Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 33
Found at i:5775309 original size:14 final size:14
Alignment explanation
Indices: 5775290--5775457 Score: 66
Period size: 14 Copynumber: 12.1 Consensus size: 14
5775280 TTTGATTTAG
*
5775290 TAATGATTTGATAA
1 TAATGATTTAATAA
5775304 TAATGA-TT--TAA
1 TAATGATTTAATAA
* *
5775315 TAATGATTTTATAT
1 TAATGATTTAATAA
*
5775329 TTATGATTTAATAA
1 TAATGATTTAATAA
* * *
5775343 TGATTATTATTAATATT
1 TAATGA-T-TTAATA-A
* *
5775360 TAATGATTTGATAT
1 TAATGATTTAATAA
*
5775374 TAATGA-TT-A-AG
1 TAATGATTTAATAA
*
5775385 TAATGA-TTAGTAA
1 TAATGATTTAATAA
*
5775398 TAATGAAATT-ATAA
1 TAATG-ATTTAATAA
*
5775412 TAATAATTTAATCATTAA
1 TAATGATTT-A--A-TAA
5775430 TAATGA-TTAATAA
1 TAATGATTTAATAA
* *
5775443 TAATTATTAAATAA
1 TAATGATTTAATAA
5775457 T
1 T
5775458 TATTAAATAT
Statistics
Matches: 119, Mismatches: 19, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
11 18 0.15
12 3 0.03
13 21 0.18
14 46 0.39
15 8 0.07
16 8 0.07
17 7 0.06
18 8 0.07
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.46
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:5775311 original size:25 final size:25
Alignment explanation
Indices: 5775282--5775392 Score: 119
Period size: 25 Copynumber: 4.6 Consensus size: 25
5775272 TGATATCATT
* *
5775282 TGATTTAGTAATGATTTGATAATAA
1 TGATTTAATAATGATTTGATATTAA
* *
5775307 TGATTTAATAATGATTTTATATTTA
1 TGATTTAATAATGATTTGATATTAA
5775332 TGATTTAATAATGA-TT-ATTATTAA
1 TGATTTAATAATGATTTGA-TATTAA
5775356 T-A-TT--TAATGATTTGATATTAA
1 TGATTTAATAATGATTTGATATTAA
5775377 TGA-TTAAGTAATGATT
1 TGATTTAA-TAATGATT
5775393 AGTAATAATG
Statistics
Matches: 74, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
20 6 0.08
21 9 0.12
22 6 0.08
23 2 0.03
24 8 0.11
25 43 0.58
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.50
Consensus pattern (25 bp):
TGATTTAATAATGATTTGATATTAA
Found at i:5775438 original size:10 final size:10
Alignment explanation
Indices: 5775409--5775459 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
5775399 AATGAAATTA
5775409 TAATAATAAT
1 TAATAATAAT
*
5775419 T--TAATCAT
1 TAATAATAAT
*
5775427 TAATAATGAT
1 TAATAATAAT
5775437 TAATAATAAT
1 TAATAATAAT
*
5775447 TATTAAATAAT
1 TAAT-AATAAT
5775458 TA
1 TA
5775460 TTAAATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
8 7 0.21
10 19 0.56
11 8 0.24
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (10 bp):
TAATAATAAT
Found at i:5775457 original size:11 final size:11
Alignment explanation
Indices: 5775441--5775466 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
5775431 AATGATTAAT
5775441 AATAATTATTA
1 AATAATTATTA
5775452 AATAATTATTA
1 AATAATTATTA
5775463 AATA
1 AATA
5775467 TTTAAATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AATAATTATTA
Found at i:5775517 original size:16 final size:16
Alignment explanation
Indices: 5775496--5775534 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5775486 ATTTAAATCA
* *
5775496 AATTTATAAATATTTG
1 AATTTATAAATAGTCG
*
5775512 AATTTATAACTAGTCG
1 AATTTATAAATAGTCG
5775528 AATTTAT
1 AATTTAT
5775535 CTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (16 bp):
AATTTATAAATAGTCG
Found at i:5778228 original size:21 final size:21
Alignment explanation
Indices: 5778175--5778214 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5778165 TTTATGTATG
5778175 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
5778196 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
5778215 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:5778295 original size:17 final size:18
Alignment explanation
Indices: 5778266--5778299 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5778256 AACAAACTAA
5778266 TAATTTAAAATAATAAAC
1 TAATTTAAAATAATAAAC
5778284 TAATTT-AAATAATAAA
1 TAATTTAAAATAATAAA
5778300 AAAACTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATTTAAAATAATAAAC
Found at i:5782004 original size:22 final size:22
Alignment explanation
Indices: 5781979--5782020 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5781969 CAATTCATTT
5781979 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
5782001 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
5782021 CCAGCACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:5782614 original size:22 final size:22
Alignment explanation
Indices: 5782589--5782630 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5782579 CAATTCATTT
5782589 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
5782611 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
5782631 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:5784437 original size:21 final size:21
Alignment explanation
Indices: 5784413--5784452 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5784403 ATCCATCGCA
*
5784413 AAAAGGGACCGATCCTTTTAG
1 AAAAGGGACCAATCCTTTTAG
*
5784434 AAAAGGGATCAATCCTTTT
1 AAAAGGGACCAATCCTTTT
5784453 CCTGAAAAAT
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:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (21 bp):
AAAAGGGACCAATCCTTTTAG
Found at i:5786915 original size:124 final size:124
Alignment explanation
Indices: 5786695--5786944 Score: 500
Period size: 124 Copynumber: 2.0 Consensus size: 124
5786685 AAATAAAATT
5786695 TTTGCACATCAATTTAGAGTAGTTCGACTTCAAGTCTACATCCACTATCTTAACTTCCACACTAA
1 TTTGCACATCAATTTAGAGTAGTTCGACTTCAAGTCTACATCCACTATCTTAACTTCCACACTAA
5786760 GAATTTCTCAAATCCACTATTTGCTTACCTTTAAGGATAAGGTGTAACCTTACAAACAC
66 GAATTTCTCAAATCCACTATTTGCTTACCTTTAAGGATAAGGTGTAACCTTACAAACAC
5786819 TTTGCACATCAATTTAGAGTAGTTCGACTTCAAGTCTACATCCACTATCTTAACTTCCACACTAA
1 TTTGCACATCAATTTAGAGTAGTTCGACTTCAAGTCTACATCCACTATCTTAACTTCCACACTAA
5786884 GAATTTCTCAAATCCACTATTTGCTTACCTTTAAGGATAAGGTGTAACCTTACAAACAC
66 GAATTTCTCAAATCCACTATTTGCTTACCTTTAAGGATAAGGTGTAACCTTACAAACAC
5786943 TT
1 TT
5786945 CAAGGTTTAT
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 126 1.00
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (124 bp):
TTTGCACATCAATTTAGAGTAGTTCGACTTCAAGTCTACATCCACTATCTTAACTTCCACACTAA
GAATTTCTCAAATCCACTATTTGCTTACCTTTAAGGATAAGGTGTAACCTTACAAACAC
Found at i:5787465 original size:20 final size:20
Alignment explanation
Indices: 5787399--5787470 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 20
5787389 ATTTTCATCG
* *
5787399 AGGGATCGATTCTTTTGGTGA
1 AGGGATCGATCCTTTT-GAGA
* ***
5787420 AGGGATTGATCCTTTT-CCT
1 AGGGATCGATCCTTTTGAGA
*
5787439 CGGGATCGATCCTTTTGAGA
1 AGGGATCGATCCTTTTGAGA
5787459 AGGGATCGATCC
1 AGGGATCGATCC
5787471 CAAACTTTCT
Statistics
Matches: 39, Mismatches: 11, Indels: 3
0.74 0.21 0.06
Matches are distributed among these distances:
19 14 0.36
20 11 0.28
21 14 0.36
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.33
Consensus pattern (20 bp):
AGGGATCGATCCTTTTGAGA
Found at i:5790035 original size:17 final size:17
Alignment explanation
Indices: 5790013--5790059 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
5790003 AAATATTTGA
5790013 AGGAATTGGAATCTGTC
1 AGGAATTGGAATCTGTC
5790030 AGGAATTGGAATCTGTC
1 AGGAATTGGAATCTGTC
*
5790047 AGGAATTGAAATC
1 AGGAATTGGAATC
5790060 CAATTTCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.28
Consensus pattern (17 bp):
AGGAATTGGAATCTGTC
Found at i:5790491 original size:35 final size:35
Alignment explanation
Indices: 5790452--5790519 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
5790442 GAACCCAACC
**
5790452 CGACCCGAATATCACATTTAAAAAAACCGACCCCT
1 CGACCCGAATATCACACATAAAAAAACCGACCCCT
* *
5790487 CGACCCTAATATCACACATAAAAAACCCGACCC
1 CGACCCGAATATCACACATAAAAAAACCGACCC
5790520 GAAAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.41, C:0.37, G:0.07, T:0.15
Consensus pattern (35 bp):
CGACCCGAATATCACACATAAAAAAACCGACCCCT
Found at i:5798657 original size:20 final size:21
Alignment explanation
Indices: 5798632--5798724 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
5798622 TTTTCCCAAT
*
5798632 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
5798652 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
5798673 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
5798693 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
5798714 TCGCAATGCGA
1 TCGCAATGCGA
5798725 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:5798738 original size:20 final size:20
Alignment explanation
Indices: 5798713--5798827 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
5798703 AATTGGGAAA
*
5798713 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
5798733 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* * *
5798754 ATCTCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
5798774 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
5798794 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
5798814 TTCGCAACGCGATA
1 ATCGCAACGCGATA
5798828 ATACATAATC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 66 0.84
21 13 0.16
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:5798739 original size:41 final size:41
Alignment explanation
Indices: 5798632--5798724 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
5798622 TTTTCCCAAT
5798632 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
5798673 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
5798714 TCGCAATGCGA
1 TCGCAATGCGA
5798725 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:5799043 original size:22 final size:22
Alignment explanation
Indices: 5799015--5799058 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5799005 CACTCTCTCA
*
5799015 CCCATCTCTGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
5799037 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
5799059 TATCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:5799347 original size:20 final size:20
Alignment explanation
Indices: 5799322--5799359 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5799312 CGATTCTCTC
5799322 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
5799342 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
5799360 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:5800723 original size:18 final size:18
Alignment explanation
Indices: 5800679--5800723 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
5800669 TCCACTTCGG
*
5800679 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
5800697 AAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
5800715 GAGCCATCA
1 GAGCCATCA
5800724 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.44, G:0.13, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:5801253 original size:19 final size:20
Alignment explanation
Indices: 5801199--5801265 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
5801189 TAGTTTACTT
* *
5801199 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
5801219 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
5801239 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
5801258 TCGCAACG
1 TCGCAACG
5801266 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:5801273 original size:14 final size:14
Alignment explanation
Indices: 5801254--5801311 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
5801244 ATGCGAAATG
*
5801254 AAAATCGCAACGAC
1 AAAATCGCAACGAA
5801268 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAA
5801284 ATGAAATCGCAACGAA
1 A--AAATCGCAACGAA
5801300 AAAATCGCAACG
1 AAAATCGCAACG
