Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000358.1 Hibiscus syriacus cultivar Beakdansim tig00000654_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 134106
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:7306 original size:13 final size:13
Alignment explanation
Indices: 7288--7312 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7278 ATTTATGCTT
7288 GAAGATCTTCATG
1 GAAGATCTTCATG
7301 GAAGATCTTCAT
1 GAAGATCTTCAT
7313 CGATCAAGTA
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
GAAGATCTTCATG
Found at i:22774 original size:18 final size:18
Alignment explanation
Indices: 22751--22785 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22741 TAGTTGATAA
22751 TATATGTTAAATCTGAAG
1 TATATGTTAAATCTGAAG
*
22769 TATATGTTAAATTTGAA
1 TATATGTTAAATCTGAA
22786 AGACTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (18 bp):
TATATGTTAAATCTGAAG
Found at i:42144 original size:594 final size:595
Alignment explanation
Indices: 39127--43904 Score: 8901
Period size: 602 Copynumber: 8.0 Consensus size: 595
39117 TGTTTCAGTA
*
39127 CCTAAATTTTTATTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
1 CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
*
39192 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAACTGGAAGTTTAGGTATTAAAATGGACCAAAAAC
66 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAACTGGAAGTTTAGGTACTAAAATGGACC-AAAAC
* * *
39257 TTATAGTTTATGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAATAAACACTAA
130 TGATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACTAA
* * *
39322 ATGTAAGGTGTTATTTTAAAAAAGTAAAATTTTAGGTACTAAACGCGTAATTCACCCATAAGTTT
195 ATGTTAGGTATTATTTT-AAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTTT
*
39387 AATATATCAAATTCAACTTATCATATACGATATATATATATATATATGCATCAGATGTTCCTGTA
259 AATATATCAAATTCAACTTATCAGATACGA-ATATATATATATATATGCATCAGATGTTCCTGTA
39452 CTTTTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACTCAAA
323 CTTTTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACTCAAA
* *
39517 AACAAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACAGGCTTGCC
388 AACAAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCTTTCC
*
39582 AGTTCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAGATTATCTATCATGTTTGAGTA
453 ATTTCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAGATTATCTATCATGTTTGAGTA
*
39647 ATCAATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATGTCAA
518 GTCAATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATGTCAA
39712 CATTGTGAATTGC
583 CATTGTGAATTGC
39725 CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
1 CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
*
39790 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAACTGGAAGTTTAGGTACTAAAATGGACTAAAACT
66 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAACTGGAAGTTTAGGTACTAAAATGGACCAAAACT
39855 GATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACTAAA
131 GATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACTAAA
39920 TGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTTTAA
196 TGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTTTAA
39985 TATATCAAATTCAACTTATCAGATACGATATATATATATATATATATATATGCATCAGATGTTCC
261 TATATCAAATTCAACTTATCAGATACG------A-ATATATATATATATATGCATCAGATGTTCC
*
40050 TGTACTTTTGAAAATAACCAATGTGACATTCGTATTATTTTTTTTCTCAATGTGACCATCTAACT
319 TGTACTTTTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACT
40115 CAAAAACAAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCT
384 CAAAAACAAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCT
*
40180 TTCCATTTCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAAATTATCTATCATGTTTG
449 TTCCATTTCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAGATTATCTATCATGTTTG
40245 AGTAGTCAATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATG
514 AGTAGTCAATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATG
*
40310 TCAACATTGTGAATTGT
579 TCAACATTGTGAATTGC
40327 CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
