Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008168.1 Hibiscus syriacus cultivar Beakdansim tig00110749_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: 82183
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1472 original size:19 final size:19
Alignment explanation
Indices: 1450--1498 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
1440 GACTTATAAC
1450 TGTATTACTTGTTCGATTG
1 TGTATTACTTGTTCGATTG
1469 TGTATTACTTGTTCGATTG
1 TGTATTACTTGTTCGATTG
1488 TGTA-TACTTGT
1 TGTATTACTTGT
1499 ACATATATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 7 0.23
19 23 0.77
ACGTcount: A:0.16, C:0.10, G:0.20, T:0.53
Consensus pattern (19 bp):
TGTATTACTTGTTCGATTG
Found at i:3510 original size:13 final size:14
Alignment explanation
Indices: 3482--3510 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3472 ACAAATGATG
3482 ATTTCATTTTTATT
1 ATTTCATTTTTATT
3496 ATTTCATTTTT-TT
1 ATTTCATTTTTATT
3509 AT
1 AT
3511 CAAGCATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTCATTTTTATT
Found at i:4591 original size:157 final size:159
Alignment explanation
Indices: 4312--4619 Score: 505
Period size: 157 Copynumber: 1.9 Consensus size: 159
4302 AAGCCACCCA
* *
4312 TCGTTAAAAATTAATGGAACATGTGACGTGCAGTTAAAAATATTTAGGTATAATTAAAACAATTG
1 TCGTTAAAAATTAACGGAACATGTGACGTGCAGTTAAAAACATTTAGGTATAATTAAAACAATTG
* *
4377 GTATAGGTTACTTATATATTCCTTCGATTTGGTCCTCATTTTAATAAATTAAAATAATCTGGTTG
66 GTATAGGTTACTTATATATTCCTTCAATTTGGTCCTCATTTTAATAAATTAAAATAATCAGGTTG
4442 -AA-AAAATAAACCAACACTATCCACCTG
131 AAAGAAAATAAACCAACACTATCCACCTG
* *
4469 TCGTTAACAATTAACGGAACATGTGACGTGACAGTTAAAAACATTTAGGTATAATT-ACACAATT
1 TCGTTAAAAATTAACGGAACATGTGACGTG-CAGTTAAAAACATTTAGGTATAATTAAAACAATT
* * *
4533 GGTATATGTTACTTGTATATTCTTTCAATTTGGTCCTCATTTTAATAAATTAAAATAATCAGGTT
65 GGTATAGGTTACTTATATATTCCTTCAATTTGGTCCTCATTTTAATAAATTAAAATAATCAGGTT
4598 GAAAGAAAATAAACCAACACTA
130 GAAAGAAAATAAACCAACACTA
4620 AAAGGGGGCC
Statistics
Matches: 139, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
157 96 0.69
158 26 0.19
159 17 0.12
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (159 bp):
TCGTTAAAAATTAACGGAACATGTGACGTGCAGTTAAAAACATTTAGGTATAATTAAAACAATTG
GTATAGGTTACTTATATATTCCTTCAATTTGGTCCTCATTTTAATAAATTAAAATAATCAGGTTG
AAAGAAAATAAACCAACACTATCCACCTG
Found at i:4928 original size:21 final size:19
Alignment explanation
Indices: 4904--4943 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
4894 TATTCATATT
*
4904 ATATTAATAAATATATATTAA
1 ATATTAACAAA-A-ATATTAA
4925 ATATTAACAAAAATATTAA
1 ATATTAACAAAAATATTAA
4944 TATGTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
ATATTAACAAAAATATTAA
Found at i:5672 original size:19 final size:18
Alignment explanation
Indices: 5648--5690 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
5638 ATTAAAAAAT
*
5648 GGTTAAAAATAGTGTGATC
1 GGTTAAAAATA-AGTGATC
5667 GGTT--AAATAAGTGATC
1 GGTTAAAAATAAGTGATC
5683 GGTTAAAA
1 GGTTAAAA
5691 TTTAGACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 10 0.48
17 5 0.24
18 2 0.10
19 4 0.19
ACGTcount: A:0.40, C:0.05, G:0.26, T:0.30
Consensus pattern (18 bp):
GGTTAAAAATAAGTGATC
Found at i:5795 original size:23 final size:23
Alignment explanation
Indices: 5748--5796 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
5738 AATAACATAT
* **
5748 TAGGTACCGCTTATATAATGTAA
1 TAGGTAACGCTTATATAATAAAA
5771 TAGGTAACGCTTATATAATAAAA
1 TAGGTAACGCTTATATAATAAAA
5794 TAG
1 TAG
5797 ATTACTAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (23 bp):
TAGGTAACGCTTATATAATAAAA
Found at i:5845 original size:23 final size:23
Alignment explanation
Indices: 5819--5875 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
5809 ATTATCAAGC
*
5819 ATAATATAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAACGCTTAT
*
5842 ATAATGTAATAGGTAACGCTTAT
1 ATAATATAATAGGTAACGCTTAT
*
5865 ATAATAAAATA
1 ATAATATAATA
5876 TGTTAATTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.33
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:5858 original size:80 final size:81
Alignment explanation
Indices: 5739--5960 Score: 295
Period size: 80 Copynumber: 2.7 Consensus size: 81
5729 ATCAAATACA
* *
5739 ATAACATATTAGGTACCGCTTATATAATGTAATAGGTAACGCTTATATAATAAAATAG-ATTACT
1 ATAATATATTAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATATAATAAAATAGTATTACT
*
5803 AGAAATATTATCAAGC
