Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018851.1 Corchorus olitorius cultivar O-4 contig18884, 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: 118118
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:1596 original size:5 final size:5
Alignment explanation
Indices: 1586--1640 Score: 74
Period size: 5 Copynumber: 10.2 Consensus size: 5
1576 TTATAATTGT
1586 TTAGA TTAGA TTAGA TTTAGA TTTAGA TTAGA TTAGA TTTAGA TTAGA
1 TTAGA TTAGA TTAGA -TTAGA -TTAGA TTAGA TTAGA -TTAGA TTAGA
1634 TTTAGA T
1 -TTAGA T
1641 ATATAAGGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
5 26 0.55
6 21 0.45
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (5 bp):
TTAGA
Found at i:1607 original size:11 final size:11
Alignment explanation
Indices: 1586--1640 Score: 87
Period size: 11 Copynumber: 5.1 Consensus size: 11
1576 TTATAATTGT
1586 TTAGA-TTAGA
1 TTAGATTTAGA
1596 TTAGATTTAGA
1 TTAGATTTAGA
1607 TTTAGA-TTAGA
1 -TTAGATTTAGA
1618 TTAGATTTAGA
1 TTAGATTTAGA
1629 TTAGATTTAGA
1 TTAGATTTAGA
1640 T
1 T
1641 ATATAAGGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.24
11 27 0.64
12 5 0.12
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (11 bp):
TTAGATTTAGA
Found at i:1610 original size:22 final size:22
Alignment explanation
Indices: 1585--1640 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 22
1575 ATTATAATTG
1585 TTTAGATTAGATTAGATTTAGA
1 TTTAGATTAGATTAGATTTAGA
1607 TTTAGATTAGATTAGATTTAGA
1 TTTAGATTAGATTAGATTTAGA
1629 -TTAGATTTAGAT
1 TTTAGA-TTAGAT
1641 ATATAAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 5 0.15
22 28 0.85
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (22 bp):
TTTAGATTAGATTAGATTTAGA
Found at i:2064 original size:60 final size:60
Alignment explanation
Indices: 1991--2111 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
1981 CCTCTAAACA
1991 GACATTCATTTCTGTGGTGTGGCACATAGAATGCAAGCAAGCTTTCTCTTTTGTGGAGTT
1 GACATTCATTTCTGTGGTGTGGCACATAGAATGCAAGCAAGCTTTCTCTTTTGTGGAGTT
*
2051 GACATTCATTTCTGTGGTGTGGCACATAGAATGCTAGCAAGCTTTCTCTTTTGTGGAGTT
1 GACATTCATTTCTGTGGTGTGGCACATAGAATGCAAGCAAGCTTTCTCTTTTGTGGAGTT
2111 G
1 G
2112 TTTGGTAATT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.37
Consensus pattern (60 bp):
GACATTCATTTCTGTGGTGTGGCACATAGAATGCAAGCAAGCTTTCTCTTTTGTGGAGTT
Found at i:9828 original size:50 final size:50
Alignment explanation
Indices: 9753--9899 Score: 267
Period size: 50 Copynumber: 2.9 Consensus size: 50
9743 TGGCTCGACC
* * *
9753 ATGCTCATCATCTTGTCTTGCTGCAATGTGGAACTTCTTTGTGACTTGAT
1 ATGCTCATCATCTTGGCTTGCTGCAATGTGGAATTTCCTTGTGACTTGAT
9803 ATGCTCATCATCTTGGCTTGCTGCAATGTGGAATTTCCTTGTGACTTGAT
1 ATGCTCATCATCTTGGCTTGCTGCAATGTGGAATTTCCTTGTGACTTGAT
9853 ATGCTCATCATCTTGGCTTGCTGCAATGTGGAATTTCCTTGTGACTT
1 ATGCTCATCATCTTGGCTTGCTGCAATGTGGAATTTCCTTGTGACTT
9900 ATCATGTTTG
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 94 1.00
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (50 bp):
ATGCTCATCATCTTGGCTTGCTGCAATGTGGAATTTCCTTGTGACTTGAT
Found at i:11193 original size:27 final size:27
Alignment explanation
Indices: 11155--11272 Score: 191
Period size: 27 Copynumber: 4.4 Consensus size: 27
11145 GTACTTGAAG
*
11155 TGACCAAAATGCCCCTGGATGTGCAAA
1 TGACCAAAATGCCCCTGGACGTGCAAA
* *
11182 TGACTAAGATGCCCCTGGACGTGCAAA
1 TGACCAAAATGCCCCTGGACGTGCAAA
11209 TGACCAAAATGCCCCTGGACGTGCAAA
1 TGACCAAAATGCCCCTGGACGTGCAAA
* *
11236 TGACCAAAATGCCCCTGGACATGTAAA
1 TGACCAAAATGCCCCTGGACGTGCAAA
11263 TGACCAAAAT
1 TGACCAAAAT
11273 AATAAGTAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 84 1.00
