Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008641.1 Hibiscus syriacus cultivar Beakdansim tig00111617_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: 241015
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:153547 original size:17 final size:16
Alignment explanation
Indices: 153525--153559 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
153515 TATATATAGT
153525 TTATATATAAACTTATA
1 TTATATATAAA-TTATA
*
153542 TTATATATATATTATA
1 TTATATATAAATTATA
153558 TT
1 TT
153560 TTTCAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATATAAATTATA
Found at i:153701 original size:4 final size:4
Alignment explanation
Indices: 153692--153717 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
153682 TATGTATTCA
153692 ATGC ATGC ATGC ATGC ATGC ATGC AT
1 ATGC ATGC ATGC ATGC ATGC ATGC AT
153718 ACATACATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (4 bp):
ATGC
Found at i:153722 original size:4 final size:4
Alignment explanation
Indices: 153715--154722 Score: 1932
Period size: 4 Copynumber: 255.0 Consensus size: 4
153705 TGCATGCATG
153715 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
153763 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
153811 CATA CATA CATA CATA CATA CATA CATA C--A CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
153857 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
153905 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
153953 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154001 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154049 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154097 CATA CATA CATA CATA CATA CATA CATA C-TA C-TA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154143 CATA CATA CATA CATA CATA CATA CATA CATA C--A CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154189 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154237 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154285 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154333 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154381 CATA CATA CATA CATA CAT- -ATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154427 CATA CATA CATA CATA CATA CATA CATA CAT- -ATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154473 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154521 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154569 CATA CATA C--A CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154615 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154663 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
154711 CATA CATA CATA
1 CATA CATA CATA
154723 ATTTATATAT
Statistics
Matches: 993, Mismatches: 0, Indels: 22
0.98 0.00 0.02
Matches are distributed among these distances:
2 10 0.01
3 6 0.01
4 977 0.98
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:154781 original size:11 final size:11
Alignment explanation
Indices: 154748--154793 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
154738 TTATAATAAT
154748 TATATAGTTTA
1 TATATAGTTTA
154759 TA-ATA---TA
1 TATATAGTTTA
*
154766 AATATAGTTTA
1 TATATAGTTTA
154777 TATATAGTTTA
1 TATATAGTTTA
154788 TATATA
1 TATATA
154794 AACTTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
7 3 0.10
8 3 0.10
10 3 0.10
11 20 0.69
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:154789 original size:18 final size:18
Alignment explanation
Indices: 154749--154782 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
154739 TATAATAATT
154749 ATATAGTTTATAATATAA
1 ATATAGTTTATAATATAA
154767 ATATAGTTTAT-ATATA
1 ATATAGTTTATAATATA
154783 GTTTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
ATATAGTTTATAATATAA
Found at i:157898 original size:28 final size:29
Alignment explanation
Indices: 157867--157921 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
157857 TTAGTTTGCT
*
157867 ATAGATGATTATGTTTT-TGTTTAAATGA
1 ATAGATGAATATGTTTTATGTTTAAATGA
* * *
157895 ATAGTTTAATATTTTTTATGTTTAAAT
1 ATAGATGAATATGTTTTATGTTTAAAT
157922 ATTTTCTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 13 0.59
29 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.55
Consensus pattern (29 bp):
ATAGATGAATATGTTTTATGTTTAAATGA
Found at i:160386 original size:32 final size:32
Alignment explanation
Indices: 160284--160388 Score: 95
Period size: 32 Copynumber: 3.3 Consensus size: 32
160274 AACATATCAG
* * * *
160284 TATTGCATTCAAACAATCCACAACAGAGTCAA
1 TATTGCATTTAAATAATGCATAACAGAGTCAA
* * * * * *
160316 TATTACATTCT-GATAATGCATAACATAATTAT
1 TATTGCATT-TAAATAATGCATAACAGAGTCAA
160348 TATTGCATTTAAATAATGCATAACAGAGTCAA
1 TATTGCATTTAAATAATGCATAACAGAGTCAA
*
160380 TGTTGCATT
1 TATTGCATT
160389 CAGATAGTGA
Statistics
Matches: 54, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
31 1 0.02
32 53 0.98
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.33
Consensus pattern (32 bp):
TATTGCATTTAAATAATGCATAACAGAGTCAA
Found at i:163665 original size:23 final size:24
Alignment explanation
Indices: 163625--163670 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
163615 TTTTTATAAC
** *
163625 TCATTTCATTCTCGTCATTTTTCT
1 TCATTTCATTCTAATCATCTTTCT
163649 TCATTTC-TTCTAATCATCTTTC
1 TCATTTCATTCTAATCATCTTTC
163671 CTCTACAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.15, C:0.26, G:0.02, T:0.57
Consensus pattern (24 bp):
TCATTTCATTCTAATCATCTTTCT
Found at i:165416 original size:32 final size:32
