Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009084.1 Hibiscus syriacus cultivar Beakdansim tig00112528_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: 881682
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 4
Found at i:169183 original size:979 final size:979
Alignment explanation
Indices: 167181--169914 Score: 4739
Period size: 979 Copynumber: 2.8 Consensus size: 979
167171 TTATAATATG
*
167181 TTGAAAGTGTCCATA-TTTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATG
1 TTGAAAGTGTCCATACTTTTTATA-AAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATG
*
167245 TTTCAA-TTTTTTAATAGTGTTTCATGTTTTTGACCTACAATATTAATTTAATAATTTCATTTGC
65 TTTCAATTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTGC
*
167309 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATTTTTAGAATTTAAATTTAACAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
*
167374 TTAACCAAATATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATGATAATATA
195 TTAACCAAATATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
* ** * *
167439 TACCGTAACATAAAAAATAAATCATTAGATACATATAATTACTAAATTGATATCTTAAAACTCAC
260 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
* * *
167504 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAATAAGTATGGACACTTCTATAAAAAGA
325 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
** *
167569 ATAGATACTTTACAATATAAGTGCTACCTATTACATTATATAAGCGCTACCTATTACATTATATA
390 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
* * * ** *
167634 AGCGCTACATATTACATTATATTTTTACCTGA-TATATTGTAAAGTATTGATCCTTTTTATAAAA
455 AGCGCTACCTATTACATCATATTTTTACCT-ATTATATTG-AAAGTGTCCATACTTTTTA-AAAA
167698 ATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGTGTTTCATGT
517 ATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGT
*
167762 TTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATAT
582 TTTCTACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATAT
*
167827 TTTATAAAATATTATTTATAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAA
647 TTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAA
*
167892 TATATATGTTTAATGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAG
712 TATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAG
*
167957 ACACCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACTTTAAATTAATGTTTT
777 ACACCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTT
* *
168022 CTACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAACACTACC
842 CCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAAATACTTTACAATATAAACACTACC
* *
168087 TATTACATTATATAAACGCTACTTATTACATTATATAAGTGCTACCTATTACATCATGTTTTTAC
907 TATTACATTATATAAACGCTACTTATTACATTATATAAGCGCTACCTATTACATCATATTTTTAC
168152 CTATTATA
972 CTATTATA
168160 TTGAAAGTGTCCATACTTTTTAT-AAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
*
168224 TTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TTCAATTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTGCA
* *
168289 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAAAATTTAAATTTAATAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
168354 TAACCAAATATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
196 TAACCAAATATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
168419 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
* * *
168484 CAAAAGATAACATTAAATTAATGTTTTCCACGGTGAAAAAATTATGGACACTTTTATAAAAAGGA
326 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
* *
168549 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACATATTATATTATATAA
391 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
* *
168614 GCGCTACCTATTACATCATATTTTTACATATTATATTGAAAGTGTCCATACATTTTAAAAAATGA
456 GCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTAAAAAATGA
*
168679 TCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAATGTTTCATGTTTTC
521 TCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTC
*
168744 TACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTA
586 TACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTA
*
168809 TAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATA
651 TAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATA
* * *
168874 TATGTTTATTGGTTTTAATTTAATAATAATATATACCGTAACGTAAAACATAAATCATTAGACGC
716 TATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACAC
*
168939 CTATAATTACTAAATTAATATTTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCAC
781 CTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCAC
*
169004 AGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAAATACTTTACAATATAAGCACTACCTATT
846 AGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAAATACTTTACAATATAAACACTACCTATT
169069 ACATTATATAAACGCTACTTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTAT
911 ACATTATATAAACGCTACTTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTAT
169134 TATA
976 TATA
* *
169138 TTGAAAGTGTCCATACTTTTTATAAAAAATGATCGATATTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
* * *
169203 TTCAATTTTTTTTAACAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTTATTTAC
66 TTCAA-TTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTGC
* *
169268 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGTATTTAAATTTAACAATA
130 ACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
*
169333 TTAACCAAAGATAATAAT-AATATGT-A-ATATATGTTTATTGTTTTTAATTTAATAATAATATA
195 TTAACCAAATATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
* *
169395 TACCGTAACGTAAAACATAAATCATTAGACGCCTATAATTACTAAATTAATATTTTAAAACTCAC
260 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
*
169460 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATG
325 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
*
169525 ATAAATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
390 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
*
169590 AGTGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAA
455 AGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATAC-TTTT-TAAAAAA
* * *
169655 GGATCGATATTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAACAGTGTTTCATGTT
518 TGATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTT
*
169720 TT-TCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGGTTTGATAT
583 TTCT-ACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATAT
*
169784 TTTATAAAATATTATTTAGTATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAA
647 TTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAA
169849 TATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAG
712 TATATATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAG
169914 A
777 A
169915 TACTTTAAAT
Statistics
Matches: 1664, Mismatches: 82, Indels: 18
0.94 0.05 0.01
Matches are distributed among these distances:
977 317 0.19
978 493 0.30
979 715 0.43
980 139 0.08
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (979 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
TTCAATTTTTTTAATAGTGTTTCATGTTTTTCACCTACAATATTAATTTAATAATTTCATTTGCA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
TAACCAAATATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
GCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTTAAAAAATGA
TCGATACTTTTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTC
TACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTA
TAAAATATTATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATGTAATATA
TATGTTTATTGTTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACAC
CTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCAC
AGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAAATACTTTACAATATAAACACTACCTATT
ACATTATATAAACGCTACTTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTAT
TATA
Found at i:169574 original size:23 final size:23
Alignment explanation
Indices: 169539--169611 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
169529 ATACTTTACA
*
169539 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
169562 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
169585 ATATAAGTGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
169608 ATAT
1 ATAT
169612 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:170511 original size:14 final size:14
Alignment explanation
Indices: 170492--170522 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
170482 TATGTTTATA
170492 TTTTTAAAAAATAT
1 TTTTTAAAAAATAT
*
170506 TTTTTAAATAATAT
1 TTTTTAAAAAATAT
170520 TTT
1 TTT
170523 ATTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTTAAAAAATAT
Found at i:176618 original size:70 final size:66
Alignment explanation
Indices: 176536--176715 Score: 181
Period size: 64 Copynumber: 2.7 Consensus size: 66
176526 AGATGATAAT
*
176536 TCTTTTGAATATCTCAAATTTAAAGGTATTCATTATCTATTTAACTTTGAA-AATTAAAAGAAAA
1 TCTTTTGAATATCTCAAATTTAAA--TATT-ATTATCTATTTAACTTTGAATAA-AAAAAGAAAA
176600 TTATA
62 TTATA
* * * ** *
176605 TCATTTTGAATATCTCAAA-TTAAA-A-TAATATATATTTAAGTTTGAATAAAAAAAGCTACTTA
1 TC-TTTTGAATATCTCAAATTTAAATATTATTATCTATTTAACTTTGAATAAAAAAAGAAAATTA
176667 TA
65 TA
*
176669 TCTTTTGAATAT-TACAAATTAAAATATATTATTATCTATTTAACTTT