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (27 bp):
TGACCAAAATGCCCCTGGACGTGCAAA
Found at i:11500 original size:19 final size:20
Alignment explanation
Indices: 11451--11500 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
11441 ATTTTTTTAT
11451 TATTTTTAAATTTTTAAATA
1 TATTTTTAAATTTTTAAATA
* *
11471 TAATTTAAAATTTTTAAA-A
1 TATTTTTAAATTTTTAAATA
11490 TATTTTTAAAT
1 TATTTTTAAAT
11501 CGGTTCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTTTTAAATTTTTAAATA
Found at i:11540 original size:31 final size:31
Alignment explanation
Indices: 11505--11570 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
11495 TTAAATCGGT
11505 TCAAATAGATACTAAA-CTTTTCAAAATTGGC
1 TCAAATAGATACTAAACCTTTT-AAAATTGGC
* *
11536 TCAAATAGGTACTAAACCTTTTAAAATTGGG
1 TCAAATAGATACTAAACCTTTTAAAATTGGC
11567 TCAA
1 TCAA
11571 TTTAGATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 27 0.84
32 5 0.16
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (31 bp):
TCAAATAGATACTAAACCTTTTAAAATTGGC
Found at i:12153 original size:24 final size:24
Alignment explanation
Indices: 12121--12168 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
12111 AGTTAAAAAT
12121 TTAGAAAGTTAGAAATGATTTGAG
1 TTAGAAAGTTAGAAATGATTTGAG
12145 TTAGAAAGTTAGAAATGATTTGAG
1 TTAGAAAGTTAGAAATGATTTGAG
12169 AGAATTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (24 bp):
TTAGAAAGTTAGAAATGATTTGAG
Found at i:15717 original size:18 final size:19
Alignment explanation
Indices: 15696--15732 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
15686 ACTAGACTCG
15696 AAACTGACACAAAA-AAAC
1 AAACTGACACAAAACAAAC
*
15714 AAACTGACTCAAAACAAAC
1 AAACTGACACAAAACAAAC
15733 TCAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.62, C:0.24, G:0.05, T:0.08
Consensus pattern (19 bp):
AAACTGACACAAAACAAAC
Found at i:18138 original size:117 final size:117
Alignment explanation
Indices: 17928--18141 Score: 349
Period size: 117 Copynumber: 1.8 Consensus size: 117
17918 CAATGCAATA
* * *
17928 TACCTCCATCAAACAAAGAACTTGAGTTACCATCATTCATTTTATAAGCTGATTAACATCAAAGT
1 TACCTCCATCAAACAAAGAACTTGAGTTACCATCATTCATGTTATAAGATGACTAACATCAAAGT
* *
17993 TTGGTACAAATATGAATTTTTTCGGAGAAAATTTAGCTACTAGCTGATTAAG
66 TTGGTACAAATATCAATTTTTTCAGAGAAAATTTAGCTACTAGCTGATTAAG
* *
18045 TACCTCCATCAAACAAAGACCTTGAGTTACCATCATTCATGTTATAAGATGACTGACATCAAAAG
1 TACCTCCATCAAACAAAGAACTTGAGTTACCATCATTCATGTTATAAGATGACTAACATC-AAAG
18110 TTTGGTACAAATATCAA-TTTTTCAGAGAAAAT
65 TTTGGTACAAATATCAATTTTTTCAGAGAAAAT
18142 GCATATACTA
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
117 69 0.78
118 20 0.22
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (117 bp):
TACCTCCATCAAACAAAGAACTTGAGTTACCATCATTCATGTTATAAGATGACTAACATCAAAGT
TTGGTACAAATATCAATTTTTTCAGAGAAAATTTAGCTACTAGCTGATTAAG
Found at i:19235 original size:23 final size:23
Alignment explanation
Indices: 19208--19284 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
19198 CAAACATACC
19208 ATCATAAAGATTTTCATTATTTA
1 ATCATAAAGATTTTCATTATTTA
* * **
19231 ATCATAAAAATTGAATCA-TA-ACA
1 ATCATAAAGATT--TTCATTATTTA
*
19254 ATCATAAAGATTTTCATCATTTA
1 ATCATAAAGATTTTCATTATTTA
*
19277 ATTATAAA
1 ATCATAAA
19285 CCATACCCTT
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
21 3 0.08
22 1 0.03
23 31 0.77
24 2 0.05
25 3 0.08
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.39
Consensus pattern (23 bp):
ATCATAAAGATTTTCATTATTTA
Found at i:21611 original size:2 final size:2
Alignment explanation
Indices: 21604--21636 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21594 TTTAACACTA
