Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021824.1 Corchorus olitorius cultivar O-4 contig21857, 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: 83716
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:7017 original size:19 final size:18
Alignment explanation
Indices: 6993--7028 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6983 TGAAGATTTA
6993 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
7012 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
7029 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:12335 original size:18 final size:18
Alignment explanation
Indices: 12312--12348 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12302 AAAGGGTAAT
*
12312 TAAAAAAAATTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
*
12330 TAAAAAGAAGTGTTTTCA
1 TAAAAAAAAGTGTTTTCA
12348 T
1 T
12349 GATATAGGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
TAAAAAAAAGTGTTTTCA
Found at i:23611 original size:19 final size:18
Alignment explanation
Indices: 23578--23613 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
23568 TTGAGATAAT
23578 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
23596 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
23614 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:24540 original size:18 final size:18
Alignment explanation
Indices: 24517--24553 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
24507 CTCCTCTTGC
*
24517 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
*
24535 ATGAAAACAATTTTTTTT
1 ATGAAAACAATTCTTTTT
24553 A
1 A
24554 AACTACCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:29670 original size:18 final size:19
Alignment explanation
Indices: 29647--29683 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
29637 ACACCCTAGT
29647 CTAAAACTAGAAGA-AAAA
1 CTAAAACTAGAAGAGAAAA
29665 CTAAAACTAGAAGAGAAAA
1 CTAAAACTAGAAGAGAAAA
29684 ATAGATGAAG
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:0.14, T:0.11
Consensus pattern (19 bp):
CTAAAACTAGAAGAGAAAA
Found at i:34865 original size:20 final size:20
Alignment explanation
Indices: 34840--34881 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
34830 AAGTAATTTT
34840 AATTAGCAATAAATATTGAA
1 AATTAGCAATAAATATTGAA
34860 AATTAGCAATAAATATTGAA
1 AATTAGCAATAAATATTGAA
34880 AA
1 AA
34882 ATAATAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.29
Consensus pattern (20 bp):
AATTAGCAATAAATATTGAA
Found at i:43105 original size:942 final size:941
Alignment explanation
Indices: 39133--44367 Score: 8048
Period size: 942 Copynumber: 5.6 Consensus size: 941
39123 AGCGTGACCA
* * * * ** *
39133 TCTCATTCTCGGTCTCTTCCTCTGCTTTTGTTAATTGGCGCATCGAGACTAAATGTTGCTTAACA
1 TCTCATTCTCGGCCTCTTCCTCTACTTTTGTTAGTTGGCGCACCGAGGTTAAATGTTGCTTGACA
* *
39198 TAGGAATAGGTCGCAAATTTGGTGCTTTCTGAACGTGATGTGGTGGGGACCGTGGGGTTGGATGT
66 TAGGAATAGGTCGCAAATTTGGTGCTTTCTGAAAGTGATGTGGTGGGGACCGTGGGGTTGGATAT
* * *
39263 GATCTTTCTGAGCACAACGTCAAATAGTCGTATGTCGACCACCATAATTTGTTCCCCA--C--C-
131 GATCTTTCTGAGCACAACGCCAAATAGTCGTATGTCGACCACCATAAATTGCTCCCCATTCTGCT
*
39323 CAATGACCTCTTTTAATTTGAACCAATCAAAATCAAAAACAAAGATTAAGGAATCGAATGCA-TA
196 CAATGACCTCTTTTAATTTGAACCAATCAAAAACAAAAACAAAGATTAAGGAATCGAATG-AGTA
* * *
39387 ACCTAAAACAGCGACATAGAGGCAGCTAGCCGCTCTGAGTACGCTGCCTACCCAAGCGAATATTT
260 AACTAAAACGGCGACATAGACGCAGCTAGCCGCTCTGAGTACGCTGCCTACCCAAGCGAATATTT
* * *
39452 CATCATATATTAATTTTGAAAAGACCATAAAAGCGATGGCCTTAGGCAAAATTATGAGGATATTC
325 CATCATATATTAATTCTGAAAAGACCATAAAAGCGATGGCCTCAGGCGAAATTATGAGGATATTC
39517 AATATAATGTTCAATTGTGATATAAATGATCCTTTCTTCTATATATTATTTTTATGATATCAGAG
390 AATATAATGTTCAATTGTGATATAAATGATCCTTTCTTCTATATATTATTTTTATGATATCAGAG
