTATTAGTACGTTAGTGCT
1 CTCTGATTATTAGCACGTTAGTGCT
* *
29232762 CTCTGATTACTAGCACGTCAGTGCT
1 CTCTGATTATTAGCACGTTAGTGCT
29232787 CTCTGATTA
1 CTCTGATTA
29232796 GCACATCTGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.39
Consensus pattern (25 bp):
CTCTGATTATTAGCACGTTAGTGCT
Found at i:29232807 original size:22 final size:23
Alignment explanation
Indices: 29232732--29232835 Score: 104
Period size: 22 Copynumber: 4.4 Consensus size: 23
29232722 TAGCACGTTG
* * *
29232732 GTGCTCTCTGATTATTAGTACGTTA
1 GTGCTCTCTGA-TA-TAGCACATCA
*
29232757 GTGCTCTCTGATTACTAGCACGTCA
1 GTGCTCTCTGA-TA-TAGCACATCA
*
29232782 GTGCTCTCTGAT-TAGCACATCT
1 GTGCTCTCTGATATAGCACATCA
*
29232804 GTGCTCTCTG-TATAGCACTTCA
1 GTGCTCTCTGATATAGCACATCA
29232826 GTGCTCTCTG
1 GTGCTCTCTG
29232836 TTCATTAGTG
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
21 1 0.01
22 36 0.51
24 1 0.01
25 33 0.46
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (23 bp):
GTGCTCTCTGATATAGCACATCA
Found at i:29232843 original size:47 final size:48
Alignment explanation
Indices: 29232712--29232843 Score: 130
Period size: 50 Copynumber: 2.8 Consensus size: 48
29232702 TTAGCGCGCG
* ** * *
29232712 CTCTGATTATTAGCACGTTGGTGCTCTCTGATTATTAGTACGTTAGTGCT
1 CTCTGA-TACTAGCACGTCAGTGCTCTCTG-TTATTAGCACATTAGTGCT
29232762 CTCTGATTACTAGCACGTCAGTGCTCTCTG--ATTAGCACATCT-GTGCT
1 CTCTGA-TACTAGCACGTCAGTGCTCTCTGTTATTAGCACAT-TAGTGCT
*
29232809 CTCTG-TA-TAGCACTTCAGTGCTCTCTGTTCATTAG
1 CTCTGATACTAGCACGTCAGTGCTCTCTGTT-ATTAG
29232844 TGCATAATAA
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
44 19 0.26
45 2 0.03
47 23 0.32
48 1 0.01
50 27 0.38
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (48 bp):
CTCTGATACTAGCACGTCAGTGCTCTCTGTTATTAGCACATTAGTGCT
Found at i:29236210 original size:23 final size:24
Alignment explanation
Indices: 29236167--29236211 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
29236157 TATTTATTTT
29236167 ATTTAATATTACTGATTATATAAA
1 ATTTAATATTACTGATTATATAAA
* *
29236191 ATTTAATTTTA-TTATTATATA
1 ATTTAATATTACTGATTATATA
29236212 TTTTAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTTAATATTACTGATTATATAAA
Found at i:29238180 original size:6 final size:7
Alignment explanation
Indices: 29238152--29238181 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
29238142 ACTAGAATAT
29238152 AATTTTA
1 AATTTTA
29238159 AATTTTA
1 AATTTTA
29238166 AATTTTA
1 AATTTTA
29238173 AA-TTTA
1 AATTTTA
29238179 AAT
1 AAT
29238182 ATTATCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AATTTTA
Found at i:29252089 original size:49 final size:49
Alignment explanation
Indices: 29252036--29252129 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
29252026 TTGTTTGAAC
*
29252036 ATTTGTGTTTGATATGCAAAAAAATAGAGAAAGTTAAATTTATATAAAA
1 ATTTGTGTTTAATATGCAAAAAAATAGAGAAAGTTAAATTTATATAAAA
* *
29252085 ATTTGTGTTTAATATGCAAATAAATGGAGAAAGTTAAATTTATAT
1 ATTTGTGTTTAATATGCAAAAAAATAGAGAAAGTTAAATTTATAT
29252130 CTACTTCCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.37
Consensus pattern (49 bp):
ATTTGTGTTTAATATGCAAAAAAATAGAGAAAGTTAAATTTATATAAAA
Found at i:29253534 original size:14 final size:16
Alignment explanation
Indices: 29253506--29253544 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
29253496 TGTACAAACG
29253506 AAATATTTATGTTTA-
1 AAATATTTATGTTTAT
*
29253521 AAAT-TTTATTTTTAT
1 AAATATTTATGTTTAT
29253536 AAATATTTA
1 AAATATTTA
29253545 AATTGTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 9 0.43
15 8 0.38
16 4 0.19
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
AAATATTTATGTTTAT
Found at i:29258345 original size:20 final size:20
Alignment explanation
Indices: 29258320--29258357 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
29258310 CGTAGTTGAT
29258320 GAAAAATTGAAAGTTTGAAC
1 GAAAAATTGAAAGTTTGAAC
*
29258340 GAAAAATTGAATGTTTGA
1 GAAAAATTGAAAGTTTGA
29258358 TTGAAAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.21, T:0.29
Consensus pattern (20 bp):
GAAAAATTGAAAGTTTGAAC
Found at i:29258363 original size:20 final size:19
Alignment explanation
Indices: 29258315--29258364 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
29258305 GTTACCGTAG
29258315 TTGATGAAAAATTGAAAGT
1 TTGATGAAAAATTGAAAGT
* *
29258334 TTGAACGAAAAATTGAATGT
1 TTG-ATGAAAAATTGAAAGT
29258354 TTGATTGAAAA
1 TTGA-TGAAAA
29258365 CCTGAAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (19 bp):
TTGATGAAAAATTGAAAGT
Found at i:29258494 original size:27 final size:27
Alignment explanation
Indices: 29258455--29258514 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
29258445 GGAATGACAG
29258455 AAATATAAGGAATTAAGTTTGGGAATCA
1 AAAT-TAAGGAATTAAGTTTGGGAATCA
29258483 AAATTAAGGAATTAAGTTTGGGAATCA
1 AAATTAAGGAATTAAGTTTGGGAATCA
29258510 AAATT
1 AAATT
29258515 GAATTAGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 28 0.88
28 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (27 bp):
AAATTAAGGAATTAAGTTTGGGAATCA
Found at i:29270698 original size:19 final size:19
Alignment explanation
Indices: 29270669--29270712 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29270659 TTAATAAACG
29270669 ATATT-AAAATAAGAA-AAA
1 ATATTAAAAATAA-AATAAA
29270687 ATATTAAAAATAAAATAAA
1 ATATTAAAAATAAAATAAA
*
29270706 ATTTTAA
1 ATATTAA
29270713 TTGAGTGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
ATATTAAAAATAAAATAAA
Found at i:29276249 original size:3 final size:3
Alignment explanation
Indices: 29276241--29276280 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
29276231 TGAAAGTGAA
*
29276241 GAT GAT GAT GAT GAT GAT GAT GAT GAC GAT G-T AGAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT -GAT GAT G
29276281 TTCTTTATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 31 0.94
4 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.35, T:0.30
Consensus pattern (3 bp):
GAT
Found at i:29276619 original size:105 final size:105
Alignment explanation
Indices: 29276484--29276693 Score: 395
Period size: 105 Copynumber: 2.0 Consensus size: 105
29276474 TGCCATAAAG
*
29276484 CTGCTAGTAAAAATTGACTTATTCAGTGGTTGAAAATCTGTTGGACCTAATAGGTTAAACTCGTG
1 CTGCTAGTAAAAATTGACTTATTCAGTGGTTGAAAATCTGTTGGACCTAATAGGTAAAACTCGTG
29276549 ATTCG-GGTAGTTGATACTTTTTAGTTTTCTGGTCAGTGTT
66 ATT-GAGGTAGTTGATACTTTTTAGTTTTCTGGTCAGTGTT
29276589 CTGCTAGTAAAAATTGACTTATTCAGTGGTTGAAAATCTGTTGGACCTAATAGGTAAAACTCGTG
1 CTGCTAGTAAAAATTGACTTATTCAGTGGTTGAAAATCTGTTGGACCTAATAGGTAAAACTCGTG
29276654 ATTGAGGTAGTTGATACTTTTTAGTTTTCTGGTCAGTGTT
66 ATTGAGGTAGTTGATACTTTTTAGTTTTCTGGTCAGTGTT
29276694 GCAAATCTGA
Statistics
Matches: 103, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
104 1 0.01
105 102 0.99
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.40
Consensus pattern (105 bp):
CTGCTAGTAAAAATTGACTTATTCAGTGGTTGAAAATCTGTTGGACCTAATAGGTAAAACTCGTG
