Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_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: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 49
Found at i:215725 original size:10 final size:10
Alignment explanation
Indices: 215713--215767 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
215703 TTTATGTTTG
*
215713 TTTACGTTCG
1 TTTACGTTCA
215723 TTTACGTTCA
1 TTTACGTTCA
*
215733 TTTATGTTCA
1 TTTACGTTCA
*
215743 TTTATTGTGTTCA
1 TTTA---CGTTCA
215756 TTTACGTTCA
1 TTTACGTTCA
215766 TT
1 TT
215768 CGTTCGTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
10 29 0.74
13 10 0.26
ACGTcount: A:0.16, C:0.15, G:0.13, T:0.56
Consensus pattern (10 bp):
TTTACGTTCA
Found at i:227393 original size:20 final size:20
Alignment explanation
Indices: 227368--227428 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
227358 TTTTGGTGCA
*
227368 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
227388 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
227409 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
227429 TACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:227437 original size:21 final size:21
Alignment explanation
Indices: 227390--227451 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
227380 ACCCCCATGA
227390 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--TGAAG
227413 GGGAACCGATTCCCCCT-ACAG
1 GGGAACCGATTCCCCCTGA-AG
* *
227434 GGGAATCGATACCCCCTG
1 GGGAACCGATTCCCCCTG
227452 GGGTTCTGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 1 0.03
21 18 0.51
23 16 0.46
ACGTcount: A:0.23, C:0.34, G:0.26, T:0.18
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTGAAG
Found at i:237501 original size:14 final size:14
Alignment explanation
Indices: 237482--237513 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
237472 AGAGGCTCAG
237482 CGATGAATATCAAA
1 CGATGAATATCAAA
237496 CGATGAATATCAAA
1 CGATGAATATCAAA
237510 CGAT
1 CGAT
237514 TTTAAACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.22
Consensus pattern (14 bp):
CGATGAATATCAAA
Found at i:240112 original size:20 final size:21
Alignment explanation
Indices: 240080--240123 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
240070 TTGGGTTAAA
240080 TTAGTTTGTTTGTAAATT-TT
1 TTAGTTTGTTTGTAAATTCTT
*
240100 TTAGTCTTG-TTGTCAATTCTT
1 TTAGT-TTGTTTGTAAATTCTT
240121 TTA
1 TTA
240124 AAGACTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.18, C:0.07, G:0.14, T:0.61
Consensus pattern (21 bp):
TTAGTTTGTTTGTAAATTCTT
Found at i:249680 original size:52 final size:53
Alignment explanation
Indices: 249615--249721 Score: 162
Period size: 52 Copynumber: 2.0 Consensus size: 53
249605 CACAAGATGG
* * *
249615 GGCACATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAA
1 GGCACATA-AAATAGGAAACTAGCATAGAGTTAGGGAATTACAACTAATCACAA
*
249669 GGCACAT-AAATAGGAGACTAGCATAGAGTTAGGGAATTACAACTAATCACAA
1 GGCACATAAAATAGGAAACTAGCATAGAGTTAGGGAATTACAACTAATCACAA
249721 G
1 G
249722 AATATTATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 42 0.86
54 7 0.14
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (53 bp):
GGCACATAAAATAGGAAACTAGCATAGAGTTAGGGAATTACAACTAATCACAA
Found at i:254277 original size:52 final size:53
Alignment explanation
Indices: 254212--254318 Score: 162
Period size: 52 Copynumber: 2.0 Consensus size: 53
254202 CACAAGATGG
* * *
254212 GGCACATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAA
1 GGCACATA-AAATAGGAAACTAGCCTAGAGTTAGAGAATTACAACTAATCACAA
*
254266 GGCACAT-AAATAGGAGACTAGCCTAGAGTTAGAGAATTACAACTAATCACAA
1 GGCACATAAAATAGGAAACTAGCCTAGAGTTAGAGAATTACAACTAATCACAA
254318 G
1 G
254319 AATATTATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 42 0.86
54 7 0.14
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (53 bp):
GGCACATAAAATAGGAAACTAGCCTAGAGTTAGAGAATTACAACTAATCACAA
Found at i:272258 original size:44 final size:44
Alignment explanation
Indices: 272205--272293 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
272195 ATGAAACTAT
*
272205 TCTTTGTAATTTTATTTCACAATACAGAAA-ACAGATCCAAAAAC
1 TCTTCGTAATTTTATTTCACAATACA-AAACACAGATCCAAAAAC
* * *
272249 TCTTCGTAATTTTATTTCATAATCCAAAACCCAGATCCAAAAAC
1 TCTTCGTAATTTTATTTCACAATACAAAACACAGATCCAAAAAC
272293 T
1 T
272294 AAAGAGTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 3 0.08
44 37 0.93
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (44 bp):
TCTTCGTAATTTTATTTCACAATACAAAACACAGATCCAAAAAC
Found at i:273742 original size:25 final size:24
Alignment explanation
Indices: 273705--273759 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
273695 TATAATTATC
* *
273705 ATATGTTATTATAATATAACTAAGT
1 ATATATTAATATAATATAA-TAAGT
* *
273730 ATATATTAATATAATATTATAATT
1 ATATATTAATATAATATAATAAGT
273754 ATATAT
1 ATATAT
273760 ATATTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
ATATATTAATATAATATAATAAGT
Found at i:277610 original size:26 final size:26
Alignment explanation
Indices: 277571--277623 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
277561 TTATTTTCTC
**
277571 TAATATATTTTAAAAGAAATTCTCTT
1 TAATATATGCTAAAAGAAATTCTCTT
*
277597 TAATATATGCTAAAAGAAATTTTCTT
1 TAATATATGCTAAAAGAAATTCTCTT
277623 T
1 T
277624 TTTTTTGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (26 bp):
TAATATATGCTAAAAGAAATTCTCTT
Found at i:286307 original size:16 final size:16
Alignment explanation
Indices: 286273--286308 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
286263 ATTTAATTTA
*
286273 TTTTTTATTTTTTATT
1 TTTTTTATTTTTCATT
286289 TTTTTTATTTTCTCATT
1 TTTTTTATTTT-TCATT
286306 TTT
1 TTT
286309 ATATTGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTATTTTTCATT
Found at i:286485 original size:21 final size:21
Alignment explanation
Indices: 286459--286758 Score: 141
Period size: 21 Copynumber: 14.6 Consensus size: 21
286449 GCGTTGCATT
* *
286459 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATATTTCAAAA
* *
286480 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATATTTCAAAA
* * **
286501 TCGCGTTACGAT-TTTCCATT
1 TCGCGTTGCGATATTTCAAAA
* **
286521 TCGCGTTGCGAT-TTTCCAGT
1 TCGCGTTGCGATATTTCAAAA
* * *
286541 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATATTTCAAAA
* **
286562 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATATTTCAAAA
* * **
286582 TCACGTTGCGAT-TTTCCAGT
1 TCGCGTTGCGATATTTCAAAA
* *
286602 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATATTTCAAAA
* * *
286623 TCGCGTTGCGATA-GTCTATA
1 TCGCGTTGCGATATTTCAAAA
* * *
286643 GCTGTCGATGCGAT-TTTCCAAA
1 TC-G-CGTTGCGATATTTCAAAA
* * **
286665 T-TCGTTGCGAT-TTTCCAGT
1 TCGCGTTGCGATATTTCAAAA
* * *
286684 TCGCGTTGTGATAGTTGAAAA
1 TCGCGTTGCGATATTTCAAAA
* *
286705 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATATTTCAAAA
* * **
286726 TCGCGTTGCGCT-TTTCCAGT
1 TCGCGTTGCGATATTTCAAAA
286746 TCGCGTTGCGATA
1 TCGCGTTGCGATA
286759 GTCTACAGTT
Statistics
Matches: 213, Mismatches: 58, Indels: 16
0.74 0.20 0.06
Matches are distributed among these distances:
19 15 0.07
20 90 0.42
21 96 0.45
22 12 0.06
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATATTTCAAAA
Found at i:286526 original size:20 final size:20
Alignment explanation
Indices: 286501--286785 Score: 128
Period size: 20 Copynumber: 13.9 Consensus size: 20
286491 TAGTTGAAAA
* *
286501 TCGCGTTACGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
286521 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* * ** **
286541 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
*
286562 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
*
286582 TCACGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* ** **
286602 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
** *
286623 TCGCGTTGCGATAGTCTA-T
1 TCGCGTTGCGATTTTCCAGT
* * *
286642 AGCTGTCGATGCGATTTTCCAAAT
1 -TC-G-CGTTGCGATTTTCC-AGT
286666 T--CGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* * ** **
286684 TCGCGTTGTGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
* ** **
286705 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
*
286726 TCGCGTTGCGCTTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
286746 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
286768 T-GTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
286786 AATTCGTTGC
Statistics
Matches: 199, Mismatches: 53, Indels: 26
0.72 0.19 0.09
Matches are distributed among these distances:
18 3 0.02
19 13 0.07
20 90 0.45
21 65 0.33
22 26 0.13
23 1 0.01
24 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:286566 original size:61 final size:61
Alignment explanation
Indices: 286480--286634 Score: 283
Period size: 61 Copynumber: 2.5 Consensus size: 61
286470 TAATTGAAAA
* *
286480 TCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCATTTCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACGTTGCGATTTTCCAGT
*
286541 TCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACGTTGCGATTTTCCAGT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACGTTGCGATTTTCCAGT
286602 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
286635 AGTCTATAGC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 90 1.00
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (61 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACGTTGCGATTTTCCAGT
Found at i:286630 original size:41 final size:40
Alignment explanation
Indices: 286480--286716 Score: 136
Period size: 41 Copynumber: 5.8 Consensus size: 40
286470 TAATTGAAAA
* * *
286480 TCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCATT
1 TCGCGTTGCGAT-GTTCAAAATCGCGTTGCGATTTTCCAGT
* * ** * * ** **
286521 TCGCGTTGCGATTTTCCAGTTCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATGTTCAAAATCGCGTTGCGAT-TTTCCAGT
* * ** *
286562 TCGCGTTGCGATTTTCCATTTCACGTTGCGATTTTCCAGT
1 TCGCGTTGCGATGTTCAAAATCGCGTTGCGATTTTCCAGT
* ** *
286602 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTA-T
1 TCGCGTTGCGAT-GTTCAAAATCGCGTTGCGATTTTCCAGT
* * * * *
286642 AGCTGTCGATGCGATTTTCCAAAT-TCGTTGCGATTTTCCAGT
1 -TC-G-CGTTGCGATGTTCAAAATCGCGTTGCGATTTTCCAGT
* *
286684 TCGCGTTGTGATAGTTGAAAATCGCGTTGCGAT
1 TCGCGTTGCGAT-GTTCAAAATCGCGTTGCGAT
286717 AGTTGAAAAT
Statistics
Matches: 143, Mismatches: 45, Indels: 16
0.70 0.22 0.08
Matches are distributed among these distances:
39 7 0.05
40 36 0.25
41 84 0.59
42 8 0.06
43 8 0.06
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (40 bp):
TCGCGTTGCGATGTTCAAAATCGCGTTGCGATTTTCCAGT
Found at i:286632 original size:82 final size:82
Alignment explanation
Indices: 286459--286757 Score: 329
Period size: 82 Copynumber: 3.6 Consensus size: 82
286449 GCGTTGCATT
* * ** * * *
286459 TCGCGTTGCGATAATTGAAAATCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCATTTCG
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCAATTCGCGTTGCGATTTTCCAGTTCG
* ** **
286524 CGTTGCGAT-TTTCCAGT
65 CGTTGCGATAGTTGAAAA
* * *