39582 CCCAAATATATATTTTAAGCCATT-GATGCTTAGTATAGAGATTGTCAACTTTAAGCAATATTTA
455 CCCAAATATATATTTTAAGCCATTAG-TGCTTAGTATAGAGATTGTCAACTTTAAGCAATATTTA
* *
39646 TTTTATGCCGACAAAAATGATGTCGAACAATGTCATGAAAAATAAAAATACA--A-CAACAGAAG
519 TTTTATGCCGAC-AAAATGATGTCGAACAATATCATG-GAAA-AAAAATACAGCAGCAACAGAAG
* *
39708 CAATCGAGCCTGTTACATGGATAGATAGCATGTCAATCTATCCTATAAACATCGCTACAGTTTTT
581 CAATCGAGCCTGTTACATGGATAGATAGCATGTCAATCCATCCTATAAACATCGCTACAGTTATT
* *
39773 AAAACCCCAATGATATAGAGCATTCTACTGAGTATTAAAACTCCAATGGTATATTATTCATTTTT
646 AAAACCCCAATGATGTAGAGCATTCTGCTGAGTATTAAAACTCCAATGGTATATTATTCATTTTT
** *
39838 AGTATAATAATGAATAATATACCAAATCCTGATACCATGGTTGAGGATAGAGTGTACAGGGTTTC
711 TTTATAATAATGAATAATATACCAAATCCTGATGCCATGGTTGAGGATAGAGTGTACAGGGTTTC
*
39903 ATTATTATTGAAATAAAAAA-ATTAAATTTTGTACAGACTCTCCCCAAGGAAATAATGATCACAA
776 ATTATTATTAAAATAAAAAATATTAAATTTTGTACAGACTCTCCCCAAGGAAATAATGATCACAA
* * ** *
39967 CCCAAAAAGAAAAAAAGAAAAAAAAGAGAGCCATTAACGTTCGCCAAAAAAACACAGTTGCGACC
841 CCCAAAAAG------A-AAAAAAAAGACACCCATTAACGGCCGCCAAAAAAACACAGTTGC-AAC
* * * *
40032 AAACTCACATTTTTCCTTCCTTTTCATCCCAGCTCTGGTCAG-CC
898 AAACTCACATCTTCCCTGCCTTTTCATCCCAGCTCTGGT-GGCCC
*
40076 TCTCATTCTCGGCCTCTTCCTCTGCTTTTGTTAGTTGGCGCACCGAGGTTAAATGTTGCTTGACA
1 TCTCATTCTCGGCCTCTTCCTCTACTTTTGTTAGTTGGCGCACCGAGGTTAAATGTTGCTTGACA
* *
40141 TAGGAATAGATCACAAATTTGGTGCTTTCTGAAAGTGATGTGGTGGGGACCGTGGGGTTGGATAT
66 TAGGAATAGGTCGCAAATTTGGTGCTTTCTGAAAGTGATGTGGTGGGGACCGTGGGGTTGGATAT
* * * *
40206 GATCTCTCTGAGCACAATGTCAAATAGTCGTATGTCGACCACCATAAATTGCTCCCCATTCTACT
131 GATCTTTCTGAGCACAACGCCAAATAGTCGTATGTCGACCACCATAAATTGCTCCCCATTCTGCT
* *
40271 CAATGACCTC-TTTAATTTGAGCCAATCAAAAACAAAAACAAAAATTAAGGAATCGAATGAGTAA
196 CAATGACCTCTTTTAATTTGAACCAATCAAAAACAAAAACAAAGATTAAGGAATCGAATGAGTAA
* *
40335 ACTAAAACGGCGACATAGACGCAGCTAGTCGCTCTGAGTACGCTGCCTACCGAAGCGAATATTTC
261 ACTAAAACGGCGACATAGACGCAGCTAGCCGCTCTGAGTACGCTGCCTACCCAAGCGAATATTTC
* * *
40400 ATCATATATTAATTTTGAAAAGAACATAAAAGCGATGGCCTCAGGCAAAATTATGAGGATATTCA
326 ATCATATATTAATTCTGAAAAGACCATAAAAGCGATGGCCTCAGGCGAAATTATGAGGATATTCA
* * * *
40465 ATATAATGTTCAATTGTGATACAAATAATCCTTTCTTCTATATATTATTTTTATGATATCTGTGC
391 ATATAATGTTCAATTGTGATATAAATGATCCTTTCTTCTATATATTATTTTTATGATATCAGAGC
*
40530 CCAAATATATATTTTAAGCCATTAGTGCTTAGTATAGAGATTGTCGACTTTAAGCAATATTTATT
456 CCAAATATATATTTTAAGCCATTAGTGCTTAGTATAGAGATTGTCAACTTTAAGCAATATTTATT
* * ** *
40595 CTCTGCCGACAAAATGATGTCGAACAATATCGGGGAAAAAAAATACAGCAGCAACAGAAGCAATT
521 TTATGCCGACAAAATGATGTCGAACAATATCATGGAAAAAAAATACAGCAGCAACAGAAGCAATC
* *
40660 GAGCCTATTACATGGATAGATAGCATGTCAATCCATCCTATAAACATCGCTTCAGTTATTAAAAC
586 GAGCCTGTTACATGGATAGATAGCATGTCAATCCATCCTATAAACATCGCTACAGTTATTAAAAC
*
40725 CCCAATGATGTAGAACATTCTGCTGAGTATTAAAACTCCAATGGTATATTATTCA-TTTTTTTAT
651 CCCAATGATGTAGAGCATTCTGCTGAGTATTAAAACTCCAATGGTATATTATTCATTTTTTTTAT
* * * *
40789 AGTAATGAATCATATACAAAATCCTGATGCCATGGTTGAGGAT-GCAGTGTACAGGGATTCATTA
716 AATAATGAATAATATACCAAATCCTGATGCCATGGTTGAGGATAG-AGTGTACAGGGTTTCATTA
* *
40853 TTATTAAAAT-AAAAATATTAAATTTTGTACAGACTTTCCCCAAGGAAATAATGATCACAACCTA
780 TTATTAAAATAAAAAATATTAAATTTTGTACAGACTCTCCCCAAGGAAATAATGATCACAACCCA
* *
40917 AAAAGAAAAAAAAAGACAGCCATTAACGGCCGCCAAAAAAATACAGTTGCAACAAACATCACATC
845 AAAAGAAAAAAAAAGACACCCATTAACGGCCGCCAAAAAAACACAGTTGCAACAAAC-TCACATC
**
40982 TTCCAGGCCTTTTCATCCCCAGCTCTGGTGGCCC
909 TTCCCTGCCTTTTCAT-CCCAGCTCTGGTGGCCC
*
41016 TCTCATTCTCGGCCTCTTCCTCTAATTTTGTTAGTTGGCGCACCGAGGTTAAATGTTGCTTGACA
1 TCTCATTCTCGGCCTCTTCCTCTACTTTTGTTAGTTGGCGCACCGAGGTTAAATGTTGCTTGACA
* *
41081 TAGGAATAGGTCGCAAATTTGGTGTTTTCTGAAAGTGATGTGATGGGGACCGTGGGGTTGGATAT
66 TAGGAATAGGTCGCAAATTTGGTGCTTTCTGAAAGTGATGTGGTGGGGACCGTGGGGTTGGATAT
* *
41146 GATCTTTCTGAGTACAACGCCAAATAGTCGAATGTCGACCACCATAAATTGCTCCCCATTCTGCT