Alignment explanation
Indices: 165369--165521 Score: 137
Period size: 32 Copynumber: 4.8 Consensus size: 32
165359 AGTGTTAGTG
*
165369 TTGCATTCAGGTAATGCACAACAGAGTCAGTA
1 TTGCATTCAGATAATGCACAACAGAGTCAGTA
* * * *
165401 TTGCATTCATATAATGCA-AAAAGAAATTAGTA
1 TTGCATTCAGATAATGCACAACAG-AGTCAGTA
* *
165433 TTGCATTCAGATAATGCACAACAGAGTTAGTG
1 TTGCATTCAGATAATGCACAACAGAGTCAGTA
* * ** *
165465 TTGCATTCAAATAGTGCACAGGAGAGTCAATA
1 TTGCATTCAGATAATGCACAACAGAGTCAGTA
* * * * *
165497 TCGTATTTAGACAATGCGCAACAGA
1 TTGCATTCAGATAATGCACAACAGA
165522 TACAGTCAGT
Statistics
Matches: 94, Mismatches: 25, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
31 4 0.04
32 86 0.91
33 4 0.04
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (32 bp):
TTGCATTCAGATAATGCACAACAGAGTCAGTA
Found at i:165469 original size:64 final size:64
Alignment explanation
Indices: 165363--165482 Score: 186
Period size: 64 Copynumber: 1.9 Consensus size: 64
165353 CATTGTAGTG
* * *
165363 TTAGTGTTGCATTCAGGTAATGCACAACAGAGTCAGTATTGCATTCATATAATGCAAAAAGAAA
1 TTAGTATTGCATTCAGATAATGCACAACAGAGTCAGTATTGCATTCAAATAATGCAAAAAGAAA
* * *
165427 TTAGTATTGCATTCAGATAATGCACAACAGAGTTAGTGTTGCATTCAAATAGTGCA
1 TTAGTATTGCATTCAGATAATGCACAACAGAGTCAGTATTGCATTCAAATAATGCA
165483 CAGGAGAGTC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 50 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (64 bp):
TTAGTATTGCATTCAGATAATGCACAACAGAGTCAGTATTGCATTCAAATAATGCAAAAAGAAA
Found at i:169811 original size:168 final size:168
Alignment explanation
Indices: 169209--170791 Score: 2156
Period size: 168 Copynumber: 9.5 Consensus size: 168
169199 AAAACAATAT
* *
169209 ACTCTCATATCTAAGAAAGGAACAAAATAGATTACTTTTTTTTTCTTTACAAGTTTCTTTGTACC
1 ACTCTCATATCTAAGAAAGGAACATAATAGATTAC-TCTTTTTTCTTTACAAGTTTCTTTGTACC
* *
169274 CTTTACTCAATTGCTTCGGTTTAAGAAAAGAATGATTCAAAGTGATGGATAACTTGAAAATGAAC
65 CTTTACTCAATTGCTTCGGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACTTGAAAACGAAC
* * * *
169339 TGACTATAAATATGATA-TCGGTATAAACTCC-TTTCTTG
130 TGACTATAAAAACGATATTC-GTACAAACTCCTTTTCTCG
* * * * *
169377 ACTATCGTATCTAGGAAAGGAACAGAATAGATTACTCTTTTTT-TTTACAAGTTTCTTTGTACCT
1 ACTCTCATATCTAAGAAAGGAACATAATAGATTACTCTTTTTTCTTTACAAGTTTCTTTGTACCC
* * * * * * * * *
169441 TTTAATCCATTGCTACAGTTTAAGTAAAGAATTATTCAAAATGATGTATAAATTGAAAATGAACT
66 TTTACTCAATTGCTTCGGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACTTGAAAACGAACT
* *
169506 GACTATAAAAAACGATATACTTACAAACTCCTTTTCTC-
131 GACTAT-AAAAACGATATTCGTACAAACTCCTTTTCTCG
* *
169544 AGGTCTCATATCTAAGAAAGGAACATAATAGATTACTCTCTTTTTCTTTACAAGTGTCTTTGTAC
1 A-CTCTCATATCTAAGAAAGGAACATAATAGATTACTCT-TTTTTCTTTACAAGTTTCTTTGTAC
* * * *
169609 CCTTTACTCAATTCCTTCGCTTTAAGTAAAGAATGATTCAAAATGATGAATAACTTGAAAACGAA
64 CCTTTACTCAATTGCTTCGGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACTTGAAAACGAA
* * *
169674 CTGACTATAAAAATGATATCCATACAAACTCCTTTTCTCG
129 CTGACTATAAAAACGATATTCGTACAAACTCCTTTTCTCG
* *
169714 ACTCGCATATCTAAGAAAGGAACATAATAGATTACTCTTTTTTCTTTACAAGTTTTTTTGTACCC
1 ACTCTCATATCTAAGAAAGGAACATAATAGATTACTCTTTTTTCTTTACAAGTTTCTTTGTACCC
* * * *
169779 TTTACTCAATTGCTTCAGTTTAAGTAAAGAATGATTCAAAGTGATTGATAACTTGAAAACTAACC
66 TTTACTCAATTGCTTCGGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACTTGAAAACGAACT
* * *
169844 GACTATAAAAACAATATTTGTACAAACTCCTTTTCTCC
131 GACTATAAAAACGATATTCGTACAAACTCCTTTTCTCG
* *
169882 ACTCTCATATATCTAAGAAAGG-A-AT-AT--ATTACTCTTTTTTTCTGTAAAAGTTTCTTTG--
1 ACTCTC--ATATCTAAGAAAGGAACATAATAGATTACTC-TTTTTTCTTTACAAGTTTCTTTGTA
* * * * *
169940 -----T--GCAATTTCTTCGATTTAAGT---GAATGATTCAAAGTGATGAATAACTTCAAAACGA
63 CCCTTTACTCAATTGCTTCGGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACTTGAAAACGA
* *
169995 ACCGACTATAAAAACGATATTTGTACAAACTCCTTTTCTCG
128 ACTGACTATAAAAACGATATTCGTACAAACTCCTTTTCTCG
* *
170036 ACTCTCATATCTAAGAAAGGAACATAATAGATTACTCTCTTTTTTTCTTTACATGTTTCTTGGTA
1 ACTCTCATATCTAAGAAAGGAACATAATAGATTA--CTC-TTTTTTCTTTACAAGTTTCTTTGTA
*
170101 CCCTTTACTCAATTGCTTTGGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACTTGAAAACGA
63 CCCTTTACTCAATTGCTTCGGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACTTGAAAACGA
*
170166 ACTGACTATAAAAACGATAGTCGTACAAACTCCTTTTCTCG
128 ACTGACTATAAAAACGATATTCGTACAAACTCCTTTTCTCG
* *
170207 ACTTTCATATCTAAAAAAGGAACATAATAGATTACTCTCTTTTTTCTTTACAAGTTTCTTTGTAC
1 ACTCTCATATCTAAGAAAGGAACATAATAGATTA--CTCTTTTTTCTTTACAAGTTTCTTTGTAC
* * *
170272 CCTTTACTCAATTGCTTCGATTTAAGTAAAAAATGATTCAAAGTGATGGATAATTTGAAAACGAA
64 CCTTTACTCAATTGCTTCGGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACTTGAAAACGAA
*
170337 CTGACTATAAAAATGATATTCGTACAAACTCCTTTTCTCG
129 CTGACTATAAAAACGATATTCGTACAAACTCCTTTTCTCG
* * * *
170377 ATTCTCATATCTAGGACAGGAACATAATATATTACTC--TTTT-TTT-CAAGTTTCTTTGTACCC
1 ACTCTCATATCTAAGAAAGGAACATAATAGATTACTCTTTTTTCTTTACAAGTTTCTTTGTACCC
*
170438 TTTACTCAATTGCATCGGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACTTGAAAACGAACC
66 TTTACTCAATTGCTTCGGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACTTGAAAACGAA-C
* *
170503 T-ACTATAAAAATGATATTCGTACAAACTCCTTTTCTCA
130 TGACTATAAAAACGATATTCGTACAAACTCCTTTTCTCG
* * *
170541 ACTCTCATATCTAAGAAACGAACATAATAGATTACTCTTTCTTCTTTAAAAGTTTCTTTGTACCC
1 ACTCTCATATCTAAGAAAGGAACATAATAGATTACTCTTTTTTCTTTACAAGTTTCTTTGTACCC
* *
170606 TTTACTCAATTACTTCGGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACTTAAAAACGAACT
66 TTTACTCAATTGCTTCGGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACTTGAAAACGAACT
* *
