Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_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: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 24
Found at i:676784 original size:26 final size:26
Alignment explanation
Indices: 676748--676807 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
676738 AATCCGAGCA
*
676748 TGATTCAGACTCAAGCCCAACATATC
1 TGATCCAGACTCAAGCCCAACATATC
676774 TGATCCAGACTCAAGCCCAACATATC
1 TGATCCAGACTCAAGCCCAACATATC
676800 TGATCCAG
1 TGATCCAG
676808 CCCCAGTAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.33, C:0.32, G:0.13, T:0.22
Consensus pattern (26 bp):
TGATCCAGACTCAAGCCCAACATATC
Found at i:676852 original size:48 final size:48
Alignment explanation
Indices: 676796--676894 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
676786 AAGCCCAACA
676796 TATCTGATCCAGCCCCAGTAACCGAGTCAGGCCCAATTCCAGCAAGCC
1 TATCTGATCCAGCCCCAGTAACCGAGTCAGGCCCAATTCCAGCAAGCC
676844 TATCTGATCCAGCCCCAGTAACCGAGTCAGGCCCAATTCCAGCAAGCC
1 TATCTGATCCAGCCCCAGTAACCGAGTCAGGCCCAATTCCAGCAAGCC
676892 TAT
1 TAT
676895 GCGAGAAACC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.27, C:0.36, G:0.18, T:0.18
Consensus pattern (48 bp):
TATCTGATCCAGCCCCAGTAACCGAGTCAGGCCCAATTCCAGCAAGCC
Found at i:681016 original size:17 final size:16
Alignment explanation
Indices: 680994--681047 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
680984 AATCAGGTAT
680994 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
**
681011 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
681026 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
681043 CGGGT
1 CGGGT
681048 CGGGACACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 11 0.35
16 4 0.13
17 16 0.52
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:684349 original size:20 final size:17
Alignment explanation
Indices: 684303--684337 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
684293 GTCAAATGTT
684303 TTACGAACCAGTAATCA
1 TTACGAACCAGTAATCA
684320 TTACGAACCAGTAATCA
1 TTACGAACCAGTAATCA
684337 T
1 T
684338 GGTGCTGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (17 bp):
TTACGAACCAGTAATCA
Found at i:685304 original size:16 final size:16
Alignment explanation
Indices: 685255--685325 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
685245 TGTTAGATAG
685255 AGAAAAAATGAAGATAA
1 AGAAAAAATGAA-ATAA
* * * *
685272 ATAATAAAGGAAGTAA
1 AGAAAAAATGAAATAA
*
685288 AGAACAAATGAAATAA
1 AGAAAAAATGAAATAA
* *
685304 A-ATAAAATAAAATAA
1 AGAAAAAATGAAATAA
*
685319 CGAAAAA
1 AGAAAAA
685326 TACGAAAAGG
Statistics
Matches: 40, Mismatches: 13, Indels: 3
0.71 0.23 0.05
Matches are distributed among these distances:
15 11 0.28
16 20 0.50
17 9 0.22
ACGTcount: A:0.70, C:0.03, G:0.13, T:0.14
Consensus pattern (16 bp):
AGAAAAAATGAAATAA
Found at i:685465 original size:27 final size:28
Alignment explanation
Indices: 685435--685491 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
685425 AATGCAAATT
*
685435 AATAAATAAATAAACAAG-AAAAAAAGA
1 AATAAATAAATAAAAAAGTAAAAAAAGA
* * *
685462 AATATATATATAAAAAAGTAAAAATAGA
1 AATAAATAAATAAAAAAGTAAAAAAAGA
685490 AA
1 AA
685492 AATAATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.18
Consensus pattern (28 bp):
AATAAATAAATAAAAAAGTAAAAAAAGA
Found at i:685491 original size:36 final size:36
Alignment explanation
Indices: 685451--685573 Score: 93
Period size: 36 Copynumber: 3.5 Consensus size: 36
685441 TAAATAAACA
685451 AGAAAAAAAGAAATATATATATAAAAAAGTAAAAAT
1 AGAAAAAAAGAAATATATATATAAAAAAGTAAAAAT
* *
685487 AG--AAAAA-TAATA-ATA-ATAACAATAA-TAACAAT
1 AGAAAAAAAGAAATATATATATAA-AA-AAGTAAAAAT
*
685519 AAGGAAAAAAAGTAATATA-ATATAAATAAAG-AGAAAAT
1 -A-GAAAAAAAGAAATATATATATAAA-AAAGTA-AAAAT
685557 A-AAAAAATAGAAATATA
1 AGAAAAAA-AGAAATATA
685574 GAAAATATAA
Statistics
Matches: 70, Mismatches: 4, Indels: 26
0.70 0.04 0.26
Matches are distributed among these distances:
31 4 0.06
32 11 0.16
33 7 0.10
34 6 0.09
35 6 0.09
36 15 0.21
37 11 0.16
38 10 0.14
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.20
Consensus pattern (36 bp):
AGAAAAAAAGAAATATATATATAAAAAAGTAAAAAT
Found at i:685502 original size:28 final size:26
Alignment explanation
Indices: 685438--685502 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 26
685428 GCAAATTAAT
*
685438 AAATA-AATAAACAAGAAAAAAAGAA
1 AAATATAATAAAAAAGAAAAAAAGAA
* *
685463 ATATATATATAAAAAAGTAAAAATAGAA
1 AAATATA-ATAAAAAAG-AAAAAAAGAA
685491 AAATAATAATAA
1 AAAT-ATAATAA
685503 TAACAATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
25 4 0.12
26 1 0.03
27 8 0.25
28 16 0.50
29 3 0.09
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.18
Consensus pattern (26 bp):
AAATATAATAAAAAAGAAAAAAAGAA
Found at i:687466 original size:114 final size:110
Alignment explanation
Indices: 687331--687538 Score: 301
Period size: 114 Copynumber: 1.9 Consensus size: 110
687321 TGGGAAATTG
*
687331 TTTGTTGACAGCCAGCTGCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCA
1 TTTGTTGACAACCAGCTGCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCA
687396 TTCGATCGATGTGAAGTTGAAATTGACTCTGAATGAAGCTGAAAAGTTA
66 TTC-A-C--TGTGAAGTTGAAATTGACTCTGAATGAAGCTGAAAAGTTA
* ** * *
687445 TTTGTTGACAATCAG-TCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATC
1 TTTGTTGACAACCAGCT-GCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATC
*
687509 ATTCACTGTGAAGTTGAAATTGGCTCTGAA
65 ATTCACTGTGAAGTTGAAATTGACTCTGAA
687539 ACTGGGAAGT
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
110 23 0.27
112 1 0.01
113 2 0.02
114 60 0.70
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (110 bp):
TTTGTTGACAACCAGCTGCCCCTTCACTATGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCA
TTCACTGTGAAGTTGAAATTGACTCTGAATGAAGCTGAAAAGTTA
Found at i:688652 original size:14 final size:13
Alignment explanation
Indices: 688629--688686 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 13
688619 TCCCACCTTA
*
688629 TTTTTATTTTCTCT
1 TTTTTCTTTTCT-T
*
688643 TTTTTCTTTTGTT
1 TTTTTCTTTTCTT
* *
688656 CTTTT-TGTTCTT
1 TTTTTCTTTTCTT
688668 TTTTTCTTTTTCTT
1 TTTTTC-TTTTCTT
688682 TTTTT
1 TTTTT
688687 TAATTTAGGG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
12 9 0.26
13 5 0.14
14 21 0.60
ACGTcount: A:0.02, C:0.12, G:0.03, T:0.83
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:688678 original size:8 final size:8
Alignment explanation
Indices: 688635--688686 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
688625 CTTATTTTTA
688635 TTTTCTCTT
1 TTTTCT-TT
688644 TTTTCTTT
1 TTTTCTTT
*
688652 TGTTCTTT
1 TTTTCTTT
688660 TTGTTCTTT
1 TT-TTCTTT
688669 TTTTC--T
1 TTTTCTTT
688675 TTTTCTTT
1 TTTTCTTT
688683 TTTT
1 TTTT
688687 TAATTTAGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
6 6 0.16
8 18 0.47
9 14 0.37
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (8 bp):
TTTTCTTT
Found at i:688687 original size:9 final size:9
Alignment explanation
Indices: 688630--688687 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
688620 CCCACCTTAT
688630 TTTTATTTTC
1 TTTT-TTTTC
*
688640 TCTTTTTTC
1 TTTTTTTTC
*
688649 -TTTTGTTC
1 TTTTTTTTC
*
688657 TTTTTGTTC
1 TTTTTTTTC
688666 -TTTTTTTC
1 TTTTTTTTC
688674 TTTTTCTTT-
1 TTTTT-TTTC
688683 TTTTT
1 TTTTT
688688 AATTTAGGGC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 13 0.32
9 22 0.54
10 6 0.15
ACGTcount: A:0.02, C:0.12, G:0.03, T:0.83
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:688687 original size:17 final size:16
Alignment explanation
Indices: 688635--688686 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
688625 CTTATTTTTA
688635 TTTTCTCTTTTTTCTTT
1 TTTTCT-TTTTTTCTTT
*
688652 TGTTCTTTTTGTTCTTT
1 TTTTCTTTTT-TTCTTT
688669 TTTTC--TTTTTCTTT
1 TTTTCTTTTTTTCTTT
688683 TTTT
1 TTTT
688687 TAATTTAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 10 0.31
15 3 0.09
16 4 0.12
17 15 0.47
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (16 bp):
TTTTCTTTTTTTCTTT
Found at i:689191 original size:15 final size:15
Alignment explanation
Indices: 689171--689212 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
689161 CTTCAATGGG
689171 TAGCACTGCTTCCAT
1 TAGCACTGCTTCCAT
689186 TAGCACTGCTTCCAT
1 TAGCACTGCTTCCAT
689201 TAGCACTGCTTC
1 TAGCACTGCTTC
689213 TATTCCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.19, C:0.33, G:0.14, T:0.33
Consensus pattern (15 bp):
TAGCACTGCTTCCAT
Found at i:705381 original size:30 final size:29
Alignment explanation
Indices: 705340--705434 Score: 136
Period size: 30 Copynumber: 3.2 Consensus size: 29
705330 ACGTGGGGGC
* *
705340 ATGGTGATGGCATGGGATATTGAATATAAA
1 ATGGTAATGGCATGGGATGTTGAATA-AAA
*
705370 ATGGTAGTGGCATGGGATGTTGAATAAAAA
1 ATGGTAATGGCATGGGATGTTGAAT-AAAA
705400 ATGGTAATGGCATGGGATGTTGAATAAAA
1 ATGGTAATGGCATGGGATGTTGAATAAAA
705429 TATGGT
1 -ATGGT
705435 GGGATAAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.07
30 54 0.92
31 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.32, T:0.29
Consensus pattern (29 bp):
ATGGTAATGGCATGGGATGTTGAATAAAA
Found at i:707700 original size:33 final size:34
Alignment explanation
Indices: 707663--707743 Score: 87
Period size: 37 Copynumber: 2.3 Consensus size: 34
707653 TAACAACTAC
*
707663 ATAAAAAAATACTAA-GATATTGC-AAAT-AAATAA
1 ATAAAAAAATA-TAAGGAGA-TGCAAAATAAAATAA
707696 ATAAAATAAATATAAGGGAGATGCAAAATAAAAATAA
1 ATAAAA-AAATATAA-GGAGATGCAAAAT-AAAATAA
707733 ATAAAAAAATA
1 ATAAAAAAATA
707744 AATAAACAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
33 9 0.22
34 8 0.20
35 7 0.17
36 5 0.12
37 12 0.29
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.21
Consensus pattern (34 bp):
ATAAAAAAATATAAGGAGATGCAAAATAAAATAA
Found at i:707741 original size:18 final size:18
Alignment explanation
Indices: 707720--707826 Score: 65
Period size: 18 Copynumber: 5.7 Consensus size: 18
707710 AGGGAGATGC
707720 AAAATAAAAATAAATAAA
1 AAAATAAAAATAAATAAA
*
