Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008295.1 Hibiscus syriacus cultivar Beakdansim tig00110962_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: 741301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:223490 original size:20 final size:19
Alignment explanation
Indices: 223456--223572 Score: 91
Period size: 20 Copynumber: 6.2 Consensus size: 19
223446 AAAATCACAA
* *
223456 CGATAGTCAAATTCGCATTG
1 CGATAGTC-ATTTCGCGTTG
*
223476 CGATAGTCATTTTCGTGTTG
1 CGATAGTCA-TTTCGCGTTG
**
223496 CGATTTTCATTTCGCGTTG
1 CGATAGTCATTTCGCGTTG
*
223515 CGAT--T-A--TCTCGTTG
1 CGATAGTCATTTCGCGTTG
*
223529 CGATAGTCAAATTCGCGTTG
1 CGATAGTC-ATTTCGCGTTG
*
223549 CGATAGTCATTATCGTGTTG
1 CGATAGTCATT-TCGCGTTG
223569 CGAT
1 CGAT
223573 TTTAAGTTTC
Statistics
Matches: 79, Mismatches: 10, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
14 11 0.14
16 2 0.03
17 1 0.01
18 1 0.01
19 16 0.20
20 48 0.61
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (19 bp):
CGATAGTCATTTCGCGTTG
Found at i:223594 original size:73 final size:73
Alignment explanation
Indices: 223456--223594 Score: 190
Period size: 73 Copynumber: 1.9 Consensus size: 73
223446 AAAATCACAA
* * * ***
223456 CGATAGTCAAATTCGCATTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTCGCGTTGCGATTA
1 CGATAGTCAAATTCGCATTGCGATAGTCATTATCGTGTTGCGATTTTAATTTCGAGAAACGATTA
223521 TCTCGTTG
66 TCTCGTTG
* *
223529 CGATAGTCAAATTCGCGTTGCGATAGTCATTATCGTGTTGCGATTTTAAGTTTC-AGAAACTATT
1 CGATAGTCAAATTCGCATTGCGATAGTCATTATCGTGTTGCGATTTTAA-TTTCGAGAAACGATT
223593 AT
65 AT
223595 TCTTCTACAA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 53 0.93
74 4 0.07
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (73 bp):
CGATAGTCAAATTCGCATTGCGATAGTCATTATCGTGTTGCGATTTTAATTTCGAGAAACGATTA
TCTCGTTG
Found at i:225592 original size:19 final size:19
Alignment explanation
Indices: 225564--225613 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
225554 AAAATGACTA
*
225564 TCGCAATGCGA-ATTTAGTT
1 TCGCATTGCGATATTTA-TT
* *
225583 TCGCGTTGCGATTTTTATT
1 TCGCATTGCGATATTTATT
225602 TCGCATTGCGAT
1 TCGCATTGCGAT
225614 TATCCCGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 22 0.85
20 4 0.15
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (19 bp):
TCGCATTGCGATATTTATT
Found at i:225614 original size:19 final size:20
Alignment explanation
Indices: 225576--225614 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
225566 GCAATGCGAA
*
225576 TTTAGTTTCGCGTTGCGATT
1 TTTAGTTTCGCATTGCGATT
225596 TTTA-TTTCGCATTGCGATT
1 TTTAGTTTCGCATTGCGATT
225615 ATCCCGTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.13, C:0.15, G:0.21, T:0.51
Consensus pattern (20 bp):
TTTAGTTTCGCATTGCGATT
Found at i:226245 original size:21 final size:21
Alignment explanation
Indices: 226154--226272 Score: 105
Period size: 21 Copynumber: 5.7 Consensus size: 21
226144 GACTCACCTG
*
226154 TCATCATTCAAGAGGCCTCTC
1 TCATCATTCAAGAGGCCCCTC
*
226175 -CTATCATTCAAGAGGCCCCTA
1 TC-ATCATTCAAGAGGCCCCTC
** *
226196 TCATCCCTCAAGAGTCCCCTC
1 TCATCATTCAAGAGGCCCCTC
* * * *
226217 CCACCGTTCAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCCCTC
* * *
226238 TCATCGTTGAAGAGGTCCCTC
1 TCATCATTCAAGAGGCCCCTC
*
226259 TCACCATTCAAGAG
1 TCATCATTCAAGAG
226273 CCCGATTCAT
Statistics
Matches: 76, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
20 1 0.01
21 74 0.97
22 1 0.01
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.24
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTC
Found at i:226251 original size:42 final size:42
Alignment explanation
Indices: 226161--226272 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
226151 CTGTCATCAT
* *
226161 TCAAGAGG-CCTCTCCTATCATTCAAGAGGCCCCTATCATCCC
1 TCAAGAGGTCC-CTCCCACCATTCAAGAGGCCCCTATCATCCC
* * **
226203 TCAAGA-GTCCCCTCCCACCGTTCAAGAGGCCCCTGTCATCGT
1 TCAAGAGGT-CCCTCCCACCATTCAAGAGGCCCCTATCATCCC
* *
226245 TGAAGAGGTCCCTCTCACCATTCAAGAG
1 TCAAGAGGTCCCTCCCACCATTCAAGAG
226273 CCCGATTCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
41 1 0.02
42 53 0.91
43 4 0.07
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (42 bp):
TCAAGAGGTCCCTCCCACCATTCAAGAGGCCCCTATCATCCC
Found at i:227689 original size:14 final size:14
Alignment explanation
Indices: 227652--227713 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
227642 TTGCTTGTTT
*
227652 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
227666 AATTGATTTGTCAA
1 AATTGATTTGTAAA
* *
227680 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
227695 TATTGATGTGTAAA
1 AATTGATTTGTAAA
227709 TAATT
1 -AATT
227714 CTTATTTGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
14 24 0.65
15 13 0.35
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:227856 original size:20 final size:20
Alignment explanation
Indices: 227827--227865 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
227817 ACGTTAAACT
*
227827 CAAAAGCGCAATGCGAAAGC
1 CAAAAGCGCAACGCGAAAGC
*
227847 CAAAATCGCAACGCGAAAG
1 CAAAAGCGCAACGCGAAAG
227866 TCAATTCACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.26, G:0.23, T:0.05
Consensus pattern (20 bp):
CAAAAGCGCAACGCGAAAGC
Found at i:227965 original size:20 final size:20
Alignment explanation
Indices: 227910--228038 Score: 126
Period size: 20 Copynumber: 6.8 Consensus size: 20
227900 AATTTTCTCA
* *
227910 TTGCGATAGTCAAATACCCG
1 TTGCGATAGTCAAATTCGCG
* *
227930 TTGCAATAATCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
227950 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
* *
227970 TTGCGAT--T----TTTGAG
1 TTGCGATAGTCAAATTCGCG
*
227984 TTGCGATAATCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
*
228004 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCG
* *
228024 TTGTGATATTCAAAT
1 TTGCGATAGTCAAAT
228039 AAATGTGTAA
Statistics
Matches: 89, Mismatches: 14, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
14 11 0.12
16 1 0.01
18 1 0.01
20 76 0.85
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:227989 original size:74 final size:74
Alignment explanation
Indices: 227868--228039 Score: 202
Period size: 74 Copynumber: 2.3 Consensus size: 74
227858 CGCGAAAGTC
* * * *
227868 AATTCACGTTGCGATAGTCTAATACGCTTTGCAATTTTCTCATTGCGATAGTCAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCAATTTTCTCATTGCGATAATCAAATACCCGTTG
227933 CAATAATCA
66 CAATAATCA
* * * * *
227942 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGAGTTGCGATAATCAAATTCGCGTT
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCAATTTTCTCA-TTGCGATAATCAAATACCCGTT
* *
228006 GCGATAGTCA
65 GCAATAATCA
* * *
228016 AATTCGCATTGTGATATTCAAATA
1 AATTCGCGTTGCGATAGTCAAATA
228040 AATGTGTAAT
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
73 2 0.02
74 80 0.98
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (74 bp):
AATTCGCGTTGCGATAGTCAAATACGCGTTGCAATTTTCTCATTGCGATAATCAAATACCCGTTG
CAATAATCA
Found at i:228261 original size:140 final size:140
Alignment explanation
Indices: 228009--228278 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
227999 TCGCGTTGCG
* *
228009 ATAGTCAAATTCGCATTGTGATATTCAAATAAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCATTGCGATATTCAAATAAATGTGTAATAAGTGATAACAACTGAACAAATCA
228074 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
228139 AATACACATA
131 AATACACATA
* *
228149 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAAATCA
1 ATAGTCAAATTCGCATTGCGATATTCAAATAAATGTGTAATAAGTGATAACAACTGAACAAATCA
228214 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
228279 TACAACGTTT
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCATTGCGATATTCAAATAAATGTGTAATAAGTGATAACAACTGAACAAATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:230416 original size:14 final size:14
Alignment explanation
Indices: 230397--230423 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
230387 TCCCGTGGCA
230397 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
230411 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
230424 TTTCTTATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:231537 original size:21 final size:21
Alignment explanation
Indices: 231512--231585 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
231502 GACAGTCAGA
*
231512 ATCGCGTTGCAATTATGTATT
1 ATCGCGTTGCGATTATGTATT
**
231533 ATCGCGTTGCGA-TA-GTTAAA
1 ATCGCGTTGCGATTATG-TATT
*
231553 ATGGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
231574 ATCGCGTTGCGA
1 ATCGCGTTGCGA
231586 ATCTGGAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.02
20 15 0.35
21 26 0.60
22 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:231542 original size:41 final size:41
Alignment explanation
Indices: 231497--231585 Score: 133
Period size: 41 Copynumber: 2.2 Consensus size: 41
231487 GAAATTCAGT
*
231497 GTTGCGACAGTCAGAATCGCGTTGCAATTATGTATTATCGC
1 GTTGCGACAGTCAAAATCGCGTTGCAATTATGTATTATCGC
* * * *
231538 GTTGCGATAGTTAAAATGGCGTTGCGATTATGTATTATCGC
1 GTTGCGACAGTCAAAATCGCGTTGCAATTATGTATTATCGC
231579 GTTGCGA
1 GTTGCGA
231586 ATCTGGAAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.34
Consensus pattern (41 bp):
GTTGCGACAGTCAAAATCGCGTTGCAATTATGTATTATCGC
Found at i:231623 original size:20 final size:19
Alignment explanation
Indices: 231600--231645 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
231590 GGAAACTGAT
* *
231600 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
231620 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
231639 TTGCGAT
1 TTGCGAT
231646 TTTGTTGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:231635 original size:19 final size:19
Alignment explanation
Indices: 231611--231647 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
231601 TGCGATACTG
*
231611 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
231630 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
231648 TGTTGGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:232594 original size:24 final size:24
Alignment explanation
Indices: 232562--232615 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
232552 GTATTCGAAA
*
232562 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
232586 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
232610 TTTGAT
1 TTTGAT
232616 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:235220 original size:20 final size:20
Alignment explanation
Indices: 235192--235244 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
235182 CGCGAAATAA
235192 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTATC
* *
235212 GCGTAGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTATC
*
235232 ACGTTGCGAATTT
1 GCGTTGCGAATTT
235245 ACCTTCAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTATC
Found at i:235742 original size:18 final size:18
Alignment explanation
Indices: 235721--235757 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
235711 GTAATTGGAG
235721 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
235739 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
235757 T
1 T
235758 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:235764 original size:24 final size:24
Alignment explanation
Indices: 235713--235765 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
235703 TTTCATATGT
* * *
235713 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
235737 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
235761 AATTT
1 AATTT
235766 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:236076 original size:35 final size:35
Alignment explanation