1 CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
*
40392 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAACTGGAAGTTTAGGTATTAAAATGGACCAAAACT
66 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAACTGGAAGTTTAGGTACTAAAATGGACCAAAACT
40457 GATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACTAAA
131 GATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACTAAA
40522 TGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTTTAA
196 TGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTTTAA
*
40587 TATATCAAATTCAACTTATCAGATATGATATATATATATATATATATATATGCATCAGATGTTCC
261 TATATCAAATTCAACTTATCAGATACG------A-ATATATATATATATATGCATCAGATGTTCC
*
40652 TATACTTTTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACT
319 TGTACTTTTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACT
40717 CAAAAACAAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCT
384 CAAAAACAAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCT
40782 TTCCATTTCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAGATTATCTATCATGTTTG
449 TTCCATTTCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAGATTATCTATCATGTTTG
40847 AGTAGTCAATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATG
514 AGTAGTCAATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATG
40912 TCAACATTGTGAATTGC
579 TCAACATTGTGAATTGC
40929 CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
1 CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
*
40994 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAACTGGAAGTTTAGGTACTAAAATGGACTAAAACT
66 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAACTGGAAGTTTAGGTACTAAAATGGACCAAAACT
41059 GATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACTAAA
131 GATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACTAAA
41124 TGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTTTAA
196 TGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTTTAA
41189 TATATCAAATTCAACTTATCAGATACG---ATATATATATATATGCATCAGATGTTCCTGTACTT
261 TATATCAAATTCAACTTATCAGATACGAATATATATATATATATGCATCAGATGTTCCTGTACTT
41251 TTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACTCAAAAAC
326 TTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACTCAAAAAC
41316 AAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCTTTCCATT
391 AAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCTTTCCATT
*
41381 TCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAAATTATCTATCATGTTTGAGTAGTC
456 TCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAGATTATCTATCATGTTTGAGTAGTC
41446 AATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATGTCAACAT
521 AATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATGTCAACAT
41511 TGTGAATTGC
586 TGTGAATTGC
*
41521 CCTAAATTTTTGTTTTTTTTCCAAAATCATATTTAATATTTAGCTTTGTTTCATTTTAATACCTC
1 CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
* *
41586 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAATTGGAAGTTTAGGTATTAAAATGGACCAAAACT
66 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAACTGGAAGTTTAGGTACTAAAATGGACCAAAACT
41651 GATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACTAAA
131 GATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACTAAA
41716 TGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTTTAA
196 TGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTTTAA
*
41781 TATATCAAATTCAACTTATCAGATACG-ATATATATATATATATGCATCAGATGTTCTTGTACTT
261 TATATCAAATTCAACTTATCAGATACGAATATATATATATATATGCATCAGATGTTCCTGTACTT
41845 TTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACTCAAAAAC
326 TTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACTCAAAAAC
41910 AAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCTTTCCATT
391 AAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCTTTCCATT
*
41975 TCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAAATTATCTATCATGTTTGAGTAGTC
456 TCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAGATTATCTATCATGTTTGAGTAGTC
