Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016005.1 Corchorus olitorius cultivar O-4 contig16038, 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: 104127
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:483 original size:27 final size:26
Alignment explanation
Indices: 448--503 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 26
438 CCAAATGAAA
448 AACTCCAAAGGTCGTTGTTTTGCTTG
1 AACTCCAAAGGTCGTTGTTTTGCTTG
474 AACTACCAAAGGTCGTTGTTTTGCTTG
1 AACT-CCAAAGGTCGTTGTTTTGCTTG
501 AAC
1 AAC
504 AGAACTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.14
27 25 0.86
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (26 bp):
AACTCCAAAGGTCGTTGTTTTGCTTG
Found at i:6904 original size:21 final size:21
Alignment explanation
Indices: 6879--6922 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
6869 CCATAGCAAT
*
6879 AGCATGAGCATCATAGAACAG
1 AGCATGAACATCATAGAACAG
6900 AGCATGAACATCATAGAACAG
1 AGCATGAACATCATAGAACAG
6921 AG
1 AG
6923 ACCATAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (21 bp):
AGCATGAACATCATAGAACAG
Found at i:7130 original size:2 final size:2
Alignment explanation
Indices: 7123--7158 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
7113 AGTAGAATCT
7123 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7159 TGTCGGTCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7398 original size:35 final size:35
Alignment explanation
Indices: 7354--7900 Score: 351
Period size: 35 Copynumber: 16.1 Consensus size: 35
7344 CCAATCAATA
*
7354 ACTTACTTAATTACCCTGAATTAAGTTACTTACTG
1 ACTTACTTAATTACCCTGAATTAAGTTATTTACTG
*
7389 ACTTGCTTAATTACCCTGAATTAAGTTATTTACTG
1 ACTTACTTAATTACCCTGAATTAAGTTATTTACTG
* **
7424 AAC-CACTTAATTACCCTGAATTAAGTTATTTACCA
1 -ACTTACTTAATTACCCTGAATTAAGTTATTTACTG
* * * * *
7459 ATTTGCTCAATTACCCTGAATTAAGTTTTTTACCG
1 ACTTACTTAATTACCCTGAATTAAGTTATTTACTG
** * * *
7494 GTTTACGTGATTACCCTGAATTAAATTATTTACTG
1 ACTTACTTAATTACCCTGAATTAAGTTATTTACTG
* * * *
7529 ATTTACTTAATTACCC-CAGATTAAGTTGTTTATTG
1 ACTTACTTAATTACCCTGA-ATTAAGTTATTTACTG
* * * *
7564 ACTTACTTAATTACCCTTAATCAAGTTACTAACTG
1 ACTTACTTAATTACCCTGAATTAAGTTATTTACTG
*
7599 ACTCTCTACTTAATTACCCTGAATTAAGTCT-TTGACTG
1 A--CT-TACTTAATTACCCTGAATTAAGT-TATTTACTG
*
7637 ATTTTACTTAATTACCCTG----AA-TTA---ACT-
1 A-CTTACTTAATTACCCTGAATTAAGTTATTTACTG
*
7664 --TTACTTACTTACCCTGAATTAAGTTGA-TTACTG
1 ACTTACTTAATTACCCTGAATTAAGTT-ATTTACTG
*
7697 TCTTACTTAATTACCCTGAATTAAG----TTA---
1 ACTTACTTAATTACCCTGAATTAAGTTATTTACTG
* ** * * *
7725 A-TTGCTTAATTGTCTTGAATTAAGTTACTTACTT
1 ACTTACTTAATTACCCTGAATTAAGTTATTTACTG
* * ** *
7759 AATTACCTTGAATTA---AGTCTT---TTATTTACTTT
1 ACTTA-CTT-AATTACCCTGAATTAAGTTATTTAC-TG
* * * *
7791 ACTGACTTAATTACCCTGAATTAAGTTAATAATTG
1 ACTTACTTAATTACCCTGAATTAAGTTATTTACTG
*
7826 ACTTACTTAATTACCCTGAATTAAGTTAATTACTG
1 ACTTACTTAATTACCCTGAATTAAGTTATTTACTG
** * * * *
7861 ACCGACTTAATTACCTTAAATTAAGTTGTTTATTG
1 ACTTACTTAATTACCCTGAATTAAGTTATTTACTG
7896 ACTTA
1 ACTTA
7901 TGCATGAGTG
Statistics
Matches: 402, Mismatches: 73, Indels: 74
0.73 0.13 0.13
Matches are distributed among these distances:
24 15 0.04
27 19 0.05
28 5 0.01
29 2 0.00
30 7 0.02
31 17 0.04
32 10 0.02
33 3 0.01
34 6 0.01
35 256 0.64
36 26 0.06
37 8 0.02
38 27 0.07
39 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.42
Consensus pattern (35 bp):
ACTTACTTAATTACCCTGAATTAAGTTATTTACTG
Found at i:7667 original size:24 final size:24
Alignment explanation
Indices: 7639--7685 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
7629 TTTGACTGAT
7639 TTTACTTAATTACCCTGAATTAAC
1 TTTACTTAATTACCCTGAATTAAC
*
7663 TTTACTTACTTACCCTGAATTAA
1 TTTACTTAATTACCCTGAATTAA
7686 GTTGATTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (24 bp):
TTTACTTAATTACCCTGAATTAAC
Found at i:7677 original size:60 final size:58
Alignment explanation
Indices: 7605--7720 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 58
7595 ACTGACTCTC
*
7605 TACTTAATTACCCTGAATTAAGTCT-TTGACTGATTTTACTTAATTACCCTGAATTAACTT
1 TACTTAATTACCCTGAATTAAGT-TATT-ACTG-TCTTACTTAATTACCCTGAATTAACTT
*
7665 TACTTACTTACCCTGAATTAAGTTGATTACTGTCTTACTTAATTACCCTGAATTAA
1 TACTTAATTACCCTGAATTAAGTT-ATTACTGTCTTACTTAATTACCCTGAATTAA
7721 GTTAATTGCT