1 TCTTTTGAATATCT-CAAATT-TAA-ATATTATTATCTATTTAACTTT
176716 CAGTATTAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
62 1 0.01
63 14 0.15
64 31 0.34
65 5 0.05
66 2 0.02
67 1 0.01
68 15 0.16
69 7 0.08
70 16 0.17
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (66 bp):
TCTTTTGAATATCTCAAATTTAAATATTATTATCTATTTAACTTTGAATAAAAAAAGAAAATTAT
A
Found at i:181001 original size:65 final size:68
Alignment explanation
Indices: 180920--181170 Score: 204
Period size: 65 Copynumber: 3.8 Consensus size: 68
180910 TTCATATTCC
* *
180920 TTTTGAATATTACAAATTAAAAGATATTTATT-TCT-TTAA-TTTGAATATTAATAGGATAA-T-
1 TTTTGAATATT-CAAATTAAAAGACATTTATTATCTATTAACTTTGAATATTAA-AAGATAATTA
*
180980 TATTG
64 TATTA
* *
180985 TTTTGAATATATCAAATTAAAAGGCATTTATTATCTACTTAACTTTGAATATTAAAATATAATTA
1 TTTTGAATAT-TCAAATTAAAAGACATTTATTATCTA-TTAACTTTGAATATTAAAAGATAATTA
181050 TATTA
64 TATTA
* * * * * * *
181055 TTTTGAATATCTCAAATTAGAATA-A--AATT-TAT-TTAAGTTTGAATAGTAAAAGCT-ATCTA
1 TTTTGAATAT-TCAAATTAAAAGACATTTATTATCTATTAACTTTGAATATTAAAAGATAAT-TA
*
181114 TA-TC
64 TATTA
* *
181118 TTTTGAATATTTCAAATTAAAAGACA-TTATTATCTTTTTAAATTTGAATATTA
1 TTTTGAATA-TTCAAATTAAAAGACATTTATTATC-TATTAACTTTGAATATTA
181171 GAATATATCT
Statistics
Matches: 150, Mismatches: 22, Indels: 25
0.76 0.11 0.13
Matches are distributed among these distances:
63 23 0.15
64 24 0.16
65 31 0.21
66 7 0.05
67 4 0.03
68 23 0.15
69 14 0.09
70 24 0.16
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (68 bp):
TTTTGAATATTCAAATTAAAAGACATTTATTATCTATTAACTTTGAATATTAAAAGATAATTATA
TTA
Found at i:182713 original size:31 final size:31
Alignment explanation
Indices: 182675--182736 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
182665 AAGTGTTCTA
*
182675 TACGAGCTGTGGCGAGAGGATGAAGTTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
*
182706 TACGAGCTGTGGTGAGAGGATGAAGCTTTGC
1 TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
182737 ATGTGCCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.13, G:0.39, T:0.26
Consensus pattern (31 bp):
TACGAGCTGTGGCGAGAGGATGAAGCTTTGC
Found at i:182769 original size:22 final size:22
Alignment explanation
Indices: 182741--182791 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
182731 CTTTGCATGT
182741 GCCATGCACGTC-AGAAGAGGTC
1 GCCATGCACGTCGA-AAGAGGTC
182763 GCCATGCACGTCGAAAGAGGTC
1 GCCATGCACGTCGAAAGAGGTC
182785 GCC-TGCA
1 GCCATGCA
182792 TGTAGTGGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.14
22 23 0.82
23 1 0.04
ACGTcount: A:0.25, C:0.29, G:0.31, T:0.14
Consensus pattern (22 bp):
GCCATGCACGTCGAAAGAGGTC
Found at i:182874 original size:29 final size:30
Alignment explanation
Indices: 182838--182925 Score: 110
Period size: 29 Copynumber: 3.0 Consensus size: 30
182828 GGGCGCAGGA
*
182838 CAAGGTCGCCCAGCGTGCATGGCGACCTAT
1 CAAGGTCGCCCGGCGTGCATGGCGACCTAT
* *
182868 C-ATGTCGCCTGGCGTGCATGGCGACCTA-
1 CAAGGTCGCCCGGCGTGCATGGCGACCTAT
*
182896 CAAGGTCGCCCGGAG-GACATGGCGACCTAT
1 CAAGGTCGCCCGGCGTG-CATGGCGACCTAT
182926 ACTGGGAAGC
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.04
29 46 0.94
30 1 0.02
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.17
Consensus pattern (30 bp):
CAAGGTCGCCCGGCGTGCATGGCGACCTAT
Found at i:189719 original size:29 final size:28
Alignment explanation
Indices: 189657--189719 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
189647 GGTTTTTATG
*
189657 TTAGGGGCGTACATGAACTTATAAGAAT
1 TTAGGGGCGAACATGAACTTATAAGAAT
* * *
189685 TCAGGGGACGAACTTGAATTTATAA-AATT
1 TTAGGGG-CGAACATGAACTTATAAGAA-T
189714 TTAGGG
1 TTAGGG
189720 AGAGAAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (28 bp):
TTAGGGGCGAACATGAACTTATAAGAAT
Found at i:194745 original size:2 final size:2
Alignment explanation
Indices: 194738--194767 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
194728 GTATTTTAAA
*
194738 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
194768 TAGTATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:207816 original size:36 final size:36
Alignment explanation
Indices: 207769--207854 Score: 163
Period size: 36 Copynumber: 2.4 Consensus size: 36
207759 TAAGTGCCTT
207769 AGATAATATGTAGCCATACACTTCCTTTTAGTTGTA
1 AGATAATATGTAGCCATACACTTCCTTTTAGTTGTA
*
207805 AGATAATATGTAGCCATACACTTTCTTTTAGTTGTA
1 AGATAATATGTAGCCATACACTTCCTTTTAGTTGTA
207841 AGATAATATGTAGC
1 AGATAATATGTAGC
207855 AATATAAGTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (36 bp):
AGATAATATGTAGCCATACACTTCCTTTTAGTTGTA
Found at i:222834 original size:34 final size:32
Alignment explanation
Indices: 222781--222850 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
222771 CCTTACAAAC
* *
222781 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAAAACCTT
*
222813 TCCCTAGCTTTTACACGGGCTAAGCTAAAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAAAACCTT
222847 TCCC
1 TCCC
222851 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAAAACCTT
Found at i:223158 original size:21 final size:21
Alignment explanation
Indices: 223133--223174 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
223123 CCAGAATGAG
*
223133 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
223154 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
223175 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:223326 original size:33 final size:35
Alignment explanation
Indices: 223287--223366 Score: 119
Period size: 33 Copynumber: 2.3 Consensus size: 35
223277 AAACCATGCA
223287 GGGGGAATCTGTACCCGAGGAATCGATA-CCCCT-
1 GGGGGAATCTGTACCCGAGGAATCGATACCCCCTG
** *
223320 GGGGGAATCTGTTTCCGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTACCCGAGGAATCGATACCCCCTG
223355 GGGGGAATCTGT
1 GGGGGAATCTGT
223367 TCCCCCTTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
33 25 0.60
34 5 0.12
35 12 0.29
ACGTcount: A:0.20, C:0.24, G:0.35, T:0.21
Consensus pattern (35 bp):
GGGGGAATCTGTACCCGAGGAATCGATACCCCCTG
Found at i:223361 original size:20 final size:21
Alignment explanation
Indices: 223336--223394 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
223326 ATCTGTTTCC
223336 GGGGAATC-GATACCCCC-TGG
1 GGGGAATCTG-TACCCCCTTGG
*
223356 GGGGAATCTGTTCCCCCTTGG
1 GGGGAATCTGTACCCCCTTGG
*
223377 GGGGAATCTGTAGCCCCT
1 GGGGAATCTGTACCCCCT
223395 GGACAATCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.15, C:0.29, G:0.34, T:0.22
Consensus pattern (21 bp):
GGGGAATCTGTACCCCCTTGG
Found at i:224498 original size:39 final size:39
Alignment explanation
Indices: 224453--224558 Score: 108
Period size: 39 Copynumber: 2.7 Consensus size: 39
224443 AGTTAAAAGA
*
224453 AATAATTTAAATTGTTGGGGTGAAATAAACTAAGAAATT
1 AATAATTTAAATTGTTGGGGTGAAATAAACTAAGAAAAT
* * **
224492 AATAATTT-AGTATGTTGTGGTGAAATAATTTAAGAAAAT
1 AATAATTTAAAT-TGTTGGGGTGAAATAAACTAAGAAAAT
* * *
224531 AAAAATTTAGAA-TGTTAGAGTGAAATAA
1 AATAATTTA-AATTGTTGGGGTGAAATAA
224559 CTTTAGAATT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
38 2 0.04
39 51 0.94
41 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.18, T:0.34
Consensus pattern (39 bp):
AATAATTTAAATTGTTGGGGTGAAATAAACTAAGAAAAT
Found at i:228407 original size:12 final size:12
Alignment explanation
Indices: 228390--228414 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
228380 CATTTCATCG
228390 AACAATTTCCCT
1 AACAATTTCCCT
228402 AACAATTTCCCT
1 AACAATTTCCCT
228414 A
1 A
228415 CATTGGAAAA
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:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (12 bp):
AACAATTTCCCT
Found at i:228509 original size:15 final size:15
Alignment explanation
Indices: 228489--228518 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
228479 GTTCAACCGT
228489 TTTTTTTATTATGCG
1 TTTTTTTATTATGCG
228504 TTTTTTTATTATGCG
1 TTTTTTTATTATGCG
228519 CGAATGGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67
Consensus pattern (15 bp):
TTTTTTTATTATGCG
Found at i:238549 original size:85 final size:84
Alignment explanation
Indices: 238447--238869 Score: 657
Period size: 84 Copynumber: 5.0 Consensus size: 84
238437 AATTGTGCCC
* * *
238447 ACCAAAGACCTTCGAGTTCAACTACGCTCAGCTCAAAGGCACAACATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
*
238512 CGAGAAGGCCTATCTACCA
66 CGAGAAGGGCTATCTACCA
* *
238531 ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
* * **
238596 TCGATAAGGGTTATCTGTCA
65 TCGAGAAGGGCTATCTACCA
*
238616 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
*
238681 CGAGAATGGCTATCTACCA
66 CGAGAAGGGCTATCTACCA
* * *
238700 ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAG
* *
238765 TCGAGAAGGGTTATCTTCCA
65 TCGAGAAGGGCTATCTACCA
238785 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
* *
238850 CAAGAAGGGCTATCTGCCA
66 CGAGAAGGGCTATCTACCA
238869 A
1 A
238870 AGATCATCGA
Statistics
Matches: 306, Mismatches: 31, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
84 155 0.51
85 151 0.49
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (84 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
CGAGAAGGGCTATCTACCA
Found at i:238662 original size:84 final size:84
Alignment explanation
Indices: 238447--238968 Score: 644