707738 AAAATAAATAA-ACAAGAAA
1 AAAATAAA-AATA-AATAAA
* *
707757 AAAAGAAATATATATATAAA
1 AAAATAAA-A-ATAAATAAA
* *
707777 AAAGTAAATATAAATAATA
1 AAAATAAAAATAAATAA-A
* *
707796 ATAATAATAAT-AATAATA
1 AAAATAAAAATAAATAA-A
* *
707814 ATAATAATAATAA
1 AAAATAAAAATAA
707827 TAATAATAAC
Statistics
Matches: 71, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
18 34 0.48
19 25 0.35
20 11 0.15
21 1 0.01
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAATAAAAATAAATAAA
Found at i:707742 original size:12 final size:12
Alignment explanation
Indices: 707725--707749 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
707715 GATGCAAAAT
707725 AAAAATAAATAA
1 AAAAATAAATAA
707737 AAAAATAAATAA
1 AAAAATAAATAA
707749 A
1 A
707750 CAAGAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATAAATAA
Found at i:707797 original size:3 final size:3
Alignment explanation
Indices: 707789--707846 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
707779 AGTAAATATA
*
707789 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
707837 AAT AAC AAT A
1 AAT AAT AAT A
707847 GGGGGAAAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:710394 original size:14 final size:14
Alignment explanation
Indices: 710358--710414 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
710348 TGAGTGACGC
* *
710358 TTATTATATATATG
1 TTATAATATATATA
*
710372 TTATTATATATATA
1 TTATAATATATATA
*
710386 TAATAATAT-TATA
1 TTATAATATATATA
710399 TTATAA-ATAT-TA
1 TTATAATATATATA
710411 TTAT
1 TTAT
710415 TTACAAAGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.21
13 10 0.26
14 20 0.53
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (14 bp):
TTATAATATATATA
Found at i:710407 original size:17 final size:19
Alignment explanation
Indices: 710373--710414 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
710363 ATATATATGT
710373 TATTATATATATATAATAA
1 TATTATATATATATAATAA
*
710392 TATTATAT-TATA-AATAT
1 TATTATATATATATAATAA
710409 TATTAT
1 TATTAT
710415 TTACAAAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
18 4 0.18
19 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTATATATATATAATAA
Found at i:713551 original size:20 final size:20
Alignment explanation
Indices: 713522--713559 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
713512 AGTTTCTGGG
* *
713522 CAAGAGTATCGATACTTTTT
1 CAAGACTATCGAAACTTTTT
713542 CAAGACTATCGAAACTTT
1 CAAGACTATCGAAACTTT
713560 GGGTCATAGT
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:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (20 bp):
CAAGACTATCGAAACTTTTT
Found at i:715734 original size:2 final size:2
Alignment explanation
Indices: 715727--715757 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
715717 TATCAAAATC
715727 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
715758 GCTGCAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:717388 original size:11 final size:12
Alignment explanation
Indices: 717375--717425 Score: 63
Period size: 11 Copynumber: 4.4 Consensus size: 12
717365 TAATTTTAAT
717375 TTATATTAAAT-
1 TTATATTAAATA
717386 TTATATT-AATA
1 TTATATTAAATA
*
717397 TTAT-TAAAATA
1 TTATATTAAATA
717408 TTATATTAATATA
1 TTATATTAA-ATA
717421 TTATA
1 TTATA
717426 ATTGAGATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 4 0.12
11 19 0.56
12 3 0.09
13 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTATATTAAATA
Found at i:717411 original size:22 final size:20
Alignment explanation
Indices: 717376--717428 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
717366 AATTTTAATT
717376 TATATT-AAATTTATATTAA
1 TATATTAAAATTTATATTAA
717395 TATTATTAAAATATTATATTAA
1 TA-TATTAAAAT-TTATATTAA
*
717417 TATATTATAATT
1 TATATTAAAATT
717429 GAGATATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.07
20 5 0.17
21 12 0.40
22 11 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATATTAAAATTTATATTAA
Found at i:717586 original size:22 final size:19
Alignment explanation
Indices: 717541--717579 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
717531 ATTGCCAATA
717541 AATTAAAAAAAATCTTAAT
1 AATTAAAAAAAATCTTAAT
717560 AATTAAAAAAAATCTTAAT
1 AATTAAAAAAAATCTTAAT
717579 A
1 A
717580 GATATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
AATTAAAAAAAATCTTAAT
Found at i:720670 original size:20 final size:20
Alignment explanation
Indices: 720645--720682 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
720635 CTAATAAAAA
* *
720645 AATATATTTATTATATTATT
1 AATATAATTAGTATATTATT
720665 AATATAATTAGTATATTA
1 AATATAATTAGTATATTA
720683 AACAATGCTT
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:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
AATATAATTAGTATATTATT
Found at i:726526 original size:11 final size:11
Alignment explanation
Indices: 726510--726534 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
726500 TTAATCTCTC
726510 TTTTTTTTCTT
1 TTTTTTTTCTT
726521 TTTTTTTTCTT
1 TTTTTTTTCTT
726532 TTT
1 TTT
726535 GAGATTCTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:732382 original size:21 final size:21
Alignment explanation
Indices: 732358--732400 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
732348 TCATAATTTT
732358 ATGTTAGAAAATAAACTTCTA
1 ATGTTAGAAAATAAACTTCTA
732379 ATGTTAGAAAATAAACTTCTA
1 ATGTTAGAAAATAAACTTCTA
732400 A
1 A
732401 AATTTTAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (21 bp):
ATGTTAGAAAATAAACTTCTA
Found at i:737881 original size:24 final size:24
Alignment explanation
Indices: 737829--737881 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
737819 TTTCAAGTTA
* *
737829 TTAAGTGAATTAATTATTTTATAT
1 TTAATTGAATTAATTATTTTAAAT
737853 TTAATTGATATTAATT-TTTTAAAT
1 TTAATTGA-ATTAATTATTTTAAAT
737877 TTAAT
1 TTAAT
737882 CTCAAAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (24 bp):
TTAATTGAATTAATTATTTTAAAT
Found at i:737940 original size:13 final size:13
Alignment explanation
Indices: 737910--737934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
737900 TAACTAAATT
737910 TAAAATTAAGTAA
1 TAAAATTAAGTAA
737923 TAAAATTAAGTA
1 TAAAATTAAGTA
737935 TGAAAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (13 bp):
TAAAATTAAGTAA
Found at i:743756 original size:62 final size:62
Alignment explanation
Indices: 743677--743800 Score: 230
Period size: 62 Copynumber: 2.0 Consensus size: 62
743667 CAAAACGACC
*
743677 AATTTGCACAGCTTATACTTAACTATAAACACAAGACTGACTTCTCAAGCTAAGGACCCAAT
1 AATTTGCACAGCATATACTTAACTATAAACACAAGACTGACTTCTCAAGCTAAGGACCCAAT
*
743739 AATTTGCACAGCATATACTTAACTATAAACACGAGACTGACTTCTCAAGCTAAGGACCCAAT
1 AATTTGCACAGCATATACTTAACTATAAACACAAGACTGACTTCTCAAGCTAAGGACCCAAT
743801 GTTTGCATTC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (62 bp):
AATTTGCACAGCATATACTTAACTATAAACACAAGACTGACTTCTCAAGCTAAGGACCCAAT
Found at i:746967 original size:54 final size:54
Alignment explanation
Indices: 746849--746972 Score: 149
Period size: 54 Copynumber: 2.3 Consensus size: 54
746839 GATACTTTCC
* * *
746849 TTCAAGGGTATCGATACCTCCTCATGGTACCGATACCGATATAACATTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCAATACCAATATAACATTCGATGT
* * * ** * *
746903 TTCAAAGGTATCGATACCTCCTCAAGGTACCAATATCAATCTGGCATTTGATTT
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCAATACCAATATAACATTCGATGT
*
746957 TTTAAGGGTATCGATA
1 TTCAAGGGTATCGATA
746973 TCATCCTTCA
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTCCTCAAGGTACCAATACCAATATAACATTCGATGT
Found at i:747000 original size:20 final size:21
Alignment explanation
Indices: 746963--747042 Score: 71
Period size: 20 Copynumber: 3.9 Consensus size: 21
746953 ATTTTTTAAG
*
746963 GGTATCGATA-TCATCCTT-CA
1 GGTATCGATACT-ACCCTTACA
746983 GGTATCGATACTACCCTTACA
1 GGTATCGATACTACCCTTACA
* *
747004 -GAATCGATAC--CTCTTCAACA
1 GGTATCGATACTACCCTT--ACA
747024 GGTATCGATACTACCCTTA
1 GGTATCGATACTACCCTTA
747043 ATAATTTCAC
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
18 4 0.08
20 27 0.56
21 13 0.27
23 4 0.08
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.30
Consensus pattern (21 bp):
GGTATCGATACTACCCTTACA
Found at i:748101 original size:21 final size:22
Alignment explanation
Indices: 748072--748145 Score: 80
Period size: 21 Copynumber: 3.3 Consensus size: 22
748062 TATTTTTTTT
748072 TATATTTTTAATAAT-TAAATAA
1 TATA-TTTTAATAATATAAATAA
748094 TATATTTTAATAATATAAAT-A
1 TATATTTTAATAATATAAATAA
* *
748115 TAAATTCTTAATATATATATATATA
1 TATATT-TTAATA-ATATAAATA-A
748140 TATATT
1 TATATT
748146 ATATATATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
21 16 0.36
22 15 0.34
23 7 0.16
25 6 0.14
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (22 bp):
TATATTTTAATAATATAAATAA
Found at i:748116 original size:19 final size:21
Alignment explanation
Indices: 748072--748162 Score: 75
Period size: 21 Copynumber: 4.3 Consensus size: 21
748062 TATTTTTTTT
*
748072 TATATTTTTAATA-ATTAAATAA
1 TATA-TTTTAATATA-TATATAA
748094 TATATTTTAATA-ATATA-AA
1 TATATTTTAATATATATATAA
748113 TATAAATTCTTAATATATATATATA
1 TAT--ATT-TTAATATATATATA-A
*
748138 TATATATT-ATATATATAT-A
1 TATATTTTAATATATATATAA
748157 TATATT
1 TATATT
748163 AATCAGGTCA
Statistics
Matches: 60, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
19 11 0.18
20 3 0.05
21 22 0.37
22 12 0.20
23 7 0.12
24 1 0.02
25 4 0.07
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (21 bp):
TATATTTTAATATATATATAA
Found at i:748132 original size:2 final size:2
Alignment explanation
Indices: 748125--748161 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
748115 TAAATTCTTA
748125 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
748162 TAATCAGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:748148 original size:17 final size:17
Alignment explanation
Indices: 748128--748163 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
748118 ATTCTTAATA
748128 TATATATATATATATAT
1 TATATATATATATATAT
748145 TATATATATATATATAT
1 TATATATATATATATAT
