Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 18 of 120
Found at i:5522412 original size:18 final size:16
Alignment explanation
Indices: 5522380--5522413 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
5522370 CAAAATATCT
5522380 AAAAATTTTAAATTTA
1 AAAAATTTTAAATTTA
5522396 AAAAATTATTAAAATTTA
1 AAAAATT-TT-AAATTTA
5522414 CTTTAGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAAATTTTAAATTTA
Found at i:5522620 original size:5 final size:5
Alignment explanation
Indices: 5522610--5522640 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
5522600 TTAATTTAGA
5522610 TATAT TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT T
5522641 TTTTTATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:5523145 original size:17 final size:17
Alignment explanation
Indices: 5523123--5523156 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5523113 TTAGATCTAT
5523123 TCTATCGAGTTATTTGA
1 TCTATCGAGTTATTTGA
5523140 TCTATCGAGTTATTTGA
1 TCTATCGAGTTATTTGA
5523157 AGATGCACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (17 bp):
TCTATCGAGTTATTTGA
Found at i:5523285 original size:19 final size:19
Alignment explanation
Indices: 5523261--5523300 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5523251 TTTTTATTTT
*
5523261 ATTAGAACT-GAAAAGTTTA
1 ATTAGAA-TGGAAAAGTATA
5523280 ATTAGAATGGAAAAGTATA
1 ATTAGAATGGAAAAGTATA
5523299 AT
1 AT
5523301 AAAAGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.30
Consensus pattern (19 bp):
ATTAGAATGGAAAAGTATA
Found at i:5524320 original size:15 final size:15
Alignment explanation
Indices: 5524296--5524329 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5524286 GATCTTTTTG
*
5524296 ACATTTTAATTCCAT
1 ACATTATAATTCCAT
5524311 ACATTATAATTCCAT
1 ACATTATAATTCCAT
5524326 ACAT
1 ACAT
5524330 AGACATAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (15 bp):
ACATTATAATTCCAT
Found at i:5528146 original size:16 final size:16
Alignment explanation
Indices: 5528121--5528154 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5528111 TGGCATAATG
5528121 ATTACCCATAATGCGC
1 ATTACCCATAATGCGC
* *
5528137 ATTACTCATAATGTGC
1 ATTACCCATAATGCGC
5528153 AT
1 AT
5528155 CCAAATATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (16 bp):
ATTACCCATAATGCGC
Found at i:5528287 original size:188 final size:188
Alignment explanation
Indices: 5527964--5528322 Score: 693
Period size: 188 Copynumber: 1.9 Consensus size: 188
5527954 AAATTTTAAT
5527964 CATCCAAATATCATACATATTATAATTTAATAAAAGAATCTTAGTTTAAAAGAAACCTTAAAGTA
1 CATCCAAATATCATACATATTATAATTTAATAAAAGAATCTTAGTTTAAAAGAAACCTTAAAGTA
5528029 ATAATATTTTGCATAAAATAATTTTACCAAAAATCAATCAACAAAGGAGAAAAACATGTCACGCA
66 ATAATATTTTGCATAAAATAATTTTACCAAAAATCAATCAACAAAGGAGAAAAACATGTCACGCA
5528094 AGGATTATAT-ATTTTTTTGGCATAATGATTACCCATAATGCGCATTACTCATAATGTG
131 AGGATTATATAATTTTTTT-GCATAATGATTACCCATAATGCGCATTACTCATAATGTG
5528152 CATCCAAATATCATACATATTATAATTTAATAAAAGAATCTTAGTTTAAAAGAAACCTTAAAGTA
1 CATCCAAATATCATACATATTATAATTTAATAAAAGAATCTTAGTTTAAAAGAAACCTTAAAGTA
*
5528217 ATAATATTTTGCATAAAATAATTTTACCAAAAATCAATCAACAAAGGAGAAAAACATGTCACGTA
66 ATAATATTTTGCATAAAATAATTTTACCAAAAATCAATCAACAAAGGAGAAAAACATGTCACGCA
5528282 AGGATTATATAATTTTTTTGCATAATGATTACCCATAATGC
131 AGGATTATATAATTTTTTTGCATAATGATTACCCATAATGC
5528323 ACGTGTCTCA
Statistics
Matches: 169, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
188 161 0.95
189 8 0.05
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.32
Consensus pattern (188 bp):
CATCCAAATATCATACATATTATAATTTAATAAAAGAATCTTAGTTTAAAAGAAACCTTAAAGTA
ATAATATTTTGCATAAAATAATTTTACCAAAAATCAATCAACAAAGGAGAAAAACATGTCACGCA
AGGATTATATAATTTTTTTGCATAATGATTACCCATAATGCGCATTACTCATAATGTG
Found at i:5529845 original size:61 final size:61
Alignment explanation
Indices: 5529780--5529907 Score: 134
Period size: 61 Copynumber: 2.1 Consensus size: 61
5529770 TGGTGGTTTT
*
5529780 TTTTTAATTTAAAAATTGAA-AAAAAAATCATTTTGTAAAGATTGAGTACTAAATTTATTG-A
1 TTTTT-ATTTAAAAATTGAACAAAAAAAT-ATTTTGTAAACATTGAGTACTAAATTTATTGAA
* * * ** ** *
5529841 TTTTTTTTTAGAATTTGAACTAAAATGATATTTTGTAAACATTGAGTGTTAAATTTGTTGAA
1 TTTTTATTTAAAAATTGAAC-AAAAAAATATTTTGTAAACATTGAGTACTAAATTTATTGAA
5529903 TTTTT
1 TTTTT
5529908 TATATTTAGG
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
60 11 0.20
61 32 0.58
62 12 0.22
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (61 bp):
TTTTTATTTAAAAATTGAACAAAAAAATATTTTGTAAACATTGAGTACTAAATTTATTGAA
Found at i:5538596 original size:12 final size:11
Alignment explanation
Indices: 5538579--5538620 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
5538569 AGTATTAAAT
5538579 TTATAAAATGTA
1 TTATAAAAT-TA
*
5538591 TTATAAAAATA
1 TTATAAAATTA
*
5538602 -TATATAATTA
1 TTATAAAATTA
5538612 TTATAAAAT
1 TTATAAAAT
5538621 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 8 0.32
11 9 0.36
12 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
TTATAAAATTA
Found at i:5538615 original size:21 final size:22
Alignment explanation
Indices: 5538575--5538619 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
5538565 TAAAAGTATT
*
5538575 AAATTTATAAAATGTATTATAA
1 AAATATATAAAATGTATTATAA
*
5538597 AAATATATATAAT-TATTATAA
1 AAATATATAAAATGTATTATAA
5538618 AA
1 AA
5538620 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATATATAAAATGTATTATAA
Found at i:5538790 original size:21 final size:21
Alignment explanation
Indices: 5538751--5538803 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
5538741 ATTAATTAAT
5538751 TTTTTATAATAATTATTTATAA
1 TTTTTATAATAATTATTTAT-A
5538773 TTTTTATAATACA-T-TTTATA
1 TTTTTATAATA-ATTATTTATA
5538793 TTTTTAGTAAT
1 TTTTTA-TAAT
5538804 TTTAATTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.24
21 9 0.31
22 12 0.41
23 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTTTATAATAATTATTTATA
Found at i:5551522 original size:21 final size:21
Alignment explanation
Indices: 5551475--5551528 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
5551465 ACCATTGTTT
** *
5551475 CTAATCTCATTGCTACAGTAT
1 CTAATCTCACCGCTACAGTAA
*
5551496 CCAATCTCACCGCTACAGTAA
1 CTAATCTCACCGCTACAGTAA
*
5551517 CTAATCTTACCG
1 CTAATCTCACCG
5551529 TCACCGTTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (21 bp):
CTAATCTCACCGCTACAGTAA
Found at i:5555052 original size:104 final size:104
Alignment explanation
Indices: 5554858--5555332 Score: 785
Period size: 104 Copynumber: 4.6 Consensus size: 104
5554848 TGTATATAAA
** * *
5554858 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCGTATCT
**
5554922 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
5554962 AGGGGTTGCTAAGTGTTGATTCCCCGATTTCATTGATGGTGCTAAGTGCGATATCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
5555027 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
5555066 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
5555131 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
5555170 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGATGCTAAGTGCAATATCCACCGTATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
5555235 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
5555274 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGGGATCCACCG
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCG
5555333 ATAACGGTTA
Statistics
Matches: 352, Mismatches: 16, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
103 43 0.12
104 268 0.76
105 40 0.11
106 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCTT
TGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:5558132 original size:16 final size:16
Alignment explanation
Indices: 5558111--5558142 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5558101 ATAGGACTTA
5558111 AATCATTTGTCGTATT
1 AATCATTTGTCGTATT
*
5558127 AATCATTTGTTGTATT
1 AATCATTTGTCGTATT
5558143 GAAATTAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.53
Consensus pattern (16 bp):
AATCATTTGTCGTATT
Found at i:5577340 original size:15 final size:15
Alignment explanation
Indices: 5577322--5577367 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
5577312 GTAGGAGGCT