Period size: 84 Copynumber: 6.2 Consensus size: 84
238437 AATTGTGCCC
* * * *
238447 ACCAAAGACCTTCGAGTTCAACTACGCTCAGCTCAAAGGCACAACATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* *
238512 CGAGAAGGCCTATCTACCA
66 CGAGAAGGGCTATCTATCA
*
238531 ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
* * *
238596 TCGATAAGGGTTATCTGTCA
65 TCGAGAAGGGCTATCTATCA
* *
238616 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* *
238681 CGAGAATGGCTATCTACCA
66 CGAGAAGGGCTATCTATCA
* *
238700 ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAACATAACTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
*
238765 TCGAGAAGGGTTATCT-TCCA
65 TCGAGAAGGGCTATCTAT-CA
*
238785 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
*
238850 CAAGAAGGGCTATC--T--
66 CGAGAAGGGCTATCTATCA
* * * * * * * * * ** * *
238865 GCCAAAGATCATCGAGTTCGATTACCCCCAGCTTCGAGGGCACATAATTAACA-AATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAG
* * *
238929 GCTAGAAGGGTTATCTATC-
65 TCGAGAAGGGCTATCTATCA
238948 ACCAAAGACCTTCGAGTTCGA
1 ACCAAAGACCTTCGAGTTCGA
238969 TTCCATTCAG
Statistics
Matches: 381, Mismatches: 50, Indels: 15
0.85 0.11 0.03
Matches are distributed among these distances:
80 46 0.12
81 15 0.04
82 1 0.00
83 19 0.05
84 150 0.39
85 150 0.39
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (84 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
CGAGAAGGGCTATCTATCA
Found at i:238726 original size:169 final size:168
Alignment explanation
Indices: 238447--238869 Score: 724
Period size: 169 Copynumber: 2.5 Consensus size: 168
238437 AATTGTGCCC
* *
238447 ACCAAAGACCTTCGAGTTCAACTACGCTCAGC-TCAAAGGCACAACATTTGCAGCATAGCTTAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATTTGCAGCATAGCTTAAG
238511 TCGAGAAGGCCTATCTACCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
65 TCGAGAAGG-CTATCTACCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
* *
238576 CATTTGCAGCATAACTTAAGTCGATAAGGGTTATCTGT-CA
129 CATTTGCAACATAACTTAAGTCGAGAAGGGTTATCT-TCCA
238616 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGT
238681 CGAGAATGGCTATCTACCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATC
66 CGAGAA-GGCTATCTACCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATC
238746 ATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTTCCA
130 ATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTTCCA
*
238785 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGT
* *
238850 CAAGAAGGGCTATCTGCCAA
66 CGAGAA-GGCTATCTACCAA
238870 AGATCATCGA
Statistics
Matches: 243, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
168 1 0.00
169 238 0.98
170 4 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (168 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGT
CGAGAAGGCTATCTACCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCA
TTTGCAACATAACTTAAGTCGAGAAGGGTTATCTTCCA
Found at i:239319 original size:5 final size:5
Alignment explanation
Indices: 239309--239349 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
239299 GTCTACAAAA
*
239309 ATATT ATATT ATATT ATATT -TATT -TATT ATTATT ATTTT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT A-TATT ATATT AT
239350 TTTTGTAGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
4 8 0.24
5 20 0.61
6 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
ATATT
Found at i:239445 original size:33 final size:33
Alignment explanation
Indices: 239408--239483 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
239398 TAAATCAACA
*
239408 TATTTGAGTCCTATTGAAATACTAAAACCAAAG
1 TATTTGAGTCCTATTGAAACACTAAAACCAAAG
*
239441 TATTTGAGTCCTATTGAAACACTAAAACCGAAG
1 TATTTGAGTCCTATTGAAACACTAAAACCAAAG
*
239474 CATTTTGAGT
1 TA-TTTGAGT
239484 TCAAGTAGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 32 0.82
34 7 0.18
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (33 bp):
TATTTGAGTCCTATTGAAACACTAAAACCAAAG
Found at i:242731 original size:3 final size:3
Alignment explanation
Indices: 242714--242754 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
242704 TGGACCTGCA
242714 AAT AA- AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
242755 AACCCATATG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:243229 original size:21 final size:22
Alignment explanation
Indices: 243187--243229 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
243177 TCCGCCATGT
**
243187 TATCAACCACTGTGAATTGTCA
1 TATCAACCACTGTGAACCGTCA
*
243209 TATCAA-CACTGTGGACCGTCA
1 TATCAACCACTGTGAACCGTCA
243230 CGTTAGCACC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (22 bp):
TATCAACCACTGTGAACCGTCA
Found at i:244434 original size:17 final size:17
Alignment explanation
Indices: 244402--244435 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
244392 TTACCCTATT
*
244402 TTTTATAACTACTTTTA
1 TTTTATAACTAATTTTA
*
244419 TTTTATAATTAATTTTA
1 TTTTATAACTAATTTTA
244436 AACTTATAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTATAACTAATTTTA
Found at i:253064 original size:20 final size:20
Alignment explanation
Indices: 253021--253058 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
253011 TCAAAATCAT
* *
253021 TTTTCAAAATTTCATTTTGA
1 TTTTCAAAATCTAATTTTGA
253041 TTTTCAAAATCTAATTTT
1 TTTTCAAAATCTAATTTT
253059 ACTTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTCAAAATCTAATTTTGA
Found at i:256009 original size:3 final size:3
Alignment explanation
Indices: 256001--256109 Score: 218
Period size: 3 Copynumber: 36.3 Consensus size: 3
255991 GCAGAACAAC
256001 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
256049 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
256097 CCA CCA CCA CCA C
1 CCA CCA CCA CCA C
256110 TAGAGATAAA
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 106 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:263638 original size:24 final size:23
Alignment explanation
Indices: 263610--263683 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
263600 TTTAATAAAT
*
263610 AAACGAACATAAACGAATACGAAC
1 AAACGAACATAAACGAAAAC-AAC
* * *
263634 GAACGAATATAAACGAAAACAAT
1 AAACGAACATAAACGAAAACAAC
*
263657 AAATGAACATAAACGAACAAC-AC
1 AAACGAACATAAACGAA-AACAAC
263680 AAAC
1 AAAC
263684 ACACAAAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 20 0.50
24 20 0.50
ACGTcount: A:0.61, C:0.19, G:0.11, T:0.09
Consensus pattern (23 bp):
AAACGAACATAAACGAAAACAAC
Found at i:267364 original size:18 final size:19
Alignment explanation
Indices: 267286--267391 Score: 144
Period size: 19 Copynumber: 5.6 Consensus size: 19
267276 GTAGAATTTA
*
267286 TCCCGAAGGACCACGTAGATG
1 TCCCGAAGGACCAC--ATATG
**
267307 TCCCGAATAACCACATATG
1 TCCCGAAGGACCACATATG
*
267326 TCCCGAATGACCACATATG
1 TCCCGAAGGACCACATATG
267345 TCCCGAAGGACCAC-TATG
1 TCCCGAAGGACCACATATG
267363 TCCCGAAGGACCAC-TATG
1 TCCCGAAGGACCACATATG
267381 TCCCGAAGGAC
1 TCCCGAAGGAC
267392 AGCGTAGACC
Statistics
Matches: 80, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
18 33 0.41
19 35 0.44
21 12 0.15
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (19 bp):
TCCCGAAGGACCACATATG
Found at i:267375 original size:37 final size:38
Alignment explanation
Indices: 267286--267391 Score: 144
Period size: 37 Copynumber: 2.8 Consensus size: 38
267276 GTAGAATTTA
* **
267286 TCCCGAAGGACCACGTAGATGTCCCGAATAACCACATATG
1 TCCCGAAGGACCAC--ATATGTCCCGAAGGACCACATATG
*
267326 TCCCGAATGACCACATATGTCCCGAAGGACCAC-TATG
1 TCCCGAAGGACCACATATGTCCCGAAGGACCACATATG
267363 TCCCGAAGGACCAC-TATGTCCCGAAGGAC
1 TCCCGAAGGACCACATATGTCCCGAAGGAC
267392 AGCGTAGACC
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
36 15 0.25
37 17 0.28
38 16 0.26
40 13 0.21
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (38 bp):
TCCCGAAGGACCACATATGTCCCGAAGGACCACATATG
Found at i:279294 original size:16 final size:16
Alignment explanation
Indices: 279273--279306 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
279263 TTACTATTCA
*
279273 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
279289 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
279305 CG
1 CG
279307 GTCGGCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:283084 original size:22 final size:22
Alignment explanation
Indices: 283056--283102 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
283046 GATTTCTGGG
* *
283056 CAAGGGGGAATCGGTACCCATT
1 CAAGGGGGAACCGATACCCATT
*
283078 CAA-GGGGAACCGATACCCCTT
1 CAAGGGGGAACCGATACCCATT
283099 CAAG
1 CAAG
283103 CGAATATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.15
Consensus pattern (22 bp):
CAAGGGGGAACCGATACCCATT
Found at i:283712 original size:18 final size:18
Alignment explanation
Indices: 283689--283723 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
283679 CTAGGAGATT
283689 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
283707 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
283724 CTAGAGGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:284778 original size:22 final size:22
Alignment explanation
Indices: 284704--284770 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
284694 TTATGGACAT
*