748162 TA
1 TA
748164 ATCAGGTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:754700 original size:18 final size:17
Alignment explanation
Indices: 754668--754736 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 17
754658 TGAATATTTA
754668 TCCCGAAGTACCACTATG
1 TCCCGAAG-ACCACTATG
* *
754686 TCCTGAATGACCACTTTG
1 TCCCGAA-GACCACTATG
754704 TCCCGAAGAACCACTATG
1 TCCCGAAG-ACCACTATG
754722 TCCCGAAGGACCACT
1 TCCCGAA-GACCACT
754737 GATAATCCCT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.02
18 41 0.93
19 2 0.05
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (17 bp):
TCCCGAAGACCACTATG
Found at i:754709 original size:36 final size:36
Alignment explanation
Indices: 754668--754736 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
754658 TGAATATTTA
* * *
754668 TCCCGAAGTACCACTATGTCCTGAATGACCACTTTG
1 TCCCGAAGAACCACTATGTCCCGAAGGACCACTTTG
754704 TCCCGAAGAACCACTATGTCCCGAAGGACCACT
1 TCCCGAAGAACCACTATGTCCCGAAGGACCACT
754737 GATAATCCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (36 bp):
TCCCGAAGAACCACTATGTCCCGAAGGACCACTTTG
Found at i:755018 original size:2 final size:2
Alignment explanation
Indices: 755013--755043 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
755003 ATATATATGC
*
755013 GT GT GT GT GC GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
755044 CACATGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.52, T:0.45
Consensus pattern (2 bp):
GT
Found at i:762074 original size:79 final size:79
Alignment explanation
Indices: 761943--762098 Score: 312
Period size: 79 Copynumber: 2.0 Consensus size: 79
761933 GGAAGCTTGG
761943 GAAATAGCGTGAGAGCTCCTTGTGAGTTCGTTGAAATGTGGGGTTGTGTTTCTAGCGTGTCTTCA
1 GAAATAGCGTGAGAGCTCCTTGTGAGTTCGTTGAAATGTGGGGTTGTGTTTCTAGCGTGTCTTCA
762008 AGGGAGGTTTCCAA
66 AGGGAGGTTTCCAA
762022 GAAATAGCGTGAGAGCTCCTTGTGAGTTCGTTGAAATGTGGGGTTGTGTTTCTAGCGTGTCTTCA
1 GAAATAGCGTGAGAGCTCCTTGTGAGTTCGTTGAAATGTGGGGTTGTGTTTCTAGCGTGTCTTCA
762087 AGGGAGGTTTCC
66 AGGGAGGTTTCC
762099 TCAACGTGTA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.19, C:0.14, G:0.33, T:0.33
Consensus pattern (79 bp):
GAAATAGCGTGAGAGCTCCTTGTGAGTTCGTTGAAATGTGGGGTTGTGTTTCTAGCGTGTCTTCA
AGGGAGGTTTCCAA
Found at i:765960 original size:28 final size:29
Alignment explanation
Indices: 765917--766005 Score: 85
Period size: 28 Copynumber: 3.1 Consensus size: 29
765907 TTATTTTCAT
765917 AAAAAACCTATGAAATT-ATTAAAATTCCAA
1 AAAAAACCT-T-AAATTCATTAAAATTCCAA
*
765947 AAAAAACCTTAAATTCCA-TAAAATTTCAA
1 AAAAAACCTTAAATT-CATTAAAATTCCAA
** * *
765976 AAAACTCC-TAAATTCCTAAAAATTCCAA
1 AAAAAACCTTAAATTCATTAAAATTCCAA
766004 AA
1 AA
766006 TACATTAGGG
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
27 1 0.02
28 22 0.44
29 17 0.34
30 10 0.20
ACGTcount: A:0.55, C:0.18, G:0.01, T:0.26
Consensus pattern (29 bp):
AAAAAACCTTAAATTCATTAAAATTCCAA
Found at i:765968 original size:29 final size:27
Alignment explanation
Indices: 765936--766005 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
765926 ATGAAATTAT
765936 TAAAATTCCAAAAAAAACCTTAAATTCC
1 TAAAATTCCAAAAAAAACC-TAAATTCC
* **
765964 ATAAAATTTCAAAAAACTCCTAAATTCC
1 -TAAAATTCCAAAAAAAACCTAAATTCC
765992 TAAAAATTCCAAAA
1 T-AAAATTCCAAAA
766006 TACATTAGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 1 0.03
28 19 0.53
29 16 0.44
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.26
Consensus pattern (27 bp):
TAAAATTCCAAAAAAAACCTAAATTCC
Found at i:768442 original size:20 final size:21
Alignment explanation
Indices: 768410--768458 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
768400 CCTAAAAAAT
*
768410 AAAA-AATAAAATAAAA-TTA
1 AAAATAATAAAATAAAAGCTA
*
768429 AAAATAATAGAATAAAAGCTA
1 AAAATAATAAAATAAAAGCTA
768450 AAAATAATA
1 AAAATAATA
768459 TATATTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.15
20 11 0.42
21 11 0.42
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (21 bp):
AAAATAATAAAATAAAAGCTA
Found at i:768551 original size:37 final size:37
Alignment explanation
Indices: 768509--768589 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
768499 ATATGATTGC
768509 AAAAATTATTTTCGAAAA-AAT-ATATATGTTTTAAAA
1 AAAAATTATTTTC-AAAACAATAATATATGTTTTAAAA
* *
768545 AGAAAATTATTTTCAAAACCATAATATATGTTTTCAAA
1 A-AAAATTATTTTCAAAACAATAATATATGTTTTAAAA
768583 AAAAATT
1 AAAAATT
768590 TAAAAACCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
36 5 0.12
37 20 0.50
38 15 0.38
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37
Consensus pattern (37 bp):
AAAAATTATTTTCAAAACAATAATATATGTTTTAAAA
Found at i:768789 original size:36 final size:35
Alignment explanation
Indices: 768691--768900 Score: 197
Period size: 35 Copynumber: 6.1 Consensus size: 35
768681 TTTTTAAATT
*
768691 ATTATTTTAAAAAACTATATACTATATGTTTTCAAG
1 ATTATTTT-AAAAACTATATACTATATGTTTTCAAA
* *
768727 ATTATTTT--AAACCATATACTACATGTTTTTCAAA
1 ATTATTTTAAAAACTATATACTATATG-TTTTCAAA
** *
768761 ATCGTTTTAAAAACTATATATTATATGTTTTCAAA
1 ATTATTTTAAAAACTATATACTATATGTTTTCAAA
*
768796 ATTACTTTAAAAAC----TA-TATA--TTTTCAAA
1 ATTATTTTAAAAACTATATACTATATGTTTTCAAA
* * *
768824 ACCGT-TTTAAAAAACTATATATTATATGTTTTCAAA
1 A--TTATTTTAAAAACTATATACTATATGTTTTCAAA
* *
768860 ATTACTTTAAAAACTATATACTATATATTTTCAAA
1 ATTATTTTAAAAACTATATACTATATGTTTTCAAA
768895 AGTTAT
1 A-TTAT
768901 GTTTGAAATT
Statistics
Matches: 140, Mismatches: 20, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
28 9 0.06
29 8 0.06
30 5 0.04
31 2 0.01
33 17 0.12
34 18 0.13
35 47 0.34
36 34 0.24
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (35 bp):
ATTATTTTAAAAACTATATACTATATGTTTTCAAA
Found at i:768822 original size:28 final size:28
Alignment explanation
Indices: 768782--768879 Score: 79
Period size: 28 Copynumber: 3.2 Consensus size: 28
768772 AACTATATAT
*
768782 TATATGTTTTCAAAATTACTTTAAAAAC
1 TATATATTTTCAAAATTACTTTAAAAAC
****
768810 TATATATTTTCAAAACCGTTTTAAAAAAC
1 TATATATTTTCAAAATTACTTT-AAAAAC
768839 TATATATTATATGTTTTCAAAATTACTTTAAAAAC
1 ----TA-TATA--TTTTCAAAATTACTTTAAAAAC
768874 TATATA
1 TATATA
768880 CTATATATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
28 17 0.32
29 6 0.11
30 4 0.08
31 2 0.04
33 2 0.04
34 4 0.08
35 6 0.11
36 12 0.23
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (28 bp):
TATATATTTTCAAAATTACTTTAAAAAC
Found at i:768856 original size:64 final size:64
Alignment explanation
Indices: 768695--768879 Score: 255
Period size: 64 Copynumber: 2.8 Consensus size: 64
768685 TAAATTATTA
* * * * *
768695 TTTTAAAAAACTATATACTATATGTTTTCAAGATTATTTTAAACCATATACTACATGTTTTTCAA
1 TTTTAAAAAACTATATATTATATGTTTTCAAAATTACTTT-AA--A-A-ACTATAT-ATTTTCAA
*
768760 AATCG
60 AACCG
768765 TTTT-AAAAACTATATATTATATGTTTTCAAAATTACTTTAAAAACTATATATTTTCAAAACCG
1 TTTTAAAAAACTATATATTATATGTTTTCAAAATTACTTTAAAAACTATATATTTTCAAAACCG
768828 TTTTAAAAAACTATATATTATATGTTTTCAAAATTACTTTAAAAACTATATA
1 TTTTAAAAAACTATATATTATATGTTTTCAAAATTACTTTAAAAACTATATA
768880 CTATATATTT
Statistics
Matches: 108, Mismatches: 6, Indels: 8
0.89 0.05 0.07
Matches are distributed among these distances:
63 15 0.14
64 53 0.49
65 1 0.01
66 1 0.01
68 2 0.02
69 32 0.30
70 4 0.04
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (64 bp):
TTTTAAAAAACTATATATTATATGTTTTCAAAATTACTTTAAAAACTATATATTTTCAAAACCG
Found at i:769941 original size:19 final size:18
Alignment explanation
Indices: 769917--769954 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
769907 GTAAGAATTT
769917 TAATTTGATTAAAAGTAGA
1 TAATTTGATTAAAA-TAGA
*
769936 TAATTTTATTAAAATAGA
1 TAATTTGATTAAAATAGA
769954 T
1 T
769955 TTTTACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (18 bp):
TAATTTGATTAAAATAGA
Found at i:771482 original size:2 final size:2
Alignment explanation
Indices: 771475--771499 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
771465 CTCTAGAAAA
771475 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
771500 AAACAGGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:781772 original size:4 final size:4
Alignment explanation
Indices: 781763--781793 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
781753 AGAGAGATGG
*
781763 GAGT GAGT GAGT GAGT GAGT GAGT TAGT GAG
1 GAGT GAGT GAGT GAGT GAGT GAGT GAGT GAG
781794 AAGGGAGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.48, T:0.26
Consensus pattern (4 bp):
GAGT
Found at i:785651 original size:21 final size:21
Alignment explanation
Indices: 785600--785652 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
785590 ATTATGACTA
785600 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* **
785621 TCACGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
785642 TCGCAATGCGA
1 TCGCAATGCGA
785653 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:785672 original size:41 final size:41
Alignment explanation
Indices: 785627--785858 Score: 114
Period size: 41 Copynumber: 5.7 Consensus size: 41
785617 AATTTCACGT
*
785627 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* *** * * * *
785668 TGCGAATTTGGAAAATCGCAATG-GGAT-ACTGACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * * **
785709 TGTGATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAATCGCAA
* * * *
785750 TGCAATTTTCATAATTCGCAATGCAAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
* * ** * * *
785791 CGCGA-ATTAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TAAGTAAATCGCAA
* * * *
785832 TGCGA-ATACGTAAATCGCAATGCGAAT
1 TGCGATTTTCCTAATTCGCAATGCGAAT
785859 CTTACTATCG
Statistics
Matches: 140, Mismatches: 44, Indels: 15
0.70 0.22 0.08
Matches are distributed among these distances:
39 2 0.01
40 26 0.19
41 109 0.78
42 1 0.01
43 1 0.01
44 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:785685 original size:21 final size:20
Alignment explanation
Indices: 785642--785690 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
785632 TTTTCCCAAT
*
785642 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