170671 GACTATAAAAACGATATCCTTACAAACTCCTTTTCTCG
131 GACTATAAAAACGATATTCGTACAAACTCCTTTTCTCG
170709 ACTCTCATATCTAAGAAAGGAACATAATAGATTACTCTTTTTTTCTTTACAAGTTTCTTTGTACC
1 ACTCTCATATCTAAGAAAGGAACATAATAGATTACTC-TTTTTTCTTTACAAGTTTCTTTGTACC
* *
170774 CTTTGCTCAATTACTTCG
65 CTTTACTCAATTGCTTCG
170792 TGAAGATACT
Statistics
Matches: 1254, Mismatches: 125, Indels: 71
0.86 0.09 0.05
Matches are distributed among these distances:
152 14 0.01
153 1 0.00
154 77 0.06
155 2 0.00
157 20 0.02
159 24 0.02
164 144 0.11
165 12 0.01
166 110 0.09
167 32 0.03
168 354 0.28
169 111 0.09
170 246 0.20
171 107 0.09
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (168 bp):
ACTCTCATATCTAAGAAAGGAACATAATAGATTACTCTTTTTTCTTTACAAGTTTCTTTGTACCC
TTTACTCAATTGCTTCGGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACTTGAAAACGAACT
GACTATAAAAACGATATTCGTACAAACTCCTTTTCTCG
Found at i:170824 original size:3 final size:3
Alignment explanation
Indices: 170816--170943 Score: 211
Period size: 3 Copynumber: 42.7 Consensus size: 3
170806 TTTTTATCCA
*
170816 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
170864 TAT TAT TAT TAT CAT CAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
170912 TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
170944 ATTTATATTA
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 117 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:171858 original size:17 final size:17
Alignment explanation
Indices: 171832--171864 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
171822 TGTTTGAGAG
171832 AAAGAAAAAGAAAAAAA
1 AAAGAAAAAGAAAAAAA
*
171849 AAAGAGAAAGAAAAAA
1 AAAGAAAAAGAAAAAA
171865 TGAAATGGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAAA
Found at i:172407 original size:22 final size:20
Alignment explanation
Indices: 172366--172410 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
172356 ATAGAATTAT
**
172366 TATTTTATTATATTGTTAAA
1 TATTTTATTATATTCATAAA
172386 TATTTTGATATATATTCATAAA
1 TATTTT-AT-TATATTCATAAA
172408 TAT
1 TAT
172411 ATATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 13 0.62
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTATTATATTCATAAA
Found at i:173169 original size:13 final size:15
Alignment explanation
Indices: 173138--173174 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
173128 TTATATGTTT
173138 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
173153 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
173166 TA-TTTATTT
1 TATTTTATTT
173175 TTTGTCTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:183723 original size:15 final size:15
Alignment explanation
Indices: 183703--183768 Score: 77
Period size: 15 Copynumber: 4.5 Consensus size: 15
183693 ATTATGCTTG
183703 AAGAAAAGAAAGAAA
1 AAGAAAAGAAAGAAA
183718 AAGAAAA-AAGAGAAA
1 AAGAAAAGAA-AGAAA
*
183733 AAGAGAAA-AACGAAA
1 AAGA-AAAGAAAGAAA
183748 AA-AAAAG-AAGAAA
1 AAGAAAAGAAAGAAA
183761 AAGAAAAG
1 AAGAAAAG
183769 GGTCAAGGTG
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 10 0.22
14 8 0.18
15 22 0.49
16 5 0.11
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAAAGAAA
Found at i:183759 original size:20 final size:18
Alignment explanation
Indices: 183706--183767 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 18
183696 ATGCTTGAAG
*
183706 AAAAGAAAGAAAAAGA-A
1 AAAAGAAAAAAAAAGAGA
*
183723 AAAAG--AGAAAAAGAGA
1 AAAAGAAAAAAAAAGAGA
183739 AAAACGAAAAAAAAAGAAGA
1 AAAA-GAAAAAAAAAG-AGA
183759 AAAAGAAAA
1 AAAAGAAAA
183768 GGGTCAAGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
15 9 0.23
16 5 0.13
17 6 0.15
19 12 0.31
20 7 0.18
ACGTcount: A:0.81, C:0.02, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAAAAGAGA
Found at i:185206 original size:50 final size:50
Alignment explanation
Indices: 184699--185195 Score: 805
Period size: 50 Copynumber: 9.8 Consensus size: 50
184689 ATATGTGCTC
* * * *
184699 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAAAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAG-ACAG
*
184750 ACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAG
1 A-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
* * *
184801 AACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGAAAG
1 -A-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
*
184853 AACATAGCATCTTCTGGAAGTGTTCTTTGGGTTATCTGATCTGATTAGACAG
1 -A-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
* * *
184905 AATAGCATCTTCTGGAAGTGTTCTTTGGGTTATCTGATCTGATCAAACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
184955 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
185005 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
* *
185055 AATAGCATCTTCTGGAAGTGTTCTTTGGGTTATCTGATCTGATTAAACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
185105 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
*
185155 AATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
185196 GTTTGGCAGA
Statistics
Matches: 425, Mismatches: 19, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
50 280 0.66
51 4 0.01
52 141 0.33
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
Found at i:185313 original size:50 final size:50
Alignment explanation
Indices: 185238--185439 Score: 386
Period size: 50 Copynumber: 4.0 Consensus size: 50
185228 TGAATTTGCC
185238 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
185288 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
185338 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