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
59 24 0.46
60 26 0.50
61 2 0.04
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (58 bp):
TACTTAATTACCCTGAATTAAGTTATTACTGTCTTACTTAATTACCCTGAATTAACTT
Found at i:7733 original size:27 final size:27
Alignment explanation
Indices: 7699--7776 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 27
7689 GATTACTGTC
*
7699 TTACTTAATTACCCTGAATTAAGTTAA
1 TTACTTAATTACCTTGAATTAAGTTAA
* ** *
7726 TTGCTTAATTGTCTTGAATTAAGTTAC
1 TTACTTAATTACCTTGAATTAAGTTAA
7753 TTACTTAATTACCTTGAATTAAGT
1 TTACTTAATTACCTTGAATTAAGT
7777 CTTTTATTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (27 bp):
TTACTTAATTACCTTGAATTAAGTTAA
Found at i:7856 original size:19 final size:19
Alignment explanation
Indices: 7797--7858 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
7787 CTTTACTGAC
7797 TTAATTACCCTGAATTAAG
1 TTAATTACCCTGAATTAAG
** * *
7816 TTAA-TA-ATTGACTT-AC
1 TTAATTACCCTGAATTAAG
7832 TTAATTACCCTGAATTAAG
1 TTAATTACCCTGAATTAAG
7851 TTAATTAC
1 TTAATTAC
7859 TGACCGACTT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
16 5 0.16
17 7 0.22
18 7 0.22
19 13 0.41
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (19 bp):
TTAATTACCCTGAATTAAG
Found at i:14086 original size:30 final size:31
Alignment explanation
Indices: 14019--14100 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 31
14009 TTAAGCAAAA
*
14019 CCAAAAGAAGATTTTGGAAAATAAGGTAACTC
1 CCAAAAGAAGATTTTGGAAAATAAGATAAC-C
14051 CCAAAAGAAGATTTTGGAAAATAAAGAT-A-C
1 CCAAAAGAAGATTTTGGAAAAT-AAGATAACC
14081 CCAAAAGAAGATTTTGGAAA
1 CCAAAAGAAGATTTTGGAAA
14101 TTAATAAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
30 21 0.44
32 23 0.48
33 4 0.08
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (31 bp):
CCAAAAGAAGATTTTGGAAAATAAGATAACC
Found at i:14791 original size:13 final size:13
Alignment explanation
Indices: 14775--14802 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
14765 CTTGCTTTTA
14775 TTGCTTAACTGTG
1 TTGCTTAACTGTG
14788 TTGCTTAACTGTG
1 TTGCTTAACTGTG
14801 TT
1 TT
14803 TTTTCGTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (13 bp):
TTGCTTAACTGTG
Found at i:15250 original size:28 final size:28
Alignment explanation
Indices: 15204--15300 Score: 94
Period size: 28 Copynumber: 3.4 Consensus size: 28
15194 GTCACCTAAG
*
15204 GGGGCATTTTGAT-ACTTTTGGCATGAT-A
1 GGGGCATTTTGGTCA-TTTTGGCATG-TCA
*
15232 GGGGCATTTTGGTCATTTT-GTATGTCCA
1 GGGGCATTTTGGTCATTTTGGCATGT-CA
*
15260 GGGGCATTTTGGTCATTTTGCACAT-TCA
1 GGGGCATTTTGGTCATTTTG-GCATGTCA
15288 GGGGGCATTTTGG
1 -GGGGCATTTTGG
15301 GTCACTTCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
26 1 0.02
27 4 0.07
28 38 0.64
29 14 0.24
30 2 0.03
ACGTcount: A:0.16, C:0.13, G:0.31, T:0.39
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTGGCATGTCA
Found at i:15518 original size:22 final size:21
Alignment explanation
Indices: 15492--15561 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
15482 TTAGTTCATT
15492 TAGCAAGCCTCTGTCTAGTTAG
1 TAGCAAGCCT-TGTCTAGTTAG
* * *
15514 TAGCAA---TAGTTTAGTTCATT
1 TAGCAAGCCTTGTCTAGTT-A-G
15534 TAGCAAGCCTTTGTCTAGTTAG
1 TAGCAAGCC-TTGTCTAGTTAG
15556 TAGCAA
1 TAGCAA
15562 TGGTCAATTG
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
18 7 0.19
19 2 0.06
20 6 0.17
22 12 0.33
23 1 0.03
24 8 0.22
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (21 bp):
TAGCAAGCCTTGTCTAGTTAG
Found at i:15537 original size:42 final size:42
Alignment explanation
Indices: 15478--15562 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
15468 GGTTGCCTAC
15478 TAGTTTAGTTCATTTAGCAAGCCTCTGTCTAGTTAGTAGCAA
1 TAGTTTAGTTCATTTAGCAAGCCTCTGTCTAGTTAGTAGCAA
*
15520 TAGTTTAGTTCATTTAGCAAGCCTTTGTCTAGTTAGTAGCAA
1 TAGTTTAGTTCATTTAGCAAGCCTCTGTCTAGTTAGTAGCAA
15562 T
1 T
15563 GGTCAATTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (42 bp):
TAGTTTAGTTCATTTAGCAAGCCTCTGTCTAGTTAGTAGCAA
Found at i:15552 original size:24 final size:24
Alignment explanation
Indices: 15483--15553 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
15473 CCTACTAGTT
*
15483 TAGTTCATTTAGCAAGCCTCTGTC
1 TAGTTCATTTAGCAAGCCTTTGTC
* * *
15507 TAGTT-A-GTAGCAA----TAGTT
1 TAGTTCATTTAGCAAGCCTTTGTC
15525 TAGTTCATTTAGCAAGCCTTTGTC