Indices: 236001--236076 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
235991 AATAATAACA
* **
236001 AAAATAATAAGTCCAAAATGCTTTTGAGTACTATC
1 AAAATCATAAGTCCAAAATGCTTCCGAGTACTATC
* *
236036 CAAATCATAAGTCCAAAATGCTTCCGA-TGCTCATC
1 AAAATCATAAGTCCAAAATGCTTCCGAGTACT-ATC
236071 AAAATC
1 AAAATC
236077 CAAAGCTCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 3 0.09
35 31 0.91
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.28
Consensus pattern (35 bp):
AAAATCATAAGTCCAAAATGCTTCCGAGTACTATC
Found at i:236113 original size:39 final size:39
Alignment explanation
Indices: 236068--236154 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
236058 TCCGATGCTC
*
236068 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGGAA
* *
236107 ATCAAAATCAAAATCTCATATGGTGTCAAGCAAAAGGAA
1 ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGGAA
236146 ATCAAAATC
1 ATCAAAATC
236155 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (39 bp):
ATCAAAATCAAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:236563 original size:61 final size:63
Alignment explanation
Indices: 236432--236572 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 63
236422 TTTTAGAAAC
*
236432 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACAAATCAAATT
236497 A
63 A
* * ** *
236498 AACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAAATCTTATTTCCTCATC-AATTGT
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATT-A
236559 AACAAATCAACTTT
1 AACAAATCAACTTT
236573 CAATGTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
60 4 0.06
61 35 0.51
62 3 0.04
66 26 0.38
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.31
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATTA
Found at i:238022 original size:21 final size:21
Alignment explanation
Indices: 237945--238040 Score: 86
Period size: 21 Copynumber: 4.6 Consensus size: 21
237935 GGCGGAACCA
*
237945 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * * * *
237966 CTTAAACGGTGGGAGAGGCTT
1 CTTGAACGATGAGAGGGGCCT
*
237987 CTTCG-ATGATGAGAGGGGCCT
1 CTT-GAACGATGAGAGGGGCCT
* *
238008 CTTGAACGATAAGAGGCGCCT
1 CTTGAACGATGAGAGGGGCCT
*
238029 CTTGAATGATGA
1 CTTGAACGATGA
238041 TAGGTGCATC
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 1 0.02
21 55 0.98
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:238203 original size:12 final size:12
Alignment explanation
Indices: 238184--238225 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
238174 GGGCCACTGA
238184 AAATAAATTAAT
1 AAATAAATTAAT
*
238196 ATATAAATTAAT
1 AAATAAATTAAT
*
238208 AAATAAATAAAT
1 AAATAAATTAAT
238220 AAATAA
1 AAATAA
238226 TGCCGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:238214 original size:4 final size:4
Alignment explanation
Indices: 238184--238225 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
238174 GGGCCACTGA
* * *
238184 AAAT AAAT TAAT ATAT AAAT TAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
238226 TGCCGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (4 bp):
AAAT
Found at i:240294 original size:13 final size:13
Alignment explanation
Indices: 240276--240307 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
240266 GGGTTTCTTC
*
240276 AACAAAAAGATAA
1 AACAAAAAGACAA
240289 AACAAAAAGACAA
1 AACAAAAAGACAA
240302 AACAAA
1 AACAAA
240308 GGCAAATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.78, C:0.12, G:0.06, T:0.03
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:240544 original size:22 final size:22
Alignment explanation
Indices: 240511--240561 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
240501 GATGGAGATA
* *
240511 GACGTATTTCGTCGGAAATGGG
1 GACGGATTTCGTCAGAAATGGG
* *
240533 GATGGATTTCGTCAGAGATGGG
1 GACGGATTTCGTCAGAAATGGG
240555 GACGGAT
1 GACGGAT
240562 GTCGCCGTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.39, T:0.25
Consensus pattern (22 bp):
GACGGATTTCGTCAGAAATGGG
Found at i:240714 original size:20 final size:20
Alignment explanation
Indices: 240689--240733 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
240679 GCGTAAAAAC
*
240689 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
*
240709 ATTTGACTATCGCTTTGCGA
1 ATTTGACTATCGCGTTGCGA
240729 ATTTG
1 ATTTG
240734 GAAAATCGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:240787 original size:20 final size:20
Alignment explanation
Indices: 240764--240810 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
240754 CATATTCGCA
*
240764 TTGCGAAATTGGAAATTGA-G
1 TTGCGAAATTGG-AATTCACG
240784 TTGCGAAATTGGAATTCACG
1 TTGCGAAATTGGAATTCACG
240804 TTGCGAA
1 TTGCGAA
240811 TTTGTTGGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.30
Consensus pattern (20 bp):
TTGCGAAATTGGAATTCACG
Found at i:241352 original size:35 final size:32
Alignment explanation
Indices: 241301--241390 Score: 92
Period size: 35 Copynumber: 2.7 Consensus size: 32
241291 AGTTAGTATT
* *
241301 TTTATA-AAATAGTTATTATATTTTATATTAATA
1 TTTATATAAATA-TTATT-TATTTTAAAATAATA
*
241334 TAATTATATAAATATTATTTTTTATTAAAATAATA
1 T--TTATATAAATATTATTTATT-TTAAAATAATA
*
241369 TTTATATAATTATTATTTATTT
1 TTTATATAAATATTATTTATTT
241391 AAATTTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
32 1 0.02
33 19 0.40
34 3 0.06
35 20 0.42
36 5 0.10
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (32 bp):
TTTATATAAATATTATTTATTTTAAAATAATA
Found at i:241357 original size:32 final size:32
Alignment explanation
Indices: 241314--241404 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 32
241304 ATAAAATAGT
*
241314 TATTATATTTTATATTAATATAATTATATAAA
1 TATTATTTTTTATATTAATATAATTATATAAA
* * *
241346 TATTATTTTTTAT-TAAAATAATATTTATATAAT
1 TATTATTTTTTATAT-TAAT-ATAATTATATAAA
* *
241379 TATTATTTATTTAAATTTAT-TAATTA
1 TATTATTT-TTTATATTAATATAATTA
241405 ATTATTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
31 1 0.02
32 20 0.43
33 19 0.40
34 6 0.13
35 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (32 bp):
TATTATTTTTTATATTAATATAATTATATAAA
Found at i:241360 original size:30 final size:32
Alignment explanation
Indices: 241314--241391 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
241304 ATAAAATAGT
241314 TATTATATTTTATATT-AAT-ATAATTATATAAA
1 TATTAT-TTTT-TATTAAATAATAATTATATAAA
* *
241346 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATT-AAATAATAATTATATAAA
241379 TATTATTTATTTA
1 TATTATTT-TTTA
241392 AATTTATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
30 4 0.10
31 4 0.10
32 9 0.22
33 19 0.47
34 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TATTATTTTTTATTAAATAATAATTATATAAA
Found at i:243189 original size:21 final size:22
Alignment explanation
Indices: 243138--243189 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
243128 TATGTCATCT
*
243138 CCGC-AGGGTTACATTCCTAGC
1 CCGCAAGGGTTACATGCCTAGC
*
243159 CCGCCA-GGTTACATGCCTAGC
1 CCGCAAGGGTTACATGCCTAGC
243180 CCG-AAGGGTT
1 CCGCAAGGGTT
243190 TTATACCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.19, C:0.33, G:0.27, T:0.21
Consensus pattern (22 bp):
CCGCAAGGGTTACATGCCTAGC
Found at i:243725 original size:34 final size:34
Alignment explanation
Indices: 243682--243788 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
243672 ATAAATGTTT
*
243682 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAATATTCGAAATTTAAAA
* * * *
243716 TTAAAATACAAATAATATTATTCAAAAATTAAAA
1 TTAAAATACAAATTATAATATTCGAAATTTAAAA
* *
243750 TTAAAATATAAATTATAATATTCGAAATTTAACA
1 TTAAAATACAAATTATAATATTCGAAATTTAAAA
243784 TTAAA
1 TTAAA
243789 TTCAACTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (34 bp):
TTAAAATACAAATTATAATATTCGAAATTTAAAA
Found at i:244422 original size:127 final size:127
Alignment explanation
Indices: 244196--244828 Score: 1045
Period size: 127 Copynumber: 5.0 Consensus size: 127
244186 GCGCTTTAAA
* * * *
244196 GTCCCCTAAGAAATAGTAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATATGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
* *
244261 CAATGATAACATATTCTCTGACAAAATAATGGAATGCGCGCCCCTGGGAACGCACCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCTGGGAACGCGCCTTCACG
*
244323 GTCCCCTAAGGAATAATAGGTATTGACATGAATTGTTCCCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
*
244388 CAATGATAACATATTCTCTGACAAAATAATGGAATGCGCG-CCCTCGGGAACGCGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCT-GGGAACGCGCCTTCACG
* *
244450 GTCCCCTAAGGAATAATAGGTATTTACATGAATAGTTCCCGGGGGATATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
* * *
244515 CAATGATAACATATTCTCTGACAAAATAATGGAAGGTGTG-CCCTCGGGAACGCGTCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCT-GGGAACGCGCCTTCACG
* *
244577 GTCCCCTAAGGAATAATAGGTATTGACATAAATAGTTCCCAGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
* *
244642 CAATGATAACATATTCTCTGACAAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCTGGGAACGCGCCTTCACG
* *
244704 GTCCCCTAAGAAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATATGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
* *
244769 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGAGAACGCGCCTTCA
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCTGGGAACGCGCCTTCA
244829 TGTGAATAGT
Statistics
Matches: 476, Mismatches: 28, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
126 4 0.01
127 469 0.99
128 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (127 bp):
GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCTGGGAACGCGCCTTCACG
Found at i:257262 original size:18 final size:18
Alignment explanation
Indices: 257241--257283 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
257231 CCCACCTCCG
*
257241 CCTCCACCATCACCACCT
1 CCTCCACCATCACCACCA
* * *
257259 CCTCCTCCTTCACTACCA
1 CCTCCACCATCACCACCA
257277 CCTCCAC
1 CCTCCAC
257284 TGCCCCTCCC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.19, C:0.60, G:0.00, T:0.21
Consensus pattern (18 bp):
CCTCCACCATCACCACCA
Found at i:258614 original size:3 final size:3
Alignment explanation
Indices: 258606--258678 Score: 121
Period size: 3 Copynumber: 24.7 Consensus size: 3
258596 TGTCCGGGTT
258606 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
258654 TTA TTA TTA TT- TCA TTA ATA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
258679 TAATTATATT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
2 1 0.02
3 64 0.98
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:260401 original size:16 final size:15
Alignment explanation
Indices: 260380--260411 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
260370 TTATTTAACA
260380 TATTTCCATTCGTATT
1 TATTTCCATT-GTATT
260396 TATTTCCATTGTATT
1 TATTTCCATTGTATT
260411 T
1 T
260412 CTTTATCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.19, C:0.16, G:0.06, T:0.59
Consensus pattern (15 bp):
TATTTCCATTGTATT
Found at i:261866 original size:16 final size:17
Alignment explanation
Indices: 261845--261877 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
261835 TCTTGAAAAT
*
261845 AAATCAT-TTTGGGTAG
1 AAATCATGTCTGGGTAG
261861 AAATCATGTCTGGGTAG
1 AAATCATGTCTGGGTAG
261878 GACCTCTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.33
Consensus pattern (17 bp):
AAATCATGTCTGGGTAG
Found at i:263323 original size:21 final size:22
Alignment explanation
Indices: 263293--263352 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
263283 GTTGATGGTT
*
263293 TCATATGTCCTTCGGGACA-AC
1 TCATAGGTCCTTCGGGACATAC
*
263314 TCATAGGTCCTTCGGGACATAT
1 TCATAGGTCCTTCGGGACATAC
* *
263336 TCACAGGTCCTTTGGGA
1 TCATAGGTCCTTCGGGA
263353 TAAAAATTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 18 0.53
22 16 0.47