286541 TCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACGTTGCGATTTTCCAGTTCGC
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCGCGTTGCGATTTTCCAGTTCGC
286606 GTTGCGATAGTTGAAAA
66 GTTGCGATAGTTGAAAA
* * *
286623 TCGCGTTGCGATAGTCT--ATAGCTGTCGATGCGATTTTCCAAATT--CGTTGCGATTTTCCAGT
1 TCGCGTTGCGATAGT-TGAAAATC-G-CGTTGCGATTTTCC-AATTCGCGTTGCGATTTTCCAGT
*
286684 TCGCGTTGTGATAGTTGAAAA
62 TCGCGTTGCGATAGTTGAAAA
* *
286705 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCAGTTCGCGTTGCGAT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCGCGTTGCGAT
286758 AGTCTACAGT
Statistics
Matches: 182, Mismatches: 26, Indels: 18
0.81 0.12 0.08
Matches are distributed among these distances:
80 3 0.02
81 48 0.26
82 111 0.61
83 17 0.09
84 3 0.02
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (82 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCGCGTTGCGATTTTCCAGTTCGC
GTTGCGATAGTTGAAAA
Found at i:286682 original size:143 final size:143
Alignment explanation
Indices: 286458--286760 Score: 398
Period size: 143 Copynumber: 2.1 Consensus size: 143
286448 CGCGTTGCAT
* * *
286458 TTCGCGTTGCGATAATTGAAAATCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCATTTC
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCGATACGATTTTCCAATTC
* * **
286523 GCGTTGCGATTTTCCAGTTCGCATTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCATTTCACG
66 -CGTTGCGATTTTCCAGTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATAGTTCAAAATCACG
286587 TTGCGATTTTCCAG
130 TTGCGATTTTCCAG
* * *
286601 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCT--ATAGCTGTCGATGCGATTTTCCAA
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGT-TGAAAATC-G-CGATACGATTTTCC-A
* * *
286664 ATT-CGTTGCGATTTTCCAGTTCGCGTTGTGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATC
62 ATTCCGTTGCGATTTTCCAGTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATAGTTCAAAATC
* *
286728 GCGTTGCGCTTTTCCAG
127 ACGTTGCGATTTTCCAG
286745 TTCGCGTTGCGATAGT
1 TTCGCGTTGCGATAGT
286761 CTACAGTTGT
Statistics
Matches: 140, Mismatches: 15, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
142 3 0.02
143 85 0.61
144 49 0.35
145 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (143 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCGATACGATTTTCCAATTC
CGTTGCGATTTTCCAGTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATAGTTCAAAATCACGT
TGCGATTTTCCAG
Found at i:286722 original size:164 final size:163
Alignment explanation
Indices: 286541--286838 Score: 429
Period size: 164 Copynumber: 1.8 Consensus size: 163
286531 ATTTTCCAGT
* * *
286541 TCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCACGTTGCGAT-TTTCCAGTTCG
1 TCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGTTCACGTTGCGATATCTACAGTT-G
* *
286605 -CGTTGCGATAGTTGAAAATCGCGTTGCGATAGTCTATAGCTGTCGATGCGATTTTCCAAATTCG
65 TCGTTGCGAT-GTTCAAAAT-GCGTTGCGATAGTCTACAGCTGTCGATGCGATTTTCCAAATTCG
286669 TTGCGATTTTCCAGTTCGCGTTGTGATAGTTGAAAA
128 TTGCGATTTTCCAGTTCGCGTTGTGATAGTTGAAAA
* * *
286705 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCAGTTCGCGTTGCGATAGTCTACAGTTG
1 TCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGTTCACGTTGCGATA-TCTACAGTTG
* * * * *
286770 TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTCGTT
65 TCGTTGCGATGTTCAAAATGCGTTGCGATAGTCTACAGCTGTCGATGCGATTTTCCAAATTCGTT
286835 GCGA
130 GCGA
286839 AAATTCGTTG
Statistics
Matches: 118, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
164 95 0.81
165 7 0.06
166 16 0.14
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (163 bp):
TCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGTTCACGTTGCGATATCTACAGTTGT
CGTTGCGATGTTCAAAATGCGTTGCGATAGTCTACAGCTGTCGATGCGATTTTCCAAATTCGTTG
CGATTTTCCAGTTCGCGTTGTGATAGTTGAAAA
Found at i:286774 original size:22 final size:22
Alignment explanation
Indices: 286749--286820 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
286739 TTCCAGTTCG
286749 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
286771 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
286790 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
286812 CGTTGCGAT
1 CGTTGCGAT
286821 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:286794 original size:19 final size:19
Alignment explanation
Indices: 286770--286838 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
286760 TCTACAGTTG
286770 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
286789 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
286810 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
286830 TCGTTGCGA
1 TCGTTGCGA
286839 AAATTCGTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 19 0.49
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:286794 original size:41 final size:41
Alignment explanation
Indices: 286626--286838 Score: 195
Period size: 41 Copynumber: 5.2 Consensus size: 41
286616 TTGAAAATCG
* * *
286626 CGTTGCGATAGTCTATAGCTGTCGATGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
* * * * ** *
286667 CGTTGCGAT--TTTCCAGTTCG-CGTTGTGATAGTTGAAAATCG
1 CGTTGCGATAGTCTACAGTT-GTCGTTGCGAT-TTTCCAAAT-T
* * * * *
286708 CGTTGCGATAGT-TGAAAATCG-CGTTGCGCTTTTCC-AGTT
1 CGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT
286747 CGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 --CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
286790 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
286831 CGTTGCGA
1 CGTTGCGA
286839 AAATTCGTTG
Statistics
Matches: 135, Mismatches: 26, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
39 12 0.09
40 9 0.07
41 85 0.63
42 23 0.17
43 6 0.04
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:286944 original size:6 final size:6
Alignment explanation
Indices: 286933--287003 Score: 114
Period size: 6 Copynumber: 12.5 Consensus size: 6
286923 GACACGTATT
286933 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
286981 ACC-CG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
287004 CGAGACGAGA
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.31
6 45 0.69
ACGTcount: A:0.30, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:287650 original size:22 final size:22
Alignment explanation
Indices: 287621--287674 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
287611 AATTTGGAAA
287621 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
287643 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
287665 ATCGCAACGA
1 ATCGCAACGA
287675 ATTTGGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:287753 original size:20 final size:20
Alignment explanation
Indices: 287705--287790 Score: 100
Period size: 20 Copynumber: 4.2 Consensus size: 20
287695 ATTGTAGACT
*
287705 ATCGCAACACGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
287725 ACCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
287745 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
287766 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
287786 ATCGC
1 ATCGC
287791 GTTGTGGTTT
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 37 0.71
21 15 0.29
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:287775 original size:41 final size:41
Alignment explanation
Indices: 287727--287822 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
287717 AATGGAAAAC
287727 CGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
1 CGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
*** * *
287768 CGCAACGCGAAATGGAAAATCGCGTTGTGGTTTTCAACTAT
1 CGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
287809 CGCAACGCGAAATG
1 CGCAACGCGAAATG
287823 CAACGCGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (41 bp):
CGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTAT
Found at i:288040 original size:12 final size:11
Alignment explanation
Indices: 288011--288059 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
288001 CTTTCTTAAC
288011 TTAT-TTAT-T
1 TTATATTATAT
288020 TTATATTATAT
1 TTATATTATAT
288031 TTATACTTATAT
1 TTATA-TTATAT
* *
288043 ATATATT-TAA
1 TTATATTATAT
288053 TTATATT
1 TTATATT
288060 TTTTCTACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 4 0.12
10 12 0.35
11 8 0.24
12 10 0.29
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TTATATTATAT
Found at i:290016 original size:29 final size:30
Alignment explanation
Indices: 289969--290039 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
289959 AAAATATTTT
*
289969 TTCGCCCTCCTAAAATTTT-ATAAATTCAAG
1 TTCGCCC-CCTAAAATTTTCATAAATTCAAA
* *
289999 TTCGCCCCCTGAAATTTTCATAAGTTCAAA
1 TTCGCCCCCTAAAATTTTCATAAATTCAAA
*
290029 TTCGTCCCCTA
1 TTCGCCCCCTA
290040 TCATAAAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 10 0.29
30 25 0.71
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.35
Consensus pattern (30 bp):
TTCGCCCCCTAAAATTTTCATAAATTCAAA
Found at i:290629 original size:12 final size:12
Alignment explanation
Indices: 290612--290639 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
290602 GCCGTTAATA
290612 AATTAAATTTAT
1 AATTAAATTTAT
290624 AATTAAATTTAT
1 AATTAAATTTAT
290636 AATT
1 AATT
290640 TATTCTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTAAATTTAT
Found at i:291994 original size:23 final size:23
Alignment explanation
Indices: 291968--292015 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
291958 AGGTAAAGAA
291968 AAACATGCCACAAAGACAGAGAT
1 AAACATGCCACAAAGACAGAGAT
* *
291991 AAACGTGTCACAAAGACAGAGAT
1 AAACATGCCACAAAGACAGAGAT
292014 AA
1 AA
292016 CTTCGGGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.10
Consensus pattern (23 bp):
AAACATGCCACAAAGACAGAGAT
Found at i:294434 original size:218 final size:223
Alignment explanation
Indices: 294185--294625 Score: 831
Period size: 218 Copynumber: 2.0 Consensus size: 223
294175 GAAGGTGAGT
294185 GGAATAACAAAAAAAAAAAAAAAAGAGTGAAGACGACTTAGGGATTTTGACAAAATATCAATAGA
1 GGAATAACAAAAAAAAAAAAAAAAGAGTGAAGACGACTTAGGGATTTTGACAAAATATCAATAGA
294250 ATAATAGGAAAGATGTTTAACATC-AAATGCTCTATATCATTAAAGAGAG-ACATTTATAAAATA
66 ATAATAGGAAAGATGTTTAACATCAAAATGCTCTATATCATTAAAGAGAGAACATTTATAAAATA
294313 GCCCAAAGTTCAACCAACTAACTGGGGTAAGCAAC-ATAACCTAAA-GTTGGCTAACAAGTTAAC
131 GCCCAAAGTTCAACCAACTAACT-GGGTAAGCAACAATAACCTAAAGGTTGGCTAACAAGTTAAC
294376 TGATGCAT-ACAGAAAGATGATACTTTAA
195 TGATGCATAACAGAAAGATGATACTTTAA
294404 GGAATAAC-AAAAAAAAAAAAAAAGAGTGAAGACGACTTAGGGATTTTGACAAAATATCAATAGA
1 GGAATAACAAAAAAAAAAAAAAAAGAGTGAAGACGACTTAGGGATTTTGACAAAATATCAATAGA
294468 ATAATAGGAAAGATGTTTAACATCAAAATGCTCTATATCATTAAAGAGAGAACATTTATAAAATA
66 ATAATAGGAAAGATGTTTAACATCAAAATGCTCTATATCATTAAAGAGAGAACATTTATAAAATA
294533 GCCCAAAGTTCAACCAACTAACTGGGTAAGCAACAATAACCTAAAGGTTGGCTAACAAGTTAACT
131 GCCCAAAGTTCAACCAACTAACTGGGTAAGCAACAATAACCTAAAGGTTGGCTAACAAGTTAACT
294598 GATGCATAACAGAAAGATGATACTTTAA
196 GATGCATAACAGAAAGATGATACTTTAA
294626 TATTTTCGTA
Statistics
Matches: 217, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
218 80 0.37
219 44 0.20
220 47 0.22
221 26 0.12