21604 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 A
21637 ATGAAAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23491 original size:22 final size:23
Alignment explanation
Indices: 23435--23497 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
23425 AGTCAAATCT
*
23435 TAATAAGAATACTAAAAAAATTG
1 TAATAAGATTACTAAAAAAATTG
** *
23458 TAATAACCTTACTAAAAACATT-
1 TAATAAGATTACTAAAAAAATTG
* *
23480 TAGTAAGATTACTGAAAA
1 TAATAAGATTACTAAAAA
23498 GCTTTTTAGC
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.29
Consensus pattern (23 bp):
TAATAAGATTACTAAAAAAATTG
Found at i:23655 original size:21 final size:20
Alignment explanation
Indices: 23604--23658 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
23594 TATATGGGAT
*
23604 TATTGAAATGCTTAATAAGG
1 TATTGAAAAGCTTAATAAGG
*
23624 TAATT-AGAAAGTTTAATAAGGG
1 T-ATTGA-AAAGCTTAATAA-GG
23646 TATTGAAAAGCTT
1 TATTGAAAAGCTT
23659 TTAAAGATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 2 0.07
21 22 0.79
22 4 0.14
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.35
Consensus pattern (20 bp):
TATTGAAAAGCTTAATAAGG
Found at i:24089 original size:21 final size:21
Alignment explanation
Indices: 24063--24104 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
24053 CCTCACTCAA
24063 AGGTCAACACCAATTCATTCC
1 AGGTCAACACCAATTCATTCC
24084 AGGTCAACACCAATTCATTCC
1 AGGTCAACACCAATTCATTCC
24105 CCTCGACGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.24
Consensus pattern (21 bp):
AGGTCAACACCAATTCATTCC
Found at i:38339 original size:30 final size:29
Alignment explanation
Indices: 38277--38346 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
38267 ACCGAACCGT
* ****
38277 CAAATAAGCCCCTGAACTTTTATTTCGGC
1 CAAATAAGCCCCTGAACTTTAAAAAAGGC
38306 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACT-TTAAAAAAGGC
38336 CAAATAAGCCC
1 CAAATAAGCCC
38347 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTTTAAAAAAGGC
Found at i:45301 original size:17 final size:17
Alignment explanation
Indices: 45279--45319 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
45269 TTTTTTTAAC
**
45279 AAAAATAAAATTTCAAT
1 AAAAATAAAATTAAAAT
*
45296 AAAAATAATATTAAAAT
1 AAAAATAAAATTAAAAT
45313 AAAAATA
1 AAAAATA
45320 TATAATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATAAAATTAAAAT
Found at i:45874 original size:11 final size:11
Alignment explanation
Indices: 45858--45892 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
45848 TTGACAGCGC
45858 AACAAAAACAA
1 AACAAAAACAA
*
45869 AACAAAAACGA
1 AACAAAAACAA
45880 AACAAAAACAA
1 AACAAAAACAA
45891 AA
1 AA
45893 AACAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:48480 original size:22 final size:22
Alignment explanation
Indices: 48421--49139 Score: 234
Period size: 22 Copynumber: 33.0 Consensus size: 22
48411 TGTTGTCTCT
*
48421 GTGTAGTTATCAAAATTTCATA
1 GTGTTGTTATCAAAATTTCATA
* * * *
48443 ATG-AGATTATCGAAATTTCTTA
1 GTGTTG-TTATCAAAATTTCATA
*
48465 GTGTTGTTGA-CAAAATTTCGTA
1 GTGTTGTT-ATCAAAATTTCATA
*
48487 GTGTGGTTATCAAAATTTCATA
1 GTGTTGTTATCAAAATTTCATA
*
48509 GCGTTGTTATCAAAATTTCATAA
1 GTGTTGTTATCAAAATTTCAT-A
*** *
48532 G-AAAGTTATCACAATTTCATA
1 GTGTTGTTATCAAAATTTCATA
*
48553 GTGTGGTTATCAAAATTTCATA
1 GTGTTGTTATCAAAATTTCATA
*
48575 GT-ATGATTA-CAAGAATTTCATTA
1 GTGTTG-TTATCAA-AATTTCA-TA
*
48598 G-GTAGTTTATCAAAATTTCATA
1 GTGTTG-TTATCAAAATTTCATA
* *
48620 GTGTAGTTACCAAAA-TTCATTA
1 GTGTTGTTATCAAAATTTCA-TA
** * *
48642 G-GAGGCTATTAAAATTTCA-A
1 GTGTTGTTATCAAAATTTCATA
* *
48662 -TGTGGTTTTCAAAATTTCATA
1 GTGTTGTTATCAAAATTTCATA
* ** **
48683 GAGACGTTATCCGAATTTCAT-