42040 AATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATGTCAACAT
521 AATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATGTCAACAT
42105 TGTGAATTGC
586 TGTGAATTGC
42115 CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
1 CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
* *
42180 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAACTGGAAGTTTAGGTATTAAAATAGACCAAAACT
66 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAACTGGAAGTTTAGGTACTAAAATGGACCAAAACT
42245 GATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACTAAA
131 GATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACTAAA
42310 TGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTTTAA
196 TGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTTTAA
42375 TATATCAAATTCAACTTATCAGATACGATATATATATATATATATATATATGCATCAGATGTTCC
261 TATATCAAATTCAACTTATCAGATACG------A-ATATATATATATATATGCATCAGATGTTCC
42440 TGTACTTTTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACT
319 TGTACTTTTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACT
* *
42505 CAAAAACAAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTGTAGTACCAGCT
384 CAAAAACAAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCT
*
42570 TTCCATTTCACGGTGGTGACGTGACAGTCCACGTTACTAACGTGGCAGATTATCTATCATGTTTG
449 TTCCATTTCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAGATTATCTATCATGTTTG
42635 AGTAGTCAATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATG
514 AGTAGTCAATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATG
42700 TCAACATTGTGAATTGC
579 TCAACATTGTGAATTGC
42717 CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
1 CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
*
42782 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAACTGGAAGTTTAGGTACTAAAATGGACTAAAACT
66 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAACTGGAAGTTTAGGTACTAAAATGGACCAAAACT
42847 GATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACTAAA
131 GATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACTAAA
42912 TGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTTTAA
196 TGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTTTAA
42977 TATATCAAATTCAACTTATCAGATACG-----ATATATATATATGCATCAGATGTTCCTGTACTT
261 TATATCAAATTCAACTTATCAGATACGAATATATATATATATATGCATCAGATGTTCCTGTACTT
43037 TTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACTCAAAAAC
326 TTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACTCAAAAAC
43102 AAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCTTTCCATT
391 AAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCTTTCCATT
43167 TCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAGATTATCTATCATGTTTGAGTAGTC
456 TCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAGATTATCTATCATGTTTGAGTAGTC
43232 AATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATGTCAACAT
521 AATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATGTCAACAT
43297 TGTGAATTGC
586 TGTGAATTGC
43307 CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
1 CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
*
43372 TATTAAAAACTTAAAGTTAAGTTTTGAAAAAAAAACTGGAAGTTTAGGTACTAAAATGGACTAAA
66 TATTAAAAACTTAAAGTTAAGTTTTG---AAAAAACTGGAAGTTTAGGTACTAAAATGGACCAAA
* *
43437 ACTGATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGACCAATACTAAAATTAAACAAACACT
128 ACTGATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACT
43502 AAATGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTT
193 AAATGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTT
43567 TAATATATCAAATTCAACTTATCAGATACG-ATATATATATATATATGCATCAGATGTTCCTGTA
258 TAATATATCAAATTCAACTTATCAGATACGAATATATATATATATATGCATCAGATGTTCCTGTA
43631 CTTTTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACTCAAA
323 CTTTTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACTCAAA
43696 AACAAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCTTTCC
388 AACAAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCTTTCC
*