222 20 0.09
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (223 bp):
GGAATAACAAAAAAAAAAAAAAAAGAGTGAAGACGACTTAGGGATTTTGACAAAATATCAATAGA
ATAATAGGAAAGATGTTTAACATCAAAATGCTCTATATCATTAAAGAGAGAACATTTATAAAATA
GCCCAAAGTTCAACCAACTAACTGGGTAAGCAACAATAACCTAAAGGTTGGCTAACAAGTTAACT
GATGCATAACAGAAAGATGATACTTTAA
Found at i:298297 original size:2 final size:2
Alignment explanation
Indices: 298290--298317 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
298280 GTCATCGCCA
298290 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
298318 AACTTCACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:302332 original size:20 final size:21
Alignment explanation
Indices: 302293--302336 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
302283 TTGATGTTTA
* *
302293 AATCATGTAATTATTTTTCTT
1 AATCATGTAATGATTATTCTT
302314 AATCAT-TAATGATTATTCTT
1 AATCATGTAATGATTATTCTT
302334 AAT
1 AAT
302337 TAATTATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (21 bp):
AATCATGTAATGATTATTCTT
Found at i:308133 original size:15 final size:15
Alignment explanation
Indices: 308113--308150 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
308103 TTGATGTCAG
308113 TTCAGGTCAAAACAA
1 TTCAGGTCAAAACAA
*
308128 TTCAGGTCAAAACAG
1 TTCAGGTCAAAACAA
308143 TTCAGGTC
1 TTCAGGTC
308151 CGAAGTAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (15 bp):
TTCAGGTCAAAACAA
Found at i:308800 original size:2 final size:2
Alignment explanation
Indices: 308783--309042 Score: 118
Period size: 2 Copynumber: 130.0 Consensus size: 2
308773 AATTGAATAA
* *
308783 AT AT A- AT AT GT AT AT AT AT AT AT AT AT A- AT AT A- AGT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * * *
308823 AT AT AA ACT AT AT AT AT AT AT AA ACT AT AT TT AT AT -T AT AA ACT
1 AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T
* *
308867 AT AT A- AT -T AT -T AT A- AGT -T AT AT AT AT AA AT -T AT AT TT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * *
308904 AT AT GA- ACT AT AT AT AT GA- ACT AT AT AT GT AA ACT AT AT AT GT
1 AT AT -AT A-T AT AT AT AT -AT A-T AT AT AT AT AT A-T AT AT AT AT
* * * * * *
308947 AT AA ACT AT AA AA AGT AT AT AGT TT AT AA ACT AT A- AT TT AT AT
1 AT AT A-T AT AT AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT AT
*
308990 -T A- AT AT AGT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
309031 AT AT AT AT AT AT
1 AT AT AT AT AT AT
309043 TATTTAAAGT
Statistics
Matches: 194, Mismatches: 34, Indels: 60
0.67 0.12 0.21
Matches are distributed among these distances:
1 15 0.08
2 166 0.86
3 13 0.07
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:308877 original size:18 final size:18
Alignment explanation
Indices: 308793--308881 Score: 89
Period size: 17 Copynumber: 4.9 Consensus size: 18
308783 ATATAATATG
308793 TATATATATATATATATAA-
1 TATATAT-TATATATA-AAC
308812 TATA-AGTTTATATATAAAC
1 TATATA--TTATATATAAAC
308831 TATATA-TATATATAAAC
1 TATATATTATATATAAAC
308848 TATAT-TTATATTATAAAC
1 TATATATTATA-TATAAAC
308866 TATATAATTAT-TATAA
1 TATAT-ATTATATATAA
308882 GTTATATATA
Statistics
Matches: 62, Mismatches: 0, Indels: 17
0.78 0.00 0.22
Matches are distributed among these distances:
17 20 0.32
18 20 0.32
19 16 0.26
20 6 0.10
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (18 bp):
TATATATTATATATAAAC
Found at i:309565 original size:7 final size:7
Alignment explanation
Indices: 309555--309616 Score: 67
Period size: 7 Copynumber: 9.3 Consensus size: 7
309545 TAGTCTATAA
309555 AAACCTT
1 AAACCTT
309562 AAACC-T
1 AAACCTT
309568 AAACC-T
1 AAACCTT
309574 AAACC-T
1 AAACCTT
309580 AAACCTT
1 AAACCTT
*
309587 AAACCCT
1 AAACCTT
*
309594 AAACTTT
1 AAACCTT
* *
309601 CAACCCT
1 AAACCTT
309608 AAACCTT
1 AAACCTT
309615 AA
1 AA
309617 CCCCTGAACT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
6 18 0.39
7 28 0.61
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (7 bp):
AAACCTT
Found at i:309572 original size:6 final size:6
Alignment explanation
Indices: 309555--309597 Score: 59
Period size: 6 Copynumber: 6.7 Consensus size: 6
309545 TAGTCTATAA
309555 AAACCTT AAACCT AAACCT AAACCT AAACCTT AAACCCT AAAC
1 AAACC-T AAACCT AAACCT AAACCT AAACC-T AAA-CCT AAAC
309598 TTTCAACCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 19 0.56
7 13 0.38
8 2 0.06
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.19
Consensus pattern (6 bp):
AAACCT
Found at i:309596 original size:14 final size:14
Alignment explanation
Indices: 309555--309621 Score: 86
Period size: 14 Copynumber: 5.0 Consensus size: 14
309545 TAGTCTATAA
309555 AAACCTTAAA-CCT
1 AAACCTTAAACCCT
309568 AAACC-TAAA-CCT
1 AAACCTTAAACCCT
309580 AAACCTTAAACCCT
1 AAACCTTAAACCCT
* *
309594 AAACTTTCAACCCT
1 AAACCTTAAACCCT
*
309608 AAACCTTAACCCCT
1 AAACCTTAAACCCT
309622 GAACTATACA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
12 12 0.26
13 9 0.19
14 26 0.55
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.22
Consensus pattern (14 bp):
AAACCTTAAACCCT
Found at i:309806 original size:7 final size:7
Alignment explanation
Indices: 309791--309848 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
309781 AGTTTTATAG
*
309791 AAACTCT
1 AAACCCT
309798 AAACCCT
1 AAACCCT
*
309805 AAACCTT
1 AAACCCT
**
309812 AAATACT
1 AAACCCT
*
309819 AAACCAT
1 AAACCCT
*
309826 AAACACT
1 AAACCCT
*
309833 AAACCAT
1 AAACCCT
309840 AAACCCT
1 AAACCCT
309847 AA
1 AA
309849 TATAAATGGA
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (7 bp):
AAACCCT
Found at i:309814 original size:14 final size:14
Alignment explanation
Indices: 309797--309848 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
309787 ATAGAAACTC
* *
309797 TAAACCCTAAACCT
1 TAAACACTAAACCA
*
309811 TAAATACTAAACCA
1 TAAACACTAAACCA
309825 TAAACACTAAACCA
1 TAAACACTAAACCA
*
309839 TAAACCCTAA
1 TAAACACTAA
309849 TATAAATGGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAACACTAAACCA
Found at i:310233 original size:15 final size:15
Alignment explanation
Indices: 310213--310243 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
310203 CCATGTAAAG
310213 TATATATAAACTATA
1 TATATATAAACTATA
*
310228 TATATATAACCTATA
1 TATATATAAACTATA
310243 T
1 T
310244 GCATATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (15 bp):
TATATATAAACTATA
Found at i:310358 original size:49 final size:49
Alignment explanation
Indices: 310258--310361 Score: 120
Period size: 48 Copynumber: 2.1 Consensus size: 49
310248 ATATATATAT
* * ** * **
310258 ATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTGTTC
1 ATAAACAATATAAAGTAAATAAAGTATATAATTTATAGAAACACTAATC
*
310307 ATAAACAATATAAAGT-AATAAAGTATATAATTTATAGAAACCCTAAATC
1 ATAAACAATATAAAGTAAATAAAGTATATAATTTATAGAAACACT-AATC
310356 ATAAAC
1 ATAAAC
310362 TTTAAACCAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 23 0.50
49 23 0.50
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.32
Consensus pattern (49 bp):
ATAAACAATATAAAGTAAATAAAGTATATAATTTATAGAAACACTAATC
Found at i:310367 original size:14 final size:14
Alignment explanation
Indices: 310350--310389 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
310340 ATAGAAACCC
* *
310350 TAAATCATAAACTT
1 TAAACCATAAACAT
310364 TAAACCATAAACAT
1 TAAACCATAAACAT
*
310378 TAAACCCTAAAC
1 TAAACCATAAAC
310390 CATAAACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCATAAACAT
Found at i:310395 original size:14 final size:14
Alignment explanation
Indices: 310344--310396 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
310334 TAATTTATAG
* *
310344 AAACCCTAAATCAT
1 AAACCTTAAACCAT
*
310358 AAACTTTAAACCAT
1 AAACCTTAAACCAT
* *
310372 AAACATTAAACCCT
1 AAACCTTAAACCAT
*
310386 AAACCATAAAC
1 AAACCTTAAAC
310397 TTTAATATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (14 bp):
AAACCTTAAACCAT
Found at i:310718 original size:553 final size:554
Alignment explanation
Indices: 309692--310726 Score: 1772
Period size: 553 Copynumber: 1.9 Consensus size: 554
309682 ATACATACAT
* *
309692 ATATATATATATATAAACTATATAAAGTAAATTACTTGTATAGTTTATAGAAATACTATGCATAA
1 ATATATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTATGCATAA
* * * * *
309757 ACTATATAAAGTAATAAAATATATAGTTTTATAGAAACTCTAAACCCTAAACCTTAAATACTAAA
66 ACAATATAAAGTAATAAAATATATAGATTTATAGAAACCCTAAACCATAAACCTTAAACACTAAA
309822 CCATAAACACTAAACCATAAACCCTAATATAAATGGACTAGCACTAATGCATATATATTGTAATA
131 CCATAAACACTAAACCATAAACCCTAATATAAATGGACTAGCACTAATGCATATATATTGTAATA
* * *
309887 AAATAGTGGGCTTATGTATTGGGCCTATGTAAACTAATGTAAATGGACTAGCACTAATGCAAATG
196 AAAGAGTGGACTTATGTATTGGGCCTATGTAAACTAATATAAATGGACTAGCACTAATGCAAATG
309952 GACTTATTTTTGGGTTTTATTATTACTTATTCATAACAACAAAATAAATGGACTATAAATGTGAA
261 GACTTATTTTTGGGTTTTATTATTACTTATTCATAACAACAAAATAAATGGACTATAAATGTGAA
* *
310017 TTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATATGGCATGTACTACTATT
326 TTAACCCAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATATGACATGTACTACTATT
*
310082 TATGAACCATATAATATGCAATGTGACATATTAATTATTTAACACCTAATTAATTATGTTTTATA
391 TATGAACCATATAATATGCAATGTGACATATTAATTATTTAACACCTAATTAATCATGTTTTATA
*
310147 TAATTTACATTTAAATAATTTTATTAAACAATTTTTATATAATATGTATGTATAAACCATGTAAA
456 TAATTTACATTAAAATAATTTTATTAAACAATTTTTATATAATATGTATGTATAAACCATGTAAA
310212 GTATATATAAACTATATATATATAACCTATATGC
521 GTATATATAAACTATATATATATAACCTATATGC
* *
310246 ATATATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTGTTCATAA
1 ATATATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTATGCATAA
* * *
310311 ACAATATAAAGTAATAAAGTATATA-ATTTATAGAAACCCTAAATCATAAACTTTAAAC-CATAA
66 ACAATATAAAGTAATAAAATATATAGATTTATAGAAACCCTAAACCATAAACCTTAAACAC-TAA
* **
310374 A-CATTAAACCCTAAACCATAAACTTTAATATAAATGGACTAGCACTAATGCATATATATTTGTA
130 ACCA-TAAACACTAAACCATAAACCCTAATATAAATGGACTAGCACTAATGCATATATA-TTGTA
*
310438 ATAAAAGAGTGGACTTATGTATTGGGCCTATGTAAACTAATATAAATGGACTAGCACTATTGCAA
193 ATAAAAGAGTGGACTTATGTATTGGGCCTATGTAAACTAATATAAATGGACTAGCACTAATGCAA
* ** *
310503 ATGGACTTATTTTTTGGTTTT-TTATTACTTATTCATAACAACAAAATAAATGGTTTATTAATGT
258 ATGGACTTATTTTTGGGTTTTATTATTACTTATTCATAACAACAAAATAAATGGACTATAAATGT
310567 GAATTAACCCAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATATGACATGTACTACT
323 GAATTAACCCAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATATGACATGTACTACT
310632 ATTTATGAACCATATAATATGCAATGTGACATATTAATTATTTAACACCTAATTAATCATGTTTT
388 ATTTATGAACCATATAATATGCAATGTGACATATTAATTATTTAACACCTAATTAATCATGTTTT
310697 ATATAATTTACATTAAAATAATTTTATTAA
453 ATATAATTTACATTAAAATAATTTTATTAA
310727 TTTTATTAAA
Statistics
Matches: 451, Mismatches: 27, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
552 3 0.01
553 278 0.62
554 170 0.38
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (554 bp):
ATATATATATATATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTATGCATAA
ACAATATAAAGTAATAAAATATATAGATTTATAGAAACCCTAAACCATAAACCTTAAACACTAAA
CCATAAACACTAAACCATAAACCCTAATATAAATGGACTAGCACTAATGCATATATATTGTAATA