785662 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
785683 TCGCAATG
1 TCGCAATG
785691 GGATACTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:785736 original size:21 final size:21
Alignment explanation
Indices: 785703--785769 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
785693 ATACTGACTA
* * *
785703 TCGCAATGTGATTTTCCTAAT
1 TCGCATTGCGATTTTCATAAT
* *
785724 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCATAAT
* *
785744 TCGCGTTGCAATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
785765 TCGCA
1 TCGCA
785770 ATGCAAATAC
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:785858 original size:20 final size:20
Alignment explanation
Indices: 785765--785876 Score: 129
Period size: 20 Copynumber: 5.5 Consensus size: 20
785755 TTTTCATAAT
*
785765 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
785785 TCGCAACGCGAATTA-GTAAA
1 TCGCAATGCGAA-TACGTAAA
* *
785805 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
785826 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
785846 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
785866 TCGCAATGCGA
1 TCGCAATGCGA
785877 TTTACATAGC
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
19 3 0.04
20 60 0.74
21 18 0.22
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:786455 original size:19 final size:19
Alignment explanation
Indices: 786431--786471 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
786421 AACGAGAGAA
*
786431 GCAACGCGAAATAAAAATC
1 GCAACGCGAAACAAAAATC
*
786450 GCAACGCGAAACCAAAATC
1 GCAACGCGAAACAAAAATC
786469 GCA
1 GCA
786472 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.27, G:0.17, T:0.07
Consensus pattern (19 bp):
GCAACGCGAAACAAAAATC
Found at i:786489 original size:19 final size:19
Alignment explanation
Indices: 786467--786593 Score: 85
Period size: 20 Copynumber: 7.1 Consensus size: 19
786457 GAAACCAAAA
*
786467 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
786486 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
786500 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
786519 TCGTGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
786533 TCTCGTTGCAATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
786552 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
786572 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
786592 TC
1 TC
786594 AACCAAAAGA
Statistics
Matches: 82, Mismatches: 14, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
14 18 0.22
16 5 0.06
17 6 0.07
19 22 0.27
20 30 0.37
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:786508 original size:14 final size:14
Alignment explanation
Indices: 786489--786541 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
786479 TTTCATTTCG
786489 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
786503 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
786520 CGTGTTGCGATTCTCT
1 C--GTTGCGATTCTCT
786536 CGTTGC
1 CGTTGC
786542 AATAGTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 13 0.41
16 6 0.19
17 6 0.19
19 7 0.22
ACGTcount: A:0.08, C:0.25, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:786514 original size:33 final size:33
Alignment explanation
Indices: 786472--786568 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
786462 CAAAATCGCA
786472 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
786505 TTGCGATTTTCATTTCGTGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* **
786538 TTGCAATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATTTTCATTT-CGCGTTGCGATTCTC
786569 ATTATCTCGT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:788761 original size:42 final size:42
Alignment explanation
Indices: 788685--788773 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
788675 GACTCGCCTG
*
788685 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCTATCGTTCAAGAGGCCCCTA
* * * * *
788727 TCATTCCTCGAGAGTCCCCTCCTA-CTGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCACTCCTATC-GTTCAAGAGGCCCCTA
788769 TCATC
1 TCATC
788774 GTTGAAGAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.03
42 38 0.97
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.26
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCTATCGTTCAAGAGGCCCCTA
Found at i:790173 original size:14 final size:14
Alignment explanation
Indices: 790154--790189 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
790144 ATTGTTTAAT
790154 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
790168 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
790182 TGATTTGT
1 TGATTTGT
790190 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:790367 original size:19 final size:19
Alignment explanation
Indices: 790292--790358 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
790282 AAAAAGTACT
* *
790292 ATCGCAATGCGAAATGAAG
1 ATCGCAACGCGAAATGAAA
*
790311 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
790325 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
790344 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
790359 TAAATTCGCG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 9 0.22
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 25 0.62
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:790394 original size:19 final size:19
Alignment explanation
Indices: 790363--790461 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 19
790353 CGAAATTAAA
790363 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
790382 TTCGCGTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
790397 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
790415 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
790429 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
790448 TTCGTATTGCGATT
1 TTCGCGTTGCGATT
790462 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
14 21 0.35
16 3 0.05
17 3 0.05
19 33 0.55
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:790483 original size:33 final size:33
Alignment explanation
Indices: 790367--790474 Score: 155
Period size: 33 Copynumber: 3.3 Consensus size: 33
790357 ATTAAATTCG
* *
790367 CGTTGCGATTTTCATTTCGCGTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
790400 CGTTGCGATTTTCATTTCGCATTGCGAAAT-TCG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCTCT
*
790433 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
790466 CGTTGCGAT
1 CGTTGCGAT
790475 AGTAATTTCC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
32 2 0.03
33 62 0.94
34 2 0.03
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:790483 original size:66 final size:67
Alignment explanation
Indices: 790360--790493 Score: 198
Period size: 66 Copynumber: 2.0 Consensus size: 67
790350 ACGCGAAATT
* ** *
790360 AAATTCGCGTTGCGATTTTCATTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTT-CGCATTG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATAGTAATTTCCGCATTG
790424 CG
66 CG
* * *
790426 AAATTCGCGTTGCGATTTTCATTTCGTATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCGTTG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATAGTAATTTCCGCATTG
790491 CG
66 CG
790493 A
1 A
790494 TAGACATTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
66 51 0.85
67 9 0.15
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (67 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATAGTAATTTCCGCATTG
CG
Found at i:792999 original size:24 final size:24
Alignment explanation
Indices: 792972--793018 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
792962 ATCATAAAAA
*
792972 TCCGAGTATTGACCAATATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
*
792996 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTGACCAAGATCAAA
793019 TTTCGAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:793929 original size:20 final size:20
Alignment explanation
Indices: 793882--793931 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
793872 GAGATAATAC
793882 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
793902 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
793922 AAAATCGCAA
1 AAAATCGCAA
793932 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:794170 original size:20 final size:20
Alignment explanation
Indices: 794145--794232 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
794135 CAACGGGAAA
*
794145 ATCGCAACACGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
794165 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
794185 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
794205 ATCGCAACGCGAAAATAGCT
1 ATCGCAACGCGAAAATGGCT
794225 ATCGCAAC
1 ATCGCAAC
794233 TAGAAAATCG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 5 0.09
20 45 0.83
21 4 0.07
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:794332 original size:20 final size:20
Alignment explanation
Indices: 794304--794346 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
794294 GCATTGTGAT
*
794304 TTTCTTGTTGCGATAGTCAG
1 TTTCGTGTTGCGATAGTCAG
*
794324 TTTCGTGTTGCGATAGTCTG
1 TTTCGTGTTGCGATAGTCAG
794344 TTT
1 TTT
794347 TGCCTTCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.12, C:0.14, G:0.26, T:0.49
Consensus pattern (20 bp):
TTTCGTGTTGCGATAGTCAG
Found at i:797847 original size:37 final size:37
Alignment explanation
Indices: 797805--797878 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
797795 ATATTTCAAC
797805 AAACATCTACCAAACTTTGAAAAACCA-TGTTTCAAAG
1 AAACATCTACCAAACTTT-AAAAACCATTGTTTCAAAG
* * *
797842 AAACATTTACCAAACTTTTAAAACCATTTTTTCAAAG
1 AAACATCTACCAAACTTTAAAAACCATTGTTTCAAAG
797879 TTGGTTGCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 7 0.21
37 26 0.79
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (37 bp):
AAACATCTACCAAACTTTAAAAACCATTGTTTCAAAG
Found at i:801663 original size:2 final size:2
Alignment explanation
Indices: 801656--801687 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
801646 AATAATTTTA