66 AGAAACATTATCAAGC
*
5819 ATAATATAATAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATATAATAAAATATGTTAATT
1 ATAATATATTAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATATAATAAAATA-G-T-ATT
*
5884 ACTGGAAACATTATCAAGC
63 ACTAGAAACATTATCAAGC
* * * * * *
5903 ACAATAATATTAGGTAGCGCTTATAAAACGTAATA-GTAGCGTTTATATATTAAAATAG
1 ATAAT-ATATTAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATATAATAAAATAG
5961 GTTAATTACT
Statistics
Matches: 125, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
80 54 0.43
81 1 0.01
83 1 0.01
84 43 0.34
85 26 0.21
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (81 bp):
ATAATATATTAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATATAATAAAATAGTATTACT
AGAAACATTATCAAGC
Found at i:5957 original size:84 final size:84
Alignment explanation
Indices: 5726--5970 Score: 311
Period size: 84 Copynumber: 2.9 Consensus size: 84
5716 AATCGAAAAT
** *
5726 ATTATCAAATACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAACGCTTATATAATA
1 ATTATCAAGCACAAT-A-ATATTAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATATAATA
*
5791 AAATAG---ATTACTAGAAAT
64 AAATAGTTAATTACTAGAAAC
* *
5809 ATTATCAAGCATAAT-ATAATAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATATAATAAA
1 ATTATCAAGCACAATAATATTAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATATAATAAA
*
5873 ATATGTTAATTACTGGAAAC
66 ATA-GTTAATTACTAGAAAC
* * * * *
5893 ATTATCAAGCACAATAATATTAGGTAGCGCTTATAAAACGTAATA-GTAGCGTTTATATATTAAA
1 ATTATCAAGCACAATAATATTAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATATAATAAA
5957 ATAGGTTAATTACT
66 ATA-GTTAATTACT
5971 TAATTTGTTA
Statistics
Matches: 142, Mismatches: 15, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
80 50 0.35
81 1 0.01
83 12 0.08
84 53 0.37
85 26 0.18
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (84 bp):
ATTATCAAGCACAATAATATTAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATATAATAAA
ATAGTTAATTACTAGAAAC
Found at i:6495 original size:111 final size:108
Alignment explanation
Indices: 6337--6795 Score: 588
Period size: 111 Copynumber: 4.2 Consensus size: 108
6327 TAGCGCCTAT
* * * * *
6337 AAAGTATCGATAC-TTTATAAAAATCTATCGATATTTTACAA-ATAACAGGTAAAAATATGATAA
1 AAAGTATCGATCCTTTTATAAAAA--GATAGATACTTTACAATATAACAGGT-AAAATATGACAA
* *
6400 AAACAATTTCATTATGAAAAAAACCGTAAAATTTACTTGATATGTTG
63 AAACAGTTTCATTATG-AAAAAACCGTAAAATTTACCTGATATGTTG
* *
6447 AAAGTATCGATCCTTTTATAAAAAGGATAAATACTTTACAATGTAACAGGTAAAAATATGACAAA
1 AAAGTATCGATCCTTTTATAAAAA-GATAGATACTTTACAATATAACAGGT-AAAATATGACAAA
* *
6512 ACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTG
64 AACAGTTTCATTATGA-AAAAACCGTAAAATTTACCTGATATGTTG
* * *
6558 AAAGTATCGATCATTTTATAAAAAGATAGATACTTTATAATATAAAAGGTAAAATATGACAAAAA
1 AAAGTATCGATCCTTTTATAAAAAGATAGATACTTTACAATATAACAGGTAAAATATGACAAAAA
* * *
6623 CAGTTTCATTATGACAAAACAGTAAAATTTACCTGATATGTAG
66 CAGTTTCATTATGAAAAAACCGTAAAATTTACCTGATATGTTG
*
6666 AGAGTATCGATCCTTTTATAAAAAAGATAGATAC-TTACAATATAACAGGT-AAATATGACAAAA
1 AAAGTATCGATCCTTTTAT-AAAAAGATAGATACTTTACAATATAACAGGTAAAATATGACAAAA
* * *
6729 CCAGTTTCATTATGACAAAACCGATAACATTTACC--ATATGTTG
65 ACAGTTTCATTATGAAAAAACCG-TAAAATTTACCTGATATGTTG
* *
6772 AAAGTATAGATACTTTTATAAAAA
1 AAAGTATCGATCCTTTTATAAAAA
6796 TTATCGATAC
Statistics
Matches: 312, Mismatches: 32, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
105 5 0.02
106 23 0.07
107 34 0.11
108 67 0.21
109 42 0.13
110 47 0.15
111 94 0.30
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (108 bp):
AAAGTATCGATCCTTTTATAAAAAGATAGATACTTTACAATATAACAGGTAAAATATGACAAAAA
CAGTTTCATTATGAAAAAACCGTAAAATTTACCTGATATGTTG
Found at i:7388 original size:108 final size:110
Alignment explanation
Indices: 7262--7689 Score: 590
Period size: 109 Copynumber: 4.0 Consensus size: 110
7252 ATATCGATGT
* * * *
7262 TTTACAATATAACAGGTAAAAATATGA-AAACACCAATTTTATTATGATAAAATCGGTAAAATTT
1 TTTACAATATAACAGGTAAAAATATGACAAA-ACCAGTTTCATTATGACAAAAACGGTAAAATTT
7326 ACTTGATATGTTGAAAGTATCGATCATTTTATAAAAAGGATAG-AC
65 ACTTGATATGTTGAAAGTATCGATCATTTTATAAAAAGGATAGAAC
7371 TTTACAA-ATAACAGGT-AAAATATGACAAAACCCAGTTTCATTATGACAAAAACGGTAAAATTT
1 TTTACAATATAACAGGTAAAAATATGACAAAA-CCAGTTTCATTATGACAAAAACGGTAAAATTT
* * *
7434 ACTTGATATATTGAAAGTATCGATCCTTTTATAAAAATGATAGATAC
65 ACTTGATATGTTGAAAGTATCGATCATTTTATAAAAAGGATAGA-AC