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (22 bp):
TCATAGGTCCTTCGGGACATAC
Found at i:263346 original size:22 final size:21
Alignment explanation
Indices: 263299--263352 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
263289 GGTTTCATAT
*
263299 GTCCTTCGGGACAACTCATAG
1 GTCCTTCGGGACAACTCACAG
*
263320 GTCCTTCGGGACATATTCACAG
1 GTCCTTCGGGACA-ACTCACAG
*
263342 GTCCTTTGGGA
1 GTCCTTCGGGA
263353 TAAAAATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GTCCTTCGGGACAACTCACAG
Found at i:267317 original size:36 final size:36
Alignment explanation
Indices: 267252--267382 Score: 165
Period size: 37 Copynumber: 3.6 Consensus size: 36
267242 ACAAAGTGTC
*
267252 GTCTCGCTAGAGACAATTTTTCTTAAAAATAAATTTT
1 GTCTCGCTTGAGACAATTTTTC-TAAAAATAAATTTT
* *
267289 GTCTCGCTTGAGATAATTTTCTCTAAAATTAAATTTT
1 GTCTCGCTTGAGACAATTTT-TCTAAAAATAAATTTT
* * * * *
267326 GTCTCTCTTGGGACAATTTTTCTCAAAACAAATTTC
1 GTCTCGCTTGAGACAATTTTTCTAAAAATAAATTTT
267362 GTCTCGCTTGAGAC-ATTTTTC
1 GTCTCGCTTGAGACAATTTTTC
267383 CTTTGAGATG
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.09
36 24 0.30
37 48 0.59
38 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (36 bp):
GTCTCGCTTGAGACAATTTTTCTAAAAATAAATTTT
Found at i:267600 original size:67 final size:66
Alignment explanation
Indices: 267435--267658 Score: 247
Period size: 67 Copynumber: 3.4 Consensus size: 66
267425 TTGATCTCAC
* * ** * * * **
267435 TTGAGGTTGTTTTTCTCAAAACAAA-TTTTGTCTCACTTGAGACGGTCTTC-CTTAAGACACGAA
1 TTGAGTTTGTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGT-TTCTCTTAA-AAAAAAA
*
267498 -CA
64 TCT
* *
267500 TTGAGATTATTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAATAAAAAT
1 TTGAGTTTGTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAA-AAAAAT
267565 CT
65 CT
* * *
267567 TTGAGTTTGTTTCCCTTGAAACAAAGTTTTGTCTATCTTGAGACAGTATCTCTTGAAAAAAAAAT
1 TTGAGTTTGTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT-AAAAAAAAAT
267632 CT
65 CT
*
267634 TTGAGTATGTTTTCCTTGAAACAAA
1 TTGAGTTTGTTTTCCTTGAAACAAA
267659 AATCTTTGAG
Statistics
Matches: 136, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
65 24 0.18
66 27 0.20
67 81 0.60
68 4 0.03
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (66 bp):
TTGAGTTTGTTTTCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAAAAAAATC
T
Found at i:267675 original size:30 final size:30
Alignment explanation
Indices: 267618--267684 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
267608 GACAGTATCT
*
267618 CTTGAAAAAAAAATCTTTGAGTATGTTTTC
1 CTTGAAAAAAAAATCTTTGAGTATGTTTCC
* *
267648 CTTGAAACAAAAATCTTTGAGTCTGTTTCC
1 CTTGAAAAAAAAATCTTTGAGTATGTTTCC
267678 CTTGAAA
1 CTTGAAA
267685 TAAAGTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Consensus pattern (30 bp):
CTTGAAAAAAAAATCTTTGAGTATGTTTCC
Found at i:267675 original size:97 final size:97
Alignment explanation
Indices: 267545--267755 Score: 314
Period size: 97 Copynumber: 2.2 Consensus size: 97
267535 TCTTGAGACA
* * * *
267545 GTTTCTCTTAAAATAAAAATCTTTGAGTTTGTTTCCCTTGAAACAAAGTTTTGTCTATCTTGAGA
1 GTTTCCCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTATCTTGAGA
* *
267610 CAGTATCTCTTGAAAAAAAAATCTTTGAGTAT
66 CAGTATCTCTTGAAAAAAAAATATTTAAGTAT
* * *
267642 GTTTTCCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAATAAAGTTTTGTCTCTCTTGAGA
1 GTTTCCCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTATCTTGAGA
* * *
267707 CAGTTTCTCTTGAAACAAAAATATTTAAGTTT
66 CAGTATCTCTTGAAAAAAAAATATTTAAGTAT
267739 GTTTCCCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
267756 GTTTTGTCTC
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
97 101 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (97 bp):
GTTTCCCTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTATCTTGAGA
CAGTATCTCTTGAAAAAAAAATATTTAAGTAT
Found at i:267705 original size:67 final size:67
Alignment explanation
Indices: 267644--267792 Score: 237
Period size: 67 Copynumber: 2.2 Consensus size: 67
267634 TTGAGTATGT
* * *
267644 TTTC-CTTGAAACAAAAATCTTTGAGTCTGTTTCCCTTGAAATAAAGTTTTGTCTCTCTTGAGAC
1 TTTCTCTTGAAACAAAAATATTTAAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGAC
267708 AG
66 AG
* *
267710 TTTCTCTTGAAACAAAAATATTTAAGTTTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGAA
1 TTTCTCTTGAAACAAAAATATTTAAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGAC
267775 AG
66 AG
*
267777 TTACTCTTGAAACAAA
1 TTTCTCTTGAAACAAA
267793 TCCCTAAAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
66 4 0.05
67 72 0.95
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (67 bp):
TTTCTCTTGAAACAAAAATATTTAAGTCTGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGAC
AG
Found at i:268039 original size:135 final size:132
Alignment explanation
Indices: 267791--268136 Score: 489
Period size: 135 Copynumber: 2.6 Consensus size: 132
267781 TCTTGAAACA
*
267791 AATCCCTAAAGATGGTCAGTCGTCCTCATCACGTAGAAACCGTGTCATCCACTGACCAGATTTCC
1 AATCCCTAAAGATGGTCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCAC-GACCAGA-TTCC
* * * * *
267856 TCATCACGTAGGAGTCGCATTAACCTTAGATAACCAGTCGTCCTCATCACGTAAGAACTGTATTA
64 TCATCACGTAGGAGCCGCATCAACCTTAGATAACCAGTCATCCACATCACGTAAGAACCGTATTA
267921 TCATT
129 TCA-T
* * * *
267926 TATCCCTAAAGATGGCCAGCCGTCCTTATCACGTAGGAACCGTGTCATCCATCGACCAGATCTCC
1 AATCCCTAAAGATGGTCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCA-CGACCAGAT-TCC
* * *
267991 TCATCACGTAGGAGCCGCGTCAACCTTAGATAACCAGTCATCCACATCACGTAGGAACCGTGTTA
64 TCATCACGTAGGAGCCGCATCAACCTTAGATAACCAGTCATCCACATCACGTAAGAACCGTATTA
268056 TCAT
129 TCAT
* *
268060 AATCCATAAATATGGTCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGA-T-CT
1 AATCCCTAAAGATGGTCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCA-CGACCAGATTCCT
268123 CATCACGTAGGAGC
65 CATCACGTAGGAGC
268137 TGTGTCACCC
Statistics
Matches: 189, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
131 16 0.08
132 1 0.01
134 55 0.29
135 116 0.61
136 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (132 bp):
AATCCCTAAAGATGGTCAGTCGTCCTCATCACGTAGGAACCGTGTCATCCACGACCAGATTCCTC
ATCACGTAGGAGCCGCATCAACCTTAGATAACCAGTCATCCACATCACGTAAGAACCGTATTATC
AT
Found at i:268406 original size:3 final size:3
Alignment explanation
Indices: 268400--268437 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
268390 ATTATTATTA
268400 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
268438 TCATCAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:269095 original size:13 final size:13
Alignment explanation
Indices: 269079--269119 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
269069 GAGTTTCGGA
269079 AAAGAGAAAGAAG
1 AAAGAGAAAGAAG
269092 AAAGAGAAA-AATG
1 AAAGAGAAAGAA-G
269105 AAAGAGAAAG-AG
1 AAAGAGAAAGAAG
269117 AAA
1 AAA
269120 AATCACATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.23
13 20 0.77
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (13 bp):
AAAGAGAAAGAAG
Found at i:269099 original size:6 final size:6
Alignment explanation
Indices: 269079--269119 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
269069 GAGTTTCGGA
*
269079 AAAGAG AAAGAAG AAAGAG AAAAATG AAAGAG AAAGAG AAA
1 AAAGAG AAAG-AG AAAGAG AAAGA-G AAAGAG AAAGAG AAA
269120 AATCACATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 20 0.65
7 11 0.35
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (6 bp):
AAAGAG
Found at i:269114 original size:19 final size:20
Alignment explanation
Indices: 269084--269122 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
269074 TCGGAAAAGA
269084 GAAAGAAGAAAGAGAAAAAT
1 GAAAGAAGAAAGAGAAAAAT
269104 GAAAG-AGAAAGAGAAAAAT
1 GAAAGAAGAAAGAGAAAAAT
269123 CACATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (20 bp):
GAAAGAAGAAAGAGAAAAAT
Found at i:282244 original size:12 final size:12
Alignment explanation
Indices: 282197--282242 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
282187 GGAGTTAGTG
282197 CATT-AGTTTTA
1 CATTAAGTTTTA
*
282208 CATCAAGTTTTA
1 CATTAAGTTTTA
282220 CATTAAGTCTTT-
1 CATTAAGT-TTTA
282232 CATTAAGTTTT
1 CATTAAGTTTT
282243 TCTTTTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 6 0.19
12 22 0.71
13 3 0.10
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (12 bp):
CATTAAGTTTTA
Found at i:285875 original size:18 final size:17
Alignment explanation
Indices: 285828--285877 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
285818 TCAATTTCTA
*
285828 TTTTCCTTTTTTTTATT
1 TTTTCCTTATTTTTATT
**
285845 TTTTATTTTATTTTTATT
1 TTTT-CCTTATTTTTATT
285863 TTTTCCTTGATTTTT
1 TTTTCCTT-ATTTTT
285878 CGGAGTACAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.10, C:0.08, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTCCTTATTTTTATT
Found at i:287109 original size:27 final size:28
Alignment explanation
Indices: 287045--287117 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 28
287035 GAAAAAAAAG
*
287045 AAAAAAAAGAAAAAGAAAAAGAAATCGTGC
1 AAAAGAAAGAAAAA-AAAAAG-AATCGTGC
* * *
287075 AAAGGAAAGAAAAAAAAAAG-ATTGTGT
1 AAAAGAAAGAAAAAAAAAAGAATCGTGC
287102 AAAAGAAAAGAAAAAA
1 AAAAG-AAAGAAAAAA
287118 TATTACGTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 9 0.24
28 10 0.27
29 6 0.16
30 12 0.32
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.08
Consensus pattern (28 bp):
AAAAGAAAGAAAAAAAAAAGAATCGTGC
Found at i:288677 original size:20 final size:20
Alignment explanation
Indices: 288607--288684 Score: 93
Period size: 20 Copynumber: 3.7 Consensus size: 20
288597 GCATGGGTAG
288607 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
288631 TGCATCGATGAACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
288651 TACATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
288671 TGTATCGATGCACT
1 TGCATCGATGCACT
288685 TCAAGGGGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 34 0.69
22 1 0.02
23 2 0.04
24 12 0.24
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:289032 original size:2 final size:2
Alignment explanation
Indices: 289025--289049 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
289015 AATGTATGTG
289025 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
289050 GTGATATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:289056 original size:14 final size:14
Alignment explanation
Indices: 289027--289077 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
289017 TGTATGTGAT
289027 ATAT-ATATATAT-
1 ATATGATATATATG
289039 ATAT-ATATATAGTG
1 ATATGATATATA-TG
289053 ATATGGAT-TATATG
1 ATAT-GATATATATG
289067 ATATGATATAT
1 ATATGATATAT
289078 GTGTGTGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
12 11 0.32
13 4 0.12
14 13 0.38
15 4 0.12
16 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (14 bp):
ATATGATATATATG
Found at i:289078 original size:12 final size:12
Alignment explanation
Indices: 289023--289078 Score: 57
Period size: 10 Copynumber: 4.8 Consensus size: 12
289013 ACAATGTATG
289023 TGATATAT-ATA
1 TGATATATGATA
289034 T-ATATAT-ATA
1 TGATATATGATA
289044 T-ATATAGTGATA
1 TGATATA-TGATA
289056 TGGATTATATGATA
1 T-GA-TATATGATA
289070 TGATATATG
1 TGATATATG
289079 TGTGTGTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
10 15 0.38
11 2 0.05
12 10 0.25
13 2 0.05
14 7 0.17
15 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (12 bp):
TGATATATGATA
Found at i:290015 original size:12 final size:12
Alignment explanation
Indices: 289994--290050 Score: 66
Period size: 12 Copynumber: 4.9 Consensus size: 12
289984 GGAGCTAGGG
289994 CATT-AGTTTTA
1 CATTAAGTTTTA
*
290005 CATCAAGTTTTA
1 CATTAAGTTTTA
290017 CATTAAGTCTTT-
1 CATTAAGT-TTTA