1 GTGTTGTTATCAAAATTTCATA
*
48704 GT-TGTGACTATCAAAATTTCATAA
1 GTGT-TG-TTATCAAAATTTCAT-A
* *
48728 GAAG--GTTATCAAAGTTTCATAA
1 G-TGTTGTTATCAAAATTTCAT-A
*
48750 GAAG--GTTATCAAAATTTCATA
1 G-TGTTGTTATCAAAATTTCATA
* *
48771 ATGTGGTTATCAAAATTTCAT-
1 GTGTTGTTATCAAAATTTCATA
** * * *
48792 GTGAAGATTACCAAAGTTTCACA
1 GTGTTG-TTATCAAAATTTCATA
* ** *
48815 GGGAGGTTACCAAAATTTCATA
1 GTGTTGTTATCAAAATTTCATA
48837 G-GTTGGTTAT-AAAATTTCATA
1 GTGTT-GTTATCAAAATTTCATA
* * *
48858 G-GTAGGTTACCAAAATTTTTATA
1 GTGT-TGTTATCAAAA-TTTCATA
* * * *
48881 TTG-TGATATTAAAATCTCATA
1 GTGTTGTTATCAAAATTTCATA
* * *
48902 GAGAT-TAAT-AAAATTTCATA
1 GTGTTGTTATCAAAATTTCATA
** * * *
48922 AAGATGTTACCAAAATTTTATA
1 GTGTTGTTATCAAAATTTCATA
*
48944 GTG-TGAGTATCAAAATTTCATA
1 GTGTTG-TTATCAAAATTTCATA
* ** ** *
48966 GAGAGGCAATC-AAATTTCACAA
1 GTGTTGTTATCAAAATTTCA-TA
** ** *
48988 G-GAGGCAATCAAAATTTCGTA
1 GTGTTGTTATCAAAATTTCATA
* **
49009 GAGAGGTTATCAAAATTTCATA
1 GTGTTGTTATCAAAATTTCATA
* ** *
49031 GGGAGGTTATCAAGATTGT-ATA
1 GTGTTGTTATCAAAATT-TCATA
* *
49053 GTGTGGTT-TCTGAAATTTCATA
1 GTGTTGTTATC-AAAATTTCATA
* **
49075 GAGAGGTTATCAAAATTTCATA
1 GTGTTGTTATCAAAATTTCATA
* * * *
49097 CTGTGGTTATTAAAATTTTATA
1 GTGTTGTTATCAAAATTTCATA
* * * *
49119 GGGATATTATCGAAATTTCAT
1 GTGTTGTTATCAAAATTTCAT
49140 TGGGAGATTA
Statistics
Matches: 532, Mismatches: 121, Indels: 88
0.72 0.16 0.12
Matches are distributed among these distances:
20 30 0.06
21 81 0.15
22 379 0.71
23 37 0.07
24 5 0.01
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (22 bp):
GTGTTGTTATCAAAATTTCATA
Found at i:48548 original size:66 final size:63
Alignment explanation
Indices: 48477--49209 Score: 276
Period size: 66 Copynumber: 11.2 Consensus size: 63
48467 GTTGTTGACA
* *
48477 AAATTTCGTAGTGTGGTTATCAAAATTTCATAGCGTTGTTATCAAAATTTCATAAGAAAGTTATC
1 AAATTTCATAGTGAGGTTATCAAAATTTCATAG-GTTGTTATCAAAATTTCATAAG-AAGTTATC
* * *
48542 ACAATTTCATAGTGTGGTTATCAAAATTTCATA-GTATGATTA-CAAGAATTTCATTAGGTAGTT
1 A-AATTTCATAGTGAGGTTATCAAAATTTCATAGGT-TG-TTATCAA-AATTTCA-TAAGAAG-T
48605 TATC
60 TATC
* ** * * * ** *
48609 AAAATTTCATAGTGTA-GTTACCAAAA-TTCATTAGGAGGCTATTAAAATTTCA-ATGTGGTTTT
1 -AAATTTCATAGTG-AGGTTATCAAAATTTCA-TAGGTTGTTATCAAAATTTCATAAGAAGTTAT
48671 C
63 C
* * **
48672 AAAATTTCATAGAGACGTTATCCGAATTTCAT--GTTGTGACTATCAAAATTTCATAAGAAGGTT
1 -AAATTTCATAGTGAGGTTATCAAAATTTCATAGGTTGT---TATCAAAATTTCATAAGAA-GTT
48735 ATC
61 ATC
* * * **
48738 AAAGTTTCATAAG-AAGGTTATCAAAATTTCATAATGTGGTTATCAAAATTTCATGTGAAGATTA
1 AAA-TTTCAT-AGTGAGGTTATCAAAATTTCAT-AGGTTGTTATCAAAATTTCATAAGAAG-TTA
*
48802 CC
62 TC
* * * * * *
48804 AAAGTTTCACAGGGAGGTTACCAAAATTTCATAGGTTGGTTAT-AAAATTTCATAGGTAGGTTAC
1 AAA-TTTCATAGTGAGGTTATCAAAATTTCATAGGTT-GTTATCAAAATTTCATAAG-AAGTTAT
48868 C
63 C
* * * * * * * * *
48869 AAAATTTTTATATTG-TGATATTAAAATCTCATAGAGAT-TAAT-AAAATTTCATAAAGATGTTA
1 -AAA-TTTCATAGTGAGGTTATCAAAATTTCATAG-GTTGTTATCAAAATTTCAT-AAGAAGTTA
*
48931 CC
62 TC
* * ** ** * * **
48933 AAAATTTTATAGTGTGAG-TATCAAAATTTCATAGAGAGGCAATC-AAATTTCACAAGGAGGCAA
1 -AAATTTCATAGTGAG-GTTATCAAAATTTCATAG-GTTGTTATCAAAATTTCATAA-GAAGTTA
48996 TC
62 TC
* * ** * * **
48998 AAAATTTCGTAGAGAGGTTATCAAAATTTCATAGGGAGGTTATCAAGATTGT-ATAGTGTGGTT-
1 -AAATTTCATAGTGAGGTTATCAAAATTTCATA-GGTTGTTATCAAAATT-TCATA-AGAAGTTA
49061 TC
62 TC
* * * * * *
49063 TGAAATTTCATAGAGAGGTTATCAAAATTTCATACTGTGGTTATTAAAATTTTATAGGGATA-TT
1 --AAATTTCATAGTGAGGTTATCAAAATTTCATA-GGTTGTTATCAAAATTTCATA-AGA-AGTT
49127 ATC
61 ATC
* * * * ** * * * *
49130 GAAATTTCATTGGGAGATTATCGAAATTTCATGAGGAGGTTATCGAAATTTCTTATGCAGGTTAT
1 -AAATTTCATAGTGAGGTTATCAAAATTTCAT-AGGTTGTTATCAAAATTTCATAAG-AAGTTAT