5801312 CGAAATGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:5801296 original size:32 final size:33
Alignment explanation
Indices: 5801238--5801328 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
5801228 GGAAATGGCT
*
5801238 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
5801271 ATCGCAATGCGAAATG-AAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
5801303 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
5801329 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
Found at i:5801391 original size:20 final size:19
Alignment explanation
Indices: 5801340--5801411 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
5801330 GCGATTTGTG
**
5801340 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATAGTCA
* *
5801359 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATAGTCA
5801378 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATAGTCA
5801398 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
5801412 TTTAAGTTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 29 0.63
20 17 0.37
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.39
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:5803444 original size:19 final size:19
Alignment explanation
Indices: 5803429--5803477 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
5803419 ATCGCAACGA
5803429 GAAAATCGCAATGCAAAAT
1 GAAAATCGCAATGCAAAAT
*
5803448 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCAAAAT
5803467 GAAAATCGCAA
1 GAAAATCGCAA
5803478 CGAGAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCAAAAT
Found at i:5803484 original size:19 final size:19
Alignment explanation
Indices: 5803429--5803484 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
5803419 ATCGCAACGA
5803429 GAAAATCGCAATGCA-AAAT
1 GAAAATCGCAATG-AGAAAT
*
5803448 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGAGAAAT
*
5803467 GAAAATCGCAACGAGAAA
1 GAAAATCGCAATGAGAAA
5803485 ATCGCAATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.52, C:0.16, G:0.20, T:0.12
Consensus pattern (19 bp):
GAAAATCGCAATGAGAAAT
Found at i:5803572 original size:20 final size:20
Alignment explanation
Indices: 5803515--5803572 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
5803505 TCGCATTGCG
* *
5803515 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
5803535 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
5803555 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
5803573 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:5805372 original size:33 final size:33
Alignment explanation
Indices: 5805326--5805452 Score: 166
Period size: 33 Copynumber: 3.8 Consensus size: 33
5805316 GGAAATTACT
*
5805326 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
5805359 ATCGCAATGCGAAATGAAAATCGCAATGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
5805391 TTTCGCTATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
5805425 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
5805453 CGAATTTAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
32 1 0.01
33 77 0.97
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:5805386 original size:19 final size:19
Alignment explanation
Indices: 5805326--5805456 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
5805316 GGAAATTACT
*
5805326 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5805345 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
5805359 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5805378 ATCGCAATGC----T-AAT
1 ATCGCAATGCGAAATGAAA
* *
5805392 TTCGCTATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
5805411 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
5805425 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
5805444 ATCGCAACGCGAA
1 ATCGCAATGCGAA
5805457 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 29 0.35
15 3 0.04
16 4 0.05
17 4 0.05
18 3 0.04
19 41 0.49
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:5805441 original size:66 final size:66
Alignment explanation
Indices: 5805335--5805459 Score: 214
Period size: 66 Copynumber: 1.9 Consensus size: 66
5805325 TATCGCAATA
* * *
5805335 CGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCTAATTTCGCTAT
1 CGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGCGAATTTCGCTAT
5805400 G
66 G
*
5805401 CGAAATGAAAATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACGCGAATTT
1 CGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGCGAATTT
5805460 AATTTCGCAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.17
Consensus pattern (66 bp):
CGAAATGAAAATCGCAACGAGAGAATCGCAAAGCGAAATGAAAATCGCAACGCGAATTTCGCTAT
G
Found at i:5805474 original size:19 final size:20
Alignment explanation
Indices: 5805452--5805494 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
5805442 AAATCGCAAC
5805452 GCGAATTT-AATTTCGCATT
1 GCGAATTTCAATTTCGCATT
* * *
5805471 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCATT
5805491 GCGA
1 GCGA
5805495 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCATT
Found at i:5805487 original size:20 final size:19
Alignment explanation
Indices: 5805461--5805528 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
5805451 CGCGAATTTA
5805461 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
5805480 ATTTTCGCGTTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
5805498 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
5805514 ATTTCGCATTGCGAT
1 ATTTCGCATTGCGAT
5805529 AGTACTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 6 0.15
16 7 0.17
17 4 0.10
18 3 0.08
19 8 0.20
20 12 0.30
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:5805654 original size:14 final size:14
Alignment explanation
Indices: 5805635--5805671 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
5805625 CATCAATTAA
5805635 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
5805649 ACAAATCACCTTTT
1 ACAAATCAACTTTT
5805663 ACAAATCAA
1 ACAAATCAA
5805672 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5807093 original size:21 final size:21
Alignment explanation
Indices: 5807027--5807093 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
5807017 GTGAATCGGG
*
5807027 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
5807047 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
5807069 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
5807090 CTCT
1 CTCT
5807094 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:5807112 original size:42 final size:41
Alignment explanation
Indices: 5807027--5807149 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
5807017 GTGAATCGGG
* * * * *
5807027 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
5807069 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
5807111 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
5807150 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:5809234 original size:33 final size:33
Alignment explanation
Indices: 5809177--5809276 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
5809167 ACGAGATAAT
*
5809177 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
5809211 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
5809244 GACAATCGCAACGCGAAATGAAAATCGCAACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
5809277 CGAAATAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 46 0.77
34 14 0.23
ACGTcount: A:0.40, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:5809269 original size:19 final size:19
Alignment explanation
Indices: 5809152--5809336 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
5809142 TCTTTTGGTT
*
5809152 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
5809171 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
5809191 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
5809209 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
5809225 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
5809243 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
5809258 GAAATGAAAATCGCAACCAC
1 GAAATGAAAATCGCAA-CGC
*
5809278 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
5809297 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
5809316 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
5809335 GA
1 GA
5809337 TTTTGGTTTC
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 61 0.45
20 44 0.32
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:5809301 original size:39 final size:38
Alignment explanation
Indices: 5809247--5809336 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
5809237 GCGACCAGAC
5809247 AATCGCAACGCGAAATGAAAATCGCAACCACGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CACGAAATAAA
* *
5809286 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACACGAAATAAA
*
5809324 AATCGCAATGCGA
1 AATCGCAACGCGA
5809337 TTTTGGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACACGAAATAAA
Found at i:5809357 original size:19 final size:19
Alignment explanation
Indices: 5809335--5809398 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
5809325 ATCGCAATGC
*
5809335 GATTTTGGTTTCGCGTTGT
1 GATTTTGATTTCGCGTTGT
* *
5809354 GATTTTTATTTCGCGTTGC
1 GATTTTGATTTCGCGTTGT
* *
5809373 GATAGTT-ATTTCCGCGTTGC
1 GAT-TTTGATTT-CGCGTTGT
5809393 GATTTT
1 GATTTT
5809399 CATTCTCGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 25 0.66
20 13 0.34
ACGTcount: A:0.11, C:0.14, G:0.25, T:0.50
Consensus pattern (19 bp):
GATTTTGATTTCGCGTTGT
Found at i:5809390 original size:20 final size:19
Alignment explanation
Indices: 5809343--5809395 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
5809333 GCGATTTTGG
* **
5809343 TTTCGCGTTGTGATTTTTA
1 TTTCGCGTTGCGATAGTTA
5809362 TTTCGCGTTGCGATAGTTA
1 TTTCGCGTTGCGATAGTTA
5809381 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
5809396 TTTCATTCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTTA
Found at i:5809939 original size:20 final size:20
Alignment explanation
Indices: 5809914--5809966 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
5809904 GCGCTATGTA
5809914 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
5809934 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
5809954 TATCTCGTTGCGA
1 AATCGCGTTGCGA
5809967 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:5810027 original size:41 final size:41
Alignment explanation
Indices: 5809977--5810089 Score: 129
Period size: 41 Copynumber: 2.8 Consensus size: 41
5809967 TTTTGTATTA
*
5809977 TCGCATTGCGATAGTAAGTA-TCGAATTGCGATTTTCCCAAT
1 TCGCGTTGCGAT-GTAAGTATTCGAATTGCGATTTTCCCAAT
* ** *
5810018 TCGCGTTGCGATTTACTTATTCGTATTGCGATTTTCCCAAT
1 TCGCGTTGCGATGTAAGTATTCGAATTGCGATTTTCCCAAT
* ** *
5810059 TCGCGTTGCGATTTACTTATTCGCATTGCGA
1 TCGCGTTGCGATGTAAGTATTCGAATTGCGA
5810090 ATTGGGAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 4 0.06
41 61 0.94
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATGTAAGTATTCGAATTGCGATTTTCCCAAT
Found at i:5810028 original size:21 final size:21
Alignment explanation
Indices: 5810002--5810072 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
5809992 AAGTATCGAA
5810002 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
* ** **
5810023 TTGCGA-TTTACTTATTCGTA
1 TTGCGATTTTCCCAATTCGCG
5810043 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
5810064 TTGCGATTT
1 TTGCGATTT
5810073 ACTTATTCGC
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCGCG
Found at i:5810046 original size:20 final size:20
Alignment explanation
Indices: 5810016--5810089 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
5810006 GATTTTCCCA
*
5810016 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* * **
5810036 ATTCGTATTGCGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
5810057 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
5810077 ATTCGCATTGCGA
1 ATTCGCATTGCGA
5810090 ATTGGGAAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:5811083 original size:30 final size:30
Alignment explanation
Indices: 5811036--5811114 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
5811026 TGGTTATTGG
*
5811036 AATGT-AAATTTTGAAAGTTTCTA-GACTAA
1 AATGTAAAATTTTAAAAGTTT-TAGGACTAA
*
5811065 AATGTAAAATTGTAAAAGTTTTAGGACTAA
1 AATGTAAAATTTTAAAAGTTTTAGGACTAA
*
5811095 AATGTAAATTTTTAAAAGTT
1 AATGTAAAATTTTAAAAGTT
5811115 AAATTTTGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 7 0.16
30 37 0.84
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (30 bp):
AATGTAAAATTTTAAAAGTTTTAGGACTAA
Found at i:5813710 original size:3 final size:3
Alignment explanation
Indices: 5813702--5813726 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5813692 TTTGGTAGTG
5813702 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
5813727 AACCCTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:5819468 original size:12 final size:12
Alignment explanation
Indices: 5819453--5819478 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5819443 TAATTAATAA
5819453 AATAAAATAATT
1 AATAAAATAATT
5819465 AATAAAATAATT
1 AATAAAATAATT
5819477 AA
1 AA
5819479 ATTTTAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAAAATAATT
Found at i:5819481 original size:17 final size:17
Alignment explanation
Indices: 5819442--5819474 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5819432 TATAGTGAAT
5819442 ATAATTAATAAAATAAA
1 ATAATTAATAAAATAAA
5819459 ATAATTAATAAAATAA
1 ATAATTAATAAAATAA
5819475 TTAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAATTAATAAAATAAA
Found at i:5820329 original size:115 final size:119
Alignment explanation
Indices: 5820150--5820386 Score: 304
Period size: 115 Copynumber: 2.0 Consensus size: 119
5820140 GTATGTGCAT
* * * * *
5820150 TTAATGTCTAATGGTTGAGAGTCTTTGAACATATATTACCTTATATTTACTTCATATACTATATA
1 TTAATGTCTAATGATTGAGAGTCTTTAAACAGATAATACCTTATATTTACTTCAGATACTATATA
*
5820215 AATTCACCAATGCAATTAATGTA-TTC-TACAT-TA-ATATTAAACCATTAATA
66 AATTCACCAATGCAATTAATGTATTTCATACATATATATATTAAACAATTAATA
* * * * *
5820265 TTAATTTCTGATGATTGAGGGTCTTTAAATAGATAATACCTTATATTTACCTT-AGATATTATAT
1 TTAATGTCTAATGATTGAGAGTCTTTAAACAGATAATACCTTATATTTA-CTTCAGATACTATAT
* *
5820329 AAATTCACCGATGCAATTAATGTATTTTCATATATATATATATTAAACAATTAATA
65 AAATTCACCAATGCAATTAATGTA-TTTCATACATATATATATTAAACAATTAATA
5820385 TT
1 TT
5820387 TTTTTTTTGT
Statistics
Matches: 103, Mismatches: 13, Indels: 7
0.84 0.11 0.06
Matches are distributed among these distances:
115 73 0.71
116 3 0.03
117 3 0.03
118 4 0.04
119 2 0.02
120 18 0.17
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (119 bp):
TTAATGTCTAATGATTGAGAGTCTTTAAACAGATAATACCTTATATTTACTTCAGATACTATATA
AATTCACCAATGCAATTAATGTATTTCATACATATATATATTAAACAATTAATA
Found at i:5821133 original size:60 final size:60
Alignment explanation
Indices: 5821006--5821142 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
5820996 ATAGTTATGT
* * * **
5821006 GACCATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAATAACGCCATATTGTTGGAG
1 GACCATTTTGTAACTTTTAATAGTCAGAAGACTCAACAAAATAACGCCATATAGCCGGAG
* * *
5821066 GATCATTTTGTAACTTTTAATAGTCAGAAGACTCAATAAAATATCGACCA-ATAGCC-GAGG
1 GACCATTTTGTAACTTTTAATAGTCAGAAGACTCAACAAAATAACG-CCATATAGCCGGA-G
5821126 GACCA-TTTGTATACTTT
1 GACCATTTTGTA-ACTTT
5821143 ACCCTATATT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 8 0.12
60 54 0.83
61 3 0.05
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCAGAAGACTCAACAAAATAACGCCATATAGCCGGAG
Found at i:5821618 original size:5 final size:5
Alignment explanation
Indices: 5821608--5821642 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
5821598 TAATCTTAGT
5821608 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
5821643 ACATGAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTCA
Found at i:5824603 original size:12 final size:13
Alignment explanation
Indices: 5824571--5824607 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5824561 TATGAATTAG
5824571 TGATATAAGAATA
1 TGATATAAGAATA
5824584 TGATATAA-AATA
1 TGATATAAGAATA
5824596 TGCA-ATAAGAAT
1 TG-ATATAAGAAT
5824608 CTATGTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.54, C:0.03, G:0.14, T:0.30
Consensus pattern (13 bp):
TGATATAAGAATA
Found at i:5825139 original size:23 final size:23
Alignment explanation
Indices: 5825113--5825187 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
5825103 AATCTTGTAT
*
5825113 GGCACTAAGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
5825136 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
5825159 GGCATTACGGTACAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
5825182 GGCACT
1 GGCACT
5825188 TCAGTGCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:5825318 original size:2 final size:2
Alignment explanation
Indices: 5825311--5825338 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5825301 AACGTATGAA
5825311 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
5825339 GATGTGTAAT
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:5825372 original size:12 final size:11
Alignment explanation
Indices: 5825305--5825372 Score: 54
Period size: 10 Copynumber: 6.4 Consensus size: 11
5825295 GAATACAACG
*
5825305 TATGAAATATA
1 TATGATATATA
5825316 TAT-ATATATA
1 TATGATATATA
5825326 TAT-ATATATA
1 TATGATATATA
* *
5825336 TATGATGTGTAA
1 TATGATATAT-A
*
5825348 TATGA-AT-TG
1 TATGATATATA
5825357 TATGATATGATA
1 TATGATAT-ATA
5825369 TATG
1 TATG
5825373 TGTGTTATGG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
9 5 0.11
10 22 0.48
11 8 0.17
12 11 0.24
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (11 bp):
TATGATATATA
Found at i:5833999 original size:54 final size:54
Alignment explanation
Indices: 5833831--5834218 Score: 550
Period size: 54 Copynumber: 7.2 Consensus size: 54
5833821 ATGGGTTTCT
* * * * * * *
5833831 CACACGTAGTG-CAGATACGGTAATTCA-CAACTCATAATGAATTACGTT-GGGTG
1 CACACATAGTGCCA-ATACGGAAATTCATAAACTAATTATGAATTTC-TTAGGTTG
* * *
5833884 CATACATAGTGCCAATACGGAAATTCATAAACT-ATTATGAATTTATTAGGTTA
1 CACACATAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAGGTTG
* * *
5833937 CAAACATAGTGGCAATACGAAAATTCATAAACTAATTATGAATTTCTTAGGTTG
1 CACACATAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAGGTTG
*
5833991 CACACATAGTGCCAATACGGAAATTCATAAACTAATTATGAGTTTCTTAGGTTG
1 CACACATAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAGGTTG
* * * *
5834045 CACACATAGTGCCAATATGAAAATTCATAAACTTATTATGAATTTGTTAGGTTG
1 CACACATAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAGGTTG
*
5834099 CACACATAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAGGTTC
1 CACACATAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAGGTTG
*
5834153 CACACATAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAAGTTG
1 CACACATAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAGGTTG
5834207 CACACATAGTGC
1 CACACATAGTGC
5834219 TCATTTGGTA
Statistics
Matches: 301, Mismatches: 30, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
52 2 0.01
53 63 0.21
54 236 0.78
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31
Consensus pattern (54 bp):
CACACATAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAGGTTG
Found at i:5835104 original size:21 final size:20
Alignment explanation
Indices: 5835080--5835119 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5835070 TTTCTTAGTT
* *
5835080 TTAATCCTCTTTAACCATTCC
1 TTAAGCCTCTATAA-CATTCC
5835101 TTAAGCCTCTATAACATTC
1 TTAAGCCTCTATAACATTC
5835120 AAGGTTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.30, G:0.03, T:0.40
Consensus pattern (20 bp):
TTAAGCCTCTATAACATTCC
Found at i:5839316 original size:54 final size:54
Alignment explanation
Indices: 5839245--5839430 Score: 187
Period size: 54 Copynumber: 3.5 Consensus size: 54
5839235 CAGATGCGGT
* * * *
5839245 AATTCA-CAACTCATTATGAATTAT-GTAGGGTATACACAAAGTGCTAATACGGA
1 AATTCATCAACTAATTATGAATT-TCGTAAGGTACACACAAAGTGCCAATACGGA
* * * * *
5839298 AATTCATCAACTTATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACGGA
1 AATTCATCAACTAATTATGAATTTCGTAAGGTACACACAAAGTGCCAATACGGA
* * * * * * **
5839352 AATTCCTAAACTAATTATGAATTTCTTAAGTTGCACACATAGTGCCAATACAAA
1 AATTCATCAACTAATTATGAATTTCGTAAGGTACACACAAAGTGCCAATACGGA
*
5839406 AATTCATAAACTAATTATGAATTTC
1 AATTCATCAACTAATTATGAATTTC
5839431 TTAGGTTGCA
Statistics
Matches: 117, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
53 7 0.06
54 110 0.94
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (54 bp):
AATTCATCAACTAATTATGAATTTCGTAAGGTACACACAAAGTGCCAATACGGA
Found at i:5839431 original size:54 final size:54
Alignment explanation
Indices: 5839278--5839448 Score: 270
Period size: 54 Copynumber: 3.2 Consensus size: 54
5839268 TGTAGGGTAT
* * * *
5839278 ACACAAAGTGCTAATACGGAAATTCATCAACTTATTATGAATTTCTTAAGTTGC
1 ACACATAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAAGTTGC
*
5839332 ACACATAGTGCCAATACGGAAATTCCTAAACTAATTATGAATTTCTTAAGTTGC
1 ACACATAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAAGTTGC
** *
5839386 ACACATAGTGCCAATACAAAAATTCATAAACTAATTATGAATTTCTTAGGTTGC
1 ACACATAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAAGTTGC
5839440 ACACATAGT
1 ACACATAGT
5839449 TTTAAAATCA
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 108 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.32
Consensus pattern (54 bp):
ACACATAGTGCCAATACGGAAATTCATAAACTAATTATGAATTTCTTAAGTTGC
Found at i:5839541 original size:20 final size:19
Alignment explanation
Indices: 5839494--5839549 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
5839484 ACTGATTCAA
*
5839494 GTGGTATCGATACCAAGAG
1 GTGGTATCGATACCATGAG
5839513 G-GGAATATCGATACCATGAG
1 GTGG--TATCGATACCATGAG
5839533 GATGGTATCGATACCAT
1 G-TGGTATCGATACCAT
5839550 TGAGCACATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 27 0.84
22 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (19 bp):
GTGGTATCGATACCATGAG
Found at i:5839600 original size:19 final size:21
Alignment explanation
Indices: 5839578--5839624 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
5839568 ATGGTATCAG
5839578 TACCATA-ATAG-AGTATCGA
1 TACCATAGATAGTAGTATCGA
5839597 TACCATAGTATAGTAGTATCGA
1 TACCATAG-ATAGTAGTATCGA
5839619 TACCAT
1 TACCAT
5839625 GGTGGGGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.28
21 4 0.16
22 14 0.56
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (21 bp):
TACCATAGATAGTAGTATCGA
Found at i:5840036 original size:58 final size:58
Alignment explanation
Indices: 5839973--5840241 Score: 484
Period size: 58 Copynumber: 4.6 Consensus size: 58
5839963 ATGGCACTAA
* *
5839973 GTGTGCAAAAAGTTAAGAAAATCATACTAAGTGTATGAATTTCCATATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
*
5840031 GTGTGCAAAAAGTTAAGAAATTCATATTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
*
5840089 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
5840147 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