290029 CATTAAGTTTT-
1 CATTAAGTTTTA
*
290040 CTTTAAGTTTT
1 CATTAAGTTTT
290051 TCTTTTAGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
11 16 0.39
12 22 0.54
13 3 0.07
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (12 bp):
CATTAAGTTTTA
Found at i:290045 original size:11 final size:11
Alignment explanation
Indices: 290009--290066 Score: 62
Period size: 12 Copynumber: 5.0 Consensus size: 11
289999 GTTTTACATC
*
290009 AAGTTTTACATT
1 AAGTTTT-CTTT
*
290021 AAGTCTTTCATT
1 AAGT-TTTCTTT
290033 AAGTTTTCTTT
1 AAGTTTTCTTT
290044 AAGTTTTTCTTT
1 AAG-TTTTCTTT
*
290056 TAGTTTTCTTT
1 AAGTTTTCTTT
290067 CAATTATGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
11 17 0.40
12 22 0.52
13 3 0.07
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (11 bp):
AAGTTTTCTTT
Found at i:290052 original size:23 final size:23
Alignment explanation
Indices: 289998--290066 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
289988 CTAGGGCATT
* * *
289998 AGTTTTACATCAAGTTTTACATTA
1 AGTTTTTCATTAAGTTTT-CTTTA
*
290022 AGTCTTTCATTAAGTTTTCTTTA
1 AGTTTTTCATTAAGTTTTCTTTA
* *
290045 AGTTTTTCTTTTAGTTTTCTTT
1 AGTTTTTCATTAAGTTTTCTTT
290067 CAATTATGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 23 0.61
24 15 0.39
ACGTcount: A:0.22, C:0.12, G:0.09, T:0.58
Consensus pattern (23 bp):
AGTTTTTCATTAAGTTTTCTTTA
Found at i:292254 original size:22 final size:22
Alignment explanation
Indices: 292229--292284 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
292219 CAATTGTGGA
*
292229 GTTCTGCAAGCAAGAGGGTCTT
1 GTTCTGCTAGCAAGAGGGTCTT
292251 GTTCTGCTAGCAAGAGGGTCTT
1 GTTCTGCTAGCAAGAGGGTCTT
292273 GTTCTGCTAGCA
1 GTTCTGCTAGCA
292285 GACGAGGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (22 bp):
GTTCTGCTAGCAAGAGGGTCTT
Found at i:299830 original size:2 final size:2
Alignment explanation
Indices: 299825--299856 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
299815 GTACGATAGT
299825 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
299857 TATGATTGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:300541 original size:17 final size:18
Alignment explanation
Indices: 300508--300541 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
300498 CCGCTACTAG
300508 TGAACCGATCAGAACCGC
1 TGAACCGATCAGAACCGC
*
300526 TGAACCGTTC-GAACCG
1 TGAACCGATCAGAACCG
300542 AACCGGCTAA
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:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (18 bp):
TGAACCGATCAGAACCGC
Found at i:308229 original size:35 final size:36
Alignment explanation
Indices: 308169--308239 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
308159 TATGTGCAGG
308169 GGGAACAGATTCCTCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCTCCCTGGGGGGTATCGATTCCCC
308205 GGGAACAGATTCC-CCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCTCCCTGGGGGGTATCGATTCCCC
308240 CTAAATGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 22 0.63
36 13 0.37
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.21
Consensus pattern (36 bp):
GGGAACAGATTCCTCCCTGGGGGGTATCGATTCCCC
Found at i:315086 original size:36 final size:37
Alignment explanation
Indices: 315024--315093 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 37
315014 TATGTGCAGG
* *
315024 GGGAACAGATTCTCCCCTGGGTGGGTATTGATTCTCC
1 GGGAACAGATTCTCCCCTGGGGGGGTATCGATTCTCC
315061 GGGAACAGATTC-CCCCTGGGGGGGTATCGATTC
1 GGGAACAGATTCTCCCCTGGGGGGGTATCGATTC
315094 CCCCTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 19 0.61
37 12 0.39
ACGTcount: A:0.17, C:0.24, G:0.33, T:0.26
Consensus pattern (37 bp):
GGGAACAGATTCTCCCCTGGGGGGGTATCGATTCTCC
Found at i:317217 original size:108 final size:108
Alignment explanation
Indices: 317093--317354 Score: 416
Period size: 108 Copynumber: 2.4 Consensus size: 108
317083 AATTGGTTTT
* * * *
317093 AAATGCAAATGATATCTCTCTAACAATTTATATCATTTTTTAAAATGCTTTGATTTTAAAAAATT
1 AAATACAAATGATATCTCTCTAACAATTGATATCAATTTTCAAAATGCTTTGATTTTAAAAAATT
*
317158 TAAGTTTTTGACCTAAATTTAAATGTTTATGCTTATAATTTAA
66 TAAGTTTTTGACCTAAATTTAAATGTTTATGCATATAATTTAA
* *
317201 AAATACAAATGATATCTCTCTAACAATCGATATCAATTTTCAAAATGCTTTGATTTTAAAAATTT
1 AAATACAAATGATATCTCTCTAACAATTGATATCAATTTTCAAAATGCTTTGATTTTAAAAAATT
*
317266 TAAGTTTTTGACCTAAATTTAATTGTTTATGCATATAATTTAA
66 TAAGTTTTTGACCTAAATTTAAATGTTTATGCATATAATTTAA
* *
317309 AAATACAAATTATATCTCTCTAGCAATTGATATCAAAATTTTCAAA
1 AAATACAAATGATATCTCTCTAACAATTGATATC--AATTTTCAAA
317355 TGCACAACAT
Statistics
Matches: 141, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
108 131 0.93
110 10 0.07
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (108 bp):
AAATACAAATGATATCTCTCTAACAATTGATATCAATTTTCAAAATGCTTTGATTTTAAAAAATT
TAAGTTTTTGACCTAAATTTAAATGTTTATGCATATAATTTAA
Found at i:328219 original size:3 final size:3
Alignment explanation
Indices: 328211--328329 Score: 202
Period size: 3 Copynumber: 39.7 Consensus size: 3
328201 TTAATATATT
* * * *
328211 TAA TAA TAA AAA TAA TAA TAA TAA TAT TAA TAA TAA TAT TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
328259 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
328307 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
328330 TGGATAAAAA
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 108 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:328948 original size:174 final size:174
Alignment explanation
Indices: 328737--329081 Score: 516
Period size: 174 Copynumber: 2.0 Consensus size: 174
328727 TGAATTTAAA
*
328737 CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *** *
328802 ATT-ATGAACTTTCTCTGGAAAAT-ATGATCCACCAAATGATGGA-TTCAGGTAAAAGGTTGAAC
66 ATTCATGAACTTTCTCTGG-AAATGATGATCCACCAAATGATGAATTTAAACAAAAAAGTTGAAC
328864 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATAT
130 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATAT
328909 CAAACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 CAAA-AAA-GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * ** * *
328974 TCATTCATGAATTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACAAAAAAGTTGAA
64 TCATTCATGAACTTTCTCTGGAAATGATGATCCACCAAATGATGAATTTAAACAAAAAAGTTGAA
*
329039 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
129 CAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
329082 GTTCTTCTCA
Statistics
Matches: 154, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
172 4 0.03
173 3 0.02
174 62 0.40
175 30 0.19
176 55 0.36
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.38
Consensus pattern (174 bp):
CAAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTCATGAACTTTCTCTGGAAATGATGATCCACCAAATGATGAATTTAAACAAAAAAGTTGAACA
AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATAT
Found at i:329050 original size:115 final size:113
Alignment explanation
Indices: 328909--329194 Score: 394
Period size: 115 Copynumber: 2.5 Consensus size: 113
328899 CAGATGATAT
*
328909 CAAACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 CAAA-AAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * ** * *
328974 TCATTCATGAATTTTCTTTGG-CCATGTTGATCCATCAAATGATGAATTTAAA
64 TCATT-ATGAACTTTCTCTGGAAAAT-ATGATCCACCAAATGATGAA-TTAAA
329026 CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
329091 ATTATGAACTTTCTCTGGAAAATATGATCCACCAAATGATGGATTCAG
66 ATTATGAACTTTCTCTGGAAAATATGATCCACCAAATGATGAATTAAA
** * *
329139 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
1 CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
329195 TATCAAACAA
Statistics
Matches: 154, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
113 55 0.36
114 30 0.19
115 62 0.40
116 3 0.02
117 4 0.03
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAATATGATCCACCAAATGATGAATTAAA
Found at i:329097 original size:289 final size:289
Alignment explanation
Indices: 328578--329483 Score: 1778
Period size: 289 Copynumber: 3.1 Consensus size: 289
328568 TCTTGATGAG
*
328578 TTCTTCTCATTATGAACTT-TCTCTTCTTTCTTCAGATGATATCAAACAAAGGTTGAACAAGCTC
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGATATCAAACAAAGGTTGAACAAGCTC
*
328642 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCATGAACTTTCTTTGGC
65 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCATGAATTTTCTTTGGC
328707 CATGTTGATCCATCAAATGATGAATTTAAACAAAAAAGTTGAACAAGTTCTTCTCATTATGAACT
130 CATGTTGATCCATCAAATGATGAATTTAAACAAAAAAGTTGAACAAGTTCTTCTCATTATGAACT
328772 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAATATGATCCACCAA
195 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAATATGATCCACCAA
328837 ATGATGGATTCAGGTAAAAGGTTGAACAAA
260 ATGATGGATTCAGGTAAAAGGTTGAACAAA
328867 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATATCAAACAAAGGTTGAACAAGCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATATCAAACAAAGGTTGAACAAGCTCT
328932 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCATGAATTTTCTTTGGCC
66 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCATGAATTTTCTTTGGCC
328997 ATGTTGATCCATCAAATGATGAATTTAAACAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
131 ATGTTGATCCATCAAATGATGAATTTAAACAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
329062 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAATATGATCCACCAAA
196 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAATATGATCCACCAAA
329127 TGATGGATTCAGGTAAAAGGTTGAACAAA
261 TGATGGATTCAGGTAAAAGGTTGAACAAA
329156 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATATCAAACAAAGGTTGAACAAGCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATATCAAACAAAGGTTGAACAAGCTCT
329221 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCATGAATTTTCTTTGGCC
66 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCATGAATTTTCTTTGGCC
329286 ATGTTGATCCATCAAATGATGAATTTAAACAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
131 ATGTTGATCCATCAAATGATGAATTTAAACAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
329351 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAATATGATCCACCAAA
196 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAATATGATCCACCAAA
329416 TGATGGATTCAGGTAAAAGGTTGAACAAA
261 TGATGGATTCAGGTAAAAGGTTGAACAAA
329445 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
329484 CGAGTTCTTC
Statistics
Matches: 614, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
289 613 1.00
290 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (289 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATATCAAACAAAGGTTGAACAAGCTCT
TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCATGAATTTTCTTTGGCC
ATGTTGATCCATCAAATGATGAATTTAAACAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAATATGATCCACCAAA
TGATGGATTCAGGTAAAAGGTTGAACAAA
Found at i:329253 original size:174 final size:174
Alignment explanation
Indices: 329026--329370 Score: 516
Period size: 174 Copynumber: 2.0 Consensus size: 174
329016 TGAATTTAAA
*
329026 CAAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 CAAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *** *
329091 ATT-ATGAACTTTCTCTGGAAAAT-ATGATCCACCAAATGATGGA-TTCAGGTAAAAGGTTGAAC
66 ATTCATGAACTTTCTCTGG-AAATGATGATCCACCAAATGATGAATTTAAACAAAAAAGTTGAAC
329153 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATAT
130 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATAT
329198 CAAACAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 CAAA-AAA-GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * ** * *
329263 TCATTCATGAATTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACAAAAAAGTTGAA
64 TCATTCATGAACTTTCTCTGGAAATGATGATCCACCAAATGATGAATTTAAACAAAAAAGTTGAA
*
329328 CAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