1 TAGTTCATTTAGCAAGCCTTTGTC
15549 TAGTT
1 TAGTT
15554 AGTAGCAATG
Statistics
Matches: 34, Mismatches: 7, Indels: 12
0.64 0.13 0.23
Matches are distributed among these distances:
18 7 0.21
19 1 0.03
20 6 0.18
22 6 0.18
23 1 0.03
24 13 0.38
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (24 bp):
TAGTTCATTTAGCAAGCCTTTGTC
Found at i:15940 original size:23 final size:23
Alignment explanation
Indices: 15910--15954 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
15900 CTATACATTT
*
15910 GCATTTCTGTTTGCACTCTACAC
1 GCATTTCTGTTTGCAATCTACAC
15933 GCATTTCTGTTTGCAATCTACA
1 GCATTTCTGTTTGCAATCTACA
15955 TTTGCATTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (23 bp):
GCATTTCTGTTTGCAATCTACAC
Found at i:20651 original size:18 final size:19
Alignment explanation
Indices: 20628--20664 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
20618 AACCTTAGCC
20628 CTAAAACTATAAGA-AAAA
1 CTAAAACTATAAGAGAAAA
20646 CTAAAACTATAAGAGAAAA
1 CTAAAACTATAAGAGAAAA
20665 AGAAGAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.65, C:0.11, G:0.08, T:0.16
Consensus pattern (19 bp):
CTAAAACTATAAGAGAAAA
Found at i:21306 original size:19 final size:19
Alignment explanation
Indices: 21273--21317 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
21263 TGGAAATAAT
21273 TCTTC-AATGATCTTCAAA
1 TCTTCAAATGATCTTCAAA
* *
21291 TCTTCAAATTATCTTCAAG
1 TCTTCAAATGATCTTCAAA
21310 TCTTCAAA
1 TCTTCAAA
21318 CACGAACTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.40
Consensus pattern (19 bp):
TCTTCAAATGATCTTCAAA
Found at i:30302 original size:675 final size:675
Alignment explanation
Indices: 29009--31714 Score: 4968
Period size: 675 Copynumber: 4.0 Consensus size: 675
28999 CATTCTTGGA
*
29009 TGAGATTGCCTCAGACCCGGGCATACCTTTAGTTCTAGGAGGTATAATAGCAAGCCTTCGTGGGA
1 TGAGATTGCCTCAGACCCGGGCATACCTTTAGTTCTGGGAGGTATAATAGCAAGCCTTCGTGGGA
*
29074 CTCGTTTGTCCCCGGGCAGGTTGTACGAAAAACCTCCACCCAAGGAAATCCTATTAGCCCAACAA
66 CTCGTTTGTCCCCGGGCAGGTTGTACGAAAAACCTCCACCCAAGGAAATCCTATTAGCCAAACAA
29139 TGGATGCTAGTAGGGTGAATTGGGAACCTCTAGGTGAACCTTTGCCCGACATATAGTGGATCGAC
131 TGGATGCTAGTAGGGTGAATTGGGAACCTCTAGGTGAACCTTTGCCCGACATATAGTGGATCGAC
* *
29204 TTCCAGCCTAGGTAGGGCCAAACCCGTGAGGATGAGTGCATTAGGTACACAGAAGGAACGTTACT
196 TTCCAGCCTAGGTAGGGCCAAACCCGTGAGGATGAGTGCACTAGGTACACAGAAGGAACGTTTCT
*
29269 CACTCTTGCCCTTTGTCTTTCAAAGTGATGATAAGAATCGTAGAACGAGTAAAGCGATTACTCGT
261 CACTCTTGCCCTTTGTCTTTCAAAATGATGATAAGAATCGTAGAACGAGTAAAGCGATTACTCGT
*
29334 CATGATAAGACCAGCCCTCGCCAAAATGGACACTTGGTCCAGATTTTTCAAGGAAAATTCTCGTT
326 CATGATAAGACCAGCCCTCCCCAAAATGGACACTTGGTCCAGATTTTTCAAGGAAAATTCTCGTT
29399 TTCGTAAACAAGAGGATTGATTTTAAAGCTTTGTTTTTCTCGGTTATTCCTGTTATTTCCTTTTT
391 TTCGTAAACAAGAGGATTGATTTTAAAGCTTTGTTTTTCTCGGTTATTCCTGTTATTTCCTTTTT
* * * *
29464 ATTATCTATACTAACATTGCTCTTTTTGATTTTGTTTTCTTCTTTTCTTTATCTTGCCGCATCAT
456 ATTATCTGTACTAACATTGCTCTTTTTGATTTCGTTTCCTTCTTTTCTTTATCTTGCCACATCAT
29529 TCCCATGCATCCACAGGTTGTCATATAATGTCGGAAACCAGACGAATGGATTTGATGACAGAAAT
521 TCCCATGCATCCACAGGTTGTCATATAATGTCGGAAACCAGACGAATGGATTTGATGACAGAAAT
29594 AGGACCCACGTGTTCGGGTGCTACTGCTGAGGTATCGGGTACGGACAGTGTGAATCAGAGTCCAG
586 AGGACCCACGTGTTCGGGTGCTACTGCTGAGGTATCGGGTACGGACAGTGTGAATCAGAGTCCAG
29659 TTCAGTCGGGCACTAGCATGACGGT
651 TTCAGTCGGGCACTAGCATGACGGT
29684 TGAGATTGCCTCAGACCCGGGCATACCTTTAGTTCTGGGAGGTATAATAGCAAGCCTTCGTGGGA
1 TGAGATTGCCTCAGACCCGGGCATACCTTTAGTTCTGGGAGGTATAATAGCAAGCCTTCGTGGGA
29749 CTCGTTTGTCCCCGGGCAGGTTGTACGAAAAACCTCCACCCAAGGAAATCCTATTAGCCAAACAA
66 CTCGTTTGTCCCCGGGCAGGTTGTACGAAAAACCTCCACCCAAGGAAATCCTATTAGCCAAACAA
29814 TGGATGCTAGTAGGGTGAATTGGGAACCTCTAGGTGAACCTTTGCCCGACATATAGTGGATCGAC
131 TGGATGCTAGTAGGGTGAATTGGGAACCTCTAGGTGAACCTTTGCCCGACATATAGTGGATCGAC
29879 TTCCAGCCTAGGTAGGGCCAAACCCGTGAGGATGAGTGCACTAGGTACACAGAAGGAACGTTTCT
196 TTCCAGCCTAGGTAGGGCCAAACCCGTGAGGATGAGTGCACTAGGTACACAGAAGGAACGTTTCT
29944 CACTCTTGCCCTTTGTCTTTCAAAATGATGATAAGAATCGTAGAACGAGTAAAGCGATTACTCGT
261 CACTCTTGCCCTTTGTCTTTCAAAATGATGATAAGAATCGTAGAACGAGTAAAGCGATTACTCGT
*
30009 CATGATAAGACCAGCCCTCCTCAAAATGGACACTTGGTCCAGATTTTTCAAGGAAAATTCTCGTT
326 CATGATAAGACCAGCCCTCCCCAAAATGGACACTTGGTCCAGATTTTTCAAGGAAAATTCTCGTT
*
30074 TTCGTAAACAAGAGGATTGATTTTAAAGCTTTGTTTTTCTCGGTTATTCCTATTATTTCCTTTTT