* *
185388 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
185438 AA
1 AA
185440 CCAATCATTG
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 150 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
Found at i:185363 original size:183 final size:183
Alignment explanation
Indices: 185055--185705 Score: 858
Period size: 183 Copynumber: 3.6 Consensus size: 183
185045 GATTAGACAG
* *
185055 AATAGCATCTTCTGGAAGTGTTCTTTGGGTTATCTGATCTGATTAAACAGAATAGCATCTTCTGG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
*
185120 AAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAATGTTCTTTGAGT
66 AAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGT
185185 TATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTGCC
131 TATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTGCC
185238 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
185303 AAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGT
66 AAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGT
* * * * * * * **
185368 TATCTGATCTGATTAGACAGAA--TAGCATCT---TCTGGAAG-TGTTCTTTG--
131 TATCTGATCTGGTTTGGCAGAACCAATCAT-TGAATTTAGAAGATG-AATTTGCC
* * * **** * * * ** * *
185415 AGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATT-T-AGAAGATGAATTTG-C-CAATAG
1 A-ATAGC--ATCT--TCTG---GAAGTGTTCTTTGAGTTATCTG-ATCTG-ATTAGACAGAATAG
185476 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTG
56 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTG
185541 TTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTGCC
121 TTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTGCC
185604 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
* *
185669 AAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAA
66 AAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAA
185706 CCAATCATTG
Statistics
Matches: 393, Mismatches: 51, Indels: 48
0.80 0.10 0.10
Matches are distributed among these distances:
177 1 0.00
178 5 0.01
179 10 0.03
180 4 0.01
181 19 0.05
182 9 0.02
183 297 0.76
184 9 0.02
185 19 0.05
186 4 0.01
187 10 0.03
188 5 0.01
189 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (183 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
AAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGT
TATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTTGCC
Found at i:185412 original size:233 final size:233
Alignment explanation
Indices: 185005--185561 Score: 1078
Period size: 233 Copynumber: 2.4 Consensus size: 233
184995 GATTAGACAG
185005 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
*
185070 AAGTGTTCTTTGGGTTATCTGATCTGATTAAACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGT
66 AAGTGTTCTTTGAGTTATCTGATCTGATTAAACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGT
185135 TATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTT
131 TATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTT
*
185200 GGCAGAACCAATCATTGAATTTAGAAGATGAATTTGCC
196 GACAGAACCAATCATTGAATTTAGAAGATGAATTTGCC
185238 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
*
185303 AAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGT
66 AAGTGTTCTTTGAGTTATCTGATCTGATTAAACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
185368 TATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
131 TATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTT
185433 GACAGAACCAATCATTGAATTTAGAAGATGAATTTGCC
196 GACAGAACCAATCATTGAATTTAGAAGATGAATTTGCC
185471 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
185536 AAGTGTTCTTTGAGTTATCTGATCTG
66 AAGTGTTCTTTGAGTTATCTGATCTG
185562 GTTTGGCAGA
Statistics
Matches: 320, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
233 320 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (233 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
AAGTGTTCTTTGAGTTATCTGATCTGATTAAACAGAATAGCATCTTCTGGAAGTGTTCTTTGAGT
TATCTGATCTGATTAGACAGAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTT
GACAGAACCAATCATTGAATTTAGAAGATGAATTTGCC
Found at i:185576 original size:133 final size:133
Alignment explanation
Indices: 185338--185777 Score: 853
Period size: 133 Copynumber: 3.3 Consensus size: 133
185328 GATTAGACAG
185338 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
185403 AAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTT
66 AAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTT
185468 GCC
131 GCC
185471 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
*
185536 AAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATTT
66 AAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTT
185601 GCC
131 GCC
185604 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
185669 AAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTT
66 AAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTT
**
185734 GTT
131 GCC
185737 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
185778 GTTTGGTAAG
Statistics
Matches: 303, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 303 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (133 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATAGCATCTTCTGG
AAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAATTTAGAAGATGAATTT
GCC
Found at i:185679 original size:50 final size:50
Alignment explanation
Indices: 185604--185705 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
185594 TGAATTTGCC
185604 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
* *