7481 TTTACAA-ATAACAGGTAAAAATATGAC-AAACCAGTTTCATTATGACAAAAACGGTAAAATTTA
1 TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTA
* * * *
7544 CCTGATATGTTGAAAGTATCGATCTTTTTATAAAAAGAATAGATAT
66 CTTGATATGTTGAAAGTATCGATCATTTTATAAAAAGGATAGA-AC
* *
7590 TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTGATTATGACAAAATCGGT-AAATTTA
1 TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTA
* * **
7654 C---CTATGTTGAAAATATATAT-ATTTTATAAAAAGGAT
66 CTTGATATGTTGAAAGTATCGATCATTTTATAAAAAGGAT
7690 TTATACTTTT
Statistics
Matches: 291, Mismatches: 21, Indels: 17
0.88 0.06 0.05
Matches are distributed among these distances:
106 14 0.05
107 25 0.09
108 80 0.27
109 87 0.30
110 49 0.17
111 36 0.12
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (110 bp):
TTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTA
CTTGATATGTTGAAAGTATCGATCATTTTATAAAAAGGATAGAAC
Found at i:8026 original size:21 final size:21
Alignment explanation
Indices: 8002--8041 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
7992 TTAATATTTT
8002 TTACAGTCAAA-TACCTACCTA
1 TTACA-TCAAACTACCTACCTA
*
8023 TTACATTAAACTACCTACC
1 TTACATCAAACTACCTACC
8042 GAATATGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.30, G:0.03, T:0.30
Consensus pattern (21 bp):
TTACATCAAACTACCTACCTA
Found at i:8324 original size:893 final size:889
Alignment explanation
Indices: 6234--8479 Score: 3357
Period size: 892 Copynumber: 2.5 Consensus size: 889
6224 AAAATAGGTG
* * *
6234 CTACCTATTATATTAAACTACCTA-C-AAGGTA-GTTGAAAGTATCGATTTCATTTAA-AAGTAT
1 CTACCTATTACATTAAACTACCTACCGAA--TATGTTGAAAGTATCGATTCCATTAAATAAGTAT
6295 CGACACTTTTGGAATTTAAAAG-AAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTATAAAA
64 CGA-ACTTTTGGAATTTAAAAGAAAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTATAAAA
*
6359 ATCTATCGATATTTTACAAATAACAGGTAAAAATATGATAAAAACAATTTCATTATGAAAAAAAC
128 ATATATCGATATTTTACAAATAACAGGTAAAAATATG--AAAAACAATTTCATTATGAAAAAAAC
* *
6424 CGTAAAATTTACTTGATATGTTGAAAGTATCGATCCTTTTATAAAAAGGATAAATACTTTACAAT
191 GGTAAAATTTACTTGATATGTTGAAAGTATCGATCCTTTTATAAAAAGGATAGATACTTTACAAT
*
6489 GTAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATAT
256 ATAACAGGTAAAAATATGA-AAAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATAT
* *
6554 GTTGAAAGTATCGATCATTTTATAAAAA-GATAGATACTTTATAATATAAAAGGTAAAATATGAC
320 GTTGAAAGTATCGATCCTTTTATAAAAATGATAGATACTTTATAATATAACAGGTAAAATATGAC
* * * *
6618 AAAAACAGTTTCATTATGAC-AAAACAGTAAAATTTACCTGATATGTAGAGAGTATCGATCCTTT
385 AAAACCAGTTTCATTATGACAAAAACAGTAAAATTTACCTGATATGTTGAAAGTATCGATCTTTT
6682 TATAAAAAAGATAGATACTTACAATATAACAGGTAAATATGACAAAACCAGTTTCATTATGACAA
450 TATAAAAAAGATAGATACTTACAATATAACAGGTAAATATGACAAAACCAGTTTCATTATGACAA
* **
6747 AACCGATAACATTTACCATATGTTGAAAGTATAGATACTTTTATAAAAATTATCGATACTTTTTG
515 AACCGATAACATTTACCATATGTTGAAAATATAGATACTTTTATAAAAAGGATCGATACTTTTTG
* * * *
6812 AAAGTTATGTAATTATGTTTCAAAATTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAA
580 AAAGTTATATAATTATGTTTCAAAAGTTTTTAATAGTGATTCATGTTTTCCACCTACAATATTAA
*
6877 TTTAATAATTTCATTTACATAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGA
645 TTTAATAATTTCATTTACACAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGA
*
6942 ATTTAAATTTAACAATTTTAACCAAAGATAATAATAAATAAATATCTATGTTTATTATTTTTAAT
710 ATTTAAATTTAACAATTTTAACCAAAGATAATAATAAATAAATATCTATGTTTATTAGTTTTAAT
* * **
7007 TTAATAATAATATATATCGTAACATAAAATAAATCATTAGACGTGTATAATTACTAAATTATCTT
775 TTAATAATAATATATACCGTAACATAAAATAAATCACTAGACGCATATAATTACTAAATTATCTT
* * *
7072 AAATCTCACTCAAAAGATAACCTTAAATTAATGTTTTTCACAGTGAATAC
840 AAAACTCACTCAAAAGATAACCTTAAATTAATATTTTTCACAGTAAATAC
*
7122 CTACTTATTACATTAAACTACCTACCGAATATGTTGAAAGTATCGATTCCATTTAAATAAGTATC
1 CTACCTATTACATTAAACTACCTACCGAATATGTTGAAAGTATCGATTCCA-TTAAATAAGTATC
*
7187 GAAACTTTTGGAATTTAAAAGAAAA-CAGTAATAGCGCCTATAAAGTATCGATACTTTATAAAAC
65 G-AACTTTTGGAATTTAAAAGAAAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTATAAAAA
* * * *
7251 TATATCGATGTTTTACAATATAACAGGTAAAAATATGAAAACACCAATTTTATTATGATAAAATC
129 TATATCGATATTTTACAA-ATAACAGGTAAAAATATGAAAA-A-CAATTTCATTATGAAAAAAAC
*
7316 GGTAAAATTTACTTGATATGTTGAAAGTATCGATCATTTTATAAAAAGGATAG--ACTTTACAA-
191 GGTAAAATTTACTTGATATGTTGAAAGTATCGATCCTTTTATAAAAAGGATAGATACTTTACAAT
*
7378 ATAACAGGT-AAAATATGACAAAACCCAGTTTCATTATGACAAAAACGGTAAAATTTACTTGATA
256 ATAACAGGTAAAAATATGA-AAAA-CCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATA
* *
7442 TATTGAAAGTATCGATCCTTTTATAAAAATGATAGATACTTTACAA-ATAACAGGTAAAAATATG
319 TGTTGAAAGTATCGATCCTTTTATAAAAATGATAGATACTTTATAATATAACAGGT-AAAATATG
*
7506 AC-AAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTGAAAGTATCGATCTT
383 ACAAAACCAGTTTCATTATGACAAAAACAGTAAAATTTACCTGATATGTTGAAAGTATCGATCTT
* *
7570 TTTAT-AAAAAGAATAGATATTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTGATTA
448 TTTATAAAAAAG-ATAGATA-CTTACAATATAACAGGT--AAATATGACAAAACCAGTTTCATTA
* * * **
7634 TGACAAAATCGGTAA-ATTTACC-TATGTTGAAAATATATATA-TTTTATAAAAAGGATTTATAC
509 TGACAAAACCGATAACATTTACCATATGTTGAAAATATAGATACTTTTATAAAAAGGATCGATAC
7696 TTTTTTGAAAGTTATATAATTTATGTTTCAAAAGTTTTTAATAGT-ATTCATGTTTTCCACCTAC
574 -TTTTTGAAAGTTATATAA-TTATGTTTCAAAAGTTTTTAATAGTGATTCATGTTTTCCACCTAC
*
7760 AATATTAATTTAATAATTTCATTTACACAAACATTTATTTGATTGTTTTGATATTTTATAAAATA
637 AATATTAATTTAATAATTTCATTTACACAAA-AATTATTTGATTGTTTTGATATTTTATAAAATA
* *
7825 TTATTTAGAATTTAAATTTAATAATTTTAACCAATGATAATAA-AAATATGTAATATCTATGTTT
701 TTATTTAGAATTTAAATTTAACAATTTTAACCAAAGATAATAATAAATA---AATATCTATGTTT
7889 ATT-GTTTTAATTTAAT-A-AA-ATATACCGTAACATAAAAATAAATCACTAGACGCATATAATT
763 ATTAGTTTTAATTTAATAATAATATATACCGTAACAT-AAAATAAATCACTAGACGCATATAATT
* *
7950 ACTAAATTAATATCTTAAAACTCACTC-AAAGATAATCTTAAATTAATATTTTTTACAGTCAAAT
827 ACTAAA-T--TATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATATTTTTCACAGT-AAAT
8014 AC
888 AC
*
8016 CTACCTATTACATTAAACTACCTACCGAATATGTTGAAAGTATCGATTCCATTAAATAAGTATTG
1 CTACCTATTACATTAAACTACCTACCGAATATGTTGAAAGTATCGATTCCATTAAATAAGTATCG
* *
8081 CAACTTTTGGAATTTAAAAGAAAAGAAGTAATAGTGCCTATAAAGTATCGATACTTTATAAAAAT
66 -AACTTTTGGAATTTAAAAGAAAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTATAAAAAT
* *
8146 GTATCGATATTTTTAC-AATAACAGGTAAAAATATGACAAAACTAGTTTCATTAT-AAAAAAACG
130 ATATCGATA-TTTTACAAATAACAGGTAAAAATATGA-AAAAC-AATTTCATTATGAAAAAAACG
* * *
8209 GTAAAATTTACCTGATATATTGAAAGTATTGATCCTTTTATAAAAAGGATAGATACTTTACAATA
192 GTAAAATTTACTTGATATGTTGAAAGTATCGATCCTTTTATAAAAAGGATAGATACTTTACAATA
* *
8274 TAACAAGTAAAAATATG-AAAACCAGTTTCATTATGACAAAAACAGTAAAATTTACCTGATATGT
257 TAACAGGTAAAAATATGAAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGT
8338 TGAAAGTATCGATCCTTTTATAAAAATGATAGATACTTTATAATATAACAGGTAAAATATGACAA
322 TGAAAGTATCGATCCTTTTATAAAAATGATAGATACTTTATAATATAACAGGTAAAATATGACAA
* * * * *
8403 AACCAGTTTCATTATGACAAAACCAGTAACATTTACCT-A-ATATTGAAAGTATAGATATTTTT-
387 AACCAGTTTCATTATGACAAAAACAGTAAAATTTACCTGATATGTTGAAAGTATCGATCTTTTTA
* *
8465 TAAAAATGATCGATA
452 TAAAAAAGATAGATA
8480 ATTTTTTGAA
Statistics
Matches: 1237, Mismatches: 81, Indels: 77
0.89 0.06 0.06
Matches are distributed among these distances:
888 38 0.03
889 125 0.10
890 124 0.10
891 222 0.18
892 277 0.22
893 236 0.19
894 193 0.16
895 14 0.01
896 8 0.01
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.35
Consensus pattern (889 bp):
CTACCTATTACATTAAACTACCTACCGAATATGTTGAAAGTATCGATTCCATTAAATAAGTATCG
AACTTTTGGAATTTAAAAGAAAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTATAAAAATA
TATCGATATTTTACAAATAACAGGTAAAAATATGAAAAACAATTTCATTATGAAAAAAACGGTAA
AATTTACTTGATATGTTGAAAGTATCGATCCTTTTATAAAAAGGATAGATACTTTACAATATAAC
AGGTAAAAATATGAAAAACCAGTTTCATTATGACAAAAACGGTAAAATTTACCTGATATGTTGAA
AGTATCGATCCTTTTATAAAAATGATAGATACTTTATAATATAACAGGTAAAATATGACAAAACC
AGTTTCATTATGACAAAAACAGTAAAATTTACCTGATATGTTGAAAGTATCGATCTTTTTATAAA
AAAGATAGATACTTACAATATAACAGGTAAATATGACAAAACCAGTTTCATTATGACAAAACCGA
TAACATTTACCATATGTTGAAAATATAGATACTTTTATAAAAAGGATCGATACTTTTTGAAAGTT
ATATAATTATGTTTCAAAAGTTTTTAATAGTGATTCATGTTTTCCACCTACAATATTAATTTAAT
AATTTCATTTACACAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAA
ATTTAACAATTTTAACCAAAGATAATAATAAATAAATATCTATGTTTATTAGTTTTAATTTAATA
ATAATATATACCGTAACATAAAATAAATCACTAGACGCATATAATTACTAAATTATCTTAAAACT
CACTCAAAAGATAACCTTAAATTAATATTTTTCACAGTAAATAC
Found at i:8435 original size:20 final size:20
Alignment explanation
Indices: 8395--8435 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
8385 ACAGGTAAAA
**
8395 TATGACAAAACCAGTTTCAT
1 TATGACAAAACCAGTAACAT
8415 TATGACAAAACCAGTAACAT
1 TATGACAAAACCAGTAACAT
8435 T
1 T
8436 TACCTAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.20, G:0.10, T:0.27
Consensus pattern (20 bp):
TATGACAAAACCAGTAACAT
Found at i:8466 original size:109 final size:111
Alignment explanation