801656 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
801688 TAGGTTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:803570 original size:22 final size:23
Alignment explanation
Indices: 803538--803581 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
803528 TCCATGGAAC
*
803538 ACTTGTTTGATTT-GTAATAATG
1 ACTTGTCTGATTTAGTAATAATG
803560 ACTTGTCTGATTTAGTAATAAT
1 ACTTGTCTGATTTAGTAATAAT
803582 CATTATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.48
Consensus pattern (23 bp):
ACTTGTCTGATTTAGTAATAATG
Found at i:803605 original size:14 final size:14
Alignment explanation
Indices: 803567--803708 Score: 160
Period size: 14 Copynumber: 10.9 Consensus size: 14
803557 ATGACTTGTC
*
803567 TGATTTAGTAATAA
1 TGATTTAATAATAA
*
803581 TCA-TT-ATAATAA
1 TGATTTAATAATAA
803593 TGATTTAATAATAA
1 TGATTTAATAATAA
803607 TGATTTAATAATAA
1 TGATTTAATAATAA
*
803621 TCA-TT-ATAATAA
1 TGATTTAATAATAA
*
803633 TGATTTAATACTAA
1 TGATTTAATAATAA
803647 TGA-TT--TAATAA
1 TGATTTAATAATAA
*
803658 TGATTTAGTAATAA
1 TGATTTAATAATAA
803672 T--TTT-ATAATAA
1 TGATTTAATAATAA
*
803683 TGATTTAATAGTAA
1 TGATTTAATAATAA
803697 TGATTTAATAAT
1 TGATTTAATAAT
803709 TATTACTAAT
Statistics
Matches: 108, Mismatches: 10, Indels: 20
0.78 0.07 0.14
Matches are distributed among these distances:
11 15 0.14
12 22 0.20
13 13 0.12
14 58 0.54
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (14 bp):
TGATTTAATAATAA
Found at i:803622 original size:40 final size:40
Alignment explanation
Indices: 803567--803721 Score: 189
Period size: 40 Copynumber: 4.0 Consensus size: 40
803557 ATGACTTGTC
*
803567 TGATTTAGTAATAATCATTATAATAATGATTTAATAATAA
1 TGATTTAATAATAATCATTATAATAATGATTTAATAATAA
*
803607 TGATTTAATAATAATCATTATAATAATGATTTAATACTAA
1 TGATTTAATAATAATCATTATAATAATGATTTAATAATAA
*
803647 TGATTTAATAATGAT--TTAGTAATAAT--TTT-ATAATAA
1 TGATTTAATAATAATCATTA-TAATAATGATTTAATAATAA
* * * *
803683 TGATTTAATAGTAATGATT-TAATAATTA-TTACTAATAA
1 TGATTTAATAATAATCATTATAATAATGATTTAATAATAA
803721 T
1 T
803722 TATGAAATAA
Statistics
Matches: 102, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
36 26 0.25
37 5 0.05
38 12 0.12
39 7 0.07
40 52 0.51
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.45
Consensus pattern (40 bp):
TGATTTAATAATAATCATTATAATAATGATTTAATAATAA
Found at i:803661 original size:25 final size:26
Alignment explanation
Indices: 803586--803721 Score: 163
Period size: 25 Copynumber: 5.3 Consensus size: 26
803576 AATAATCATT
803586 ATAATAATGATTTAATAATAATGATTTA
1 ATAATAATGA-TT-ATAATAATGATTTA
*
803614 ATAATAATCATTATAATAATGATTTA
1 ATAATAATGATTATAATAATGATTTA
*
803640 ATACTAATGATT-TAATAATGATTTA
1 ATAATAATGATTATAATAATGATTTA
* *
803665 GTAATAAT-TTTATAATAATGATTTA
1 ATAATAATGATTATAATAATGATTTA
* *
803690 ATAGTAATGATT-TAATAATTA-TTA
1 ATAATAATGATTATAATAATGATTTA
*
803714 CTAATAAT
1 ATAATAAT
803722 TATGAAATAA
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
24 11 0.12
25 46 0.49
26 26 0.28
27 2 0.02
28 9 0.10
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (26 bp):
ATAATAATGATTATAATAATGATTTA
Found at i:803885 original size:14 final size:12
Alignment explanation
Indices: 803842--804119 Score: 165
Period size: 14 Copynumber: 22.3 Consensus size: 12
803832 TATTTGATAC
*
803842 TAATGATT-TAC
1 TAATGATTATAA
*
803853 TAATGATTACTAG
1 TAATGATTA-TAA
803866 TAATGAAGTTATAA
1 TAATG-A-TTATAA
803880 TAATGATTTAGTAA
1 TAATGA-TTA-TAA
*
803894 TAATCATTATAA
1 TAATGATTATAA
803906 TAATGATT-TAA
1 TAATGATTATAA
*
803917 TAATGATTTTAA
1 TAATGATTATAA
* * * *
803929 TATTTAATGAT-T
1 TA-ATGATTATAA
* *
803941 TGATGATT-TAG
1 TAATGATTATAA
803952 TAATGATTTGATAA
1 TAATGA-TT-ATAA
* *
803966 TAATCATTGTAA
1 TAATGATTATAA
803978 TAATGATTTAGTAA
1 TAATGA-TTA-TAA
*
803992 TAATCATTATAA
1 TAATGATTATAA
804004 TAATGATT-TAA
1 TAATGATTATAA
* * *
804015 TACTAATGATAA
1 TAATGATTATAA
804027 TAATGATTTAATAA
1 TAATGA-TT-ATAA
*
804041 TAATCATTATAA
1 TAATGATTATAA
*
804053 TAATGATTTAATAC
1 TAATGA-TT-ATAA
*
804067 TAATGATT-TAG
1 TAATGATTATAA
*
804078 TAATGATTTTATAG
1 TAATGA--TTATAA
804092 TAATGATT-TAA
1 TAATGATTATAA
*
804103 TAATTATTACTAA
1 TAATGATTA-TAA
804116 TAAT
1 TAAT
804120 TATGAAATAA
Statistics
Matches: 209, Mismatches: 35, Indels: 44
0.73 0.12 0.15
Matches are distributed among these distances:
10 1 0.00
11 52 0.25
12 54 0.26
13 41 0.20
14 58 0.28
15 3 0.01
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (12 bp):
TAATGATTATAA
Found at i:803917 original size:23 final size:25
Alignment explanation
Indices: 803874--804514 Score: 252
Period size: 26 Copynumber: 24.9 Consensus size: 25
803864 AGTAATGAAG
803874 TTATAATAATGATTTAGTAATAATCA
1 TTATAATAATGATTTA-TAATAATCA
*
803900 TTATAATAATGA-TT-TAATAATGA
1 TTATAATAATGATTTATAATAATCA
* * * * * * * *
803923 TTTTAATATTTAATGAT-TTGATGA
1 TTATAATAATGATTTATAATAATCA
*
803947 TT-TAGTAATGATTTGATAATAATCA
1 TTATAATAATGATTT-ATAATAATCA
*
803972 TTGTAATAATGATTTAGTAATAATCA
1 TTATAATAATGATTTA-TAATAATCA
* *
803998 TTATAATAATGA-TT-TAATACTAA
1 TTATAATAATGATTTATAATAATCA
*
804021 TGATAATAATGATTTAATAATAATCA
1 TTATAATAATGATTT-ATAATAATCA
* *
804047 TTATAATAATGATTTAATACTAATGA
1 TTATAATAATGATTT-ATAATAATCA
* * *
804073 TT-TAGTAATGATTTTATAGTAATGA
1 TTATAATAATGA-TTTATAATAATCA
* *
804098 TT-TAATAATTA-TTACTAATAATTA
1 TTATAATAATGATTTA-TAATAATCA
* * *** * *
804122 TGA-AATAATAACAAATGAGT-GTACAA
1 TTATAATAATGATTTAT-AATAAT-C-A
* * * *
804148 GTGTGAACTACTCGAATTTA-AATTTATACA
1 TTAT-AA-TAAT-G-ATTTATAA-TAAT-CA
*
804178 TAGTAGAATTTAA--ATTTAATAATAA-CA
1 T--TATAA--TAATGATTT-ATAATAATCA
* * * * **
804205 TAATAAT-TTGTTATTAATATTTAATTTT
1 TTATAATAATG--ATTTATA-ATAA-TCA
* * *
804233 TTGATACTAATGA-TTACTAGTAATGAA
1 TT-ATAATAATGATTTA-TAATAAT-CA
*
804260 GTTATAATAATGATTTAATAATAATGA
1 -TTATAATAATGATTT-ATAATAATCA
*
804287 TTATAATAATGA-TT-TAATAATGA
1 TTATAATAATGATTTATAATAATCA
*
804310 TTTAATAATAATGATTTATTTAATAATGA
1 -TT-ATAATAATGATTTA--TAATAATCA
*
804339 TTTGATAGTAATGATTTGATAATAATCA
1 -TT-ATAATAATGATTT-ATAATAATCA
804367 TTATAATAATGATTTAGTAATAATCA
1 TTATAATAATGATTTA-TAATAATCA
804393 TTATAATAATGATTTAATAATAAT-A
1 TTATAATAATGATTT-ATAATAATCA
804418 --ATAATAATGATTTAATAATAATCA
1 TTATAATAATGATTT-ATAATAATCA
* * *
804442 TTATAATCATGATTTACTAATGAT-T
1 TTATAATAATGATTTA-TAATAATCA
* *
804467 TTATAATAATGATTTAATAGTAATGA
1 TTATAATAATGATTT-ATAATAATCA
*
804493 TT-TAATAATTA-TTACTAATAAT
1 TTATAATAATGATTTA-TAATAAT
804515 TATGAATAAT
Statistics
Matches: 473, Mismatches: 84, Indels: 118
0.70 0.12 0.17
Matches are distributed among these distances:
23 78 0.16
24 40 0.08
25 89 0.19
26 164 0.35
27 21 0.04
28 28 0.06
29 36 0.08
30 7 0.01
31 7 0.01
32 3 0.01
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.43
Consensus pattern (25 bp):
TTATAATAATGATTTATAATAATCA
Found at i:804016 original size:49 final size:48
Alignment explanation
Indices: 803877--804501 Score: 210
Period size: 49 Copynumber: 12.7 Consensus size: 48
803867 AATGAAGTTA
*
803877 TAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATGATT-
1 TAATAATGATTTAATAATAATCATTATAATAATGATTTAATAAT-ATTG
* * * *
803925 T--TAAT-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAATAATCATTG
1 TAATAATGATTTAAT-A-ATAATCATTATAATAATGA-TT--TAATAAT-ATTG
* * *
803975 TAATAATGATTTAGTAATAATCATTATAATAATGATTTAATACTAATG
1 TAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATATTG
804023 ATAATAATGATTTAATAATAATCATTATAATAATGATTTAATACTAATGATT-
1 -TAATAATGATTTAATAATAATCATTATAATAATGATTT-A-A-TAAT-ATTG
* * * * *
804075 TAGTAATGATTTTATAGTAATGATT-TAATAATTATTACTAATAAT-TATG
1 TAATAATGATTTAATAATAATCATTATAATAATGATT--TAATAATAT-TG
* *** * * * * * *
804124 AAATAAT-AACAAATGAGT-GTACAAGTGTGAACTACTCGAATTT-A-AAT-TTA
1 TAATAATGATTTAAT-AATAAT-C-ATTAT-AA-TAAT-G-ATTTAATAATATTG
* ** * *
804174 TACATAGTAGAATTTAAATTTAATAAT-AACATAATAAT-TTGTTATTAATATT-
1 TA-ATAAT-G-ATTT-AA--TAATAATCATTATAATAATGAT-TTAATAATATTG
* * * * *
804226 TAAT--T-TTTTGATACTAATGATTACTAGTAATGAAGTTATAATAATGATT-
1 TAATAATGATTTAATAATAATCATTA-TAATAATG-A-TT-TAATAAT-ATTG
* * *
804275 TAATAATAATGATT-ATAATAATGATT-TAATAATGATTTAATAATAATG
1 TAATAATGAT--TTAATAATAATCATTATAATAATGATTTAATAATATTG
* * * *
804323 --AT--TTATTTAATAATGAT--TTGATAGTAATGATTTGATAATAATCATTA
1 TAATAATGATTTAATAATAATCATT-ATAATAATGA-TT--TAATAAT-ATTG
* **
804370 TAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATAATAA
1 TAATAATGATTTAATAATAATCATTATAATAATGATTTAATAAT-ATTG
* * *
804419 TAATAATGATTTAATAATAATCATTATAATCATGATTTACTAATGATTTTA
1 TAATAATGATTTAATAATAATCATTATAATAATGATTTAATAAT-A--TTG
* *
804470 TAATAATGATTTAATAGTAATGATT-TAATAAT
1 TAATAATGATTTAATAATAATCATTATAATAAT
804502 TATTACTAAT
Statistics
Matches: 433, Mismatches: 77, Indels: 132
0.67 0.12 0.21
Matches are distributed among these distances:
41 2 0.00
42 2 0.00
43 21 0.05
44 7 0.02
45 13 0.03
46 25 0.06
47 14 0.03
48 23 0.05
49 130 0.30
50 26 0.06
51 89 0.21
52 38 0.09
53 29 0.07
54 5 0.01
55 5 0.01
56 2 0.00
57 2 0.00
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.43
Consensus pattern (48 bp):
TAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATATTG
Found at i:804117 original size:75 final size:74
Alignment explanation
Indices: 803828--804119 Score: 287
Period size: 75 Copynumber: 3.9 Consensus size: 74
803818 TATTAATATT
* * *
803828 TAATTATTTGATACTAATGATTTACTAATGA-TTACTAGTAATGAAGTTATAATAATGATTTAGT
1 TAATGATTTAATACTAATGATTTA-TAATGATTTAATAGTAATG-A-TT-TAATAATGATTTA-T
803892 AATAATCATTATAA
61 AATAATCATTATAA
* * *
803906 TAATGATTT-A-A-TAATGATTT-TAAT-ATTTAATGATTTGATGATTTAGTAATGATTTGATAA
1 TAATGATTTAATACTAATGATTTATAATGATTTAAT-A-GTAATGATTTAATAATGATTT-ATAA
*
803966 TAATCATTGTAA
63 TAATCATTATAA
* * * *
803978 TAATGATTTAGTAATAATCATTATAATAATGATTTAATACTAATGA--TAATAATGATTTAATAA
1 TAATGATTTAATACTAATGATT-T-ATAATGATTTAATAGTAATGATTTAATAATGATTT-ATAA
804041 TAATCATTATAA
63 TAATCATTATAA
* *
804053 TAATGATTTAATACTAATGATTTAGTAATGATTTTATAGTAATGATTTAATAATTA-TTACTAAT