5577322 GAGCAATTGGTGGAG
1 GAGCAATTGGTGGAG
* * *
5577337 GAGCCATAGGTGGCG
1 GAGCAATTGGTGGAG
*
5577352 GAGCAAGTGGTGGAG
1 GAGCAATTGGTGGAG
5577367 G
1 G
5577368 GGGTGAGGGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.24, C:0.11, G:0.50, T:0.15
Consensus pattern (15 bp):
GAGCAATTGGTGGAG
Found at i:5581022 original size:10 final size:10
Alignment explanation
Indices: 5581003--5581031 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
5580993 TGCCAAAATC
5581003 TAAA-TAAAA
1 TAAATTAAAA
5581012 TAAATTAAAA
1 TAAATTAAAA
5581022 TAAATTAAAA
1 TAAATTAAAA
5581032 ACATAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAATTAAAA
Found at i:5585557 original size:24 final size:24
Alignment explanation
Indices: 5585530--5585581 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
5585520 AATCAAAGTC
* *
5585530 AAATATATTAT-GTTAATAAATGCT
1 AAATATATTATACTT-ATAAATACT
5585554 AAATATATTATACTTATAAATACT
1 AAATATATTATACTTATAAATACT
5585578 AAAT
1 AAAT
5585582 CTTTTAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTTATAAATACT
Found at i:5592700 original size:7 final size:7
Alignment explanation
Indices: 5592688--5592735 Score: 51
Period size: 7 Copynumber: 6.3 Consensus size: 7
5592678 ATAGAAATTT
5592688 TAAAATA
1 TAAAATA
5592695 TAAAATA
1 TAAAATA
5592702 TAAAATAA
1 TAAAAT-A
5592710 TTAAAACTGA
1 -TAAAA-T-A
5592720 TAAAATA
1 TAAAATA
*
5592727 TAGAATA
1 TAAAATA
5592734 TA
1 TA
5592736 TAGACTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
7 22 0.61
8 2 0.06
9 10 0.28
10 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (7 bp):
TAAAATA
Found at i:5592722 original size:25 final size:23
Alignment explanation
Indices: 5592687--5592733 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
5592677 GATAGAAATT
5592687 TTAAAATATAAAATATAAAATAA
1 TTAAAATATAAAATATAAAATAA
*
5592710 TTAAAACTGATAAAATATAGAATA
1 TTAAAA-T-ATAAAATATAAAATA
5592734 TATAGACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 1 0.05
25 14 0.67
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (23 bp):
TTAAAATATAAAATATAAAATAA
Found at i:5595569 original size:15 final size:16
Alignment explanation
Indices: 5595546--5595587 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
5595536 ATTTTAATTC
5595546 TTTTT-AAATT-TATT
1 TTTTTAAAATTATATT
5595560 TTTTTAAAATTCATATT
1 TTTTTAAAATT-ATATT
5595577 TTTTTATAAAT
1 TTTTTA-AAAT
5595588 ACTTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.21
15 5 0.21
17 10 0.42
18 4 0.17
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTAAAATTATATT
Found at i:5599596 original size:22 final size:21
Alignment explanation
Indices: 5599554--5599603 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
5599544 TTTTTATTAA
* *
5599554 ATATATATGAAAATTAAAAAT
1 ATATATATAAAAATCAAAAAT
*
5599575 ATATATATAAAAAATCAGAAAT
1 ATATATAT-AAAAATCAAAAAT
5599597 ATATATA
1 ATATATA
5599604 AATTAAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (21 bp):
ATATATATAAAAATCAAAAAT
Found at i:5599612 original size:18 final size:19
Alignment explanation
Indices: 5599552--5599623 Score: 65
Period size: 21 Copynumber: 3.7 Consensus size: 19
5599542 TATTTTTATT
*
5599552 AAATATATATGAAAATTAAA
1 AAATATATAT-AAAATTAAG
* *
5599572 AATATATATATAAAAAATCAG
1 AA-ATATATAT-AAAATTAAG
5599593 AAATATATAT-AAATTAAG
1 AAATATATATAAAATTAAG
* *
5599611 AAAAAAATATAAA
1 AAATATATATAAA
5599624 TTATAAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
18 14 0.33
19 2 0.05
20 10 0.24
21 16 0.38
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (19 bp):
AAATATATATAAAATTAAG
Found at i:5599624 original size:18 final size:17
Alignment explanation
Indices: 5599599--5599635 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
5599589 TCAGAAATAT
5599599 ATATAAATTAAGAAAAAA
1 ATATAAATT-AGAAAAAA
*
5599617 ATATAAATTATAAAAAA
1 ATATAAATTAGAAAAAA
5599634 AT
1 AT
5599636 TTACAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
ATATAAATTAGAAAAAA
Found at i:5600357 original size:17 final size:17
Alignment explanation
Indices: 5600327--5600379 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
5600317 ATAATTTTTG
*
5600327 AAAATTCAATAATATATA
1 AAAATT-AAAAATATATA
5600345 AAAATTAAAAATATTATA
1 AAAATTAAAAATA-TATA
*
5600363 AAAATTAAAAAAATATA
1 AAAATTAAAAATATATA
5600380 TTTAAATTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 10 0.31
18 22 0.69
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAATTAAAAATATATA
Found at i:5605330 original size:24 final size:24
Alignment explanation
Indices: 5605302--5605353 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5605292 TTCGTAGATA
* *
5605302 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
5605326 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
5605350 AAAT
1 AAAT
5605354 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:5607144 original size:13 final size:13
Alignment explanation
Indices: 5607119--5607152 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5607109 AGTGAAGAGT
5607119 ACAAAAGTGTAAAC
1 ACAAAA-TGTAAAC
5607133 ACAAAATGTAAAC
1 ACAAAATGTAAAC
*
5607146 ATAAAAT
1 ACAAAAT
5607153 TCTCTAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.62, C:0.12, G:0.09, T:0.18
Consensus pattern (13 bp):
ACAAAATGTAAAC
Found at i:5607269 original size:24 final size:24
Alignment explanation
Indices: 5607242--5607293 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
5607232 TTCGTAGGTC
5607242 AAATAAATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
*
5607266 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
5607290 AAAT
1 AAAT
5607294 CTTCTAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:5608801 original size:275 final size:275
Alignment explanation
Indices: 5608310--5608848 Score: 997
Period size: 275 Copynumber: 2.0 Consensus size: 275
5608300 ATACACTTTT
*
5608310 AAAATACCATTTCACCACTGGTGTGATTAAATATAAAGGAGACCCAAGGCTTCCTTTGGATACCA
1 AAAATACCATTTCACCACTGGTGTGATTAAATATAAAGGAGACCCAAGGCTTCCTTTAGATACCA
* *
5608375 CTAAATCTGTGCATCACAACTTTCAAGATAGGAATAATTACACCCGAACCATTGTATGGTGTTGG
66 CTAAATATGTGCATCACAACTTTCAAGATAGGAATAATTACACCCGAACCATTGTATGGTGTTGA
*
5608440 ATAACATCCGTGAGATGAGATTTAAATAAATTGTCATGAGTCTAAATGAAATTAGGGATTTTGAG
131 ATAACATCCGTGAGATGAGATTTAAACAAATTGTCATGAGTCTAAATGAAATTAGGGATTTTGAG
*
5608505 AAAAAAGAACCCTAATTTTGGAAATTAAGGAAATGATGAGGAATAGATTGAGGGAAGGAAAGGTC
196 AAAAAAGAACCCTAATTTTGGAAATTAAGGAAATGATGAGGAATAGATTAAGGGAAGGAAAGGTC
5608570 GAGAGTTAATGGGAC
261 GAGAGTTAATGGGAC
*
5608585 AAAATACCATTTCACCACTGGTGTGATTGAATATAAAGGAGACCCAAGGCTTCCTTTAGATACCA
1 AAAATACCATTTCACCACTGGTGTGATTAAATATAAAGGAGACCCAAGGCTTCCTTTAGATACCA
*
5608650 TTAAATATGTGCATCACAACTTTCAAGATAGGAATAATTACACCCGAACCATTGTATGGTGTTGA
66 CTAAATATGTGCATCACAACTTTCAAGATAGGAATAATTACACCCGAACCATTGTATGGTGTTGA
*
5608715 ATAACATCCGTGAGATGAGATTTAAACAAATTGTCATGAGTCTGAATGAAATTAGGGATTTTGAG
131 ATAACATCCGTGAGATGAGATTTAAACAAATTGTCATGAGTCTAAATGAAATTAGGGATTTTGAG
*
5608780 AAAAAAGAACCCTAATTTTGGAAATTAAGGAAATGATGAGGAATAGATTAAGGTAAGGAAAGGTC
196 AAAAAAGAACCCTAATTTTGGAAATTAAGGAAATGATGAGGAATAGATTAAGGGAAGGAAAGGTC
5608845 GAGA
261 GAGA
5608849 ATGGGCCAAG
Statistics
Matches: 255, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
275 255 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (275 bp):
AAAATACCATTTCACCACTGGTGTGATTAAATATAAAGGAGACCCAAGGCTTCCTTTAGATACCA
CTAAATATGTGCATCACAACTTTCAAGATAGGAATAATTACACCCGAACCATTGTATGGTGTTGA
ATAACATCCGTGAGATGAGATTTAAACAAATTGTCATGAGTCTAAATGAAATTAGGGATTTTGAG
AAAAAAGAACCCTAATTTTGGAAATTAAGGAAATGATGAGGAATAGATTAAGGGAAGGAAAGGTC
GAGAGTTAATGGGAC
Found at i:5612311 original size:34 final size:35
Alignment explanation
Indices: 5612267--5612333 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
5612257 CAGTAAAATA
* *
5612267 TTTTCCGTAAAATGGTTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
5612301 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
5612334 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:5613692 original size:27 final size:27
Alignment explanation
Indices: 5613661--5613713 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