49195 C
63 C
*
49196 AAAATTTAATAGTG
1 -AAATTTCATAGTG
49210 TGGTATTGTG
Statistics
Matches: 518, Mismatches: 103, Indels: 93
0.73 0.14 0.13
Matches are distributed among these distances:
61 2 0.00
62 1 0.00
63 34 0.07
64 66 0.13
65 104 0.20
66 265 0.51
67 40 0.08
68 2 0.00
69 4 0.01
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (63 bp):
AAATTTCATAGTGAGGTTATCAAAATTTCATAGGTTGTTATCAAAATTTCATAAGAAGTTATC
Found at i:48932 original size:64 final size:64
Alignment explanation
Indices: 48845--48969 Score: 173
Period size: 64 Copynumber: 2.0 Consensus size: 64
48835 TAGGTTGGTT
* * *
48845 ATAAAATTTCATAGGTAGGTTACCAAAATTTTTATATTGTGA-TATTAAAATCTCATAGAGATTA
1 ATAAAATTTCATAAGTAGGTTACCAAAA-TTTTATAGTGTGAGTATCAAAATCTCATAGAGATTA
* *
48909 ATAAAATTTCATAAAG-ATGTTACCAAAATTTTATAGTGTGAGTATCAAAATTTCATAGAGA
1 ATAAAATTTCAT-AAGTAGGTTACCAAAATTTTATAGTGTGAGTATCAAAATCTCATAGAGA
48970 GGCAATCAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
63 12 0.22
64 40 0.74
65 2 0.04
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (64 bp):
ATAAAATTTCATAAGTAGGTTACCAAAATTTTATAGTGTGAGTATCAAAATCTCATAGAGATTA
Found at i:49191 original size:22 final size:22
Alignment explanation
Indices: 48951--49202 Score: 105
Period size: 22 Copynumber: 11.5 Consensus size: 22
48941 ATAGTGTGAG
* *
48951 TATCAAAATTTCA-TAGAGAGGC
1 TATCGAAATTTCATTAG-GAGGT
* ** *
48973 AATC-AAATTTCACAAGGAGGC
1 TATCGAAATTTCATTAGGAGGT
* * *
48994 AATCAAAATTTC-GTAGAGAGGT
1 TATCGAAATTTCATTAG-GAGGT
*
49016 TATCAAAATTTCA-TAGGGAGGT
1 TATCGAAATTTCATTA-GGAGGT
*
49038 TATC-AAGATTGT-A-TAGTGTGGT
1 TATCGAA-ATT-TCATTAG-GAGGT
49060 T-TCTGAAATTTCA-TAGAGAGGT
1 TATC-GAAATTTCATTAG-GAGGT
* * *
49082 TATCAAAATTTCA-TACTGTGGT
1 TATCGAAATTTCATTA-GGAGGT
** * **
49104 TATTAAAATTTTA-TAGGGATAT
1 TATCGAAATTTCATTA-GGAGGT
* *
49126 TATCGAAATTTCATTGGGAGAT
1 TATCGAAATTTCATTAGGAGGT
*
49148 TATCGAAATTTCATGAGGAGGT
1 TATCGAAATTTCATTAGGAGGT
*
49170 TATCGAAATTTC-TTATGCAGGT
1 TATCGAAATTTCATTA-GGAGGT
*
49192 TATCAAAATTT
1 TATCGAAATTT
49203 AATAGTGTGG
Statistics
Matches: 185, Mismatches: 30, Indels: 30
0.76 0.12 0.12
Matches are distributed among these distances:
21 27 0.15
22 151 0.82
23 7 0.04
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (22 bp):
TATCGAAATTTCATTAGGAGGT
Found at i:49326 original size:22 final size:22
Alignment explanation
Indices: 49297--49420 Score: 108
Period size: 22 Copynumber: 5.6 Consensus size: 22
49287 CGCAATATAA
* *
49297 TTATCAAAATTTTATATGGAGG
1 TTATCAAAATTTTATAAGAAGG
* * * *
49319 TTAACAAAATTTTGTTATG-TGG
1 TTATCAAAATTTT-ATAAGAAGG
* *
49341 TTATCAAAATTTCATAAGAATG
1 TTATCAAAATTTTATAAGAAGG
*
49363 TTATCAAAATTTTATAAGAATG
1 TTATCAAAATTTTATAAGAAGG
* * *
49385 TTATCAAAATTTCATAATG-TGA
1 TTATCAAAATTTTATAA-GAAGG
49407 TTATCAAAATTTTA
1 TTATCAAAATTTTA
49421 CAAGGACACT
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
21 3 0.04
22 76 0.90
23 5 0.06
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTTATAAGAAGG
Found at i:49624 original size:16 final size:16
Alignment explanation
Indices: 49603--49636 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
49593 ATAGAAATAA
49603 GATGGTATATTTGGTT
1 GATGGTATATTTGGTT
49619 GATGGTATATTTGGTT
1 GATGGTATATTTGGTT
49635 GA
1 GA
49637 GGGTTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (16 bp):
GATGGTATATTTGGTT
Found at i:56198 original size:24 final size:24
Alignment explanation
Indices: 56166--56220 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
56156 TGTGATCAAC
*
56166 TGATCATGATCTCTTCTCTCCGTA
1 TGATCATGATCTCTTCTCTCCATA