185654 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
185704 AA
1 AA
185706 CCAATCATTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
Found at i:186612 original size:113 final size:112
Alignment explanation
Indices: 186414--186960 Score: 936
Period size: 113 Copynumber: 4.8 Consensus size: 112
186404 TTAGCAAAGA
186414 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGGTGGATCAT-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
186479 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
186527 TGAATCCATCATTTGGTGGATCATTTTTCCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGGTGGATCATTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
186592 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
186640 TGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGGTGGATCAT-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
186705 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* *
186753 TAAATCCATCATTTGGTGGATTATTTTTCCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 TGAATCCATCATTTGGTGGATCATTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* *
186818 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
* * ** *
186866 TGAATTCATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGA
1 TGAATCCATCATTTGGTGGATC-ATTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGA
186930 AGAAGGAAG-AGAAAGTTCATAATGAGAAGAA
64 AGAAGGAAGAAG-AAGTTCATAATGAGAAGAA
186961 CTCATCAAGA
Statistics
Matches: 417, Mismatches: 11, Indels: 12
0.95 0.03 0.03
Matches are distributed among these distances:
112 11 0.03
113 399 0.96
114 7 0.02
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (112 bp):
TGAATCCATCATTTGGTGGATCATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACC
Found at i:187218 original size:3 final size:3
Alignment explanation
Indices: 187210--187329 Score: 195
Period size: 3 Copynumber: 39.7 Consensus size: 3
187200 TTTTTATCCA
187210 TAT TAT TAT TAT TAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
187256 TAT CAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
187304 TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
187330 ATTTATATTA
Statistics
Matches: 110, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
3 107 0.97
4 3 0.03
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:188240 original size:17 final size:17
Alignment explanation
Indices: 188214--188246 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
188204 TGTTTGAGAG
188214 AAAGAAAAAGAAAAAAA
1 AAAGAAAAAGAAAAAAA
*
188231 AAAGAGAAAGAAAAAA
1 AAAGAAAAAGAAAAAA
188247 TGAAATGGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAAA
Found at i:188786 original size:22 final size:20
Alignment explanation
Indices: 188745--188789 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
188735 ATAGAATTAT
**
188745 TATTTTATTATATTGTTAAA
1 TATTTTATTATATTCATAAA
188765 TATTTTGATATATATTCATAAA
1 TATTTT-AT-TATATTCATAAA
188787 TAT
1 TAT
188790 ATATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 13 0.62
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTATTATATTCATAAA
Found at i:189648 original size:169 final size:172
Alignment explanation
Indices: 189369--189707 Score: 524
Period size: 169 Copynumber: 2.0 Consensus size: 172
189359 ACGACACTTC
* *
189369 GGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACTTGAAAACGAACTGACTTTAAAAACGATA
1 GGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACATGAAAACGAACTGACTATAAAAACGATA
* * * *
189434 TCCGTACAAACTCCTTTTCTTGACTCTCATATCTAAGGAAGGAACAAAATATATTACTC-TTTTT
66 TACGTACAAACTCCTTTTCTCGACTCTCATATCTAAGAAAGGAACAAAATAAATTACTCTTTTTT
*
189498 TT-CTTTACAAGTTTCTTTGTACCCTTT-ACTTAATTGCTTG
131 TTCCTTTACAAGTTTCTTTGTACCCTTTAACTCAATTGCTTG
189538 GGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACATGAAGAA-GAACTGACTATAAAAACGAT
1 GGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACATGAA-AACGAACTGACTATAAAAACGAT
* * * *
189602 ATATGTATAAACTCTTTTTCTCGACTCTCATATCTAAGAAAGGAACAGAATAAATTACTCTTTTT
65 ATACGTACAAACTCCTTTTCTCGACTCTCATATCTAAGAAAGGAACAAAATAAATTACTC-TTTT
*
189667 TTTTCCTTTATAAGTTTCTTTGTACCCTTTAACTCAATTGC
129 TTTTCCTTTACAAGTTTCTTTGTACCCTTTAACTCAATTGC
189708 AACGTATTCT
Statistics
Matches: 153, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
169 111 0.73
170 2 0.01
171 7 0.05
172 24 0.16
173 9 0.06
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.36
Consensus pattern (172 bp):
GGTTTAAGTAAAGAATGATTCAAAGTGATGGATAACATGAAAACGAACTGACTATAAAAACGATA
TACGTACAAACTCCTTTTCTCGACTCTCATATCTAAGAAAGGAACAAAATAAATTACTCTTTTTT
TTCCTTTACAAGTTTCTTTGTACCCTTTAACTCAATTGCTTG
Found at i:190851 original size:29 final size:28
Alignment explanation
Indices: 190809--190912 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 28
190799 GAGCTAAATA
* *
190809 AGCACAAGACGAGCAACAAGTTTTTAACG
1 AGCACGAGTCGAGCAACAA-TTTTTAACG
190838 AGCACGAGTCGAGCAA-AA-TTTTAACG
1 AGCACGAGTCGAGCAACAATTTTTAACG
*
190864 AGCTTAATGAGTCGAGCAACAAATTTTTATAACG
1 AGC---ACGAGTCGAGCAAC-AA-TTTT-TAACG
*
190898 AGCACGAGTCAAGCA
1 AGCACGAGTCGAGCA
190913 CTGCCTTCAT
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
26 11 0.18
28 2 0.03
29 26 0.42
31 12 0.19
33 3 0.05
34 8 0.13
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (28 bp):
AGCACGAGTCGAGCAACAATTTTTAACG
Found at i:206358 original size:21 final size:21
Alignment explanation
Indices: 206334--206389 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
206324 CGCAACTCAG
206334 TTTCCAAATTCGCATTGCGAT