131 GATCTTTCTGAGCACAACGCCAAATAGTCGTATGTCGACCACCATAAATTGCTCCCCATTCTGCT
41211 CAATGACCTCTTTTAATTTGAACCAATCAAAAACAAAAACAAAGATTAAGGAATCGAATGAGTAA
196 CAATGACCTCTTTTAATTTGAACCAATCAAAAACAAAAACAAAGATTAAGGAATCGAATGAGTAA
* *
41276 ACTAAAACGGCGACATAGACGTAGCTAGCCGCTCTGAGTACGCTGCCTACCCAAGCGAATATTTG
261 ACTAAAACGGCGACATAGACGCAGCTAGCCGCTCTGAGTACGCTGCCTACCCAAGCGAATATTTC
* *
41341 ATCAGATATTAATTCTGAAAAGACCATAAAAGCGATGGCCTCAGGCGAAATTATGTGGATATTCA
326 ATCATATATTAATTCTGAAAAGACCATAAAAGCGATGGCCTCAGGCGAAATTATGAGGATATTCA
* *
41406 ATATAATGTTTAATTGTGATATAAATGATCCTTTCTTCTATATATTATTTTTATGATAT-ATGTG
391 ATATAATGTTCAATTGTGATATAAATGATCCTTTCTTCTATATATTATTTTTATGATATCA-GAG
* *
41470 CCCAAATATATATTTTAAGCCATTAGTGCTTAGTATAAAGATTGTCGACTTTAAGCAATATTTAT
455 CCCAAATATATATTTTAAGCCATTAGTGCTTAGTATAGAGATTGTCAACTTTAAGCAATATTTAT
*
41535 TTTATGCCGACAAAATGATGTCGAACAATATCATGGAAAAAAAAATACAGCAGCAACAGAAGAAA
520 TTTATGCCGACAAAATGATGTCGAACAATATCATGG-AAAAAAAATACAGCAGCAACAGAAGCAA
* * * *
41600 TTGAGCATGTTACATGGATAGATACCATGTCAATCCATCCTATAAACATCGCTAAAGTTATTAAA
584 TCGAGCCTGTTACATGGATAGATAGCATGTCAATCCATCCTATAAACATCGCTACAGTTATTAAA
*
41665 ACCCCAATGATGTAGTGCATTCTGCTGAGTATTAAAACTCCAATGGTATATTATTCATTTTTTTT
649 ACCCCAATGATGTAGAGCATTCTGCTGAGTATTAAAACTCCAATGGTATATTATTCATTTTTTTT
* * *
41730 ATAATAATGAATAATATACCAAATTCTGATGCCATGGTTGAGGATAGAATGTACAGGGTTTCCTT
714 ATAATAATGAATAATATACCAAATCCTGATGCCATGGTTGAGGATAGAGTGTACAGGGTTTCATT
* * *
41795 ATTATTAAAATAAAAAATACTAAATTTTGTAAAGACTCTCCCCAAGAAAATAATGATCACAACCC
779 ATTATTAAAATAAAAAATATTAAATTTTGTACAGACTCTCCCCAAGGAAATAATGATCACAACCC
* *
41860 AAAAAGGAAAAAAAAAGACACCAATTAACGGCTGCC-AAAAAACACAGTTGCAACAAACCTCACA
844 AAAAA-GAAAAAAAAAGACACCCATTAACGGCCGCCAAAAAAACACAGTTGCAACAAA-CTCACA
* * *
41924 TCTTCCCTGCCTTTTCATCCAAAGCTCTGGTGGACT
907 TCTTCCCTGCCTTTTCATCC-CAGCTCTGGTGGCCC
* * * * *
41960 TCTCATTCTCGGCTTTTTGCTCTACTTTTGTTAGTTGGCGCACCGAGGTTAAATGTAGCTTGACT
1 TCTCATTCTCGGCCTCTTCCTCTACTTTTGTTAGTTGGCGCACCGAGGTTAAATGTTGCTTGACA
* * *
42025 TATGAGTAGGTCGCATATTTGGTGCTTTCTGAAAGTGATGTGGTGGGGACCGTGGGGTTGGATAT
66 TAGGAATAGGTCGCAAATTTGGTGCTTTCTGAAAGTGATGTGGTGGGGACCGTGGGGTTGGATAT
** * * **
42090 GATCTTTCTGAGCACAACAACAAATAGTCGCATGTCAACCACCATAAATTGCTCCCGGTTCTGCT
131 GATCTTTCTGAGCACAACGCCAAATAGTCGTATGTCGACCACCATAAATTGCTCCCCATTCTGCT
* * * *
42155 CAATGACCTCTTTTAATTTGAACCAATTAAAAAGAAGAACAAAGATTAAGGAATCGAATGACTAA
196 CAATGACCTCTTTTAATTTGAACCAATCAAAAACAAAAACAAAGATTAAGGAATCGAATGAGTAA
* * * * * *
42220 ACAAAAACAGAGACATAGACGTAGCTAGCCGCTCTAAGTACGCTCCCTACCCAAGCGAATATTTC
261 ACTAAAACGGCGACATAGACGCAGCTAGCCGCTCTGAGTACGCTGCCTACCCAAGCGAATATTTC
* **
42285 ATCATATATTAATTCTGAAAAGAACATAAAAGCGATGGCCTCATACGAAATTATGAGGATATTCA
326 ATCATATATTAATTCTGAAAAGACCATAAAAGCGATGGCCTCAGGCGAAATTATGAGGATATTCA
* * *
42350 ATATAATGTTCAATTGTAATTTAAATGATCCTTTCTTCTACATATTATTTTTATGATATCAGAGC
391 ATATAATGTTCAATTGTGATATAAATGATCCTTTCTTCTATATATTATTTTTATGATATCAGAGC
* * * * *
42415 CCATATATATATTTTAAGCTATTAGTGCTTAATATAGAGATTGTCAACTTTAACCAATATTCATT
456 CCAAATATATATTTTAAGCCATTAGTGCTTAGTATAGAGATTGTCAACTTTAAGCAATATTTATT
* *
42480 TTATGCCGACAAAATGATGTCGAACAATATCGTGGAAAAAAAATACAGCAGGAACAGAAGCAATC
521 TTATGCCGACAAAATGATGTCGAACAATATCATGGAAAAAAAATACAGCAGCAACAGAAGCAATC
* * *
42545 GAGCTTGTTACATGGATAGATAACATGTCAATCCATCCTATAAACATCGCTAAAGTTATTAAAAC
586 GAGCCTGTTACATGGATAGATAGCATGTCAATCCATCCTATAAACATCGCTACAGTTATTAAAAC
* * *
42610 CCTAATGATGTAGAGTATTCTGCTGAGTATTAAAACTACAATGGTATATTATTCATTTTTTTTAT
651 CCCAATGATGTAGAGCATTCTGCTGAGTATTAAAACTCCAATGGTATATTATTCATTTTTTTTAT
* *
42675 AATAATGAATAATATACCAAATCCTGATGCCATGGTTGAGGATAGAGTGTAAAGGATTTCATTAT
716 AATAATGAATAATATACCAAATCCTGATGCCATGGTTGAGGATAGAGTGTACAGGGTTTCATTAT
* * **
42740 TATT-AAATAAAAAATACTAAATTTTGTAAAGACTCTTTCCAAGGAAATAATGATCACAACCCAA