56190 TGATCATGATCTCTTCTCTCCATA
1 TGATCATGATCTCTTCTCTCCATA
*
56214 TAATCAT
1 TGATCAT
56221 ATATATATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.22, C:0.27, G:0.09, T:0.42
Consensus pattern (24 bp):
TGATCATGATCTCTTCTCTCCATA
Found at i:58734 original size:13 final size:13
Alignment explanation
Indices: 58716--58740 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58706 TTTGAGGTCT
58716 CTCTCTCTCTCTC
1 CTCTCTCTCTCTC
58729 CTCTCTCTCTCT
1 CTCTCTCTCTCT
58741 GTGTATGTGG
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (13 bp):
CTCTCTCTCTCTC
Found at i:65371 original size:23 final size:23
Alignment explanation
Indices: 65341--65389 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
65331 TTTTAAGGCC
65341 TTATATAAGTTAAGATTGGAACA
1 TTATATAAGTTAAGATTGGAACA
65364 TTATATAAGTTAAGATTGGAACA
1 TTATATAAGTTAAGATTGGAACA
65387 TTA
1 TTA
65390 GGCCCTGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (23 bp):
TTATATAAGTTAAGATTGGAACA
Found at i:65544 original size:20 final size:20
Alignment explanation
Indices: 65519--65556 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
65509 TCAAGGTGTC
65519 TTTTTTTATTGGCCAGTTTT
1 TTTTTTTATTGGCCAGTTTT
*
65539 TTTTTTTTTTGGCCAGTT
1 TTTTTTTATTGGCCAGTT
65557 GCTACAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.11, G:0.16, T:0.66
Consensus pattern (20 bp):
TTTTTTTATTGGCCAGTTTT
Found at i:66480 original size:3 final size:3
Alignment explanation
Indices: 66458--66500 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
66448 GGTCTAAATT
*
66458 TAA T-A TAA AAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
66501 AACAAACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:66976 original size:6 final size:6
Alignment explanation
Indices: 66965--67094 Score: 65
Period size: 6 Copynumber: 23.7 Consensus size: 6
66955 GTTTTGACCA
* * *
66965 TCGAGC TCGAGC TTG-GC TCGA-A TCGAGTA TCGAGC T--A-C TCGAGC
1 TCGAGC TCGAGC TCGAGC TCGAGC TCGAG-C TCGAGC TCGAGC TCGAGC
* *
67009 TCGAGC TCG-GC TCGA-A TCGAGTA TCGAGC T--A-C TCGAGC TCGAGC
1 TCGAGC TCGAGC TCGAGC TCGAG-C TCGAGC TCGAGC TCGAGC TCGAGC
* *
67053 TCG-GC TCGA-A TCGAGTA TCGAGC T--A-C TCGAGC TCGAGC TCGA
1 TCGAGC TCGAGC TCGAG-C TCGAGC TCGAGC TCGAGC TCGAGC TCGA
67095 CAAGTTCGAT
Statistics
Matches: 98, Mismatches: 8, Indels: 36
0.69 0.06 0.25
Matches are distributed among these distances:
3 6 0.06
4 3 0.03
5 29 0.30
6 42 0.43
7 18 0.18
ACGTcount: A:0.21, C:0.28, G:0.29, T:0.22
Consensus pattern (6 bp):
TCGAGC
Found at i:67023 original size:11 final size:12
Alignment explanation
Indices: 66965--67094 Score: 65
Period size: 11 Copynumber: 11.8 Consensus size: 12
66955 GTTTTGACCA
66965 TCGAGCTCGAGC
1 TCGAGCTCGAGC
* *
66977 TTG-GCTCGA-A
1 TCGAGCTCGAGC
*
66987 TCGAGTATCGAGC
1 TCGAG-CTCGAGC
67000 T--A-CTCGAGC
1 TCGAGCTCGAGC
67009 TCGAGCTCG-GC
1 TCGAGCTCGAGC
* *
67020 TCGA-ATCGAGTA
1 TCGAGCTCGAG-C
67032 TCGAGCT--A-C
1 TCGAGCTCGAGC
67041 TCGAGCTCGAGC
1 TCGAGCTCGAGC
*
67053 TCG-GCTCGA-A
1 TCGAGCTCGAGC
*
67063 TCGAGTATCGAGC
1 TCGAG-CTCGAGC
67076 T--A-CTCGAGC
1 TCGAGCTCGAGC
67085 TCGAGCTCGA
1 TCGAGCTCGA
67095 CAAGTTCGAT
Statistics
Matches: 86, Mismatches: 14, Indels: 36
0.63 0.10 0.26
Matches are distributed among these distances:
9 21 0.24
10 8 0.09
11 27 0.31
12 27 0.31
13 3 0.03
ACGTcount: A:0.21, C:0.28, G:0.29, T:0.22
Consensus pattern (12 bp):
TCGAGCTCGAGC
Found at i:67050 original size:44 final size:38
Alignment explanation
Indices: 66965--67093 Score: 249
Period size: 38 Copynumber: 3.4 Consensus size: 38
66955 GTTTTGACCA
*