AAAGAGTGGACTTATGTATTGGGCCTATGTAAACTAATATAAATGGACTAGCACTAATGCAAATG
GACTTATTTTTGGGTTTTATTATTACTTATTCATAACAACAAAATAAATGGACTATAAATGTGAA
TTAACCCAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATATGACATGTACTACTATT
TATGAACCATATAATATGCAATGTGACATATTAATTATTTAACACCTAATTAATCATGTTTTATA
TAATTTACATTAAAATAATTTTATTAAACAATTTTTATATAATATGTATGTATAAACCATGTAAA
GTATATATAAACTATATATATATAACCTATATGC
Found at i:310750 original size:23 final size:25
Alignment explanation
Indices: 310693--310750 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 25
310683 ATTAATCATG
310693 TTTTATATAATTTACATTAAAATAA
1 TTTTATATAATTTACATTAAAATAA
*
310718 TTTTAT-TAATTT-TATT-AAATAA
1 TTTTATATAATTTACATTAAAATAA
310740 TTTTATATAAT
1 TTTTATATAAT
310751 ATGTATGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 12 0.39
23 7 0.23
24 6 0.19
25 6 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTTATATAATTTACATTAAAATAA
Found at i:310876 original size:7 final size:7
Alignment explanation
Indices: 310866--310979 Score: 210
Period size: 7 Copynumber: 16.3 Consensus size: 7
310856 TAGTTTATAG
310866 AAACCCT
1 AAACCCT
310873 AAACCCT
1 AAACCCT
310880 AAACCCT
1 AAACCCT
310887 AAACCCT
1 AAACCCT
310894 AAACCCT
1 AAACCCT
310901 AAACCCT
1 AAACCCT
310908 AAACCCT
1 AAACCCT
310915 AAACCCT
1 AAACCCT
310922 AAACCCT
1 AAACCCT
310929 AAACCCT
1 AAACCCT
310936 AAACCCT
1 AAACCCT
*
310943 AAACCAT
1 AAACCCT
310950 AAACCCT
1 AAACCCT
310957 AAACCCT
1 AAACCCT
*
310964 AAACCAT
1 AAACCCT
310971 AAACCCT
1 AAACCCT
310978 AA
1 AA
310980 TGTAAATAGA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 103 1.00
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:311164 original size:14 final size:14
Alignment explanation
Indices: 311145--311191 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
311135 ATTTTTTCTT
311145 TATATAAATTAAAC
1 TATATAAATTAAAC
311159 TATAT-AATT----
1 TATATAAATTAAAC
311168 TATATAAATTAAAC
1 TATATAAATTAAAC
*
311182 TATATTAATT
1 TATATAAATT
311192 TTCCTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:311170 original size:23 final size:24
Alignment explanation
Indices: 311143--311192 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
311133 TTATTTTTTC
311143 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
311166 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
311190 TTT
1 TTT
311193 TCCTTTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:311486 original size:16 final size:16
Alignment explanation
Indices: 311465--311495 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
311455 TCATTTACAG
311465 GTCAGGTTAAAAACAT
1 GTCAGGTTAAAAACAT
*
311481 GTCAGGTTGAAAACA
1 GTCAGGTTAAAAACA
311496 GGTCGGGTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.23
Consensus pattern (16 bp):
GTCAGGTTAAAAACAT
Found at i:312521 original size:23 final size:22
Alignment explanation
Indices: 312487--312554 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
312477 CACCACAACT
*
312487 CGTATAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACC-AAGTGCCA
* * * *
312510 CGTAGAATTGCACCTAGTGTCG
1 CGTAGAAATGCACCAAGTGCCA
312532 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACC-AAGTGCCA
312555 TATAAGGTTG
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 18 0.51
23 17 0.49
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (22 bp):
CGTAGAAATGCACCAAGTGCCA
Found at i:313030 original size:21 final size:21
Alignment explanation
Indices: 313005--313045 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
312995 ATGTGTATTC
313005 ATATA-AT-TCATATTCCTAT
1 ATATATATATCATATTCCTAT
*
313024 ATATATATATCATTTTCCTAT
1 ATATATATATCATATTCCTAT
313045 A
1 A
313046 CTTGTATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATATATATCATATTCCTAT
Found at i:314172 original size:24 final size:20
Alignment explanation
Indices: 314115--314192 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
314105 TTTCCCTTGA
*
314115 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
314135 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
*
314158 ATGTGCATCGATGCACTCCT-T
1 A-GTGCATCGATGCA-TCCTAC
314179 A-TGCATCGATGCAT
1 AGTGCATCGATGCAT
314193 TAATTGCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
18 1 0.02
19 12 0.24
20 14 0.29
21 2 0.04
22 1 0.02
23 4 0.08
24 14 0.29
25 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:315068 original size:2 final size:2
Alignment explanation
Indices: 315014--315054 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
315004 TATTTTAAAT
315014 TA TA TA TA TA 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 TA TA TA TA TA T
315055 TAATGAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:316927 original size:166 final size:166
Alignment explanation
Indices: 316653--316982 Score: 615
Period size: 166 Copynumber: 2.0 Consensus size: 166
316643 CTTAACTATC
*
316653 AGTCTCAATACTATGACCATGGTCTCGAGACTATAGACCCTTCTGGGATTTTGGTATCGAGATTG
1 AGTCTCAATACTATGACCATGGTCTCGAGACTATAAACCCTTCTGGGATTTTGGTATCGAGATTG
*
316718 GCATACTGGTCTTGAGACTGGGAGGGATTTTGGTTAAAATATAAGTGTTTTGAGCTTTAGAACAA
66 ACATACTGGTCTTGAGACTGGGAGGGATTTTGGTTAAAATATAAGTGTTTTGAGCTTTAGAACAA
*
316783 TACTTATAATTTTTGAAATTACTCAAGAACACTTGA
131 TACTTATAATTTGTGAAATTACTCAAGAACACTTGA
316819 AGTCTCAATACTATGACCATGGTCTCGAGACTATAAACCCTTCTGGGATTTTGGTATCGAGATTG
1 AGTCTCAATACTATGACCATGGTCTCGAGACTATAAACCCTTCTGGGATTTTGGTATCGAGATTG
* *
316884 ACATACTGGTCTTGAGACTGGGAGGGGTTTTGGTTAAAATATAAGTGTTTTGAGCTTTATAACAA
66 ACATACTGGTCTTGAGACTGGGAGGGATTTTGGTTAAAATATAAGTGTTTTGAGCTTTAGAACAA
316949 TACTTATAATTTGTGAAATTACTCAAGAACACTT
131 TACTTATAATTTGTGAAATTACTCAAGAACACTT
316983 AAAAACACTT
Statistics
Matches: 159, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
166 159 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.35
Consensus pattern (166 bp):
AGTCTCAATACTATGACCATGGTCTCGAGACTATAAACCCTTCTGGGATTTTGGTATCGAGATTG
ACATACTGGTCTTGAGACTGGGAGGGATTTTGGTTAAAATATAAGTGTTTTGAGCTTTAGAACAA
TACTTATAATTTGTGAAATTACTCAAGAACACTTGA
Found at i:319282 original size:21 final size:21
Alignment explanation
Indices: 319258--319307 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
319248 TTCTATGTGC
*
319258 TATGTGATAT-ATATATGAACA
1 TATGTGATATAAGATATG-ACA
319279 TATGTGA-ATAAGATATGACA
1 TATGTGATATAAGATATGACA
319299 TATGT-ATAT
1 TATGTGATAT
319308 GAACAAAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 12 0.46
21 13 0.50
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (21 bp):
TATGTGATATAAGATATGACA
Found at i:319606 original size:32 final size:31
Alignment explanation
Indices: 319565--319737 Score: 101
Period size: 32 Copynumber: 5.5 Consensus size: 31
319555 AGTCGAGGGT
*
319565 TTACCTATGTTCTACGAAACATATGGACATAA
1 TTACCTATGTTCTTC-AAACATATGGACATAA
* *
319597 TTACCTATG-TCTTTCAGGATATATGGACATAA
1 TTACCTATGTTC-TTCA-AACATATGGACATAA
* * * *
319629 TTATCTATG-TCTTTCAGGACATATGGATAGAA
1 TTACCTATGTTC-TTCA-AACATATGGACATAA
*
319661 TTACCTATGTAT-TTCAAGAGATATGGAC--AA
1 TTACCTATGT-TCTTCAA-ACATATGGACATAA
*
319691 TATACCTATGTTC-TAAGGAACATATGGACAGT--
1 T-TACCTATGTTCTTCA--AACATATGGACA-TAA
*
319723 TTACCTAGGTTCTTC
1 TTACCTATGTTCTTC
319738 GGGACCTATG
Statistics
Matches: 113, Mismatches: 15, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
30 6 0.05
31 31 0.27
32 75 0.66
34 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (31 bp):
TTACCTATGTTCTTCAAACATATGGACATAA
Found at i:327808 original size:53 final size:53
Alignment explanation
Indices: 327745--327851 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
327735 ACCTCACCAT
327745 TCCTTATTCCCTTTAGTGATGTGTTAATCACATCCTTGTAATGCATTCATACA
1 TCCTTATTCCCTTTAGTGATGTGTTAATCACATCCTTGTAATGCATTCATACA
327798 TCCTTATTCCCTTTAGTGATGTGTTAATCACATCCTTGTAATGCATTCATACA
1 TCCTTATTCCCTTTAGTGATGTGTTAATCACATCCTTGTAATGCATTCATACA
327851 T
1 T
327852 ATCCTTGTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.42
Consensus pattern (53 bp):
TCCTTATTCCCTTTAGTGATGTGTTAATCACATCCTTGTAATGCATTCATACA
Found at i:330432 original size:22 final size:22
Alignment explanation
Indices: 330402--330458 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
330392 ATATATATTT
330402 TTATGAAAATATATATGAAAAAA
1 TTAT-AAAATATATATGAAAAAA
* * *
330425 TTATAAAA-AGTATATTATAATA
1 TTATAAAATA-TATATGAAAAAA
330447 TTAT-AAATATAT
1 TTATAAAATATAT
330459 TTATTTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 7 0.24
22 18 0.62
23 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (22 bp):
TTATAAAATATATATGAAAAAA
Found at i:330649 original size:27 final size:26
Alignment explanation
Indices: 330622--330694 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 26
330612 AATATATAAT
330622 TTAAAAATAATATTATTTGAAAAAAA
1 TTAAAAATAATATTATTTGAAAAAAA
* *
330648 TT---ATTAATATTATTTGAAATAAA
1 TTAAAAATAATATTATTTGAAAAAAA
* * *
330671 TAAATAAATAATATGATTTTAAAA
1 TTAA-AAATAATATTATTTGAAAA
330695 TTTAAATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
23 20 0.56
26 2 0.06
27 14 0.39
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (26 bp):
TTAAAAATAATATTATTTGAAAAAAA
Found at i:330695 original size:20 final size:18
Alignment explanation
Indices: 330672--330717 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 18
330662 TGAAATAAAT
330672 AAATAAATAATATGATTTTA
1 AAATAAATAA-AT-ATTTTA
330692 AAATTTAAATAAATATTTTA
1 AAA--TAAATAAATATTTTA
330712 AAATAA
1 AAATAA
330718 TTTCATAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 3 0.12
20 12 0.50
21 2 0.08
22 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATAAATAAATATTTTA
Found at i:330703 original size:22 final size:20
Alignment explanation
Indices: 330675--330715 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
330665 AATAAATAAA
330675 TAAATAATATGATTTTAAAATT
1 TAAATAA-AT-ATTTTAAAATT
330697 TAAATAAATATTTTAAAAT
1 TAAATAAATATTTTAAAAT
330716 AATTTCATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TAAATAAATATTTTAAAATT
Found at i:335451 original size:34 final size:34
Alignment explanation
Indices: 335408--335475 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
335398 TTACCACTAA
*
335408 AACTACTAATTTGTTTCCGGTCGCTCTAGGTTTT
1 AACTACTAATTTGTTTCCGGTAGCTCTAGGTTTT
335442 AACTACTAATTTGTTTCCGGTAGCTCTAGGTTTT
1 AACTACTAATTTGTTTCCGGTAGCTCTAGGTTTT
335476 TGGTATAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (34 bp):
AACTACTAATTTGTTTCCGGTAGCTCTAGGTTTT
Found at i:343680 original size:134 final size:133
Alignment explanation
Indices: 343419--343866 Score: 494
Period size: 134 Copynumber: 3.3 Consensus size: 133
343409 CGTCTAAGGG
*
343419 TGACACGGCTCCTACGCGATGAGGAGATCTGGTCG-GAGTATGACACTGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGCGATGAGGAGATCTGGTCGTG-GGATGACACTGCTCATACGTGATGAAG
** * * * * * *
343483 AGTCCTTGGCCATCTTTAGGAAGTATGATAACACGGTTCCATTATGCTGTGGATGGCTAGTTATC
65 AGTTTTTGGCCATCTTTAGGAAG-ATGATAACACGGTTCCACTATGATGAGGACGACTGGTTATC
343548 TGAGT
129 TGAGT
* *