5613651 TTGATCCTTG
5613661 GGGACAAGGATTGAATCAAGAAGGGGT
1 GGGACAAGGATTGAATCAAGAAGGGGT
5613688 GGGACAAGGATTGAATCAAGAAGGGG
1 GGGACAAGGATTGAATCAAGAAGGGG
5613714 GTATTGTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.42, T:0.13
Consensus pattern (27 bp):
GGGACAAGGATTGAATCAAGAAGGGGT
Found at i:5616989 original size:16 final size:16
Alignment explanation
Indices: 5616969--5617021 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
5616959 AAAAATTATG
*
5616969 TTTTCCATCCTTCTAG
1 TTTTCCATCCTTCTAA
* *
5616985 TTTTCTACCCCTTC-AA
1 TTTTCCA-TCCTTCTAA
*
5617001 TTTTCCATCCTCCTAA
1 TTTTCCATCCTTCTAA
5617017 TTTTC
1 TTTTC
5617022 TTTCCACTCT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 4 0.14
16 20 0.69
17 5 0.17
ACGTcount: A:0.15, C:0.34, G:0.02, T:0.49
Consensus pattern (16 bp):
TTTTCCATCCTTCTAA
Found at i:5622750 original size:64 final size:64
Alignment explanation
Indices: 5622681--5622810 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
5622671 GATTAGTAGC
5622681 AATACTTCATCTCTCCAGAAGTCAAATAAACAGTAAAGATTCATCAAAGAATTGTTTGAAAACT
1 AATACTTCATCTCTCCAGAAGTCAAATAAACAGTAAAGATTCATCAAAGAATTGTTTGAAAACT
5622745 AATACTTCATCTCTCCAGAAGTCAAATAAACAGTAAAGATTCATCAAAGAATTGTTTGAAAACT
1 AATACTTCATCTCTCCAGAAGTCAAATAAACAGTAAAGATTCATCAAAGAATTGTTTGAAAACT
5622809 AA
1 AA
5622811 AAAAACCCTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.28
Consensus pattern (64 bp):
AATACTTCATCTCTCCAGAAGTCAAATAAACAGTAAAGATTCATCAAAGAATTGTTTGAAAACT
Found at i:5625842 original size:2 final size:2
Alignment explanation
Indices: 5625835--5625866 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5625825 AGCAAAACTA
5625835 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
5625867 TGGCATGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5638604 original size:34 final size:35
Alignment explanation
Indices: 5638560--5638626 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
5638550 CAGTAAAATA
* *
5638560 TTTTCCGTAAAATGGTTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
5638594 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
5638627 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:5639183 original size:8 final size:8
Alignment explanation
Indices: 5639170--5639213 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
5639160 AATTGAGAGA
5639170 AGAGAGGG
1 AGAGAGGG
5639178 AGAGA-GG
1 AGAGAGGG
5639185 -GAGAGGG
1 AGAGAGGG
*
5639192 AGGGAGGG
1 AGAGAGGG
*
5639200 AGGGAGGG
1 AGAGAGGG
5639208 AGAGAG
1 AGAGAG
5639214 AGGGAATGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 4 0.12
7 4 0.12
8 24 0.75
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (8 bp):
AGAGAGGG
Found at i:5639196 original size:4 final size:4
Alignment explanation
Indices: 5639173--5639209 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
5639163 TGAGAGAAGA
*
5639173 GAGG GAGA GAGG GA-- GAGG GAGG GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAG
5639210 AGAGAGGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.07
4 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:5639199 original size:22 final size:22
Alignment explanation
Indices: 5639164--5639218 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
5639154 GTGTTAAATT
*
5639164 GAGAGA-AGAGAGGGAGAGAGG
1 GAGAGAGAGGGAGGGAGAGAGG
* *
5639185 GAGAGGGAGGGAGGGAGGGAGG
1 GAGAGAGAGGGAGGGAGAGAGG
5639207 GAGAGAGAGGGA
1 GAGAGAGAGGGA
5639219 ATGCAAGCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 5 0.17
22 24 0.83
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (22 bp):
GAGAGAGAGGGAGGGAGAGAGG
Found at i:5648650 original size:20 final size:20
Alignment explanation
Indices: 5648606--5648655 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
5648596 AGAGCCATTA
5648606 ATATCGATACCAAGAGAAAT
1 ATATCGATACCAAGAGAAAT
* *
5648626 TTATCGATACCAA-ATAGAAT
1 ATATCGATACCAAGAGA-AAT
5648646 ATATCGATAC
1 ATATCGATAC
5648656 TTGATAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (20 bp):
ATATCGATACCAAGAGAAAT
Found at i:5658946 original size:18 final size:18
Alignment explanation
Indices: 5658923--5658958 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5658913 CAACACCTCT
5658923 ACCTCTGCCACGATAACC
1 ACCTCTGCCACGATAACC
*
5658941 ACCTCTGCCATGATAACC
1 ACCTCTGCCACGATAACC
5658959 TCTTCTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.42, G:0.11, T:0.19
Consensus pattern (18 bp):
ACCTCTGCCACGATAACC
Found at i:5660550 original size:15 final size:15
Alignment explanation
Indices: 5660505--5660551 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
5660495 TCCTAAAATG
5660505 ATAAAATTTTAATTT
1 ATAAAATTTTAATTT
**
5660520 A-AGTCATTTATAATTT
1 ATA-AAATTT-TAATTT
5660536 ATAAAATTTTAATTT
1 ATAAAATTTTAATTT
5660551 A
1 A
5660552 GAAATAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 1 0.04
15 12 0.48
16 11 0.44
17 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (15 bp):
ATAAAATTTTAATTT
Found at i:5661573 original size:14 final size:13
Alignment explanation
Indices: 5661532--5661587 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 13
5661522 AGTAATTTAA
*
5661532 ATTTTTTTCTTTT
1 ATTTTTTTCCTTT
*
5661545 ATGTTTTTTAACTTT
1 AT-TTTTTT-CCTTT
5661560 ACTTTTTTTCCTTT
1 A-TTTTTTTCCTTT
*
5661574 -TTTTTTTCCATT
1 ATTTTTTTCCTTT
5661586 AT
1 AT
5661588 CTTCTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 11 0.31
13 3 0.09
14 10 0.29
15 10 0.29
16 1 0.03
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.73
Consensus pattern (13 bp):
ATTTTTTTCCTTT
Found at i:5662945 original size:17 final size:18
Alignment explanation
Indices: 5662914--5662949 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5662904 AATTTAACTT
5662914 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
5662932 TAATT-AATTTTTTAAAA
1 TAATTAAATTATTTAAAA
5662949 T
1 T
5662950 TATAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:5663145 original size:14 final size:13
Alignment explanation
Indices: 5663132--5663174 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5663122 AACATAGAAC
5663132 CCTGAATCTTGAA
1 CCTGAATCTTGAA
* *
5663145 CTTGAACCTTGAA
1 CCTGAATCTTGAA
*
5663158 CCTTAATTCTTGAA
1 CCTGAA-TCTTGAA
5663172 CCT
1 CCT
5663175 TGAGGTTTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (13 bp):
CCTGAATCTTGAA
Found at i:5663155 original size:7 final size:7
Alignment explanation
Indices: 5663128--5663177 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
5663118 CTCAAACATA
*
5663128 GAACCCT
1 GAACCTT
*
5663135 GAATCTT
1 GAACCTT
5663142 GAA-CTT
1 GAACCTT
5663148 GAACCTT
1 GAACCTT
5663155 GAACCTT
1 GAACCTT
*
5663162 -AATTCTT
1 GAA-CCTT
5663169 GAACCTT
1 GAACCTT
5663176 GA
1 GA
5663178 GGTTTAGGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 8 0.22
7 26 0.72
8 2 0.06
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (7 bp):
GAACCTT
Found at i:5663687 original size:21 final size:21
Alignment explanation
Indices: 5663629--5663721 Score: 57
Period size: 21 Copynumber: 4.4 Consensus size: 21
5663619 CTATTATGAT
* *
5663629 ATAAATATTAAAATAATATTA
1 ATAAATATAAAAATAAAATTA
* * *
5663650 AGATGAT-TATAAAA-AAATTTA
1 ATA-AATATA-AAAATAAAATTA
5663671 ATAAATA-AAAAATAAAATTA
1 ATAAATATAAAAATAAAATTA
* * * *
5663691 CTAAATATTAAAATAATATAA
1 ATAAATATAAAAATAAAATTA
5663712 TATAAATATA
1 -ATAAATATA
5663722 TTTTTAAAAA
Statistics
Matches: 52, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
19 4 0.08
20 15 0.29
21 20 0.38
22 13 0.25
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAAATATAAAAATAAAATTA
Found at i:5663745 original size:32 final size:32
Alignment explanation
Indices: 5663709--5663772 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
5663699 TAAAATAATA
* *
5663709 TAATATAAATATATTTTTAAA-AAATTTAAATT
1 TAATATAAATAGA-TTTAAAATAAATTTAAATT
*
5663741 TAATATAGATAGATTTAAAATAAATTTAAATT
1 TAATATAAATAGATTTAAAATAAATTTAAATT
5663773 CAAACCTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 6 0.21
32 22 0.79
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (32 bp):
TAATATAAATAGATTTAAAATAAATTTAAATT