Indices: 8122--8479 Score: 466
Period size: 109 Copynumber: 3.3 Consensus size: 111
8112 TAGTGCCTAT
* * * *
8122 AAAGTATCGATAC-TTTATAAAAATGTATCGATA-TTTTTACA-ATAACAGGTAAAAATATGACA
1 AAAGTATAGATCCTTTTATAAAAATG-ATAGATACTTTATA-ATATAACAGGTAAAAATATGACA
* * *
8184 AAACTAGTTTCATTAT-AAAAAAACGGTAAAATTTACCTGATATATTG
64 AAACCAGTTTCATTATGACAAAAACAGTAAAATTTACCTGATATATTG
* * * *
8231 AAAGTATTGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAAGTAAAAATATG--AAA
1 AAAGTATAGATCCTTTTATAAAAATGATAGATACTTTATAATATAACAGGTAAAAATATGACAAA
*
8294 ACCAGTTTCATTATGACAAAAACAGTAAAATTTACCTGATATGTTG
66 ACCAGTTTCATTATGACAAAAACAGTAAAATTTACCTGATATATTG
*
8340 AAAGTATCGATCCTTTTATAAAAATGATAGATACTTTATAATATAACAGGT-AAAATATGACAAA
1 AAAGTATAGATCCTTTTATAAAAATGATAGATACTTTATAATATAACAGGTAAAAATATGACAAA
* *
8404 ACCAGTTTCATTATGACAAAACCAGTAACATTTACCT-A-ATATTG
66 ACCAGTTTCATTATGACAAAAACAGTAAAATTTACCTGATATATTG
* * *
8448 AAAGTATAGAT-ATTTTTTAAAAATGATCGATA
1 AAAGTATAGATCCTTTTATAAAAATGATAGATA
8480 ATTTTTTGAA
Statistics
Matches: 221, Mismatches: 22, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
107 18 0.08
108 39 0.18
109 94 0.43
110 70 0.32
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (111 bp):
AAAGTATAGATCCTTTTATAAAAATGATAGATACTTTATAATATAACAGGTAAAAATATGACAAA
ACCAGTTTCATTATGACAAAAACAGTAAAATTTACCTGATATATTG
Found at i:10220 original size:27 final size:27
Alignment explanation
Indices: 10170--10221 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
10160 ATACGGCCTA
*
10170 ATTCGAGAATCATATACACTCCACTGG
1 ATTCGAGAATCATATACACACCACTGG
* * *
10197 ATTCGAGAATTATATGCTCACCACT
1 ATTCGAGAATCATATACACACCACT
10222 TGACATGAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (27 bp):
ATTCGAGAATCATATACACACCACTGG
Found at i:12219 original size:228 final size:227
Alignment explanation
Indices: 11819--12332 Score: 884
Period size: 228 Copynumber: 2.3 Consensus size: 227
11809 CAGTTATATG
* *
11819 GTATTCTTTTCCAATCTACAATGATCTTGTTCTCAACCTCTTTTTGCCATTTTTTCCTTACGAAT
1 GTATTCTTTTCCAATCTACAATGATCTTGTTCTCAACCTCTTTTTGCCTTTTTTTCTTTACGAAT
* **
11884 TCATTATTTAAGGCTTACAACTAATAAATGGTTAAGTGATATTTGTTATCTTTAAAGGTCTCGGG
66 TCATTATTTAAGGCTTAAAACTAATAAATGGTTAAGTGATATTTGTTATCTTTAAAGGTCTCAAG
* * *
11949 TTTGAGCATGACGTTTGAAGGATTGTTTGAACATTTATTGTCAAATTATTGAGAGTTTCTCGAAT
131 TTTGAGCATGACGTCTGAAGGAGTGTTTGAACATTCATTGTCAAATTATTGAGAGTTTCTCGAAT
12014 TTATTGCTTGTCATTTGATTGTTCTTTATTCA
196 TTATTGCTTGTCATTTGATTGTTCTTTATTCA
12046 GTATTCTTTTCCAATCTACAATGATCTTGTTCTCAACCTCTTTTTGCCTTTTTTTTCTTTACGAA
1 GTATTCTTTTCCAATCTACAATGATCTTGTTCTCAACCTCTTTTTGCC-TTTTTTTCTTTACGAA
*
12111 TTCATTATTTAAGGCTTAAAACTAATAAATGGTTAAGTGATGTTTGTTATCTTTAAAGGTCTCAA
65 TTCATTATTTAAGGCTTAAAACTAATAAATGGTTAAGTGATATTTGTTATCTTTAAAGGTCTCAA
* * * *
12176 GTTTGAGCATGACGTCTGTATGAGTGTTTGAACATTCATTGTCAAATTATTTAGAGTTTCTTGAA
130 GTTTGAGCATGACGTCTGAAGGAGTGTTTGAACATTCATTGTCAAATTATTGAGAGTTTCTCGAA
*
12241 TTTATTGCTTGTCATTTTATTGTTCTTTATTCA
195 TTTATTGCTTGTCATTTGATTGTTCTTTATTCA
*
12274 ATATTCTTTTCCAATCTACAATGATCTTGTTCTCAACCTCTTTTTGCCTTTTTTTCTTT
1 GTATTCTTTTCCAATCTACAATGATCTTGTTCTCAACCTCTTTTTGCCTTTTTTTCTTT
12333 GAACTAATAA
Statistics
Matches: 271, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
227 59 0.22
228 212 0.78
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.47
Consensus pattern (227 bp):
GTATTCTTTTCCAATCTACAATGATCTTGTTCTCAACCTCTTTTTGCCTTTTTTTCTTTACGAAT
TCATTATTTAAGGCTTAAAACTAATAAATGGTTAAGTGATATTTGTTATCTTTAAAGGTCTCAAG
TTTGAGCATGACGTCTGAAGGAGTGTTTGAACATTCATTGTCAAATTATTGAGAGTTTCTCGAAT
TTATTGCTTGTCATTTGATTGTTCTTTATTCA
Found at i:20313 original size:17 final size:17
Alignment explanation
Indices: 20293--20327 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
20283 ACACAACCAG
20293 ATTCTAAACACTGATCA
1 ATTCTAAACACTGATCA
20310 ATTCTAAACACTGATCA
1 ATTCTAAACACTGATCA
20327 A
1 A
20328 GATCAAGAAT
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:0.43, C:0.23, G:0.06, T:0.29
Consensus pattern (17 bp):
ATTCTAAACACTGATCA
Found at i:32791 original size:3 final size:3
Alignment explanation
Indices: 32783--32825 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
32773 ATATATACGT
*
32783 ATA ATA ATA ATA ATA ACA ATA ATA ATA TATA TATA TATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -ATA -ATA ATA A
32826 AACGTATAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 26 0.70