129 CAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
329371 GTTCTTCTCA
Statistics
Matches: 154, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
172 4 0.03
173 3 0.02
174 62 0.40
175 30 0.19
176 55 0.36
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.38
Consensus pattern (174 bp):
CAAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTCATGAACTTTCTCTGGAAATGATGATCCACCAAATGATGAATTTAAACAAAAAAGTTGAACA
AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATAT
Found at i:329536 original size:116 final size:112
Alignment explanation
Indices: 329203--329874 Score: 766
Period size: 113 Copynumber: 5.9 Consensus size: 112
329193 GATATCAAAC
*
329203 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * ** ***
329268 CATGAATTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACAA
66 -ATGAACTTTCTCTGGAAATGTTGATCCATC-AATGATGAA-TTAAGGTA
*
329318 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
329383 ATGAACTTTCTCTGGAAAAT-ATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGG-AAATGTTGATCCATC-AATGATGAATTAAGGTA
*
329431 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTC
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTC
*
329496 ATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAA-ATA
63 ATTATGAACTTTCTCTGGAAATGTTGATCCATCAA-TGATGAATT-AAGGTA
**
329547 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
**** * *
329612 ATGAACTCGAACTGGTAATGCTGAATCC-TCGAATGATGAATTTAAGCG-A
66 ATGAACTTTCTCTGGAAATGTTG-ATCCATC-AATGATGAA-TTAAG-GTA
** *
329661 AAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATGAGATCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
**** * * * * *
329725 ATGAACTCGAACTGGTAATGCTGATCCATCGAATGATGGATT-TGAGCA
66 ATGAACTTTCTCTGGAAATGTTGATCCATC-AATGATGAATTAAG-GTA
* *
329773 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** *
329838 ATGAACTCGAC-CTGG-AATGTTGATCCATTGAATGATG
66 ATGAACT-TTCTCTGGAAATGTTGATCCA-TCAATGATG
329875 GATTTAAACT
Statistics
Matches: 496, Mismatches: 44, Indels: 37
0.86 0.08 0.06
Matches are distributed among these distances:
111 2 0.00
112 28 0.06
113 257 0.52
114 42 0.08
115 71 0.14
116 95 0.19
117 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (112 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGTTGATCCATCAATGATGAATTAAGGTA
Found at i:329800 original size:226 final size:225
Alignment explanation
Indices: 329203--329881 Score: 873
Period size: 229 Copynumber: 3.0 Consensus size: 225
329193 GATATCAAAC
* *
329203 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGATCTTCTCATT
* * ** *
329268 CATGAATTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACAAAAAAGTTGAACAAGT
66 -ATGAACTTTCTCTGGAAATGTTGATCCATC-AATGATGAATTTAAAC-AAAAGGTTGAACAAGT
****
329333 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
128 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG
* * *
329398 AAAAT-ATGATCCACCAAATGATGGA-TTCAGGTA
193 --AATGATGATCCATCGAATGATGGATTTAAGGTA
*
329431 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTC
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-GA--TCTTCTC
* *
329496 ATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAATAAAAGGTTGAACAAG
63 ATTATGAACTTTCTCTGGAAATGTTGATCCATCAA-TGATGAATTTAAACAAAAGGTTGAACAAG
**
329561 TTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
127 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* *
329626 GTAATGCTGAATCC-TCGAATGATGAATTTAAGCG-A
192 G-AATGATG-ATCCATCGAATGATGGATTTAAG-GTA
**
329661 AAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTTTTCTTCAGATGAGATCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGATCTTCTCATT
**** * * * * * *
329725 ATGAACTCGAACTGGTAATGCTGATCCATCGAATGATGGATTTGAGCAAAAGGTTGAACAAATTC
66 ATGAACTTTCTCTGGAAATGTTGATCCATC-AATGATGAATTTAAACAAAAGGTTGAACAAGTTC
* *
329790 TTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGAA
130 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAA
* *
329855 TGTTGATCCATTGAATGATGGATTTAA
195 TGATGATCCATCGAATGATGGATTTAA
329882 ACTTTGCTAA
Statistics
Matches: 397, Mismatches: 44, Indels: 23
0.86 0.09 0.05
Matches are distributed among these distances:
224 4 0.01
225 21 0.05
226 119 0.30
227 2 0.01
228 56 0.14
229 134 0.34
230 50 0.13
231 11 0.03
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (225 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGATCTTCTCATT
ATGAACTTTCTCTGGAAATGTTGATCCATCAATGATGAATTTAAACAAAAGGTTGAACAAGTTCT
TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAT
GATGATCCATCGAATGATGGATTTAAGGTA
Found at i:330306 original size:22 final size:22
Alignment explanation
Indices: 330281--330357 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
330271 GATAAAGCTT
* *
330281 TCATCTTTGAAAAGAGAATATG
1 TCATCTTTGAAAAGAGAATCTA
* *
330303 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
330325 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
330347 TCATCTTTGAA
1 TCATCTTTGAA
330358 GAGTGTAGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:330799 original size:54 final size:54
Alignment explanation
Indices: 330717--330828 Score: 179
Period size: 54 Copynumber: 2.1 Consensus size: 54
330707 AGAATAGCAG
** *
330717 GTTCGTAAAACATTTGACGGCGCATTCATCCTTTCCTGTAGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTAGTTTCTGCTCAGAT
* *
330771 GTTCGTAAAACATTTGACAACACATTCATCTTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTAGTTTCTGCTCAGAT
330825 GTTC
1 GTTC
330829 TCAATCATTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTAGTTTCTGCTCAGAT
Found at i:333114 original size:83 final size:83
Alignment explanation
Indices: 332974--333238 Score: 460
Period size: 83 Copynumber: 3.2 Consensus size: 83
332964 CTTATTTCTA
* *
332974 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATTAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTG-CCAAACCAGATCAGATAACTCAA
333038 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* *
333057 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
333122 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
333140 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
333205 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
333223 CTATGAGCACATTCAT
1 CTATGAGCAAATTCAT
333239 TTGTTCCATT
Statistics
Matches: 174, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
82 2 0.01
83 172 0.99
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:338607 original size:14 final size:15
Alignment explanation
Indices: 338582--338624 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
338572 AAAGATGCCA
*
338582 AATGCAAATGTAAAT
1 AATGTAAATGTAAAT
*
338597 -ATGTGAATGT-AAT
1 AATGTAAATGTAAAT
338610 AATGTAAATGTAAAT
1 AATGTAAATGTAAAT
338625 TATTTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 3 0.13
14 17 0.74
15 3 0.13
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (15 bp):
AATGTAAATGTAAAT
Found at i:342350 original size:3 final size:3
Alignment explanation
Indices: 342342--342481 Score: 244
Period size: 3 Copynumber: 46.7 Consensus size: 3
342332 TTAATATATT
* * * *
342342 TAA TAA TAA AAA TAA TAA TAA TAA TAT TAA TAA TAA TAT TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
342390 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
342438 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
342482 TGGATAAAAA
Statistics
Matches: 129, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 129 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:348194 original size:39 final size:37
Alignment explanation
Indices: 348110--348213 Score: 99
Period size: 37 Copynumber: 2.8 Consensus size: 37
348100 TTGACAAACG
*
348110 GTTTTTGAAAATACGTATATAATATATAGTTTCTAAAAA
1 GTTTTT-AAAA-ACTTATATAATATATAGTTTCTAAAAA
** * *
348149 CATTTTAAAAACTTATATAATATATAGTGTTTTGAAAAT
1 GTTTTTAAAAACTTATATAATATATAGT-TTCT-AAAAA
348188 GTTTTTAAAAA-TT-TAT--TATATAGTTT
1 GTTTTTAAAAACTTATATAATATATAGTTT
348214 TTTAAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
34 2 0.04
35 8 0.14
37 20 0.36
38 9 0.16
39 17 0.30
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (37 bp):
GTTTTTAAAAACTTATATAATATATAGTTTCTAAAAA
Found at i:348257 original size:16 final size:16
Alignment explanation
Indices: 348236--348284 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
348226 TACTTTTTTA
348236 TATTTATTATTATTAT
1 TATTTATTATTATTAT
* *
348252 TATTTACTATTATTAA
1 TATTTATTATTATTAT
348268 TATTT-TTATTAATTAT
1 TATTTATTATT-ATTAT
348284 T
1 T
348285 TTTTGCAGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 4 0.14
16 24 0.86
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTATTATTATTAT
Found at i:353707 original size:94 final size:94
Alignment explanation
Indices: 353541--354422 Score: 1244
Period size: 94 Copynumber: 9.0 Consensus size: 94
353531 TTCAGAGTCT
* * *
353541 ATTTCAACTTCGCAACGAAGAAAATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
353606 ACCGCTGGTTGTCAATAAACAATTTCCCA
66 ACCGCTGGTTGTCAATAAACAATTTCCCA
* * *
353635 ATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
353700 ACTGCTGGTTGTCAATAAACAATTTCCCA
66 ACCGCTGGTTGTCAATAAACAATTTCCCA
* *
353729 ATTTCAATTTCACAACGAAGGATATTGAGA-TCCAGACAACGCAAGTTAAACTTCACGACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTG-GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
353793 GACCGCTGGTTGTCAATAAACAATTTCCCA
65 GACCGCTGGTTGTCAATAAACAATTTCCCA
*
353823 ATTTCAACTTCACAACGAAGGATATTGGGCTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
353888 ACCGCTGGTTGTCAATAAACAATTTCCCA
66 ACCGCTGGTTGTCAATAAACAATTTCCCA
* * *
353917 ATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
353982 ACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAGTCA
66 ACCGCTGGTTGTCAATAAACAATTT--C-----C-----CA
354023 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
354088 AACGCTGGTTGTCAACAAATAATTTCCCGATTTCAGAGCCA
66 ACCGCTGGTTGT---C-AATAA----ACAATTTC----CCA
* *
354129 ATTTCAACTTCACAATGAAGGATATTGGACTCCAGACGACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
354194 ACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAGCCA
66 ACCGCTGGTTGTCAATAAAC-A-------ATTTC----CCA
354235 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
354300 ACCGCTGGTTGTCAATAAACAATTTCCCA
66 ACCGCTGGTTGTCAATAAACAATTTCCCA
* *
354329 ATTTCAACTTCAGAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
354394 ACCGCTGGTTGTCAATAAACAATTTCCCA
66 ACCGCTGGTTGTCAATAAACAATTTCCCA
354423 GTTCCAGAGC
Statistics
Matches: 720, Mismatches: 38, Indels: 60
0.88 0.05 0.07
Matches are distributed among these distances:
93 1 0.00
94 442 0.61
95 2 0.00
96 1 0.00
98 6 0.01
101 1 0.00
102 5 0.01
103 1 0.00
105 1 0.00
106 246 0.34
109 1 0.00
110 5 0.01
111 2 0.00
112 1 0.00
114 5 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (94 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAATAAACAATTTCCCA
Found at i:354100 original size:106 final size:106
Alignment explanation
Indices: 353914--354465 Score: 869
Period size: 106 Copynumber: 5.3 Consensus size: 106
353904 AAACAATTTC
* * *
353914 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCGGACAACACAAGTTCAACTTCACAACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
353979 GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAG
*
354020 TCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
354085 GGGAACGCTGGTTGTCAACAAATAATTTCCCGATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAG
* *
354126 CCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACGACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