391 TTCGTAAACAAGAGGATTGATTTTAAAGCTTTGTTTTTCTCGGTTATTCCTGTTATTTCCTTTTT
* * *
30139 ATTATCTGTACTAACATTGCTCTTTTTTATTTCGTTTTCTTCTTTTCTTTATCTTGCCAAATCAT
456 ATTATCTGTACTAACATTGCTCTTTTTGATTTCGTTTCCTTCTTTTCTTTATCTTGCCACATCAT
*
30204 TCCCATGCATCCACAGGTTGTCATATAATGTCGGAAACCAGACGAATGTATTTGATGACAGAAAT
521 TCCCATGCATCCACAGGTTGTCATATAATGTCGGAAACCAGACGAATGGATTTGATGACAGAAAT
*
30269 AGGACCCACGTGTTCGGGTGCTACTGTTGAGGTATCGGGTACGGACAGTGTGAATCAGAGTCCAG
586 AGGACCCACGTGTTCGGGTGCTACTGCTGAGGTATCGGGTACGGACAGTGTGAATCAGAGTCCAG
30334 TTCAGTCGGGCACTAGCATGACGGT
651 TTCAGTCGGGCACTAGCATGACGGT
*
30359 TGAGATTGCCTCAGACCCGGGCATACCTTTAGTTCTGGGTGGTATAATAGCAAGCCTTCGTGGGA
1 TGAGATTGCCTCAGACCCGGGCATACCTTTAGTTCTGGGAGGTATAATAGCAAGCCTTCGTGGGA
*
30424 CTCGCTTGTCCCCGGGCAGGTTGTACGAAAAACCTCCATCCC-AGGAAATCCTATTAGCCAAACA
66 CTCGTTTGTCCCCGGGCAGGTTGTACGAAAAACCTCCA-CCCAAGGAAATCCTATTAGCCAAACA
30488 ATGGATGCTAGTAGGGTGAATTGGGAACCTCTAGGTGAACCTTTGCCCGACATATAGTGGATCGA
130 ATGGATGCTAGTAGGGTGAATTGGGAACCTCTAGGTGAACCTTTGCCCGACATATAGTGGATCGA
*
30553 CTTCCAGCCTAGGTAGGGCCAAACCCGTGAGGATGAGTGCACTAGGTACACAGAAGGTACGTTTC
195 CTTCCAGCCTAGGTAGGGCCAAACCCGTGAGGATGAGTGCACTAGGTACACAGAAGGAACGTTTC
30618 TCACTCTTGCCCTTTGTCTTTCAAAATGATGATAAGAATCGTAGAACGAGTAAAGCGATTACTCG
260 TCACTCTTGCCCTTTGTCTTTCAAAATGATGATAAGAATCGTAGAACGAGTAAAGCGATTACTCG
30683 TCATGATAAGACCAGCCCTCCCCAAAATGGACACTTGGTCCAGATTTTTCAAGGAAAATTCTCGT
325 TCATGATAAGACCAGCCCTCCCCAAAATGGACACTTGGTCCAGATTTTTCAAGGAAAATTCTCGT
30748 TTTCGTAAACAAGAGGATTGATTTTAAAGCTTTTGTTTTTCTCGGTTATTCCTGTTATTTCCTTT
390 TTTCGTAAACAAGAGGATTGATTTTAAAGC-TTTGTTTTTCTCGGTTATTCCTGTTATTTCCTTT
30813 TTATTATCTGTACTAACATTGCTCTTTTTGATTTCGTTTCCTTCTTTTCTTTATCTTG-CAGCAT
454 TTATTATCTGTACTAACATTGCTCTTTTTGATTTCGTTTCCTTCTTTTCTTTATCTTGCCA-CAT
* * *
30877 CATTCCCATGCATCCACAGGTTGTCATATAATGTCGGAAACCAGAAGAATAGATTT-TTGACAGA
518 CATTCCCATGCATCCACAGGTTGTCATATAATGTCGGAAACCAGACGAATGGATTTGATGACAGA
30941 AATAGGACCCACGTGTTCGGGTGCTACTGCTGAGGTATCGGGTACGGACAGTGTGAATCAGAGTC
583 AATAGGACCCACGTGTTCGGGTGCTACTGCTGAGGTATCGGGTACGGACAGTGTGAATCAGAGTC
* *
31006 CAATTCAGTCGGACACTAGCATGACGGT
648 CAGTTCAGTCGGGCACTAGCATGACGGT
* *
31034 TGAGATTGCCTCAGACCCGGGTATACCTTTAGTTCTGAGAGGTATAATAGCAAGCCTTCGTGGGA
1 TGAGATTGCCTCAGACCCGGGCATACCTTTAGTTCTGGGAGGTATAATAGCAAGCCTTCGTGGGA
*
31099 CTCGTTTGTCCCCGGGCAGGTTGTACGAAAAACCTCCACCCAAGGAAATCCTATTAGCCCAACAA
66 CTCGTTTGTCCCCGGGCAGGTTGTACGAAAAACCTCCACCCAAGGAAATCCTATTAGCCAAACAA
*
31164 TGGATGCTAGTAGGGTGAATTGGGAACCTCTAGGTGAACCTTCGCCCGACATATAGTGGATCGAC
131 TGGATGCTAGTAGGGTGAATTGGGAACCTCTAGGTGAACCTTTGCCCGACATATAGTGGATCGAC
* *
31229 TTCCAGCCTAGGTAGGGCCAAACCTGTGAGGATGAGTGCATTAGGTACACAGAAGGAACGTTTCT
196 TTCCAGCCTAGGTAGGGCCAAACCCGTGAGGATGAGTGCACTAGGTACACAGAAGGAACGTTTCT
31294 CACTCTTGCCCTTTGTCTTTCAAAATGATGATAAGAATCGTAGAACGAGTAAAGCGATTACTCGT
261 CACTCTTGCCCTTTGTCTTTCAAAATGATGATAAGAATCGTAGAACGAGTAAAGCGATTACTCGT
31359 CATGATAAGACCAGCCCTCCCCAAAATGGACACTTGGTCCAGATTTTTCAAGGAAAATTCTCGTT
326 CATGATAAGACCAGCCCTCCCCAAAATGGACACTTGGTCCAGATTTTTCAAGGAAAATTCTCGTT
* * * * *
31424 TTCGTAAACAAGGGGATTGATTTTAAAACTTTATTTTTCTCAGTTATTCCTGTTATTTCCTTGTT
391 TTCGTAAACAAGAGGATTGATTTTAAAGCTTTGTTTTTCTCGGTTATTCCTGTTATTTCCTTTTT
* * * * *
31489 GTTATCTGTACTGACATTGCTCTTTTTGTTTTCGTTTCCTTCTCTTCTTTATCTTGCCGCATCAT
456 ATTATCTGTACTAACATTGCTCTTTTTGATTTCGTTTCCTTCTTTTCTTTATCTTGCCACATCAT
** *
31554 TCCCATGCATTTACAGGTTGTCATATAATGTCGGAAACCAGAGGAATGGATTTGATGACAGAAAT
521 TCCCATGCATCCACAGGTTGTCATATAATGTCGGAAACCAGACGAATGGATTTGATGACAGAAAT
31619 AGGACCCACGTGTTCGGGTGCTACTGCTGAGGTATCGGGTACGGACAGTGTGAATCAGAGTCCAG
586 AGGACCCACGTGTTCGGGTGCTACTGCTGAGGTATCGGGTACGGACAGTGTGAATCAGAGTCCAG
31684 TTCAGTCGGGCACTAGCATGACGGT
651 TTCAGTCGGGCACTAGCATGACGGT
31709 TGAGAT
1 TGAGAT
31715 GGAACTCCCA
Statistics
Matches: 1969, Mismatches: 56, Indels: 12
0.97 0.03 0.01
Matches are distributed among these distances:
674 143 0.07
675 1679 0.85
676 147 0.07
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (675 bp):
TGAGATTGCCTCAGACCCGGGCATACCTTTAGTTCTGGGAGGTATAATAGCAAGCCTTCGTGGGA
CTCGTTTGTCCCCGGGCAGGTTGTACGAAAAACCTCCACCCAAGGAAATCCTATTAGCCAAACAA
TGGATGCTAGTAGGGTGAATTGGGAACCTCTAGGTGAACCTTTGCCCGACATATAGTGGATCGAC
TTCCAGCCTAGGTAGGGCCAAACCCGTGAGGATGAGTGCACTAGGTACACAGAAGGAACGTTTCT