4 11 0.30
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:33916 original size:18 final size:16
Alignment explanation
Indices: 33885--33925 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
33875 AAAAAAAATG
33885 TAAATATAATTTATAA
1 TAAATATAATTTATAA
33901 TAAATATATATATTAT-A
1 TAAATATA-AT-TTATAA
33918 T-AATATAA
1 TAAATATAA
33926 GGATGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 14 0.61
17 4 0.17
18 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATATAATTTATAA
Found at i:34163 original size:20 final size:20
Alignment explanation
Indices: 34140--34181 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
34130 GAATCCTTCG
34140 TCGTGAAATTGAAATCGAAC
1 TCGTGAAATTGAAATCGAAC
* *
34160 TCGTGAAGTTGAAGTCGAAC
1 TCGTGAAATTGAAATCGAAC
34180 TC
1 TC
34182 AGAGTTCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (20 bp):
TCGTGAAATTGAAATCGAAC
Found at i:34424 original size:105 final size:105
Alignment explanation
Indices: 34262--35186 Score: 1778
Period size: 105 Copynumber: 8.8 Consensus size: 105
34252 ATTGTTTATC
* * *
34262 GACAACCAGCGGTCCCTTCGTCATGAAGTTGAACCTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
34327 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
34367 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
34432 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
*
34472 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
34537 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
34577 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
34642 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
34682 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
*
34747 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTAGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
34787 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
34852 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
34892 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
*
34957 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTAGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
34997 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
*
35062 GTGAAGTTGAAATTGGCTTTAAATTTGAGAAATGTTTGGT
66 GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
*
35102 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTT
1 GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
35167 GTGAAGTTGAAATTGGCTCT
66 GTGAAGTTGAAATTGGCTCT
35187 GGGTAAAACC
Statistics
Matches: 808, Mismatches: 12, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 808 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
GACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
GTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGGT
Found at i:35385 original size:1 final size:1
Alignment explanation
Indices: 35379--35404 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
35369 TGTTTGATGA
35379 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
35405 GAAGATGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:35991 original size:1 final size:1
Alignment explanation
Indices: 35985--36009 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
35975 ACCCTAAACG
35985 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
36010 CAACTTAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:47339 original size:31 final size:31
Alignment explanation
Indices: 47281--47342 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
47271 TATAAAAAGA
47281 AATAAAATATACATATATATACGTATAATAAT
1 AATAAAATATACATATATATAC-TATAATAAT
47313 AATAACAATAATA-ATATATATA-TATAATAA
1 AATAA-AAT-ATACATATATATACTATAATAA
47343 AACGTATAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 8 0.29
32 5 0.18
33 12 0.43
34 3 0.11
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.34
Consensus pattern (31 bp):
AATAAAATATACATATATATACTATAATAAT
Found at i:48442 original size:18 final size:16
Alignment explanation
Indices: 48411--48451 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
48401 AAAAAAAATG
48411 TAAATATAATTTATAA
1 TAAATATAATTTATAA
48427 TAAATATATATATTAT-A
1 TAAATATA-AT-TTATAA
48444 T-AATATAA
1 TAAATATAA
48452 GGATGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 14 0.61
17 4 0.17
18 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATATAATTTATAA
Found at i:48514 original size:24 final size:24