354191 GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAG
354232 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
354297 GGGACCGCTGGTTGTCAATAAAC-A-------ATTTC----
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAG
* *
354326 CCAATTTCAACTTCAGAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
354391 GGGACCGCTGGTTGTCAATAAACAATTTCCC-AGTTCCAGAG
66 GGGACCGCTGGTTGTCAATAAACAATTTCCCGA-TTTCAGAG
** *
354432 CCAATTTCAACTTCACGGCGGAGGATATTGGACT
1 CCAATTTCAACTTCACAACGAAGGATATTGGACT
354466 TGGAACAATA
Statistics
Matches: 412, Mismatches: 22, Indels: 24
0.90 0.05 0.05
Matches are distributed among these distances:
94 86 0.21
95 1 0.00
98 5 0.01
101 1 0.00
102 3 0.01
105 1 0.00
106 315 0.76
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTCAGAG
Found at i:354281 original size:212 final size:200
Alignment explanation
Indices: 353820--354465 Score: 1015
Period size: 200 Copynumber: 3.2 Consensus size: 200
353810 AAACAATTTC
*
353820 CCAATTTCAACTTCACAACGAAGGATATTGGGCTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
353885 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 GGGAACGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * *
353950 GGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCGATTT
131 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCGATTT
354015 CAGAG
196 CAGAG
*
354020 TCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
354085 GGGAACGCTGGTTGTCAACAAATAATTTCCCGATTTCAGAGCCAATTTCAACTTCACAATGAAGG
66 GGGAACGCTGGTTGT---C-AATAA----ACAATTTC----CCAATTTCAACTTCACAACGAAGG
*
354150 ATATTGGACTCCAGACGACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
119 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
354215 ATTTCCCGATTTCAGAG
184 ATTTCCCGATTTCAGAG
354232 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
354297 GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCAGAACGAAGGATATTGGACTCC
66 GGGAACGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
354362 AGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC-AGTT
131 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCGA-TT
*
354426 CCAGAG
195 TCAGAG
** *
354432 CCAATTTCAACTTCACGGCGGAGGATATTGGACT
1 CCAATTTCAACTTCACAACGAAGGATATTGGACT
354466 TGGAACAATA
Statistics
Matches: 411, Mismatches: 22, Indels: 26
0.90 0.05 0.06
Matches are distributed among these distances:
199 1 0.00
200 207 0.50
203 1 0.00
204 11 0.03
208 11 0.03
209 1 0.00
212 179 0.44
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (200 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
GGGAACGCTGGTTGTCAATAAACAATTTCCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCGATTT
CAGAG
Found at i:354298 original size:43 final size:43
Alignment explanation
Indices: 354237--354392 Score: 125
Period size: 43 Copynumber: 3.4 Consensus size: 43
354227 CAGAGCCAAT
*
354237 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAG
*** ** * * * *
354280 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACGACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
*
354331 TTCAACTTCA-GAACGAAGGATATTGGACTCCAGACAACGTAAG
1 TTCAACTTCACG-ACGAAGGATATTGGACTCCAGACAACGCAAG
354374 TTCAACTTCACGACGAAGG
1 TTCAACTTCACGACGAAGG
354393 GACCGCTGGT
Statistics
Matches: 83, Mismatches: 20, Indels: 20
0.67 0.16 0.16
Matches are distributed among these distances:
43 36 0.43
44 4 0.05
45 3 0.04
46 7 0.08
48 7 0.08
49 3 0.04
50 4 0.05
51 19 0.23
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:355065 original size:165 final size:165
Alignment explanation
Indices: 354666--355283 Score: 615
Period size: 165 Copynumber: 3.7 Consensus size: 165
354656 TCTACCAACA
* * * * *
354666 AAAGACCTTTGAGTTCGACTACGCTCAGC-TCAATGACACATCATTTGCAGCATAGCTTAAGTCG
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTTCAA-GGCATATCATTTGCAGTATAACTTAAGTCG
* * * * ** * * * *
354730 AGAAGGGCTATCTGCTAA--ATA-CCCCCT-AGTTCGATTACACTCAGCTTCGAGGGCATATCAT
65 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCGA-GGCACATCAT
* * ** * * * *
354791 TTACAGTATAACGCAAGGCTAGAAGGGTTATTTGCAACC
129 TTGCAGTACAACTTAAGTCGAGAAGGGCTATCTGC--CC
* * *
354830 AAAGACCTTCGAATTCGACTACGCTCAGCTTCAAGGCATA-CATTTGCAGTACAACTTAAGTTTG
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCATATCATTTGCAGTATAACTTAAG-TCG
* *
354894 -GAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCGAGGCACATCATT
65 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCGAGGCACATCATT
* * *
354958 TGTAGTATAGCTTAAGTCGAGAAGGGCTATCTG-CC
130 TGCAGTACAACTTAAGTCGAGAAGGGCTATCTGCCC
** * * * *
354993 AAAGACCTTCGAGTTTAATTACACTCAGCTTCGAGGGCACATCATTTGCAGTATAACTTAAGTCG
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTTC-AAGGCATATCATTTGCAGTATAACTTAAGTCG
* * *
355058 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
65 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCGAGGCACATCATT
* * * *
355123 TGCAGTACAACTTAAGTCTAGAGGGGTTGTCTGCCAAC
130 TGCAGTACAACTTAAGTCGAGAAGGGCTATCTGCC--C
* * *
355161 AAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCG
1 -AAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCATATCATTTGCAGTATAACTTAAGTCG
* * * * *
355226 AGAAGGGTTATCTGCCAACCGAAGA-CTTTCGAGCTCGATTACACTCAGCTCAGAGGCA
65 AGAAGGGTTATCTGCCAACCAAAGACCTTT-GAGTTCGACTACGCTCAGCTCCGAGGCA
355284 AACCAAGTTT
Statistics
Matches: 375, Mismatches: 65, Indels: 24
0.81 0.14 0.05
Matches are distributed among these distances:
163 60 0.16
164 41 0.11
165 110 0.29
166 38 0.10
167 23 0.06
168 77 0.21
169 26 0.07
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (165 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCATATCATTTGCAGTATAACTTAAGTCGA
GAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCGAGGCACATCATTT
GCAGTACAACTTAAGTCGAGAAGGGCTATCTGCCC
Found at i:355208 original size:249 final size:247
Alignment explanation
Indices: 354646--355243 Score: 903
Period size: 247 Copynumber: 2.4 Consensus size: 247
354636 TCCAACTCAA
* *
354646 AGAAGGAG-TGTCTACCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAATGACACATCA
1 AGAAGG-GTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCA
* * * *
354709 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCTAAATACCCCCTAGTTCGATTACACTCAG
64 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCAATTACACTCAG
* * *
354774 CTTCGAGGGCATATCATTTACAGTATAACGCAAGGCTAGAAGGGTTATTTGCAACCAAAGACCTT
129 CTTCGAGGGCACATCATTTACAGTATAACGCAAGGCGAGAAGGGTTATCTGCAACCAAAGACCTT
* *
354839 CGAATTCGACTACGCTCAGCTTCAAGGCATACATTTGCAGTACAACTTAAGTTT
194 CGAATTCGACTACGCTCAGCTCCAAGGCATACATTTGCAGTACAACTTAAGTCT
* *
354893 GGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCGAGGCACATCATT
1 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * ** *
354958 TGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTTAATTACACTCAGCT
66 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCAATTACACTCAGCT
* ** *
355023 TCGAGGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTC
131 TCGAGGGCACATCATTTACAGTATAACGCAAGGCGAGAAGGGTTATCTG-CAACCAAAGACCTTC
*
355088 GAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTACAACTTAAGTCT
195 GAATTCGACTACGCTCAGCTCCAAGGCATA-CATTTGCAGTACAACTTAAGTCT
* *
355142 AGAGGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
355207 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
66 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
355244 CCGAAGACTT
Statistics
Matches: 316, Mismatches: 31, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
246 1 0.00
247 154 0.49
248 45 0.14
249 116 0.37
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (247 bp):
AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCAATTACACTCAGCT
TCGAGGGCACATCATTTACAGTATAACGCAAGGCGAGAAGGGTTATCTGCAACCAAAGACCTTCG
AATTCGACTACGCTCAGCTCCAAGGCATACATTTGCAGTACAACTTAAGTCT
Found at i:355276 original size:84 final size:84
Alignment explanation
Indices: 354660--355276 Score: 637
Period size: 84 Copynumber: 7.4 Consensus size: 84
354650 GGAGTGTCTA
* * * * * *
354660 CCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAATGACACATCATTTGCAGCATAGCTT
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCATATCATTTGCAGTATAACTT
*
354724 AAGTCGAGAAGGGCTATCTG
65 AAGTCGAGAAGGGTTATCTG
* * ** * * * * * * **
354744 ----CTAAATACCCCCTAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGTATAACGC
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGTATAACTT
* * *
354805 AAGGCTAGAAGGGTTATTTG
65 AAGTCGAGAAGGGTTATCTG
* * *
354825 -CAACCAAAGACCTTCGAATTCGACTACGCTCAGCTTCAAGGCATA-CATTTGCAGTACAACTTA
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTA
* *
354888 AGTTTG-GAAGGGTTGTCTG
66 AG-TCGAGAAGGGTTATCTG
* * * * * *
354907 CCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCGAGGCACATCATTTGTAGTATAGCTTA
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTA
*
354972 AGTCGAGAAGGGCTATCTG
66 AGTCGAGAAGGGTTATCTG
** * * * * *
354991 ----CCAAAGACCTTCGAGTTTAATTACACTCAGCTTCGAGGGCACATCATTTGCAGTATAACTT
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGTATAACTT
355052 AAGTCGAGAAGGGTTATCTG
65 AAGTCGAGAAGGGTTATCTG
*
355072 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTACAACTTA
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTA
* * *
355137 AGTCTAGAGGGGTTGTCTG
66 AGTCGAGAAGGGTTATCTG
* * *
355156 CCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTA
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTA
355221 AGTCGAGAAGGGTTATCTG
66 AGTCGAGAAGGGTTATCTG
* * * * *
355240 CCAACCGAAGACTTTCGAGCTCGATTACACTCAGCTC
1 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
355277 AGAGGCAAAC
Statistics
Matches: 429, Mismatches: 90, Indels: 28
0.78 0.16 0.05
Matches are distributed among these distances:
80 48 0.11
81 77 0.18
82 28 0.07
83 49 0.11
84 200 0.47
85 27 0.06
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (84 bp):
CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTA
AGTCGAGAAGGGTTATCTG
Found at i:355998 original size:39 final size:37
Alignment explanation
Indices: 355929--356017 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 37
355919 TGAAAATATG
355929 TATATAATATATAGTTTCTAAAAACATTTTAAAAACT
1 TATATAATATATAGTTTCTAAAAACATTTTAAAAACT
* * *
355966 TATATAATATATAGTGTTTTGAAAACGTTTTTAAAAA-T
1 TATATAATATATAGT-TTCTAAAAAC-ATTTTAAAAACT
356004 T-TAT--TATATAGTTT
1 TATATAATATATAGTTT
356018 TTTAAAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
34 2 0.04
35 8 0.17
37 18 0.38
38 10 0.21
39 9 0.19
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (37 bp):
TATATAATATATAGTTTCTAAAAACATTTTAAAAACT
Found at i:356050 original size:3 final size:3
Alignment explanation
Indices: 356042--356087 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
356032 CTTTTTATAT
* *
356042 TTA TTA TTA TTA TTA TTTA TTA TTA TTA ATA TTT TTA TTAA TTA TT
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT-A TTA TT
356088 TTTTGCAGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:356060 original size:16 final size:16
Alignment explanation
Indices: 356039--356087 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
356029 ATACTTTTTA
356039 TATTTATTATTATTAT
1 TATTTATTATTATTAT
*
356055 TATTTATTATTATTAA
1 TATTTATTATTATTAT
356071 TATTT-TTATTAATTAT
1 TATTTATTATT-ATTAT
356087 T
1 T
356088 TTTTGCAGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 5 0.17
16 25 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTATTATTATTAT
Found at i:356085 original size:22 final size:22
Alignment explanation
Indices: 356042--356087 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
356032 CTTTTTATAT
* *