1 TAATGATTTAATACTAATGATTTA-TAATGATTTAATAGTAATGATTTAATAATGATTTA-TAAT
804117 AAT
64 AAT
804120 TATGAAATAA
Statistics
Matches: 180, Mismatches: 19, Indels: 33
0.78 0.08 0.14
Matches are distributed among these distances:
72 35 0.19
73 12 0.07
74 23 0.13
75 74 0.41
76 10 0.06
77 6 0.03
78 13 0.07
79 7 0.04
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (74 bp):
TAATGATTTAATACTAATGATTTATAATGATTTAATAGTAATGATTTAATAATGATTTATAATAA
TCATTATAA
Found at i:804272 original size:14 final size:12
Alignment explanation
Indices: 804240--804514 Score: 216
Period size: 14 Copynumber: 21.3 Consensus size: 12
804230 TTTTTGATAC
*
804240 TAATGATTACTAG
1 TAATGATTA-TAA
804253 TAATGAAGTTATAA
1 TAATG-A-TTATAA
804267 TAATGATTTAATAA
1 TAATGA-TT-ATAA
804281 TAATGATTATAA
1 TAATGATTATAA
804293 TAATGATT-TAA
1 TAATGATTATAA
804304 TAATGATTTAATAA
1 TAATGA-TT-ATAA
804318 TAATGATTTATTTAA
1 TAATGA-TTA--TAA
*
804333 TAATGATTTGATAG
1 TAATGA-TT-ATAA
804347 TAATGATTTGATAA
1 TAATGA-TT-ATAA
*
804361 TAATCATTATAA
1 TAATGATTATAA
804373 TAATGATTTAGTAA
1 TAATGA-TTA-TAA
*
804387 TAATCATTATAA
1 TAATGATTATAA
804399 TAATGATT-TAA
1 TAATGATTATAA
* *
804410 TAATAATAATAA
1 TAATGATTATAA
804422 TAATGATTTAATAA
1 TAATGA-TT-ATAA
*
804436 TAATCATTATAA
1 TAATGATTATAA
* *
804448 TCATGATT-TAC
1 TAATGATTATAA
804459 TAATGATTTTATAA
1 TAATGA--TTATAA
*
804473 TAATGATTTAATAG
1 TAATGA-TT-ATAA
804487 TAATGATT-TAA
1 TAATGATTATAA
*
804498 TAATTATTACTAA
1 TAATGATTA-TAA
804511 TAAT
1 TAAT
804515 TATGAATAAT
Statistics
Matches: 221, Mismatches: 21, Indels: 40
0.78 0.07 0.14
Matches are distributed among these distances:
11 34 0.15
12 51 0.23
13 36 0.16
14 84 0.38
15 15 0.07
16 1 0.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (12 bp):
TAATGATTATAA
Found at i:804439 original size:398 final size:390
Alignment explanation
Indices: 803575--804583 Score: 1450
Period size: 398 Copynumber: 2.5 Consensus size: 390
803565 TCTGATTTAG
* *
803575 TAATAATCA-TTA-TAATAATGATTTAATAATAATGATTTAATAATAATCATTATAATAATGATT
1 TAATAATGATTTAGTAATAATCA-TT-ATAATAATGATTTAATAATAAT-A--ATAATAATGATT
* * * *
803638 TAATACTAATGATT-TAATAATGATTTAGTAATAAT-TTTATAATAATGATTTAATAGTAATGAT
61 TAATAATAATCATTATAATAATGATTTA-TACTAATGATT-T-ATAATGATTTAATAGTAATGAT
*
803701 TTAATAATTATTACTAATAATTATGAAATAATAACAAATGAGTGTACAAGTGTGGACTACTCGGA
123 TTAATAATTATTACTAATAATTATGAAATAATAACAAATGAGTGTACAAGTGT-GACTACTCGAA
* *
803766 TTTAAATTTATACATAGTCGAATTTAAATTAAATAATAACATAATGATTTATTATTAATATTTAA
187 TTTAAATTTATACATAGTAGAATTTAAATTAAATAATAACATAATAATTTATTATTAATATTTAA
*
803831 TTATTTGATACTAATGATTTACTAATGATTACTAGTAATGAAGTTATAATAATGATTTAGTAATA
252 -TATTT-ATA-T-ATGA-TTACTAATGATTACTAGTAATGAAGTTATAATAATGATTTAATAATA
* * *
803896 ATCATTATAATAATGATTTAATAATGATTTTAATATTTAATGATTTGATGATTTAGTAATGATTT
312 ATCATTATAATAATGATTTAATAATGATTTTAATAATGAATGATTTAATGATTTAGTAATGATTT
*
803961 GATAATAATCATTG
377 GATAATAATCATTA
* *
803975 TAATAATGATTTAGTAATAATCATTATAATAATGATTTAATACTAATGATAATAATGATTTAATA
1 TAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATAATAATAATAATGATTTAATA
*
804040 ATAATCATTATAATAATGATTTAATACTAATGATTTAGTAATGATTTTATAGTAATGATTTAATA
66 ATAATCATTATAATAATGATTT-ATACTAATGATTTA-TAATGATTTAATAGTAATGATTTAATA
804105 ATTATTACTAATAATTATGAAATAATAACAAATGAGTGTACAAGTGTGAACTACTCGAATTTAAA
129 ATTATTACTAATAATTATGAAATAATAACAAATGAGTGTACAAGTGTG-ACTACTCGAATTTAAA
* *
804170 TTTATACATAGTAGAATTTAAATTTAATAATAACATAATAATTTGTTATTAATATTT-A-ATTT-
193 TTTATACATAGTAGAATTTAAATTAAATAATAACATAATAATTTATTATTAATATTTAATATTTA
*
804232 T-T-TGA-TACTAATGATTACTAGTAATGAAGTTATAATAATGATTTAATAATAATGATTATAAT
258 TATATGATTACTAATGATTACTAGTAATGAAGTTATAATAATGATTTAATAATAATCATTATAAT
* *
804294 AATGATTTAATAATGATTTAATAATAATGATTTATTTAATAATGATTTGATAGTAATGATTTGAT
323 AATGATTTAATAATGATTT--TAATAATGAATGA-TT--TAATGA-TT--TAGTAATGATTTGAT
804359 AATAATCATTA
380 AATAATCATTA
804370 TAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATAATAATAATAATGATTTAATA
1 TAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATAATAATAATAATGATTTAATA
*
804435 ATAATCATTATAATCATGA-TT-TACTAATGATTTTATAATAATGATTTAATAGTAATGATTTAA
66 ATAATCATTATAATAATGATTTATACTAATGA--TT-T-ATAATGATTTAATAGTAATGATTTAA
804498 TAATTATTACTAATAATTATG-AATAATAACAAATGAGTGTACAAGTGTTGACTACTCGAATTTA
127 TAATTATTACTAATAATTATGAAATAATAACAAATGAGTGTACAAGTG-TGACTACTCGAATTTA
804562 AATTTATACATAGTAGAATTTA
191 AATTTATACATAGTAGAATTTA
804584 TTAATGATTT
Statistics
Matches: 563, Mismatches: 26, Indels: 46
0.89 0.04 0.07
Matches are distributed among these distances:
387 74 0.13
389 12 0.02
390 2 0.00
391 1 0.00
392 14 0.02
393 3 0.01
394 66 0.12
395 158 0.28
396 1 0.00
397 27 0.05
398 160 0.28
399 3 0.01
400 29 0.05
401 5 0.01
402 8 0.01
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42
Consensus pattern (390 bp):
TAATAATGATTTAGTAATAATCATTATAATAATGATTTAATAATAATAATAATAATGATTTAATA
ATAATCATTATAATAATGATTTATACTAATGATTTATAATGATTTAATAGTAATGATTTAATAAT
TATTACTAATAATTATGAAATAATAACAAATGAGTGTACAAGTGTGACTACTCGAATTTAAATTT
ATACATAGTAGAATTTAAATTAAATAATAACATAATAATTTATTATTAATATTTAATATTTATAT
ATGATTACTAATGATTACTAGTAATGAAGTTATAATAATGATTTAATAATAATCATTATAATAAT
GATTTAATAATGATTTTAATAATGAATGATTTAATGATTTAGTAATGATTTGATAATAATCATTA
Found at i:804650 original size:38 final size:37
Alignment explanation
Indices: 804603--804730 Score: 104
Period size: 38 Copynumber: 3.5 Consensus size: 37
804593 TTTAAATATT
804603 TAATGATTTAATACTAATGATTTAGTAATTATTATTAA
1 TAATGATTTAATACTAATGATTTAGTAATTATTA-TAA
* * * * * *
804641 TAATGATTTATTATTAAT-ATTTAATTATT-TGATAC
1 TAATGATTTAATACTAATGATTTAGTAATTATTATAA
*
804676 TAATGA-TT--TACTAATGATTACTAGTAATGAAATTATAA
1 TAATGATTTAATACTAATGATT--TAGTAAT--TATTATAA
*
804714 TAATGATTTGATACTAA
1 TAATGATTTAATACTAA
804731 AAATCATTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
32 6 0.09
33 3 0.04
34 2 0.03
35 13 0.19
36 2 0.03
37 9 0.13
38 26 0.38
39 2 0.03
41 6 0.09
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (37 bp):
TAATGATTTAATACTAATGATTTAGTAATTATTATAA
Found at i:804653 original size:14 final size:14
Alignment explanation
Indices: 804603--804663 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 14
804593 TTTAAATATT
* *
804603 TAATGATTTAATAC
1 TAATGATTTATTAA
*
804617 TAATGATTTAGTAA
1 TAATGATTTATTAA
804631 T--T-A-TTATTAA
1 TAATGATTTATTAA
*
804641 TAATGATTTATTAT
1 TAATGATTTATTAA
804655 TAAT-ATTTA
1 TAATGATTTA
804664 ATTATTTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 7 0.18
11 1 0.03
12 2 0.05
13 6 0.15
14 23 0.59
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (14 bp):
TAATGATTTATTAA
Found at i:804660 original size:59 final size:56
Alignment explanation
Indices: 804585--804705 Score: 161
Period size: 59 Copynumber: 2.1 Consensus size: 56
804575 TAGAATTTAT
* * *
804585 TAATGATTTTTAAATATTTAATGATTTAATACTAATGATTTAGTAATTATTATTAA
1 TAATGATTTTTAAATATTTAATGATTTAATACTAATGATTTACTAATGATTACTAA
* * *
804641 TAATGATTTATTATTAATATTTAATTATTTGATACTAATGATTTACTAATGATTACTAG
1 TAATGATTT-TTA--AATATTTAATGATTTAATACTAATGATTTACTAATGATTACTAA
804700 TAATGA
1 TAATGA
804706 AATTATAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
56 9 0.16
57 3 0.05
59 44 0.79
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (56 bp):
TAATGATTTTTAAATATTTAATGATTTAATACTAATGATTTACTAATGATTACTAA
Found at i:804665 original size:24 final size:24
Alignment explanation
Indices: 804617--804661 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
804607 GATTTAATAC
*
804617 TAATGATTTAGTAATTATTATTAA
1 TAATGATTTAGTAATTAATATTAA
*
804641 TAATGATTTA-TTATTAATATT
1 TAATGATTTAGTAATTAATATT
804662 TAATTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (24 bp):
TAATGATTTAGTAATTAATATTAA
Found at i:804668 original size:17 final size:17
Alignment explanation
Indices: 804628--804669 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
804618 AATGATTTAG
804628 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
804645 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
804662 TAATTATT
1 TAATTATT
804670 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:805699 original size:23 final size:20
Alignment explanation
Indices: 805657--805705 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 20
805647 AAAATTACAA
*
805657 AAATAAAATAAAATTGATTT
1 AAATAAAATAAAATTAATTT
805677 AAATAAAATAATATAGTTAATTT
1 AAATAAAATAA-A-A-TTAATTT
805700 AAATAA
1 AAATAA
805706 TAATTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 11 0.44
21 1 0.04
22 1 0.04
23 12 0.48
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
AAATAAAATAAAATTAATTT
Found at i:807027 original size:30 final size:29
Alignment explanation
Indices: 806993--807079 Score: 98
Period size: 30 Copynumber: 3.2 Consensus size: 29
806983 TTCCTTAAAC
806993 AACTATTAAACTATTCTTTAATATAACTTT
1 AACTA-TAAACTATTCTTTAATATAACTTT
807023 AAC--T--A-T-TT-TTTAATATAACTTT
1 AACTATAAACTATTCTTTAATATAACTTT
*
807045 AACTAATAAACTATTCTTTAATATAACTTA
1 AACT-ATAAACTATTCTTTAATATAACTTT
807075 AACTA
1 AACTA
807080 AAAAACTAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 17
0.73 0.02 0.26
Matches are distributed among these distances:
22 17 0.35
23 2 0.04
24 1 0.02
25 2 0.04
27 2 0.04
28 1 0.02
29 3 0.06
30 20 0.42
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.45
Consensus pattern (29 bp):
AACTATAAACTATTCTTTAATATAACTTT
Found at i:807029 original size:22 final size:22
Alignment explanation
Indices: 807001--807049 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
806991 ACAACTATTA
807001 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
*
807023 AACTATTTTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
807045 AACTA
1 AACTA
807050 ATAAACTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (22 bp):
AACTATTCTTTAATATAACTTT
Found at i:807080 original size:30 final size:30
Alignment explanation
Indices: 807023--807087 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
807013 ATATAACTTT
* * *