Alignment explanation
Indices: 48482--48533 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
48472 AAGTGGTTTT
*
48482 CGTACATCTAACGTAACCCGTATG
1 CGTACATCTAACGTAACCCATATG
48506 CGTACATCTAACGTAACCCATATG
1 CGTACATCTAACGTAACCCATATG
48530 CGTA
1 CGTA
48534 GACTGTCCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (24 bp):
CGTACATCTAACGTAACCCATATG
Found at i:49103 original size:2 final size:2
Alignment explanation
Indices: 49098--49133 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
49088 TATATAAAAT
49098 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
49134 ATCGGGGCGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49991 original size:31 final size:31
Alignment explanation
Indices: 49918--49983 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
49908 AGTTACGTCG
* **
49918 GGGACCATATTGCAAATGGACTAAATGTTGA
1 GGGATCATATTGCAAACAGACTAAATGTTGA
*
49949 GGGATCATATTGCAAACAGACTAAATGTTGG
1 GGGATCATATTGCAAACAGACTAAATGTTGA
49980 GGGA
1 GGGA
49984 ATGTATTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (31 bp):
GGGATCATATTGCAAACAGACTAAATGTTGA
Found at i:51064 original size:31 final size:31
Alignment explanation
Indices: 51029--51095 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
51019 TAAAACTTGT
**
51029 AATATAATCCCCCAACATTTAGTCTTTTTGC
1 AATATAATCCCCCAACATTTAGTCCGTTTGC
** *
51060 AATATGGTCCCTCAACATTTAGTCCGTTTGC
1 AATATAATCCCCCAACATTTAGTCCGTTTGC
51091 AATAT
1 AATAT
51096 GGTCCCCGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.37
Consensus pattern (31 bp):
AATATAATCCCCCAACATTTAGTCCGTTTGC
Found at i:51096 original size:31 final size:31
Alignment explanation
Indices: 51036--51102 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
51026 TGTAATATAA
**
51036 TCCCCCAACATTTAGTCTTTTTGCAATATGG
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
*
51067 TCCCTCAACATTTAGTCCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
51098 TCCCC
1 TCCCC
51103 GATATAACTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.36
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCGTTTGCAATATGG
Found at i:59266 original size:155 final size:153
Alignment explanation
Indices: 59033--59379 Score: 482
Period size: 155 Copynumber: 2.2 Consensus size: 153
59023 TGTGGTATAT
* *
59033 GAGCATGTGGTTCAAATTTGGTAAAAAATTGACTTAAAATAAATTACAAATTGAAGGAATAAGGA
1 GAGCATGTGGTTCAAATTTGGT-AAAAA-TGACTTAAAATAAATGACAAATTGAAGAAATAAGGA
* *
59098 GGTTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTGTTATAAAAAAGAGGAATTGAAA
64 GATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAA--ATTATAAAAAAGAGGAATTGAAA
* *
59163 GTAGACATGTATTCTACTATGGTTTAG
127 GTACACATGTATTCTACTATGGTTTAA
* * * * * *
59190 GAGCATGTGGCTCAAATTTGATAAAAATGACTTAAAATAAATGACGAATTGGAGAAATAATGATA
1 GAGCATGTGGTTCAAATTTGGTAAAAATGACTTAAAATAAATGACAAATTGAAGAAATAAGGAGA
* * *
59255 TTATGAAAAATTGAAGGACTAAATTTAAAAATAAAAAAATTATCAAAAAGTGGAATTGAAAGTAC
66 TTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAAATTATAAAAAAGAGGAATTGAAAGTAC
59320 ACATGTATTCTACTATGGTTTAA
131 ACATGTATTCTACTATGGTTTAA
* *
59343 GTGCATGTGATTCAAA--TGGTAAAAATGGACTTAAAAT
1 GAGCATGTGGTTCAAATTTGGTAAAAAT-GACTTAAAAT
59380 GAAGGAGGAA
Statistics
Matches: 170, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
151 9 0.05
152 10 0.06
153 58 0.34
155 68 0.40
156 5 0.03
157 20 0.12
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.29
Consensus pattern (153 bp):
GAGCATGTGGTTCAAATTTGGTAAAAATGACTTAAAATAAATGACAAATTGAAGAAATAAGGAGA
TTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAAATTATAAAAAAGAGGAATTGAAAGTAC
ACATGTATTCTACTATGGTTTAA
Found at i:59401 original size:153 final size:153
Alignment explanation
Indices: 59033--59410 Score: 436
Period size: 153 Copynumber: 2.4 Consensus size: 153
59023 TGTGGTATAT
** * ** * ** *
59033 GAGCATGTGGTTCAAATTTGGTAAAAAATTGACTTAAAATAAATTACAAATTGAAGGAATAAGGA
1 GAGCATGTGACTCAAA-TTGAT-AAAAA-TGACTTAAAATAAAGGACGAATTGAAAAAATAATGA
** *
59098 GGTTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTGTTATAAAAAAGAGGAATTGAAA
63 AATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAA-TATTATAAAAAAGAGGAATTGAAA
* *
59163 GTAGACATGTATTCTACTATGGTTTAG
127 GTACACATGTATTCTACTATGGTTTAA
* * * * *
59190 GAGCATGTGGCTCAAATTTGATAAAAATGACTTAAAATAAATGACGAATTGGAGAAATAATGATA
1 GAGCATGTGACTCAAA-TTGATAAAAATGACTTAAAATAAAGGACGAATTGAAAAAATAATGAAA