356042 TTATTATTATTATTATTTATTA
1 TTATTAATATTATTATTAATTA
*
356064 TTATTAATATTTTTATTAATTA
1 TTATTAATATTATTATTAATTA
356086 TT
1 TT
356088 TTTTGCAGGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATTAATATTATTATTAATTA
Found at i:362381 original size:30 final size:30
Alignment explanation
Indices: 362345--362403 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
362335 CAGCAGATGT
*
362345 GCATGGAAG-CGTGGATCTCTCGGCATCTTG
1 GCATGGAAGTC-TGGATATCTCGGCATCTTG
*
362375 GCATGGAAGTCTGGATATCTCGGCGTCTT
1 GCATGGAAGTCTGGATATCTCGGCATCTT
362404 TAACGCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.17, C:0.22, G:0.32, T:0.29
Consensus pattern (30 bp):
GCATGGAAGTCTGGATATCTCGGCATCTTG
Found at i:362500 original size:34 final size:34
Alignment explanation
Indices: 362457--362539 Score: 148
Period size: 34 Copynumber: 2.4 Consensus size: 34
362447 TATGATTGAT
362457 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
362491 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
* *
362525 ATCTCGGTGTCTTCA
1 CTCTCGGCGTCTTCA
362540 TAGGACTGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (34 bp):
CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
Found at i:362634 original size:23 final size:23
Alignment explanation
Indices: 362608--362651 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
362598 TGAGCAGGGG
362608 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
*
362631 CTGCACGTCTGTATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
362652 GCATGCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.23, G:0.41, T:0.27
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:362658 original size:23 final size:22
Alignment explanation
Indices: 362604--362658 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
362594 GGGTTGAGCA
362604 GGGGCTGCACGTCTGCATGTGG
1 GGGGCTGCACGTCTGCATGTGG
* *
362626 GGGTCCTGCACGTCTGTATGTGG
1 GGG-GCTGCACGTCTGCATGTGG
362649 GGGGCATGCA
1 GGGGC-TGCA
362659 ATTGTTGGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.11, C:0.22, G:0.44, T:0.24
Consensus pattern (22 bp):
GGGGCTGCACGTCTGCATGTGG
Found at i:363369 original size:173 final size:173
Alignment explanation
Indices: 363080--363439 Score: 605
Period size: 173 Copynumber: 2.1 Consensus size: 173
363070 TTGTAAAGTT
* *
363080 TTAGGGACCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTGCTAT
1 TTAGGGATCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGCTAT
*
363145 ACTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTA-T
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
* *
363209 GGATTAAATTGCTAAGTTTGAAAATGTTGAGAACCAAATAGTAA
131 -GATTAAATTGCAAAGTTTGAAAATATTGAGAACCAAATAGTAA
* * *
363253 TTAGGGATCGTTTTGTAAAATTTGAGGAATTTAAGGAATTAGAGTAAATTATAAAAAGTTGGTAT
1 TTAGGGATCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGCTAT
*
363318 ACTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
66 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
*
363383 GATTAAATTGCAAAGTTTGAAAATATTGAGAAGCAAATAGTAA
131 GATTAAATTGCAAAGTTTGAAAATATTGAGAACCAAATAGTAA
*
363426 TTAGGGATCATTTT
1 TTAGGGATCGTTTT
363440 ATATTTGATG
Statistics
Matches: 175, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
173 174 0.99
174 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.38
Consensus pattern (173 bp):
TTAGGGATCGTTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATAAAAAGTTGCTAT
ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
GATTAAATTGCAAAGTTTGAAAATATTGAGAACCAAATAGTAA
Found at i:365177 original size:6 final size:6
Alignment explanation
Indices: 365170--365206 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
365160 CAAGAAGGAC
* *
365170 TGGGAC TGGGAG TGGGAG TGGGAG TGGGAG TAGGAG T
1 TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG TGGGAG T
365207 TCTTCTCACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.19, C:0.03, G:0.59, T:0.19
Consensus pattern (6 bp):
TGGGAG
Found at i:365197 original size:18 final size:18
Alignment explanation
Indices: 365165--365206 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
365155 GAAACCAAGA
*
365165 AGGACTGGGACTGGGAGT
1 AGGAGTGGGACTGGGAGT
* *
365183 GGGAGTGGGAGTGGGAGT
1 AGGAGTGGGACTGGGAGT
365201 AGGAGT
1 AGGAGT
365207 TCTTCTCACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.57, T:0.17
Consensus pattern (18 bp):
AGGAGTGGGACTGGGAGT
Found at i:365709 original size:42 final size:42
Alignment explanation
Indices: 365660--365853 Score: 205
Period size: 42 Copynumber: 4.4 Consensus size: 42
365650 ATATATTTAC
* *
365660 TATTATTATATCAGT-AAATATAAATCATTAAAGTCAAGTAAT
1 TATTATTAAATCATTAAAAT-TAAATCATTAAAGTCAAGTAAT
* *
365702 TATTATTAAATCATTAAAATTAAATCATTAAAATTAAGTAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTAAT
* *
365744 TATTATTAAATTATTAAAATTAAATCATTAAAGT-AATTATTAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTA--AT
*
365787 TAAATCATTAAATCATTAAATAATTAAATCATTAAA-TCATTAAAGTAAT
1 T--ATTATTAAATCATT-AA-AATTAAATCATTAAAGTC----AAGTAAT
365836 TATTATTAAATCATTAAA
1 TATTATTAAATCATTAAA
365854 TCATTAAAGT
Statistics
Matches: 129, Mismatches: 11, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
41 4 0.03
42 65 0.50
43 7 0.05
45 13 0.10
46 5 0.04
47 28 0.22
49 3 0.02
51 4 0.03
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.41
Consensus pattern (42 bp):
TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTAAT
Found at i:365717 original size:14 final size:14
Alignment explanation
Indices: 365700--366140 Score: 139
Period size: 14 Copynumber: 30.9 Consensus size: 14
365690 AAGTCAAGTA
*
365700 ATTATTATTAAATC
1 ATTATAATTAAATC
*
365714 ATTAAAATTAAATC
1 ATTATAATTAAATC
* * *
365728 ATTAAAATTAAGTA
1 ATTATAATTAAATC
* *
365742 ATTATTATTAAATT
1 ATTATAATTAAATC
*
365756 ATTAAAATTAAATC
1 ATTATAATTAAATC
* *
365770 ATTA-AAGTAATTATT
1 ATTATAATTAA--ATC
*
365785 ATTAAATCATTAAATC
1 ATT--ATAATTAAATC
365801 ATTAAATAATTAAATC
1 ATT--ATAATTAAATC
* *
365817 ATTAAATCATTAAAGTA
1 ATT--ATAATTAAA-TC
*
365834 ATTATTATTAAATC
1 ATTATAATTAAATC
* *
365848 ATTAAATCATTAAAGTA
1 ATT--ATAATTAAA-TC
* *
365865 ATTATTATTAAAGC
1 ATTATAATTAAATC
365879 ATTA-AAGTTAAATC
1 ATTATAA-TTAAATC
* *
365893 ATTA-AAGTAATTATT
1 ATTATAATTAA--ATC
* *
365908 ATTAAATCATTAAAGTA
1 ATT--ATAATTAAA-TC
* **
365925 ATTATTATTAAAGA
1 ATTATAATTAAATC
365939 ATTA-AAGTTAAATC
1 ATTATAA-TTAAATC
*
365953 ATTAAATCATTAAA--
1 ATT--ATAATTAAATC
* *
365967 ATTAAATCATTAAAGTA
1 ATT--ATAATTAAA-TC
*
365984 ATTATTATTAAATC
1 ATTATAATTAAATC
*
365998 ATTAAAATTAAATC
1 ATTATAATTAAATC
*
366012 ATTA-AAGT--A--
1 ATTATAATTAAATC
*
366021 ATTATTATTAAATC
1 ATTATAATTAAATC
366035 ATTA-AAGTTAAATC
1 ATTATAA-TTAAATC
*
366049 ATTA-AAGT--A--
1 ATTATAATTAAATC
*
366058 ATTATTATTAAATC
1 ATTATAATTAAATC
*
366072 ATTA-AAGTTAAATA
1 ATTATAA-TTAAATC
*
366086 ATTATTATTAAATC
1 ATTATAATTAAATC
*
366100 ATTA-AAGTTAAATA
1 ATTATAA-TTAAATC
*
366114 ATTA-AATTTAAATA
1 ATTATAA-TTAAATC
*
366128 ATTATTATTAAAT
1 ATTATAATTAAAT
366141 ATGTACTCGA
Statistics
Matches: 331, Mismatches: 58, Indels: 76
0.71 0.12 0.16
Matches are distributed among these distances:
9 8 0.02
10 4 0.01
11 2 0.01
12 2 0.01
13 17 0.05
14 183 0.55
15 44 0.13
16 45 0.14
17 18 0.05
18 8 0.02
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.41
Consensus pattern (14 bp):
ATTATAATTAAATC
Found at i:365765 original size:9 final size:8
Alignment explanation
Indices: 365703--366140 Score: 111
Period size: 8 Copynumber: 57.2 Consensus size: 8
365693 TCAAGTAATT
365703 ATTATTAA
1 ATTATTAA
*
365711 ATCATTAA
1 ATTATTAA
365719 A--ATTAA
1 ATTATTAA
*
365725 ATCATTAAA
1 ATTATT-AA
*
365734 ATTAAGTAA
1 ATT-ATTAA
365743 TTATTATTAA
1 --ATTATTAA
365753 ATTATTAA
1 ATTATTAA
365761 A--ATTAA
1 ATTATTAA
*
365767 ATCATTAA
1 ATTATTAA
*
365775 AGTAATT--
1 A-TTATTAA
365782 ATTATTAA
1 ATTATTAA
*
365790 ATCATTAA
1 ATTATTAA
*
365798 ATCATTAA
1 ATTATTAA
*
365806 ATAATTAA
1 ATTATTAA
*
365814 ATCATTAA
1 ATTATTAA
*
365822 ATCATTAA
1 ATTATTAA
*
365830 AGTAATT--
1 A-TTATTAA
365837 ATTATTAA
1 ATTATTAA
*
365845 ATCATTAA
1 ATTATTAA
*
365853 ATCATTAA
1 ATTATTAA
*
365861 AGTAATT--
1 A-TTATTAA
365868 ATTATTAA
1 ATTATTAA
**
365876 AGCATTAA
1 ATTATTAA
*
365884 A--GTTAA
1 ATTATTAA
*
365890 ATCATTAA
1 ATTATTAA
*
365898 AGTAATT--
1 A-TTATTAA
365905 ATTATTAA
1 ATTATTAA
*
365913 ATCATTAA
1 ATTATTAA
*
365921 AGTAATT--
1 A-TTATTAA
365928 ATTATTAA
1 ATTATTAA
**
365936 AGAATTAA
1 ATTATTAA
*
365944 A--GTTAA
1 ATTATTAA
*
365950 ATCATTAA
1 ATTATTAA
*
365958 ATCATTAA
1 ATTATTAA
365966 A--ATTAA
1 ATTATTAA
*
365972 ATCATTAA
1 ATTATTAA
*
365980 AGTAATT--
1 A-TTATTAA
365987 ATTATTAA
1 ATTATTAA
*
365995 ATCATTAA
1 ATTATTAA
366003 A--ATTAA
1 ATTATTAA
*
366009 ATCATTAA
1 ATTATTAA
*
366017 AGTAATT--
1 A-TTATTAA
366024 ATTATTAA
1 ATTATTAA
*
366032 ATCATTAA
1 ATTATTAA
*
366040 A--GTTAA
1 ATTATTAA
*
366046 ATCATTAA
1 ATTATTAA
*
366054 AGTAATT--
1 A-TTATTAA
366061 ATTATTAA
1 ATTATTAA
*
366069 ATCATTAA
1 ATTATTAA
*
366077 AGTTAAATAA
1 A-TT-ATTAA
366087 TTATTATTAA
1 --ATTATTAA
*
366097 ATCATTAA
1 ATTATTAA
*
366105 A--GTTAA
1 ATTATTAA
*
366111 ATAATTAA
1 ATTATTAA
366119 A-T-TTAA
1 ATTATTAA
*
366125 ATAATT--
1 ATTATTAA
366131 ATTATTAA
1 ATTATTAA
366139 AT
1 AT
366141 ATGTACTCGA
Statistics
Matches: 331, Mismatches: 47, Indels: 104
0.69 0.10 0.22
Matches are distributed among these distances:
6 86 0.26
7 8 0.02
8 178 0.54
9 39 0.12
10 14 0.04
11 5 0.02
12 1 0.00
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.41
Consensus pattern (8 bp):
ATTATTAA
Found at i:365787 original size:37 final size:37
Alignment explanation
Indices: 365737--366089 Score: 384
Period size: 37 Copynumber: 9.0 Consensus size: 37
365727 CATTAAAATT
*
365737 AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
*
365774 AAGTAATTATTATTAAATCATTAAATCATTAAATAATTAA
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATT-A
* * * *
365814 ATCATTAAATCATTAAAGTAATTATTATTAAATCATTAAATCATTA
1 A--AGT-AATTATT--ATTAA--ATCATTAAA--ATTAAATCATTA
* *
365860 AAGTAATTATTATTAAAGCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* *
365897 AAGTAATTATTATTAAATCATT-AAAGTAATTATTATTA
1 AAGTAATTATTATTAAATCATTAAAATTAA--ATCATTA
*
365935 AAGAATTAAAGTTAAATCATTAAATCATTAAAATTAAATCATTA
1 AAG---T-AA-TT--ATTATTAAATCATTAAAATTAAATCATTA
365979 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
*
366016 AAGTAATTATTATTAAATCATTAAAGTTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* *
366053 AAGTAATTATTATTAAATCATTAAAGTTAAATAATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
366090 TTATTAAATC
Statistics
Matches: 273, Mismatches: 23, Indels: 40
0.81 0.07 0.12
Matches are distributed among these distances:
36 5 0.02
37 156 0.57
38 9 0.03
39 19 0.07
40 4 0.01
41 6 0.02
42 4 0.01
43 14 0.05
44 11 0.04
45 17 0.06
46 8 0.03
47 20 0.07
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.40
Consensus pattern (37 bp):
AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
Found at i:365788 original size:23 final size:23
Alignment explanation
Indices: 365762--366140 Score: 159
Period size: 23 Copynumber: 16.3 Consensus size: 23
365752 AATTATTAAA
365762 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
* *
365785 ATTAAATCATTAAA-TCATTAAATA
1 ATTAAATCATTAAAGTAATT--ATT
* *
365809 ATTAAATCATTAAA-TCATTA-A
1 ATTAAATCATTAAAGTAATTATT
* * * *
365830 AGT-AATTATT--ATTAA--ATC
1 ATTAAATCATTAAAGTAATTATT
365848 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
* *
365871 ATTAAAGCATTAAAGTTAAATCATT
1 ATTAAATCATTAAAG-T-AATTATT
* * * *