343553 TGACACGGCTCATACGTGATGAGGAGATCTGGTCGTGGGATGACACTGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGCGATGAGGAGATCTGGTCGTGGGATGACACTGCTCATACGTGATGAAGA
* * * * * *
343618 GTTTTTGGCCATCTTTTGAAATGATGATAACATGGTTCCACTCTGTTGGGGACGACTGGTTATCT
66 GTTTTTGGCCATCTTTAGGAA-GATGATAACACGGTTCCACTATGATGAGGACGACTGGTTATCT
343683 GAGT
130 GAGT
* * * *
343687 TGATACGTCTCCTACGTGATGAGGAGATCTGGTCGAT-GGATGACAC-GACTCGTACGTGATGAA
1 TGACACGGCTCCTACGCGATGAGGAGATCTGGTCG-TGGGATGACACTG-CTCATACGTGATGAA
* * ** * *
343750 GTG-TTCTGGCCATCTTTAGGAAGGGCGATAACACAGTTCCTAC-GTGATGAGGACGACTGGTTA
64 GAGTTTTTGGCCATCTTTAGGAA-GATGATAACACGGTTCC-ACTATGATGAGGACGACTGGTTA
343813 TCT-ATGGT
127 TCTGA--GT
* * * *
343821 TGACGCGACTCCTACACGATGAGGAGATCTGGTCGGGGGATGACAC
1 TGACACGGCTCCTACGCGATGAGGAGATCTGGTCGTGGGATGACAC
343867 GGTTCCTAAG
Statistics
Matches: 269, Mismatches: 37, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
132 1 0.00
133 50 0.19
134 215 0.80
135 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (133 bp):
TGACACGGCTCCTACGCGATGAGGAGATCTGGTCGTGGGATGACACTGCTCATACGTGATGAAGA
GTTTTTGGCCATCTTTAGGAAGATGATAACACGGTTCCACTATGATGAGGACGACTGGTTATCTG
AGT
Found at i:343964 original size:34 final size:34
Alignment explanation
Indices: 343919--344042 Score: 101
Period size: 36 Copynumber: 3.6 Consensus size: 34
343909 TGATTTTAAG
*
343919 AGAAACCGACTCAAAGATTGGATTTTGTTTCCAA
1 AGAAACAGACTCAAAGATTGGATTTTGTTTCCAA
*
343953 AGAAACAGACTCAAAGATTTTTG-TTTTGTTT-CAA
1 AGAAACAGACTCAAAGA--TTGGATTTTGTTTCCAA
* * * *
343987 GGGAAATAGACTCACATA-TGGTAAATTTTGTTTCCAA
1 -AGAAACAGACTCAAAGATTGG---ATTTTGTTTCCAA
* *
344024 AGAAACAAAATCAAAGATT
1 AGAAACAGACTCAAAGATT
344043 TTTCTCAAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
32 2 0.03
34 19 0.28
35 21 0.31
36 22 0.32
37 4 0.06
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (34 bp):
AGAAACAGACTCAAAGATTGGATTTTGTTTCCAA
Found at i:344462 original size:71 final size:68
Alignment explanation
Indices: 344303--344448 Score: 161
Period size: 68 Copynumber: 2.1 Consensus size: 68
344293 AAGATTTTTT
* *
344303 TTTCCAAAAGAAAT-TGTCTCAAGAGAGACAAAATGTGTTTCAATGGAAACAATCTCAATGTTTT
1 TTTCAAAAAG-AATCTGTCTCAAGAGAGACAAAATGTGTTTCAATGGAAACAATATCAATGTTTT
*
344367 TATG
65 TATA
* * * *
344371 TTTCAAAAAGAATTTGTCTCAAGCGAGACAAAACTTTGTTTCAA-GAGAAACACTATCAAAGTGT
1 TTTCAAAAAGAATCTGTCTCAAGAGAGACAAAA-TGTGTTTCAATG-GAAACAATATC-AA-TG-
344435 TTTTTATA
61 TTTTTATA
344443 TTTCAA
1 TTTCAA
344449 GATAAACTGT
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
67 3 0.05
68 28 0.42
69 18 0.27
70 2 0.03
71 2 0.03
72 13 0.20
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (68 bp):
TTTCAAAAAGAATCTGTCTCAAGAGAGACAAAATGTGTTTCAATGGAAACAATATCAATGTTTTT
ATA
Found at i:344602 original size:36 final size:36
Alignment explanation
Indices: 344561--344632 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
344551 GGAAAAACTG
344561 TCTCAAGAGAGATGAAATTTGCTTT-AAGAGAAATAA
1 TCTCAAGAGAGATGAAATTTG-TTTCAAGAGAAATAA
* * * *
344597 TCTCAAGTGAGATTAATTTTGTTTCAAGTGAAATAA
1 TCTCAAGAGAGATGAAATTTGTTTCAAGAGAAATAA
344633 ATTCAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 3 0.10
36 28 0.90
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.33
Consensus pattern (36 bp):
TCTCAAGAGAGATGAAATTTGTTTCAAGAGAAATAA
Found at i:347309 original size:19 final size:18
Alignment explanation
Indices: 347285--347374 Score: 67
Period size: 19 Copynumber: 4.7 Consensus size: 18
347275 TTTGTCCTCT
347285 TTTTGTTCTTTGTTTTTTC
1 TTTTGTTCTTT-TTTTTTC
347304 TTTTGTTCTTTTTCTTTGT-
1 TTTTGTTCTTTTT-TTT-TC
*
347323 TTCTTTTTCTTTGCTTTTTTC
1 TT-TTGTTCTTT--TTTTTTC
* *
347344 TCTTTGCTCTTTATTTTTC
1 T-TTTGTTCTTTTTTTTTC
*
347363 -TTTGTTGTTTTT
1 TTTTGTTCTTTTT
347375 CTCTTTGTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
17 9 0.16
18 2 0.04
19 22 0.39
20 10 0.18
21 11 0.19
22 3 0.05
ACGTcount: A:0.01, C:0.13, G:0.09, T:0.77
Consensus pattern (18 bp):
TTTTGTTCTTTTTTTTTC
Found at i:347315 original size:14 final size:15
Alignment explanation
Indices: 347272--347383 Score: 69
Period size: 14 Copynumber: 7.6 Consensus size: 15
347262 ATTGTTTGTG
347272 CTCTTTGTCCTCTTTTT
1 CTCTTTGT--TCTTTTT
*
347289 GTTCTTTG-T-TTTTT
1 -CTCTTTGTTCTTTTT
347303 CT-TTTGTTC-TTTT
1 CTCTTTGTTCTTTTT
347316 -TCTTTGTT-TCTTTT
1 CTCTTTGTTCT-TTTT
*
347330 -TCTTTGCT-TTTTT
1 CTCTTTGTTCTTTTT
*
347343 CTCTTTGCTCTTTATTT
1 CTCTTTGTTC-TT-TTT
* *
347360 TTCTTTGTTGTTTTT
1 CTCTTTGTTCTTTTT
347375 CTCTTTGTT
1 CTCTTTGTT
347384 TTGATTTTAT
Statistics
Matches: 78, Mismatches: 7, Indels: 21
0.74 0.07 0.20
Matches are distributed among these distances:
12 5 0.06
13 16 0.21
14 25 0.32
15 12 0.15
16 4 0.05
17 10 0.13
18 6 0.08
ACGTcount: A:0.01, C:0.17, G:0.09, T:0.73
Consensus pattern (15 bp):
CTCTTTGTTCTTTTT
Found at i:347339 original size:25 final size:25
Alignment explanation
Indices: 347290--347341 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
347280 CCTCTTTTTG
*
347290 TTCTTTGTTTTTTCTTTTGTTCTTT
1 TTCTTTGTTTTTTCTTTTGTGCTTT
347315 TTCTTTGTTTCTTT-TTCTT-TGCTTT
1 TTCTTTGTTT-TTTCTT-TTGTGCTTT
347340 TT
1 TT
347342 TCTCTTTGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (25 bp):
TTCTTTGTTTTTTCTTTTGTGCTTT
Found at i:349426 original size:31 final size:32
Alignment explanation
Indices: 349368--349428 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
349358 ATGAAAAATG
*
349368 ACACAAACAAATGAGAAAAAATAAGTTAGTGT
1 ACACAAACAAAAGAGAAAAAATAAGTTAGTGT
*
349400 ACACAAACAAAAGA-AAAAAATTAGTTAGT
1 ACACAAACAAAAGAGAAAAAATAAGTTAGT
349429 ACATGTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAAAAATAAGTTAGTGT
Found at i:352835 original size:31 final size:31
Alignment explanation
Indices: 352746--352874 Score: 125
Period size: 31 Copynumber: 4.1 Consensus size: 31
352736 AGAACCTCGA
* * *
352746 AAACTGTCCATAGGTCCCGAAGAACCTAGGT
1 AAACTGTTCATATGTCCCGAAGAACATAGGT
* **
352777 AAACTGTTCATATGTTCCTTAGAACATAGGT
1 AAACTGTTCATATGTCCCGAAGAACATAGGT
*
352808 ATACTGTTCATATGTCCCGAA-AGACATAGGT
1 AAACTGTTCATATGTCCCGAAGA-ACATAGGT
** * * *
352839 AATTTTGTCCATATGTTCCGTAGAACATAGGT
1 AA-ACTGTTCATATGTCCCGAAGAACATAGGT
352871 AAAC
1 AAAC
352875 CCTTGACTCT
Statistics
Matches: 77, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
30 1 0.01
31 51 0.66
32 24 0.31
33 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (31 bp):
AAACTGTTCATATGTCCCGAAGAACATAGGT
Found at i:354281 original size:28 final size:28
Alignment explanation
Indices: 354249--354305 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
354239 ACTTTAAATC
*
354249 AACAAATAATCAACTAATTATAAAACTT
1 AACAAATAATCAACTAATTAGAAAACTT
354277 AACAAATAATCAACTAATTAGAAAACTT
1 AACAAATAATCAACTAATTAGAAAACTT
354305 A
1 A
354306 CCTTTGCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (28 bp):
AACAAATAATCAACTAATTAGAAAACTT
Found at i:356523 original size:36 final size:36
Alignment explanation
Indices: 356447--356773 Score: 313
Period size: 36 Copynumber: 9.2 Consensus size: 36
356437 TATATTTCGA
* * *
356447 AAAATGTTTTCGAAATCTATACA-TATGATATATTTCC
1 AAAATGTTTTC-AAAACTATATATTAT-ATATATTTTC
* * *
356484 AAAAACGTTTT-AAAATTATGTATTATATATATTTTC
1 -AAAATGTTTTCAAAACTATATATTATATATATTTTC
*
356520 AAAATGTTTTCAAAGCTATATA-TATTATATATATTTC
1 AAAATGTTTTCAAAACTATATATTA-TATATAT-TTTC
*
356557 AAAATGTTTTTAAAACTATATATTATATATATTTTC
1 AAAATGTTTTCAAAACTATATATTATATATATTTTC
356593 AAAATGTTTTCAAAACTATATATTATATATATTTTC
1 AAAATGTTTTCAAAACTATATATTATATATATTTTC
* * *
356629 AAAATATTTTCAAAGC--TATATTATATATA-TAT-
1 AAAATGTTTTCAAAACTATATATTATATATATTTTC
* * * *
356661 -ATAT-ATAT--ATA-TATATA-TATATATATATTT-
1 AAAATGTTTTCAAAACTATATATTATATATAT-TTTC
*
356691 AAAATGTTTTCAAAAACTATATATTATATATGTTTTC
1 AAAATGTTTTC-AAAACTATATATTATATATATTTTC
* *
356728 AAAATGTTTTCAAAAACTATATATTGTATATATTTTT
1 AAAATGTTTTC-AAAACTATATATTATATATATTTTC
*
356765 GAAATGTTT
1 AAAATGTTT
356774 AAAAAATATT
Statistics
Matches: 241, Mismatches: 31, Indels: 35
0.79 0.10 0.11
Matches are distributed among these distances:
28 9 0.04
29 4 0.02
30 4 0.02
31 6 0.02
32 2 0.01
33 2 0.01
34 13 0.05
35 13 0.05
36 93 0.39
37 84 0.35
38 11 0.05
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (36 bp):
AAAATGTTTTCAAAACTATATATTATATATATTTTC
Found at i:356635 original size:11 final size:11
Alignment explanation
Indices: 356585--356642 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
356575 TATATTATAT
356585 ATATTTTCAAA
1 ATATTTTCAAA
*
356596 ATGTTTTCAAA
1 ATATTTTCAAA
*
356607 ACTATATATT-ATAT
1 A-TAT-T-TTCA-AA
356621 ATATTTTCAAA
1 ATATTTTCAAA
356632 ATATTTTCAAA
1 ATATTTTCAAA
356643 GCTATATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
11 25 0.66
12 4 0.11
13 5 0.13
14 4 0.11
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (11 bp):
ATATTTTCAAA
Found at i:356657 original size:2 final size:2
Alignment explanation
Indices: 356645--356688 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
356635 TTTTCAAAGC
356645 TA TA T- 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 TA TA TA
356686 TA T
1 TA T
356689 TTAAAATGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:356711 original size:26 final size:26
Alignment explanation
Indices: 356682--356731 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
356672 TATATATATA
356682 TATATATT-TAAAATGTTTTCAAAAAC
1 TATATATTAT-AAATGTTTTCAAAAAC
*
356708 TATATATTATATATGTTTTCAAAA
1 TATATATTATAAATGTTTTCAAAA
356732 TGTTTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (26 bp):
TATATATTATAAATGTTTTCAAAAAC
Found at i:356770 original size:37 final size:37
Alignment explanation
Indices: 356670--356773 Score: 154
Period size: 37 Copynumber: 2.8 Consensus size: 37
356660 TATATATATA
*
356670 TATATATATATATATATATTTAAAATGTTTTCAAAAAC
1 TATATAT-TATATATATTTTTAAAATGTTTTCAAAAAC
* *
356708 TATATATTATATATGTTTTCAAAATGTTTTCAAAAAC
1 TATATATTATATATATTTTTAAAATGTTTTCAAAAAC
* *
356745 TATATATTGTATATATTTTTGAAATGTTT
1 TATATATTATATATATTTTTAAAATGTTT
356774 AAAAAATATT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
37 52 0.88
38 7 0.12
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (37 bp):
TATATATTATATATATTTTTAAAATGTTTTCAAAAAC
Found at i:370935 original size:14 final size:14
Alignment explanation
Indices: 370916--370943 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
370906 TAACAGACTT
370916 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
370930 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
370944 TGGTATCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:374615 original size:237 final size:239
Alignment explanation
Indices: 374200--374677 Score: 942
Period size: 237 Copynumber: 2.0 Consensus size: 239
374190 TGCAAGCTCA
374200 ATAAATCCTTATATGGCTTAAAACAGTCTCCCAGGGCTTGGTTTGATCGATTTGCTAAGGCCATG
1 ATAAATCCTTATATGGCTTAAAACAGTCTCCCAGGGCTTGGTTTGATCGATTTGCTAAGGCCATG
374265 ACACAGAATGGTTTCAAACAAAGCCAAGCGGATCACACATTATTCAGAAAAATTGCACCGAGTGG