ATTGAGGTAGTTGATACTTTTTAGTTTTCTGGTCAGTGTT
Found at i:29282313 original size:5 final size:5
Alignment explanation
Indices: 29282303--29282332 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
29282293 AATTCACGTT
29282303 AGAAG AGAAG AGAAG AGAAG AGAAG A-AAG A
1 AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG A
29282333 AAGTTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:29284924 original size:30 final size:29
Alignment explanation
Indices: 29284890--29284947 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
29284880 AAAATTTATT
* *
29284890 TTATTTGAATATCAATTAAAGTTTAAATGC
1 TTATTTGAA-ACCAATTAAAGTATAAATGC
*
29284920 TTATTTGAAGCCAATTAAAGTATAAATG
1 TTATTTGAAACCAATTAAAGTATAAATG
29284948 TATAATTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (29 bp):
TTATTTGAAACCAATTAAAGTATAAATGC
Found at i:29291663 original size:14 final size:14
Alignment explanation
Indices: 29291644--29291678 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
29291634 ATTTTATTTT
*
29291644 TTCTAATGATACTA
1 TTCTAACGATACTA
29291658 TTCTAACGATACTA
1 TTCTAACGATACTA
29291672 TTCTAAC
1 TTCTAAC
29291679 ATGTAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:29292990 original size:62 final size:62
Alignment explanation
Indices: 29292902--29293069 Score: 282
Period size: 62 Copynumber: 2.7 Consensus size: 62
29292892 CAACATTACA
* * * * *
29292902 ACATTAAAACACTAAAACTTGTAACAAAGTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
29292964 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
*
29293026 ACATTACAATATTAAAAATTGGAACAAACTTTGTAATATAAATT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATT
29293070 AGGTACATTG
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 100 1.00
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (62 bp):
ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
Found at i:29296334 original size:27 final size:27
Alignment explanation
Indices: 29296296--29296374 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
29296286 TATACTAGGT
29296296 GTGCCGCCTATCAGATAGGCACCACCA
1 GTGCCGCCTATCAGATAGGCACCACCA
* *** *
29296323 GTGCCGCCTATCATATAGGGGTCACTA
1 GTGCCGCCTATCAGATAGGCACCACCA
*
29296350 GTGCCGCCTATCAGATAAGCACCAC
1 GTGCCGCCTATCAGATAGGCACCAC
29296375 ACCCGCTTCG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.19
Consensus pattern (27 bp):
GTGCCGCCTATCAGATAGGCACCACCA
Found at i:29296774 original size:18 final size:18
Alignment explanation
Indices: 29296737--29296775 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29296727 TATAAATTGT
* * *
29296737 TTTTATATGTTTTTTTTA
1 TTTTATATGATTTATATA
29296755 TTTTATATGATTTATATA
1 TTTTATATGATTTATATA
29296773 TTT
1 TTT
29296776 ATAAAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (18 bp):
TTTTATATGATTTATATA
Found at i:29302054 original size:21 final size:21
Alignment explanation
Indices: 29302028--29302070 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
29302018 TTTGGGTGGA
* *
29302028 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTCACGAGCTTATGT
29302049 TCAGCTCTCACGAGCTTATGT
1 TCAGCTCTCACGAGCTTATGT
29302070 T
1 T
29302071 GGCGTGTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.37
Consensus pattern (21 bp):
TCAGCTCTCACGAGCTTATGT
Found at i:29307379 original size:3 final size:3
Alignment explanation
Indices: 29307364--29307435 Score: 58
Period size: 3 Copynumber: 24.3 Consensus size: 3
29307354 AATACTAACG
* * ** * *
29307364 ATA ATA GTA ATA ATA AAA ACC ATA ATA ATA GTA A-A CTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
29307411 TTTA A-A ATA ATA ATA ATA ATA ATA A
1 -ATA ATA ATA ATA ATA ATA ATA ATA A
29307436 CATAAAATTG
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
2 3 0.06
3 48 0.91
4 2 0.04
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:29307492 original size:29 final size:29
Alignment explanation
Indices: 29307447--29307534 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 29
29307437 ATAAAATTGC
29307447 TAAAATAT-GGGCTAAATCGAAATAAAACA
1 TAAAATATAGGGCTAAATCGAAATAAAA-A
* * *
29307476 -AAAATATAGGGCGAAATTGAAAGAAAAA
1 TAAAATATAGGGCTAAATCGAAATAAAAA
* *
29307504 TAAAATAAAAGGGACTAAATCAAAATAAAAA
1 TAAAAT-ATAGGG-CTAAATCGAAATAAAAA
29307535 AAGAAACTGG
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
28 8 0.17
29 21 0.45
30 5 0.11
31 13 0.28
ACGTcount: A:0.61, C:0.07, G:0.15, T:0.17
Consensus pattern (29 bp):
TAAAATATAGGGCTAAATCGAAATAAAAA
Found at i:29309056 original size:44 final size:43
Alignment explanation
Indices: 29308997--29309377 Score: 230
Period size: 44 Copynumber: 8.8 Consensus size: 43
29308987 ACCTGACACG
* * * *
29308997 ATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTCATTTTA
1 ATCTGCTCTACTGTAATC-TCAGAGAGATAAGAT-CTACATTTCA
* * * *
29309041 ATCCGCTCCACTGTAATCTCA-AGGAGATAGGAT-TACTAGCTTCA
1 ATCTGCTCTACTGTAATCTCAGA-GAGATAAGATCTAC-A-TTTCA
* * *
29309085 ATCTGCTCTTCTATAATCTCAGGGAGATAAGATCTGACA---CA
1 ATCTGCTCTACTGTAATCTCAGAGAGATAAGATCT-ACATTTCA
* * * *
29309126 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTCGTTTTA
1 ATCTGCTCTACTGTAATC-TCAGAGAGATAAGAT-CTACATTTCA
* * * * *
29309170 ATCCGCTCCACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCA
1 ATCTGCTCTACTGTAATCTCAGAGAGATAAGATCTAC-A-TTTCA
* * *
29309214 ATCTGCTCTTCTGTAATCTCAGGGAGATAAGATCTGACA---CG
1 ATCTGCTCTACTGTAATCTCAGAGAGATAAGATCT-ACATTTCA
* * * *
29309255 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTCGTTTTA
1 ATCTGCTCTACTGTAATC-TCAGAGAGATAAGAT-CTACATTTCA
* * * *
29309299 ATCTGCTCCACTGTAATATCAGGGAGATAGGAT-TACTATCTTCA
1 ATCTGCTCTACTGTAATCTCAGAGAGATAAGATCTAC-AT-TTCA
** *
29309343 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
1 ATCTGCTCTACTGTAATCTCAGAGAGATAAGATCT
29309378 GAAATTCTTC
Statistics
Matches: 258, Mismatches: 53, Indels: 51
0.71 0.15 0.14
Matches are distributed among these distances:
40 2 0.01
41 60 0.23
42 10 0.04
43 3 0.01
44 172 0.67
45 7 0.03
46 4 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (43 bp):
ATCTGCTCTACTGTAATCTCAGAGAGATAAGATCTACATTTCA
Found at i:29309132 original size:129 final size:129
Alignment explanation
Indices: 29308966--29309379 Score: 720
Period size: 129 Copynumber: 3.2 Consensus size: 129
29308956 GTCTATTCCA
* * *
29308966 CTGTAATCTCAGGGAAATAAGACCTGACACGATCTACTCTGCTGTAACTTCAGAGAGATAAGATC
1 CTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
* *
29309031 CTTCATTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCTT
66 CTTCGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTT
* *
29309095 CTATAATCTCAGGGAGATAAGATCTGACACAATCTACTCTACTGTAACTTCAGAGAGATAAGATC
1 CTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
29309160 CTTCGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTT
66 CTTCGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTT
29309224 CTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
1 CTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
* * * **
29309289 CTTCGTTTTAATCTGCTCCACTGTAATATCAGGGAGATAGGATTACTATCTTCAATCTGCTCCG
66 CTTCGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTT
29309353 CTGTAATCTCAGGGAGATAAGATCTGA
1 CTGTAATCTCAGGGAGATAAGATCTGA
29309380 AATTCTTCGG
Statistics
Matches: 271, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 271 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (129 bp):
CTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTACTGTAACTTCAGAGAGATAAGATC
CTTCGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTT
Found at i:29309139 original size:85 final size:85
Alignment explanation
Indices: 29309040--29309379 Score: 230
Period size: 85 Copynumber: 4.0 Consensus size: 85
29309030 CCTTCATTTT
* * * ** *
29309040 AATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGCTTCAATCTGCTCTTCTATAATCTC
1 AATCTGCTCTACTGTAATCTCAAGGAGATAAGA-TACTAGCTTCAATCTGCTCCACTGTAATCTC
*
29309105 AGGGAGATAAGAT-CTGACAC
65 AGGGAGATAAGATACTGACTC
* * * * * *
29309125 AATCTACTCTACTGTAA-CTTC-AGAGAGATAAGATCCTTCGTTTTAATCCGCTCCACTGTAATC
1 AATCTGCTCTACTGTAATC-TCAAG-GAGATAAGATAC-TAGCTTCAATCTGCTCCACTGTAATC
*
29309188 TCAGGGAGATAGGATTACT-AGCTTC
63 TCAGGGAGATAAGA-TACTGA-C-TC
* * * * * *
29309213 AATCTGCTCTTCTGTAATCTCAGGGAGATAAGAT-CT-GAC-ACGATCTACTCTACTGTAA-CTT
1 AATCTGCTCTACTGTAATCTCAAGGAGATAAGATACTAG-CTTCAATCTGCTCCACTGTAATC-T
* * ** *
29309274 CAGAGAGATAAGATCCTTCGTTTT
64 CAGGGAGATAAGATAC-T-GACTC
* * * * * *
29309298 AATCTGCTCCACTGTAATATCAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTC
1 AATCTGCTCTACTGTAATCTCAAGGAGATAAGA-TACTAGCTTCAATCTGCTCCACTGTAATCTC
29309363 AGGGAGATAAGAT-CTGA
65 AGGGAGATAAGATACTGA
29309380 AATTCTTCGG
Statistics
Matches: 194, Mismatches: 42, Indels: 38
0.71 0.15 0.14
Matches are distributed among these distances:
84 8 0.04
85 114 0.59
86 5 0.03
87 8 0.04
88 56 0.29
89 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (85 bp):
AATCTGCTCTACTGTAATCTCAAGGAGATAAGATACTAGCTTCAATCTGCTCCACTGTAATCTCA
GGGAGATAAGATACTGACTC
Found at i:29322365 original size:3 final size:3
Alignment explanation
Indices: 29322350--29322424 Score: 73
Period size: 3 Copynumber: 25.3 Consensus size: 3
29322340 AATACTAACG
* ** * *
29322350 ATA ATA GTA ATA ATA ATA ACC ATA ATA ATA ATA GTA A-A CTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
29322397 ATA TTTA A-A ATA ATA ATA ATA ATA ATA A
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA A
29322425 CATAAAATTG
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
2 3 0.05
3 52 0.91
4 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29322481 original size:29 final size:28
Alignment explanation
Indices: 29322437--29322525 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 28
29322427 TAAAATTGCT
29322437 AAAATAT-GGGCTAAATCGAAATAAAACA
1 AAAATATAGGGCTAAATCGAAATAAAA-A
* * *
29322465 AAAATATAGGGCGAAATTGAAAGAAAAA
1 AAAATATAGGGCTAAATCGAAATAAAAA
* * *
29322493 TAAAATAAAAGGACTAAATCAAAATAAAAA
1 -AAAAT-ATAGGGCTAAATCGAAATAAAAA
29322523 AAA
1 AAA
29322526 GAAACTGGGC
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
28 8 0.16
29 24 0.49
30 17 0.35
ACGTcount: A:0.64, C:0.07, G:0.13, T:0.16
Consensus pattern (28 bp):
AAAATATAGGGCTAAATCGAAATAAAAA
Found at i:29332452 original size:28 final size:28
Alignment explanation
Indices: 29332420--29332516 Score: 149
Period size: 28 Copynumber: 3.5 Consensus size: 28
29332410 AATAAGTTCA
* * *
29332420 CACACTTAGTGCTTAATAATCAAACTCG
1 CACACTTAGTGCTTTACAATTAAACTCG
*
29332448 CACACTTAGTGCTTTACCATTAAACTCG
1 CACACTTAGTGCTTTACAATTAAACTCG
*
29332476 CACACTTAGTGCTTTACAATTAAACTCA
1 CACACTTAGTGCTTTACAATTAAACTCG
29332504 CACACTTAGTGCT
1 CACACTTAGTGCT
29332517 AATCTCATTA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.31
Consensus pattern (28 bp):
CACACTTAGTGCTTTACAATTAAACTCG
Found at i:29336042 original size:5 final size:5
Alignment explanation
Indices: 29336032--29336069 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
29336022 TCAACTAAAG
*
29336032 TTTTA TTTTA TTTTA TTTTA TTTTA -TATA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
29336070 TATTGGCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 27 0.90
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:29336072 original size:15 final size:14
Alignment explanation
Indices: 29336032--29336069 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
29336022 TCAACTAAAG
*
29336032 TTTTATTTTATTTTA
1 TTTTATTTTA-TATA
29336047 TTTTATTTTATATA
1 TTTTATTTTATATA
29336061 TTTTATTTT
1 TTTTATTTT
29336070 TATTGGCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTATTTTATATA
Found at i:29337376 original size:19 final size:20
Alignment explanation
Indices: 29337352--29337390 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29337342 ACTATTTTAA
*
29337352 ATATAA-AACAATAAATTTT
1 ATATAATAAAAATAAATTTT
*
29337371 ATATAATAAAAATTAATTTT
1 ATATAATAAAAATAAATTTT
29337391 TAAGCATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATAATAAAAATAAATTTT
Found at i:29337707 original size:14 final size:15
Alignment explanation
Indices: 29337688--29337717 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
29337678 ATTTTAATCA
29337688 TTAATTTA-ATTTTT
1 TTAATTTATATTTTT
29337702 TTAATTTATATTTTT
1 TTAATTTATATTTTT
29337717 T
1 T
29337718 GTCAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTAATTTATATTTTT
Found at i:29337877 original size:21 final size:21
Alignment explanation
Indices: 29337844--29337924 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
29337834 TTAAAAATTA
* *
29337844 AAAAAATATAAAAATTATTTT
1 AAAAATTAAAAAAATTATTTT
*
29337865 AAAAATT-AAAAAATATATATT
1 AAAAATTAAAAAAAT-TATTTT
*
29337886 AAAAAGTATAAAAAA-TATTTTT
1 AAAAATTA-AAAAAATTA-TTTT
*
29337908 AAAATTTAAAAAAATTA
1 AAAAATTAAAAAAATTA
29337925 ATTAAATGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 6 0.12
21 25 0.52
22 11 0.23
23 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (21 bp):
AAAAATTAAAAAAATTATTTT
Found at i:29338377 original size:35 final size:35
Alignment explanation
Indices: 29338320--29338387 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
29338310 AAAGCCTACT
**
29338320 GAATCTTAACTCGATTAATATTAGTATAATTGTTA
1 GAATCTTAACTCGATTAATATTAACATAATTGTTA
* **
29338355 GAATCTTAACTTGATTGGTATTAACATAATTGT
1 GAATCTTAACTCGATTAATATTAACATAATTGT
29338388 CAGTACAAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (35 bp):
GAATCTTAACTCGATTAATATTAACATAATTGTTA
Found at i:29344275 original size:21 final size:22
Alignment explanation
Indices: 29344236--29344278 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
29344226 TATATTATTA
29344236 CAATAACAATGAAAAATATTGT