Found at i:5668474 original size:10 final size:10
Alignment explanation
Indices: 5668444--5668484 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
5668434 ATCACAAGTC
5668444 TTGTGATATA
1 TTGTGATATA
*
5668454 GTGTGATATA
1 TTGTGATATA
5668464 TTGTGATATA
1 TTGTGATATA
*
5668474 TATATGATATA
1 T-TGTGATATA
5668485 AGTAGAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (10 bp):
TTGTGATATA
Found at i:5673106 original size:51 final size:51
Alignment explanation
Indices: 5673030--5673133 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
5673020 TTTTTGGGAC
5673030 TTAACAATTGAAATTGAGTCTTATTTGGGAAAGGAAGAAAGAATTCTACTA
1 TTAACAATTGAAATTGAGTCTTATTTGGGAAAGGAAGAAAGAATTCTACTA
5673081 TTAACAATTGAAATTGAGTCTTATTTGGGAAAGGAAGAAAGAATTCTACTA
1 TTAACAATTGAAATTGAGTCTTATTTGGGAAAGGAAGAAAGAATTCTACTA
5673132 TT
1 TT
5673134 CTTTTGGAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (51 bp):
TTAACAATTGAAATTGAGTCTTATTTGGGAAAGGAAGAAAGAATTCTACTA
Found at i:5676268 original size:17 final size:17
Alignment explanation
Indices: 5676228--5676276 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
5676218 TTTAGATAGT
*
5676228 AAAAGAAAAAGAAGAGG
1 AAAAGAAAAAGAAGAAG
** *
5676245 AGGAGAAGAAGAAGAAG
1 AAAAGAAAAAGAAGAAG
*
5676262 AAAAGAAAAATAAGA
1 AAAAGAAAAAGAAGA
5676277 GAAGAAATAG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (17 bp):
AAAAGAAAAAGAAGAAG
Found at i:5677363 original size:21 final size:21
Alignment explanation
Indices: 5677339--5677409 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
5677329 TGTTGATGAG
*
5677339 TTGGGGCAGCTTTTTGCTGAA
1 TTGGGGCAGCTTATTGCTGAA
* * *
5677360 TTGGAGTAGCTTATTGCTGAG
1 TTGGGGCAGCTTATTGCTGAA
*
5677381 TTGGGGCAGCTTCTTGCTGAA
1 TTGGGGCAGCTTATTGCTGAA
*
5677402 TCGGGGCA
1 TTGGGGCA
5677410 ACCTTGATTA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.34
Consensus pattern (21 bp):
TTGGGGCAGCTTATTGCTGAA
Found at i:5679910 original size:26 final size:27
Alignment explanation
Indices: 5679875--5679989 Score: 90
Period size: 27 Copynumber: 4.3 Consensus size: 27
5679865 CAAAAGGGCA
* **
5679875 TTCTCTTCATAAATCGCC-CAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
* * * *
5679901 TTCTTTTCATAGATAGCTATAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
* *
5679928 GTCTTTTCA-AAGATAACCATAAAGGCT
1 TTCTTTTCATAA-ATAACCACAAAGGCT
* * *
5679955 TCCTTTTCATAGATCACCACAAAGGCT
1 TTCTTTTCATAAATAACCACAAAGGCT
*
5679982 TCCTTTTC
1 TTCTTTTC
5679990 TAGCGTGTTT
Statistics
Matches: 72, Mismatches: 14, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
26 15 0.21
27 56 0.78
28 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (27 bp):
TTCTTTTCATAAATAACCACAAAGGCT
Found at i:5679924 original size:27 final size:27
Alignment explanation
Indices: 5679894--5679989 Score: 120
Period size: 27 Copynumber: 3.6 Consensus size: 27
5679884 TAAATCGCCC
* *
5679894 AAAGGCTTTCTTTTCATAGATAGCTAT
1 AAAGGCTTTCTTTTCATAGATAACCAT
* *
5679921 AAAGGCTGTCTTTTCAAAGATAACCAT
1 AAAGGCTTTCTTTTCATAGATAACCAT
* * *
5679948 AAAGGCTTCCTTTTCATAGATCACCAC
1 AAAGGCTTTCTTTTCATAGATAACCAT
*
5679975 AAAGGCTTCCTTTTC
1 AAAGGCTTTCTTTTC
5679990 TAGCGTGTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (27 bp):
AAAGGCTTTCTTTTCATAGATAACCAT
Found at i:5682696 original size:25 final size:25
Alignment explanation
Indices: 5682667--5682754 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
5682657 TGTACAATAG
5682667 CCAAACAATAATCATGCACTTTAAT
1 CCAAACAATAATCATGCACTTTAAT
* * *
5682692 CCAAAACAGT-ATCATGTACATGGTAGACAAT
1 CC-AAACAATAATCATGCAC-T--T---TAAT
5682723 AACCAAACAATAATCATGCACTTTAAT
1 --CCAAACAATAATCATGCACTTTAAT
5682750 CCAAA
1 CCAAA
5682755 TCATATTTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 20
0.64 0.08 0.27
Matches are distributed among these distances:
25 15 0.32
26 7 0.15
27 3 0.06
28 1 0.02
30 1 0.02
31 3 0.06
32 7 0.15
33 10 0.21
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.24
Consensus pattern (25 bp):
CCAAACAATAATCATGCACTTTAAT
Found at i:5683585 original size:45 final size:45
Alignment explanation
Indices: 5683521--5683638 Score: 168
Period size: 45 Copynumber: 2.6 Consensus size: 45
5683511 GGAAGGAAGA
* *
5683521 ATTAGTGGCTTCGTCCACAACCTACAT-GACAGCTTGTCTATGAAT
1 ATTAGTGGCTTCATCCACAACCTACATAG-CAACTTGTCTATGAAT
* *
5683566 ATTAGTGGCTTCATCCACAACCTACATAGCAACTTGTTTGTGAAT
1 ATTAGTGGCTTCATCCACAACCTACATAGCAACTTGTCTATGAAT
*
5683611 ATTAGTGG-TTTATCCACAACCTACATAG
1 ATTAGTGGCTTCATCCACAACCTACATAG
5683639 TAGCTTATCT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
44 19 0.28
45 47 0.70
46 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (45 bp):
ATTAGTGGCTTCATCCACAACCTACATAGCAACTTGTCTATGAAT
Found at i:5698600 original size:139 final size:139
Alignment explanation
Indices: 5698339--5698611 Score: 354
Period size: 139 Copynumber: 2.0 Consensus size: 139
5698329 AAACTTAGGC
* * *
5698339 TTAATATATAGATTGGCTCCTAAACTTGGCAACTTTTCTCAAATTAGCTCCTAAACTTTTTTTTG
1 TTAATATACAGATTGGCCCCTAAACTTGGCAACTTTTCTCAAATTAGCCCCTAAACTTTTTTTTG
* * * * * *
5698404 GATCACATCTGTCCCTAAGGTTGGCATCCGTTACACAAATTGGTCCCTATAGTTAACACCGTTAG
66 GATCACATCGGTCCCTAAGGTTGGCATCCATTACACAAATTAGTCCCTACAGCTAACACAGTTAG
5698469 TTTTAAGGT
131 TTTTAAGGT
* *
5698478 TTAATATACAGATTGGCCCCTAAACTTGGCAGCTTTTCTCACATT-GTCCCCTAAACTCTTTTTT
1 TTAATATACAGATTGGCCCCTAAACTTGGCAACTTTTCTCAAATTAG-CCCCTAAACT-TTTTTT
* * * *
5698542 TGGGTCATAGT-GGTCCCTAAGGTTGGCATCCATTGCATAAATTAGTCCCTACA-CTAACACAGT
64 TGGATCACA-TCGGTCCCTAAGGTTGGCATCCATTACACAAATTAGTCCCTACAGCTAACACAGT
*
5698605 TTGTTTT
128 TAGTTTT
5698612 TGAAGATTTT
Statistics
Matches: 115, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
138 1 0.01
139 64 0.56
140 49 0.43
141 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (139 bp):
TTAATATACAGATTGGCCCCTAAACTTGGCAACTTTTCTCAAATTAGCCCCTAAACTTTTTTTTG
GATCACATCGGTCCCTAAGGTTGGCATCCATTACACAAATTAGTCCCTACAGCTAACACAGTTAG
TTTTAAGGT
Found at i:5699244 original size:35 final size:35
Alignment explanation
Indices: 5699172--5699244 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
5699162 AAATTTGATA
* * *
5699172 TTTTTATTTTCAATTTATACATATTCTTTTTTATT
1 TTTTTATTTTCAATTTATACATATTATATTCTATT
5699207 TTTTTATTTTCAATTTATATACATA-TATATTCT-TT
1 TTTTTATTTTCAA-TT-TATACATATTATATTCTATT
5699242 TTT
1 TTT
5699245 AAAGTTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 18 0.55
36 7 0.21
37 8 0.24
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (35 bp):
TTTTTATTTTCAATTTATACATATTATATTCTATT
Found at i:5699722 original size:19 final size:19
Alignment explanation
Indices: 5699680--5699747 Score: 86
Period size: 19 Copynumber: 3.5 Consensus size: 19
5699670 ATTACAAAAT
5699680 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTT-AAA
5699700 AATTCAAAATAAGTTTT-AA
1 AATTCAAAATAA-TTTTAAA
5699719 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TAAA
5699738 AATTCTAAAA
1 AATTC-AAAA
5699748 ATTATATTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.07
18 2 0.05
19 19 0.43
20 16 0.36
21 4 0.09
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.35
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:5701063 original size:15 final size:17
Alignment explanation
Indices: 5701037--5701074 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
5701027 AGCTCAAAGC
5701037 ATAAGTAGAAAAGAAAT
1 ATAAGTAGAAAAGAAAT
*
5701054 A-AAGTA-AAAATAAAT
1 ATAAGTAGAAAAGAAAT
5701069 ATAAGT
1 ATAAGT
5701075 TGTAGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 9 0.47
16 9 0.47
17 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (17 bp):
ATAAGTAGAAAAGAAAT
Found at i:5704551 original size:27 final size:27
Alignment explanation
Indices: 5704521--5704587 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
5704511 CCTATCAGGT
*
5704521 AGGCGCCAATGAAGGTGCCTCACAGAG
1 AGGCGCCAATGAAGGCGCCTCACAGAG
*
5704548 AGGCGCCAATGAAGGCGCCTCATAGAG
1 AGGCGCCAATGAAGGCGCCTCACAGAG
5704575 AGGCGCCAATGAA
1 AGGCGCCAATGAA
5704588 TATTGTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.31, C:0.25, G:0.33, T:0.10
Consensus pattern (27 bp):
AGGCGCCAATGAAGGCGCCTCACAGAG