* * *
59255 TTATGAAAAATTGAAGGACTAAATTTAAAAATAAAAAA-ATTATCAAAAAGTGGAATTGAAAGTA
65 TTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATATTATAAAAAAGAGGAATTGAAAGTA
59319 CACATGTATTCTACTATGGTTTAA
130 CACATGTATTCTACTATGGTTTAA
* * * * *
59343 GTGCATGTGATTCAAA-TGGTAAAAATGGACTTAAAATGAAGGAGGAATTGAAAAAAATAATGAA
1 GAGCATGTGACTCAAATTGATAAAAAT-GACTTAAAATAAAGGACGAATTG-AAAAAATAATGAA
59407 ATTA
64 ATTA
59411 GGGACTAAAT
Statistics
Matches: 194, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
151 9 0.05
152 20 0.10
153 72 0.37
155 68 0.35
156 5 0.03
157 20 0.10
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (153 bp):
GAGCATGTGACTCAAATTGATAAAAATGACTTAAAATAAAGGACGAATTGAAAAAATAATGAAAT
TATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATATTATAAAAAAGAGGAATTGAAAGTAC
ACATGTATTCTACTATGGTTTAA
Found at i:59416 original size:142 final size:150
Alignment explanation
Indices: 59033--59430 Score: 402
Period size: 155 Copynumber: 2.6 Consensus size: 150
59023 TGTGGTATAT
** * ** * * *
59033 GAGCATGTGGTTCAAATTTGGTAAAAAATTGACTTAAAATAAATTACAAATTGAAGGAATAAGGA
1 GAGCATGTGACTCAAA-TTGAT-AAAAA-TGACTTAAAATAAAGGACGAATTGGAGAAATAA-GA
* *
59098 GGT-TATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTGTTATAAAAAAGAGGAATTGAA
62 --TATATG-AAAATTGAAGGACTAAATTTAAAAATAAAAAA-TATTATAAAAAAGAGGAATTGAA
* *
59162 AGTAGACATGTATTCTACTATGGTTTAG
123 AGTACACATGTATTCTACTATGGTTTAA
* *
59190 GAGCATGTGGCTCAAATTTGATAAAAATGACTTAAAATAAATGACGAATTGGAGAAATAATGATA
1 GAGCATGTGACTCAAA-TTGATAAAAATGACTTAAAATAAAGGACGAATTGGAGAAATAA-GATA
* *
59255 TTATGAAAAATTGAAGGACTAAATTTAAAAATAAAAAA-ATTATCAAAAAGTGGAATTGAAAGTA
64 -TATG-AAAATTGAAGGACTAAATTTAAAAATAAAAAATATTATAAAAAAGAGGAATTGAAAGTA
59319 CACATGTATTCTACTATGGTTTAA
127 CACATGTATTCTACTATGGTTTAA
* * * * *
59343 GTGCATGTGATTCAAA-TGGTAAAAATGGACTTAAAATGAAGGAGGAATT-GA-AAA-AA-ATA-
1 GAGCATGTGACTCAAATTGATAAAAAT-GACTTAAAATAAAGGACGAATTGGAGAAATAAGATAT
*
59402 ATG-AAATT-AGGGACTAAATTGTAAAAATA
65 ATGAAAATTGAAGGACTAAATT-TAAAAATA
59431 TCAAAGTATT
Statistics
Matches: 216, Mismatches: 21, Indels: 22
0.83 0.08 0.08
Matches are distributed among these distances:
142 11 0.05
143 13 0.06
145 3 0.01
147 3 0.01
149 2 0.01
150 3 0.01
151 11 0.05
152 19 0.09
153 59 0.27
155 67 0.31
156 5 0.02
157 20 0.09
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (150 bp):
GAGCATGTGACTCAAATTGATAAAAATGACTTAAAATAAAGGACGAATTGGAGAAATAAGATATA
TGAAAATTGAAGGACTAAATTTAAAAATAAAAAATATTATAAAAAAGAGGAATTGAAAGTACACA
TGTATTCTACTATGGTTTAA
Found at i:59517 original size:14 final size:15
Alignment explanation
Indices: 59493--59528 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
59483 TTTCAACCCG
59493 ACTCGAACTCAAATA
1 ACTCGAACTCAAATA
59508 ACTC-AACTCAAATA
1 ACTCGAACTCAAATA
59522 ACTCGAA
1 ACTCGAA
59529 AATGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.47, C:0.28, G:0.06, T:0.19
Consensus pattern (15 bp):
ACTCGAACTCAAATA
Found at i:64311 original size:17 final size:16
Alignment explanation
Indices: 64278--64309 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
64268 ATTACTCGAT
64278 TTAAATAATTAAAAAA
1 TTAAATAATTAAAAAA
*
64294 TTAAATGATTAAAAAA
1 TTAAATAATTAAAAAA
64310 ATAACCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
TTAAATAATTAAAAAA
Found at i:65501 original size:38 final size:39
Alignment explanation
Indices: 65450--65548 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 39
65440 AAAAAACCTG
* * *
65450 AAAGAAAACTAATAATCCTAGCCCTAGATTTAAGCCC-A
1 AAAGATAACTAATAATCCTAGCCCTAGATTGAAACCCTA
**
65488 AAAGATAACTAATAATCCTAAACCTAGATTGAAACCCTA
1 AAAGATAACTAATAATCCTAGCCCTAGATTGAAACCCTA
* * *
65527 AAA-ATACCTTATAATCTTAGCC
1 AAAGATAACTAATAATCCTAGCC
65549 GTCCATAAGG
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
38 46 0.92
39 4 0.08
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.24
Consensus pattern (39 bp):
AAAGATAACTAATAATCCTAGCCCTAGATTGAAACCCTA
Found at i:80264 original size:23 final size:24
Alignment explanation
Indices: 80234--80283 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
80224 CTACTAAGGG
80234 CACGTAGAATTTGT-CCGAAGGAC
1 CACGTAGAATTTGTCCCGAAGGAC
*
80257 CACGTAGAATTTGTCCCGAATGAC
1 CACGTAGAATTTGTCCCGAAGGAC
80281 CAC
1 CAC
80284 ATATAAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (24 bp):
CACGTAGAATTTGTCCCGAAGGAC
Done.