66965 TCGAGCTCGAGCTTGGCTCGAATCGAGTATCGAGCTAC
1 TCGAGCTCGAGCTCGGCTCGAATCGAGTATCGAGCTAC
67003 TCGAGCTCGAGCTCGGCTCGAATCGAGTATCGAGCTAC
1 TCGAGCTCGAGCTCGGCTCGAATCGAGTATCGAGCTAC
67041 TCGAGCTCGAGCTCGGCTCGAATCGAGTATCGAGCTAC
1 TCGAGCTCGAGCTCGGCTCGAATCGAGTATCGAGCTAC
67079 TCGAGCTCGAGCTCG
1 TCGAGCTCGAGCTCG
67094 ACAAGTTCGA
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 90 1.00
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.22
Consensus pattern (38 bp):
TCGAGCTCGAGCTCGGCTCGAATCGAGTATCGAGCTAC
Found at i:67165 original size:18 final size:18
Alignment explanation
Indices: 67144--67192 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
67134 TTTCAGCTAA
67144 AATTCGAGCTCGAGCTCG
1 AATTCGAGCTCGAGCTCG
* *
67162 AATTCGATAC-CGAGTTCG
1 AATTCGA-GCTCGAGCTCG
*
67180 AGTTCGAGCTCGA
1 AATTCGAGCTCGA
67193 CAGGTATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 1 0.04
18 23 0.92
19 1 0.04
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (18 bp):
AATTCGAGCTCGAGCTCG
Found at i:67246 original size:18 final size:18
Alignment explanation
Indices: 67223--67258 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
67213 TTTTAATTAA
67223 ATATATA-ATATTATGTAT
1 ATATATATATATT-TGTAT
67241 ATATATATATATTTGTAT
1 ATATATATATATTTGTAT
67259 CGAGTAGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATATATATATATTTGTAT
Found at i:67517 original size:29 final size:30
Alignment explanation
Indices: 67463--67522 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
67453 ATTAACAAGC
*
67463 ACATTAGACCCTTAATTGATTGAAATTGAA
1 ACATTAGACCCTTAATTGACTGAAATTGAA
*
67493 ACATTAGGCCC-TAATTCGACT-AAATTGAA
1 ACATTAGACCCTTAATT-GACTGAAATTGAA
67522 A
1 A
67523 GGGTGAGCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (30 bp):
ACATTAGACCCTTAATTGACTGAAATTGAA
Found at i:70266 original size:12 final size:12
Alignment explanation
Indices: 70249--70273 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
70239 CGTCATTGCT
70249 TAATGACACAAG
1 TAATGACACAAG
70261 TAATGACACAAG
1 TAATGACACAAG
70273 T
1 T
70274 CAGCAACTAA
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:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (12 bp):
TAATGACACAAG
Found at i:70469 original size:21 final size:21
Alignment explanation
Indices: 70443--70487 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
70433 ATTTGAGCCT
70443 TCTAAAAAATTAAACAAAACA
1 TCTAAAAAATTAAACAAAACA
70464 TCTAAAAAATTAAACAAAACA
1 TCTAAAAAATTAAACAAAACA
70485 TCT
1 TCT
70488 TAAGAAGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (21 bp):
TCTAAAAAATTAAACAAAACA
Found at i:87144 original size:34 final size:34
Alignment explanation
Indices: 87100--87185 Score: 163
Period size: 34 Copynumber: 2.5 Consensus size: 34
87090 GGGAGTGTGA
*
87100 GCTAAATCCTTCCAACTTGATGCCAAAAAAGAAG
1 GCTAAGTCCTTCCAACTTGATGCCAAAAAAGAAG
87134 GCTAAGTCCTTCCAACTTGATGCCAAAAAAGAAG
1 GCTAAGTCCTTCCAACTTGATGCCAAAAAAGAAG
87168 GCTAAGTCCTTCCAACTT
1 GCTAAGTCCTTCCAACTT
87186 TGCTATTACT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (34 bp):
GCTAAGTCCTTCCAACTTGATGCCAAAAAAGAAG
Found at i:92511 original size:53 final size:53
Alignment explanation
Indices: 92431--92536 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
92421 GAAGGAGATG
92431 AAAGTGCTGGTGCTATAGTGCTAAGTAGGATGAATGGCATTCAGAGAACTGTC
1 AAAGTGCTGGTGCTATAGTGCTAAGTAGGATGAATGGCATTCAGAGAACTGTC
92484 AAAGTGCTGGTGCTATAGTGCTAAGTAGGATGAATGGCATTCAGAGAACTGTC
1 AAAGTGCTGGTGCTATAGTGCTAAGTAGGATGAATGGCATTCAGAGAACTGTC
92537 GGCTGTTGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.26