807023 AACTATTTTTTAATATAACTTTAACTAATA
1 AACTATTCTTTAATATAACTTAAACTAAAA
807053 AACTATTCTTTAATATAACTTAAACTAAAA
1 AACTATTCTTTAATATAACTTAAACTAAAA
807083 AACTA
1 AACTA
807088 ATTAACTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (30 bp):
AACTATTCTTTAATATAACTTAAACTAAAA
Found at i:807094 original size:52 final size:52
Alignment explanation
Indices: 806993--807094 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 52
806983 TTCCTTAAAC
* * *****
806993 AACTATTAAACTATTCTTTAATATAACTTTAACTATTTTTTAATATAACTTT
1 AACTAATAAACTATTCTTTAATATAACTTAAACTAAAAACTAATATAACTTT
807045 AACTAATAAACTATTCTTTAATATAACTTAAACTAAAAAACTAAT-TAACT
1 AACTAATAAACTATTCTTTAATATAACTTAAACT-AAAAACTAATATAACT
807095 AATTTTTTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 37 0.88
53 5 0.12
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (52 bp):
AACTAATAAACTATTCTTTAATATAACTTAAACTAAAAACTAATATAACTTT
Found at i:807291 original size:21 final size:21
Alignment explanation
Indices: 807265--807304 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
807255 TTTCTATATG
*
807265 ATATAACTTAAACTAACAATA
1 ATATAAATTAAACTAACAATA
807286 ATATAAATTAAACTAACAA
1 ATATAAATTAAACTAACAA
807305 ACTAATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAAATTAAACTAACAATA
Found at i:807440 original size:35 final size:38
Alignment explanation
Indices: 807401--807473 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
807391 TCTTTTATAT
807401 AACTT-AA-ACTAATAAACT-A-TTTTTTATTATAATAA
1 AACTTAAACACTAATAAACTAATTTTTTTA-TATAATAA
807436 AACTTAAACTACTAATAAACTAATTTTTTTATATAATA
1 AACTTAAAC-ACTAATAAACTAATTTTTTTATATAATA
807474 TAAATTCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
35 5 0.15
36 2 0.06
38 11 0.33
39 8 0.24
40 7 0.21
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (38 bp):
AACTTAAACACTAATAAACTAATTTTTTTATATAATAA
Found at i:807533 original size:27 final size:29
Alignment explanation
Indices: 807498--807562 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
807488 AAAATATAAC
*
807498 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
807525 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
807553 TTAATTATTT
1 TTAAATATTT
807563 TTTTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:807676 original size:9 final size:9
Alignment explanation
Indices: 807644--807681 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
807634 CTAACAAACT
807644 AATAATTTAA
1 AATAA-TTAA
807654 AATAA-TAA
1 AATAATTAA
*
807662 ACTAATTAA
1 AATAATTAA
807671 AATAATTAA
1 AATAATTAA
807680 AA
1 AA
807682 AACTTACCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:807765 original size:26 final size:25
Alignment explanation
Indices: 807702--807765 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 25
807692 GATGTTGTGC
*
807702 TCTCCCTTTCTTCTTCTTCCTCTTT
1 TCTCCCTTTCTTCTTCTTCCTATTT
* * *
807727 TCTCTGCTATCTTC-TCATTTGCTATTT
1 TCTC-CCTTTCTTCTTC--TTCCTATTT
807754 TCTCCCTTTCTT
1 TCTCCCTTTCTT
807766 TCTCTCTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
25 6 0.20
26 13 0.43
27 11 0.37
ACGTcount: A:0.05, C:0.34, G:0.03, T:0.58
Consensus pattern (25 bp):
TCTCCCTTTCTTCTTCTTCCTATTT
Found at i:807904 original size:12 final size:11
Alignment explanation
Indices: 807873--807906 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
807863 ACGTTCACGG
807873 GCTGCAATAAT
1 GCTGCAATAAT
*
807884 GCAGCAATAAGT
1 GCTGCAATAA-T
807896 GCTGCAATAAT
1 GCTGCAATAAT
807907 ACAGTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (11 bp):
GCTGCAATAAT
Found at i:808080 original size:23 final size:23
Alignment explanation
Indices: 808053--808103 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
808043 TACCCAACGT
*
808053 TGCCATGCTGCCACCCAGACCCA
1 TGCCATACTGCCACCCAGACCCA
808076 TGCCATACTGCCACCCAGACCCA
1 TGCCATACTGCCACCCAGACCCA
808099 TGCCA
1 TGCCA
808104 CGTTGACATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.47, G:0.16, T:0.14
Consensus pattern (23 bp):
TGCCATACTGCCACCCAGACCCA
Found at i:808526 original size:32 final size:32
Alignment explanation
Indices: 808480--808541 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
808470 ATATGCATAG
808480 TCAGGGATAAAGCCATGTAGGCCCGAGGGGCA
1 TCAGGGATAAAGCCATGTAGGCCCGAGGGGCA
* *
808512 TCAGGGATAGAGCCATGTAGGCCCGGGGGG
1 TCAGGGATAAAGCCATGTAGGCCCGAGGGG
808542 TATTGCCCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.24, C:0.21, G:0.42, T:0.13
Consensus pattern (32 bp):
TCAGGGATAAAGCCATGTAGGCCCGAGGGGCA
Found at i:812094 original size:2 final size:2
Alignment explanation
Indices: 812087--812123 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
812077 TGTGTAGTTA
812087 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
812124 ATTTTAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:813013 original size:12 final size:12
Alignment explanation
Indices: 812996--813036 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
812986 ATTTACCTTT
812996 AAAAATTATTTA
1 AAAAATTATTTA
*
813008 AAAAATT-GTTA
1 AAAAATTATTTA
813019 AAAAA-TATTATA
1 AAAAATTATT-TA
813031 AAAAAT
1 AAAAAT
813037 AATGTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
10 1 0.04
11 9 0.38
12 14 0.58
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (12 bp):
AAAAATTATTTA
Found at i:813022 original size:22 final size:23
Alignment explanation
Indices: 812994--813036 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
812984 TAATTTACCT
*
812994 TTAAAAATTATT-TAAAAAATTG
1 TTAAAAAATATTATAAAAAATTG
813016 TTAAAAAATATTATAAAAAAT
1 TTAAAAAATATTATAAAAAAT
813037 AATGTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TTAAAAAATATTATAAAAAATTG
Found at i:813037 original size:12 final size:11
Alignment explanation
Indices: 812993--813037 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
812983 ATAATTTACC
*
812993 TTTAAAAATTA
1 TTTAAAAAATA
813004 TTTAAAAAAT-
1 TTTAAAAAATA
813014 TGTTAAAAAATA
1 T-TTAAAAAATA
813026 TTATAAAAAATA
1 TT-TAAAAAATA
813038 ATGTAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 1 0.03
11 19 0.63
12 10 0.33
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
TTTAAAAAATA
Found at i:819056 original size:156 final size:155
Alignment explanation
Indices: 818754--819282 Score: 721
Period size: 156 Copynumber: 3.5 Consensus size: 155
818744 CAAGAGGAAT
* * * * *
818754 ACTGAAGAGAGTAAGTTGTATGAGTCTGAGAATGATAAGAAGCAATTGGATTCTGAAGTTGGAC-
1 ACTGAAGAGAGTAAGTCGGATGAGTCTAAGAAGGATAAGAAGCAATTGGATTCTGAAGGTGGACA
* * * * *
818818 G--GAC-A-AACAACAATAGTGGGGAGAATTTACCCAAGGATGCTAGTGGGGCTAAAGATGGAGG
66 GACAACAACAACAACAAGAGTGGTGAGAATTTTCCCAAGGATGCTAGTGGGGCTAAAGATGGTGG
818879 CACTGGCAACTTAAACACACCAGAA
131 CACTGGCAACTTAAACACACCAGAA
* *
818904 ACTGAAGATAGTAAGTTGGATGAGTCTAAGAAGGATAAGAAGCAATTGGATTCTGAAGGTGGACA
1 ACTGAAGAGAGTAAGTCGGATGAGTCTAAGAAGGATAAGAAGCAATTGGATTCTGAAGGTGGACA
* *
818969 GACAATCAACAACAACAAGAGTGGTGAGAATTTTCCCAATGATGCTAGTGAGGCTAAAGATGGTG
66 GACAA-CAACAACAACAAGAGTGGTGAGAATTTTCCCAAGGATGCTAGTGGGGCTAAAGATGGTG
*
819034 GCACTAGCAACTTAAACACACCAGAA
130 GCACTGGCAACTTAAACACACCAGAA
** *
819060 ACTGAAGAGAGTAAGTCAAATGAGTCTAAGAAGGATAAGAAACAATTGGATTCTGAAGGTGGACA
1 ACTGAAGAGAGTAAGTCGGATGAGTCTAAGAAGGATAAGAAGCAATTGGATTCTGAAGGTGGACA
* * *
819125 GAC-A-AACAATAACAAGAGTGGTGAGAATTTTCCTAAGGATGCTAGCGGGGCTAAAGATGGTGG
66 GACAACAACAACAACAAGAGTGGTGAGAATTTTCCCAAGGATGCTAGTGGGGCTAAAGATGGTGG
*
819188 TACTGGCAACTTAAACACACCAGAA
131 CACTGGCAACTTAAACACACCAGAA
* * ** * * * * *
819213 ACTGGAGAAAGCGAGTCGGACGAGTCTAAAAAGGATAAAAAGCAATTGAATTCTGAAGGAGGACA
1 ACTGAAGAGAGTAAGTCGGATGAGTCTAAGAAGGATAAGAAGCAATTGGATTCTGAAGGTGGACA
819278 GACAA
66 GACAA
819283 ACGTCAGTGG
Statistics
Matches: 335, Mismatches: 37, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
150 59 0.18
151 1 0.00
153 134 0.40
154 2 0.01
155 2 0.01
156 137 0.41
ACGTcount: A:0.40, C:0.14, G:0.27, T:0.19
Consensus pattern (155 bp):
ACTGAAGAGAGTAAGTCGGATGAGTCTAAGAAGGATAAGAAGCAATTGGATTCTGAAGGTGGACA
GACAACAACAACAACAAGAGTGGTGAGAATTTTCCCAAGGATGCTAGTGGGGCTAAAGATGGTGG
CACTGGCAACTTAAACACACCAGAA
Found at i:819238 original size:153 final size:152
Alignment explanation
Indices: 818754--819284 Score: 708
Period size: 153 Copynumber: 3.5 Consensus size: 152
818744 CAAGAGGAAT
* * * * * * * *
818754 ACTGAAGAGAGTAAGTTGTATGAGTCTGAGAATGATAAGAAGCAATTGGATTCTGAAGTTGGACG
1 ACTGAAGAAAGTAAGTCGGATGAGTCTAAGAAGGATAAGAAACAATTGGATTCTGAAGGTGGACA
* * * *
818819 GACAAAC--AACAATAGTGGGGAGAATTTACCCAAGGATGCTAGTGGGGCTAAAGATGGAGGCAC
66 GACAAACAAAACAAGAGTGGTGAGAATTTTCCCAAGGATGCTAGTGGGGCTAAAGATGGTGGCAC
818882 TGGCAACTTAAACACACCAGAA
131 TGGCAACTTAAACACACCAGAA
* * *
818904 ACTGAAGATAGTAAGTTGGATGAGTCTAAGAAGGATAAGAAGCAATTGGATTCTGAAGGTGGACA
1 ACTGAAGAAAGTAAGTCGGATGAGTCTAAGAAGGATAAGAAACAATTGGATTCTGAAGGTGGACA
* *
818969 GACAATCAACAACAACAAGAGTGGTGAGAATTTTCCCAATGATGCTAGTGAGGCTAAAGATGGTG
66 GAC-A--AACAA-AACAAGAGTGGTGAGAATTTTCCCAAGGATGCTAGTGGGGCTAAAGATGGTG
*
819034 GCACTAGCAACTTAAACACACCAGAA
127 GCACTGGCAACTTAAACACACCAGAA
* **
819060 ACTGAAGAGAGTAAGTCAAATGAGTCTAAGAAGGATAAGAAACAATTGGATTCTGAAGGTGGACA
1 ACTGAAGAAAGTAAGTCGGATGAGTCTAAGAAGGATAAGAAACAATTGGATTCTGAAGGTGGACA
* * *
819125 GACAAACAATAACAAGAGTGGTGAGAATTTTCCTAAGGATGCTAGCGGGGCTAAAGATGGTGGTA
66 GACAAACAA-AACAAGAGTGGTGAGAATTTTCCCAAGGATGCTAGTGGGGCTAAAGATGGTGGCA
819190 CTGGCAACTTAAACACACCAGAA
130 CTGGCAACTTAAACACACCAGAA
* ** * * * *
819213 ACTGGAGAAAGCGAGTCGGACGAGTCTAAAAAGGATAA-AAAGCAATTGAATTCTGAAGGAGGAC
1 ACTGAAGAAAGTAAGTCGGATGAGTCTAAGAAGGATAAGAAA-CAATTGGATTCTGAAGGTGGAC
819277 AGACAAAC
65 AGACAAAC
819285 GTCAGTGGTG
Statistics
Matches: 339, Mismatches: 35, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
150 62 0.18
151 1 0.00
152 3 0.01
153 138 0.41
155 1 0.00
156 134 0.40
ACGTcount: A:0.40, C:0.14, G:0.27, T:0.19
Consensus pattern (152 bp):
ACTGAAGAAAGTAAGTCGGATGAGTCTAAGAAGGATAAGAAACAATTGGATTCTGAAGGTGGACA
GACAAACAAAACAAGAGTGGTGAGAATTTTCCCAAGGATGCTAGTGGGGCTAAAGATGGTGGCAC