781 TATTAAAATAAAAAATATTAAATTTTGTACAGACTCTCCCCAAGGAAATAATGATCACAACCCAA
*
42804 AAAGAAAAAAAAAGTCACCCATTAACGGCCGCCAAAAAAACACAGTTGCAACAAAGCTCACATCT
846 AAAGAAAAAAAAAGACACCCATTAACGGCCGCCAAAAAAACACAGTTGCAACAAA-CTCACATCT
*
42869 TCCCTACCTTTTCATGCCCAGCTCTGGTGGCCC
910 TCCCTGCCTTTTCAT-CCCAGCTCTGGTGGCCC
**
42902 TCTCATTCTCGGCCTCTTCCTCTACTTTTGTTAGTTGGCATACCGAGGTTAAATGTTGCTTGACA
1 TCTCATTCTCGGCCTCTTCCTCTACTTTTGTTAGTTGGCGCACCGAGGTTAAATGTTGCTTGACA
* *
42967 TAGGAATAGGTCGCATATTTGGTGCTTTCTGAAAGTGATCTGGTGGGGACCGTGGGGTTGGATAT
66 TAGGAATAGGTCGCAAATTTGGTGCTTTCTGAAAGTGATGTGGTGGGGACCGTGGGGTTGGATAT
*
43032 GATCTTTCTGAGCACAACGCCAAATAGTCGTATGTCGACCACCATAAATTGCTCCCCATTCTACT
131 GATCTTTCTGAGCACAACGCCAAATAGTCGTATGTCGACCACCATAAATTGCTCCCCATTCTGCT
*
43097 CAATGACCTCTTTTAATTTGAATCAATCAAAAACAAAAACAAAGATTAAGGAATCGAATGAGTAA
196 CAATGACCTCTTTTAATTTGAACCAATCAAAAACAAAAACAAAGATTAAGGAATCGAATGAGTAA
* * * *
43162 CCTAAACCTGCGACATAGACGCAGCTAGCCGCTCTGAGTACGCTGCCTACTCAAGCGAATATTTC
261 ACTAAAACGGCGACATAGACGCAGCTAGCCGCTCTGAGTACGCTGCCTACCCAAGCGAATATTTC
* * * * * *
43227 ATCATATATCAATTCTGAAAAGACCATAAAAGCGATGGCCTTAAGTGAAATTATTAAGATATTCA
326 ATCATATATTAATTCTGAAAAGACCATAAAAGCGATGGCCTCAGGCGAAATTATGAGGATATTCA
43292 ATATAATGTTCAATTGTGATATAAATGATCCTTTCTTCTATATATTATTTTTATGATATCAGAGC
391 ATATAATGTTCAATTGTGATATAAATGATCCTTTCTTCTATATATTATTTTTATGATATCAGAGC
* *
43357 CCAAATATATATTTTAAGCCATTAGTGCTTAGTATATAGATTGTCAACTTTAAGCAATATTTACT
456 CCAAATATATATTTTAAGCCATTAGTGCTTAGTATAGAGATTGTCAACTTTAAGCAATATTTATT
43422 TTATGCCGACAAAATGATGTCGAACAATATCATGGTAAAAAAAATACAGCAGCAACAGAAGCAAT
521 TTATGCCGACAAAATGATGTCGAACAATATCATGG-AAAAAAAATACAGCAGCAACAGAAGCAAT
* * *
43487 CGAGTCTGTTACATGGATAGATATCATGTCAATCCACCCTATAAACATCGCTACAGTTATTAAAA
585 CGAGCCTGTTACATGGATAGATAGCATGTCAATCCATCCTATAAACATCGCTACAGTTATTAAAA
* * * *** **
43552 CCCCAATGATATAGAGCATTTTGCTGAGTATTAAAACTCTAATAAAAAATATTATTCATTTTTCA
650 CCCCAATGATGTAGAGCATTCTGCTGAGTATTAAAACTCCAAT--GGTATATTATTCATTTTTTT
** * *
43617 TATAATAATGAATAATATACCAAATTATGATGCCATGGTTGATGATGGAGTGTACAGGGTTTCAT
713 TATAATAATGAATAATATACCAAATCCTGATGCCATGGTTGAGGATAGAGTGTACAGGGTTTCAT
* * *
43682 TATTATTAAAATAAAAAAAATTAAATTTTCTACAGACTCTCTCCAAGGAAATAATGATCACAACC
778 TATTATTAAAATAAAAAATATTAAATTTTGTACAGACTCTCCCCAAGGAAATAATGATCACAACC
* ** *
43747 CAAAAAGAAAAAAAAA-ACAACCATTAACGGCCGCCAAAAAAACACAACTGCAACCAAACTCGCA
843 CAAAAAGAAAAAAAAAGACACCCATTAACGGCCGCCAAAAAAACACAGTTGCAA-CAAACTCACA
* *
43811 TCTTCCTTGCCTTTTCATCCCCAGCTCTGGTGGGCC
907 TCTTCCCTGCCTTTTCAT-CCCAGCTCTGGTGGCCC
* * * *
43847 TCTCATTCTCGACAT-TCTCCTCTGCTTTTGTTAGTTGGCGCACCGAGGTTAATTGTTGCTTGAC
1 TCTCATTCTCGGCCTCT-TCCTCTACTTTTGTTAGTTGGCGCACCGAGGTTAAATGTTGCTTGAC
* *
43911 ATAGGAATAGGTCGCAAATTTGGTGCTTTCTGAAAGCGATATGGTGGGGACCGTGGGGTTGGATA
65 ATAGGAATAGGTCGCAAATTTGGTGCTTTCTGAAAGTGATGTGGTGGGGACCGTGGGGTTGGATA
* * **
43976 TGATCTTTCTGAGCTCAACGCCAAAAAGTTATATGTCGACCACCATAAATTGCTCCCCATTCTGC
130 TGATCTTTCTGAGCACAACGCCAAATAGTCGTATGTCGACCACCATAAATTGCTCCCCATTCTGC
* *
44041 TCAATGACCTCTTTTAATTTGAACTAATAAAAAACAAAAACAAAGATTAAGGAATCGAATGAGTA
195 TCAATGACCTCTTTTAATTTGAACCAATCAAAAACAAAAACAAAGATTAAGGAATCGAATGAGTA
* * *
44106 AACTAAATCGGTGACATAGACAG-AGCCAGCCGCTCTGAGTACGCTGCCTACCCAAGCGAATATT
260 AACTAAAACGGCGACATAGAC-GCAGCTAGCCGCTCTGAGTACGCTGCCTACCCAAGCGAATATT
* *
44170 TTATCATATATTAATTCTGAAAAGATCATAAAAGCGATGGCCTCAGGCGAAATTATGAGGATATT
324 TCATCATATATTAATTCTGAAAAGACCATAAAAGCGATGGCCTCAGGCGAAATTATGAGGATATT
* * *
44235 CAATATAATGTTCAATTGTGATATAAATGATCCTTTTTTCTATATATTATTTTAATGATATTAGA
389 CAATATAATGTTCAATTGTGATATAAATGATCCTTTCTTCTATATATTATTTTTATGATATCAGA
* * *
44300 TCCCAAATATATATTTTAAGCCATTGGTGCTTTGTATAGAGATTGTCAACTTTAAGCAATATTTA
454 GCCCAAATATATATTTTAAGCCATTAGTGCTTAGTATAGAGATTGTCAACTTTAAGCAATATTTA