284704 AATTCTACGGGTACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
284726 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
284748 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
284770 A
1 A
284771 TTTATACGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.28
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:287926 original size:22 final size:22
Alignment explanation
Indices: 287898--287944 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
287888 GATTTCTGGG
* *
287898 CAAGGGGGAATCGGTACCCATT
1 CAAGGGGGAACCGATACCCATT
*
287920 CAA-GGGGAACCGATACCCCTT
1 CAAGGGGGAACCGATACCCATT
287941 CAAG
1 CAAG
287945 CGAATATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.30, C:0.28, G:0.28, T:0.15
Consensus pattern (22 bp):
CAAGGGGGAACCGATACCCATT
Found at i:288553 original size:18 final size:18
Alignment explanation
Indices: 288530--288564 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
288520 CTAGGAGATT
288530 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
288548 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
288565 CTAGAGGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:289625 original size:22 final size:22
Alignment explanation
Indices: 289551--289617 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
289541 TTATGGACAT
289551 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
289573 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
289595 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
289617 A
1 A
289618 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:291410 original size:30 final size:31
Alignment explanation
Indices: 291350--291411 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
291340 GAAATAGTTG
* *
291350 TTGTTGTAATGACTGCAAGAACCAATATCAA
1 TTGTTGTAATGACTGCAAGAACAAACATCAA
*
291381 TTGTTGTAATGACT-CGAGAACAAACATCAA
1 TTGTTGTAATGACTGCAAGAACAAACATCAA
291411 T
1 T
291412 GAAAAAAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (31 bp):
TTGTTGTAATGACTGCAAGAACAAACATCAA
Found at i:292406 original size:21 final size:21
Alignment explanation
Indices: 292380--292453 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
292370 GTTTCCAAAT
292380 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
*
292401 TCGCAATGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
* * *
292422 TCGCAATGTGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
292443 TCGCAACGCGA
1 TCGCAACGCGA
292454 TTTAGTTGGT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:296098 original size:16 final size:16
Alignment explanation
Indices: 296077--296110 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
296067 TTACTATTCA
*
296077 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
296093 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
296109 CG
1 CG
296111 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:305808 original size:12 final size:12
Alignment explanation
Indices: 305791--305854 Score: 55
Period size: 12 Copynumber: 5.6 Consensus size: 12
305781 TAATACTAAC
*
305791 AAAAATGAAAAT
1 AAAAATAAAAAT
305803 AAAAATAAAAAT
1 AAAAATAAAAAT
*
305815 -AAAATAAAACT
1 AAAAATAAAAAT
* *
305826 TATAA-AAAAAT
1 AAAAATAAAAAT
305837 -AAAAT-AAAAT
1 AAAAATAAAAAT
305847 AAGAAATA
1 AA-AAATA
305855 CATCTACAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
10 8 0.19
11 16 0.38
12 18 0.43
ACGTcount: A:0.77, C:0.02, G:0.03, T:0.19
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:305812 original size:5 final size:5
Alignment explanation
Indices: 305792--305848 Score: 53
Period size: 5 Copynumber: 10.4 Consensus size: 5
305782 AATACTAACA
305792 AAAAT GAAAAT AAAAAT AAAAAT AAAAT AAAACTT ATAAA- AAAAT AAAAT
1 AAAAT -AAAAT -AAAAT -AAAAT AAAAT AAAA--T A-AAAT AAAAT AAAAT
305842 AAAAT AA
1 AAAAT AA
305849 GAAATACATC
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
4 3 0.07
5 22 0.48
6 16 0.35
7 2 0.04
8 3 0.07
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:305854 original size:17 final size:17
Alignment explanation
Indices: 305791--305845 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
305781 TAATACTAAC
305791 AAAAATGAAAATAAAAAT
1 AAAAAT-AAAATAAAAAT
*
305809 AAAAATAAAATAAAACTT
1 AAAAATAAAATAAAA-AT
*
305827 ATAAA-AAAAT-AAAAT
1 AAAAATAAAATAAAAAT
305842 AAAA
1 AAAA
305846 TAAGAAATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 14 0.44
18 11 0.34
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (17 bp):
AAAAATAAAATAAAAAT
Found at i:306470 original size:16 final size:17
Alignment explanation
Indices: 306446--306483 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
306436 ATGTCTTTTT
*
306446 AAATAATTTTAAGA-AA
1 AAATTATTTTAAGACAA
306462 AAATTATTTTAAGACAA
1 AAATTATTTTAAGACAA
306479 AAATT
1 AAATT
306484 GGTATGCGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (17 bp):
AAATTATTTTAAGACAA
Found at i:306899 original size:5 final size:5
Alignment explanation
Indices: 306884--306943 Score: 59
Period size: 5 Copynumber: 11.4 Consensus size: 5
306874 AATACTAACA
* *
306884 AAAATT AAAAT AAAAT AAAAT AAAACAT ATAAA- AATAC AAAAT AAAAT
1 AAAA-T AAAAT AAAAT AAAAT -AAA-AT A-AAAT AAAAT AAAAT AAAAT
306932 AAAAT AAAAT AA
1 AAAAT AAAAT AA
306944 GAAATACCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
4 2 0.04
5 32 0.68
6 9 0.19
7 4 0.09
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:314847 original size:6 final size:7
Alignment explanation
Indices: 314830--314861 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
314820 TGCCCTAATT
314830 TTTTTAA
1 TTTTTAA
314837 TTTTTAA
1 TTTTTAA
314844 TTTTTAA
1 TTTTTAA
314851 -TTTTAA
1 TTTTTAA
314857 TTTTT
1 TTTTT
314862 TAAAATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTAA
Found at i:314854 original size:13 final size:14
Alignment explanation
Indices: 314830--314861 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
314820 TGCCCTAATT
314830 TTTTTAATTTTTAA
1 TTTTTAATTTTTAA
314844 TTTTTAA-TTTTAA
1 TTTTTAATTTTTAA
314857 TTTTT
1 TTTTT
314862 TAAAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTAATTTTTAA
Found at i:314862 original size:14 final size:15
Alignment explanation
Indices: 314829--314864 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
314819 TTGCCCTAAT
314829 TTTTTTAATTTTTAA
1 TTTTTTAATTTTTAA
314844 -TTTTTAA-TTTTAA
1 TTTTTTAATTTTTAA
314857 TTTTTTAA
1 TTTTTTAA
314865 AATATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTTAATTTTTAA
Found at i:316167 original size:46 final size:45
Alignment explanation
Indices: 316126--316217 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
316116 CTTTATGAGC
* *
316126 TAGGT-AGGTTTAGGGTTTTTTTTTTCTTTCAAATTCATTTATGTA
1 TAGGTGAGGCTTAGGG-GTTTTTTTTCTTTCAAATTCATTTATGTA
** *
316171 TATTTGATGCTTAGGGGTTTTTTTTCTTTCAAATTCATTTATGTA
1 TAGGTGAGGCTTAGGGGTTTTTTTTCTTTCAAATTCATTTATGTA
316216 TA
1 TA
316218 TTTGATGCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
45 33 0.80
46 8 0.20
ACGTcount: A:0.21, C:0.08, G:0.16, T:0.55
Consensus pattern (45 bp):
TAGGTGAGGCTTAGGGGTTTTTTTTCTTTCAAATTCATTTATGTA
Found at i:319288 original size:18 final size:18
Alignment explanation
Indices: 319262--319300 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
319252 GATTGTATGC
*
319262 AAAAAAGAGGAAGGAACT
1 AAAAAAGAGGAAGAAACT
* *
319280 AAAAGAGAGGCAGAAACT
1 AAAAAAGAGGAAGAAACT
319298 AAA
1 AAA
319301 GGTGACTGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.08, G:0.26, T:0.05
Consensus pattern (18 bp):
AAAAAAGAGGAAGAAACT
Found at i:322706 original size:24 final size:24
Alignment explanation
Indices: 322679--322726 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
322669 CACGTTTGTA
*
322679 CAAATACGTTCAAATTATATAATT
1 CAAATACGTTAAAATTATATAATT
*
322703 CAAATATGTTAAAATTATATAATT
1 CAAATACGTTAAAATTATATAATT
322727 TCATCCAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (24 bp):
CAAATACGTTAAAATTATATAATT
Found at i:323536 original size:23 final size:24
Alignment explanation
Indices: 323493--323550 Score: 93
Period size: 22 Copynumber: 2.5 Consensus size: 24
323483 AAATAGACTT
323493 ATTATATAAAATTATTTAATG-AA
1 ATTATATAAAATTATTTAATGTAA
323516 ATTA-ATAAAATTATTTAAATGTAA
1 ATTATATAAAATTATTT-AATGTAA
323540 ATTATATAAAA
1 ATTATATAAAA
323551 CATGATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 12 0.38
23 8 0.25
24 6 0.19
25 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (24 bp):
ATTATATAAAATTATTTAATGTAA
Found at i:324923 original size:37 final size:38
Alignment explanation
Indices: 324882--324962 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 38
324872 TTCATTAAAC
* *
324882 ATTTTTAT-ATTTTCAATTTTGTAAA-AAAATTATATAA
1 ATTTTTATGAATTTAAATTTTGTAAAGAAAA-TATATAA
*
324919 A-TTTTATGAATTTAAATTTTTTAAAGAAAATATATAA
1 ATTTTTATGAATTTAAATTTTGTAAAGAAAATATATAA
324956 ATATTTT
1 AT-TTTT
324963 CCAACTTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
36 6 0.16
37 23 0.62
38 4 0.11
39 4 0.11
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (38 bp):
ATTTTTATGAATTTAAATTTTGTAAAGAAAATATATAA
Found at i:327022 original size:2 final size:2