66 ACACAGAATGGTTTCAAACAAAGCCAAGCGGATCACACATTATTCAGAAAAATTGCACCGAGTGG
374330 TAAGATAACTCTCCTAATTGTCTATGTAGATGATATGATTATAACTGGCAGTTATATAG-A-AAA
131 TAAGATAACTCTCCTAATTGTCTATGTAGATGATATGATTATAACTGGCAGTTATATAGAAGAAA
374393 TAGAAAAGCTAAAGATGAATCTTGCAAAGGAGTTGAAACCAAGG
196 TAGAAAAGCTAAAGATGAATCTTGCAAAGGAGTTGAAACCAAGG
374437 ATAAATCCTTATATGGCTTAAAACAGTCTCCCAGGGCTTGGTTTGATCGATTTGCTAAGGCCATG
1 ATAAATCCTTATATGGCTTAAAACAGTCTCCCAGGGCTTGGTTTGATCGATTTGCTAAGGCCATG
374502 ACACAGAATGGTTTCAAACAAAGCCAAGCGGATCACACATTATTCAGAAAAATTGCACCGAGTGG
66 ACACAGAATGGTTTCAAACAAAGCCAAGCGGATCACACATTATTCAGAAAAATTGCACCGAGTGG
374567 TAAGATAACTCTCCTAATTGTCTATGTAGATGATATGATTATAACTGGCAGTTATATAGAAGAAA
131 TAAGATAACTCTCCTAATTGTCTATGTAGATGATATGATTATAACTGGCAGTTATATAGAAGAAA
374632 TAGAAAAGCTAAAGATGAATCTTGCAAAGGAGTTGAAACCAAGG
196 TAGAAAAGCTAAAGATGAATCTTGCAAAGGAGTTGAAACCAAGG
374676 AT
1 AT
374678 TTAGGGAGTA
Statistics
Matches: 239, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
237 189 0.79
238 1 0.00
239 49 0.21
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (239 bp):
ATAAATCCTTATATGGCTTAAAACAGTCTCCCAGGGCTTGGTTTGATCGATTTGCTAAGGCCATG
ACACAGAATGGTTTCAAACAAAGCCAAGCGGATCACACATTATTCAGAAAAATTGCACCGAGTGG
TAAGATAACTCTCCTAATTGTCTATGTAGATGATATGATTATAACTGGCAGTTATATAGAAGAAA
TAGAAAAGCTAAAGATGAATCTTGCAAAGGAGTTGAAACCAAGG
Found at i:375792 original size:14 final size:14
Alignment explanation
Indices: 375771--375812 Score: 68
Period size: 14 Copynumber: 3.0 Consensus size: 14
375761 TAACAGACTT
375771 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
375785 -TCCTGTTTTCTACA
1 GT-CTGTTTTCTACA
375799 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
375813 ACTACTGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.14, C:0.24, G:0.12, T:0.50
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:380084 original size:50 final size:50
Alignment explanation
Indices: 379985--380084 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 50
379975 TAAAGGAGCG
**
379985 GATCAATGTTGAAGCATGAAACTGAAATTTGGCGGGGACTGTCGGTCACC
1 GATCAATGTTGAAGCATGAAACTGAAATTTGGCGGGGACTGTCAATCACC
* * * *
380035 GATCACTGTTGAAGCATGAAACTGAAGTTTGGTGGGGATTGTCAATCACC
1 GATCAATGTTGAAGCATGAAACTGAAATTTGGCGGGGACTGTCAATCACC
380085 TTGAACTCTG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (50 bp):
GATCAATGTTGAAGCATGAAACTGAAATTTGGCGGGGACTGTCAATCACC
Found at i:381274 original size:130 final size:131
Alignment explanation
Indices: 381041--381304 Score: 503
Period size: 130 Copynumber: 2.0 Consensus size: 131
381031 ATTCAGCAAG
381041 TTCAAATAGATTTAGTCGGAAATGGAGAAATAAGAATGCAGAGCCTATATACTCACGGGAGATGA
1 TTCAAATAGATTTAGTCGGAAATGGAGAAATAAGAATGCAGAGCCTATATACTCACGGGAGATGA
381106 CTTGGGGCTCTTGCTCTTCAAAGCCTGAGACAGACTCTTGAGATTCAG-TTCCATCCTCTTCTTG
66 CTTGGGGCTCTTGCTCTTCAAAGCCTGAGACAGACTCTTGAGATTCAGTTTCCATCCTCTTCTTG
381170 T
131 T
381171 TTCAAATAGATTTAGTCGGAAATGGAGAAATAAGAATGCAGAGCCTATATACTCACGGGAGATGA
1 TTCAAATAGATTTAGTCGGAAATGGAGAAATAAGAATGCAGAGCCTATATACTCACGGGAGATGA
381236 CTTGGGGCTCTTGCTCTTCAAAGCCTGAGACAGACTCTTGAGATTCAGTTCTTCCATCCTCTTCT
66 CTTGGGGCTCTTGCTCTTCAAAGCCTGAGACAGACTCTTGAGATTCAG-T-TTCCATCCTCTTCT
381301 TGT
129 TGT
381304 T
1 T
381305 CTCTTCTAAC
Statistics
Matches: 131, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
130 113 0.86
133 18 0.14
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (131 bp):
TTCAAATAGATTTAGTCGGAAATGGAGAAATAAGAATGCAGAGCCTATATACTCACGGGAGATGA
CTTGGGGCTCTTGCTCTTCAAAGCCTGAGACAGACTCTTGAGATTCAGTTTCCATCCTCTTCTTG
T
Found at i:384044 original size:3 final size:3
Alignment explanation
Indices: 384032--384089 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
384022 TCTATAAAAA
384032 TAT T-T TAT TAT TAT TAT TA- TAT TAT TAT TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
384077 TAT TAT TTT TAT T
1 TAT TAT TAT TAT T
384090 TTTGTAGGTC
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 6 0.12
3 44 0.88
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:384054 original size:11 final size:11
Alignment explanation
Indices: 384040--384083 Score: 79
Period size: 11 Copynumber: 3.9 Consensus size: 11
384030 AATATTTTAT
384040 TATTATTATTA
1 TATTATTATTA
384051 TATTATTATTA
1 TATTATTATTA
384062 TATTATTATTA
1 TATTATTATTA
384073 TTATTATTATT
1 -TATTATTATT
384084 TTTATTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTATTATTA
Found at i:384054 original size:14 final size:14
Alignment explanation
Indices: 384036--384089 Score: 74
Period size: 14 Copynumber: 3.8 Consensus size: 14
384026 TAAAAATATT
384036 TTATTATTATTAT-
1 TTATTATTATTATA
384049 TATATTATTATTATA
1 T-TATTATTATTATA
384064 TTATTATTATTATTA
1 TTATTATTATTA-TA
*
384079 TTATTTTTATT
1 TTATTATTATT
384090 TTTGTAGGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
13 1 0.03
14 23 0.62
15 13 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:384743 original size:7 final size:7
Alignment explanation
Indices: 384739--384797 Score: 66
Period size: 7 Copynumber: 8.1 Consensus size: 7
384729 ACATTATTTA
384739 TTATTAT
1 TTATTAT
384746 TTATTTAT
1 TTA-TTAT
384754 TTATTAT
1 TTATTAT
384761 TTATTTAT
1 TTA-TTAT
*
384769 TT-TAAT
1 TTATTAT
384775 ATTATTAT
1 -TTATTAT
*
384783 TTAATAT
1 TTATTAT
384790 TTATTAT
1 TTATTAT
384797 T
1 T
384798 CATTTTTAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
6 3 0.07
7 25 0.57
8 16 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTATTAT
Found at i:384749 original size:4 final size:4
Alignment explanation
Indices: 384732--384770 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
384722 TGATAATACA
384732 TTAT TTA- TTA- TTAT TTAT TTAT TTA- TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
384771 TAATATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 9 0.27
4 24 0.73
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:384765 original size:29 final size:29
Alignment explanation
Indices: 384732--384794 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
384722 TGATAATACA
*
384732 TTATTTATTATT-AT-TTATTTATTTATTAT
1 TTATTTATT-TTAATATTA-TTATTTAATAT
384761 TTATTTATTTTAATATTATTATTTAATAT
1 TTATTTATTTTAATATTATTATTTAATAT
384790 TTATT
1 TTATT
384795 ATTCATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 2 0.06
29 26 0.84
30 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (29 bp):
TTATTTATTTTAATATTATTATTTAATAT
Found at i:384802 original size:11 final size:10
Alignment explanation
Indices: 384731--384802 Score: 68
Period size: 11 Copynumber: 7.7 Consensus size: 10
384721 ATGATAATAC
384731 ATTATTTATT
1 ATTATTTATT
384741 ATTATTTA-T
1 ATTATTTATT
384750 -TTATTTATT
1 ATTATTTATT
384759 ATTTATTTATT
1 A-TTATTTATT
*
384770 -TTA-ATATT
1 ATTATTTATT
384778 ATTATTTA--
1 ATTATTTATT
384786 A-TATTTATT
1 ATTATTTATT
384795 ATTCATTT
1 ATT-ATTT
384803 TTAGCATTCA
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
7 6 0.12
8 12 0.24
9 9 0.18
10 11 0.22
11 13 0.25
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTATTTATT
Found at i:388823 original size:111 final size:110
Alignment explanation
Indices: 388514--388929 Score: 642
Period size: 110 Copynumber: 3.8 Consensus size: 110
388504 GTGGTTGCTT
*
388514 AACTTCACAGCGAA-GGG-G-C-GACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTCTCAGTTTCATTCAGAGTCAATT
* *
388575 TCAACTTCACAACGAATGATATTGGACTCGAGACAACACAAGCTC
66 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTC
* * *
388620 AACTTCACAGCGAAGGGGCGATTGACTGTCAACAAATAACTTCTCAGTTTCCTTCAGAGTCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTCTCAGTTTCATTCAGAGTCAATT
* *
388685 CCAACTTCACAGCTAAGGATATTGGACTCGAGACAACACAAGCTC
66 TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTC
* *
388730 AACTTCACAACGAAGGGGCGACTGACTGTCAAACAAACAACTTTTCAGTTTCATTCAGAGTCAAT
1 AACTTCACAGCGAAGGGGCGACTGACTGTC-AACAAACAACTTCTCAGTTTCATTCAGAGTCAAT
388795 TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTC
65 TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTC
* * * * * *
388841 AACTTCACAGCGAAGGGGCGGCTGACTGTCAGCAAACAACTTCCCAATTTTATTCAGAGCCAATT
1 AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTCTCAGTTTCATTCAGAGTCAATT
*
388906 TCAACTTCACAGTGAAGGATATTG
66 TCAACTTCACAGCGAAGGATATTG
388930 AACTTGAAAC
Statistics
Matches: 281, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
106 14 0.05
107 3 0.01
108 1 0.00
110 160 0.57
111 103 0.37
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (110 bp):
AACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTCTCAGTTTCATTCAGAGTCAATT
TCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTC
Found at i:388899 original size:221 final size:216
Alignment explanation
Indices: 388514--388929 Score: 654
Period size: 221 Copynumber: 1.9 Consensus size: 216
388504 GTGGTTGCTT
*
388514 AACTTCACAGCGAAGGGGCGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAA
1 AACTTCACAACGAAGGGGCGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAA
* *
388579 CTTCACAACGAATGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGATTG
66 CTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGACTG
* * * * *
388644 ACTGTCAACAAATAACTTCTCAGTTTCCTTCAGAGTCAATTCCAACTTCACAGCT-AAGGATATT
131 ACTGTCAACAAACAACTTCCCAATTTCATTCAGAGCCAATTCCAACTTCACAG-TGAAGGATATT
388708 GGACTCGAGACAACACAAGCTC
195 GGACTCGAGACAACACAAGCTC
388730 AACTTCACAACGAAGGGGCGACTGACTGTCAAACAAACAACTTTTCAGTTTCATTCAGAGTCAAT
1 AACTTCACAACGAA-GGG-G-C-GACTGTC-AACAAACAACTTTTCAGTTTCATTCAGAGTCAAT
*
388795 TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGC
61 TTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGC
* * * *
388860 GGCTGACTGTCAGCAAACAACTTCCCAATTTTATTCAGAGCCAATTTCAACTTCACAGTGAAGGA
126 GACTGACTGTCAACAAACAACTTCCCAATTTCATTCAGAGCCAATTCCAACTTCACAGTGAAGGA
388925 TATTG
191 TATTG
388930 AACTTGAAAC
Statistics
Matches: 181, Mismatches: 13, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
216 13 0.07
217 3 0.02
218 1 0.01
219 1 0.01
220 8 0.04
221 155 0.86
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (216 bp):
AACTTCACAACGAAGGGGCGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAA
CTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGACTG
ACTGTCAACAAACAACTTCCCAATTTCATTCAGAGCCAATTCCAACTTCACAGTGAAGGATATTG
GACTCGAGACAACACAAGCTC
Found at i:389313 original size:241 final size:241
Alignment explanation
Indices: 388893--389750 Score: 1371
Period size: 241 Copynumber: 3.6 Consensus size: 241
388883 CCCAATTTTA
* * * * *
388893 TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGAACTTGAAACAATAC-A--TACTTGGAT
1 TTCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTCGAAACAATACAACTTACTTGGAT
388955 TTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
66 TTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
* *
389020 TTTCAACTCCACAACGGAGGATATCGTACCCACACATCCATAATTTCAACTCCATGACGGAGGAT
131 TTTCAACTCCACAACGGAGGATATCGTACCCACACATCCATGATTTCAACTCCACGACGGAGGAT
*
389085 ATCATGCCATTTGAGGCTTAACTTCACGACGAAGGGGCTTCCCAGT