1 CAATAACAATGAAAAATATTGT
**
29344258 CAAT-ACAATGAATTATATTGT
1 CAATAACAATGAAAAATATTGT
29344279 TGAAGGTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (22 bp):
CAATAACAATGAAAAATATTGT
Found at i:29346911 original size:37 final size:37
Alignment explanation
Indices: 29346861--29346942 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
29346851 TATTTCCTAG
* *
29346861 AATAAAATCTTTAAAAGATAATATAATATTAAATTAA
1 AATAAAATATTTAAAAGATAATATAATATTAAAATAA
* * *
29346898 AATAAAATATTTAAAGGATAATATTATTTTAAAATAA
1 AATAAAATATTTAAAAGATAATATAATATTAAAATAA
29346935 AATAAAAT
1 AATAAAAT
29346943 TTGAAAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (37 bp):
AATAAAATATTTAAAAGATAATATAATATTAAAATAA
Found at i:29346920 original size:19 final size:19
Alignment explanation
Indices: 29346861--29346942 Score: 60
Period size: 18 Copynumber: 4.4 Consensus size: 19
29346851 TATTTCCTAG
*
29346861 AATAAAATCTTTAAAAGAT
1 AATAAAATATTTAAAAGAT
* ** *
29346880 AATATAATA-TTAAATTAA
1 AATAAAATATTTAAAAGAT
*
29346898 AATAAAATATTTAAAGGAT
1 AATAAAATATTTAAAAGAT
** * *
29346917 AATATTAT-TTTAAAATAA
1 AATAAAATATTTAAAAGAT
29346935 AATAAAAT
1 AATAAAAT
29346943 TTGAAAAAAA
Statistics
Matches: 46, Mismatches: 16, Indels: 3
0.71 0.25 0.05
Matches are distributed among these distances:
18 27 0.59
19 19 0.41
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (19 bp):
AATAAAATATTTAAAAGAT
Found at i:29347217 original size:21 final size:21
Alignment explanation
Indices: 29347154--29347217 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
29347144 ATCATATATA
* * *
29347154 TTACAATTTTTTATATATTTC
1 TTACAAATTTTTATATTTTTT
* *
29347175 TTA-ATAAATTTTA-ATTAATTT
1 TTACA-AATTTTTATATT-TTTT
29347196 TTACAAATTTTTATATTTTTT
1 TTACAAATTTTTATATTTTTT
29347217 T
1 T
29347218 ACCAGGTTGT
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
20 3 0.09
21 25 0.78
22 4 0.12
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
TTACAAATTTTTATATTTTTT
Found at i:29350274 original size:31 final size:31
Alignment explanation
Indices: 29350238--29350299 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
29350228 AGATAATTTT
29350238 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
29350269 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
29350300 TAATTTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:29355419 original size:5 final size:5
Alignment explanation
Indices: 29355411--29355481 Score: 60
Period size: 5 Copynumber: 14.8 Consensus size: 5
29355401 GGTACTAAAC
* * *
29355411 TACTT TACTC TAC-- TACTT TACTC TACTT TACTC TAC-- TACTT TACTT
1 TACTT TACTT TACTT TACTT TACTT TACTT TACTT TACTT TACTT TACTT
* *
29355457 TACTC TACTAC TACTT TACTT TACT
1 TACTT TACT-T TACTT TACTT TACT
29355482 AAACCCTCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
3 6 0.11
5 44 0.80
6 5 0.09
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.49
Consensus pattern (5 bp):
TACTT
Found at i:29355436 original size:10 final size:10
Alignment explanation
Indices: 29355423--29355481 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
29355413 CTTTACTCTA
29355423 CTACTTTACT
1 CTACTTTACT
29355433 CTACTTTACT
1 CTACTTTACT
29355443 CTAC--TACT
1 CTACTTTACT
*
29355451 TTACTTTACT
1 CTACTTTACT
*
29355461 CTACTACTACT
1 CTACT-TTACT
*
29355472 TTACTTTACT
1 CTACTTTACT
29355482 AAACCCTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
8 7 0.17
10 26 0.63
11 8 0.20
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (10 bp):
CTACTTTACT
Found at i:29355436 original size:23 final size:23
Alignment explanation
Indices: 29355410--29355481 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
29355400 AGGTACTAAA
29355410 CTACTTTACTCTACTACTTTACT
1 CTACTTTACTCTACTACTTTACT
29355433 CTACTTTACTCTACTACTTTACT
1 CTACTTTACTCTACTACTTTACT
* *
29355456 TTACTCTA--CTACTACTTTACT
1 CTACTTTACTCTACTACTTTACT
*
29355477 TTACT
1 CTACT
29355482 AAACCCTCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 18 0.38
23 29 0.62
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (23 bp):
CTACTTTACTCTACTACTTTACT
Found at i:29355481 original size:13 final size:12
Alignment explanation
Indices: 29355409--29355482 Score: 77
Period size: 13 Copynumber: 6.3 Consensus size: 12
29355399 TAGGTACTAA
29355409 ACTACTTTACTCT
1 ACTACTTTACT-T
29355422 ACTACTTTAC-T
1 ACTACTTTACTT
29355433 -CTACTTTACTCT
1 ACTACTTTACT-T
29355445 ACTACTTTACTT
1 ACTACTTTACTT
*
29355457 --TACTCTAC-T
1 ACTACTTTACTT
29355466 ACTACTTTACTTT
1 ACTACTTTAC-TT
29355479 ACTA
1 ACTA
29355483 AACCCTCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
9 1 0.02
10 16 0.31
11 8 0.15
12 2 0.04
13 25 0.48
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.47
Consensus pattern (12 bp):
ACTACTTTACTT
Found at i:29356459 original size:31 final size:31
Alignment explanation
Indices: 29356423--29356484 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
29356413 AGATAATTTT
29356423 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
29356454 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGGATTCAATTACTCTTG
29356485 TAATTTTCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGAGTTTTATTAGGATTCAATTACTCTTG
Found at i:29359092 original size:469 final size:468
Alignment explanation
Indices: 29358203--29359619 Score: 2406
Period size: 469 Copynumber: 3.0 Consensus size: 468
29358193 TACAAATCCC
* * * *
29358203 ACCTTAAAAACAGATACATCATGCAAATAACAGATAACAGATACAAAAACACATGATTAACTTAC
1 ACCTAAAAAACAGATACATCATGCAAATAACAGATAACAGATACAAAATCACATGATTAACATGC
*
29358268 TCGTATACAGATATTGTACTTACTTATG-TAGAATAGTCAGACATATATATCGATTTCCTACTCA
66 TCGTATACAGATATTGTACTTACTTATGCT-GAATAGTCAGACATATATATTGATTTCCTACTCA
* * * *
29358332 GATCAAACTATTAGAATAACAGATCACATACAATGGGTTTAGTTAGCCCTTATGGACCTTAAGGT
130 GATCAAACTATTAGATTAACAGATCACATACAATGGGTTTAGTTAGCCCTTATCGACCCTACGGT
* *
29358397 AGGCGTACAGTCGATCAGAATGACCTGTGCTACCCTAAAGAAATTTTTAGAATTATGGGCCCACA
195 AGGCGTACAGTCGATCGGAATGACCTGTGCTACCCTAAAGAAATTTTTAGAATTTTGGGCCCACA
*
29358462 CGCCCAATCCGGCCTAGCCCGTGTGGCCCACACGGCCACACAATCTCCGTCACATGGCTATGTCT
260 CGCCCAATCCGGCCTAGCCCGTGTGGCCCACACGGCCACACAATCTCCGTCACATGGCTGTGTCT
29358527 CACACACAGCCAGCCGCACGACCGACCACACGCCTGTGTGGTGTCGACAGACCAAATTTTTAGCT
325 CACACACAGCCAGCCGCACGACCGACCACACGCC-GTGTGGTGTCGACAGACCAAATTTTTAGCT
*
29358592 TTCGTCGAACCTTATTTTCTCATGTTTTAGGTATACACCTGGTACAGTTTTGATGTGAAAGTAAT
389 TTCGTCGAACCTTATTTTCTCATGTTTTAGGTATACACCTGGTACAGTTTTGATGCGAAAGTAAT
*
29358657 TCTGAGCCCTTCCAA
454 TCCGAGCCCTTCCAA
* * *
29358672 ACCTAAAAAATAGATACATTATGCAAATAACAGATAATAGATACAAAATCACATGATTAACATGC
1 ACCTAAAAAACAGATACATCATGCAAATAACAGATAACAGATACAAAATCACATGATTAACATGC
29358737 TCGTATACAGATATTGTACTTACTTATGCTGAATAGTCAGACATATATATTGATTTCCTACTCAG
66 TCGTATACAGATATTGTACTTACTTATGCTGAATAGTCAGACATATATATTGATTTCCTACTCAG