Alignment explanation
Indices: 327015--327045 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
327005 GTTATTACAT
327015 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
327046 TATCTTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 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):
TA
Found at i:333793 original size:2 final size:2
Alignment explanation
Indices: 333786--333815 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
333776 ATTACATTGA
333786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
333816 CTTTATACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:334280 original size:20 final size:20
Alignment explanation
Indices: 334257--334299 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
334247 TTCATCCCTA
*
334257 TATAATTTATTTTAATAAAT
1 TATAATTTATATTAATAAAT
334277 TATAATTTATATTAATAAAT
1 TATAATTTATATTAATAAAT
334297 TAT
1 TAT
334300 TTAATCAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATAATTTATATTAATAAAT
Found at i:334422 original size:31 final size:31
Alignment explanation
Indices: 334384--334446 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
334374 TATAATTTGT
334384 AATTAATATTAATATAAAATATAATCTATAA
1 AATTAATATTAATATAAAATATAATCTATAA
* * *
334415 AATTAATATTAATATAAATTATATTTTATAA
1 AATTAATATTAATATAAAATATAATCTATAA
334446 A
1 A
334447 TTATATAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (31 bp):
AATTAATATTAATATAAAATATAATCTATAA
Found at i:334630 original size:36 final size:36
Alignment explanation
Indices: 334573--334663 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 36
334563 ATATGTTAAT
* * *
334573 ATTAATAAAAACTATAGTTTATAAATTATCTACTAC
1 ATTAATAAAAATTATAGTTTATAAACTATATACTAC
* * * *
334609 ATTAATACAAATTATATTTTATAAACTATATGCTAT
1 ATTAATAAAAATTATAGTTTATAAACTATATACTAC
*
334645 ATTAATATAAATTATAGTT
1 ATTAATAAAAATTATAGTT
334664 AAGATAATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (36 bp):
ATTAATAAAAATTATAGTTTATAAACTATATACTAC
Found at i:334660 original size:15 final size:15
Alignment explanation
Indices: 334642--334696 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
334632 AACTATATGC
334642 TATATTAATATAAAT
1 TATATTAATATAAAT
*
334657 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
* *
334672 TAACATTAATATAAAC
1 T-ATATTAATATAAAT
334688 TATATTAAT
1 TATATTAAT
334697 GTGTTAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
15 21 0.66
16 11 0.34
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:334694 original size:21 final size:22
Alignment explanation
Indices: 334670--334713 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
334660 AGTTAAGATA
334670 ATTAA-CATTAATATAAACTAT
1 ATTAAGCATTAATATAAACTAT
**
334691 ATTAATGTGTTAATATAAACTAT
1 ATTAA-GCATTAATATAAACTAT
334714 CATTTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (22 bp):
ATTAAGCATTAATATAAACTAT
Found at i:334726 original size:23 final size:23
Alignment explanation
Indices: 334676--334729 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
334666 GATAATTAAC
*
334676 ATTAATATAAACTATATTAATGT
1 ATTAATATAAACTATATTAATGA
* *
334699 GTTAATATAAACTATCATTTAT-A
1 ATTAATATAAACTAT-ATTAATGA
334722 ATTAATAT
1 ATTAATAT
334730 TAATAATAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (23 bp):
ATTAATATAAACTATATTAATGA
Found at i:334734 original size:29 final size:28
Alignment explanation
Indices: 334700--334824 Score: 84
Period size: 31 Copynumber: 4.5 Consensus size: 28
334690 TATTAATGTG
*
334700 TTAATATAAACTATCATTTATAATTAATA
1 TTAATATAAA-TATAATTTATAATTAATA
*
334729 TT-A-AT--A-ATAACTTAT-ATTAATA
1 TTAATATAAATATAATTTATAATTAATA
** *
334751 -TAATATAGTTTATAATTTCTAATTAATA
1 TTAATATA-AATATAATTTATAATTAATA
* *
334779 TTAATATAAAATATAATCTATAAAACTAATA
1 TTAATAT-AAATATAAT-T-TATAATTAATA
*
334810 TTAATATTAATATAA
1 TTAATATAAATATAA
334825 ACTATTTTAT
Statistics
Matches: 74, Mismatches: 11, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
21 1 0.01
22 8 0.11
23 9 0.12
25 1 0.01
27 9 0.12
28 8 0.11
29 14 0.19
30 9 0.12
31 15 0.20
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (28 bp):
TTAATATAAATATAATTTATAATTAATA
Found at i:334861 original size:16 final size:17
Alignment explanation
Indices: 334830--334861 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
334820 TATAAACTAT
334830 TTTATAAATATATAGTA
1 TTTATAAATATATAGTA
334847 TTTATAAAT-TATAGT
1 TTTATAAATATATAGT
334862 TAATATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
TTTATAAATATATAGTA
Found at i:334942 original size:15 final size:17
Alignment explanation
Indices: 334909--334952 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
334899 ACTATAATTA
334909 ATATTAATATTATATACT
1 ATATTAATA-TATATACT
334927 ATATTAATATA-A-ACT
1 ATATTAATATATATACT
334942 ATAGTTAATAT
1 ATA-TTAATAT
334953 GTTAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.24
16 8 0.32
17 2 0.08
18 9 0.36
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (17 bp):
ATATTAATATATATACT
Found at i:335011 original size:36 final size:36
Alignment explanation
Indices: 334971--335049 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
334961 TAATGTAAAC
*
334971 TATAGTTTATAAACTATCTACTACATTAATACAAAT
1 TATAGTTTATAAACTATATACTACATTAATACAAAT
* * *
335007 TATAGTTTATAAACTATATGCTATATTAATATAAAT
1 TATAGTTTATAAACTATATACTACATTAATACAAAT
335043 TATAGTT
1 TATAGTT
335050 AAGATAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (36 bp):
TATAGTTTATAAACTATATACTACATTAATACAAAT
Found at i:335046 original size:15 final size:15
Alignment explanation
Indices: 335028--335078 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
335018 AACTATATGC
335028 TATATTAATATAAAT
1 TATATTAATATAAAT
*
335043 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
*
335058 TAACATTAATATAAAT
1 T-ATATTAATATAAAT
335074 TATAT
1 TATAT
335079 AGTACATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:335118 original size:21 final size:21
Alignment explanation
Indices: 335089--335136 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
335079 AGTACATTAA
* * *
335089 TATAAACTATAGTTTATAAAT
1 TATATACTATAGGTTATAAAC
335110 TATATACTATAGGTTATAAAC
1 TATATACTATAGGTTATAAAC
335131 TATATA
1 TATATA
335137 GGACACTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (21 bp):
TATATACTATAGGTTATAAAC
Found at i:335277 original size:52 final size:54
Alignment explanation
Indices: 335220--335380 Score: 200
Period size: 52 Copynumber: 2.9 Consensus size: 54
335210 ATATTACATA
*
335220 ATACATATACTATAGGTTACATATATAGTTTACATATA-AATACAT-TGTATAT
1 ATACATATACTATAGGTTACATATATAGTTTACATATACAATACATATGTATAC
* * * *
335272 ATACATATACTATAGGTTATATATATAGTTTATATATACTATACATAGTTTATAC
1 ATACATATACTATAGGTTACATATATAGTTTACATATACAATACATA-TGTATAC
* *
335327 ATACATATACAATAAGTTACATATATAGTTTACATGTATACATATACTATATGT
1 ATACATATACTATAGGTTACATATATAGTTTACA--TATACA-ATAC-ATATGT
335381 TGCATATATT
Statistics
Matches: 91, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
52 36 0.40
53 6 0.07
55 35 0.38
57 5 0.05
58 6 0.07
59 3 0.03
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (54 bp):
ATACATATACTATAGGTTACATATATAGTTTACATATACAATACATATGTATAC
Found at i:335305 original size:11 final size:13
Alignment explanation
Indices: 335276--335309 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
335266 GTATATATAC
335276 ATATACTATAGGTT
1 ATATA-TATAGGTT
*
335290 ATATATATAGTTT
1 ATATATATAGGTT
335303 ATATATA
1 ATATATA
335310 CTATACATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (13 bp):
ATATATATAGGTT
Found at i:335314 original size:20 final size:20
Alignment explanation
Indices: 335291--335335 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
335281 CTATAGGTTA
*
335291 TATATATAGTTTATATATAC
1 TATATATAGTTTATACATAC
*
335311 TATACATAGTTTATACATAC
1 TATATATAGTTTATACATAC
335331 -ATATA
1 TATATA
335336 CAATAAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (20 bp):
TATATATAGTTTATACATAC
Found at i:335452 original size:16 final size:17
Alignment explanation
Indices: 335425--335465 Score: 66
Period size: 16 Copynumber: 2.4 Consensus size: 17
335415 TAAGGTTACA
335425 TATATAATTTATATAAAC
1 TATAT-ATTTATATAAAC
335443 TA-ATATTTATATAAAC
1 TATATATTTATATAAAC
335459 TATATAT
1 TATATAT
335466 GAATTATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 14 0.64
17 6 0.27
18 2 0.09
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
TATATATTTATATAAAC
Found at i:335712 original size:21 final size:21
Alignment explanation
Indices: 335683--335755 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
335673 ATGTATAGTT
*
335683 TATACATATATAATTTATTTA
1 TATATATATATAATTTATTTA
* *
335704 TATATATATATAATATATATA
1 TATATATATATAATTTATTTA
335725 T-TA-ATATA-AATTATAGTTTA
1 TATATATATATAATT-TA-TTTA
*
335745 TAAACTATATA
1 TATA-TATATA
335756 CTTTTTATAG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
18 3 0.07
19 7 0.17
20 6 0.15
21 20 0.49
23 5 0.12
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (21 bp):
TATATATATATAATTTATTTA
Found at i:335739 original size:15 final size:18
Alignment explanation