CACTCTTGCCCTTTGTCTTTCAAAATGATGATAAGAATCGTAGAACGAGTAAAGCGATTACTCGT
CATGATAAGACCAGCCCTCCCCAAAATGGACACTTGGTCCAGATTTTTCAAGGAAAATTCTCGTT
TTCGTAAACAAGAGGATTGATTTTAAAGCTTTGTTTTTCTCGGTTATTCCTGTTATTTCCTTTTT
ATTATCTGTACTAACATTGCTCTTTTTGATTTCGTTTCCTTCTTTTCTTTATCTTGCCACATCAT
TCCCATGCATCCACAGGTTGTCATATAATGTCGGAAACCAGACGAATGGATTTGATGACAGAAAT
AGGACCCACGTGTTCGGGTGCTACTGCTGAGGTATCGGGTACGGACAGTGTGAATCAGAGTCCAG
TTCAGTCGGGCACTAGCATGACGGT
Found at i:35198 original size:17 final size:18
Alignment explanation
Indices: 35162--35199 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
35152 TGAAGAAGAC
* *
35162 AAAAAGAAGGAAAAGAGA
1 AAAAAAAAGAAAAAGAGA
35180 AAAAAAAAGAAAAAG-GA
1 AAAAAAAAGAAAAAGAGA
35197 AAA
1 AAA
35200 GGAAAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAAGAGA
Found at i:41706 original size:23 final size:23
Alignment explanation
Indices: 41679--41758 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
41669 GGAGCGAATT
41679 GGAAGACAGTTCAAAGGATAAGC
1 GGAAGACAGTTCAAAGGATAAGC
* ** **
41702 GGAAGACGGTCCTTTTAA-GATTGAATT
1 GGAAGACAG---TTCAAAGGA-T-AAGC
41729 GGAAGACAGTTCAAAGGATAAGC
1 GGAAGACAGTTCAAAGGATAAGC
41752 GGAAGAC
1 GGAAGAC
41759 GATCCTTTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
23 17 0.41
24 5 0.12
25 4 0.10
26 5 0.12
27 10 0.24
ACGTcount: A:0.39, C:0.12, G:0.30, T:0.19
Consensus pattern (23 bp):
GGAAGACAGTTCAAAGGATAAGC
Found at i:41732 original size:50 final size:50
Alignment explanation
Indices: 41674--41818 Score: 254
Period size: 50 Copynumber: 2.9 Consensus size: 50
41664 ATCAAGGAGC
41674 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT
1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT
*
41724 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGATCCTTTTAAGATT
1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT
* *
41774 GAATTGGAAGACAATTCAAAGGATAAGCGAAAGACGGTCCCTTTT
1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGT-CCTTTT
41819 TATATTGGAA
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
50 84 0.93
51 6 0.07
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.23
Consensus pattern (50 bp):
GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT
Found at i:42107 original size:27 final size:27
Alignment explanation
Indices: 42077--42128 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
42067 AGCATTGGGG
*
42077 ACATCTAGGGGCATTTTGGTCATTTGC
1 ACATCCAGGGGCATTTTGGTCATTTGC
42104 ACATCCAGGGGCATTTTGGTCATTT
1 ACATCCAGGGGCATTTTGGTCATTT
42129 CAAGTGCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (27 bp):
ACATCCAGGGGCATTTTGGTCATTTGC
Found at i:48625 original size:30 final size:31
Alignment explanation
Indices: 48558--48639 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 31
48548 TTAAGCAAAT
* *
48558 CCAAAAGAAGATTTTGGAAACTAAGGTAACTC
1 CCAAAAGAAGATTTTGGAAAATAAGATAAC-C
48590 CCAAAAGAAGATTTTGGAAAATAAAGAT-A-C
1 CCAAAAGAAGATTTTGGAAAAT-AAGATAACC
48620 CCAAAAGAAGATTTTGGAAA
1 CCAAAAGAAGATTTTGGAAA
48640 TTAATAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
30 21 0.45
32 22 0.47
33 4 0.09
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21
Consensus pattern (31 bp):
CCAAAAGAAGATTTTGGAAAATAAGATAACC
Found at i:55046 original size:17 final size:18
Alignment explanation
Indices: 55013--55048 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55003 CTCCTCTTGC
*
55013 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
55031 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
55048 A
1 A
55049 ACCACCATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:56287 original size:21 final size:21
Alignment explanation
Indices: 56245--56296 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
56235 GCAGGCTTGA
*
56245 CCGAGCAAGTGGTGCGGATGG
1 CCGAGCATGTGGTGCGGATGG
*
56266 CCGAGCATGTGGCT-CGGGTGG
1 CCGAGCATGTGG-TGCGGATGG
*
56287 CCGGGCATGT
1 CCGAGCATGT
56297 AGCTTGGTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.17
Consensus pattern (21 bp):
CCGAGCATGTGGTGCGGATGG
Found at i:58191 original size:28 final size:27
Alignment explanation
Indices: 58118--58191 Score: 67
Period size: 28 Copynumber: 2.7 Consensus size: 27
58108 GGTCACCCAG
* ** *