43761 AGTTCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAGATTATCTATCATGTTTGAGTA
453 ATTTCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAGATTATCTATCATGTTTGAGTA
*
43826 ATCAATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATGTCAA
518 GTCAATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATGTCAA
43891 CATTGTGAATTGC
583 CATTGTGAATTGC
43904 C
1 C
43905 ACATCAACAC
Statistics
Matches: 4105, Mismatches: 52, Indels: 47
0.98 0.01 0.01
Matches are distributed among these distances:
590 391 0.10
592 586 0.14
593 194 0.05
594 588 0.14
596 74 0.02
597 384 0.09
598 121 0.03
602 1767 0.43
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (595 bp):
CCTAAATTTTTGTTTTTTTTCCAAAATCATATCTAATATTTAGCTTTGTTTCATTTTAATACCTC
TATTAAAAACTTAAAGTTAAGTTTTGAAAAAACTGGAAGTTTAGGTACTAAAATGGACCAAAACT
GATAGTTTAGGTGCTAATCCTGTTAAGTTTTTAACGGCCAATACTAAAATGAAACAAACACTAAA
TGTTAGGTATTATTTTAAAAAGTAAAATTTTAGGTACTAAACACGTAATTCACCCATAAGTTTAA
TATATCAAATTCAACTTATCAGATACGAATATATATATATATATGCATCAGATGTTCCTGTACTT
TTGAAAATAACCAATGTGACATTCGTATTATTTTTTCTCTCAATGTGACCATCTAACTCAAAAAC
AAACCCAATGTAGCCCTTCAACCAACATTTTTCGTCATTGATCGTTATAGTACCGGCTTTCCATT
TCACGGTGGTGACGTGACAGTCCACGGTACTAACGTGGCAGATTATCTATCATGTTTGAGTAGTC
AATTTAATCAATCTCCCATGACATCCGTCATGTTAATCTGTCACCCTAGATTGTCATGTCAACAT
TGTGAATTGC
Found at i:46136 original size:35 final size:35
Alignment explanation
Indices: 46090--46158 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
46080 CTAATTTTAT
46090 TAAAAATAGAAAACATTGAATTACAATATGAACAC
1 TAAAAATAGAAAACATTGAATTACAATATGAACAC
46125 TAAAAATAGAAAACATTGAATTACAATATGAACA
1 TAAAAATAGAAAACATTGAATTACAATATGAACA
46159 TTCAGAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.58, C:0.10, G:0.09, T:0.23
Consensus pattern (35 bp):
TAAAAATAGAAAACATTGAATTACAATATGAACAC
Found at i:46182 original size:12 final size:12
Alignment explanation
Indices: 46165--46190 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
46155 AACATTCAGA
46165 ATTACAATATTC
1 ATTACAATATTC
46177 ATTACAATATTC
1 ATTACAATATTC
46189 AT
1 AT
46191 AATTACAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTACAATATTC
Found at i:46195 original size:15 final size:14
Alignment explanation
Indices: 46158--46200 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
46148 CAATATGAAC
46158 ATTCAGAATTACAAT
1 ATTCA-AATTACAAT
46173 ATTC--ATTACAAT
1 ATTCAAATTACAAT
46185 ATTCATAATTACAAT
1 ATTCA-AATTACAAT
46200 A
1 A
46201 CGAAGATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.48
15 13 0.52
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (14 bp):
ATTCAAATTACAAT
Found at i:47038 original size:13 final size:14
Alignment explanation
Indices: 47010--47039 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
47000 ATATCTTATC
47010 TTTTCATTTATAAT
1 TTTTCATTTATAAT
47024 TTTTCATTTAT-AT
1 TTTTCATTTATAAT
47037 TTT
1 TTT
47040 CAACATGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTCATTTATAAT
Found at i:48983 original size:37 final size:36
Alignment explanation
Indices: 48911--48984 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
48901 GTTGGAAAAT
* *
48911 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
*
48947 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTGAAAATCATAAA
48984 A
1 A
48985 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 8 0.24
37 15 0.45
38 10 0.30
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Found at i:54899 original size:2 final size:2
Alignment explanation
Indices: 54892--54923 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
54882 TTCTCTACCC
54892 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
54924 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:54928 original size:2 final size:2
Alignment explanation
Indices: 54923--54974 Score: 70
Period size: 2 Copynumber: 26.0 Consensus size: 2
54913 TCTCTCTCTC
* *
54923 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A GTT TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
54965 TA TA TA TA TA