* * *
29358802 ATCAGACTATTAGATTAACAGATTACATACAATGGGTTTAGTTAGCCCTTATCAACCCTACGGTA
131 ATCAAACTATTAGATTAACAGATCACATACAATGGGTTTAGTTAGCCCTTATCGACCCTACGGTA
* *
29358867 GGCGTACAGTCGATCGGAATGACTTGTGCTACCCTAAAGAAATTTTCAGAATTTTGGGCCCACAC
196 GGCGTACAGTCGATCGGAATGACCTGTGCTACCCTAAAGAAATTTTTAGAATTTTGGGCCCACAC
* *
29358932 GCCCAATCCGGCCTAGCCCGTGTGGCCCACACGGCCACACAATCTCTGTCACATGGCTGCGTCTC
261 GCCCAATCCGGCCTAGCCCGTGTGGCCCACACGGCCACACAATCTCCGTCACATGGCTGTGTCTC
* * * *
29358997 ACACACAGCCAGCCGCACAACCGGCCACACGCTCATGTGGCGTCGACAGACCAAATTTTTAGCTT
326 ACACACAGCCAGCCGCACGACCGACCACACGC-CGTGTGGTGTCGACAGACCAAATTTTTAGCTT
*
29359062 TCGCCGAACCTTATTTTCTCATGTTTTAGGTATACACCTGGTACAGTTTTGATGCGAAAGTAATT
390 TCGTCGAACCTTATTTTCTCATGTTTTAGGTATACACCTGGTACAGTTTTGATGCGAAAGTAATT
29359127 CCGAGCCCTTCCAA
455 CCGAGCCCTTCCAA
*
29359141 ACCTAAAAAACAGATACATCATGCAAATAACAGATAACAGATACAAAATCACATGATTAACATGA
1 ACCTAAAAAACAGATACATCATGCAAATAACAGATAACAGATACAAAATCACATGATTAACATGC
*
29359206 TCGTATACAGATATTGTACTTGCTTATGCTGAATAGTCAGACATATATATCT-ATTTCCTACTCA
66 TCGTATACAGATATTGTACTTACTTATGCTGAATAGTCAGACATATATAT-TGATTTCCTACTCA
*
29359270 GATCAAACTATTAGATTAACAGATCACATACAATGGGTTTAGTTAGCCCTTATCGACCCTACGAT
130 GATCAAACTATTAGATTAACAGATCACATACAATGGGTTTAGTTAGCCCTTATCGACCCTACGGT
*
29359335 AGGCGTACAGTCGATCGGAATGACCTGTGCTACCCTAAACAAATTTTTAGAATTTTGGGCCCACA
195 AGGCGTACAGTCGATCGGAATGACCTGTGCTACCCTAAAGAAATTTTTAGAATTTTGGGCCCACA
* *
29359400 CGCCCAATCTGGCCTAGCCCGTGTGGCCCACACGGCCACAGAATCTCCGTCACATGGCTGTGTCT
260 CGCCCAATCCGGCCTAGCCCGTGTGGCCCACACGGCCACACAATCTCCGTCACATGGCTGTGTCT
* * *
29359465 CACACACAGCCAGCCGCACGATCGACCACATGCCCGTGTGGTGTCGATAGACCAAATTTTTAGCT
325 CACACACAGCCAGCCGCACGACCGACCACACG-CCGTGTGGTGTCGACAGACCAAATTTTTAGCT
* * *
29359530 TTCATCGAACCTTATTTTCTCATGTTTTAGGTATACAGCTGGTACAGTTTTGATACGAAAGTAAT
389 TTCGTCGAACCTTATTTTCTCATGTTTTAGGTATACACCTGGTACAGTTTTGATGCGAAAGTAAT
29359595 TCCGAGCCCTTCCAA
454 TCCGAGCCCTTCCAA
29359610 ACCTAAAAAA
1 ACCTAAAAAA
29359620 TAGTACCTCA
Statistics
Matches: 888, Mismatches: 56, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
469 884 1.00
470 4 0.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (468 bp):
ACCTAAAAAACAGATACATCATGCAAATAACAGATAACAGATACAAAATCACATGATTAACATGC
TCGTATACAGATATTGTACTTACTTATGCTGAATAGTCAGACATATATATTGATTTCCTACTCAG
ATCAAACTATTAGATTAACAGATCACATACAATGGGTTTAGTTAGCCCTTATCGACCCTACGGTA
GGCGTACAGTCGATCGGAATGACCTGTGCTACCCTAAAGAAATTTTTAGAATTTTGGGCCCACAC
GCCCAATCCGGCCTAGCCCGTGTGGCCCACACGGCCACACAATCTCCGTCACATGGCTGTGTCTC
ACACACAGCCAGCCGCACGACCGACCACACGCCGTGTGGTGTCGACAGACCAAATTTTTAGCTTT
CGTCGAACCTTATTTTCTCATGTTTTAGGTATACACCTGGTACAGTTTTGATGCGAAAGTAATTC
CGAGCCCTTCCAA
Found at i:29368056 original size:22 final size:22
Alignment explanation
Indices: 29368031--29368077 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
29368021 TATACTTTTA
* *
29368031 AATAATAACCTTATTATTATTG
1 AATAATAACCGTATTATCATTG
29368053 AATAATAACCGTATTATCATTG
1 AATAATAACCGTATTATCATTG
29368075 AAT
1 AAT
29368078 TGGGTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (22 bp):
AATAATAACCGTATTATCATTG
Found at i:29371912 original size:3 final size:3
Alignment explanation
Indices: 29371904--29371935 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29371894 CATGGCTGAA
29371904 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29371936 ATTTGTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:29372221 original size:9 final size:9
Alignment explanation
Indices: 29372207--29372237 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29372197 GTTAAACTAA
29372207 TCGAGTTAT
1 TCGAGTTAT
*
29372216 TCGAGTTAA
1 TCGAGTTAT
29372225 TCGAGTTAT
1 TCGAGTTAT
29372234 TCGA
1 TCGA
29372238 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:29372409 original size:33 final size:33
Alignment explanation
Indices: 29372372--29372441 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
29372362 TTTTACTTTT
*
29372372 CCCCCAAAACTTTTACTCTCCTCCCCTCCCAAC
1 CCCCCAAAACTTTTACTCCCCTCCCCTCCCAAC
29372405 CCCCCAAAACTTTTACTCCCCTCCCCTCCCAAC
1 CCCCCAAAACTTTTACTCCCCTCCCCTCCCAAC
29372438 CCCC
1 CCCC
29372442 AATCTACCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.20, C:0.59, G:0.00, T:0.21
Consensus pattern (33 bp):
CCCCCAAAACTTTTACTCCCCTCCCCTCCCAAC
Found at i:29374557 original size:20 final size:20
Alignment explanation
Indices: 29374519--29374557 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29374509 TCTTTCTTTT
* **
29374519 TTCTTTTCTTTTTGGTTCTG
1 TTCTATTCTTTTTCCTTCTG
29374539 TTCTATTCTTTTTCCTTCT
1 TTCTATTCTTTTTCCTTCT
29374558 TCTTTTTCCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.21, G:0.08, T:0.69
Consensus pattern (20 bp):
TTCTATTCTTTTTCCTTCTG
Found at i:29386595 original size:21 final size:21
Alignment explanation
Indices: 29386569--29386630 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
29386559 AAAACACGCC
* *
29386569 AACAGAAGCTCGTGAGTGCTA
1 AACAGAAGCTCATGAGAGCTA
*
29386590 AACAGAAGCTCATGAGAGTTA
1 AACAGAAGCTCATGAGAGCTA
* *
29386611 AACAGAAGGTCATTAGAGCT
1 AACAGAAGCTCATGAGAGCT
29386631 GATCCACCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.19
Consensus pattern (21 bp):
AACAGAAGCTCATGAGAGCTA
Found at i:29387094 original size:35 final size:34
Alignment explanation
Indices: 29387021--29387248 Score: 294
Period size: 35 Copynumber: 6.6 Consensus size: 34
29387011 TACATGACAT
* * *
29387021 GAGAGATTCCCTGCAAGAAATGATGTGTGAACAG
1 GAGAGATTCCCTGCAAAAAATAATGCGTGAACAG
*
29387055 GAGAGATTCCCTGCAACAAAATAATGCGTGAACAT
1 GAGAGATTCCCTGCAA-AAAATAATGCGTGAACAG
* * *
29387090 GAGAGATTCCCTGCAAGAAATGATGTGTGAACAG
1 GAGAGATTCCCTGCAAAAAATAATGCGTGAACAG
29387124 GAGAGATTCCCTGCAACAAAATAATGCGTGAACAG
1 GAGAGATTCCCTGCAA-AAAATAATGCGTGAACAG
* * * *
29387159 GAGGGATTCCCTGCAATAAATGATGTGTGAACAG
1 GAGAGATTCCCTGCAAAAAATAATGCGTGAACAG
*
29387193 GAGAGATTCCCTACAACAAAATAATGCGTGAACAG
1 GAGAGATTCCCTGCAA-AAAATAATGCGTGAACAG
* *
29387228 GAAATATTCCCTGCAAGAAAA
1 GAGAGATTCCCTGCAA-AAAA
29387249 GACAAGTGGA
Statistics
Matches: 167, Mismatches: 24, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
34 75 0.45
35 92 0.55
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.20
Consensus pattern (34 bp):
GAGAGATTCCCTGCAAAAAATAATGCGTGAACAG
Found at i:29387128 original size:69 final size:69
Alignment explanation
Indices: 29387021--29387247 Score: 400
Period size: 69 Copynumber: 3.3 Consensus size: 69
29387011 TACATGACAT
29387021 GAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGA
1 GAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGA
*
29387086 ACAT
66 ACAG
29387090 GAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGA
1 GAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGA
29387155 ACAG
66 ACAG
* * *