44365 TTT
519 TTT
44368 AGAATTCATA
Statistics
Matches: 3936, Mismatches: 322, Indels: 66
0.91 0.07 0.02
Matches are distributed among these distances:
938 6 0.00
939 59 0.01
940 208 0.05
941 355 0.09
942 763 0.19
943 592 0.15
944 624 0.16
945 668 0.17
946 220 0.06
947 430 0.11
948 11 0.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (941 bp):
TCTCATTCTCGGCCTCTTCCTCTACTTTTGTTAGTTGGCGCACCGAGGTTAAATGTTGCTTGACA
TAGGAATAGGTCGCAAATTTGGTGCTTTCTGAAAGTGATGTGGTGGGGACCGTGGGGTTGGATAT
GATCTTTCTGAGCACAACGCCAAATAGTCGTATGTCGACCACCATAAATTGCTCCCCATTCTGCT
CAATGACCTCTTTTAATTTGAACCAATCAAAAACAAAAACAAAGATTAAGGAATCGAATGAGTAA
ACTAAAACGGCGACATAGACGCAGCTAGCCGCTCTGAGTACGCTGCCTACCCAAGCGAATATTTC
ATCATATATTAATTCTGAAAAGACCATAAAAGCGATGGCCTCAGGCGAAATTATGAGGATATTCA
ATATAATGTTCAATTGTGATATAAATGATCCTTTCTTCTATATATTATTTTTATGATATCAGAGC
CCAAATATATATTTTAAGCCATTAGTGCTTAGTATAGAGATTGTCAACTTTAAGCAATATTTATT
TTATGCCGACAAAATGATGTCGAACAATATCATGGAAAAAAAATACAGCAGCAACAGAAGCAATC
GAGCCTGTTACATGGATAGATAGCATGTCAATCCATCCTATAAACATCGCTACAGTTATTAAAAC
CCCAATGATGTAGAGCATTCTGCTGAGTATTAAAACTCCAATGGTATATTATTCATTTTTTTTAT
AATAATGAATAATATACCAAATCCTGATGCCATGGTTGAGGATAGAGTGTACAGGGTTTCATTAT
TATTAAAATAAAAAATATTAAATTTTGTACAGACTCTCCCCAAGGAAATAATGATCACAACCCAA
AAAGAAAAAAAAAGACACCCATTAACGGCCGCCAAAAAAACACAGTTGCAACAAACTCACATCTT
CCCTGCCTTTTCATCCCAGCTCTGGTGGCCC
Found at i:45116 original size:21 final size:21
Alignment explanation
Indices: 45075--45117 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
45065 TCTGCTATGC
*
45075 AACTTGAATCTGCTATGTCTG
1 AACTTGAATCTGCTATATCTG
* *
45096 AACTTGATTCTGCTGTATCTG
1 AACTTGAATCTGCTATATCTG
45117 A
1 A
45118 TTTACCTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (21 bp):
AACTTGAATCTGCTATATCTG
Found at i:46125 original size:23 final size:23
Alignment explanation
Indices: 46105--46245 Score: 148
Period size: 23 Copynumber: 6.1 Consensus size: 23
46095 CCAAGGCCGG
46105 GTGCCGAGTCCAAGGGTGGCCAA
1 GTGCCGAGTCCAAGGGTGGCCAA
46128 GTGCC-A-TCGCCAAGGGTGGCCAA
1 GTGCCGAGT--CCAAGGGTGGCCAA
* *
46151 GTCCCGTCG-CCAAGGGTGGCCAA
1 GTGCCG-AGTCCAAGGGTGGCCAA
*
46174 GTGCCGAGTCCAAGAGTGGCCAA
1 GTGCCGAGTCCAAGGGTGGCCAA
* **
46197 GTGTC-A-TCACCATTGGTGGCCAA
1 GTGCCGAGT--CCAAGGGTGGCCAA
46220 GTGCCGAGTCCAAGGGTGGCCAA
1 GTGCCGAGTCCAAGGGTGGCCAA
46243 GTG
1 GTG
46246 TAATCTGAAT
Statistics
Matches: 96, Mismatches: 12, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
21 2 0.02
22 3 0.03
23 89 0.93
24 1 0.01
25 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.35, T:0.16
Consensus pattern (23 bp):
GTGCCGAGTCCAAGGGTGGCCAA
Found at i:46187 original size:69 final size:69
Alignment explanation
Indices: 46105--46245 Score: 203
Period size: 69 Copynumber: 2.0 Consensus size: 69
46095 CCAAGGCCGG
* * *
46105 GTGCCGAGTCCAAGGGTGGCCAAGTGCCATCGCCAAGGGTGGCCAAGTCCCGTCG-CCAAGGGTG
1 GTGCCGAGTCCAAGAGTGGCCAAGTGCCATCACCAAGGGTGGCCAAGTCCCG-AGTCCAAGGGTG
46169 GCCAA
65 GCCAA
* ** *
46174 GTGCCGAGTCCAAGAGTGGCCAAGTGTCATCACCATTGGTGGCCAAGTGCCGAGTCCAAGGGTGG
1 GTGCCGAGTCCAAGAGTGGCCAAGTGCCATCACCAAGGGTGGCCAAGTCCCGAGTCCAAGGGTGG
46239 CCAA
66 CCAA
46243 GTG
1 GTG
46246 TAATCTGAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
68 1 0.02
69 63 0.98
ACGTcount: A:0.21, C:0.28, G:0.35, T:0.16
Consensus pattern (69 bp):
GTGCCGAGTCCAAGAGTGGCCAAGTGCCATCACCAAGGGTGGCCAAGTCCCGAGTCCAAGGGTGG
CCAA
Found at i:46245 original size:46 final size:46
Alignment explanation
Indices: 46114--46246 Score: 171
Period size: 46 Copynumber: 2.9 Consensus size: 46
46104 GGTGCCGAGT
** * *
46114 CCAAGGGTGGCCAAGTGCC-A-TCGCCAAGGGTGGCCAAGTCCCGTCG
1 CCAAGGGTGGCCAAGTGCCGAGT--CCAAGGGTGGCCAAGTGTCATCA
*
46160 CCAAGGGTGGCCAAGTGCCGAGTCCAAGAGTGGCCAAGTGTCATCA