1 TTTCCAAATTCGCATTGCGAT
*
206355 TTTCCAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCATTGCGAT
206376 TTTCCAAATTCGCA
1 TTTCCAAATTCGCA
206390 ACACTGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (21 bp):
TTTCCAAATTCGCATTGCGAT
Found at i:206608 original size:14 final size:15
Alignment explanation
Indices: 206589--206626 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
206579 TCCCCATCTC
206589 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
206603 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
206619 TAATTTTT
1 TAATTTTT
206627 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:209603 original size:18 final size:18
Alignment explanation
Indices: 209580--209615 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
209570 AAGCAAAAGG
*
209580 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
209598 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
209616 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:209921 original size:20 final size:20
Alignment explanation
Indices: 209894--209974 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
209884 AAATCGCAAC
**
209894 GCGAATTTGACTTTCGTGTT
1 GCGAATTTGACTTTCACGTT
*
209914 GGGAATTTGACTTTCACGTT
1 GCGAATTTGACTTTCACGTT
* * ***
209934 GCGAATTTGACTATCGCAAC
1 GCGAATTTGACTTTCACGTT
*
209954 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCACGTT
209974 G
1 G
209975 TGAAAGTGTA
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GCGAATTTGACTTTCACGTT
Found at i:210138 original size:64 final size:64
Alignment explanation
Indices: 210037--210183 Score: 233
Period size: 64 Copynumber: 2.3 Consensus size: 64
210027 AATTTAAAAC
*
210037 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAACCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*** * *
210101 AACAAATCAACTTTTACAAACCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAACCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
210165 AACAAATCAAC-TTTACAAA
1 AACAAATCAACTTTTACAAA
210184 TGAACTTTTA
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
63 8 0.10
64 69 0.90
ACGTcount: A:0.52, C:0.18, G:0.02, T:0.27
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAACCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:210182 original size:13 final size:14
Alignment explanation
Indices: 210166--210198 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
210156 CATCAATTAA
210166 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
210179 ACAAATGAACTTTT
1 ACAAATCAACTTTT
210193 ACAAAT
1 ACAAAT
210199 ACATCAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:211567 original size:21 final size:21
Alignment explanation
Indices: 211543--211670 Score: 64
Period size: 21 Copynumber: 6.1 Consensus size: 21
211533 GAACGGTGGG
*
211543 AGGGACCTCTTGAATAATGAC
1 AGGGACCTCTTGAATGATGAC
* * * **
211564 AGGGGCCTCTTAAATGGTGTG
1 AGGGACCTCTTGAATGATGAC
* * *
211585 AGGGATCTCTTGAAGGATGAT
1 AGGGACCTCTTGAATGATGAC
* * * *
211606 AGGGATCTCTTGAAGGAAGATA
1 AGGGACCTCTTGAATGATGA-C
* *
211628 AGGG-CCTTTTGAACGATAGA-
1 AGGGACCTCTTGAATGAT-GAC
*
211648 AGAGG-CCTCTTGAACGATGAC
1 AG-GGACCTCTTGAATGATGAC
211669 AG
1 AG
211671 TTGAATCGGG
Statistics
Matches: 83, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
20 4 0.05
21 73 0.88
22 6 0.07
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (21 bp):
AGGGACCTCTTGAATGATGAC
Found at i:211616 original size:42 final size:42
Alignment explanation
Indices: 211537--211616 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 42
211527 GCTCTCGAAC
* *
211537 GGTGGGAGGGACCTCTTGAATAATGACAGGGGCCTCTTAAAT
1 GGTGGGAGGGACCTCTTGAAGAATGACAGGGACCTCTTAAAT
* * * * *
211579 GGTGTGAGGGATCTCTTGAAGGATGATAGGGATCTCTT
1 GGTGGGAGGGACCTCTTGAAGAATGACAGGGACCTCTT
211617 GAAGGAAGAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 31 1.00
ACGTcount: A:0.24, C:0.14, G:0.35, T:0.28
Consensus pattern (42 bp):
GGTGGGAGGGACCTCTTGAAGAATGACAGGGACCTCTTAAAT
Found at i:212099 original size:21 final size:21
Alignment explanation
Indices: 212075--212124 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
212065 ATCATTGTCT
* *
212075 TCACGTAAAGTACCGACCTCC
1 TCACGTAAAGCACCGACCTCA
* **
212096 TCACGCAAAGCATTGACCTCA
1 TCACGTAAAGCACCGACCTCA
212117 TCACGTAA
1 TCACGTAA
212125 CTCACCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.34, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:213829 original size:27 final size:27
Alignment explanation
Indices: 213789--213858 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
213779 GAATAGTTTA
213789 TGAAACTTAAAATCGCAACGCGAAAACG
1 TGAAAC-TAAAATCGCAACGCGAAAACG
*
213817 TGAAACTAAAATCGCAACTCGAAAACG
1 TGAAACTAAAATCGCAACGCGAAAACG
*
213844 CGAAACTAAAATCGC
1 TGAAACTAAAATCGC
213859 GTTGCGATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 34 0.85
28 6 0.15
ACGTcount: A:0.47, C:0.23, G:0.16, T:0.14
Consensus pattern (27 bp):
TGAAACTAAAATCGCAACGCGAAAACG
Found at i:214240 original size:20 final size:21
Alignment explanation
Indices: 214215--214272 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
214205 TCTGAGAGAT
214215 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
214235 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
* *
214257 AGAGATGGGGACGGAT
1 GGAGAT-GAGACGGAT
214273 GTCACCGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 6 0.18
22 27 0.82
ACGTcount: A:0.24, C:0.14, G:0.43, T:0.19