29387159 GAGGGATTCCCTGCAATAAATGATGTGTGAACAGGAGAGATTCCCTACAACAAAATAATGCGTGA
1 GAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGA
29387224 ACAG
66 ACAG
* *
29387228 GAAATATTCCCTGCAAGAAA
1 GAGAGATTCCCTGCAAGAAA
29387248 AGACAAGTGG
Statistics
Matches: 150, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 150 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (69 bp):
GAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGA
ACAG
Found at i:29393462 original size:20 final size:22
Alignment explanation
Indices: 29393432--29393475 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
29393422 AGAAAAAGAG
29393432 AAATACAAAAA-AGAATAG-ATC
1 AAATACAAAAAGA-AATAGAATC
29393453 AAAT-CAAAAAGAAATAGAATC
1 AAATACAAAAAGAAATAGAATC
29393474 AA
1 AA
29393476 CAATTTGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.68, C:0.09, G:0.09, T:0.14
Consensus pattern (22 bp):
AAATACAAAAAGAAATAGAATC
Found at i:29396305 original size:34 final size:34
Alignment explanation
Indices: 29396262--29396439 Score: 230
Period size: 34 Copynumber: 5.2 Consensus size: 34
29396252 CAGGTCCAAA
* *
29396262 AAGAAATGATACATGAACAGGAGAGATTCCCTGC
1 AAGAAATGATGCGTGAACAGGAGAGATTCCCTGC
* *
29396296 AAGAAATGATGTGTGAACAGGAGAGATTCCCCGC
1 AAGAAATGATGCGTGAACAGGAGAGATTCCCTGC
* *
29396330 AACAAAATAATGCGTGAACAGGAGAGATTCCCTGC
1 AA-GAAATGATGCGTGAACAGGAGAGATTCCCTGC
* *
29396365 AATAAATGATGTGTGAACAGGAGAGATTCCCTGC
1 AAGAAATGATGCGTGAACAGGAGAGATTCCCTGC
* * * *
29396399 AACAAAATAATGCGTGAACAGGAAATATTCCCTGC
1 AA-GAAATGATGCGTGAACAGGAGAGATTCCCTGC
29396434 AAGAAA
1 AAGAAA
29396440 AGACAAGTGA
Statistics
Matches: 125, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
34 66 0.53
35 59 0.47
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (34 bp):
AAGAAATGATGCGTGAACAGGAGAGATTCCCTGC
Found at i:29396354 original size:35 final size:34
Alignment explanation
Indices: 29396275--29396440 Score: 224
Period size: 35 Copynumber: 4.8 Consensus size: 34
29396265 AAATGATACA
* * *
29396275 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAAAAAATAATGCG
*
29396309 TGAACAGGAGAGATTCCCCGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAA-AAAATAATGCG
* * *
29396344 TGAACAGGAGAGATTCCCTGCAATAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAAAAAATAATGCG
29396378 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAA-AAAATAATGCG
* *
29396413 TGAACAGGAAATATTCCCTGCAAGAAAA
1 TGAACAGGAGAGATTCCCTGCAA-AAAA
29396441 GACAAGTGAA
Statistics
Matches: 116, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
34 53 0.46
35 63 0.54
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (34 bp):
TGAACAGGAGAGATTCCCTGCAAAAAATAATGCG
Found at i:29396450 original size:69 final size:69
Alignment explanation
Indices: 29396275--29396439 Score: 294
Period size: 69 Copynumber: 2.4 Consensus size: 69
29396265 AAATGATACA
29396275 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCCGCAACAAAATAA
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCCGCAACAAAATAA
29396340 TGCG
66 TGCG
* *
29396344 TGAACAGGAGAGATTCCCTGCAATAAATGATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAA
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCCGCAACAAAATAA
29396409 TGCG
66 TGCG
* *
29396413 TGAACAGGAAATATTCCCTGCAAGAAA
1 TGAACAGGAGAGATTCCCTGCAAGAAA
29396440 AGACAAGTGA
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 91 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (69 bp):
TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCCGCAACAAAATAA
TGCG
Found at i:29396669 original size:18 final size:18
Alignment explanation
Indices: 29396646--29396701 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
29396636 AAGTTTCTCA
29396646 AAGTTTCTCAAAACTTTT
1 AAGTTTCTCAAAACTTTT
*
29396664 AAGTTT-ACAAAA--TTT
1 AAGTTTCTCAAAACTTTT
29396679 -AGTTTCTCAAAACTTTT
1 AAGTTTCTCAAAACTTTT
29396696 AAGTTT
1 AAGTTT
29396702 ACAAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 5 0.16
15 8 0.25
17 8 0.25
18 11 0.34
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (18 bp):
AAGTTTCTCAAAACTTTT
Found at i:29396684 original size:32 final size:32
Alignment explanation
Indices: 29396647--29396711 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
29396637 AGTTTCTCAA
29396647 AGTTTCTCAAAACTTTTAAGTTTACAAAATTT
1 AGTTTCTCAAAACTTTTAAGTTTACAAAATTT
29396679 AGTTTCTCAAAACTTTTAAGTTTACAAAATTT
1 AGTTTCTCAAAACTTTTAAGTTTACAAAATTT
29396711 A
1 A
29396712 ATTTTTAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.43
Consensus pattern (32 bp):
AGTTTCTCAAAACTTTTAAGTTTACAAAATTT
Found at i:29396706 original size:17 final size:17
Alignment explanation
Indices: 29396654--29396707 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
29396644 CAAAGTTTCT
29396654 CAAAACTTTTAAGTTTA
1 CAAAACTTTTAAGTTTA
*
29396671 CAAAA--TTT-AGTTTCT
1 CAAAACTTTTAAGTTT-A
29396686 CAAAACTTTTAAGTTTA
1 CAAAACTTTTAAGTTTA
29396703 CAAAA
1 CAAAA
29396708 TTTAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 5 0.16
15 8 0.26
17 13 0.42
18 5 0.16
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.39
Consensus pattern (17 bp):
CAAAACTTTTAAGTTTA
Found at i:29396816 original size:17 final size:17
Alignment explanation
Indices: 29396794--29396827 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29396784 CTTTGGCTCA
*
29396794 AAACTTAGAATTATTTC
1 AAACTTAGAATCATTTC
29396811 AAACTTAGAATCATTTC
1 AAACTTAGAATCATTTC
29396828 TCAAAAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.38
Consensus pattern (17 bp):
AAACTTAGAATCATTTC
Found at i:29401054 original size:13 final size:14
Alignment explanation
Indices: 29401024--29401057 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
29401014 ATATTTGTAA
29401024 TTTGAAAACTTAAG
1 TTTGAAAACTTAAG
29401038 TTTGAAAACTT-AG
1 TTTGAAAACTTAAG
29401051 TTTGAAA
1 TTTGAAA
29401058 TTTTGGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (14 bp):
TTTGAAAACTTAAG
Found at i:29401117 original size:32 final size:32
Alignment explanation
Indices: 29401076--29401140 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
29401066 ACTTAAAAAT
29401076 TAAATTTTGTAAACTTAAAAGTTTTGAGAAAC
1 TAAATTTTGTAAACTTAAAAGTTTTGAGAAAC
29401108 TAAATTTTGTAAACTTAAAAGTTTTGAGAAAC
1 TAAATTTTGTAAACTTAAAAGTTTTGAGAAAC
29401140 T
1 T
29401141 TTGCTGATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.38
Consensus pattern (32 bp):
TAAATTTTGTAAACTTAAAAGTTTTGAGAAAC
Found at i:29401126 original size:15 final size:15
Alignment explanation
Indices: 29401075--29401126 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
29401065 AACTTAAAAA
29401075 TTAAATTTTGTAAAC
1 TTAAATTTTGTAAAC
*
29401090 TTAAAAGTTTTGAGAAAC
1 TT-AAA-TTTTG-TAAAC
29401108 -TAAATTTTGTAAAC
1 TTAAATTTTGTAAAC
29401122 TTAAA
1 TTAAA
29401127 AGTTTTGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 4 0.13