Indices: 335683--335731 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 18
335673 ATGTATAGTT
*
335683 TATACATATATAAT-TTA
1 TATATATATATAATATTA
* *
335700 TTTATATATAT-ATATAA
1 TATATATATATAATATTA
335717 TATATATAT-TAATAT
1 TATATATATATAATAT
335732 AAATTATAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.12
17 23 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATATATATAATATTA
Found at i:335739 original size:17 final size:19
Alignment explanation
Indices: 335683--335739 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
335673 ATGTATAGTT
* * *
335683 TATACATATATAATTTATT
1 TATATATATATAAATTATA
335702 TATATATATATATAA-TATA
1 TATATATATATA-AATTATA
335721 TATAT-TAATATAAATTATA
1 TATATAT-ATATAAATTATA
335740 GTTTATAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 3 0.09
19 28 0.88
20 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATATATATAAATTATA
Found at i:335793 original size:13 final size:13
Alignment explanation
Indices: 335761--335841 Score: 90
Period size: 13 Copynumber: 5.9 Consensus size: 13
335751 ATATACTTTT
335761 TATAGTTTATACCTA
1 TATAGTTTATA--TA
335776 TATAGTTTATATA
1 TATAGTTTATATA
*
335789 CATAGTTTATATA
1 TATAGTTTATATA
*
335802 TATAGTTCATATAAA
1 TATAGTT--TATATA
*
335817 CATAGTTTATATA
1 TATAGTTTATATA
*
335830 TGTAGTTTATAT
1 TATAGTTTATAT
335842 TAATTATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
13 35 0.61
15 22 0.39
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:335796 original size:28 final size:26
Alignment explanation
Indices: 335762--335841 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 26
335752 TATACTTTTT
335762 ATAGTTTATACCTATATAGTTTATATAC
1 ATAGTTTATA--TATATAGTTTATATAC
*
335790 ATAGTTTATATATATAGTTCATATAAAC
1 ATAGTTTATATATATAGTT--TATATAC
*
335818 ATAGTTTATATATGTAGTTTATAT
1 ATAGTTTATATATATAGTTTATAT
335842 TAATTATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
26 13 0.28
28 34 0.72
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (26 bp):
ATAGTTTATATATATAGTTTATATAC
Found at i:335805 original size:85 final size:84
Alignment explanation
Indices: 335612--335805 Score: 237
Period size: 85 Copynumber: 2.3 Consensus size: 84
335602 ATAGATTACC
* * *
335612 TATATTACTTATACATATATATGCTATATTAATATAAATTATAATTTATAAACTATAACTGATGT
1 TATA-TACATATATATATATAT-ATATATTAATATAAATTATAATTTATAAACTATAACTGATGT
335677 ATAGTTTATACATATATAATT
64 ATAGTTTATACATATATAATT
* * * * *
335698 TATTTATATATATATATAATATATATATTAATATAAATTATAGTTTATAAACTATATACT-TTTT
1 TATATACATATATATAT-ATATATATATTAATATAAATTATAATTTATAAACTATA-ACTGATGT
* *
335762 ATAGTTTATACCTATATAGTT
64 ATAGTTTATACATATATAATT
*
335783 TATATACATAGTTTATATATATA
1 TATATACATA-TATATATATATA
335806 GTTCATATAA
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
85 76 0.83
86 16 0.17
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (84 bp):
TATATACATATATATATATATATATATTAATATAAATTATAATTTATAAACTATAACTGATGTAT
AGTTTATACATATATAATT
Found at i:335869 original size:20 final size:18
Alignment explanation
Indices: 335827--335878 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
335817 CATAGTTTAT
*
335827 ATATGTAGTTTATATTAA
1 ATATATAGTTTATATTAA
*
335845 TTATATAGTTTATAATATAA
1 ATATATAGTTTAT-AT-TAA
335865 ATATA-A-TTTATATT
1 ATATATAGTTTATATT
335879 GGTTGTCTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.03
17 2 0.07
18 16 0.55
19 3 0.10
20 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
ATATATAGTTTATATTAA
Found at i:336299 original size:11 final size:11
Alignment explanation
Indices: 336283--336316 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
336273 GTTTATTAAC
*
336283 AAACTACATGT
1 AAACTACATAT
336294 AAACTACATAT
1 AAACTACATAT
*
336305 AAACTATATAT
1 AAACTACATAT
336316 A
1 A
336317 TTATATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.29
Consensus pattern (11 bp):
AAACTACATAT
Found at i:346021 original size:22 final size:22
Alignment explanation
Indices: 345996--346038 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
345986 GGAAGTTAAC
345996 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
346018 GGTCAACTGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
346039 AGACCGGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.23, G:0.47, T:0.21
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:346098 original size:9 final size:9
Alignment explanation
Indices: 346035--346113 Score: 59
Period size: 10 Copynumber: 8.3 Consensus size: 9
346025 TGTCGGGTCG
*
346035 GGTCAGACC
1 GGTCAAACC
*
346044 GGTTCAGACC
1 GG-TCAAACC
*
346054 GGTCAAATC
1 GGTCAAACC
*
346063 GGTTCGAACC
1 GG-TCAAACC
346073 GGTCGAAACC
1 GGTC-AAACC
**
346083 GAACAAACC
1 GGTCAAACC
*
346092 GGTCAAAATC
1 GGTC-AAACC
346102 GGTCAAACC
1 GGTCAAACC
346111 GGT
1 GGT
346114 TTTCAGCCAC
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
9 25 0.45
10 30 0.55
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:346108 original size:19 final size:18
Alignment explanation
Indices: 346051--346113 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
346041 ACCGGTTCAG
*
346051 ACCGGTCAAATCGGTTCGA
1 ACCGGTCAAATCGG-TCAA
* **
346070 ACCGGTCGAAACCGAACAA
1 ACCGGTC-AAATCGGTCAA
346089 ACCGGTCAAAATCGGTCAA
1 ACCGGTC-AAATCGGTCAA
346108 ACCGGT
1 ACCGGT
346114 TTTCAGCCAC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
19 30 0.86
20 5 0.14
ACGTcount: A:0.33, C:0.29, G:0.24, T:0.14
Consensus pattern (18 bp):
ACCGGTCAAATCGGTCAA
Found at i:352918 original size:18 final size:21
Alignment explanation
Indices: 352895--352949 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 21
352885 ATTCCTGAGA
352895 GAATTGAAATCTGT-GAA-T-
1 GAATTGAAATCTGTAGAATTG
352913 GAATTGAAATCTGTAGGAATTG
1 GAATTGAAATCTGTA-GAATTG
352935 GAATTTGAAATCTGT
1 GAA-TTGAAATCTGT
352950 TTGGTTGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 14 0.44
20 3 0.09
21 1 0.03
22 3 0.09
23 11 0.34
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (21 bp):
GAATTGAAATCTGTAGAATTG
Found at i:353573 original size:32 final size:33
Alignment explanation
Indices: 353503--353606 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
353493 CCTAAACCTG
* *
353503 AACCCGACCCAAAAATCACACTTAAAAAAGCCC
1 AACCCGACCCGAAAATCAAACTTAAAAAAGCCC
* * *
353536 GACCCGACCCGAATATTAAACTTAAAAAA-CCC
1 AACCCGACCCGAAAATCAAACTTAAAAAAGCCC
* * * **
353568 AACCCGACCCG-AACTCGAATTTAAAAAAATCC
1 AACCCGACCCGAAAATCAAACTTAAAAAAGCCC
353600 AACCCGA
1 AACCCGA
353607 TCCTGAAATT
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
31 12 0.21
32 22 0.38
33 24 0.41
ACGTcount: A:0.45, C:0.34, G:0.09, T:0.12
Consensus pattern (33 bp):
AACCCGACCCGAAAATCAAACTTAAAAAAGCCC
Found at i:355958 original size:128 final size:128
Alignment explanation
Indices: 355730--356588 Score: 1463
Period size: 128 Copynumber: 6.7 Consensus size: 128
355720 AATCTCATTT
* * *
355730 GGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCTCTATTATGTCACTCATGT
1 GGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
**
355795 CCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCC
66 CCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTAGGCACATGAAGGCGCGTTCCC
*
355858 GGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
1 GGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
* *
355923 CCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTGGGGACATGAAGGCGCGTTCCC
66 CCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTAGGCACATGAAGGCGCGTTCCC
*
355986 GGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
1 GGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
**
356051 CCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCC
66 CCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTAGGCACATGAAGGCGCGTTCCC
*
356114 GGGGG-GCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
1 GGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
** *
356178 CCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGTGCGTTCCC
66 CCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTAGGCACATGAAGGCGCGTTCCC
*
356241 GGGGGCGCGCCTTCCATTATTTCGTTAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
1 GGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
* * **
356306 CCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC-AGGGGACATGAAGGCGTATTCCC
66 CCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA-GGCACATGAAGGCGCGTTCCC
*
356369 GGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
1 GGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
* * *
356434 CCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC-AGGGGACAGGAAGGCGCGTTCCC
66 CCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA-GGCACATGAAGGCGCGTTCCC
356497 GGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
1 GGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
356562 CCCTCGGGGACACTAGATATATCAGTA
66 CCCTCGGGGACACTAGATATATCAGTA
356589 AATCAGGTAA
Statistics
Matches: 700, Mismatches: 29, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
127 126 0.18
128 574 0.82
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (128 bp):
GGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
CCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTAGGCACATGAAGGCGCGTTCCC
Found at i:356438 original size:383 final size:383
Alignment explanation
Indices: 355731--356588 Score: 1565
Period size: 383 Copynumber: 2.2 Consensus size: 383
355721 ATCTCATTTG
*
355731 GGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCTCTATTATGTCACTCATGTC
1 GGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTC
355796 CCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGG
66 CCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGG
355861 GGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
131 GGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
* *
355926 TCGGGGACACTAGATATATCAGTACCTATTATTTCACTGGGGACATGAAGGCGCGTTCCCGGGGG
196 TCGGGGACACTAGATATATCAGTACCTATTATTTCACAGGGGACATGAAGGCGCATTCCCGGGGG
355991 GGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTC
261 GGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTC
** *
356056 GGGGACACTAGATATATCAGTACCTATTATTTCACTA-TTCACATGAAGGCGCGTTCCC
326 GGGGACACTAGATATATCAGTACCTATTATTTCAC-AGGGCACAGGAAGGCGCGTTCCC
356114 GGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTC
1 GGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTC
*
356179 CCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGTGCGTTCCCGGG
66 CCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGG
* *
356244 GGCGCGCCTTCCATTATTTCGTTAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
131 GGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
* *
356309 TCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACATGAAGGCGTATTCCCGGGGG
196 TCGGGGACACTAGATATATCAGTACCTATTATTTCACAGGGGACATGAAGGCGCATTCCCGGGGG
356374 GGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTC
261 GGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTC
* *
356439 GGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACAGGAAGGCGCGTTCCC
326 GGGGACACTAGATATATCAGTACCTATTATTTCACAGGGCACAGGAAGGCGCGTTCCC
*
356497 GGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
1 GGGGG-GCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGT
356562 CCCTCGGGGACACTAGATATATCAGTA
65 CCCTCGGGGACACTAGATATATCAGTA
356589 AATCAGGTAA
Statistics
Matches: 459, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
382 1 0.00
383 373 0.81
384 85 0.19
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (383 bp):
GGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTC
CCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATTCACATGAAGGCGCGTTCCCGGG
GGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCC
TCGGGGACACTAGATATATCAGTACCTATTATTTCACAGGGGACATGAAGGCGCATTCCCGGGGG
GGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTC
GGGGACACTAGATATATCAGTACCTATTATTTCACAGGGCACAGGAAGGCGCGTTCCC
Found at i:357027 original size:34 final size:34
Alignment explanation
Indices: 356989--357088 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 34
356979 AAATTTAATG
*
356989 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* * * *
357023 TTAAA-TTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* *
357056 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTTGAATAATATAATTTATATTTTAAA
357089 AACATTTATC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (34 bp):
TTAAATTTTGAATAATATAATTTATATTTTAAAT
Found at i:357641 original size:21 final size:20
Alignment explanation
Indices: 357610--357679 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
357600 GGTATAAAAC
* *
357610 CCTGCGCGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
357630 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
357651 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
357672 CCCTGCGG
1 -CCTGCGG
357680 AGATGGCATA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.19, C:0.29, G:0.34, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:359490 original size:32 final size:31
Alignment explanation
Indices: 359449--359534 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 31
359439 ATAATAATTC
* *
359449 TAAATAATAATAATATATAAATATTATT-TTAA
1 TAAAAAATAATAATATATAAATA-TATTAAT-A
* *
359481 TAAAAAATAATATTTACATAAATATATTAATA
1 TAAAAAATAATA-ATATATAAATATATTAATA
*
359513 TAAAAAATAATAACTATTTAAA
1 TAAAAAATAATAA-TATATAAA
359535 AAAATACTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
32 34 0.77
33 10 0.23
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAATAATAATATATAAATATATTAATA
Found at i:360589 original size:9 final size:9
Alignment explanation
Indices: 360577--360628 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
360567 TAATATTTTA
360577 TATTTAATT
1 TATTTAATT
*
360586 TATTTAA-G
1 TATTTAATT
360594 TATTTAATT
1 TATTTAATT
360603 TATTTAA--
1 TATTTAATT
*
360610 TATTTTATT
1 TATTTAATT
*
360619 TAATTAATT
1 TATTTAATT
360628 T
1 T
360629 TTTTTTGCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:360599 original size:17 final size:16
Alignment explanation
Indices: 360570--360626 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
360560 ATATTTTTAA
*
360570 TATTTTATATTTAATT
1 TATTTAATATTTAATT
360586 TATTTAAGTATTTAATT
1 TATTTAA-TATTTAATT
*
360603 TATTTAATATTTTATT
1 TATTTAATATTTAATT
*
360619 TAATTAAT
1 TATTTAAT
360627 TTTTTTTTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 21 0.57
17 16 0.43
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TATTTAATATTTAATT
Found at i:362879 original size:26 final size:26
Alignment explanation
Indices: 362824--362889 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
362814 ATAGATTCTG
* *
362824 TTTTTTATTATATTTGTATTTAGTAC
1 TTTTTTATTATAGTTGTATTTAGGAC
*
362850 -TTTTTATTATAGTTGT-TTATTGGAC
1 TTTTTTATTATAGTTGTATT-TAGGAC
*
362875 TTTTTTATTGTAGTT
1 TTTTTTATTATAGTT
362890 TTTTTTTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 2 0.06
25 19 0.56
26 13 0.38
ACGTcount: A:0.20, C:0.03, G:0.12, T:0.65
Consensus pattern (26 bp):
TTTTTTATTATAGTTGTATTTAGGAC
Found at i:362891 original size:13 final size:13
Alignment explanation
Indices: 362850--362893 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
362840 TATTTAGTAC
*
362850 TTTTTATTATAGT
1 TTTTTATTGTAGT
* * *
362863 TGTTTATTGGACT
1 TTTTTATTGTAGT
362876 TTTTTATTGTAGT
1 TTTTTATTGTAGT
362889 TTTTT
1 TTTTT
362894 TTTATTATTT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAGT
Found at i:371984 original size:19 final size:20
Alignment explanation
Indices: 371946--371984 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
371936 TAAAGGAAAA
*
371946 GAAAGGAAAGGAAAGTTAAG
1 GAAAGGAAAGGAAAGATAAG
*
371966 GAAA-GAAAGGAAGGATAAG
1 GAAAGGAAAGGAAAGATAAG
371985 TAAGGGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (20 bp):
GAAAGGAAAGGAAAGATAAG
Found at i:394484 original size:31 final size:31
Alignment explanation
Indices: 394424--394484 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
394414 TGATAGAGTA
** * *
394424 ACCATTTTGTTATAAATCGATAATGTTAGTG
1 ACCATTTTGTTATAAATAAAAAATATTAGTG
394455 ACCATTTTGTTATAAATAAAAAATATTAGT
1 ACCATTTTGTTATAAATAAAAAATATTAGT
394485 AATCAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.41
Consensus pattern (31 bp):
ACCATTTTGTTATAAATAAAAAATATTAGTG
Found at i:395041 original size:21 final size:20
Alignment explanation
Indices: 394981--395034 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 20
394971 TCTTGTATAG
394981 TGCTACCTAAAATGTTATTT
1 TGCTACCTAAAATGTTATTT
* *
395001 T-TTACCGAAAATGTTAATTT
1 TGCTACCTAAAATGTT-ATTT
395021 TGCTACCTAAAATG
1 TGCTACCTAAAATG
395035 AATATTTCCG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 12 0.43
20 6 0.21
21 10 0.36
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (20 bp):
TGCTACCTAAAATGTTATTT
Found at i:395825 original size:16 final size:16
Alignment explanation
Indices: 395804--395836 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
395794 GGTGATTTTT
395804 AAAAAATGAGAGATGA
1 AAAAAATGAGAGATGA
395820 AAAAAATGAGAGATGA
1 AAAAAATGAGAGATGA
395836 A
1 A
395837 TATTCATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.12
Consensus pattern (16 bp):
AAAAAATGAGAGATGA
Found at i:411924 original size:34 final size:35
Alignment explanation
Indices: 411861--411945 Score: 118
Period size: 34 Copynumber: 2.4 Consensus size: 35
411851 TAAAATACGA
*
411861 TATGAACAATACCGTATGAACATTAATGAACAATAC
1 TATGAACAATACCG-ATGAACAGTAATGAACAATAC
* *
411897 TATGAACAGTACC-ATGAACAGTGATGAACAATAC
1 TATGAACAATACCGATGAACAGTAATGAACAATAC
*
411931 CATGAACAATACCGA
1 TATGAACAATACCGA
411946 ATGTTAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
34 30 0.70
35 1 0.02
36 12 0.28
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (35 bp):
TATGAACAATACCGATGAACAGTAATGAACAATAC
Found at i:411943 original size:12 final size:12
Alignment explanation
Indices: 411862--411943 Score: 73
Period size: 12 Copynumber: 7.0 Consensus size: 12
411852 AAAATACGAT
411862 ATGAACAATACC
1 ATGAACAATACC
*
411874 GTATGAACATTA--
1 --ATGAACAATACC
*
411886 ATGAACAATACT
1 ATGAACAATACC
*
411898 ATGAACAGTACC
1 ATGAACAATACC
* *
411910 ATGAACAGT--G
1 ATGAACAATACC