365896 AAAGTAATTATTATTAAA-TCATTA-A
1 --ATTAA--ATCATTAAAGTAATTATT
* * *
365921 AGTAATTATTATTAAAG-AATTA-A
1 ATTAA--ATCATTAAAGTAATTATT
* **
365944 AGTTAAATCATTAAA-TCATTAAA
1 A-TTAAATCATTAAAGTAATTATT
365967 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
* *
365990 ATTAAATCATTAAAATTAAATCATT
1 ATTAAATCATT-AAAGT-AATTATT
* * * *
366015 AAAGTAATTATTATTAAA-TCATTA-A
1 --ATTAA--ATCATTAAAGTAATTATT
366040 AGTTAAATCATTAAAGTAATTATT
1 A-TTAAATCATTAAAGTAATTATT
366064 ATTAAATCATTAAAGTTAAATAATTATT
1 ATTAAATCATTAAAG-----TAATTATT
*
366092 ATTAAATCATTAAAGTTAA--ATA
1 ATTAAATCATTAAAG-TAATTATT
366114 ATTAAAT--TTAAA-TAATTATT
1 ATTAAATCATTAAAGTAATTATT
366134 ATTAAAT
1 ATTAAAT
366141 ATGTACTCGA
Statistics
Matches: 281, Mismatches: 39, Indels: 75
0.71 0.10 0.19
Matches are distributed among these distances:
17 1 0.00
18 6 0.02
19 8 0.03
20 20 0.07
21 7 0.02
22 47 0.17
23 90 0.32
24 36 0.13
25 12 0.04
26 6 0.02
27 10 0.04
28 26 0.09
29 12 0.04
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (23 bp):
ATTAAATCATTAAAGTAATTATT
Found at i:365845 original size:15 final size:15
Alignment explanation
Indices: 365825--365877 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
365815 TCATTAAATC
365825 ATTAAAGTAATTATT
1 ATTAAAGTAATTATT
* *
365840 ATTAAA-TCATTAAATC
1 ATTAAAGTAATT--ATT
365856 ATTAAAGTAATTATT
1 ATTAAAGTAATTATT
365871 ATTAAAG
1 ATTAAAG
365878 CATTAAAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 4 0.13
15 15 0.48
16 8 0.26
17 4 0.13
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (15 bp):
ATTAAAGTAATTATT
Found at i:365994 original size:74 final size:72
Alignment explanation
Indices: 365748--366131 Score: 178
Period size: 74 Copynumber: 5.1 Consensus size: 72
365738 AGTAATTATT
*
365748 ATTAAATTATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAATCATTAAATAATTA
1 ATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATT-AA--ATTAAATAATTA
*
365813 AATCATTAAATC
63 AA--GTTAAATC
* ** *
365825 ATTAAAGTAATTATTATTAAATCATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAGTTAA
1 ATTAAA-TCATTAAAATT--------AAATCATTAAAGTAATTATTATTAAATCATTAAA-TTAA
* *
365890 ATCATTAAAG-TAATTATT
56 ATAATTAAAGTTAA--ATC
* * * *
365908 ATTAAATCATT-AAAGTAATTATTATTAAAG-AATTA-AAGTTAAATC-----ATTAAATCATTA
1 ATTAAATCATTAAAATTAA--ATCATTAAAGTAATTATTA-TTAAATCATTAAATTAAATAATTA
*
365965 AAATTAAATC
63 AAGTTAAATC
* ** * * * * *
365975 ATTAAAGTAATTATTATTAAATCATTAAAATTAA--ATCATTAAAGTAATTATTATTAAATCATT
1 ATTAAA-TCATTAAAATTAAATCATT-AAAGTAATTATTATTAAA-TCATTA-AATTAAATAATT
366038 AAAGTTAAATC
62 AAAGTTAAATC
* **
366049 ATTAAAGTAATTATTATTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAAGTTAAATA
1 ATTAAA-TCATTAAAATTAAATCATTAAAG-----TAATTATTATTAAATCATTAAA-TTAAATA
* *
366114 ATTAAATTTAAATA
59 ATTAAAGTTAAATC
366128 ATTA
1 ATTA
366132 TTATTAAATA
Statistics
Matches: 239, Mismatches: 32, Indels: 70
0.70 0.09 0.21
Matches are distributed among these distances:
67 19 0.08
68 22 0.09
69 10 0.04
73 6 0.03
74 58 0.24
75 9 0.04
77 6 0.03
78 12 0.05
79 27 0.11
80 8 0.03
81 5 0.02
82 4 0.02
83 9 0.04
84 12 0.05
85 2 0.01
86 30 0.13
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (72 bp):
ATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAAATCATTAAATTAAATAATTAAAG
TTAAATC
Found at i:366009 original size:119 final size:119
Alignment explanation
Indices: 365848--366077 Score: 376
Period size: 119 Copynumber: 1.9 Consensus size: 119
365838 TTATTAAATC
*
365848 ATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAGTTAAATCATTAAAGTAATTATTATTAA
1 ATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAATTAAATCATTAAAGTAATTATTATTAA
*
365913 ATCATTAAAG-TAATTATTATTAAAG-AATTA-AAGTTAAATCATTAAATCATTAAA
66 ATCATTAAAGTTAA--ATCATTAAAGTAATTATAA-TTAAATCATTAAATCATTAAA
*
365967 ATTAAATCATTAAAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAGTAATTATTATTAA
1 ATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAATTAAATCATTAAAGTAATTATTATTAA
*
366032 ATCATTAAAGTTAAATCATTAAAGTAATTATTATTAAATCATTAAA
66 ATCATTAAAGTTAAATCATTAAAGTAATTATAATTAAATCATTAAA
366078 GTTAAATAAT
Statistics
Matches: 104, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
118 9 0.09
119 91 0.88
120 4 0.04
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (119 bp):
ATTAAATCATTAAAGTAATTATTATTAAAGCATTAAAATTAAATCATTAAAGTAATTATTATTAA
ATCATTAAAGTTAAATCATTAAAGTAATTATAATTAAATCATTAAATCATTAAA
Found at i:366089 original size:119 final size:117
Alignment explanation
Indices: 365793--366089 Score: 367
Period size: 119 Copynumber: 2.5 Consensus size: 117
365783 TTATTAAATC
** * *
365793 ATTAAATCATTAAA-TAATTAAATCATTAAATCATTAAAG-T-AATTATT--ATTAAATCATTAA
1 ATTAAATCATTAAAGTAA-T--ATCATTAAAGAATTAAAGTTAAATCATTAAATTAAATAATTAA
*
365853 ATCATTAAAGTAATTATTATTAAAGCATTAAAGTTAAATCATTAAAGTAATTATT
63 ATCATTAAAGTAATTATTATTAAAGCATTAAAATTAAATCATTAAAGTAATTATT
* *
365908 ATTAAATCATTAAAGTAATTATTATTAAAGAATTAAAGTTAAATCATTAAATCATTAA-AATTAA
1 ATTAAATCATTAAAGTAA-TATCATTAAAGAATTAAAGTTAAATCATTAAAT--TAAATAATTAA
*
365972 ATCATTAAAGTAATTATTATTAAATCATTAAAATTAAATCATTAAAGTAATTATT
63 ATCATTAAAGTAATTATTATTAAAGCATTAAAATTAAATCATTAAAGTAATTATT
*
366027 ATTAAATCATTAAAGTTAA-ATCATTAAAGTAATTATTA-TTAAATCATTAAAGTTAAATAATTA
1 ATTAAATCATTAAAG-TAATATCATTAAAG-AATTA-AAGTTAAATCATTAAA-TTAAATAATTA
366090 TTATTAAATC
Statistics
Matches: 159, Mismatches: 11, Indels: 20
0.84 0.06 0.11
Matches are distributed among these distances:
114 15 0.09
115 15 0.09
116 11 0.07
118 14 0.09
119 96 0.60
120 8 0.05
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (117 bp):
ATTAAATCATTAAAGTAATATCATTAAAGAATTAAAGTTAAATCATTAAATTAAATAATTAAATC
ATTAAAGTAATTATTATTAAAGCATTAAAATTAAATCATTAAAGTAATTATT
Found at i:366234 original size:28 final size:28
Alignment explanation
Indices: 366202--366256 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
366192 AGATTACTAC
366202 TGAGGTCTATACTGTGGAAGGTTTGGAG
1 TGAGGTCTATACTGTGGAAGGTTTGGAG
366230 TGAGGTCTATACTGTGGAAGGTTTGGA
1 TGAGGTCTATACTGTGGAAGGTTTGGA
366257 AAATTTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.07, G:0.38, T:0.33
Consensus pattern (28 bp):
TGAGGTCTATACTGTGGAAGGTTTGGAG
Found at i:369680 original size:42 final size:42
Alignment explanation
Indices: 369621--369705 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
369611 AACAAATCTC
*
369621 ACGCTTCAGGCGAATCTCACGCTTCGGCCCCAAAGCATACAG
1 ACGCTTCAGGCGAATCTCACGCTTCGGCCACAAAGCATACAG
369663 ACGCTTCAGGCGAATCTCACGCTTCGGCCACAAAGCATACAG
1 ACGCTTCAGGCGAATCTCACGCTTCGGCCACAAAGCATACAG
369705 A
1 A
369706 TTCACGTAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.28, C:0.34, G:0.21, T:0.16
Consensus pattern (42 bp):
ACGCTTCAGGCGAATCTCACGCTTCGGCCACAAAGCATACAG
Found at i:374149 original size:75 final size:75
Alignment explanation
Indices: 374060--374223 Score: 206
Period size: 76 Copynumber: 2.2 Consensus size: 75
374050 TAAACTCAAG
* *
374060 TTTAGGATAATATTTTAAACATTATATTT-TATCTT-TGTATTTTAGTTTAAATATGTTTTAGTA
1 TTTAGGATATTATTTTAAACATTATATTTGT-T-TTAGGTATTTTAGTTTAAATATGTTTTAGTA
*
374123 TTTTAATTAAGT
64 TTTTAATTAAGA
* **
374135 TTTAGGATATTATTTTTATATTTTATATTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAGTAT
1 TTTAGGATATTA-TTTTAAACATTATATTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAGTAT
* *
374200 TTTTATTAGGA
65 TTTAATTAAGA
*
374211 TTTAGAATATTAT
1 TTTAGGATATTAT
374224 ATTATTTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
75 14 0.18
76 62 0.81
77 1 0.01
ACGTcount: A:0.30, C:0.01, G:0.11, T:0.58
Consensus pattern (75 bp):
TTTAGGATATTATTTTAAACATTATATTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAGTATT
TTAATTAAGA
Found at i:374158 original size:32 final size:32
Alignment explanation
Indices: 374115--374176 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
374105 TTTAAATATG
374115 TTTTAGTATTTTA-ATTAAGTTTTAGGATATTAT
1 TTTTAGTATTTTATATT-AGTTTTAGG-TATTAT
*
374148 TTTTA-TATTTTATATTTGTTTTAGGTATT
1 TTTTAGTATTTTATATTAGTTTTAGGTATT
374177 TTAGTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 4 0.15
32 15 0.56
33 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (32 bp):
TTTTAGTATTTTATATTAGTTTTAGGTATTAT
Found at i:374224 original size:63 final size:64
Alignment explanation
Indices: 374157--374278 Score: 185
Period size: 64 Copynumber: 1.9 Consensus size: 64
374147 TTTTTATATT
* *
374157 TTATATT-TGTTTTAGGTATTTTAGTTTAAATATGTTTT-AGTATTTTTATTAGGATTTAGAATA
1 TTATATTATGTTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTATTTTAATTAAGATTTAGAATA
* *
374220 TTATATTATTTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAAGATTTA
1 TTATATTATGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAAGATTTA
374279 AGATGTTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
63 12 0.23
64 41 0.77
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (64 bp):
TTATATTATGTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAAGATTTAGAATA
Found at i:374890 original size:19 final size:19
Alignment explanation
Indices: 374861--374910 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
374851 AATCTCTTTA
*
374861 ATTTGTTTATTTAATTATT
1 ATTTTTTTATTTAATTATT
*
374880 -TTTCTTTTATTTAATTCTT
1 ATTT-TTTTATTTAATTATT
374899 ATTTTTTTATTT
1 ATTTTTTTATTT
374911 TAAAAATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 21 0.78
20 3 0.11
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (19 bp):
ATTTTTTTATTTAATTATT
Found at i:377913 original size:14 final size:14
Alignment explanation
Indices: 377889--377934 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
377879 CCCATTTCGT
377889 TTTATTTTCATTTTA
1 TTTA-TTTCATTTTA
**
377904 TTTATTTCATTCCA
1 TTTATTTCATTTTA
*
377918 TTTATTTTATTTTA
1 TTTATTTCATTTTA
377932 TTT
1 TTT
377935 TATCAGATGC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTTCATTTTA
Found at i:377956 original size:5 final size:5
Alignment explanation
Indices: 377888--377937 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
377878 ACCCATTTCG
* **
377888 TTTTA TTTTCA TTTTA -TTTA TTTCA TTCCA -TTTA TTTTA TTTTA TTTTA
1 TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
377937 T
1 T
377938 CAGATGCTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
4 6 0.16
5 27 0.71
6 5 0.13
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:379211 original size:16 final size:16
Alignment explanation
Indices: 379186--379231 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
379176 TTACTTTAAA
379186 TTTT-CTTGGTTGTAT
1 TTTTGCTTGGTTGTAT
379201 TTTTGCTTGGTTGTAT
1 TTTTGCTTGGTTGTAT
* *
379217 CTTTGCTTGATTGTA
1 TTTTGCTTGGTTGTA
379232 ACATGAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 4 0.14
16 24 0.86
ACGTcount: A:0.09, C:0.09, G:0.22, T:0.61
Consensus pattern (16 bp):
TTTTGCTTGGTTGTAT
Found at i:380428 original size:19 final size:18
Alignment explanation
Indices: 380379--380425 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
380369 AATCTCTTTA
380379 ATTTTTTA-TTAATTATT
1 ATTTTTTATTTAATTATT
* *
380396 TTTCTTTTATTTAATTCTT
1 ATT-TTTTATTTAATTATT
380415 ATTTTTTATTT
1 ATTTTTTATTT
380426 TAAAAATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 2 0.08
18 13 0.52
19 10 0.40
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:389887 original size:2 final size:2
Alignment explanation
Indices: 389875--389927 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
389865 GAACCGGATT
*
389875 TA TA TA CA 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
389917 TA TA TA TA TA T
1 TA TA TA TA TA T
389928 TGTACATAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.