58118 GGGGCATTTTAGTCATTTGCACGTCTA
1 GGGGCATTTTAGTCATTTTCAAATCCA
* * * *
58145 AGGGAATTTTGGTCGTTTTCAAAATCCA
1 GGGGCATTTTAGTCATTTTC-AAATCCA
58173 GGGGCATTTTAGTCATTTT
1 GGGGCATTTTAGTCATTTT
58192 TACAAAAAAG
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
27 15 0.44
28 19 0.56
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (27 bp):
GGGGCATTTTAGTCATTTTCAAATCCA
Found at i:61325 original size:41 final size:41
Alignment explanation
Indices: 61278--61367 Score: 110
Period size: 41 Copynumber: 2.2 Consensus size: 41
61268 GTGTGAATTC
**
61278 ATTCAATTGGGTCCCTAATTTAG-GCTGTTATTTATTCATTG
1 ATTCAATTGGGTCCCTAATTTAGAG-TAATATTTATTCATTG
** * *
61319 ATTCAATTTTGTCCCTAATTTTGAGTAATATTTATTTATTG
1 ATTCAATTGGGTCCCTAATTTAGAGTAATATTTATTCATTG
61360 ATTCAATT
1 ATTCAATT
61368 TCGTCCCGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 41 0.98
42 1 0.02
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.50
Consensus pattern (41 bp):
ATTCAATTGGGTCCCTAATTTAGAGTAATATTTATTCATTG
Found at i:61392 original size:41 final size:41
Alignment explanation
Indices: 61278--61392 Score: 104
Period size: 41 Copynumber: 2.8 Consensus size: 41
61268 GTGTGAATTC
** * ** *
61278 ATTCAATTGGGTCCCTAATTTAGGCTGTTATTTATTCATTG
1 ATTCAATTTCGTCCCGAATTTAGAATATTATTTATTCATTG
* * * * * *
61319 ATTCAATTTTGTCCCTAATTTTGAGTAATATTTATTTATTG
1 ATTCAATTTCGTCCCGAATTTAGAATATTATTTATTCATTG
* *
61360 ATTCAATTTCGTCCCGGATTTAGAATTTTATTT
1 ATTCAATTTCGTCCCGAATTTAGAATATTATTT
61393 TTAATTTATG
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.50
Consensus pattern (41 bp):
ATTCAATTTCGTCCCGAATTTAGAATATTATTTATTCATTG
Found at i:63858 original size:28 final size:25
Alignment explanation
Indices: 63807--63867 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
63797 AGGAAAATAA
*
63807 TTTTTTTTTTGAAAACGCAGAAACAAT
1 TTTTTTTTTTGAAAACGCA-AAA-ACT
* *
63834 TTTTTTTTTTAGAAGACGTAAAAACT
1 TTTTTTTTTT-GAAAACGCAAAAACT
63860 TTTTTTTT
1 TTTTTTTT
63868 AAACACTAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 10 0.33
27 13 0.43
28 7 0.23
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (25 bp):
TTTTTTTTTTGAAAACGCAAAAACT
Found at i:64916 original size:34 final size:34
Alignment explanation
Indices: 64878--64946 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
64868 TGATTGAATT
64878 CACCAAAGGATAAGAAGTATTAAAAATTTAGCTA
1 CACCAAAGGATAAGAAGTATTAAAAATTTAGCTA
*
64912 CACCAAAGGATAAGAAGTATTAAGAATTTAGCTA
1 CACCAAAGGATAAGAAGTATTAAAAATTTAGCTA
64946 C
1 C
64947 TCATGGATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (34 bp):
CACCAAAGGATAAGAAGTATTAAAAATTTAGCTA
Found at i:68888 original size:24 final size:25
Alignment explanation
Indices: 68842--68892 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
68832 ATTGGAGTAT
*
68842 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
68867 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
68891 TT
1 TT
68893 GTTCACATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:82934 original size:40 final size:41
Alignment explanation
Indices: 82873--82964 Score: 102
Period size: 40 Copynumber: 2.3 Consensus size: 41
82863 TCAAATTGAA
* * *
82873 TAAAGCAGGGA-TCAGATTGCATTAAATTAAGAAA-AAAACT-
1 TAAATCAGGGACTAAGATTGCA-TAAATCAA-AAATAAAACTC
*
82913 TAAATCAGGGACTAAGA-TGCATAAATCAAAAATAAAATTC
1 TAAATCAGGGACTAAGATTGCATAAATCAAAAATAAAACTC
82953 TAAATCAGGGAC
1 TAAATCAGGGAC
82965 AAAATTGAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
38 3 0.07
39 12 0.27
40 26 0.58
41 4 0.09
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (41 bp):
TAAATCAGGGACTAAGATTGCATAAATCAAAAATAAAACTC
Found at i:87862 original size:13 final size:13
Alignment explanation
Indices: 87844--87873 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
87834 ATAGAGTAAT
*
87844 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
87857 AAAGAAAAAGAAA
1 AAAGAAAAAGAAA
87870 AAAG
1 AAAG
87874 GTTAGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:88507 original size:22 final size:23
Alignment explanation
Indices: 88479--88522 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
88469 AGAGATAGAA
*
88479 AAAGATC-AAAATCAAAAAAGAG
1 AAAGATCAAAAATAAAAAAAGAG
88501 AAAGATCAGAAAATAAAAAAAG
1 AAAGATCA-AAAATAAAAAAAG