1 TA TA TA TA TA
54975 ATTTTATGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55623 original size:23 final size:23
Alignment explanation
Indices: 55590--55645 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
55580 TTATATTTAG
55590 TATTTTGTTAATAATTTATTTAAC
1 TATTTT-TTAATAATTTATTTAAC
* *
55614 TATTTTTTAATATTTTATTTAAT
1 TATTTTTTAATAATTTATTTAAC
55637 TAATTTTTT
1 T-ATTTTTT
55646 TTACAGATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
TATTTTTTAATAATTTATTTAAC
Found at i:55634 original size:12 final size:12
Alignment explanation
Indices: 55578--55636 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
55568 AGGTATATTT
* *
55578 TATTATATTTAG
1 TATTTTATTTAA
*
55590 TATTTT-GTTAA
1 TATTTTATTTAA
*
55601 TAATTTATTTAA
1 TATTTTATTTAA
55613 CTA-TTT-TTTAA
1 -TATTTTATTTAA
55624 TATTTTATTTAA
1 TATTTTATTTAA
55636 T
1 T
55637 TAATTTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
10 2 0.05
11 16 0.42
12 18 0.47
13 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (12 bp):
TATTTTATTTAA
Found at i:61794 original size:26 final size:27
Alignment explanation
Indices: 61750--61804 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
61740 TTTTAAAAAA
**
61750 ATAATTTTTTCAAAATATATGAAATTT
1 ATAATTTTTTCAAAATATAAAAAATTT
61777 ATAA-TTTTT-AAAATTATAAAAAATTT
1 ATAATTTTTTCAAAA-TATAAAAAATTT
61803 AT
1 AT
61805 TATTATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.16
26 17 0.68
27 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
ATAATTTTTTCAAAATATAAAAAATTT
Found at i:73445 original size:2 final size:2
Alignment explanation
Indices: 73438--73473 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
73428 CAACTATAAT
73438 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73474 AAAGCATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:74090 original size:84 final size:82
Alignment explanation
Indices: 73822--74134 Score: 383
Period size: 84 Copynumber: 3.8 Consensus size: 82
73812 GGTTCAGCCA
* * * * * ** * *
73822 TAGTGGTGTTTTTTAAACAAACGCCGCTAAAGACTCATACTTTAGTGGTGTTTTTGAAACAAACG
1 TAGTGGCG-TTTTTATACAAACGTCGCTATACACTTGTACTTTAGTGGCGTTTTT-ATACAAACG
*
73887 CCGCTAAAGACTCATACTT
64 CCGCTAAAGACTCGTACTT
* * * * **
73906 TAGTGGCGTTTTTATACAAACGTTGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGAA
1 TAGTGGCGTTTTTATACAAACGTCGCTATACACTTGTACTTTAGTGGCGTTTTTATACAAACGCC
73971 GCTAAAGACTCGTACTT
66 GCTAAAGACTCGTACTT
** * *
73988 TAGTGGCGTTTTTATACAAACACCGCTATACACTTGTACTTTAGTGGCGTTTGTGTTTAGAAACG
1 TAGTGGCGTTTTTATACAAACGTCGCTATACACTTGTACTTTAGTGGCGTTT-T-TATACAAACG
74053 CCGCTAAAGACTCGTACTT
64 CCGCTAAAGACTCGTACTT
* * *
74072 TAGTGGCATTTATATACAAACGTCGCTATACACTTATACTTTAGTGGCGTTTTTATACAAACG
1 TAGTGGCGTTTTTATACAAACGTCGCTATACACTTGTACTTTAGTGGCGTTTTTATACAAACG
74135 TCACTATACA
Statistics
Matches: 200, Mismatches: 27, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
82 78 0.39
83 43 0.22
84 79 0.40
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (82 bp):
TAGTGGCGTTTTTATACAAACGTCGCTATACACTTGTACTTTAGTGGCGTTTTTATACAAACGCC
GCTAAAGACTCGTACTT
Found at i:74142 original size:125 final size:123
Alignment explanation
Indices: 73838--74145 Score: 391
Period size: 125 Copynumber: 2.5 Consensus size: 123
73828 TGTTTTTTAA
* * * * *
73838 ACAAACGCCGCTAAAGACTCATACTTTAGTGGTGTTTTTGAAACAAACGCCGCTAAAGACTCATA
1 ACAAACGACGCTAAAGACTCATACTTTAGTGGCGTTTTT-ATACAAACGCCGCTATACACTCATA
** * *
73903 CTTTAGTGGCGTTTTTATACAAACGTTGCTAAAGACTCGTACTTTAGTGGCGTTTTTAT
65 CTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTATAT
* * * **
73962 ACAAACGAAGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACACCGCTATACACTTGTAC
1 ACAAACGACGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACGCCGCTATACACTCATAC
* *
74027 TTTAGTGGCGTTTGTGTTTAGAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTATAT
66 TTTAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTATAT
* * * * * *
74087 ACAAACGTCGCTATACACTTATACTTTAGTGGCGTTTTTATACAAACGTCACTATACAC