15 11 0.35
16 6 0.19
17 6 0.19
18 4 0.13
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (15 bp):
TTAAATTTTGTAAAC
Found at i:29401141 original size:18 final size:18
Alignment explanation
Indices: 29401086--29401141 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
29401076 TAAATTTTGT
29401086 AAACTTAAAAGTTTTGAG
1 AAACTTAAAAGTTTTGAG
*
29401104 AAAC-T-AAA-TTTTG-T
1 AAACTTAAAAGTTTTGAG
29401118 AAACTTAAAAGTTTTGAG
1 AAACTTAAAAGTTTTGAG
29401136 AAACTT
1 AAACTT
29401142 TGCTGATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 4 0.12
15 6 0.19
16 6 0.19
17 6 0.19
18 10 0.31
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (18 bp):
AAACTTAAAAGTTTTGAG
Found at i:29401740 original size:34 final size:34
Alignment explanation
Indices: 29401697--29401874 Score: 194
Period size: 34 Copynumber: 5.2 Consensus size: 34
29401687 CAGGTCCAAA
* * *
29401697 AAGAAATGATACATGAACAAGAGAGATTTCCTGC
1 AAGAAATGATACGTGAACAGGAGAGATTCCCTGC
**
29401731 AAGAAATGATGTGTGAACAGGAGAGATTCCCTGC
1 AAGAAATGATACGTGAACAGGAGAGATTCCCTGC
* *
29401765 AACAAAATAATACGTGAACAGGAGAGATTCCCTGC
1 AA-GAAATGATACGTGAACAGGAGAGATTCCCTGC
* ** *
29401800 AATAAATGATGTGTGAACAGGAGAGATTTCCTGC
1 AAGAAATGATACGTGAACAGGAGAGATTCCCTGC
* * * * *
29401834 AACAAAATAATGCGTGAACAGGAAATATTCCCTGC
1 AA-GAAATGATACGTGAACAGGAGAGATTCCCTGC
29401869 AAGAAA
1 AAGAAA
29401875 ATACAAGTGA
Statistics
Matches: 121, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
34 63 0.52
35 58 0.48
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (34 bp):
AAGAAATGATACGTGAACAGGAGAGATTCCCTGC
Found at i:29401789 original size:35 final size:34
Alignment explanation
Indices: 29401710--29401877 Score: 201
Period size: 35 Copynumber: 4.9 Consensus size: 34
29401700 AAATGATACA
* * * * *
29401710 TGAACAAGAGAGATTTCCTGCAAGAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAAAAAATAATGCG
*
29401744 TGAACAGGAGAGATTCCCTGCAACAAAATAATACG
1 TGAACAGGAGAGATTCCCTGCAA-AAAATAATGCG
* * *
29401779 TGAACAGGAGAGATTCCCTGCAATAAATGATGTG
1 TGAACAGGAGAGATTCCCTGCAAAAAATAATGCG
*
29401813 TGAACAGGAGAGATTTCCTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAA-AAAATAATGCG
* *
29401848 TGAACAGGAAATATTCCCTGCAAGAAAATA
1 TGAACAGGAGAGATTCCCTGCAA-AAAATA
29401878 CAAGTGAATA
Statistics
Matches: 114, Mismatches: 18, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
34 50 0.44
35 64 0.56
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (34 bp):
TGAACAGGAGAGATTCCCTGCAAAAAATAATGCG
Found at i:29401792 original size:69 final size:69
Alignment explanation
Indices: 29401700--29401874 Score: 269
Period size: 69 Copynumber: 2.5 Consensus size: 69
29401690 GTCCAAAAAG
* * * *
29401700 AAATGATACATGAACAAGAGAGATTTCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCTGC
1 AAATAATACGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCTGC
29401765 AACA
66 AACA
* *
29401769 AAATAATACGTGAACAGGAGAGATTCCCTGCAATAAATGATGTGTGAACAGGAGAGATTTCCTGC
1 AAATAATACGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCTGC
29401834 AACA
66 AACA
* * *
29401838 AAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAA
1 AAATAATACGTGAACAGGAGAGATTCCCTGCAAGAAA
29401875 ATACAAGTGA
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 96 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (69 bp):
AAATAATACGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGTGAACAGGAGAGATTCCCTGC
AACA
Found at i:29402140 original size:13 final size:14
Alignment explanation
Indices: 29402122--29402156 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
29402112 AGTTTCCAAA
29402122 TTTTCAAAC-TAAG
1 TTTTCAAACTTAAG
29402135 TTTTCAAACTTAAG
1 TTTTCAAACTTAAG
29402149 TTTTCAAA
1 TTTTCAAA
29402157 TTACAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (14 bp):
TTTTCAAACTTAAG
Found at i:29402822 original size:5 final size:5
Alignment explanation
Indices: 29402812--29402838 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
29402802 GCTTTAATGT
29402812 TTTAA TTTAA TTTAA TTTAA TTTAA TT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TT
29402839 CATCAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTTAA
Found at i:29404613 original size:12 final size:12
Alignment explanation
Indices: 29404580--29404624 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
29404570 AAATGGAAAT
* *
29404580 ATAATGATAATA
1 ATAATAATACTA
*
29404592 ACAATAATACTA
1 ATAATAATACTA
*
29404604 ATAGTAATACTA
1 ATAATAATACTA
29404616 ATAATAATA
1 ATAATAATA
29404625 TATTAGTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (12 bp):
ATAATAATACTA
Found at i:29405327 original size:14 final size:14
Alignment explanation
Indices: 29405308--29405337 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29405298 TTCAGGTACC
*
29405308 TTCTCTTTTCTTTT
1 TTCTCTATTCTTTT
29405322 TTCTCTATTCTTTT
1 TTCTCTATTCTTTT
29405336 TT
1 TT
29405338 TGTTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (14 bp):
TTCTCTATTCTTTT
Found at i:29406519 original size:5 final size:5
Alignment explanation
Indices: 29406509--29406533 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29406499 AATTATATAG
29406509 ATTAA ATTAA ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA
29406534 GAGAAACACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTAA
Found at i:29406844 original size:13 final size:13
Alignment explanation
Indices: 29406826--29406855 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29406816 ACTAAGTTTA
29406826 AATTTTAGTACTC
1 AATTTTAGTACTC
*
29406839 AATTTTATTACTC
1 AATTTTAGTACTC
29406852 AATT
1 AATT
29406856 AGAATCCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.03, T:0.50
Consensus pattern (13 bp):
AATTTTAGTACTC
Found at i:29409374 original size:29 final size:30
Alignment explanation
Indices: 29409342--29409430 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 30
29409332 TTGATTTAAT
*
29409342 GTGCAATTGTATACATG-AACTTTAATTTG
1 GTGCAATTATATACATGAAACTTTAATTTG
* * *
29409371 GTGCAATTATACACGTGAAACTCTAATTGTG
1 GTGCAATTATATACATGAAACTTTAATT-TG
* * * *
29409402 GTTCAAATCTATACTTGAAACTTTAATTT
1 GTGCAATTATATACATGAAACTTTAATTT
29409431 TGATTTAATC
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 14 0.29
30 10 0.21
31 24 0.50
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (30 bp):
GTGCAATTATATACATGAAACTTTAATTTG
Found at i:29410921 original size:43 final size:43
Alignment explanation
Indices: 29410873--29411167 Score: 376
Period size: 43 Copynumber: 6.9 Consensus size: 43
29410863 TTATGTGGAA
* * * * * *
29410873 AAACACCGCTATAGAACATGACATTTACCAGTGCTCTT-CCCAT
1 AAACACCGCTAAAGAACATGACCTTTAGCGGCGCT-TTCCCCAC
29410916 AAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
1 AAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
* * *