88523 GCAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.09
Consensus pattern (23 bp):
AAAGATCAAAAATAAAAAAAGAG
Found at i:88718 original size:30 final size:31
Alignment explanation
Indices: 88648--88732 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 31
88638 TTTCTTAAGC
*
88648 AAATCCAAAAGACA-ATTTTGGAAAATAAGGT
1 AAATCCAAAAGA-AGATTTTGGAAAATAAAGT
*
88679 AATTCCAAAAGAAGATTTTGGAAAATAAAG-
1 AAATCCAAAAGAAGATTTTGGAAAATAAAGT
*
88709 AAATCCAAAAGAAGGTTTTGGAAA
1 AAATCCAAAAGAAGATTTTGGAAA
88733 TTAATAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
30 23 0.47
31 26 0.53
ACGTcount: A:0.52, C:0.08, G:0.18, T:0.22
Consensus pattern (31 bp):
AAATCCAAAAGAAGATTTTGGAAAATAAAGT
Found at i:89259 original size:27 final size:27
Alignment explanation
Indices: 89221--89272 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
89211 CCACCTATCC
89221 AAGGTCGTCTCGGCAGGGTTCCCCGTA
1 AAGGTCGTCTCGGCAGGGTTCCCCGTA
*
89248 AAGGTCGTCTCGGTAGGGTTCCCCG
1 AAGGTCGTCTCGGCAGGGTTCCCCG
89273 GACCCGAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.29, G:0.35, T:0.23
Consensus pattern (27 bp):
AAGGTCGTCTCGGCAGGGTTCCCCGTA
Found at i:97254 original size:47 final size:47
Alignment explanation
Indices: 97200--97811 Score: 699
Period size: 47 Copynumber: 12.5 Consensus size: 47
97190 ATGTCAGAGC
* * * *
97200 AATTAAACTAAATAGTAAAAGAAGAAGAGGTCAGTTTAATTCAGAGC
1 AATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGT
*
97247 AATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTCATTCTGGGT
1 AATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGT
* * *
97294 AATTAAACTAAATAGTAAAAGAAGAGGA-ATTAGTTTAATGCTGGGT
1 AATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGT
97340 AATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGT
1 AATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGT
* *
97387 AATTAAACTAAAGAGTAAAAGAAGAAGA-ATTAGTTTAATTCTGGGT
1 AATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGT
* * *
97433 AATTAAACTAAACATTAAAACAAGAAGAGGTTAGTTTAATTCTGGGT
1 AATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGT
* * *
97480 AATTAAACTAAAGAGTAAAAGAAGAAGA-ATTAGTTTAATTCTGGGA
1 AATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGT
*
97526 AATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTATGGGT
1 AATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGT
*
97573 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
1 AATTAAACTAAATAGT--AA-AAGAAG---A-AGAGGTTAGTTTAATTCTGGGT
* * *
97627 AATTAAACTAAAGAATAAAAGAAGAAGTAAACAGTAATTAGTTTAATTCTGGGT
1 AATTAAACTAAATAGTAAAAGAAGAAG-----AG--GTTAGTTTAATTCTGGGT
* **
97681 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAATAATTAGTTTAATTCTGGGT
1 AATTAAACTAAATAGTAAAAGAAGAAG------A-GGTTAGTTTAATTCTGGGT
* * *
97735 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGTAACCAGTTTAATTCTGGGT
1 AATTAAACTAAATAGTAAAAGAAGAAG---A-GGT---TAGTTTAATTCTGGGT
*
97789 AATTAAACTAAAGAGTAAAAGAA
1 AATTAAACTAAATAGTAAAAGAA
97812 AGAGTAAACG
Statistics
Matches: 502, Mismatches: 41, Indels: 37
0.87 0.07 0.06
Matches are distributed among these distances:
46 127 0.25
47 186 0.37
48 1 0.00
49 2 0.00
50 6 0.01
51 10 0.02
52 4 0.01
53 1 0.00
54 162 0.32
55 3 0.01
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (47 bp):
AATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGT
Found at i:97361 original size:93 final size:93
Alignment explanation
Indices: 97200--97811 Score: 756
Period size: 93 Copynumber: 6.2 Consensus size: 93
97190 ATGTCAGAGC
* * * * * *
97200 AATTAAACTAAATAGTAAAAGAAGAAGAGGTCAGTTTAATTCAGAGCAATTAAACTAAATAGTAA
1 AATTAAACTAAAGAGTAAAAGAAGAAGA-ATTAGTTTAATTCTGGGTAATTAAACTAAATAGTAA
*
97265 AAGAAGAAGAGGTTAGTTTCATTCTGGGT
65 AAGAAGAAGAGGTTAGTTTAATTCTGGGT
* * *
97294 AATTAAACTAAATAGTAAAAGAAGAGGAATTAGTTTAATGCTGGGTAATTAAACTAAATAGTAAA
1 AATTAAACTAAAGAGTAAAAGAAGAAGAATTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAA
97359 AGAAGAAGAGGTTAGTTTAATTCTGGGT
66 AGAAGAAGAGGTTAGTTTAATTCTGGGT
* *
97387 AATTAAACTAAAGAGTAAAAGAAGAAGAATTAGTTTAATTCTGGGTAATTAAACTAAACATTAAA
1 AATTAAACTAAAGAGTAAAAGAAGAAGAATTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAA
*
97452 ACAAGAAGAGGTTAGTTTAATTCTGGGT
66 AGAAGAAGAGGTTAGTTTAATTCTGGGT