Found at i:5704580 original size:15 final size:15
Alignment explanation
Indices: 5704537--5704581 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
5704527 CAATGAAGGT
*
5704537 GCCTCACAGAGAGGC
1 GCCTCATAGAGAGGC
*
5704552 GCC-AAT-GA-AGGC
1 GCCTCATAGAGAGGC
5704564 GCCTCATAGAGAGGC
1 GCCTCATAGAGAGGC
5704579 GCC
1 GCC
5704582 AATGAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
12 7 0.29
13 4 0.17
14 3 0.12
15 10 0.42
ACGTcount: A:0.27, C:0.31, G:0.33, T:0.09
Consensus pattern (15 bp):
GCCTCATAGAGAGGC
Found at i:5704686 original size:21 final size:21
Alignment explanation
Indices: 5704657--5704700 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5704647 TGGATTAGTA
*
5704657 TTTTGTATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
5704678 TTTTATATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
5704699 TT
1 TT
5704701 GTGTTTGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (21 bp):
TTTTATATGAATATTGTAATT
Found at i:5704834 original size:16 final size:16
Alignment explanation
Indices: 5704791--5704834 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
5704781 AAAATCAAAT
*
5704791 AAAATTTAATTATATA
1 AAAATTAAATTATATA
* *
5704807 AAAGTTACATTATATA
1 AAAATTAAATTATATA
5704823 AAAATTAAATTA
1 AAAATTAAATTA
5704835 GTTAACAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAATTAAATTATATA
Found at i:5704909 original size:38 final size:38
Alignment explanation
Indices: 5704867--5704939 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
5704857 AAAAAGTCAG
5704867 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
*
5704905 TTATAATTAAACTTTTAATAAGATGATTTTTAATT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATT
5704940 ACTAATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:5704963 original size:38 final size:38
Alignment explanation
Indices: 5704868--5704959 Score: 125
Period size: 38 Copynumber: 2.4 Consensus size: 38
5704858 AAAAGTCAGT
* **
5704868 TATAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
1 TATAATTAAACTTTTAATAAAATGATTTTTAATTCTAA
*
5704906 TATAATTAAACTTTTAATAAGATGATTTTTAATTACTAA
1 TATAATTAAACTTTTAATAAAATGATTTTTAATT-CTAA
5704945 TA-AATTAAA-TTTTAA
1 TATAATTAAACTTTTAA
5704960 ATAATTACAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
37 6 0.12
38 40 0.82
39 3 0.06
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (38 bp):
TATAATTAAACTTTTAATAAAATGATTTTTAATTCTAA
Found at i:5705057 original size:8 final size:8
Alignment explanation
Indices: 5705044--5705155 Score: 50
Period size: 8 Copynumber: 13.4 Consensus size: 8
5705034 CATACAAAAA
5705044 ATTACAAT
1 ATTACAAT
5705052 ATTACAAT
1 ATTACAAT
* * *
5705060 ATATCCCGAC
1 AT-T-ACAAT
5705070 ATTACAAT
1 ATTACAAT
*
5705078 ATTCATACAAA
1 A-T--TACAAT
5705089 ATTACAAT
1 ATTACAAT
5705097 ATTACAAT
1 ATTACAAT
*
5705105 ATTCATACAAA
1 A-T--TACAAT
* *
5705116 ATTATAAA
1 ATTACAAT
5705124 ATTACAAT
1 ATTACAAT
5705132 ATT-C-AT
1 ATTACAAT
* *
5705138 A-TAAAAA
1 ATTACAAT
5705145 ATTACAAT
1 ATTACAAT
5705153 ATT
1 ATT
5705156 CATACAAGAT
Statistics
Matches: 77, Mismatches: 16, Indels: 22
0.67 0.14 0.19
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
7 3 0.04
8 48 0.62
9 4 0.05
10 6 0.08
11 12 0.16
ACGTcount: A:0.51, C:0.14, G:0.01, T:0.34
Consensus pattern (8 bp):
ATTACAAT
Found at i:5705094 original size:19 final size:19
Alignment explanation
Indices: 5705070--5705162 Score: 72
Period size: 19 Copynumber: 4.9 Consensus size: 19
5705060 ATATCCCGAC
5705070 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
5705089 ATTACAATA-T--TACAATA
1 ATTACAATATTCATACAA-A
* *
5705106 TTCATACAAAATT-AT--AAA
1 AT--TACAATATTCATACAAA
*
5705124 ATTACAATATTCATATAAAAA
1 ATTACAATATTC--ATACAAA
5705145 ATTACAATATTCATACAA
1 ATTACAATATTCATACAA
5705163 GATACTAATC
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
16 13 0.22
17 2 0.03
18 3 0.05
19 24 0.41
20 1 0.02
21 16 0.27
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:5705106 original size:27 final size:27
Alignment explanation
Indices: 5705070--5705155 Score: 127
Period size: 27 Copynumber: 3.1 Consensus size: 27
5705060 ATATCCCGAC
5705070 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
* *
5705097 ATTACAATATTCATACAAAATTATAAA
1 ATTACAATATTCATACAAAATTACAAT
*
5705124 ATTACAATATTCATATAAAAAATTACAAT
1 ATTACAATATTC--ATACAAAATTACAAT
5705153 ATT
1 ATT
5705156 CATACAAGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
27 37 0.71
29 15 0.29
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:5705217 original size:19 final size:19
Alignment explanation
Indices: 5705198--5705235 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5705188 AAATTTAATT
5705198 ATAAAATAATTACAATATTA
1 ATAAAA-AATTACAATATTA
*
5705218 ATACAAAATTACAATATT
1 ATAAAAAATTACAATATT
5705236 CATTGGCGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAAAAATTACAATATTA
Found at i:5705338 original size:27 final size:27
Alignment explanation
Indices: 5705234--5705323 Score: 171
Period size: 27 Copynumber: 3.3 Consensus size: 27
5705224 AATTACAATA
*
5705234 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTGTGAGGCACC
5705261 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTGTGAGGCACC
5705288 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTGTGAGGCACC
5705315 TTCATTGGC
1 TTCATTGGC
5705324 ACCTACCTGA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.12, C:0.32, G:0.24, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTGTGAGGCACC
Found at i:5705803 original size:21 final size:21
Alignment explanation
Indices: 5705779--5705837 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
5705769 ATCTAATTAA
5705779 AAATATTTAATAATTATA-TTT
1 AAATATTTAATAA-TATAGTTT
5705800 AAATATTTAA-AATATAGTTT
1 AAATATTTAATAATATAGTTT
*
5705820 ATATATTCTAATTAATAT
1 AAATATT-TAA-TAATAT
5705838 TTAATATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.12
20 11 0.33
21 13 0.39
23 5 0.15
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATATTTAATAATATAGTTT
Found at i:5706088 original size:12 final size:13
Alignment explanation
Indices: 5706070--5706103 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
5706060 CTTAAATTAA
*
5706070 AATTTTTAAAAGT
1 AATTTTTAAAAAT
5706083 -ATTTTTAAAAAT
1 AATTTTTAAAAAT
5706095 AATTTTTAA
1 AATTTTTAA
5706104 GCAATGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
AATTTTTAAAAAT
Found at i:5710406 original size:51 final size:51
Alignment explanation
Indices: 5710323--5710501 Score: 207
Period size: 51 Copynumber: 3.4 Consensus size: 51
5710313 ACTTCTGATC
* * *
5710323 AGTGATAAGTGATAAGT-AGTAGCTTCAACTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGA-TAGCTTTAGCTACACTTATCTGATCAGTGACA
*
5710374 AGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
* *
5710425 GGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGAT-A--GCT---TTAGCTACACTTATCTGATCAGTGACA
* * *
5710482 AGAGATAAATGATAAGTGAT
1 AGTGACAAGTGATAAGTGAT
5710502 TCCGTGTAAG
Statistics
Matches: 110, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
51 63 0.57
52 2 0.02
54 2 0.02
57 43 0.39
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:5710430 original size:58 final size:57
Alignment explanation
Indices: 5710368--5710481 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 57
5710358 TATCTGATCA
*
5710368 GTGACAAGTGGCAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAG
1 GTGACAAGTGACAAGTGATAAGTGATAGC-TTAGCTACACTTATCTGATCAGTGACAG
* *
5710426 GTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
1 GTGACAAGTGACAAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAGTGACA
5710482 AGAGATAAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 27 0.51
58 26 0.49
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (57 bp):
GTGACAAGTGACAAGTGATAAGTGATAGCTTAGCTACACTTATCTGATCAGTGACAG
Found at i:5710495 original size:57 final size:58
Alignment explanation
Indices: 5710380--5710501 Score: 192
Period size: 57 Copynumber: 2.1 Consensus size: 58
5710370 GACAAGTGGC
* * *
5710380 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAGGTGACAAGTGAT
1 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGAGACAAATGAT
* *
5710438 AAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACAAGAGATAAATGAT
1 AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGAGACAAATGAT
5710495 AAGTGAT
1 AAGTGAT
5710502 TCCGTGTAAG
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
57 43 0.73
58 16 0.27
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (58 bp):
AAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAGTGACAAGAGACAAATGAT
Found at i:5713188 original size:13 final size:13
Alignment explanation
Indices: 5713165--5713206 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5713155 CTGGCTTTCT
*
5713165 TACACAAATAATA
1 TACAAAAATAATA
*
5713178 TATAAAAATAAT-
1 TACAAAAATAATA
5713190 TACAAAAATAAGTA
1 TACAAAAATAA-TA
5713204 TAC
1 TAC
5713207 TGAACAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.42
13 11 0.46
14 3 0.12
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (13 bp):
TACAAAAATAATA
Found at i:5713658 original size:17 final size:18
Alignment explanation
Indices: 5713621--5713661 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5713611 GTATATTATT
**
5713621 AAAAAAAAGTTGAAAATA
1 AAAAAAAAACTGAAAATA
5713639 AAAAAAAAACTGAAAA-A
1 AAAAAAAAACTGAAAATA
5713656 AAAAAA
1 AAAAAA
5713662 GAAGGGAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.10
Consensus pattern (18 bp):
AAAAAAAAACTGAAAATA
Found at i:5714631 original size:25 final size:26
Alignment explanation
Indices: 5714578--5714633 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
5714568 AATTTTAAAA
* *
5714578 TATTTTTAAAATACTTTTTTTATTTTT
1 TATTTTTAAAATAC-TTTTTTAGTGTT
*
5714605 TATTTTTAAAATA-TTTTTTGGTGTT
1 TATTTTTAAAATACTTTTTTAGTGTT
5714630 TATT
1 TATT
5714634 AAAAAAATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 13 0.50
27 13 0.50
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (26 bp):
TATTTTTAAAATACTTTTTTAGTGTT
Found at i:5716925 original size:16 final size:13
Alignment explanation
Indices: 5716899--5716946 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 13
5716889 TTTTATAGAT
5716899 ATTTTTCTTTTTC
1 ATTTTTCTTTTTC
5716912 ATGTTCTCTCTTTTTC
1 AT-TT-T-TCTTTTTC
5716928 ATTTTTCTTTTTC
1 ATTTTTCTTTTTC
5716941 -TTTTTC
1 ATTTTTC
5716947 CTACCCTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.19
13 10 0.31
14 3 0.09
15 3 0.09
16 10 0.31
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (13 bp):
ATTTTTCTTTTTC
Found at i:5718100 original size:20 final size:19
Alignment explanation
Indices: 5718062--5718106 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
5718052 AATAATAATT
5718062 TAATATTTTACTAAAAATAA
1 TAATATTTTACTAAAAAT-A
*
5718082 TAATATTTTA-TAAGTAATA
1 TAATATTTTACTAA-AAATA
5718101 TAATAT
1 TAATAT
5718107 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
TAATATTTTACTAAAAATA
Found at i:5718105 original size:19 final size:18
Alignment explanation
Indices: 5718053--5718106 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
5718043 TTTTTGTTAA
*
5718053 ATAATAATTTAATATTTT
1 ATAATAATATAATATTTT
*
5718071 ACTAAAAATAATAATATTTT
1 A-TAATAAT-ATAATATTTT
5718091 ATAAGTAATATAATAT
1 ATAA-TAATATAATAT
5718107 ATATATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.03
19 16 0.53
20 13 0.43
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
ATAATAATATAATATTTT
Found at i:5718761 original size:26 final size:25
Alignment explanation
Indices: 5718720--5718778 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
5718710 CAAATATAAT
5718720 AAATA-TTTTTATTTTTTATT-TTA
1 AAATATTTTTTATTTTTTATTGTTA
5718743 AAATACTTTTTTATTTTTTATTGTTA
1 AAATA-TTTTTTATTTTTTATTGTTA
5718769 AAATATTTTT
1 AAATATTTTT
5718779 AAATATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.15
25 20 0.61
26 8 0.24
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (25 bp):
AAATATTTTTTATTTTTTATTGTTA
Found at i:5719073 original size:34 final size:34
Alignment explanation
Indices: 5719010--5719074 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
5719000 TGTATGTTTA
* * *
5719010 AATCAATTGTCATGTTGTAATACTGCTTCTTTTG
1 AATCAATTGTCATGGTGGAATACTACTTCTTTTG
* *
5719044 AATCAATTGTTATGGTGGAATATTACTTCTT
1 AATCAATTGTCATGGTGGAATACTACTTCTT
5719075 CTTCTTTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.46
Consensus pattern (34 bp):
AATCAATTGTCATGGTGGAATACTACTTCTTTTG
Found at i:5729580 original size:9 final size:9
Alignment explanation
Indices: 5729566--5729650 Score: 116
Period size: 9 Copynumber: 9.4 Consensus size: 9
5729556 TTTGGTTAAA
5729566 AATTAACCG
1 AATTAACCG
*
5729575 AATTAACCA
1 AATTAACCG
5729584 AATTAACCG
1 AATTAACCG
*
5729593 AATTACCCG
1 AATTAACCG
5729602 AATTAACCG
1 AATTAACCG
*
5729611 AATTACCCG
1 AATTAACCG
*
5729620 AATTACCCG
1 AATTAACCG
*
5729629 AATTACCCG
1 AATTAACCG
*
5729638 AATTAACCT
1 AATTAACCG
5729647 AATT
1 AATT
5729651 GAATCATACC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 69 1.00
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:5729588 original size:18 final size:18
Alignment explanation
Indices: 5729566--5729650 Score: 134
Period size: 18 Copynumber: 4.7 Consensus size: 18
5729556 TTTGGTTAAA
* *
5729566 AATTAACCGAATTAACCA
1 AATTAACCGAATTACCCG
5729584 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
5729602 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
5729620 AATTACCCGAATTACCCG
1 AATTAACCGAATTACCCG
*
5729638 AATTAACCTAATT
1 AATTAACCGAATT
5729651 GAATCATACC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:5736650 original size:2 final size:2
Alignment explanation
Indices: 5736645--5736675 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5736635 CTAAGCTTGC
5736645 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5736676 ATCTGTGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5756041 original size:15 final size:15
Alignment explanation
Indices: 5756023--5756066 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
5756013 TTTGAAGGTC
5756023 CAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAA
* *
5756038 CAAAACAAAACAAAA
1 CAAAAAAAAAAAAAA
5756053 CAAAAACAAAAAAA
1 CAAAAA-AAAAAAA
5756067 GAAGAAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAAAAAAA
Found at i:5756042 original size:10 final size:10
Alignment explanation
Indices: 5756024--5756066 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
5756014 TTGAAGGTCC
5756024 AAAAA-AAAA
1 AAAAACAAAA
5756033 AAAAACAAAA
1 AAAAACAAAA
*
5756043 CAAAACAAAA
1 AAAAACAAAA
5756053 CAAAAACAAAA
1 -AAAAACAAAA
5756064 AAA
1 AAA
5756067 GAAGAAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 5 0.17
10 16 0.53
11 9 0.30
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:5757341 original size:46 final size:44
Alignment explanation
Indices: 5757274--5757389 Score: 115
Period size: 46 Copynumber: 2.6 Consensus size: 44
5757264 ATTATACAGG
* * **
5757274 TCTTATTTCCCTGAGACTACAGTGGAACAGACCAAAGAATTTTAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAG-ATAGTA-A
* * ***
5757320 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGATAGTAA
* *
5757364 TCCTATCTCCCTGATATTACAGTGGA
1 TCTTATCTCCCTGAGATTACAGTGGA
5757390 GCGGATTAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
44 24 0.41
45 4 0.07
46 30 0.52
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGATAGTAA
Found at i:5757383 original size:44 final size:44
Alignment explanation
Indices: 5757323--5757513 Score: 146
Period size: 44 Copynumber: 4.4 Consensus size: 44
5757313 TTTTAGATCT
5757323 TATCTCCCTGAGATTACAGCGGAGCAGATTGAAGAT-AGTAATCC
1 TATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAAG-AATCC
* * * * *
5757367 TATCTCCCTGATATTACAGTGGAGCGGATT-AAAACTAAGAATCT
1 TATCTCCCTGAGATTACAGCGGAGCAGATTGAAGA-TAAGAATCC
* ** * * * *
5757411 TATCTCTCTGA-AGTTACAGTAGAGTAGATCG-TG-TCAGATAT--
1 TATCTCCCTGAGA-TTACAGCGGAGCAGATTGAAGATAAGA-ATCC
* * *
5757452 TGTCTCCCTGATATTGCAGCGGAGCAGATTGAAGAT-AGTAATCC
1 TATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAAG-AATCC
5757496 TATCTCCCTGAGATTACA
1 TATCTCCCTGAGATTACA
5757514 CATTGCGTCG