196 ATCGTGCCATTTGAGGCTTAACTTCACGACGAAGGGGCTTCCCAGT
*
389131 TTCAGAGCCAATTTTAACTTCACGGCGGAGGATATTGGACTCGAAACAATACAACTTACTTGGAT
1 TTCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTCGAAACAATACAACTTACTTGGAT
* * *
389196 TTCAACTTCACGATGAAGGATATTCAAGTCAAGGCTCAACTTCACGATGAATGGGCCATCCACGA
66 TTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
* * *
389261 TTTCAACTCCACAACGGAGGATATCATACCCACACATCCATGATTCCAACTCCACGATGGAGGAT
131 TTTCAACTCCACAACGGAGGATATCGTACCCACACATCCATGATTTCAACTCCACGACGGAGGAT
* * *
389326 ATCGTGTCATTTGAGGCTCAACTTCATGACGAAGGGGCTTCCCAGT
196 ATCGTGCCATTTGAGGCTTAACTTCACGACGAAGGGGCTTCCCAGT
* * *
389372 TTCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGATTCAAAACAATACAACTTACTTAGAT
1 TTCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTCGAAACAATACAACTTACTTGGAT
* * *
389437 TTCAACTTCACGATGAAGGATATTCAAGTCAAGGCTCAAATTCACGACGAATGGGCCATCCACGA
66 TTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
* * *
389502 TTTCAACTCCACGACAGAGGATATCGTACCCACACATCCACGATTTCAACTCCACGACGGAGGAT
131 TTTCAACTCCACAACGGAGGATATCGTACCCACACATCCATGATTTCAACTCCACGACGGAGGAT
* *
389567 ATCGTGCCATTTGAGGCTTAACTTCACAACGAAGGGGCTTCCCAAT
196 ATCGTGCCATTTGAGGCTTAACTTCACGACGAAGGGGCTTCCCAGT
*
389613 TTCAGAGCCAATTTCAACTTCACGGTGGAGGATATTGGACTCGAAACAATACAACTTACTTGGAT
1 TTCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTCGAAACAATACAACTTACTTGGAT
* * * * * *
389678 TTGAACTTTACGACGAAGGATATCCAATTCAAGGCTCAACTTCACGACGGAGGGGCCATCAACGA
66 TTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
389743 TTTCAACT
131 TTTCAACT
389751 TCACGACGAA
Statistics
Matches: 569, Mismatches: 48, Indels: 3
0.92 0.08 0.00
Matches are distributed among these distances:
238 46 0.08
239 1 0.00
241 522 0.92
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (241 bp):
TTCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGGACTCGAAACAATACAACTTACTTGGAT
TTCAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
TTTCAACTCCACAACGGAGGATATCGTACCCACACATCCATGATTTCAACTCCACGACGGAGGAT
ATCGTGCCATTTGAGGCTTAACTTCACGACGAAGGGGCTTCCCAGT
Found at i:390348 original size:33 final size:34
Alignment explanation
Indices: 390311--390392 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 34
390301 GAAAATAAAT
*
390311 CAACGTATTTGAGTCCTATTGAAACACT-AAACC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAACC
*
390344 CAACGTATTCGAGTCCTATTAAAACACTAAAACC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAACC
* *
390378 GAA-GCATTTGAGTCC
1 CAACGTATTTGAGTCC
390393 AAGTAGGACT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 36 0.84
34 7 0.16
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (34 bp):
CAACGTATTTGAGTCCTATTAAAACACTAAAACC
Found at i:390937 original size:4 final size:4
Alignment explanation
Indices: 390928--390973 Score: 51
Period size: 4 Copynumber: 11.2 Consensus size: 4
390918 TGATAATACA
390928 TTAT TTAT TTAT TTAT TTATT TTAAT ATTA- TTAT TTA- TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTA-T TT-AT -TTAT TTAT TTAT TTAT TTAT T
390974 ATTCATTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
3 6 0.16
4 23 0.62
5 5 0.14
6 3 0.08
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:390967 original size:7 final size:7
Alignment explanation
Indices: 390927--390976 Score: 57
Period size: 7 Copynumber: 6.9 Consensus size: 7
390917 ATGATAATAC
390927 ATTATTT
1 ATTATTT
390934 ATTTATTT
1 A-TTATTT
390942 ATTTATTT
1 A-TTATTT
*
390950 -TAATATT
1 ATTAT-TT
390957 ATTATTT
1 ATTATTT
390964 ATTATTT
1 ATTATTT
390971 ATTATT
1 ATTATT
390977 CATTTTTAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 3 0.08
7 18 0.47
8 17 0.45
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
ATTATTT
Found at i:393268 original size:199 final size:199
Alignment explanation
Indices: 392928--393325 Score: 796
Period size: 199 Copynumber: 2.0 Consensus size: 199
392918 ATCTTTGAGG
392928 CCCTTCACATCTCTCTCTTGTGTGAAAAACCCAGAAAAGAATAAACCTTAGTCCTCCGTTTGAGG
1 CCCTTCACATCTCTCTCTTGTGTGAAAAACCCAGAAAAGAATAAACCTTAGTCCTCCGTTTGAGG
392993 GACATGGGATTTTGGCCGAGAAAGCGTTGATATTTATATTGGAAGTTACTGATGAAAAAAGGGGT
66 GACATGGGATTTTGGCCGAGAAAGCGTTGATATTTATATTGGAAGTTACTGATGAAAAAAGGGGT
393058 TTTGATGATGAGGTTAAAAGGGAAGGAGAAAGAGTGGTGGGTTCTTTTTGAGATTGGAGATGAGA
131 TTTGATGATGAGGTTAAAAGGGAAGGAGAAAGAGTGGTGGGTTCTTTTTGAGATTGGAGATGAGA
393123 TTTT
196 TTTT
393127 CCCTTCACATCTCTCTCTTGTGTGAAAAACCCAGAAAAGAATAAACCTTAGTCCTCCGTTTGAGG
1 CCCTTCACATCTCTCTCTTGTGTGAAAAACCCAGAAAAGAATAAACCTTAGTCCTCCGTTTGAGG
393192 GACATGGGATTTTGGCCGAGAAAGCGTTGATATTTATATTGGAAGTTACTGATGAAAAAAGGGGT
66 GACATGGGATTTTGGCCGAGAAAGCGTTGATATTTATATTGGAAGTTACTGATGAAAAAAGGGGT
393257 TTTGATGATGAGGTTAAAAGGGAAGGAGAAAGAGTGGTGGGTTCTTTTTGAGATTGGAGATGAGA
131 TTTGATGATGAGGTTAAAAGGGAAGGAGAAAGAGTGGTGGGTTCTTTTTGAGATTGGAGATGAGA
393322 TTTT
196 TTTT
393326 AGCCGAGTGG
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
199 199 1.00
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (199 bp):
CCCTTCACATCTCTCTCTTGTGTGAAAAACCCAGAAAAGAATAAACCTTAGTCCTCCGTTTGAGG
GACATGGGATTTTGGCCGAGAAAGCGTTGATATTTATATTGGAAGTTACTGATGAAAAAAGGGGT
TTTGATGATGAGGTTAAAAGGGAAGGAGAAAGAGTGGTGGGTTCTTTTTGAGATTGGAGATGAGA
TTTT
Found at i:395087 original size:22 final size:22
Alignment explanation
Indices: 395057--395101 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
395047 AGTCGAGGGT
* *
395057 TACATAGGTCTTTCAGGACATA
1 TACACAGGTCCTTCAGGACATA
*
395079 TACACAGGTCCTTCTGGACATA
1 TACACAGGTCCTTCAGGACATA
395101 T
1 T
395102 TTCACATGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (22 bp):
TACACAGGTCCTTCAGGACATA
Found at i:396525 original size:18 final size:18
Alignment explanation
Indices: 396422--396521 Score: 164
Period size: 18 Copynumber: 5.6 Consensus size: 18
396412 ACGTAGAATT
* *
396422 TGTCCCGTAGGACCACTG
1 TGTCCCGAAGGACCACTA
*
396440 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
396458 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
396476 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
396494 TGTCCCGAAGAACCACTA
1 TGTCCCGAAGGACCACTA
396512 TGTCCCGAAG
1 TGTCCCGAAG
396522 AACCGCGTAG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 77 1.00
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:398682 original size:16 final size:16
Alignment explanation
Indices: 398661--398712 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
398651 ACATTATGCC
398661 TAGTTTATAATACATA
1 TAGTTTATAATACATA
* *
398677 TAGTTTACAA-ATTATA
1 TAGTTTATAATA-CATA
398693 TAGTTTATATATAACATA
1 TAGTTTATA-AT-ACATA
398711 TA
1 TA
398713 TAGTAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 1 0.04
16 20 0.71
17 1 0.04
18 5 0.18
19 1 0.04
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (16 bp):
TAGTTTATAATACATA
Found at i:398703 original size:2 final size:2
Alignment explanation
Indices: 398698--398787 Score: 54
Period size: 2 Copynumber: 48.0 Consensus size: 2
398688 TTATATAGTT
* * *
398698 TA TA TA TA -A CA TA TA TA GTA -A TA TA AA CTA TA TA T- TT TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
*
398739 TA TA TA T- TA TA T- TA T- TA TA TA GTT TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
398778 -A TA TA T- TA TA
1 TA TA TA TA TA TA
398788 ATTGTTTTAA
Statistics
Matches: 70, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
1 9 0.13
2 57 0.81
3 4 0.06
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:398739 original size:28 final size:28
Alignment explanation
Indices: 398708--398783 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
398698 TATATATAAC
*
398708 ATATATAGTAATATA-AACTATATATTTT
1 ATATATA-TAATATATAACTATATAGTTT
* * *
398736 ATATATATATTATATTATTATATAGTTT
1 ATATATATAATATATAACTATATAGTTT
398764 ATATATAT-ATAT-TAA-TATAT
1 ATATATATAATATATAACTATAT
398784 TATAATTGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
25 5 0.12
26 2 0.05
27 9 0.22
28 25 0.61
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (28 bp):
ATATATATAATATATAACTATATAGTTT
Found at i:398785 original size:30 final size:30
Alignment explanation
Indices: 398687--398787 Score: 100
Period size: 30 Copynumber: 3.2 Consensus size: 30
398677 TAGTTTACAA
398687 ATTATATAGTTTATATATAACATATATAGTAATAT
1 ATTATATAGTTTATATAT---ATATAT--TAATAT
*
398722 AAACTATATA-TTT-TATATATATATT-ATATT
1 --ATTATATAGTTTATATATATATATTAATA-T
398752 ATTATATAGTTTATATATATATATTAATAT
1 ATTATATAGTTTATATATATATATTAATAT
398782 ATTATA
1 ATTATA
398788 ATTGTTTTAA
Statistics
Matches: 58, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
28 7 0.12
29 6 0.10
30 21 0.36
31 3 0.05
32 6 0.10
35 5 0.09
36 3 0.05
37 7 0.12
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (30 bp):
ATTATATAGTTTATATATATATATTAATAT
Found at i:402079 original size:21 final size:21
Alignment explanation
Indices: 402053--402105 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
402043 GCTTGGATAG
402053 GTGTTCTCAACCCTTCTTCAA
1 GTGTTCTCAACCCTTCTTCAA
402074 GTGTTCTCAACCCTTCTTCAA
1 GTGTTCTCAACCCTTCTTCAA
402095 GTGTTCTCAAC
1 GTGTTCTCAAC
402106 TTATTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.32, G:0.11, T:0.38
Consensus pattern (21 bp):
GTGTTCTCAACCCTTCTTCAA
Found at i:402838 original size:135 final size:135
Alignment explanation
Indices: 402592--402860 Score: 398
Period size: 135 Copynumber: 2.0 Consensus size: 135
402582 TAATTCAGTC
* * * *
402592 ATTTTTATATTAATTTCAAACTCATATTTTAAAATTATTTTGATTTGGTCCATCAACAATGTGTG
1 ATTTTTATATTAATTTCAAACTCACATTTTAAAATTATTTCGATTTGATCCATCAACAATGTGCG
* * * *
402657 TTGTTTAATTTATTTAATTTTTTTTTCGTAATTTCATATTTGTTCAATTTAGTTCTTAAAATTAT
66 TTGTTTAATTTATTTAAATTTTATTTCGTAATTTCATATTTATTCAATTTAGTCCTTAAAATTAT
402722 ATTTG
131 ATTTG
* * *
402727 ATTTTTATATTAATTTC-AACATCACATTTTAAAATTATTTCGATTTGATCCCTTAGCAATGTGC
1 ATTTTTATATTAATTTCAAAC-TCACATTTTAAAATTATTTCGATTTGATCCATCAACAATGTGC
402791 GTTGTTTAATTTATTTAAAATTTTATTT-GTAATTTCATATTTATTCAATTTAGTCCTTAAAATT
65 GTTGTTTAATTTATTT-AAATTTTATTTCGTAATTTCATATTTATTCAATTTAGTCCTTAAAATT
*
402855 TTATTT
129 ATATTT
402861 TTATCAATAT
Statistics
Matches: 120, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
134 3 0.03
135 108 0.90
136 9 0.08
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (135 bp):
ATTTTTATATTAATTTCAAACTCACATTTTAAAATTATTTCGATTTGATCCATCAACAATGTGCG
TTGTTTAATTTATTTAAATTTTATTTCGTAATTTCATATTTATTCAATTTAGTCCTTAAAATTAT
ATTTG
Found at i:405744 original size:43 final size:43
Alignment explanation
Indices: 405679--405822 Score: 146
Period size: 43 Copynumber: 3.4 Consensus size: 43
405669 GATGGGAAAG
* * * * *
405679 ACGCCGCAATAGGTCAAGATATATCGCGACGTTTTTGGAACAA
1 ACGCCGCAAAAGGTCGATATATATAGCGGCGTTTTTGGAACAA
* * *
405722 ACGCCGCAAAAGATCGATATATATAGCGGCATTTTTTGAACAA
1 ACGCCGCAAAAGGTCGATATATATAGCGGCGTTTTTGGAACAA
** * **
405765 AAACCGCAAAAGGTTGATACCTATAGCGGCGTTTTTGG-ACAA
1 ACGCCGCAAAAGGTCGATATATATAGCGGCGTTTTTGGAACAA
* *
405807 ACGTCACAAAAGGTCG
1 ACGCCGCAAAAGGTCG