1 ACAAACGACGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACGCCGCTATACAC
74146 ACTACAACAA
Statistics
Matches: 157, Mismatches: 25, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
123 33 0.21
124 36 0.23
125 88 0.56
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (123 bp):
ACAAACGACGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACGCCGCTATACACTCATAC
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTATAT
Found at i:74145 original size:41 final size:41
Alignment explanation
Indices: 73822--74134 Score: 383
Period size: 41 Copynumber: 7.5 Consensus size: 41
73812 GGTTCAGCCA
* * *
73822 TAGTGGTGTTTTTTAAACAAACGCCGCTAAAGACTCATACTT
1 TAGTGGCG-TTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * *
73864 TAGTGGTGTTTTTGAAACAAACGCCGCTAAAGACTCATACTT
1 TAGTGGCGTTTTT-ATACAAACGCCGCTAAAGACTCGTACTT
**
73906 TAGTGGCGTTTTTATACAAACGTTGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
**
73947 TAGTGGCGTTTTTATACAAACGAAGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * *
73988 TAGTGGCGTTTTTATACAAACACCGCTATACACTTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* *
74029 TAGTGGCGTTTGTGTTTAGAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGTACTT
* * * * * **
74072 TAGTGGCATTTATATACAAACGTCGCTATACACTTATACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
74113 TAGTGGCGTTTTTATACAAACG
1 TAGTGGCGTTTTTATACAAACG
74135 TCACTATACA
Statistics
Matches: 238, Mismatches: 30, Indels: 7
0.87 0.11 0.03
Matches are distributed among these distances:
41 156 0.66
42 49 0.21
43 33 0.14
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
Found at i:74360 original size:41 final size:40
Alignment explanation
Indices: 74315--74442 Score: 118
Period size: 41 Copynumber: 3.1 Consensus size: 40
74305 CGTTTGTTTC
*
74315 ACAAACGCCACAACATATAA-GTACTTTAGTGGCATTT-TAAA
1 ACAAACGCCACAACA-A-AACCTACTTTAGTGGCATTTCT-AA
*
74356 ACAAACGCCACAACAAAATCCTACTTTAGTGGCGTTTCTAA
1 ACAAACGCCACAACAAAA-CCTACTTTAGTGGCATTTCTAA
* * * * *
74397 ACAAATGCCACAA-AAGAATCATTCTTTAGTGGCGTTTATAA
1 ACAAACGCCACAACAA-AA-CCTACTTTAGTGGCATTTCTAA
74438 ACAAA
1 ACAAA
74443 TGCCGCAATA
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
39 2 0.03
40 3 0.04
41 71 0.92
42 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (40 bp):
ACAAACGCCACAACAAAACCTACTTTAGTGGCATTTCTAA
Found at i:74443 original size:41 final size:40
Alignment explanation
Indices: 74336--74446 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 40
74326 AACATATAAG
* * *
74336 TACTTTAGTGGCATTTTAAAACAAACGCCACAACAAAATCC
1 TACTTTAGTGGCGTTTT-AAACAAATGCCACAACAAAATCA
74377 TACTTTAGTGGCGTTTCTAAACAAATGCCACAA-AAGAATCA
1 TACTTTAGTGGCGTTT-TAAACAAATGCCACAACAA-AATCA
*
74418 TTCTTTAGTGGCGTTTATAAACAAATGCC
1 TACTTTAGTGGCGTTT-TAAACAAATGCC
74447 GCAATAGAGT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
40 2 0.03
41 60 0.95
42 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (40 bp):
TACTTTAGTGGCGTTTTAAACAAATGCCACAACAAAATCA
Found at i:77720 original size:16 final size:17
Alignment explanation
Indices: 77691--77742 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
77681 ATCTTAAGTT
*
77691 TAAAAAACTATATTTATAA
1 TAAAAAA-T-TATTAATAA
77710 -AAAAAATTATTAATAA
1 TAAAAAATTATTAATAA
*
77726 TTAAAAAATTATAAATA
1 -TAAAAAATTATTAATA
77743 TATATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 8 0.28
17 1 0.03
18 20 0.69
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAAAATTATTAATAA
Found at i:84408 original size:43 final size:42
Alignment explanation
Indices: 84335--84450 Score: 151
Period size: 43 Copynumber: 2.7 Consensus size: 42
84325 GCGTTTGTAT
* * * *
84335 TAAAGACGCCGCTAAACCTCAACGCCTATTGCGGCATTTTAGC
1 TAAAAACG-CGCTAAATCTCAACACATATTGCGGCATTTTAGC
*
84378 TAAAAACGTCGCTAAATCTCAACACATATTGCGGCATTTTCGC
1 TAAAAACG-CGCTAAATCTCAACACATATTGCGGCATTTTAGC
*
84421 TAAAAACGCTGCTAAATCTCAAGACATATT
1 TAAAAACGC-GCTAAATCTCAACACATATT
84451 ATAGCGTTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 1 0.02
43 64 0.98