Statistics
Matches: 112, Mismatches: 24, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
41 22 0.20
42 10 0.09
43 8 0.07
44 70 0.62
45 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAAGAATCC
Found at i:5767832 original size:6 final size:6
Alignment explanation
Indices: 5767821--5767845 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5767811 AAGTGTCAAT
5767821 ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA A
5767846 ATAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:5781287 original size:23 final size:23
Alignment explanation
Indices: 5781252--5781301 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
5781242 TAACACAGTT
**
5781252 CGGATTCCTCAATCCTATATCTA
1 CGGATTCAACAATCCTATATCTA
5781275 CGGATTCAACAATCCTATATCTA
1 CGGATTCAACAATCCTATATCTA
5781298 CGGA
1 CGGA
5781302 GCCTTGCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (23 bp):
CGGATTCAACAATCCTATATCTA
Found at i:5785994 original size:2 final size:2
Alignment explanation
Indices: 5785987--5786014 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5785977 AAAATTATTC
5785987 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
5786015 TCTTACGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5794322 original size:29 final size:28
Alignment explanation
Indices: 5794284--5794339 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
5794274 TTGTGTTAAT
5794284 AATTTAC-AAATCAAAATCCCATGTATAA
1 AATTTACAAAATCAAAAT-CCATGTATAA
*
5794312 AATTTCACAAAATCAAAATTCATGTATA
1 AATTT-ACAAAATCAAAATCCATGTATA
5794340 GTTTTGGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 10 0.40
30 10 0.40
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (28 bp):
AATTTACAAAATCAAAATCCATGTATAA
Found at i:5800560 original size:24 final size:22
Alignment explanation
Indices: 5800531--5800611 Score: 65
Period size: 24 Copynumber: 3.4 Consensus size: 22
5800521 CTATATAGCG
5800531 GGAAGCTCATAAGAGCCATAAT
1 GGAAGCTCATAAGAGCCATAAT
**
5800553 CAGGAAGCTCATGCGAGCCAATAAT
1 --GGAAGCTCATAAGAGCC-ATAAT
5800578 GGATAGCTCCA-AAGAGCCATTAATT
1 GGA-AGCT-CATAAGAGCCA-TAA-T
5800603 GGAAAGCTC
1 GG-AAGCTC
5800612 TGGACAATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
23 4 0.09
24 28 0.60
25 14 0.30
26 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (22 bp):
GGAAGCTCATAAGAGCCATAAT
Found at i:5800676 original size:26 final size:26
Alignment explanation
Indices: 5800640--5800694 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
5800630 GAAGCTCCGG
*
5800640 AGAGCCTTTAATCAGGAAGCTCACAA
1 AGAGCCCTTAATCAGGAAGCTCACAA
* *
5800666 AGAGCCCTTAATCATGAAGCTCACGA
1 AGAGCCCTTAATCAGGAAGCTCACAA
5800692 AGA
1 AGA
5800695 ACCATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (26 bp):
AGAGCCCTTAATCAGGAAGCTCACAA
Found at i:5801360 original size:20 final size:20
Alignment explanation
Indices: 5801322--5801361 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5801312 CCATGTGTTT
* *
5801322 CATAAAATTTAGAATTTTTC
1 CATAAAATTTACAACTTTTC
*
5801342 CATAAATTTTACAACTTTTC
1 CATAAAATTTACAACTTTTC
5801362 AATTTAGTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (20 bp):
CATAAAATTTACAACTTTTC
Found at i:5802482 original size:24 final size:24
Alignment explanation
Indices: 5802436--5802487 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
5802426 ATTTTTATTT
* **
5802436 AAATAATTCTTTAAATTTGTATAA
1 AAATAATTATTTAAATTAATATAA
* *
5802460 AAATAATTATTTACATTAATATAT
1 AAATAATTATTTAAATTAATATAA
5802484 AAAT
1 AAAT
5802488 TTCTAATGAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (24 bp):
AAATAATTATTTAAATTAATATAA
Found at i:5823997 original size:36 final size:36
Alignment explanation
Indices: 5823949--5824042 Score: 109
Period size: 37 Copynumber: 2.6 Consensus size: 36
5823939 GGGTCTCCAA
* *
5823949 AATCACATTTCAATTCAATTTCACTTTTTCACTTTC
1 AATCACAATTCAATTCAATTTCACTTTTCCACTTTC
* *
5823985 AATCACAATTCAATTCAAAATTCACTTTTCCATTTTC
1 AATCACAATTCAATTC-AATTTCACTTTTCCACTTTC
*
5824022 AAGTCA-ATATTCATTTCAATT
1 AA-TCACA-ATTCAATTCAATT
5824043 CCACACATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
36 15 0.31
37 23 0.47
38 11 0.22
ACGTcount: A:0.33, C:0.22, G:0.01, T:0.44
Consensus pattern (36 bp):
AATCACAATTCAATTCAATTTCACTTTTCCACTTTC
Found at i:5824043 original size:36 final size:35
Alignment explanation
Indices: 5823949--5824043 Score: 102
Period size: 36 Copynumber: 2.6 Consensus size: 35
5823939 GGGTCTCCAA
* *
5823949 AATCACATTTCAATTCAATTTCACTTTTTCACTTTC
1 AATCACAATTCAATTCAA-TTCACTTTTCCACTTTC
*
5823985 AATCACAATTCAATTCAAAATTCACTTTTCCATTTTC
1 AATCACAATTCAATTC--AATTCACTTTTCCACTTTC
*
5824022 AAGTCA-ATATTCATTTCAATTC
1 AA-TCACA-ATTCAATTCAATTC
5824044 CACACATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
36 20 0.39
37 18 0.35
38 13 0.25
ACGTcount: A:0.33, C:0.23, G:0.01, T:0.43
Consensus pattern (35 bp):
AATCACAATTCAATTCAATTCACTTTTCCACTTTC
Found at i:5824357 original size:17 final size:18
Alignment explanation
Indices: 5824325--5824358 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5824315 ATTTTCTTTT
5824325 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
5824343 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
5824359 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:5824741 original size:4 final size:4
Alignment explanation
Indices: 5824732--5824765 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
5824722 TTAGTTTTTC
5824732 CTTT CTTT CTTT CTTTT CTTT CTTT CCTTT CTTT
1 CTTT CTTT CTTT C-TTT CTTT CTTT -CTTT CTTT
5824766 TCTCCCTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:5824749 original size:9 final size:9
Alignment explanation
Indices: 5824727--5824768 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
5824717 AAACTTTAGT
5824727 TTTTCCTTTC
1 TTTT-CTTTC
5824737 -TTTCTTTC
1 TTTTCTTTC
5824745 TTTTCTTTC
1 TTTTCTTTC
*
5824754 TTTCCTTTC
1 TTTTCTTTC
5824763 TTTTCT
1 TTTTCT
5824769 CCCTGTTTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 5 0.17
9 24 0.83
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:5824749 original size:13 final size:13
Alignment explanation
Indices: 5824728--5824765 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
5824718 AACTTTAGTT
5824728 TTTCCTTTCTTTC
1 TTTCCTTTCTTTC
*
5824741 TTTCTTTTCTTTC
1 TTTCCTTTCTTTC
5824754 TTTCCTTTCTTT
1 TTTCCTTTCTTT
5824766 TCTCCCTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCCTTTCTTTC
Found at i:5825112 original size:31 final size:28
Alignment explanation
Indices: 5825077--5825164 Score: 88
Period size: 31 Copynumber: 3.0 Consensus size: 28
5825067 TACATTTTTC
5825077 ATAATTCAATTTATTTATTAATATAATATTT
1 ATAATT-AATTTATTTATTAATAT-A-ATTT
* * *
5825108 ATAATATAATTAATTTAATAATATACTTT
1 ATAAT-TAATTTATTTATTAATATAATTT
* *
5825137 ATAATTAATTTATATATTTATA-AATTT
1 ATAATTAATTTATTTATTAATATAATTT
5825164 A
1 A
5825165 AATCATTGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
27 5 0.10
28 13 0.27
29 8 0.17
30 1 0.02
31 20 0.42
32 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAATTAATTTATTTATTAATATAATTT
Found at i:5825114 original size:14 final size:15
Alignment explanation
Indices: 5825087--5825132 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 15
5825077 ATAATTCAAT
5825087 TTATTTATTAATATAA
1 TTATTTA-TAATATAA
5825103 -TATTTATAATATAA
1 TTATTTATAATATAA
5825117 TTAATTTAATAATATA
1 TT-ATTT-ATAATATA
5825133 CTTTATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 8 0.30
15 7 0.26
16 4 0.15
17 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATTTATAATATAA
Found at i:5825150 original size:11 final size:11
Alignment explanation
Indices: 5825112--5825150 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
5825102 ATATTTATAA
5825112 TATAATTAATT
1 TATAATTAATT
*
5825123 TAATAATATACTT
1 T-ATAAT-TAATT
5825136 TATAATTAATT
1 TATAATTAATT
5825147 TATA
1 TATA
5825151 TATTTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATTAATT
Found at i:5829627 original size:14 final size:14
Alignment explanation
Indices: 5829608--5829636 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5829598 TTGAAAACAA