5840205 GTGTACAAAAAGTTAAGAGATTCATACTAAGTGTATG
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATG
5840242 TATCTCCATG
Statistics
Matches: 203, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 203 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (58 bp):
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:5840863 original size:68 final size:68
Alignment explanation
Indices: 5840476--5840846 Score: 519
Period size: 68 Copynumber: 5.5 Consensus size: 68
5840466 GATTAAAGGT
** * **
5840476 CTAACTGTATATTTGATAGAAATATGTCAATCATGTCAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGTCAGTTAGATGAAAGGCTAAGTGCCTTTGA
5840541 GGC
66 GGC
* * *
5840544 CTAACTGTGGATTTGACAGAAAGGTGTCAATCATGTCAGTTAGATGAAAGGCTAAGTGTCTTTAA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGTCAGTTAGATGAAAGGCTAAGTGCCTTTGA
5840609 GGC
66 GGC
* * * *
5840612 CTAACTGTGCATTTGATAGAAAGGTGCCAATCAAGTCAGTTAGATGAAATGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGTCAGTTAGATGAAAGGCTAAGTGCCTTTGA
5840677 GGC
66 GGC
* * * *
5840680 CTAACTATGCATTTGACATAAAGGTGTCAATCATGTCAGTTAGATAAAAGGCT-AGATTCCTTTG
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGTCAGTTAGATGAAAGGCTAAG-TGCCTTTG
5840744 AGGC
65 AGGC
* * *
5840748 CTAACTGTGCATTTGATAGAAAGGTCTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGTCAGTTAGATGAAAGGCTAAGTGCCTTTGA
5840813 GGC
66 GGC
* * * *
5840816 TTGATTGTGCATTTGACAAAAAGGTGTCAAT
1 CTAACTGTGCATTTGACAGAAAGGTGTCAAT
5840847 TATGCCATTT
Statistics
Matches: 266, Mismatches: 35, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
67 2 0.01
68 262 0.98
69 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (68 bp):
CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGTCAGTTAGATGAAAGGCTAAGTGCCTTTGA
GGC
Found at i:5840982 original size:45 final size:45
Alignment explanation
Indices: 5840925--5841149 Score: 351
Period size: 45 Copynumber: 5.0 Consensus size: 45
5840915 GTATAAAAGA
5840925 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
* * * * *
5840970 CATTAAATGATGCCATAGTTGAAATGTATATGGGTGAATTATCGG
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
* * * *
5841015 CATGAAAGAATGTCATAATTGAAATGCATGTGGGTGCATTATCGA
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
* *
5841060 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGTATTATAGG
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
5841105 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
5841150 TATAAAAAGA
Statistics
Matches: 158, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 158 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (45 bp):
CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGG
Found at i:5841173 original size:135 final size:135
Alignment explanation
Indices: 5840923--5841173 Score: 387
Period size: 135 Copynumber: 1.9 Consensus size: 135
5840913 TTGTATAAAA
* * * *
5840923 GACATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGGCATTAAATGATGCCATAG
1 GACATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATAGGCATGAAAGGATGCCATAA
* * *
5840988 TTGAAATGTATATGGGTGAATTATCGGCATGAAAGAATGTCATAATTGAAATGCATGTGGGTGCA
66 TTGAAATGCATATGGGTGAATTATCGGCATAAAAGAATGTCATAAATGAAATGCATGTGGGTGCA
5841053 TTATC
131 TTATC
*
5841058 GACATGAAAGGATGCCATAATTGAAATGCATATGGGTGTATTATAGGCATGAAAGGATGCCATAA
1 GACATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATAGGCATGAAAGGATGCCATAA
* * *
5841123 TTGAAATGCATATGGGTGCATTATCGGTATAAAA-AGATGTTATAAATGAAA
66 TTGAAATGCATATGGGTGAATTATCGGCATAAAAGA-ATGTCATAAATGAAA
5841174 AGGCATAATG
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
134 1 0.01
135 103 0.99
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.29
Consensus pattern (135 bp):
GACATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATAGGCATGAAAGGATGCCATAA
TTGAAATGCATATGGGTGAATTATCGGCATAAAAGAATGTCATAAATGAAATGCATGTGGGTGCA
TTATC
Found at i:5843159 original size:30 final size:29
Alignment explanation
Indices: 5843100--5843160 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
5843090 AATTTTGGAT
* * *
5843100 TCGAATTTAATCAAATTTCACTATGGTCC
1 TCGAATTTAATAAAATTTCAATATAGTCC
*
5843129 TCGAATTTAATTAAAATTTCAATTTAGTCC
1 TCGAATTTAA-TAAAATTTCAATATAGTCC
5843159 TC
1 TC
5843161 AAAATAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (29 bp):
TCGAATTTAATAAAATTTCAATATAGTCC
Found at i:5845579 original size:23 final size:23
Alignment explanation
Indices: 5845532--5845579 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5845522 AATAACATAT
* **
5845532 TAGGTAACGTTTATATAATGTAA
1 TAGGTAACGATTATATAATAAAA
*
5845555 TAGGTAGCGATTATATAATAAAA
1 TAGGTAACGATTATATAATAAAA
5845578 TA
1 TA
5845580 TGCATTTAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (23 bp):
TAGGTAACGATTATATAATAAAA
Found at i:5845645 original size:23 final size:23
Alignment explanation
Indices: 5845610--5845680 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 23
5845600 ATCAAATACA
* *
5845610 ATAACATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
* *
5845633 ATAATATAATAGGTACCGTTTAT
1 ATAATATAATAGGTAGCGCTTAT
* *
5845656 ATAATGTAATAGGCAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
5845679 AT
1 AT
5845681 TAACCTATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:5846148 original size:199 final size:198
Alignment explanation
Indices: 5845698--5846393 Score: 780
Period size: 199 Copynumber: 3.5 Consensus size: 198
5845688 TTTTATAAAT
* * * * * *
5845698 AAACCGGTATATTTATACAGGTAACATTGCAAATTTACCTATTACATTATATTTATCGGTTTCAA
1 AAACCGATATATTTATACAGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
* * * *
5845763 TGGTTTT-GGATCGATACAATTT--TAAATGTATCGACACTTTATGCGTGTACCTCG-TTGAGCA
66 TGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGTGTGCACCTCGTTTG-GCA
* *
5845824 TTCATTCTGGA-AACAAGTATCGACACAAACTTAAAGAGTGTCGATACATTATAT-AT-ACCTAT
129 TTCATTATGGACAACAAGTATCGACACAAA-TTAAA-AGTGTCGATAC-TT-TATGATGACATAT
5845886 TTT-TCATA
190 TTTCTCATA
* * * *
5845894 AAACCGGTATATTTCTATCAGG-TACATTGTAAATTTACATATCACATTGTAATTATCGGTTTCG
1 AAACCGATATATTTATA-CAGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCG
5845958 ATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTGCACC-CGTTTGGCAT
65 ATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGCAT
*
5846022 TCATTATGGACAA-AATGTATCTACACAAATTTAATAAGTGTCGATACTTTATGATGACATATTT
130 TCATTATGGACAACAA-GTATCGACACAAA-TTAA-AAGTGTCGATACTTTATGATGACATATTT
5846086 TCTCATA
192 TCTCATA
* *
5846093 AAACCGATATATTTTTACCGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
1 AAACCGATATATTTATACAGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
* * * *
5846158 T-TTTATTGGGATGGACACTTTTAATAATTGTATCGACAC-TTAT-TACGTGCACCTCATTTAGG
66 TGTTT-TTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGT--GTGCACCTCGTTT-GG
* * * *
5846220 CATTCATTTTGGACAATAAGTATCGACACAAATTACACAAGTGTCGATACATTATGTTGACATAT
127 CATTCATTATGGACAACAAGTATCGACACAAATTA-A-AAGTGTCGATACTTTATGATGACATAT
*
5846285 TTTCTAAT-
190 TTTCTCATA
* * * * *
5846293 TAACC-AGTATATTTATACTGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCG
1 AAACCGA-TATATTTATACAGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCG
* *
5846357 AAGTTTTTTGGG-TCGATACTTTTAGA-AAAAGTATCGA
65 ATG-TTTTTGGGATCGATACTTTTA-ATAAATGTATCGA
5846394 TATATATATT
Statistics
Matches: 435, Mismatches: 42, Indels: 42
0.84 0.08 0.08
Matches are distributed among these distances:
196 64 0.15
197 36 0.08
198 77 0.18
199 102 0.23
200 83 0.19
201 68 0.16
202 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (198 bp):
AAACCGATATATTTATACAGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGCATT
CATTATGGACAACAAGTATCGACACAAATTAAAAGTGTCGATACTTTATGATGACATATTTTCTC
ATA
Found at i:5852907 original size:402 final size:396
Alignment explanation
Indices: 5852123--5853291 Score: 1367
Period size: 402 Copynumber: 2.9 Consensus size: 396
5852113 TGTTATTTAC
* * ** * *
5852123 AAGTATCGCCACAA-A-TCTAAAACGTGTCGATACATT-TGTTCACCTATTTTCTCATAAAA-CA
1 AAGTATCGACACAATATTC-AAAA-GTGTCGACACATTATGTAGACCTATTCTCACATAAAACCA
* * * * ** * *
5852184 GGTACATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
64 -GTATATTTACACCGGTTATATTACAAAATTAACTATTACATTATAATTAT-GGTTTCGATG-TT
* * * ** * **
5852249 TTGGGATCGATATTTTTTAAAAAATGTATCGACACTATATGCTTGCAACCC-TTTTGGCTTTAAT
126 TTAGGATCGATACTTTTT--AAAATGTATCGACACTTTATGGGTGC-ACCCTTTTTGGATTTCCT
* * *
5852313 TTTGGACAAAAAGTATCGACACAAA-TCTAAAATGTGTCGATACATTATGT-TCACCTATTTTAA
188 TCTGGACAAAAAGTATCGACACAAATTCTAAAA-GTGTCGATACATTATGTAT-ATCTATTTTCA
* * *
5852376 CATAAAACCGGTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTT
251 CAAAAAATCGGTTTATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTA-TGGTT
* * *
5852441 TCGATGTTTTTAGAATCGATACTTTTTATAAATGTATCGACACTTTATTCGTTCACCCTTTTGGG
315 TCGATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGG
5852506 CATTCATTATGGACAAA
380 CATTCATTATGGACAAA
* *
5852523 ACA-TATCGACAC-ATCATTCAAAAGTGTCGACACATTATGTAGACCTATTCTGACATAAAACCG
1 A-AGTATCGACACAAT-ATTCAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCA
* * *
5852586 GTATGTTTACACCGGTTATATTACAAAATTAATTATTACATTATATTTATGTGTTTCGATGTTTT
64 GTATATTTACACCGGTTATATTACAAAATTAACTATTACATTATAATTATG-GTTTCGATGTTTT
* *
5852651 AAGGATCGATACTGTTTAAACATGTATCGACACTTTATGGGTGCACCCTTTTTGGATTTTCCTTG
128 -AGGATCGATACTTTTTAAA-ATGTATCGACACTTTATGGGTGCACCCTTTTTGGA-TTTCCTTC
* * *
5852716 TGGACCAAAAGTATCGACACAAATTCTACAAGTGTCGATACATTATGTATATCTATTTTCTCAAA
190 TGGACAAAAAGTATCGACACAAATTCTAAAAGTGTCGATACATTATGTATATCTATTTTCACAAA
*
5852781 AAATCGGTTTTATTTATA-TCGGTTACATTTTAAATTTACCTATTACATTATAATTATCGGTTTC
255 AAATCGG-TTTATTTATACT-GGTTACATTGTAAATTTACCTATTACATTATAATTAT-GGTTTC
*
5852845 GATATTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCA
317 GATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCA
*
5852910 TTCATTCTGGACAAA
382 TTCATTATGGACAAA
* * *
5852925 AAGTATCGACACAATATTCAAAAGTGTCGACATATTATGTAGACCTATTTTCACATAAAACTAGT
1 AAGTATCGACACAATATTCAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCAGT
* * * * *
5852990 ATATTTATATCTGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
66 ATATTTACACCGGTTATATTACAAAATTAACTATTACATTATAATTAT-GGTTTCGATGTTTTAG
* * *
5853055 AGATCAATACTTTTTTAAAAAGTATCGACACTTTATGGGTGCACCCTTTTGGGCA-TTCCTTCTG
130 -GATCGATAC-TTTTTAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGG-ATTTCCTTCTG
* * * * * * * *
5853119 GATAAACAGTATCGACACAAATTCCAGAAGTGTCGATACATTATATAGAAT-TATTCTCGCATAA
192 GACAAAAAGTATCGACACAAATTCTAAAAGTGTCGATACATTATGTA-TATCTATTTTCACA-AA
* * *
5853183 AACAT--GTTTAGTTATACTGGTTATATTGTAAATTTACCTATTACATTATATTTATGGATTTCG
255 AA-ATCGGTTTATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATGG-TTTCG
* * *
5853246 ATGTTTTTGGGATCAATATTTTTTAAAAATGTATCGACACTTTATG
318 ATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATG
5853292 GGAAACTTTA
Statistics
Matches: 664, Mismatches: 78, Indels: 54
0.83 0.10 0.07
Matches are distributed among these distances:
399 10 0.02
400 142 0.21
401 209 0.31
402 290 0.44
403 13 0.02
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (396 bp):
AAGTATCGACACAATATTCAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAACCAGT
ATATTTACACCGGTTATATTACAAAATTAACTATTACATTATAATTATGGTTTCGATGTTTTAGG
ATCGATACTTTTTAAAATGTATCGACACTTTATGGGTGCACCCTTTTTGGATTTCCTTCTGGACA
AAAAGTATCGACACAAATTCTAAAAGTGTCGATACATTATGTATATCTATTTTCACAAAAAATCG
GTTTATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATGGTTTCGATGTTTTT
GGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTATG
GACAAA
Found at i:5853293 original size:200 final size:199
Alignment explanation
Indices: 5852123--5853291 Score: 1286
Period size: 200 Copynumber: 5.8 Consensus size: 199
5852113 TGTTATTTAC
* * ** * *
5852123 AAGTATCGCCACAAA-TCTAAAACGTGTCGATACATT-TGTTCACCTATTTTCTCATAAAACAGG
1 AAGTATCGACACAAATTCCAAAA-GTGTCGATACATTATGTAGACCTATTTTCACATAAAACATG
*
5852186 TACATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
65 TATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTAT-GGTTTCGATGTTTTT
* * * * * *
5852251 GGGATCGATATTTTTTAAAAAATGTATCGACACTATATGCTTGCAACCCTTTT-GGCTTTAATTT
129 GGGATCGATACTTTTT-AAAAATGTATCGACACTTTATGCGTGC-ACCCTTTTGGGCATTCATTC
5852315 TGGACAAA
192 TGGACAAA
* ** * **
5852323 AAGTATCGACACAAA-TCTAAAATGTGTCGATACATTATGTTCACCTATTTTAACATAAAACCGG
1 AAGTATCGACACAAATTCCAAAA-GTGTCGATACATTATGTAGACCTATTTTCACATAAAACATG
5852387 TATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTT
65 TATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTA-TGGTTTCGATGTTTTT
* * * * * *
5852452 AGAATCGATACTTTTTATAAATGTATCGACACTTTATTCGTTCACCCTTTTGGGCATTCATTATG
129 GGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATTCTG
5852517 GACAAA
194 GACAAA
* * * * **
5852523 ACA-TATCGACACATCATT-CAAAAGTGTCGACACATTATGTAGACCTATTCTGACATAAAACCG
1 A-AGTATCGACACA-AATTCCAAAAGTGTCGATACATTATGTAGACCTATTTTCACATAAAACAT
* * * * ** * ** *
5852586 GTATGTTTACACCGGTTATATTACAAAATTAATTATTACATTATATTTATGTGTTTCGATGTTTT
64 GTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATG-GTTTCGATGTTTT
** * * * * *
5852651 AAGGATCGATACTGTTTAAACATGTATCGACACTTTATGGGTGCACCCTTTTTGG-ATTTTCCTT
128 TGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCA--TTCATT
* *
5852715 GTGGACCAA
191 CTGGACAAA
* * * * *
5852724 AAGTATCGACACAAATTCTACAAGTGTCGATACATTATGTATATCTATTTTCTCA-AAAA-ATCG
1 AAGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTTTCACATAAAACAT--
* * *
5852787 GTTTTATTTATA-TCGGTTACATTTTAAATTTACCTATTACATTATAATTATCGGTTTCGATATT
64 G-TATATTTATACT-GGTTACATTGTAAATTTACCTATTACATTATAATTAT-GGTTTCGATGTT
* *
5852851 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATT
126 TTTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATT
5852916 CTGGACAAA
191 CTGGACAAA
* *
5852925 AAGTATCGACACAATATT-CAAAAGTGTCGACATATTATGTAGACCTATTTTCACATAAAAC-TA
1 AAGTATCGACACAA-ATTCCAAAAGTGTCGATACATTATGTAGACCTATTTTCACATAAAACAT-
* ** *
5852988 GTATATTTATATCT-GTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
64 GTATATTTATA-CTGGTTACATTGTAAATTTACCTATTACATTATAATTAT-GGTTTCGATGTTT
* * * *
5853052 TTGAGATCAATACTTTTTTAAAAA-GTATCGACACTTTATGGGTGCACCCTTTTGGGCATTCCTT
127 TTGGGATCGATAC-TTTTTAAAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATT
*
5853116 CTGGATAAA
191 CTGGACAAA
* * * ** * *
5853125 CAGTATCGACACAAATTCCAGAAGTGTCGATACATTATATAGAATTATTCTCGCATAAAACATGT
1 AAGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTTTCACATAAAACATGT
* * * *
5853190 TTAGTTATACTGGTTATATTGTAAATTTACCTATTACATTATATTTATGGATTTCGATGTTTTTG
66 ATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATGG-TTTCGATGTTTTTG
* *
5853255 GGATCAATATTTTTTAAAAATGTATCGACACTTTATG
130 GGATCGATACTTTTTAAAAATGTATCGACACTTTATG
5853292 GGAAACTTTA
Statistics
Matches: 822, Mismatches: 119, Indels: 56
0.82 0.12 0.06
Matches are distributed among these distances:
199 28 0.03
200 460 0.56
201 225 0.27
202 107 0.13
203 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (199 bp):
AAGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTTTCACATAAAACATGT
ATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATGGTTTCGATGTTTTTGG
GATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATTCTGGA
CAAA
Found at i:5855605 original size:2 final size:2
Alignment explanation
Indices: 5855598--5855627 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5855588 TAGTTTCCAG
5855598 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
5855628 CCTTCTCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5856695 original size:200 final size:198
Alignment explanation
Indices: 5855991--5857073 Score: 1272
Period size: 200 Copynumber: 5.4 Consensus size: 198
5855981 ATTTAAAATG
* * * * *
5855991 GTATCGACACAAATTTAACAATTGTCGATACTTTATG-ATGACATATTTTCTCATAAAACTGGTA
1 GTATCGACACAAA-TTAACAAGTGTCGATACATTATGTA-GACCTATTCTCTCATAAAACCGGTA
* * * * * *
5856055 TATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAATATTTTTGG
64 TATGTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCT-G
* * *
5856120 GATCGACACTTTTTAAAAATGTATCGACACTTTATGCGTTCAACCCTTTT-GGCATTCCTTCAGG
128 GATCGACACTTTTTATAAATGTATCGACACTTTATGCGTTC-ACCCTTTTGGGCATTCATTCTGG
*
5856184 ATAAAAA
192 ACAAAAA
* **
5856191 GTATCGACACAAATTCACAAGCATCGATACATGT-TGTAGACCTATTCTCTCATAAAACCGGTAT
1 GTATCGACACAAATTAACAAGTGTCGATACAT-TATGTAGACCTATTCTCTCATAAAACCGGTAT
* * *
5856255 A-GTTATATCGGTTACATTTTAAATTTACCTATTACATTATATTTATGGGTTTCGATGTTTCTGG
65 ATG-TATACCGGTTACATTATAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* * *
5856319 TATCGACACTTTTTATAAATATATCGACACTTTATGCGTTCATCCTTTTGGACATTCATTCTGGA
129 -ATCGACACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCTGGA
5856384 CAAAAA
193 CAAAAA
*
5856390 GTATCGACAC-AA--AA-AAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATA
1 GTATCGACACAAATTAACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATA
* * * * * * * *
5856451 TTTATATCGGTTATATTAAAAAATTACCTATTACATTATAATTATGGGTTTAGATATTTTTAGGA
66 TGTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCT-GGA
* * * *
5856516 TCGACACTTTTTATAAATGTTTCGACACTTAATG-GTGCACCCTTTTTGGGCATTCATTTTGGAC
130 TCGACACTTTTTATAAATGTATCGACACTTTATGCGTTCACCC-TTTTGGGCATTCATTCTGGAC
*
5856580 CAAAA
194 AAAAA
* * *
5856585 GTATCGACACAAATTACACAAGTATCGATACA-TATTGTAGACCTATTCTCTCATAAAACTGATA
1 GTATCGACACAAATTA-ACAAGTGTCGATACATTA-TGTAGACCTATTCTCTCATAAAACCGGTA
* *
5856649 TATGTATACCGGTTACATTAAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
64 TATGTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* ** * * * *
5856714 AATCGATACTTGTTTATAAATGTATCGGTACTTGT-TGTGTGCTCCCTTTTTGGGCATTCCTTCT
129 -ATCGACACTT-TTTATAAATGTATCGACACTT-TATGCGTTCACCC-TTTTGGGCATTCATTCT
*
5856778 GGACAAATA
190 GGACAAAAA
* * *
5856787 GTATCGACACAAATTACATAAGTGTCGATACATTATGTAGACCTATTCTTTCATAAAACCGGTTT
1 GTATCGACACAAATTA-ACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
* * * **
5856852 A-GTTATACCAGTTACATTGTAAATTTACCTATTACATTATATTTATCAGTTTCGATGTTTCTGG
65 ATG-TATACCGGTTACATTATAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCT-G
** * * *
5856916 GATCGACACTTTCAATAAATGTATCGACATTTTATGCGTTCATCATTTTGGGCATTCATTCTGGA
128 GATCGACACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCTGGA
5856981 CAAAAA
193 CAAAAA
* * * *
5856987 GTATCGACACATAATGAAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCAGTAT
1 GTATCGACACA-AATTAACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
* **
5857052 ATTTATACCTATTACATTATAA
65 ATGTATACCGGTTACATTATAA
5857074 TTATGGGTTT
Statistics
Matches: 758, Mismatches: 100, Indels: 50
0.83 0.11 0.06
Matches are distributed among these distances:
194 7 0.01
195 158 0.21
196 5 0.01
198 12 0.02
199 162 0.21
200 215 0.28
201 47 0.06
202 148 0.20
203 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (198 bp):
GTATCGACACAAATTAACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATA
TGTATACCGGTTACATTATAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGAT
CGACACTTTTTATAAATGTATCGACACTTTATGCGTTCACCCTTTTGGGCATTCATTCTGGACAA
AAA
Found at i:5856967 original size:402 final size:397
Alignment explanation
Indices: 5855986--5857070 Score: 1343
Period size: 402 Copynumber: 2.7 Consensus size: 397
5855976 ACGATATTTA
* * * *
5855986 AAATGGTATCGACACAAATTTAACAATTGTCGATACTTTATG-ATGACATATT-TTCTCATAAAA
1 AAATAGTATCGACACAAA-TTAA-AAGTGTCGATACATTATGTA-GACCTATTCTT-TCATAAAA
* *
5856049 CTGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAATAT
62 CCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATAT
*
5856114 TTTTGGGATCGACACTTTTTAA-AAATGTATCGACACTTTATGCGTTCAACCCTTTT-GGCATTC
127 TTTTGGGATCGACAC-TTTTAATAAATGTATCGACACTTTATGCGTTC-ACCATTTTGGGCATTC
* * * *
5856177 CTTCAGGATAAAAAGTATCGACACAAATT-CACAAGCATCGATACATGTTGTAGACCTATTCTCT
190 ATTCTGGACAAAAAGTATCGACACAAATTACACAAGTATCGATACAT-TTGTAGACCTATTCTCT
* * ** * *
5856241 CATAAAACCGGTATAGTTATATCGGTTACATTTTAAATTTACCTATTACATTATATTTATGGGTT
254 CATAAAACCGATATAGTTATACCGGTTACATTAAAAAATTACCTATTACATTATAATTATGGGTT
* *
5856306 TCGATGTTTCTGGTATCGACACTTTTTATAAATATATCGACACTTTATGCGTTCATCCTTTTGGA
319 TCGATGTTTCTGGAATCGACACTTTTTATAAATATATCGACACTTTATGCGTGCATCCTTTTGGA
5856371 CATTCATTCTGGAC
384 CATTCATTCTGGAC
* **
5856385 AAAAAGTATCGACAC-AA--AAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGG
1 AAATAGTATCGACACAAATTAAAAGTGTCGATACATTATGTAGACCTATTCTTTCATAAAACCGG
* * ** * * *
5856447 TATATTTATATCGGTTATATTAAAAAATTACCTATTACATTATAATTATGGGTTTAGATATTTTT
66 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTT
* * * * * * *
5856512 AGGATCGACACTTTTTATAAATGTTTCGACACTTAATG-GTGCACCCTTTTTGGGCATTCATTTT
131 GGGATCGACACTTTTAATAAATGTATCGACACTTTATGCGTTCA-CCATTTTGGGCATTCATTCT
*
5856576 GGACCAAAAGTATCGACACAAATTACACAAGTATCGATACATATTGTAGACCTATTCTCTCATAA
195 GGACAAAAAGTATCGACACAAATTACACAAGTATCGATACAT-TTGTAGACCTATTCTCTCATAA
*
5856641 AACTGATATA-TGTATACCGGTTACATTAAAAAATTACCTATTACATTATAATTATGGGTTTCGA
259 AACCGATATAGT-TATACCGGTTACATTAAAAAATTACCTATTACATTATAATTATGGGTTTCGA
* * ** * *
5856705 TGTTTCTGGAATCGATACTTGTTTATAAATGTATCGGTACTTGT-TGTGTGC-TCCCTTTTTGGG
323 TGTTTCTGGAATCGACACTT-TTTATAAATATATCGACACTT-TATGCGTGCAT-CC-TTTTGGA
*
5856768 CATTCCTTCTGGAC
384 CATTCATTCTGGAC
5856782 AAATAGTATCGACACAAATTACATAAGTGTCGATACATTATGTAGACCTATTCTTTCATAAAACC
1 AAATAGTATCGACACAAATTA-A-AAGTGTCGATACATTATGTAGACCTATTCTTTCATAAAACC
* * * * * *
5856847 GGTTTAGTTATACCAGTTACATTGTAAATTTACCTATTACATTATATTTATCAGTTTCGATGTTT
64 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTT
* * * *
5856912 CTGGGATCGACACTTTCAATAAATGTATCGACATTTTATGCGTTCATCATTTTGGGCATTCATTC
129 TTGGGATCGACACTTTTAATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTC
* * * *
5856977 TGGACAAAAAGTATCGACACATAATGA-AAAAGTGTCGATACATTATGTAGACCTATTCTCACAT
194 TGGACAAAAAGTATCGACACA-AATTACACAAGTATCGATACATT-TGTAGACCTATTCTCTCAT
* **
5857041 AAAACC-AGTATATTTATACCTATTACATTA
257 AAAACCGA-TATAGTTATACCGGTTACATTA
5857071 TAATTATGGG
Statistics
Matches: 585, Mismatches: 80, Indels: 39
0.83 0.11 0.06
Matches are distributed among these distances:
392 1 0.00
393 14 0.02
394 150 0.26
395 116 0.20
396 25 0.04
397 34 0.06
398 4 0.01
399 13 0.02
400 1 0.00
401 3 0.01
402 215 0.37
403 9 0.02
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (397 bp):
AAATAGTATCGACACAAATTAAAAGTGTCGATACATTATGTAGACCTATTCTTTCATAAAACCGG
TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTT
GGGATCGACACTTTTAATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCTG
GACAAAAAGTATCGACACAAATTACACAAGTATCGATACATTTGTAGACCTATTCTCTCATAAAA
CCGATATAGTTATACCGGTTACATTAAAAAATTACCTATTACATTATAATTATGGGTTTCGATGT
TTCTGGAATCGACACTTTTTATAAATATATCGACACTTTATGCGTGCATCCTTTTGGACATTCAT
TCTGGAC
Found at i:5857505 original size:19 final size:19
Alignment explanation
Indices: 5857477--5857525 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
5857467 TTACATCCAC