1 CCAAGGGTGGCCAAGTGCCGAGTCCAAGGGTGGCCAAGTGTCATCA
**
46206 CCATTGGTGGCCAAGTGCCGAGTCCAAGGGTGGCCAAGTGT
1 CCAAGGGTGGCCAAGTGCCGAGTCCAAGGGTGGCCAAGTGT
46247 AATCTGAATT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
46 75 0.97
47 1 0.01
48 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.35, T:0.16
Consensus pattern (46 bp):
CCAAGGGTGGCCAAGTGCCGAGTCCAAGGGTGGCCAAGTGTCATCA
Found at i:55757 original size:57 final size:56
Alignment explanation
Indices: 55662--55869 Score: 171
Period size: 57 Copynumber: 3.8 Consensus size: 56
55652 TCTTCCTACG
* * * * * *
55662 TATTATTAGATGAGTCTGTCCCTAGTCCCGGGGAAGGCAATGCCCTTAGTCACGGTA
1 TATTATTACAAGAGTCCGTCCCGAGTCCAGGAGAAGGCAATGCCCTTAGTCACGG-A
*
55719 TATTATTACAAGAGTCCGTCCCGAGTCCAGGAGCAGGCAATGCCC---G-CA---A
1 TATTATTACAAGAGTCCGTCCCGAGTCCAGGAGAAGGCAATGCCCTTAGTCACGGA
* * * * * *
55768 -ATTATTAGATGAGTCTGTCCCAAGTCCTGGGGAAGGCAATGCCCTTAGTCACGGCA
1 TATTATTACAAGAGTCCGTCCCGAGTCCAGGAGAAGGCAATGCCCTTAGTCACGG-A
* * *
55824 GATTATTACAACAAGAGTCCGTCCCGAGTCGAGGAGCAGGCAATGC
1 TATTATT---ACAAGAGTCCGTCCCGAGTCCAGGAGAAGGCAATGC
55870 TCGCAAATTA
Statistics
Matches: 117, Mismatches: 22, Indels: 21
0.73 0.14 0.13
Matches are distributed among these distances:
48 37 0.32
49 1 0.01
51 1 0.01
52 2 0.02
53 2 0.02
54 1 0.01
56 1 0.01
57 44 0.38
60 28 0.24
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (56 bp):
TATTATTACAAGAGTCCGTCCCGAGTCCAGGAGAAGGCAATGCCCTTAGTCACGGA
Found at i:55773 original size:48 final size:48
Alignment explanation
Indices: 55720--55917 Score: 162
Period size: 48 Copynumber: 3.9 Consensus size: 48
55710 GTCACGGTAT
*
55720 ATTATTACAAGAGTCCGTCCCGAGTCCAGGAGCAGGCAATGCCCGCAA
1 ATTATTACAAGAGTCCGTCCCAAGTCCAGGAGCAGGCAATGCCCGCAA
* * * * * *
55768 ATTATTAGATGAGTCTGTCCCAAGTCCTGGGGAAGGCAATGCCCTTAGTCACGGCA
1 ATTATTACAAGAGTCCGTCCCAAGTCCAGGAGCAGGCAATGCCC---G-CA----A
* * *
55824 GATTATTACAACAAGAGTCCGTCCCGAGTCGAGGAGCAGGCAATGCTCGCAA
1 -ATTATT---ACAAGAGTCCGTCCCAAGTCCAGGAGCAGGCAATGCCCGCAA
* * * *
55876 ATTATTAGATGAGTCTGTCCCAAGTCCAGGAACAGGCAATGC
1 ATTATTACAAGAGTCCGTCCCAAGTCCAGGAGCAGGCAATGC
55918 TATTCGTCAT
Statistics
Matches: 116, Mismatches: 22, Indels: 24
0.72 0.14 0.15
Matches are distributed among these distances:
48 67 0.58
51 7 0.06
52 3 0.03
56 3 0.03
57 7 0.06
60 29 0.25
ACGTcount: A:0.29, C:0.25, G:0.26, T:0.21
Consensus pattern (48 bp):
ATTATTACAAGAGTCCGTCCCAAGTCCAGGAGCAGGCAATGCCCGCAA
Found at i:55867 original size:108 final size:105
Alignment explanation
Indices: 55663--55902 Score: 399
Period size: 108 Copynumber: 2.3 Consensus size: 105
55653 CTTCCTACGT
* * *
55663 ATTATTAGATGAGTCTGTCCCTAGTCCCGGGGAAGGCAATGCCCTTAGTCACGGTATATTATTAC
1 ATTATTAGATGAGTCTGTCCCAAGTCCCGGGGAAGGCAATGCCCTTAGTCACGGCAGATTATTAC
55728 AAGAGTCCGTCCCGAGTCCAGGAGCAGGCAATGCCCGCAA
66 AAGAGTCCGTCCCGAGTCCAGGAGCAGGCAATGCCCGCAA
*
55768 ATTATTAGATGAGTCTGTCCCAAGTCCTGGGGAAGGCAATGCCCTTAGTCACGGCAGATTATTAC
1 ATTATTAGATGAGTCTGTCCCAAGTCCCGGGGAAGGCAATGCCCTTAGTCACGGCAGATTATT--
* *
55833 AACAAGAGTCCGTCCCGAGTCGAGGAGCAGGCAATGCTCGCAA
64 -ACAAGAGTCCGTCCCGAGTCCAGGAGCAGGCAATGCCCGCAA
55876 ATTATTAGATGAGTCTGTCCCAAGTCC
1 ATTATTAGATGAGTCTGTCCCAAGTCC
55903 AGGAACAGGC
Statistics
Matches: 126, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
105 59 0.47
108 67 0.53
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (105 bp):
ATTATTAGATGAGTCTGTCCCAAGTCCCGGGGAAGGCAATGCCCTTAGTCACGGCAGATTATTAC
AAGAGTCCGTCCCGAGTCCAGGAGCAGGCAATGCCCGCAA
Found at i:55937 original size:108 final size:105
Alignment explanation
Indices: 55663--55939 Score: 394
Period size: 108 Copynumber: 2.6 Consensus size: 105
55653 CTTCCTACGT
* * *
55663 ATTATTAGATGAGTCTGTCCCTAGTCCCGGGGAAGGCAATGCCCTTAGTCACGGTATATTATT-A