TGGCAACTTAAACACACCAGAA
Found at i:826068 original size:16 final size:17
Alignment explanation
Indices: 826040--826072 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
826030 ATTGCTGACA
826040 AAATTTCACTATTCACG
1 AAATTTCACTATTCACG
826057 AAATTT-ACTATTCACG
1 AAATTTCACTATTCACG
826073 TGAATAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (17 bp):
AAATTTCACTATTCACG
Found at i:826724 original size:18 final size:19
Alignment explanation
Indices: 826687--826724 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
826677 GTTTCTTATT
*
826687 AACTCTGCTATAAAACCAA
1 AACTCTGCTATAAAAACAA
*
826706 AACTCTGGT-TAAAAACAA
1 AACTCTGCTATAAAAACAA
826724 A
1 A
826725 TCTAACACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.50, C:0.21, G:0.08, T:0.21
Consensus pattern (19 bp):
AACTCTGCTATAAAAACAA
Found at i:829102 original size:17 final size:17
Alignment explanation
Indices: 829080--829115 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
829070 TATCTTGAAA
829080 ATTTTAAATTATTTTAT
1 ATTTTAAATTATTTTAT
829097 ATTTTAAATTATTTTAT
1 ATTTTAAATTATTTTAT
829114 AT
1 AT
829116 GTATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTAAATTATTTTAT
Found at i:829122 original size:28 final size:28
Alignment explanation
Indices: 829080--829139 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
829070 TATCTTGAAA
*
829080 ATTTTAAATTATTTTATATTTTAAAT-T
1 ATTTTAAATTATTTTATATTATAAATCT
* *
829107 ATTTTATATGTATTTTTTATTATAAATCT
1 ATTTTAAAT-TATTTTATATTATAAATCT
829136 ATTT
1 ATTT
829140 CAATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 8 0.29
28 15 0.54
29 5 0.18
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
ATTTTAAATTATTTTATATTATAAATCT
Found at i:844234 original size:31 final size:31
Alignment explanation
Indices: 844198--844256 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
844188 AACTTAAATG
* * *
844198 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATATAAATAATTTT
844229 AGTTTTACAATACTGAAATATAAATAAT
1 AGTTTTACAATACTGAAATATAAATAAT
844257 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATATAAATAATTTT
Found at i:844307 original size:22 final size:22
Alignment explanation
Indices: 844281--844323 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
844271 TAATAAATTA
844281 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
844303 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
844324 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:844330 original size:54 final size:54
Alignment explanation
Indices: 844271--844849 Score: 454
Period size: 54 Copynumber: 10.7 Consensus size: 54
844261 ACAACTACAA
844271 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*** * * *
844325 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
* ** * *
844378 -CAT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAA--A--T-AAATCAATCCATAC
* * * *
844432 T-ATATAACTA--CAATAATAAATGAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATA-AATTATTTAA-AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * * ** * ** * **
844485 AAATAAATTACTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATAC
** **
844540 -AATCCA-TATTTTAAAATAAATCAATTTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
844593 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCGTAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
844647 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
844701 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** ** *
844758 TTTTAAAATAAAT-CAATCCATACTAATAAAT-TATTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATAC
844813 TAATAAATTATTTTAAAATAAATCAATCCATATTTTA
1 TAATAAATTA-TTTAAAATAAATCAATCCATATTTTA
844850 TAATTTATTT
Statistics
Matches: 414, Mismatches: 76, Indels: 69
0.74 0.14 0.12
Matches are distributed among these distances:
48 26 0.06
49 1 0.00
50 2 0.00
52 18 0.04
53 18 0.04
54 236 0.57
55 38 0.09
56 13 0.03
57 26 0.06
58 36 0.09
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:844332 original size:22 final size:22
Alignment explanation
Indices: 844283--844331 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
844273 ATAAATTATT
**
844283 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
844305 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
844328 TAAA
1 TAAA
844332 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:844341 original size:32 final size:30
Alignment explanation
Indices: 844303--844844 Score: 236
Period size: 32 Copynumber: 19.7 Consensus size: 30
844293 CAATCCATAT
844303 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
*
844335 TTTAAAATAAATCAATCCATAC-AACTACAA
1 TTTAAAATAAATCAATCCATACTAA-TAAAA
844365 --T--AATAAATCAATCC--A-T-AT----
1 TTTAAAATAAATCAATCCATACTAATAAAA
844383 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
* *
844415 TTTAAAATAAATCAATCTATA-TAACTACAA
1 TTTAAAATAAATCAATCCATACTAA-TAAAA
* * **
844445 --T--AATAAATGAATTCATA-T--TTTAA
1 TTTAAAATAAATCAATCCATACTAATAAAA
*
844468 ---AA--TAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
* *
844495 CTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
844527 TTTAAAATAAATCAATCC--A-T-AT----
1 TTTAAAATAAATCAATCCATACTAATAAAA
** **
844549 TTTAAAATAAATCAATTTATA-TTTTAAAA
1 TTTAAAATAAATCAATCCATACTAATAAAA
844578 -------TAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
844603 TTTAAAATAAATCAATCC--A-T-AT----
1 TTTAAAATAAATCAATCCATACTAATAAAA
*
844625 TTTAAAATAAATCAATCCGTACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
844657 TTTAAAATAAATCAATCC--A-T-AT----
1 TTTAAAATAAATCAATCCATACTAATAAAA
844679 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
*
844711 TTTAAAATAAATCAATCCATAC-AACTACAA
1 TTTAAAATAAATCAATCCATACTAA-TAAAA
844741 --T--AATAAATCAATCC--A-T-AT----
1 TTTAAAATAAATCAATCCATACTAATAAAA
844759 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
*
844791 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA--A
844823 TTTTAAAATAAATCAATCCATA
1 -TTTAAAATAAATCAATCCATA
844845 TTTTATAATT
Statistics
Matches: 400, Mismatches: 27, Indels: 165
0.68 0.05 0.28
Matches are distributed among these distances:
20 2 0.00
22 104 0.26
23 10 0.03
24 8 0.02
25 8 0.02
26 48 0.12
27 1 0.00
28 9 0.02
29 3 0.01
30 8 0.02
31 7 0.02
32 172 0.43
33 20 0.05
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (30 bp):
TTTAAAATAAATCAATCCATACTAATAAAA
Found at i:844376 original size:80 final size:83
Alignment explanation
Indices: 844271--844844 Score: 517
Period size: 80 Copynumber: 7.0 Consensus size: 83
844261 ACAACTACAA
844271 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
844336 TTAAAATAAATCAATCCATAC
63 TTAAAATAAATCAATCCATAC
*
844357 -AACTACA-A-T-AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT
1 TAA-TAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT
*
844418 AAAATAAATCAATCTATA-
65 AAAATAAATCAATCCATAC
* * * * *
844436 TAACTACA-A-T-AATAAATGAATTCATATTTTAAAATAAATCAATCCATACAAATAAATTACTT
1 TAA-TAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT
*
844498 AAAATAAATCAATCTATAC
65 AAAATAAATCAATCCATAC
844517 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT---T--T-AT--A-T-T
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
844572 TTAAAATAAATCAATCCATAC
63 TTAAAATAAATCAATCCATAC
*
844593 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCGTACTAATAAATTAT
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
844658 TTAAAATAAATCAATCCATA-
63 TTAAAATAAATCAATCCATAC
** * * * *
844678 TTTTAAA-A-TAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTACA
1 TAATAAATATTAAATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAA-TAAA
844740 --A--T--AATAAATCAATCCATA-
59 TTATTTAAAATAAATCAATCCATAC
** * * * *
844758 TTTTAAA-A-TAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACTAATAAAT
1 TAATAAATATTAAATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAATAAAT
844821 TATTTTAAAATAAATCAATCCATA
60 TA-TTTAAAATAAATCAATCCATA
844845 TTTTATAATT
Statistics
Matches: 433, Mismatches: 21, Indels: 67
0.83 0.04 0.13
Matches are distributed among these distances:
76 68 0.16
77 1 0.00
78 1 0.00
79 1 0.00
80 232 0.54
81 8 0.02
82 8 0.02
83 2 0.00
84 5 0.01
85 12 0.03
86 79 0.18
87 16 0.04
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (83 bp):
TAATAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTA
AAATAAATCAATCCATAC
Found at i:844412 original size:22 final size:23
Alignment explanation
Indices: 844337--844411 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
844327 ATAAATTATT
844337 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
844359 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
844385 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
844408 TAAA
1 TAAA
844412 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:844593 original size:76 final size:76
Alignment explanation
Indices: 844496--844640 Score: 281
Period size: 76 Copynumber: 1.9 Consensus size: 76
844486 AATAAATTAC
*
844496 TTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
1 TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
844561 CAATTTATATT
66 CAATTTATATT
844572 TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
1 TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
844637 CAAT
66 CAAT
844641 CCGTACTAAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.37
Consensus pattern (76 bp):
TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAAT
CAATTTATATT
Found at i:844600 original size:22 final size:22
Alignment explanation
Indices: 844527--844591 Score: 112
Period size: 22 Copynumber: 3.0 Consensus size: 22
844517 TAATAAATTA
844527 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
**
844549 TTTAAAATAAATCAATTTATAT
1 TTTAAAATAAATCAATCCATAT
844571 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
844592 CTAATAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Done.