5857477 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
* *
5857496 ATATAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
5857515 ATACAAAATTA
1 ATACAAAATTA
5857526 ACTCTATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:5858896 original size:13 final size:13
Alignment explanation
Indices: 5858878--5858910 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
5858868 TGTCATCAAT
5858878 TCCGCTTGGAATA
1 TCCGCTTGGAATA
5858891 TCCGCTTGGAATA
1 TCCGCTTGGAATA
5858904 TCCGCTT
1 TCCGCTT
5858911 TTTCAACCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.33
Consensus pattern (13 bp):
TCCGCTTGGAATA
Found at i:5859115 original size:18 final size:18
Alignment explanation
Indices: 5859092--5859130 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
5859082 TCATCCTCAT
5859092 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
5859110 TTCCTCCCTCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
5859128 TTC
1 TTC
5859131 ATATTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:5859350 original size:33 final size:33
Alignment explanation
Indices: 5859305--5859369 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
5859295 CCATCTTAAG
5859305 TTCACCCCTCAACACCTCAACTTCTTTCACCAT
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAT
*
5859338 TTCACCCTTCAACACCTCAACTTCTTTCACCA
1 TTCACCCCTCAACACCTCAACTTCTTTCACCA
5859370 CTCCATCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.25, C:0.45, G:0.00, T:0.31
Consensus pattern (33 bp):
TTCACCCCTCAACACCTCAACTTCTTTCACCAT
Found at i:5859366 original size:18 final size:18
Alignment explanation
Indices: 5859313--5859366 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 18
5859303 AGTTCACCCC
5859313 TCAACACCTCAACTTCTT
1 TCAACACCTCAACTTCTT
* ** *
5859331 TCACCATTTC-AC--CCT
1 TCAACACCTCAACTTCTT
5859346 TCAACACCTCAACTTCTT
1 TCAACACCTCAACTTCTT
5859364 TCA
1 TCA
5859367 CCACTCCATC
Statistics
Matches: 25, Mismatches: 8, Indels: 6
0.64 0.21 0.15
Matches are distributed among these distances:
15 9 0.36
16 2 0.08
17 2 0.08
18 12 0.48
ACGTcount: A:0.26, C:0.41, G:0.00, T:0.33
Consensus pattern (18 bp):
TCAACACCTCAACTTCTT
Found at i:5859430 original size:21 final size:21
Alignment explanation
Indices: 5859405--5859448 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5859395 CCCCTTATGC
*
5859405 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCAACT
*
5859426 CTCTCAAGTTTCTCTTCAACT
1 CTCTCAAGTGTCTCTTCAACT
5859447 CT
1 CT
5859449 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.34, G:0.09, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTCTCTTCAACT
Found at i:5859864 original size:22 final size:23
Alignment explanation
Indices: 5859836--5859891 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
5859826 AACCTGCATT
5859836 TATAATAAAAT-TTATAATTTTA
1 TATAATAAAATATTATAATTTTA
* *
5859858 TATAATAACTATATTATCATTTTA
1 TATAATAA-AATATTATAATTTTA
*
5859882 TATAAAAAAA
1 TATAATAAAA
5859892 CAAAAACGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 8 0.29
23 3 0.11
24 17 0.61
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATAAAATATTATAATTTTA
Found at i:5863090 original size:182 final size:181
Alignment explanation
Indices: 5862783--5863637 Score: 1058
Period size: 182 Copynumber: 4.7 Consensus size: 181
5862773 TACGTTTACT
* * * * *
5862783 TATTAAAGTATCGACACTTTCAATATATCCAGTAGCGCTTTACCGGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTATACCGGTTTTGTCCTTTAGATACCG
*
5862848 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGA-CTGATACATTGTTATAAAGTATCGACAC
66 GTTTTGTCATATTTTTA-CTGTTATATCGTTGTGGATC-GATACATTTTTATAAAGTATCGACAC
* **
5862912 TTTATAGGCGCTAAAGTTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
129 TTTATAGACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * *
5862965 TATTAAAGTATCGACACTTTAAATATATACGGTCGCTCTATACCGGTTTTGTCCTTTAGATACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTATACCGGTTTTGTCCTTTAGATACCG
* * *
5863030 GTTTTGTCATATTTTTATCTGTTATATCGTTATGGTTCAATACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTA-CTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
* *
5863095 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATCCACAAAGTGTCGATACTTA
130 TTATAGACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * ** * ** * *
5863147 TGTTAAAATATCGACACTTTCAATATATTTGGTCGTTCTATAACGGTTTTGTCCTTTAGATACCA
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTATACCGGTTTTGTCCTTTAGATACCG
* * * * *
5863212 GTTTTGTCATATTTTTACATGTTATATCGTTGTGTATTGATACATTGTTATAAAATATCGACACG
66 GTTTTGTCATATTTTTAC-TGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACT
*
5863277 TTATAGAAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
130 TTATAGACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* ** * * *
5863329 TATTAAAGTATCGACACTTTCAATATATCCGCTAATGC-CT-TACCCAATTTTGTCTTTTCGAGA
1 TATTAAAGTATCGACACTTTCAATATATCCGGT-A-GCGCTATA-CCGGTTTTGTCCTTTAGATA
* * *
5863392 CTGGTTTTGTCATATTTTTACATGTTATATCGTTGTGGATCGATACATATTTATAAAGAATCGAC
63 CCGGTTTTGTCATATTTTTAC-TGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGAC
* * * *
5863457 ACTTTATAGACGCTAAAACTGTTTCTCCTTTAAATTCACAATGTGTCGACACTTA
127 ACTTTATAGACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * *
5863512 TATTAACGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCGG--TTGTCTTTTCATGAT--
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTATACCGGTTTTGTCCTTT-A-GATAC
* * * * * *
5863573 CGGTTTTGTCATATTTTTTCCTGTTATATTGATGTGGATCAATATATTTTTATAAAATATCGACA
64 CGGTTTTGTCATA-TTTTTACTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACA
5863638 TAAACTGACA
Statistics
Matches: 584, Mismatches: 79, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
180 58 0.10
181 9 0.02
182 361 0.62
183 155 0.27
184 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (181 bp):
TATTAAAGTATCGACACTTTCAATATATCCGGTAGCGCTATACCGGTTTTGTCCTTTAGATACCG
GTTTTGTCATATTTTTACTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCGACACTT
TATAGACGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Found at i:5864287 original size:15 final size:15
Alignment explanation
Indices: 5864267--5864340 Score: 85
Period size: 15 Copynumber: 4.9 Consensus size: 15
5864257 AATTTTAATT
5864267 TATTTAAATAATTAA
1 TATTTAAATAATTAA
* **
5864282 TATTTATATAATTCG
1 TATTTAAATAATTAA
*
5864297 TATTTAAATAATTGA
1 TATTTAAATAATTAA
*
5864312 TATTTCAAATAATTAG
1 TATTT-AAATAATTAA
*
5864328 TAGTTAAATAATT
1 TATTTAAATAATT
5864341 CATGTTTATA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
15 37 0.76
16 12 0.24
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (15 bp):
TATTTAAATAATTAA
Found at i:5864335 original size:31 final size:30
Alignment explanation
Indices: 5864270--5864340 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 30
5864260 TTTAATTTAT
* * *
5864270 TTAAATAATTAATATTTATATAATTCGTAT
1 TTAAATAATTAATATTTAAATAATTAGTAG
*
5864300 TTAAATAATTGATATTTCAAATAATTAGTAG
1 TTAAATAATTAATATTT-AAATAATTAGTAG
5864331 TTAAATAATT
1 TTAAATAATT
5864341 CATGTTTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 16 0.44
31 20 0.56
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (30 bp):
TTAAATAATTAATATTTAAATAATTAGTAG
Found at i:5866878 original size:13 final size:13
Alignment explanation
Indices: 5866856--5866891 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
5866846 TTAAAATCTT
*
5866856 TATTAATAATTTA
1 TATTATTAATTTA
5866869 TATTATTAATTTA
1 TATTATTAATTTA
5866882 -ATTATTAATT
1 TATTATTAATT
5866892 AATTAAGACG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATTATTAATTTA
Found at i:5866887 original size:12 final size:12
Alignment explanation
Indices: 5866857--5866896 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 12
5866847 TAAAATCTTT
*
5866857 ATTAATAATTTA
1 ATTATTAATTTA
5866869 TATTATTAATTTA
1 -ATTATTAATTTA
5866882 ATTATTAA-TTA
1 ATTATTAATTTA
5866893 ATTA
1 ATTA
5866897 AGACGATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 7 0.27
12 8 0.31
13 11 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTATTAATTTA
Found at i:5878933 original size:21 final size:22
Alignment explanation
Indices: 5878889--5878933 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
5878879 TATTCTATAT
* *
5878889 TTATGACACAATTTTTTCTGTC
1 TTATGACACAATTTTCTCTCTC
*
5878911 TTATGACAC-GTTTTCTCTCTC
1 TTATGACACAATTTTCTCTCTC
5878932 TT
1 TT
5878934 TGTTATCAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.18, C:0.22, G:0.09, T:0.51
Consensus pattern (22 bp):
TTATGACACAATTTTCTCTCTC
Found at i:5879753 original size:15 final size:14
Alignment explanation
Indices: 5879724--5879768 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
5879714 GACCCGCTTG
*
5879724 ACCCGACTTAGTCA
1 ACCCGACTGAGTCA
5879738 ACCCGCACTGAGTCA
1 ACCCG-ACTGAGTCA
* *
5879753 ACTCGGCTGAGTCA
1 ACCCGACTGAGTCA
5879767 AC
1 AC
5879769 TCACTAGGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.27, C:0.36, G:0.20, T:0.18
Consensus pattern (14 bp):
ACCCGACTGAGTCA
Found at i:5879809 original size:23 final size:23
Alignment explanation
Indices: 5879776--5879834 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
5879766 AACTCACTAG
* *
5879776 GTCAACTTGTTGACTTAAACCGA
1 GTCAACCTGTTGACTTAAACAGA
**
5879799 GTCAACCTGTTGACTTTGACAGA
1 GTCAACCTGTTGACTTAAACAGA
5879822 GTCAACCTGTTGA
1 GTCAACCTGTTGA
5879835 TCGTTGACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (23 bp):
GTCAACCTGTTGACTTAAACAGA
Found at i:5881936 original size:24 final size:23
Alignment explanation
Indices: 5881909--5881970 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
5881899 TTTTGATTTG
5881909 GATTATGTTATGATACATGACCT
1 GATTATGTTATGATACATGACCT
* * *
5881932 AGATTCTGTTCTAATACATGACCT
1 -GATTATGTTATGATACATGACCT
*
5881956 GAATTATGTTTTGAT
1 G-ATTATGTTATGAT
5881971 TTATGATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (23 bp):
GATTATGTTATGATACATGACCT
Found at i:5882277 original size:153 final size:153
Alignment explanation
Indices: 5881996--5882462 Score: 609
Period size: 153 Copynumber: 3.0 Consensus size: 153
5881986 TTATTGACGG
*
5881996 AAAATGTTTTATTTAGGGGTATTATTGGAGGAAGTATACTTGCATGCTCCTCGGCTTTGTGCTGC
1 AAAATGTTTTATTTAGGGGTATTGTTGGAGGAAGTATACTTGCATGCTCCTCGGC-TT-T-CTGC
* * * * * *
5882061 TGAGGGCCTTACTGGATGTGGCGGTGGTTGTATAGTTCTGGGGAACCTACACATTTGGACGTGTT
63 TCAGAGCCTTACTGGACGTGACGGTTGTTGTATGGTTCTGGGGAACCTACACATTTGGACGTGTT
5882126 CGGTTGGAGGGATTACTATGGTTTTT
128 CGGTTGGAGGGATTACTATGGTTTTT
* * * * *
5882152 AAAATGTTTTATTT-GGGAGTATTGTTGGAGGAAGTATACTTACATGCTTCTCGACTTTCAGTTC
1 AAAATGTTTTATTTAGGG-GTATTGTTGGAGGAAGTATACTTGCATGCTCCTCGGCTTTCTGCTC
* *
5882216 AGAGCCTTACTGGACGTGACGGTTGTTCTATGGTTCTGGGGAACCTACACATTTGGACGTGTTCT
65 AGAGCCTTACTGGACGTGACGGTTGTTGTATGGTTCTGGGGAACCTACACATTTGGACGTGTTCG
*
5882281 GTTGGAGGAATTACTATGGTTTTT
130 GTTGGAGGGATTACTATGGTTTTT
* * * *
5882305 AAAATGTTTTATTTGGGGGGTATTGTTGGAGGAAGTATACTTGTAGGCTCCTCGGCTTTGTGCTC
1 AAAATGTTTTATTT-AGGGGTATTGTTGGAGGAAGTATACTTGCATGCTCCTCGGCTTTCTGCTC
* * * * * *
5882370 AGTGCCTTACTGGACTTGACGG-TGAGTGTATGGTTTTGGGGAACCTACATATTTGGACTTG-TC
65 AGAGCCTTACTGGACGTGACGGTTG-TTGTATGGTTCTGGGGAACCTACACATTTGGACGTGTTC
5882433 GGTTGG-GGGAATTACTATGGTTTTT
129 GGTTGGAGGG-ATTACTATGGTTTTT
*
5882458 GAAAT
1 AAAAT
5882463 TTAAAAATAT
Statistics
Matches: 273, Mismatches: 33, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