411920 ATGAACAATACC
1 ATGAACAATACC
411932 ATGAACAATACC
1 ATGAACAATACC
411944 GAATGTTAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
10 17 0.30
12 31 0.54
14 9 0.16
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (12 bp):
ATGAACAATACC
Found at i:412864 original size:32 final size:32
Alignment explanation
Indices: 412812--412918 Score: 171
Period size: 32 Copynumber: 3.4 Consensus size: 32
412802 GTTCTTTAGA
*
412812 ACATAGGT-ATATTGTCCATATGTCTCAAAAG
1 ACATAGGTAATTTTGTCCATATGTCTCAAAAG
412843 ACATAGGTAATTTTGTCCATATGTCTCAAAAG
1 ACATAGGTAATTTTGTCCATATGTCTCAAAAG
* * *
412875 ACATAGGTAATTATGTCCATATGTCCCGAAAG
1 ACATAGGTAATTTTGTCCATATGTCTCAAAAG
412907 ACATAGGTAATT
1 ACATAGGTAATT
412919 CCTCGACTCT
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
31 8 0.11
32 63 0.89
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.32
Consensus pattern (32 bp):
ACATAGGTAATTTTGTCCATATGTCTCAAAAG
Found at i:413401 original size:16 final size:16
Alignment explanation
Indices: 413376--413408 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
413366 TACTATTATG
*
413376 TATTCTCATATACATA
1 TATTCACATATACATA
413392 TATTCACATATACATA
1 TATTCACATATACATA
413408 T
1 T
413409 CATTTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTCACATATACATA
Found at i:414787 original size:18 final size:18
Alignment explanation
Indices: 414764--414806 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
414754 ACCGGTCACA
414764 ACCCGACCCAACCCGTTT
1 ACCCGACCCAACCCGTTT
*
414782 ACCCGACCCGACCCGTTT
1 ACCCGACCCAACCCGTTT
414800 ACCCGAC
1 ACCCGAC
414807 TCGTTGACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.51, G:0.14, T:0.14
Consensus pattern (18 bp):
ACCCGACCCAACCCGTTT
Found at i:414790 original size:13 final size:13
Alignment explanation
Indices: 414786--414848 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
414776 CCGTTTACCC
414786 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
414799 TACCCGACTCGTT
1 GACCCGACCCGTT
414812 GACCCGACTCGACTCGTT
1 GACCCGA--C--C-CGTT
414830 GACCCGACCCGTT
1 GACCCGACCCGTT
414843 GACCCG
1 GACCCG
414849 TTGACCGTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 27 0.66
14 1 0.02
15 1 0.02
16 1 0.02
18 11 0.27
ACGTcount: A:0.16, C:0.43, G:0.22, T:0.19
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:414817 original size:31 final size:31
Alignment explanation
Indices: 414768--414848 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
414758 GTCACAACCC
* *
414768 GACCCAACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * * *
414799 TACCCGACTCGTTGACCCGACTCGACTCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
414830 GACCCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
414849 TTGACCGTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.17, C:0.44, G:0.20, T:0.19
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:414824 original size:18 final size:18
Alignment explanation
Indices: 414803--414837 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
414793 CCCGTTTACC
414803 CGACTCGTTGACCCGACT
1 CGACTCGTTGACCCGACT
414821 CGACTCGTTGACCCGAC
1 CGACTCGTTGACCCGAC
414838 CCGTTGACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.40, G:0.23, T:0.20
Consensus pattern (18 bp):
CGACTCGTTGACCCGACT
Found at i:414848 original size:8 final size:8
Alignment explanation
Indices: 414835--414875 Score: 68
Period size: 8 Copynumber: 5.4 Consensus size: 8
414825 TCGTTGACCC
414835 GACCCGTT
1 GACCCGTT
414843 GACCCGTT
1 GACCCGTT
414851 GA-CCGTT
1 GACCCGTT
414858 GACCCGTT
1 GACCCGTT
414866 GA-CCGTT
1 GACCCGTT
414873 GAC
1 GAC
414876 TACTGTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 14 0.45
8 17 0.55
ACGTcount: A:0.15, C:0.34, G:0.27, T:0.24
Consensus pattern (8 bp):
GACCCGTT
Found at i:414858 original size:7 final size:7
Alignment explanation
Indices: 414838--414875 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
414828 TTGACCCGAC
414838 CCGTTGA
1 CCGTTGA
414845 CCCGTTGA
1 -CCGTTGA
414853 CCGTTGA
1 CCGTTGA
414860 CCCGTTGA
1 -CCGTTGA
414868 CCGTTGA
1 CCGTTGA
414875 C
1 C
414876 TACTGTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:414858 original size:15 final size:15
Alignment explanation
Indices: 414838--414875 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
414828 TTGACCCGAC
414838 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
414853 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
414868 CCGTTGAC
1 CCGTTGAC
414876 TACTGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:416005 original size:18 final size:18
Alignment explanation
Indices: 415979--416013 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
415969 TCGAAAGGAC
*
415979 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
415997 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
416014 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:419698 original size:18 final size:18
Alignment explanation
Indices: 419675--419717 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
419665 ACCGGTCACA
419675 ACCCGACCCAACCCGTTT
1 ACCCGACCCAACCCGTTT
*
419693 ACCCGACCCGACCCGTTT
1 ACCCGACCCAACCCGTTT
419711 ACCCGAC
1 ACCCGAC
419718 TCGTTGACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.51, G:0.14, T:0.14
Consensus pattern (18 bp):
ACCCGACCCAACCCGTTT
Found at i:419701 original size:13 final size:13
Alignment explanation
Indices: 419697--419757 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
419687 CCGTTTACCC
419697 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
419710 TACCCGACTCGTT
1 GACCCGACCCGTT
419723 GACCCGACTCGACTCGTT
1 GACCCGA--C--C-CGTT
419741 GACCCGACCCGTT
1 GACCCGACCCGTT
419754 GACC
1 GACC
419758 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 25 0.64
14 1 0.03
15 1 0.03
16 1 0.03
18 11 0.28
ACGTcount: A:0.16, C:0.43, G:0.21, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:419728 original size:31 final size:31
Alignment explanation
Indices: 419679--419757 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
419669 GTCACAACCC
* *
419679 GACCCAACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * * *
419710 TACCCGACTCGTTGACCCGACTCGACTCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
419741 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
419758 GTTGACCGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.18, C:0.44, G:0.19, T:0.19
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:419735 original size:18 final size:18
Alignment explanation
Indices: 419714--419748 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
419704 CCCGTTTACC
419714 CGACTCGTTGACCCGACT
1 CGACTCGTTGACCCGACT
419732 CGACTCGTTGACCCGAC
1 CGACTCGTTGACCCGAC
419749 CCGTTGACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.40, G:0.23, T:0.20
Consensus pattern (18 bp):
CGACTCGTTGACCCGACT
Found at i:419761 original size:7 final size:7
Alignment explanation
Indices: 419749--419785 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
419739 TTGACCCGAC
419749 CCGTTGA
1 CCGTTGA
419756 CCGTTGA
1 CCGTTGA
419763 CCGTTGA
1 CCGTTGA
419770 CCCGTTGA
1 -CCGTTGA
419778 CCGTTGA
1 CCGTTGA
419785 C
1 C
419786 TACTGTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (7 bp):
CCGTTGA
Found at i:419774 original size:15 final size:15
Alignment explanation
Indices: 419749--419785 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
419739 TTGACCCGAC
419749 CCGTTGA-CCGTTGA
1 CCGTTGACCCGTTGA
419763 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
419778 CCGTTGAC
1 CCGTTGAC
419786 TACTGTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:420915 original size:18 final size:18
Alignment explanation
Indices: 420889--420923 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
420879 TCGAAAGGAC
*
420889 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
420907 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
420924 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:429484 original size:3 final size:3
Alignment explanation
Indices: 429471--429529 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
429461 TTTTTATCCA
* *
429471 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
429519 TAT TAT TAT TA
1 TAT TAT TAT TA
429530 ATAAATATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:429544 original size:14 final size:14
Alignment explanation
Indices: 429525--429565 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
429515 TTATTATTAT
429525 TATTAATAAATATA
1 TATTAATAAATATA
429539 TATTAAATAAATATA
1 TATT-AATAAATATA
*
429554 TATAAATAAATA
1 TATTAATAAATA
429566 ATTACAGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATTAATAAATATA
Found at i:429549 original size:15 final size:15
Alignment explanation
Indices: 429525--429565 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
429515 TTATTATTAT
429525 TATT-AATAAATATA
1 TATTAAATAAATATA
429539 TATTAAATAAATATA
1 TATTAAATAAATATA
429554 TA-TAAATAAATA
1 TATTAAATAAATA
429566 ATTACAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATTAAATAAATATA
Done.