5829608 TTTTTATTTATTGT
1 TTTTTATTTATTGT
5829622 TTTTTATTTATTGT
1 TTTTTATTTATTGT
5829636 T
1 T
5829637 CTTCAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTTATTTATTGT
Found at i:5832614 original size:20 final size:20
Alignment explanation
Indices: 5832591--5832628 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5832581 GGTTTTCGAT
*
5832591 TTTTCATTTTAATTTTGATG
1 TTTTAATTTTAATTTTGATG
*
5832611 TTTTAATTTTATTTTTGA
1 TTTTAATTTTAATTTTGA
5832629 CAGAATAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.68
Consensus pattern (20 bp):
TTTTAATTTTAATTTTGATG
Found at i:5833247 original size:6 final size:6
Alignment explanation
Indices: 5833238--5833270 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
5833228 TTAAATTAAT
5833238 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
5833271 CGTAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:5833416 original size:17 final size:17
Alignment explanation
Indices: 5833378--5833410 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5833368 AATAAAAAAT
*
5833378 ATTTATAAAAATTATAG
1 ATTTATAAAAAATATAG
5833395 ATTTATAAAAAATATA
1 ATTTATAAAAAATATA
5833411 TTTTTAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATTTATAAAAAATATAG
Found at i:5835365 original size:2 final size:2
Alignment explanation
Indices: 5835358--5835386 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5835348 ATGTGAATCT
5835358 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 T
5835387 CCTTCCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5838027 original size:105 final size:105
Alignment explanation
Indices: 5837912--5838153 Score: 265
Period size: 105 Copynumber: 2.3 Consensus size: 105
5837902 CGCAACTACG
*
5837912 AAACAGCTCGCAGACTTATGTTCTCAGTTGATGTTTAAAGGTTAGTTGCA-TTAAGTTCGCAACC
1 AAACAGCTCGCAGACTTATGTTCTCAGTTGATGTTTAAAGGTTAGTTG-AGTTAAGCTCGCAACC
* * * * * ***
5837976 TCTAGATTATTCGAGTTAACTTAGTTAAGCTTGTAACTCTA
65 TCCAAATTATTCAAGTTAACTGAATTAAGCTCACAACTCTA
* * * ** *
5838017 AAACAACTCGCAAACTTACGTT-TCCAACTGATGTTTAAAGGTTAGTTGAGTTAAGCTCGCAGCC
1 AAACAGCTCGCAGACTTATGTTCT-CAGTTGATGTTTAAAGGTTAGTTGAGTTAAGCTCGCAACC
* *
5838081 TCCAAATTATTCAAGTTAGCTGAATTAAGCTCACAACTCTG
65 TCCAAATTATTCAAGTTAACTGAATTAAGCTCACAACTCTA
* *
5838122 AAACAGCTCGC-GAACCTATGTTCCCAGTTGAT
1 AAACAGCTCGCAG-ACTTATGTTCTCAGTTGAT
5838154 TCTACTAAGG
Statistics
Matches: 109, Mismatches: 24, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
104 2 0.02
105 107 0.98
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (105 bp):
AAACAGCTCGCAGACTTATGTTCTCAGTTGATGTTTAAAGGTTAGTTGAGTTAAGCTCGCAACCT
CCAAATTATTCAAGTTAACTGAATTAAGCTCACAACTCTA
Found at i:5838665 original size:104 final size:103
Alignment explanation
Indices: 5838532--5838892 Score: 359
Period size: 104 Copynumber: 3.5 Consensus size: 103
5838522 ACAGCTCACA
* * * ** *
5838532 AACCTACGTTCCCAGCTCAT-TCTACTAAGGTTTACTGAATTAAGATCGCAATCTCCGATTATTT
1 AACCTACGTTCACAGCTGATAT-TACTAAGGCTCGCTGATTTAAGATCGCAATCTCCGATTATTT
* *
5838596 AAGTTCACTGATTTAAGATCGCAACTCTTAACAACTTACT
65 GAGTTCACTGATTTAAGATCGCAACTC-TAACAACTTGCT
* * * *
5838636 AACCTACGTTCACAGCTGATATTACTAAGGCTCGTTGATTTAAGATGGCAACCTCCAATTATTTG
1 AACCTACGTTCACAGCTGATATTACTAAGGCTCGCTGATTTAAGATCGCAATCTCCGATTATTTG
* * *
5838701 AGTTCGCTGATTTAAGAACGCAACTGCTAACAACTCGCT
66 AGTTCACTGATTTAAGATCGCAACT-CTAACAACTTGCT
* ** * * * * * * *
5838740 GATTTATGTTCACAACTGATGTTACTAAGGCTCGCTGATTTAATATTGCAGTTTCCGATTATTTG
1 AACCTACGTTCACAGCTGATATTACTAAGGCTCGCTGATTTAAGATCGCAATCTCCGATTATTTG
* *
5838805 AGTT-AGTTGATTTAAGATCGCAATTCCTAACAACTTGCT
66 AGTTCA-CTGATTTAAGATCGCAACT-CTAACAACTTGCT
* * * * * *
5838844 GACATACGTTCAGAGTTGATATTACTAAAGCTCG-TGATTTGAGATCGCA
1 AACCTACGTTCACAGCTGATATTACTAAGGCTCGCTGATTTAAGATCGCA
5838893 GCCTCCGAAT
Statistics
Matches: 209, Mismatches: 45, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
103 12 0.06
104 195 0.93
105 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (103 bp):
AACCTACGTTCACAGCTGATATTACTAAGGCTCGCTGATTTAAGATCGCAATCTCCGATTATTTG
AGTTCACTGATTTAAGATCGCAACTCTAACAACTTGCT
Found at i:5842454 original size:11 final size:11
Alignment explanation
Indices: 5842440--5842498 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
5842430 AATTATTTTA
5842440 TCAATTTCCTC
1 TCAATTTCCTC
*
5842451 TCAATTTCCTT
1 TCAATTTCCTC
* *
5842462 TCAAATTGCTC
1 TCAATTTCCTC
*
5842473 TCAATTTCCTT
1 TCAATTTCCTC
5842484 TCAAATTT-CTC
1 TC-AATTTCCTC
5842495 TCAA
1 TCAA
5842499 ATCCATATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
10 2 0.05
11 32 0.82
12 5 0.13
ACGTcount: A:0.24, C:0.29, G:0.02, T:0.46
Consensus pattern (11 bp):
TCAATTTCCTC
Found at i:5842473 original size:22 final size:22
Alignment explanation
Indices: 5842448--5842498 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
5842438 TATCAATTTC
5842448 CTCTCAATTTCCTTTCAAATTG
1 CTCTCAATTTCCTTTCAAATTG
*
5842470 CTCTCAATTTCCTTTCAAATTT
1 CTCTCAATTTCCTTTCAAATTG
5842492 CTCTCAA
1 CTCTCAA
5842499 ATCCATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.29, G:0.02, T:0.45
Consensus pattern (22 bp):
CTCTCAATTTCCTTTCAAATTG
Found at i:5842536 original size:29 final size:28
Alignment explanation
Indices: 5842487--5842541 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
5842477 TTTCCTTTCA
*
5842487 AATTTCTCTCAAATCCATATTTAATCTC
1 AATTTCTCTCAAATCCATATTAAATCTC
*
5842515 AATTTGCTCTCAATTTCC-TATTAAATC
1 AATTT-CTCTCAA-ATCCATATTAAATC
5842542 CCTATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.22
29 15 0.65
30 3 0.13
ACGTcount: A:0.31, C:0.24, G:0.02, T:0.44
Consensus pattern (28 bp):
AATTTCTCTCAAATCCATATTAAATCTC
Found at i:5842541 original size:40 final size:40
Alignment explanation
Indices: 5842471--5842548 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
5842461 TTCAAATTGC
* *
5842471 TCTCAATTTCCTTTCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTCCTCTCAAATTTCTATCAAATCCATATTTAA
* * *
5842511 TCTCAATTTGCTCTC-AATTTCCTATTAAATCCCTATTT
1 TCTCAATTTCCTCTCAAATTT-CTATCAAATCCATATTT
5842549 TTAATTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 5 0.16
40 27 0.84
ACGTcount: A:0.27, C:0.26, G:0.01, T:0.46
Consensus pattern (40 bp):
TCTCAATTTCCTCTCAAATTTCTATCAAATCCATATTTAA
Found at i:5844559 original size:24 final size:24
Alignment explanation
Indices: 5844520--5844576 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
5844510 TTCCTTTTAC
* * *
5844520 CAAACACCATCACCGTATGG-GTTT
1 CAAACACCTTCACCGT-TGGTGATG
*
5844544 CAAACACCTTCGCCGTTGGTGATG
1 CAAACACCTTCACCGTTGGTGATG
5844568 CAAACACCT
1 CAAACACCT
5844577 CCACATTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.23
Consensus pattern (24 bp):
CAAACACCTTCACCGTTGGTGATG
Found at i:5847568 original size:7 final size:7
Alignment explanation
Indices: 5847556--5847584 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
5847546 AAAACCCTAA
5847556 AAACCCT
1 AAACCCT
5847563 AAACCCT
1 AAACCCT
5847570 AAACCCT
1 AAACCCT
5847577 -AACCCT
1 AAACCCT
5847583 AA
1 AA
5847585 TCCTAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.45, C:0.41, G:0.00, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:5858801 original size:93 final size:91
Alignment explanation
Indices: 5858636--5858824 Score: 236
Period size: 93 Copynumber: 2.1 Consensus size: 91
5858626 TGAAATTGAG
* ** * *
5858636 TTTCATATGATAATGGCTTCTTGCTTTCTTCCCCATGTTTATTTTCTTCTTATTTATACTGATGT
1 TTTCATATGATAACGGCTTCTTGCTTTCTTCCCCATCATTATTTGCTTCTTATCTATACTGATGT
* * *
5858701 TTGATAGTTAATTTTTTTTTTGTAGATAT
66 TTAATAG-T--TGTTTCTTTTGTAGATAT
* ** *
5858730 TTTCATATGATAACGGC-TCTTGCTTTCTTCCCCCTCATTATTTGCTTCTTATCTATTTTGATTT
1 TTTCATATGATAACGGCTTCTTGCTTTCTTCCCCATCATTATTTGCTTCTTATCTATACTGATGT
5858794 TTAATAGTTGTTTCTTTTGTAGATAT
66 TTAATAGTTGTTTCTTTTGTAGATAT
5858820 TTTCA
1 TTTCA
5858825 CTTTAATCTA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
90 21 0.25
92 1 0.01
93 45 0.54
94 16 0.19
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.55
Consensus pattern (91 bp):
TTTCATATGATAACGGCTTCTTGCTTTCTTCCCCATCATTATTTGCTTCTTATCTATACTGATGT
TTAATAGTTGTTTCTTTTGTAGATAT
Done.