Consensus pattern (53 bp):
AAAGTGCTGGTGCTATAGTGCTAAGTAGGATGAATGGCATTCAGAGAACTGTC
Found at i:101654 original size:31 final size:30
Alignment explanation
Indices: 101619--101687 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
101609 TTTTTTAAAG
*
101619 GAATGATAGTAAATTTTATTTTTT-GGT-AGAA
1 GAATGATAGT--ATTTT-TTTTTTGGGTAAAAA
101650 GAATGATAGTATTTTTTTTTTGGGTAAAAA
1 GAATGATAGTATTTTTTTTTTGGGTAAAAA
101680 GAATGATA
1 GAATGATA
101688 CTAGTATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
28 6 0.17
29 8 0.23
30 11 0.31
31 10 0.29
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.43
Consensus pattern (30 bp):
GAATGATAGTATTTTTTTTTTGGGTAAAAA
Found at i:101668 original size:28 final size:27
Alignment explanation
Indices: 101599--101687 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 27
101589 ATATAAGTAG
101599 TAGTATTTTTTTTTT--TAAAGGAATGA
1 TAGTATTTTTTTTTTGGTAAA-GAATGA
101625 TAGTAAATTTTATTTTTTGGTAGAAGAATGA
1 TAGT--ATTTT-TTTTTTGGTA-AAGAATGA
101656 TAGTATTTTTTTTTTGGGTAAAAAGAATGA
1 TAGTATTTTTTTTTT-GGT--AAAGAATGA
101686 TA
1 TA
101688 CTAGTATTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
26 4 0.07
28 11 0.20
29 14 0.26
30 10 0.19
31 13 0.24
32 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (27 bp):
TAGTATTTTTTTTTTGGTAAAGAATGA
Found at i:103640 original size:4 final size:4
Alignment explanation
Indices: 103631--103678 Score: 96
Period size: 4 Copynumber: 12.0 Consensus size: 4
103621 CTAACCGACA
103631 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
103679 TGAACAATAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:106813 original size:16 final size:17
Alignment explanation
Indices: 106785--106817 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
106775 TTTAGTAACT
106785 TTAGAAGTTTTTTTGAA
1 TTAGAAGTTTTTTTGAA
106802 TTAGAA-TTTTTTTGAA
1 TTAGAAGTTTTTTTGAA
106818 CTTCTTAAAA
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:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (17 bp):
TTAGAAGTTTTTTTGAA
Found at i:109315 original size:5 final size:5
Alignment explanation
Indices: 109305--109334 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
109295 CATAGCTGTG
109305 ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT
1 ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT
109335 CAGACATCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
ATCAT
Found at i:115578 original size:94 final size:95
Alignment explanation
Indices: 115478--115666 Score: 335
Period size: 95 Copynumber: 2.0 Consensus size: 95
115468 TATCAATATG
115478 TAATAACATGAA-TTTTTTTTATAAATCTTATTATATAATAAAAAAATCTAAATCCAAATAAATT
1 TAATAACATGAATTTTTTTTTATAAATCTTATTATATAATAAAAAAATCTAAATCCAAATAAATT
*
115542 TTTTGAGATAAGAATAATTTTAATTTCTTA
66 TTTTGAGATAAAAATAATTTTAATTTCTTA
*
115572 TAATAACATGAATTTTTTTTTATAAATCTTATTATATAATAAAAAAATTTAAATCCAAATAAATT
1 TAATAACATGAATTTTTTTTTATAAATCTTATTATATAATAAAAAAATCTAAATCCAAATAAATT
* *
115637 TTTTGAGATAAAAATCATTTTCATTTCTTA
66 TTTTGAGATAAAAATAATTTTAATTTCTTA
115667 AAGAGATTGA
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
94 12 0.13
95 78 0.87
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (95 bp):
TAATAACATGAATTTTTTTTTATAAATCTTATTATATAATAAAAAAATCTAAATCCAAATAAATT
TTTTGAGATAAAAATAATTTTAATTTCTTA
Found at i:117623 original size:2 final size:2
Alignment explanation
Indices: 117616--117643 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
117606 ATTTTAGGTG
117616 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
117644 ACGCTACATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.