*
97480 AATTAAACTAAAGAGTAAAAGAAGAAGAATTAGTTTAATTCTGGGAAATTAAACTAAATAGTAAA
1 AATTAAACTAAAGAGTAAAAGAAGAAGAATTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAA
*
97545 AGAAGAAGAGGTTAGTTTAATTATGGGT
66 AGAAGAAGAGGTTAGTTTAATTCTGGGT
97573 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGTAATTAAACTAA
1 AATTAAACTAAAGAGTAAAAGAAGAAG-----A-A--TTAGTTTAATTCTGGGTAATTAAACTAA
* * *
97638 AGAATAAAAGAAGAAGTAAACAGTAATTAGTTTAATTCTGGGT
58 ATAGTAAAAGAAGAAG-----AG--GTTAGTTTAATTCTGGGT
97681 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAATAATTAGTTTAATTCTGGGTAATTAAACTAA
1 AATTAAACTAAAGAGTAAAAGAAGAAG--------AATTAGTTTAATTCTGGGTAATTAAACTAA
* * *
97746 AGAGTAAAAGAAGAAGTAAACAGTAACCAGTTTAATTCTGGGT
58 ATAGTAAAAGAAGAAG---A-GGT---TAGTTTAATTCTGGGT
97789 AATTAAACTAAAGAGTAAAAGAA
1 AATTAAACTAAAGAGTAAAAGAA
97812 AGAGTAAACG
Statistics
Matches: 463, Mismatches: 33, Indels: 30
0.88 0.06 0.06
Matches are distributed among these distances:
93 260 0.56
94 27 0.06
98 1 0.00
99 1 0.00
101 41 0.09
105 1 0.00
106 4 0.01
108 124 0.27
110 1 0.00
111 3 0.01
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (93 bp):
AATTAAACTAAAGAGTAAAAGAAGAAGAATTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAA
AGAAGAAGAGGTTAGTTTAATTCTGGGT
Found at i:97704 original size:108 final size:107
Alignment explanation
Indices: 97463--97861 Score: 517
Period size: 108 Copynumber: 3.8 Consensus size: 107
97453 CAAGAAGAGG
97463 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGT--AA-AAGAAG---A-AGAATTAGTTTAATTC
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAATTAGTTTAATTC
* * * *
97521 TGGGAAATTAAACTAAATAGTAAAAGAAGAAG-----AG--G
66 TGGGTAATTAAACTAAAGAATAAAAGAAGAAGTAAACAGTAA
* *
97556 TTAGTTTAATTATGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTTAGTTTAATT
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGA-ATTAGTTTAATT
97621 CTGGGTAATTAAACTAAAGAATAAAAGAAGAAGTAAACAGTAA
65 CTGGGTAATTAAACTAAAGAATAAAAGAAGAAGTAAACAGTAA
*
97664 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAATAATTAGTTTAATT
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAAC-AGAATTAGTTTAATT
*
97729 CTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGTAA
65 CTGGGTAATTAAACTAAAGAATAAAAGAAGAAGTAAACAGTAA
** *
97772 CCAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAA-AGAGTAAACGGTAATTAG-TTAAT
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGA-AGTAAACAG-AATTAGTTTAAT
* *
97835 TTTGAGTAATTAAACTAAA-AAGTAAAA
64 TCTGGGTAATTAAACTAAAGAA-TAAAA
97862 AGCAAAAATA
Statistics
Matches: 270, Mismatches: 17, Indels: 24
0.87 0.05 0.08
Matches are distributed among these distances:
93 32 0.12
95 2 0.01
96 6 0.02
99 1 0.00
100 3 0.01
101 41 0.15
106 3 0.01
107 28 0.10
108 152 0.56
109 2 0.01
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.28
Consensus pattern (107 bp):
TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAATTAGTTTAATTC
TGGGTAATTAAACTAAAGAATAAAAGAAGAAGTAAACAGTAA
Found at i:97863 original size:54 final size:54
Alignment explanation
Indices: 97556--97861 Score: 483
Period size: 54 Copynumber: 5.7 Consensus size: 54
97546 GAAGAAGAGG
* *
97556 TTAGTTTAATTATGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAG-AGG
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGTA-A
*
97610 TTAGTTTAATTCTGGGTAATTAAACTAAAGAATAAAAGAAGAAGTAAACAGTAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGTAA
*
97664 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAATAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGTAA
97718 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGTAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGTAA
** *
97772 CCAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAA-AGAGTAAACGGTAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGA-AGTAAACAGTAA
* * *
97826 TTAG-TTAATTTTGAGTAATTAAACTAAAAAGTAAAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAA
97862 AGCAAAAATA
Statistics
Matches: 236, Mismatches: 14, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
53 30 0.13
54 205 0.87
55 1 0.00
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.28
Consensus pattern (54 bp):
TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGTAA
Done.