152 2 0.01
153 126 0.46
154 90 0.33
155 8 0.03
156 47 0.17
ACGTcount: A:0.20, C:0.13, G:0.30, T:0.37
Consensus pattern (153 bp):
AAAATGTTTTATTTAGGGGTATTGTTGGAGGAAGTATACTTGCATGCTCCTCGGCTTTCTGCTCA
GAGCCTTACTGGACGTGACGGTTGTTGTATGGTTCTGGGGAACCTACACATTTGGACGTGTTCGG
TTGGAGGGATTACTATGGTTTTT
Found at i:5884849 original size:21 final size:21
Alignment explanation
Indices: 5884825--5884888 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
5884815 GCAAATTCGC
5884825 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
5884846 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
5884866 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
5884887 GT
1 GT
5884889 CTATAGTTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:5885560 original size:6 final size:6
Alignment explanation
Indices: 5885539--5885575 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
5885529 TCTCGTCTCG
*
5885539 GGTCG- GGTCG- GGTCGT GGTCGT GATCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
5885576 AATACGTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.03, C:0.16, G:0.51, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:5885671 original size:19 final size:19
Alignment explanation
Indices: 5885647--5885729 Score: 85
Period size: 19 Copynumber: 4.2 Consensus size: 19
5885637 TTAACTATCA
5885647 CAACAAATTTGGAAAATCG
1 CAACAAATTTGGAAAATCG
* * **
5885666 CAACAACAACTGTAGACTATCG
1 CAAC-A-AA-TTTGGAAAATCG
*
5885688 CAACGAATTTGGAAAATCG
1 CAACAAATTTGGAAAATCG
*
5885707 CAACGAATTTGGAAAATCG
1 CAACAAATTTGGAAAATCG
5885726 CAAC
1 CAAC
5885730 GACAACTGTA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
19 35 0.67
20 3 0.06
21 2 0.04
22 12 0.23
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.19
Consensus pattern (19 bp):
CAACAAATTTGGAAAATCG
Found at i:5885730 original size:19 final size:19
Alignment explanation
Indices: 5885684--5885731 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
5885674 ACTGTAGACT
5885684 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
5885703 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
5885722 ATCGCAACGA
1 ATCGCAACGA
5885732 CAACTGTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:5886786 original size:12 final size:11
Alignment explanation
Indices: 5886756--5886870 Score: 50
Period size: 11 Copynumber: 9.9 Consensus size: 11
5886746 AAGATAATTC
*
5886756 AATAATAAAAA
1 AATAAAAAAAA
5886767 AATAAAAAAACA
1 AATAAAAAAA-A
*
5886779 AATCAAAATAAA
1 AAT-AAAAAAAA
* *
5886791 TACAAAAGAAAA
1 AATAAAA-AAAA
* ** *
5886803 AAGAGGAAAAG
1 AATAAAAAAAA
5886814 AATAAATAAAAAA
1 AAT-AA-AAAAAA
* *
5886827 AATAAAATAAG
1 AATAAAAAAAA
** *
5886838 CTTAAAAATAA
1 AATAAAAAAAA
*
5886849 AATAAAAAATA
1 AATAAAAAAAA
5886860 AATAGAAAAAA
1 AATA-AAAAAA
5886871 TGATAAATAA
Statistics
Matches: 72, Mismatches: 26, Indels: 11
0.66 0.24 0.10
Matches are distributed among these distances:
11 39 0.54
12 20 0.28
13 13 0.18
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (11 bp):
AATAAAAAAAA
Found at i:5886916 original size:14 final size:15
Alignment explanation
Indices: 5886897--5886932 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
5886887 GATTTTTTTA
5886897 AAAAAAAT-ATAAAG
1 AAAAAAATGATAAAG
*
5886911 AAAAAAATGATAATG
1 AAAAAAATGATAAAG
5886926 AAAAAAA
1 AAAAAAA
5886933 GAAAATAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (15 bp):
AAAAAAATGATAAAG
Found at i:5886916 original size:15 final size:16
Alignment explanation
Indices: 5886896--5886932 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
5886886 GGATTTTTTT
5886896 AAAAAAAAT-ATAAAG
1 AAAAAAAATGATAAAG
*
5886911 -AAAAAAATGATAATG
1 AAAAAAAATGATAAAG
5886926 AAAAAAA
1 AAAAAAA
5886933 GAAAATAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 8 0.42
15 5 0.26
16 6 0.32
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (16 bp):
AAAAAAAATGATAAAG
Found at i:5888291 original size:13 final size:13
Alignment explanation
Indices: 5888273--5888298 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5888263 GGTGAATAAT
5888273 AATAAATAAAAAC
1 AATAAATAAAAAC
5888286 AATAAATAAAAAC
1 AATAAATAAAAAC
5888299 TATATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAATAAAAAC
Found at i:5888414 original size:32 final size:31
Alignment explanation
Indices: 5888345--5888443 Score: 130
Period size: 31 Copynumber: 3.2 Consensus size: 31
5888335 AACTATATAC
* *
5888345 TATAT-ATTTTCAAAAATGTTTTTCAAAAAAC
1 TATATAATTTTTAAAAATGTTTTT-AAAAAAT
*
5888376 TA-ATAATTTTTAAAAATGTTCTTTTAAAAAT
1 TATATAATTTTTAAAAATGTT-TTTAAAAAAT
*
5888407 TATATAATTTTTAAAAATGTTTTAAAAAAAT
1 TATATAATTTTTAAAAATGTTTTTAAAAAAT
5888438 TATATA
1 TATATA
5888444 TTATATATAA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
30 2 0.03
31 37 0.62
32 21 0.35
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (31 bp):
TATATAATTTTTAAAAATGTTTTTAAAAAAT
Found at i:5888534 original size:32 final size:34
Alignment explanation
Indices: 5888470--5888623 Score: 149
Period size: 35 Copynumber: 4.5 Consensus size: 34
5888460 AAAATGCTCT
* *
5888470 AAAATTATATATTATAAGTTTTCAAAATGTTTTTC
1 AAAAATATATATTAT-AGTTTTTAAAATGTTTTTC
5888505 AAAAAT-TATATTATA-TTTTTAAAATGTTTTTC
1 AAAAATATATATTATAGTTTTTAAAATGTTTTTC
* *
5888537 AAAAATTATATATTATATATTTTTTAAAATG--TTTG
1 AAAAA-TATATA-T-TATAGTTTTTAAAATGTTTTTC
*
5888572 AAAATATATATAATATAGTTTTTAAAA-GTGTTTT-
1 AAAA-ATATATATTATAGTTTTTAAAATGT-TTTTC
5888606 AAAACCATATATATTATA
1 AAAA--ATATATATTATA
5888624 TACGTATTTT
Statistics
Matches: 102, Mismatches: 7, Indels: 20
0.79 0.05 0.16
Matches are distributed among these distances:
32 22 0.22
33 15 0.15
34 16 0.16
35 33 0.32
36 5 0.05
37 11 0.11
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (34 bp):
AAAAATATATATTATAGTTTTTAAAATGTTTTTC
Found at i:5888621 original size:70 final size:68
Alignment explanation
Indices: 5888470--5888625 Score: 178
Period size: 70 Copynumber: 2.3 Consensus size: 68
5888460 AAAATGCTCT
*
5888470 AAAATTATATATTATA-AGTTTTCAAAATGTTTTTCAAAAATTATATTATATTTTTAAAATGTTT
1 AAAATTATATATTATATAGTTTTCAAAATG-TTTTCAAAAATTATAATATATTTTTAAAATGTTT
5888534 TTCA
65 TTCA
* * *
5888538 AAAATTATATATTATATATTTTTTAAAATG-TTTGAAAATATATATAATATAGTTTTTAAAA-GT
1 AAAATTATATATTATATAGTTTTCAAAATGTTTTCAAAA-AT-TATAATATA-TTTTTAAAATGT
5888601 GTTTT-A
63 -TTTTCA
5888607 AAACCA-TATATATTATATA
1 AAA--ATTATATATTATATA
5888626 CGTATTTTCA
Statistics
Matches: 77, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
67 7 0.09
68 18 0.23
69 25 0.32
70 26 0.34
71 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (68 bp):
AAAATTATATATTATATAGTTTTCAAAATGTTTTCAAAAATTATAATATATTTTTAAAATGTTTT
TCA
Found at i:5889393 original size:84 final size:82
Alignment explanation
Indices: 5889253--5890006 Score: 712
Period size: 84 Copynumber: 9.2 Consensus size: 82
5889243 TGCCTTGAGC
* * * *
5889253 TATGCTGTAAATGATGTG-CCTTGGAGTTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCATAGA
1 TATGCTGCAAATGATGTGCCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTC-CAGA
* *
5889317 TAACCCTTCTAGCCTTGAGT
63 TAACCCTTCTAGACTTAAGT
* * * * **
5889337 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG--CAGATA
1 TATGCTGCAAATGATGTGCCCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCCAGATA
* * *
5889400 GCCCTTCTCGACTTAAGC
65 ACCCTTCTAGACTTAAGT
* * * * * *
5889418 TATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGTTGCCAGAC
1 TATGCTGCAAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGT-CCAGAT
5889483 AACCCTTCTAGACTTAAGT
64 AACCCTTCTAGACTTAAGT
* * * *
5889502 TGTGCTGCAAATGATATG-CCTTGGAGCTGATCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGA
1 TATGCTGCAAATGATGTGCCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-T-CCAGA
*
5889566 T-ACCCTTC--GGCTTAAGT
63 TAACCCTTCTAGACTTAAGT
* * * * **
5889583 TATGCTGCGAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGTGGTCTTTGG--CAGATA
1 TATGCTGCAAATGATGTGCCCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCCAGATA
* * *
5889646 GCCCTTCTCGACTTAAGC
65 ACCCTTCTAGACTTAAGT
* * ** *
5889664 TATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAATCGAACTCGGGGGTC-TTGG--CAGATAG
1 TATGCTGCAAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCCAGATAA
*
5889726 CCCTTC--GACTTAAGC
66 CCCTTCTAGACTTAAGT
* * * * * *
5889741 TATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGTTGGCAGAC
1 TATGCTGCAAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGT-CCAGAT
5889806 AACCCTTCTAGACTTAAGT
64 AACCCTTCTAGACTTAAGT
* ** **
5889825 TGTGCTGCAAATGAAATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT-TGGCAT
1 TATGCTGCAAATGATGTGCCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCCAG-AT
*
5889888 AAACCCTTCTCGACTTAAGT
64 -AACCCTTCTAGACTTAAGT
* * * *
5889908 TATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTGACAGAT
1 TATGCTGCAAATGATGTGCCCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT-CCAGAT
* *
5889973 AACCCTTCTAGCCTTGAGT
64 AACCCTTCTAGACTTAAGT
5889992 TATGCTGCAAATGAT
1 TATGCTGCAAATGAT
5890007 TGTTTTAAAA
Statistics
Matches: 556, Mismatches: 87, Indels: 54
0.80 0.12 0.08
Matches are distributed among these distances:
77 55 0.10
78 5 0.01
79 26 0.05
80 46 0.08
81 95 0.17
82 42 0.08
83 56 0.10
84 204 0.37
85 26 0.05
86 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (82 bp):
TATGCTGCAAATGATGTGCCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCCAGATAA
CCCTTCTAGACTTAAGT
Found at i:5889629 original size:246 final size:244
Alignment explanation
Indices: 5889253--5890006 Score: 912
Period size: 246 Copynumber: 3.1 Consensus size: 244
5889243 TGCCTTGAGC
* * ***
5889253 TATGCTGTAAATGATGTGCCTTGGAGTTGAGCGTAGTCGAACTCAAAGGTCTTTTGG-TCATAGA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTTGGCAGA
* * *
5889317 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC
65 T-ACCCTTC-AGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC
* *
5889382 GGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTG
128 GGAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTG
* * * *
5889447 AGCGTAGTCAAACTCAAAGGTCTTTTGTTGCCAGACAACCCTTCTAGACTTAAGT
193 AGCGTAATCGAACTCGAAGGTC-TTTG-TG-CAGATAACCCTTCTAGACTTAAGT
* * * *
5889502 TGTGCTGCAAATGATATGCCTTGGAGCTGATCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGAT
* * *
5889567 ACCCTTC-GGCTTAAGTTATGCTGCGAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGT
66 ACCCTTCAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGA
5889631 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
131 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
** * *
5889696 GTAATCGAACTCGGGGGTC-TTG-GCAGATAGCCCTTC--GACTTAAGC
196 GTAATCGAACTCGAAGGTCTTTGTGCAGATAACCCTTCTAGACTTAAGT
* *
5889741 TATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGTTGGCAGA
1 TATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGA
* * ** * * * *
5889805 CAACCCTTCTAGACTTAAGTTGTGCTGCAAATGAAATG-CCTTGGAGCTGAGCGTAGTCGAACTC
65 -TACCCTTC-AGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC
* ** * * * *
5889869 GAAGGTCTTTGGTTGGCATAAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAA
128 GGAGGTCTTTGG-CAG-AT-AGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG-A
* * *
5889934 GCTGAGTGTAATCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGT
189 GCTGAGCGTAATCGAACTCGAAGGTCTTT-GTG-CAGATAACCCTTCTAGACTTAAGT
5889992 TATGCTGCAAATGAT
1 TATGCTGCAAATGAT