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (42 bp):
TAAAAACGCGCTAAATCTCAACACATATTGCGGCATTTTAGC
Found at i:90192 original size:38 final size:38
Alignment explanation
Indices: 90150--90224 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 38
90140 AATTTTCTAA
* *
90150 TTTAT-ATAAAAATTAAATATTTTATAATTAAAAAATAG
1 TTTATAAT-AAAATTAAATAATATATAATTAAAAAATAG
* * *
90188 TTTATAATCAATTTAAATAATATATAATTATAAAATA
1 TTTATAATAAAATTAAATAATATATAATTAAAAAATA
90225 AAAATATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 29 0.94
39 2 0.06
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (38 bp):
TTTATAATAAAATTAAATAATATATAATTAAAAAATAG
Found at i:98340 original size:19 final size:19
Alignment explanation
Indices: 98292--98347 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
98282 TGAAAACTAT
*
98292 TTTAATAAA-AATAAAATAA
1 TTTAAGAAATAATAAAA-AA
* *
98311 ATT-AGACATAATAAAAAA
1 TTTAAGAAATAATAAAAAA
98329 TTTAAGAAATAAATAAAAA
1 TTTAAGAAAT-AATAAAAA
98348 TCAAACGTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 7 0.24
19 14 0.48
20 8 0.28
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (19 bp):
TTTAAGAAATAATAAAAAA
Found at i:103751 original size:7 final size:7
Alignment explanation
Indices: 103739--103763 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
103729 TTGTCGTGTG
103739 AGACGAA
1 AGACGAA
103746 AGACGAA
1 AGACGAA
103753 AGACGAA
1 AGACGAA
103760 AGAC
1 AGAC
103764 AAGCCATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.28, T:0.00
Consensus pattern (7 bp):
AGACGAA
Found at i:113117 original size:23 final size:22
Alignment explanation
Indices: 113091--113133 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
113081 TCTAACAAAC
*
113091 TAAAAATCCTAATTAATAAATAT
1 TAAAAATCCTAAATAA-AAATAT
113114 TAAAAATCCTAAATAAAAAT
1 TAAAAATCCTAAATAAAAAT
113134 TCTATGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAATCCTAAATAAAAATAT
Found at i:114770 original size:20 final size:20
Alignment explanation
Indices: 114725--114863 Score: 109
Period size: 20 Copynumber: 6.8 Consensus size: 20
114715 AGAAGTCGAA
*
114725 TTCGCAACTCGAATTTGACATT
1 TTCGCAACACGAATTT--CATT
*
114747 TTCGCAACACGAATTTCTTT
1 TTCGCAACACGAATTTCATT
* * * * **
114767 TTCGCGACTCGATTTTTAAA
1 TTCGCAACACGAATTTCATT
* *
114787 TTCGCAACACGAGTTTCGTT
1 TTCGCAACACGAATTTCATT
** *
114807 TTCGCAATGC-AAGTTTCAAT
1 TTCGCAACACGAA-TTTCATT
*
114827 TTCGCAACACGAATTTCGTT
1 TTCGCAACACGAATTTCATT
*
114847 TTCGCAACGCGAATTTC
1 TTCGCAACACGAATTTC
114864 GAATTAGCAC
Statistics
Matches: 89, Mismatches: 26, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
19 1 0.01
20 71 0.80
21 2 0.02
22 15 0.17
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (20 bp):
TTCGCAACACGAATTTCATT
Found at i:114798 original size:40 final size:40
Alignment explanation
Indices: 114747--114884 Score: 136
Period size: 40 Copynumber: 3.5 Consensus size: 40
114737 ATTTGACATT
* * * * *
114747 TTCGCAACACGAATTTCTTTTTCGCGACT-CGATTTTTAAA
1 TTCGCAACACGAATTTCGTTTTCGC-AATGCAAGTTTCAAA
* *
114787 TTCGCAACACGAGTTTCGTTTTCGCAATGCAAGTTTCAAT
1 TTCGCAACACGAATTTCGTTTTCGCAATGCAAGTTTCAAA
* *
114827 TTCGCAACACGAATTTCGTTTTCGCAACGCGAA-TTTCGAA
1 TTCGCAACACGAATTTCGTTTTCGCAATGC-AAGTTTCAAA
* * *
114867 TTAGCACCGCGAATTTCG
1 TTCGCAACACGAATTTCG
114885 AATTAGTAAC
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.02
40 78 0.95
41 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (40 bp):
TTCGCAACACGAATTTCGTTTTCGCAATGCAAGTTTCAAA
Found at i:114864 original size:20 final size:20
Alignment explanation
Indices: 114746--114920 Score: 118
Period size: 20 Copynumber: 8.8 Consensus size: 20
114736 AATTTGACAT
* **
114746 TTTCGCAACACGAATTTCTT
1 TTTCGCAACGCGAATTTCGA
* * * **
114766 TTTCGCGACTCGATTTTTAA
1 TTTCGCAACGCGAATTTCGA
* * * *
114786 ATTCGCAACACGAGTTTCGT
1 TTTCGCAACGCGAATTTCGA
* *
114806 TTTCGCAATGC-AAGTTTCAA
1 TTTCGCAACGCGAA-TTTCGA
* *
114826 TTTCGCAACACGAATTTCGT
1 TTTCGCAACGCGAATTTCGA
114846 TTTCGCAACGCGAATTTCGA
1 TTTCGCAACGCGAATTTCGA
* * *