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:214249 original size:22 final size:22
Alignment explanation
Indices: 214222--214272 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
214212 GATGGAGATA
*
214222 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
214244 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
214266 GACGGAT
1 GACGGAT
214273 GTCACCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:214405 original size:19 final size:20
Alignment explanation
Indices: 214383--214420 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
214373 AATATTGTGT
214383 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
*
214402 TTCGCATTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
214421 CGCGCTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:214452 original size:20 final size:20
Alignment explanation
Indices: 214427--214472 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
214417 TAAACGCGCT
214427 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
214447 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
214467 TTGCGA
1 TTGCGA
214473 TTTACATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.43
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:214529 original size:20 final size:21
Alignment explanation
Indices: 214480--214530 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
214470 CGATTTACAT
*
214480 ATTCGCGTTGCAAATTTGGAA
1 ATTCGCGTTGCAAAATTGGAA
*
214501 ATT-GAGTTGCAAAATTGG-A
1 ATTCGCGTTGCAAAATTGGAA
*
214520 GTTCGCGTTGC
1 ATTCGCGTTGC
214531 GAATTTATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 3 0.12
20 19 0.76
21 3 0.12
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.33
Consensus pattern (21 bp):
ATTCGCGTTGCAAAATTGGAA
Found at i:215737 original size:3 final size:3
Alignment explanation
Indices: 215729--215763 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
215719 TCTTTATTTT
215729 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
215764 CATTTACACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:216925 original size:13 final size:13
Alignment explanation
Indices: 216893--216931 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
216883 GTCATAAATC
* *
216893 TATGACACGTATT
1 TATGACGCGCATT
216906 TATGACGCGCATT
1 TATGACGCGCATT
*
216919 TATGACGCTCATT
1 TATGACGCGCATT
216932 GCGCGTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:217523 original size:86 final size:86
Alignment explanation
Indices: 217417--217637 Score: 279
Period size: 85 Copynumber: 2.6 Consensus size: 86
217407 CAACAGTGTA
* * * *
217417 TCATAAATCTATGACGCGCAT-TAATAACGTT-CATTGAGTGTCATTGAAGCCCCCCGTCATAAA
1 TCATAAATTTATGACACGCATGT-ATAAC-TTACATTGCGTGTCATTGAAGCCCCCCATCATAAA
*
217480 T-TAAGATGACACACATTTGTGCG
64 TCT-ACATGACACACATTTGTGCG
* * *
217503 TCATAAATTTATGACACGCATGTATAACTTGCATTGCGCGTCATTGAAG-TCCCCATCATAAATC
1 TCATAAATTTATGACACGCATGTATAACTTACATTGCGTGTCATTGAAGCCCCCCATCATAAATC
* * *
217567 TACTTGACATACATTTGTGTG
66 TACATGACACACATTTGTGCG
*
217588 TCATAAATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGC
1 TCATAAATTTATGACACGCATGTATAACTTACATTGCGTGTCATTGAAGC
217638 ACACGTCATT
Statistics
Matches: 118, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
85 76 0.64
86 41 0.35
87 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (86 bp):
TCATAAATTTATGACACGCATGTATAACTTACATTGCGTGTCATTGAAGCCCCCCATCATAAATC
TACATGACACACATTTGTGCG
Found at i:217672 original size:85 final size:83
Alignment explanation
Indices: 217412--217674 Score: 251
Period size: 85 Copynumber: 3.1 Consensus size: 83
217402 ACACGCAACA
* * * *
217412 GTGTATCATAAATCTATGACGCGCAT-TAATAACGTTCATTGAGTGTCATTGAAGCCCCCCGTCA
1 GTGTGTCATAAATTTATGACACGCATGT-ATAAC-TTCATTGCGTGTCATTGAAG-CCCCCGTCA
* * *
217476 TAAATTAAGATGACACACATTT
63 TAAA-AAAGACGACAAACATTT
* * * *
217498 GTGCGTCATAAATTTATGACACGCATGTATAACTTGCATTGCGCGTCATTGAAGTCCCCATCAT-
1 GTGTGTCATAAATTTATGACACGCATGTATAACTT-CATTGCGTGTCATTGAAGCCCCCGTCATA
*** *
217562 AAATCTACTTGACATACATTT
65 AAAAAGAC--GACAAACATTT
* * *
217583 GTGTGTCATAAATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACACGTCATT
1 GTGTGTCATAAATTTATGACACGCATGTATAACTT-CATTGCGTGTCATTGAAGCCCCCGTCA-T
* *
217648 AAAAAAGACGACAAACGTTC
64 AAAAAAGACGACAAACATTT
217668 GTGTGTC
1 GTGTGTC
217675 GTGATTGTAT
Statistics
Matches: 143, Mismatches: 28, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
83 1 0.01
84 2 0.01
85 90 0.63
86 44 0.31
87 6 0.04
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (83 bp):
GTGTGTCATAAATTTATGACACGCATGTATAACTTCATTGCGTGTCATTGAAGCCCCCGTCATAA
AAAAGACGACAAACATTT
Found at i:217701 original size:2 final size:2
Alignment explanation
Indices: 217694--217752 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
217684 TTTCGTAAAT
* *
217694 TA TA TA TA TA CA TA CA 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
217736 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
217753 TGTAGATTGA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:220711 original size:2 final size:2
Alignment explanation
Indices: 220704--220728 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
220694 TCCTACAAAT
220704 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
220729 TAATTGCAGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:224099 original size:15 final size:15
Alignment explanation
Indices: 224074--224128 Score: 83
Period size: 15 Copynumber: 3.6 Consensus size: 15
224064 TATGCTTTCT