405823 CAGTCTATAG
Statistics
Matches: 80, Mismatches: 21, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
42 15 0.19
43 65 0.81
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (43 bp):
ACGCCGCAAAAGGTCGATATATATAGCGGCGTTTTTGGAACAA
Found at i:405964 original size:41 final size:41
Alignment explanation
Indices: 405869--405982 Score: 117
Period size: 41 Copynumber: 2.8 Consensus size: 41
405859 ACAGGTCATA
* * *
405869 TCTATAGCGGCATTT-TTAGAAAAACGCCACTAAAGTATGAG
1 TCTATCGCGGCGTTTGTT-GAAAAACGCCACTAAAGTATGAC
* *
405910 TCTATCGCTGCGTTTGTAT-AAAAACGCCACTAAAGTGCT-AC
1 TCTATCGCGGCGTTTGT-TGAAAAACGCCACTAAAGT-ATGAC
* *
405951 TCTGTTGCGGCGTTTGTTGAAAAACGCCACTA
1 TCTATCGCGGCGTTTGTTGAAAAACGCCACTA
405983 TGGATGAACC
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
40 1 0.02
41 57 0.93
42 2 0.03
43 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (41 bp):
TCTATCGCGGCGTTTGTTGAAAAACGCCACTAAAGTATGAC
Found at i:407360 original size:19 final size:16
Alignment explanation
Indices: 407331--407376 Score: 92
Period size: 16 Copynumber: 2.9 Consensus size: 16
407321 TGATTGAACA
407331 TGTAAAGTATTATTGC
1 TGTAAAGTATTATTGC
407347 TGTAAAGTATTATTGC
1 TGTAAAGTATTATTGC
407363 TGTAAAGTATTATT
1 TGTAAAGTATTATT
407377 TGATTTTGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (16 bp):
TGTAAAGTATTATTGC
Found at i:408732 original size:26 final size:26
Alignment explanation
Indices: 408696--408759 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
408686 TACTGTATTG
* * *
408696 TAATATAATGTAGGAGTTAATGTTTT
1 TAATGTAATGTAGGAGTTAATGTCTC
*
408722 TAATGTGATGTAGGAGTTAATGTCTC
1 TAATGTAATGTAGGAGTTAATGTCTC
408748 TAATGTAATGTA
1 TAATGTAATGTA
408760 ATGTATAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.42
Consensus pattern (26 bp):
TAATGTAATGTAGGAGTTAATGTCTC
Found at i:410534 original size:24 final size:23
Alignment explanation
Indices: 410507--410560 Score: 54
Period size: 25 Copynumber: 2.2 Consensus size: 23
410497 AAATTTATCT
*
410507 TTTATTCTATTTAAAAATTTAAAA
1 TTTATT-TATTTAAAAAGTTAAAA
* *
410531 TTTAAATTTTTTTAAAAAGTTAAAT
1 TTT--ATTTATTTAAAAAGTTAAAA
410556 TTTAT
1 TTTAT
410561 AATCCTGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 2 0.08
24 3 0.12
25 17 0.68
26 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTATTTATTTAAAAAGTTAAAA
Found at i:410700 original size:3 final size:3
Alignment explanation
Indices: 410692--410755 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
410682 ATTTTTCTCA
410692 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
410740 CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT C
410756 CAAAAATCAC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.34, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:425042 original size:46 final size:46
Alignment explanation
Indices: 424989--425079 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
424979 TGAGATTTGA
* *
424989 TAAAATTTAATCGCAGAATCTCAAACGACTATCATATCTCAAACAG
1 TAAAATTTAATCGCAAAATCTCAAACGACTATCATACCTCAAACAG
* ** *
425035 TAAAATTTGATTTCAAAATCTTAAACGACTATCATACCTCAAACA
1 TAAAATTTAATCGCAAAATCTCAAACGACTATCATACCTCAAACA
425080 ACAGTTTACA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.29
Consensus pattern (46 bp):
TAAAATTTAATCGCAAAATCTCAAACGACTATCATACCTCAAACAG
Found at i:429738 original size:190 final size:190
Alignment explanation
Indices: 429434--429779 Score: 491
Period size: 190 Copynumber: 1.8 Consensus size: 190
429424 TAAATATGTC
* *
429434 TTATTTTAATTTGAAAAATACAAAAATATATAATTATCTTTAATATAAAAAGTTAAAAAGGTAAC
1 TTATTTTAATTTGAAAAATACAAAAACATATAATTATCTTTAATATAAAAAGTCAAAAAGGTAAC
* * * * * * *
429499 AATTACCTTTTTAAGTTGACATATTCAAAGAGTAATTATCCTACTAATATTTAAATTAAATAATA
66 AAATACCTTTTTAAATTAACATATTAAAAGAATAATTATCCTACTAATATTCAAATTAAAAAATA
* *
429564 T-ATTTAATTTGCAATGGTCAAAAGGTAAACTTCTTTTACTATTCAAATTTAAACAAATA
131 TCATTTAATTCGCAATAGTCAAAAGGTAAACTTCTTTTACTATTCAAATTTAAACAAATA
* * *
429623 TTATTTTAATTTGAAATATACAAAAACATATAATTATCTTTTAATATTCAAAA-TCAAAAAGATT
1 TTATTTTAATTTGAAAAATACAAAAACATATAATTATC-TTTAATA-TAAAAAGTCAAAAAG-GT
*
429687 AA-AAATACCTTTTTAAATTAACTTATTAAAAGAATAATTATCCTACTAATATTCAAATTAAAAA
63 AACAAATACCTTTTTAAATTAACATATTAAAAGAATAATTATCCTACTAATATTCAAATTAAAAA
* *
429751 ATATCTTTTAATTCGCAATATTCAAAAGG
128 ATATCATTTAATTCGCAATAGTCAAAAGG
429780 ACTATGAATT
Statistics
Matches: 136, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
189 36 0.26
190 72 0.53
191 28 0.21
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (190 bp):
TTATTTTAATTTGAAAAATACAAAAACATATAATTATCTTTAATATAAAAAGTCAAAAAGGTAAC
AAATACCTTTTTAAATTAACATATTAAAAGAATAATTATCCTACTAATATTCAAATTAAAAAATA
TCATTTAATTCGCAATAGTCAAAAGGTAAACTTCTTTTACTATTCAAATTTAAACAAATA
Found at i:433037 original size:55 final size:55
Alignment explanation
Indices: 432944--433086 Score: 193
Period size: 55 Copynumber: 2.6 Consensus size: 55
432934 CAAAGGGAGG
*
432944 TATCGATACACTCTTTGATGTCTCGATACACCCACAACATTGAATGCATTTTGTC
1 TATCGATACACTCTTTGATGTATCGATACACCCACAACATTGAATGCATTTTGTC
* * *
432999 TA-CTGATACACTCTTTTATGTATCGA-ATCACCCCCAACATTGAATGCATTTTGTG
1 TATC-GATACACTCTTTGATGTATCGATA-CACCCACAACATTGAATGCATTTTGTC
*
433054 TATCGATACACT-TTCTGATGTACCGATACACCC
1 TATCGATACACTCTT-TGATGTATCGATACACCC
433087 CTCGCTTAGG
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
54 4 0.05
55 71 0.92
56 2 0.03
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (55 bp):
TATCGATACACTCTTTGATGTATCGATACACCCACAACATTGAATGCATTTTGTC
Found at i:434588 original size:189 final size:192
Alignment explanation
Indices: 434352--434722 Score: 545
Period size: 191 Copynumber: 1.9 Consensus size: 192
434342 AACAATATCT
*
434352 TTTAATTTGAAATATTCAAAAGATAAAACTCCTTTTACCATTCAAACTT-AA-ATATGCATTATT
1 TTTAATTTGAAATAGTCAAAAGATAAAACTCCTTTTACCATTCAAACTTAAACATATG--TTATT
* *
434415 TTAATTTGAAATATACAAAAGTATATAATTATC-TTTAATATTCAAAGTT-AAAAAGATAACAAA
64 TTAATTTGAAATATACAAAAGTATATAATTATCTTTTAATATTCAAAATTAAAAAAAATAACAAA
* * * *
434478 TTCATTTTTAAGTTGACAAATTCAAAGAGTAATTATCCTACTAATATTCAAATTAAATAATATA
129 TACATTTTTAAATTCACAAATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAATAATATA
* * * *
434542 TTTAATTTGCAATGGTCAAAAGGT-AAACTCCTTTTACTATTCAAACTTAAACATATGTTATTTT
1 TTTAATTTGAAATAGTCAAAAGATAAAACTCCTTTTACCATTCAAACTTAAACATATGTTATTTT
434606 AATTTGAAATATACAAAAGTATATAATTATCTTTTAATATTCAAAATTAAAAAAAATAACAAATA
66 AATTTGAAATATACAAAAGTATATAATTATCTTTTAATATTCAAAATTAAAAAAAATAACAAATA
* ** * *
434671 CCTTTTTAAATTCACTTATTAAAATAGTAATTATCTTACTAATATTCAAATT
131 CATTTTTAAATTCACAAATTAAAAGAGTAATTATCCTACTAATATTCAAATT
434723 GAATTCACAA
Statistics
Matches: 161, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
189 61 0.38
190 37 0.23
191 63 0.39
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (192 bp):
TTTAATTTGAAATAGTCAAAAGATAAAACTCCTTTTACCATTCAAACTTAAACATATGTTATTTT
AATTTGAAATATACAAAAGTATATAATTATCTTTTAATATTCAAAATTAAAAAAAATAACAAATA
CATTTTTAAATTCACAAATTAAAAGAGTAATTATCCTACTAATATTCAAATTAAATAATATA
Found at i:443171 original size:18 final size:18
Alignment explanation
Indices: 443136--443169 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
443126 ACTTGATTGG
*
443136 ATTATCTTCCATCATTTC
1 ATTATCATCCATCATTTC
443154 ATTATCATCC-TCATTT
1 ATTATCATCCATCATTT
443170 TCTTGAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.26, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTATCATCCATCATTTC
Found at i:455714 original size:22 final size:21
Alignment explanation
Indices: 455683--455753 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
455673 CATCAATAAG
*
455683 TCTTTTGAGCATGATGCTTAAA
1 TCTTTAGAGCATGATG-TTAAA
* *
455705 TCTTTAGAGCCATCA-G-TAAG
1 TCTTTAGAG-CATGATGTTAAA
*
455725 TCTTTCGAGCATGATGATTAAA
1 TCTTTAGAGCATGATG-TTAAA
*
455747 TCCTTAG
1 TCTTTAG
455754 GATAATTTGT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 4 0.11
20 12 0.32
22 17 0.46
23 4 0.11
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (21 bp):
TCTTTAGAGCATGATGTTAAA
Found at i:455734 original size:20 final size:20
Alignment explanation
Indices: 455655--455734 Score: 54
Period size: 20 Copynumber: 3.9 Consensus size: 20
455645 AATTTCACAC
* * *
455655 TCAGTAAGTCATTCGGGACA
1 TCAGTAAGTCTTTCGAGCCA
* *
455675 TCAATAAGTCTTTTGAG-CA
1 TCAGTAAGTCTTTCGAGCCA
* * *
455694 TGATGCTTAAATCTTTAGAGCCA
1 TCA-G--TAAGTCTTTCGAGCCA
455717 TCAGTAAGTCTTTCGAGC
1 TCAGTAAGTCTTTCGAGC
455735 ATGATGATTA
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
19 4 0.09
20 25 0.56
22 12 0.27
23 4 0.09
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (20 bp):
TCAGTAAGTCTTTCGAGCCA
Found at i:455766 original size:42 final size:42
Alignment explanation
Indices: 455674--455972 Score: 167
Period size: 42 Copynumber: 6.9 Consensus size: 42
455664 CATTCGGGAC
* * * * *
455674 ATCAATAAGTCTTTTGAGCATGATGCTTAAATCTTTAGAGCC
1 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGAGCA
*
455716 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAG-GATA
1 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGAG-CA
** * * ** * *
455758 ATTTGTAAGCCTTCACGGAAG-A-GTAGTGAAGCAAACCCATCAGTAAGTGTCA
1 ATCAGTAAGTCTT-TC-G-AGCATG-A-TG-ATTAAATCC-T---T-AGAG-CA
* * *
455810 -TCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCAG-GCC
1 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT-AGAGCA
* * * * * *
455851 ATCAATAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGCC
1 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGAGCA
* * * * *
455893 ATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTTTTGGGCC
1 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCC--TTAGAGCA
455937 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
1 ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
455973 CGAGTAATTT
Statistics
Matches: 207, Mismatches: 31, Indels: 38
0.75 0.11 0.14
Matches are distributed among these distances:
41 3 0.01
42 117 0.57
43 5 0.02
44 42 0.20
45 4 0.02
46 7 0.03
47 6 0.03
48 4 0.02
49 3 0.01
50 3 0.01
51 11 0.05
52 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (42 bp):
ATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTAGAGCA
Found at i:455888 original size:22 final size:22
Alignment explanation
Indices: 455815--455928 Score: 98
Period size: 22 Copynumber: 5.4 Consensus size: 22
455805 TGTCATCAGT
*
455815 AAGTCTTTCGAGCATGATGATG
1 AAGTCCTTCGAGCATGATGATG
*
455837 AAGTCCTTC-AGGCCATCA--AT-
1 AAGTCCTTCGA-G-CATGATGATG
*
455857 AAGTCTTTCGAGCATGATGATG
1 AAGTCCTTCGAGCATGATGATG
* *
455879 AAGTCCTTCGGGCCATCA-G-T-
1 AAGTCCTTCGAG-CATGATGATG
*
455899 AAGTCTTTCGAGCATGATGATG
1 AAGTCCTTCGAGCATGATGATG
455921 AAGTCCTT
1 AAGTCCTT
455929 TTTGGGCCAT
Statistics
Matches: 71, Mismatches: 11, Indels: 20
0.70 0.11 0.20
Matches are distributed among these distances:
19 8 0.11
20 20 0.28
21 8 0.11
22 27 0.38
23 8 0.11
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (22 bp):
AAGTCCTTCGAGCATGATGATG
Done.