114866 ATTAGCACCGCGAATTTCGA
1 TTTCGCAACGCGAATTTCGA
* * *
114886 ATTAGTAACGCGAATTTCGA
1 TTTCGCAACGCGAATTTCGA
* *
114906 ATTAGCAACGCGAAT
1 TTTCGCAACGCGAAT
114921 CCTGCTATGT
Statistics
Matches: 122, Mismatches: 31, Indels: 4
0.78 0.20 0.03
Matches are distributed among these distances:
19 1 0.01
20 119 0.98
21 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (20 bp):
TTTCGCAACGCGAATTTCGA
Found at i:115492 original size:20 final size:20
Alignment explanation
Indices: 115467--115549 Score: 94
Period size: 20 Copynumber: 4.2 Consensus size: 20
115457 AGGATTTGCA
*
115467 TTGCGAATTCAAAAATCGAG
1 TTGCGAATTTAAAAATCGAG
** * * *
115487 TTGCGAAAATGAAACTCGTG
1 TTGCGAATTTAAAAATCGAG
* *
115507 TTGTGAATTTAAAAATCGAA
1 TTGCGAATTTAAAAATCGAG
115527 TTGCGAATTTAAAAATCGAG
1 TTGCGAATTTAAAAATCGAG
115547 TTG
1 TTG
115550 TGAAAAAGAA
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (20 bp):
TTGCGAATTTAAAAATCGAG
Found at i:115574 original size:20 final size:21
Alignment explanation
Indices: 115546--115595 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
115536 TAAAAATCGA
* *
115546 GTTGTGAAAAAG-AAATTCGT
1 GTTGCGAAAAAGCAAATTCGG
*
115566 GTTGCGAAAATGTCAAATTCGG
1 GTTGCGAAAAAG-CAAATTCGG
115588 GTTGCGAA
1 GTTGCGAA
115596 TTCGACTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.40
22 15 0.60
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (21 bp):
GTTGCGAAAAAGCAAATTCGG
Found at i:115613 original size:20 final size:20
Alignment explanation
Indices: 115588--115698 Score: 84
Period size: 20 Copynumber: 5.6 Consensus size: 20
115578 TCAAATTCGG
*
115588 GTTGCGAATTCGACTTCTGT
1 GTTGCGAATTCGAATTCTGT
* *
115608 GTTGCGAATTCCAAATTC-GA
1 GTTGCGAATT-CGAATTCTGT
**
115628 GTTGCGAATTCGAAAACTGT
1 GTTGCGAATTCGAATTCTGT
* * **
115648 GTTACGAAATTGGCTTTC-GT
1 GTTGCG-AATTCGAATTCTGT
* *
115668 GTTGCGAATTCGAAAT-TGA
1 GTTGCGAATTCGAATTCTGT
115687 GTTGCGAATTCG
1 GTTGCGAATTCG
115699 TTGGTAATTT
Statistics
Matches: 68, Mismatches: 19, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
19 23 0.34
20 34 0.50
21 11 0.16
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTCGAATTCTGT
Found at i:115648 original size:40 final size:40
Alignment explanation
Indices: 115579--115697 Score: 109
Period size: 40 Copynumber: 3.0 Consensus size: 40
115569 GCGAAAATGT
* ***
115579 CAAATTCGGGTTGCGAATTCGACTTCTGTGTTGCGAATTC
1 CAAATTCGAGTTGCGAATTCGAAAACTGTGTTGCGAATTC
* *
115619 CAAATTCGAGTTGCGAATTCGAAAACTGTGTTACGAAATTGG
1 CAAATTCGAGTTGCGAATTCGAAAACTGTGTTGCG-AATT-C
* * * *
115661 C--TTTCGTGTTGCGAATTCG-AAATTGAGTTGCGAATTC
1 CAAATTCGAGTTGCGAATTCGAAAACTGTGTTGCGAATTC
115698 GTTGGTAATT
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
38 4 0.06
39 10 0.15
40 46 0.71
41 4 0.06
42 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (40 bp):
CAAATTCGAGTTGCGAATTCGAAAACTGTGTTGCGAATTC
Found at i:124044 original size:18 final size:18
Alignment explanation
Indices: 124021--124064 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
124011 AAATTATTGA
124021 TGTTTTGGATACATTTAG
1 TGTTTTGGATACATTTAG
124039 TGTTTTGGATACATTTAG
1 TGTTTTGGATACATTTAG
*
124057 TGTCTTGG
1 TGTTTTGG
124065 TAGAGCTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.07, G:0.25, T:0.50
Consensus pattern (18 bp):
TGTTTTGGATACATTTAG
Found at i:132530 original size:69 final size:66
Alignment explanation
Indices: 132391--132520 Score: 206
Period size: 69 Copynumber: 1.9 Consensus size: 66
132381 CTCTAGGTCC
* * *
132391 TCTTTCTCTTCACTTCCATTTCCAGCTTCTTCTTCTTGCTCCTCTTGTTCATCTTGTTGTTCTTT
1 TCTTTCTCATCACTTCCATTTCCAGCTTCTTCTTCTTGCTCCTCTTGTTCATCTTCTTGTTCTGT
132456 A
66 A
132457 TCTTTCTCATCACTTCCATTTCCAGCTTCTTCTTCTTCTTGCTCCTCTTGTTCATCTTCTTGTT
1 TCTTTCTCATCACTTCCATTTCCAG---CTTCTTCTTCTTGCTCCTCTTGTTCATCTTCTTGTT
132521 GGTGTTCTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
66 24 0.41
69 35 0.59
ACGTcount: A:0.08, C:0.32, G:0.07, T:0.54
Consensus pattern (66 bp):
TCTTTCTCATCACTTCCATTTCCAGCTTCTTCTTCTTGCTCCTCTTGTTCATCTTCTTGTTCTGT
A
Done.