1 ATTATTAGATGAGTCTGTCCCAAGT-CCGGGGAAGGCAATGCCCTTAGTCACGGCAAATTATTAA
55727 CAAGAGTCCGTCCCGAGTCCAGGAGCAGGCAATGCCCGCAA
65 CAAGAGTCCGTCCCGAGTCCAGGAGCAGGCAATGCCCGCAA
*
55768 ATTATTAGATGAGTCTGTCCCAAGTCCTGGGGAAGGCAATGCCCTTAGTCACGGCAGATTATTAC
1 ATTATTAGATGAGTCTGTCCCAAGTCC-GGGGAAGGCAATGCCCTTAGTCACGGCAAATTATT--
* *
55833 AACAAGAGTCCGTCCCGAGTCGAGGAGCAGGCAATGCTCGCAA
63 AACAAGAGTCCGTCCCGAGTCCAGGAGCAGGCAATGCCCGCAA
* * ** * *
55876 ATTATTAGATGAGTCTGTCCCAAGTCCAGGAACAGGCAATGCTATTCGTCATGGCAAATTATTA
1 ATTATTAGATGAGTCTGTCCCAAGTCCGGGGA-AGGCAATGCCCTTAGTCACGGCAAATTATTA
55940 GCCTTGTCTG
Statistics
Matches: 155, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
104 2 0.01
105 57 0.37
106 1 0.01
107 3 0.02
108 92 0.59
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (105 bp):
ATTATTAGATGAGTCTGTCCCAAGTCCGGGGAAGGCAATGCCCTTAGTCACGGCAAATTATTAAC
AAGAGTCCGTCCCGAGTCCAGGAGCAGGCAATGCCCGCAA
Found at i:59647 original size:50 final size:50
Alignment explanation
Indices: 59560--59666 Score: 121
Period size: 50 Copynumber: 2.2 Consensus size: 50
59550 GTTCTTCATA
** *
59560 TTTT-TCTTGTTCAGATCTTGTCTCAGGACACCCAAACACTCTTTTAGTG
1 TTTTCTCTTGTTCAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTG
* * * *
59609 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATAAAAACACTGTATTCGTG
1 TTTTCTCTTG-TTCAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTG
59659 -TTTCTCTT
1 TTTTCTCTT
59667 TCCGAAATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
49 12 0.24
50 33 0.67
51 4 0.08
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.44
Consensus pattern (50 bp):
TTTTCTCTTGTTCAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTG
Found at i:65602 original size:51 final size:50
Alignment explanation
Indices: 65501--65603 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 50
65491 GTTCTTCATA
* *
65501 TTTTTCTTGTTCAGATCTTGTCTCAGGACACTCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTCAGATCTTGTCTCAGGACACTAAAACACTCTATTAGTGT
* * *
65551 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACA-TAAAAACACTGTATTCGTGT
1 TTTT-TCTTG-TTCAGATCTTGTCTCAGGACACT-AAAACACTCTATTAGTGT
65602 TT
1 TT
65604 CTCTTTCAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
50 5 0.11
51 36 0.80
52 4 0.09
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (50 bp):
TTTTTCTTGTTCAGATCTTGTCTCAGGACACTAAAACACTCTATTAGTGT
Found at i:67701 original size:49 final size:48
Alignment explanation
Indices: 67625--67755 Score: 169
Period size: 49 Copynumber: 2.7 Consensus size: 48
67615 GAGCGTGCCA
*
67625 ATCAATTTTGTC-AAAAAATTGATAAAAAGTGCAA-TAAAAAGTAAAAG
1 ATCAATTTTGTCTAAAAAATTGAGAAAAAGTGCAAGTAAAAA-TAAAAG
*
67672 ATCAATTTTGTCTTAAAAAATTGAGAAAAAGGGGCAAGTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAAATTGAGAAAAA-GTGCAAGTAAAAATAAAAG
* *
67722 TTCAATTTTGTAGT-AAAAATTGAGAAAAAGTGCA
1 ATCAATTTTGT-CTAAAAAATTGAGAAAAAGTGCA
67756 GGAAAAGTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
47 12 0.16
48 4 0.05
49 30 0.41
50 22 0.30
51 6 0.08
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (48 bp):
ATCAATTTTGTCTAAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
Found at i:69051 original size:9 final size:9
Alignment explanation
Indices: 69031--69059 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
69021 TTAATTTCTT
69031 TAATTTCC-
1 TAATTTCCA
69039 TAATTTCCA
1 TAATTTCCA
69048 TAATTTCCA
1 TAATTTCCA
69057 TAA
1 TAA
69060 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:70389 original size:15 final size:15
Alignment explanation
Indices: 70369--70446 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
70359 AGCAAACACT
70369 TTCGGTGCCATCATC
1 TTCGGTGCCATCATC
* *
70384 TTCGGTGCCGTCGA-A
1 TTCGGTGCCATC-ATC
*
70399 TTGGGTGCCATCATC