29410959 AAACGCCGCTATAGAATATGACCTTTAGCGGCGCTTTCCCCAC
1 AAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
29411002 AAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
1 AAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
* * * * * * * *
29411045 AAACGCTGCTATAGAATATGACGTTTAGCTGCACTTTTCCCAC
1 AAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
* *
29411088 AAACACTGCTAAAGAACATGACCTTTAGCAGCGCTTTCCCCAC
1 AAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
** *
29411131 AAATGCCGCTAAATAACATGACCTTTAGCGGCGCTTT
1 AAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTT
29411168 TAATAAAAGT
Statistics
Matches: 219, Mismatches: 32, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
42 2 0.01
43 217 0.99
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (43 bp):
AAACACCGCTAAAGAACATGACCTTTAGCGGCGCTTTCCCCAC
Found at i:29411168 original size:86 final size:86
Alignment explanation
Indices: 29410873--29411168 Score: 421
Period size: 86 Copynumber: 3.4 Consensus size: 86
29410863 TTATGTGGAA
* * * * * * * *
29410873 AAACACCGCTATAGAACATGACATTTACCAGTGCTCTTCCCATAAACACCGCTAAAGAACATGAC
1 AAACGCCGCTATAGAATATGACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGAACATGAC
29410938 CTTTAGCGGCGCTTTCCCCAC
66 CTTTAGCGGCGCTTTCCCCAC
*
29410959 AAACGCCGCTATAGAATATGACCTTTAGCGGCGCTTTCCCCACAAACACCGCTAAAGAACATGAC
1 AAACGCCGCTATAGAATATGACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGAACATGAC
29411024 CTTTAGCGGCGCTTTCCCCAC
66 CTTTAGCGGCGCTTTCCCCAC
* * * * *
29411045 AAACGCTGCTATAGAATATGACGTTTAGCTGCACTTTTCCCACAAACACTGCTAAAGAACATGAC
1 AAACGCCGCTATAGAATATGACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGAACATGAC
*
29411110 CTTTAGCAGCGCTTTCCCCAC
66 CTTTAGCGGCGCTTTCCCCAC
* * * *
29411131 AAATGCCGCTAAATAACATGACCTTTAGCGGCGCTTTT
1 AAACGCCGCTATAGAATATGACCTTTAGCGGCGCTTTT
29411169 AATAAAAGTA
Statistics
Matches: 186, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 186 1.00
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.24
Consensus pattern (86 bp):
AAACGCCGCTATAGAATATGACCTTTAGCGGCGCTTTTCCCACAAACACCGCTAAAGAACATGAC
CTTTAGCGGCGCTTTCCCCAC
Found at i:29418840 original size:2 final size:2
Alignment explanation
Indices: 29418835--29418874 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
29418825 GGAGGAGGAA
* * *
29418835 AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29418875 GAATATTCAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29418875 original size:8 final size:8
Alignment explanation
Indices: 29418836--29418880 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
29418826 GAGGAGGAAA
*
29418836 TATATATA
1 TATATATG
*
29418844 TATATATA
1 TATATATG
29418852 TATATATG
1 TATATATG
*
29418860 TATGTATG
1 TATATATG
29418868 TATATATG
1 TATATATG
*
29418876 AATAT
1 TATAT
29418881 TCAGTTAGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (8 bp):
TATATATG
Found at i:29422812 original size:9 final size:9
Alignment explanation
Indices: 29422798--29422845 Score: 51
Period size: 9 Copynumber: 4.9 Consensus size: 9
29422788 TAAGTATAAT
29422798 TAAGTTATG
1 TAAGTTATG
29422807 TAAGTTATG
1 TAAGTTATG
*
29422816 ATATATATTTATG
1 ---TA-AGTTATG
29422829 TAAGTTATG
1 TAAGTTATG
29422838 TAAGTTAT
1 TAAGTTAT
29422846 AAAATTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 23 0.70
10 2 0.06
12 2 0.06
13 6 0.18
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (9 bp):
TAAGTTATG
Found at i:29423552 original size:29 final size:30
Alignment explanation
Indices: 29423493--29423564 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
29423483 GATTTGGATT
*
29423493 TAAATTTTTAAAATAATATAATTTGAGTAA
1 TAAATTTTTAAAATAATATAATTTCAGTAA
29423523 TAAATTATTT-AAA-AATATAATATTCA-TAA
1 TAAATT-TTTAAAATAATATAAT-TTCAGTAA
*
29423552 T-TATTTTTAAAAT
1 TAAATTTTTAAAAT
29423565 TTATGAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
27 3 0.08
28 6 0.17
29 12 0.33
30 12 0.33
31 3 0.08
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (30 bp):
TAAATTTTTAAAATAATATAATTTCAGTAA
Found at i:29429392 original size:110 final size:111
Alignment explanation
Indices: 29429192--29429419 Score: 300
Period size: 110 Copynumber: 2.0 Consensus size: 111
29429182 CAAATTATAC
* **
29429192 AATTACAAGTCATGCACATCATCTAAGATAGGTAATGTATCCAAGAATGGTTCAAAATATAATAT
1 AATTACAAGTCATGCACATCATCTAAGATAGGTAACGTA--CAAGAAAAGTTCAAAATATAATAT
*
29429257 TATCAAAGAAAGTTCAAAGAGGAAGTA-TCCAAAGTCCTAACAAAACCT
64 TACCAAAGAAAGTTCAAAGAGGAAGTACT-CAAAGTCCTAACAAAACCT
** *
29429305 AATTACAAGTCATGCGTATCATTTAAGATTA-GTAACGTA-AAGAAAAGTTCAAAATATAATATT
1 AATTACAAGTCATGCACATCATCTAAGA-TAGGTAACGTACAAGAAAAGTTCAAAATATAATATT
** * *
29429368 ACCATGGAAAGTTCAAAGATGAAGTACTCAAAGTTCTAACAAAACCT
65 ACCAAAGAAAGTTCAAAGAGGAAGTACTCAAAGTCCTAACAAAACCT
29429415 AATTA
1 AATTA
29429420 TACAAAGCCC
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
110 67 0.66
111 1 0.01
113 32 0.31
114 2 0.02
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (111 bp):
AATTACAAGTCATGCACATCATCTAAGATAGGTAACGTACAAGAAAAGTTCAAAATATAATATTA
CCAAAGAAAGTTCAAAGAGGAAGTACTCAAAGTCCTAACAAAACCT
Found at i:29446599 original size:17 final size:16
Alignment explanation
Indices: 29446521--29446611 Score: 53
Period size: 17 Copynumber: 5.4 Consensus size: 16
29446511 AAATAATGAG
29446521 TATTTTATATAATTAAT
1 TATTTTATAT-ATTAAT
*
29446538 TAATATTTTTATATTTAAAAT
1 T-AT-TTTATATA-TT--AAT
*
29446559 TA-TTTA-AT-CTAAT
1 TATTTTATATATTAAT
*
29446572 TCATTTAATATATTCAAT
1 T-ATTTTATATATT-AAT
*
29446590 TATTTTATATATTAAA
1 TATTTTATATATTAAT
29446606 TATTTT
1 TATTTT
29446612 TAAAAAAACA
Statistics
Matches: 57, Mismatches: 7, Indels: 21
0.67 0.08 0.25
Matches are distributed among these distances:
13 4 0.07
14 1 0.02
15 4 0.07
16 10 0.18
17 15 0.26
18 10 0.18
19 8 0.14
20 1 0.02
21 4 0.07
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTTATATATTAAT
Found at i:29457690 original size:21 final size:18
Alignment explanation
Indices: 29457649--29457691 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 18
29457639 AATAAATTTT
*
29457649 TTTTATTATTTTAAATTA
1 TTTTATTATTTTAAATAA
29457667 TTTTATTAATTTTTACAATAA
1 TTTTATT-A-TTTTA-AATAA
29457688 TTTT
1 TTTT
29457692 GTAATTACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
20 5 0.24
21 8 0.38
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTATTATTTTAAATAA
Found at i:29458011 original size:13 final size:15
Alignment explanation
Indices: 29457993--29458026 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
29457983 TAAATAATAA
29457993 ATTTAATTCT-TTT-
1 ATTTAATTCTATTTC
29458006 ATTTAATTCTATTTC
1 ATTTAATTCTATTTC
29458021 ATTTAA
1 ATTTAA
29458027 GATTATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 3 0.16
15 6 0.32
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTAATTCTATTTC
Done.