5890007 TGTTTTAAAA
Statistics
Matches: 436, Mismatches: 54, Indels: 28
0.84 0.10 0.05
Matches are distributed among these distances:
239 63 0.14
240 9 0.02
241 43 0.10
242 24 0.06
243 2 0.00
244 42 0.10
245 24 0.06
246 132 0.30
247 1 0.00
248 13 0.03
249 62 0.14
251 21 0.05
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (244 bp):
TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGAT
ACCCTTCAGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGA
GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGC
GTAATCGAACTCGAAGGTCTTTGTGCAGATAACCCTTCTAGACTTAAGT
Found at i:5893244 original size:18 final size:19
Alignment explanation
Indices: 5893208--5893248 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
5893198 AATGTGAATA
5893208 CAAAGAAAATAACAAAATG
1 CAAAGAAAATAACAAAATG
5893227 CAAAGAAAATAA-AAAATG
1 CAAAGAAAATAACAAAATG
5893245 CAAA
1 CAAA
5893249 ATGTCTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (19 bp):
CAAAGAAAATAACAAAATG
Found at i:5894984 original size:23 final size:23
Alignment explanation
Indices: 5894915--5894985 Score: 58
Period size: 23 Copynumber: 3.1 Consensus size: 23
5894905 AAATCAAAAT
* *
5894915 AAATACAAAAGAAAA-AAGA-GGA
1 AAATA-AAAAAAAAATAAGATGAA
* *
5894937 AAATAAAAAAAAAATAAGCTTAA
1 AAATAAAAAAAAAATAAGATGAA
*
5894960 AAATAAAATAAAAATAA-ATAGAA
1 AAATAAAAAAAAAATAAGAT-GAA
5894983 AAA
1 AAA
5894986 AATGATAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
21 8 0.21
22 9 0.23
23 22 0.56
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (23 bp):
AAATAAAAAAAAAATAAGATGAA
Found at i:5896397 original size:13 final size:13
Alignment explanation
Indices: 5896379--5896404 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5896369 GGTGAATAAT
5896379 AATAAATAAAAAC
1 AATAAATAAAAAC
5896392 AATAAATAAAAAC
1 AATAAATAAAAAC
5896405 TATATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAATAAAAAC
Found at i:5896536 original size:33 final size:31
Alignment explanation
Indices: 5896455--5896555 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
5896445 CTATATACTA
* *
5896455 TATATAAATTTTCAAAAATGTTTTTCAAAAAAC
1 TATAT-AATTTTTAAAAATGTTTTT-AAAAAAT
*
5896488 TA-ATAATTTTTAAAAATGTTCTTTTAAAAAT
1 TATATAATTTTTAAAAATGTT-TTTAAAAAAT
5896519 TATATAATTTTTTAAAAATG-TTTTAAAAAAT
1 TATATAA-TTTTTAAAAATGTTTTTAAAAAAT
5896550 TATATA
1 TATATA
5896556 TTATATATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
31 37 0.61
32 10 0.16
33 14 0.23
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (31 bp):
TATATAATTTTTAAAAATGTTTTTAAAAAAT
Found at i:5896623 original size:35 final size:35
Alignment explanation
Indices: 5896495--5896744 Score: 210
Period size: 35 Copynumber: 7.0 Consensus size: 35
5896485 AACTAATAAT
5896495 TTTTAAAAATGTTCTTTTAAAAATTATATA--AT-T-
1 TTTTAAAAATG-T-TTTTAAAAATTATATATTATATG
*
5896528 TTTTAAAAATGTTTTAAAAAATTATATATTATATATAAG
1 TTTTAAAAATGTTTTTAAAAATTATATA-T-TATAT--G
* *
5896567 TTTTCAAAAATG-CTCTAAAAATTATATATTATATG
1 TTTT-AAAAATGTTTTTAAAAATTATATATTATATG
* * *
5896602 TTTTCAAAATGTTTTTCAAAATTATATATTATATA
1 TTTTAAAAATGTTTTTAAAAATTATATATTATATG
* *
5896637 TTTTTAAAATGTTTTTCAAAAATTATAT-TATATATT
1 TTTTAAAAATGTTTTT-AAAAATTATATAT-TATATG
* *
5896673 TTTTAAAAATG-TTTTGAAAATATATATAATATATAG
1 TTTTAAAAATGTTTTTAAAAAT-TATATATTATAT-G
* *
5896709 TTTTTAAAA-GTGTTTTAAAAACCATATATATTATAT
1 TTTTAAAAATGT-TTTTAAAAA--TTATATATTATAT
5896745 ACATATTTTC
Statistics
Matches: 178, Mismatches: 20, Indels: 33
0.77 0.09 0.14
Matches are distributed among these distances:
31 15 0.08
32 1 0.01
33 11 0.06
34 11 0.06
35 57 0.32
36 34 0.19
37 13 0.07
38 12 0.07
39 17 0.10
40 7 0.04
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (35 bp):
TTTTAAAAATGTTTTTAAAAATTATATATTATATG
Found at i:5896699 original size:71 final size:69
Alignment explanation
Indices: 5896493--5896739 Score: 238
Period size: 71 Copynumber: 3.5 Consensus size: 69
5896483 AAAACTAATA
*
5896493 ATTTTTAAAAATGTTCTTTTAAAAA-T-TATATA-ATTTTTTAAAAATGTTTTAAAAAATTATAT
1 ATTTTTAAAAATG-T-TTTTAAAAATTATATATATATTTTTTAAAAATGTTTTAAAATA-TATAT
5896555 ATTATAT
63 ATTATAT
* * * *
5896562 ATAAGTTTTCAAAAATG-CTCTAAAAATTATATATTATATGTTTTCAAAATGTTTTTCAAAAT-T
1 AT---TTTT-AAAAATGTTTTTAAAAATTATATA-TATATTTTTTAAAAATG-TTTT-AAAATAT
5896625 ATATATTATAT
59 ATATATTATAT
5896636 ATTTTT-AAAATGTTTTTCAAAAATTATATTATATATTTTTTAAAAATGTTTTGAAAATATATAT
1 ATTTTTAAAAATGTTTTT-AAAAATTATA-TATATATTTTTTAAAAATGTTTT-AAAATATATAT
*
5896700 AATATAT
63 ATTATAT
* **
5896707 AGTTTTTAAAAGTG-TTTTAAAAACCATATATAT
1 A-TTTTTAAAAATGTTTTTAAAAATTATATATAT
5896740 TATATACATA
Statistics
Matches: 148, Mismatches: 14, Indels: 31
0.77 0.07 0.16
Matches are distributed among these distances:
69 8 0.05
70 23 0.16
71 50 0.34
72 19 0.13
73 14 0.09
74 26 0.18
75 4 0.03
76 4 0.03
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (69 bp):
ATTTTTAAAAATGTTTTTAAAAATTATATATATATTTTTTAAAAATGTTTTAAAATATATATATT
ATAT
Found at i:5897649 original size:24 final size:26
Alignment explanation
Indices: 5897616--5897730 Score: 91
Period size: 24 Copynumber: 4.4 Consensus size: 26
5897606 ATATATATAA
5897616 TTTATCATTTTAT-AAATTTTAATATT
1 TTTAT-ATTTTATAAAATTTTAATATT
*
5897642 TTTA-ATTTTATAAAAATTT--TATT
1 TTTATATTTTATAAAATTTTAATATT
5897665 TTTATATTTTATAAATATTTTAATGATAT
1 TTTATATTTTATAAA-ATTTTAAT-AT-T
*
5897694 TGTT-TAATTTTA-ATAATTTCTTAAT-TT
1 T-TTAT-ATTTTATA-AAATT-TTAATATT
5897721 TTTATATTTT
1 TTTATATTTT
5897731 TACTTAAAGA
Statistics
Matches: 74, Mismatches: 3, Indels: 24
0.73 0.03 0.24
Matches are distributed among these distances:
23 8 0.11
24 17 0.23
25 10 0.14
26 11 0.15
27 4 0.05
28 3 0.04
29 6 0.08
30 15 0.20
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTATATTTTATAAAATTTTAATATT
Found at i:5900931 original size:21 final size:21
Alignment explanation
Indices: 5900907--5900979 Score: 137
Period size: 21 Copynumber: 3.5 Consensus size: 21
5900897 ACCAATTTGT
*
5900907 ATTTGTTTTTCCAAATGTTTC
1 ATTTGTTCTTCCAAATGTTTC
5900928 ATTTGTTCTTCCAAATGTTTC
1 ATTTGTTCTTCCAAATGTTTC
5900949 ATTTGTTCTTCCAAATGTTTC
1 ATTTGTTCTTCCAAATGTTTC
5900970 ATTTGTTCTT
1 ATTTGTTCTT
5900980 GAATTGTGAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.56
Consensus pattern (21 bp):
ATTTGTTCTTCCAAATGTTTC
Found at i:5901398 original size:21 final size:21
Alignment explanation
Indices: 5901347--5901401 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
5901337 CAAATGAATA
* *
5901347 ACTACGTTAACATCATAGACC
1 ACTACGTTAGCATAATAGACC
*
5901368 CCTACGTTAGCATAATAGACC
1 ACTACGTTAGCATAATAGACC
*
5901389 ACTATGTTAGCAT
1 ACTACGTTAGCAT
5901402 TGTAATGGCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (21 bp):
ACTACGTTAGCATAATAGACC
Found at i:5902299 original size:19 final size:19
Alignment explanation
Indices: 5902275--5902348 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
5902265 ATGCAAATAT
5902275 GGTATCGATACCATAGGAG
1 GGTATCGATACCATAGGAG
* *
5902294 GGTATCGATACTATAGTATG
1 GGTATCGATACCATAGGA-G
5902314 GTAGTATCGATACCAT-GGTAAG
1 G--GTATCGATACCATAGG--AG
*
5902336 GGTATTGATACCA
1 GGTATCGATACCA
5902349 GGTAACATCG
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
19 16 0.36
20 13 0.29
21 1 0.02
22 14 0.31
23 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (19 bp):
GGTATCGATACCATAGGAG
Found at i:5902827 original size:59 final size:59
Alignment explanation
Indices: 5902772--5903174 Score: 682
Period size: 59 Copynumber: 6.8 Consensus size: 59
5902762 ATGGCACTAA
* *
5902772 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATCAATTTTCGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
*
5902831 GTGTGCTAAAATGATAAGAAGTTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
*
5902890 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAAGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
5902949 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
* *
5903008 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAAGGCACTTC
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
* *
5903067 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACCTT-
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCA-CTTC
* * * *
5903126 GTGTGCTAAAATAATGAGAAATTCATACTAAGTGTATAAATTTCCGTAT
1 GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
5903175 GGGAAATATA
Statistics
Matches: 330, Mismatches: 13, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
59 327 0.99
60 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTC
Found at i:5912373 original size:31 final size:31
Alignment explanation
Indices: 5912330--5912575 Score: 352
Period size: 31 Copynumber: 8.0 Consensus size: 31
5912320 GAGTCGATGG
* *
5912330 TTACCTACGTTCTTCAGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
5912361 TTACCTATGTTCTTCGGGATATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
5912392 TTACCTATGTTCTTCGGGATATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
5912423 TTACCTATGTTCTTCGGGACATATGAACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* * *
5912454 TTACCTATGTTCTTCGAGATATATGAACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
5912485 TTACCTATGTTCTTC--GATCATATGGACTGA
1 TTACCTATGTTCTTCGGGA-CATATGGACTGT
*
5912515 TTACCTATGTTCTTGGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
5912546 TTACCTATGTTCTTCGGAACATATGGACTG
1 TTACCTATGTTCTTCGGGACATATGGACTG
5912576 GTCCTTCAGG
Statistics
Matches: 196, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
29 2 0.01
30 23 0.12
31 169 0.86
32 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:5913388 original size:21 final size:22
Alignment explanation
Indices: 5913353--5913405 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
5913343 ATATATGTTT
* *
5913353 ACTGTATCAAGGGTATCGGTA-C
1 ACTGTAGC-AGGGTATCGATACC
5913375 ACTGTAGCAGGGTATCGATACC
1 ACTGTAGCAGGGTATCGATACC
*
5913397 CCTGTAGCA
1 ACTGTAGCA
5913406 TTCTAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (22 bp):
ACTGTAGCAGGGTATCGATACC
Found at i:5913868 original size:17 final size:17
Alignment explanation
Indices: 5913826--5913881 Score: 62
Period size: 16 Copynumber: 3.2 Consensus size: 17
5913816 TTTAATTTTT
5913826 AATATTTTAATATTTAAA
1 AATATTTTAA-ATTTAAA
*
5913844 TTATATTTTAAATTTAAA
1 -AATATTTTAAATTTAAA
5913862 AATATTTCT--ATTTAAA
1 AATATTT-TAAATTTAAA
5913878 AATA
1 AATA
5913882 AATAAATAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 11 0.32
17 6 0.18
18 8 0.24
19 9 0.26
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATTTTAAATTTAAA
Found at i:5921605 original size:15 final size:15
Alignment explanation
Indices: 5921587--5921642 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
5921577 TAACCGGTTT
5921587 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
5921602 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
5921619 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
5921634 CGATTTTAA
1 CGGTTTTAA
5921643 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:5921615 original size:17 final size:17
Alignment explanation
Indices: 5921590--5921640 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
5921580 CCGGTTTCGG
5921590 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
5921607 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
5921622 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
5921639 TT
1 TT
5921641 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Done.