1 TTCGGTGCCATCATC
* *
70414 TTCGGTGCCGTTGAT-
1 TTCGGTGCC-ATCATC
*
70429 TTTGGTGCCATCATC
1 TTCGGTGCCATCATC
70444 TTC
1 TTC
70447 TTCCATGACA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 4 0.09
15 39 0.83
16 4 0.09
ACGTcount: A:0.12, C:0.27, G:0.26, T:0.36
Consensus pattern (15 bp):
TTCGGTGCCATCATC
Found at i:70408 original size:30 final size:30
Alignment explanation
Indices: 70372--70446 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
70362 AAACACTTTC
70372 GGTGCCATCATCTTCGGTGCCGTCGAATTG
1 GGTGCCATCATCTTCGGTGCCGTCGAATTG
* * *
70402 GGTGCCATCATCTTCGGTGCCGTTGATTTT
1 GGTGCCATCATCTTCGGTGCCGTCGAATTG
70432 GGTGCCATCATCTTC
1 GGTGCCATCATCTTC
70447 TTCCATGACA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.12, C:0.27, G:0.27, T:0.35
Consensus pattern (30 bp):
GGTGCCATCATCTTCGGTGCCGTCGAATTG
Found at i:71699 original size:18 final size:18
Alignment explanation
Indices: 71674--71759 Score: 118
Period size: 18 Copynumber: 4.8 Consensus size: 18
71664 GTGTGACAAT
71674 TTGGTGCGGTGCGACCAC
1 TTGGTGCGGTGCGACCAC
*
71692 TGGGTGCGGTGCGACCAC
1 TTGGTGCGGTGCGACCAC
* *
71710 TTGGTGTGGTGCGACCAT
1 TTGGTGCGGTGCGACCAC
* **
71728 TTGGTGTGGTGCGAATAC
1 TTGGTGCGGTGCGACCAC
71746 TTGGTGCGGTGCGA
1 TTGGTGCGGTGCGA
71760 TTTGTTGTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.12, C:0.20, G:0.42, T:0.27
Consensus pattern (18 bp):
TTGGTGCGGTGCGACCAC
Found at i:72530 original size:49 final size:49
Alignment explanation
Indices: 72466--72594 Score: 156
Period size: 49 Copynumber: 2.7 Consensus size: 49
72456 TAATTTTGCC
** **
72466 AAAAAATTGTTAAAAAGTGCAA-TAAAAAGTAAAAGATCAATTTTGTCTT
1 AAAAAATTGAGAAAAAGTGCAAGT-AAAAGTAAAAGATCAATTTTGTAGT
* *
72515 AAAAAATTGAGAAAAAGGTGCAAGTAAAATTAAAAGTTCAATTTTGTAGT
1 AAAAAATTGAGAAAAA-GTGCAAGTAAAAGTAAAAGATCAATTTTGTAGT
*
72565 -AAAAATTGAGAAAAAGTGC-AGGAAAAGTAA
1 AAAAAATTGAGAAAAAGTGCAAGTAAAAGTAA
72595 GGATTGCTTG
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
47 9 0.13
48 4 0.06
49 29 0.41
50 27 0.39
51 1 0.01
ACGTcount: A:0.53, C:0.05, G:0.17, T:0.26
Consensus pattern (49 bp):
AAAAAATTGAGAAAAAGTGCAAGTAAAAGTAAAAGATCAATTTTGTAGT
Found at i:73879 original size:9 final size:9
Alignment explanation
Indices: 73859--73887 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
73849 TTAATATCTT
73859 TAATTTCC-
1 TAATTTCCA
73867 TAATTTCCA
1 TAATTTCCA
73876 TAATTTCCA
1 TAATTTCCA
73885 TAA
1 TAA
73888 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:74095 original size:2 final size:2
Alignment explanation
Indices: 74088--74120 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
74078 GTATACATTC
*
74088 AT AT AT AT AT AT AT AT AT TT 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
74121 AAGGGCTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:74733 original size:2 final size:2
Alignment explanation
Indices: 74697--74725 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
74687 CACAAACAGA
74697 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 A
74726 GCTATATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76753 original size:21 final size:21
Alignment explanation
Indices: 76727--76839 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
76717 TGCTAGAAGT
76727 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
76748 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
76769 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
76790 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
76811 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
76832 TCATTGGA
1 TCATTGGA
76840 AATGCCTAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
20 1 0.01
21 84 0.99
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Done.