224074 TTTTCCTTCTTTGACG
1 TTTT-CTTCTTTGACG
224090 TTTTCTTCTTTGACG
1 TTTTCTTCTTTGACG
*
224105 TTTTCTTCTTAGACG
1 TTTTCTTCTTTGACG
*
224120 TTGTCTTCT
1 TTTTCTTCT
224129 AACCCCCATG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
15 33 0.89
16 4 0.11
ACGTcount: A:0.07, C:0.22, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTTCTTCTTTGACG
Found at i:234741 original size:29 final size:29
Alignment explanation
Indices: 234699--234785 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
234689 GTCCCGGGGG
*
234699 TAGGTCGCCATGCACGCCCGGCGACCTAC
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
**
234728 TAGGTCGCCATGCACGCCCAGCGACCTGG
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
* *
234757 TAGGTCGCCATGCATGCCCTGCGACCTAC
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
234786 CAGCACCTCC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.17, C:0.39, G:0.28, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCAGCGACCTAC
Found at i:234801 original size:10 final size:10
Alignment explanation
Indices: 234794--234875 Score: 59
Period size: 10 Copynumber: 8.3 Consensus size: 10
234784 ACCAGCACCT
234794 CCATGCACGC
1 CCATGCACGC
234804 CCATGCACGC
1 CCATGCACGC
*
234814 CCAGGCACGC
1 CCATGCACGC
*
234824 CCA-ACGAC-C
1 CCATGC-ACGC
234833 TCCATG-AC-C
1 -CCATGCACGC
234842 TACCA-GCAC-C
1 --CCATGCACGC
234852 TCCATGCACGC
1 -CCATGCACGC
234863 CCATGCACGC
1 CCATGCACGC
234873 CCA
1 CCA
234876 ACGACCTCCA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
9 9 0.15
10 50 0.83
11 1 0.02
ACGTcount: A:0.23, C:0.50, G:0.17, T:0.10
Consensus pattern (10 bp):
CCATGCACGC
Found at i:235566 original size:21 final size:21
Alignment explanation
Indices: 235541--235584 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
235531 AATTTAGTTA
235541 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
235562 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
235583 AT
1 AT
235585 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:238751 original size:60 final size:59
Alignment explanation
Indices: 238679--239096 Score: 562
Period size: 60 Copynumber: 7.2 Consensus size: 59
238669 TTTATAAGAT
* *
238679 TTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTAATAGTAATTTGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAA--TGA
*
238740 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAA-TATTTAATGATTTGATAGTAATGA
*
238798 TTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTTAATGATTTGATATTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
238857 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
* *
238917 TTTACTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAA-TATTTAATGATTTGATAGTAATGA
*
238977 TTTAGTAATGATTAGTAATAATG-AATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
*
239036 TTAG---T-A--A-TAATAAT----TTATTATTAATATTTAATGATTTGATATTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
239084 TTTAGTAATGATT
1 -TTAGTAATGATT
239097 TGATAGTAAT
Statistics
Matches: 329, Mismatches: 14, Indels: 34
0.87 0.04 0.09
Matches are distributed among these distances:
48 32 0.10
49 4 0.01
51 7 0.02
52 2 0.01
53 1 0.00
54 1 0.00
55 1 0.00
58 12 0.04
59 85 0.26
60 177 0.54
61 7 0.02
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (59 bp):
TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
Found at i:238888 original size:119 final size:118
Alignment explanation
Indices: 238676--239096 Score: 602
Period size: 119 Copynumber: 3.6 Consensus size: 118
238666 GTATTTATAA
* *
238676 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTAATAGTAAT--TTG
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT-
238739 ATAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
65 -TAGTAATGATTAGTAATAATGAAATTATTATTAATT-T-TATGATTTGATAGTAAT
*
238796 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTTAATGATTTGATATTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
238860 AGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
66 AGTAATGATTAGTAATAATGAAATTATTATTAA-TTTT-ATGATTTGATAGTAAT
* *
238915 GATTTACTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAATGATT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAA-TATTTAATGATTTGATAGTAATGATT
*
238979 TAGTAATGATTAGTAATAATG-AATTATTATTAATTTT-T-A-ATGAT--T--T
65 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTATGATTTGATAGTAAT
* *
239025 GA--TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
239087 AGTAATGATT
66 AGTAATGATT
239097 TGATAGTAAT
Statistics
Matches: 283, Mismatches: 11, Indels: 27
0.88 0.03 0.08
Matches are distributed among these distances:
106 4 0.01
107 42 0.15
108 19 0.07
110 3 0.01
112 1 0.00
114 4 0.01
115 1 0.00
116 1 0.00
118 5 0.02
119 118 0.42
120 81 0.29
121 4 0.01
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (118 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
AGTAATGATTAGTAATAATGAAATTATTATTAATTTTATGATTTGATAGTAAT
Found at i:238976 original size:179 final size:170
Alignment explanation
Indices: 238676--239096 Score: 645
Period size: 179 Copynumber: 2.4 Consensus size: 170
238666 GTATTTATAA
* *
238676 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTAATAGTAAT--TTG
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT-
238739 ATAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTTAGT
65 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTTAGT
*
238804 AATGATTAGTAATAATGAAATTATTATTAATTTTAATGATTTGATATTAAT
129 AATGATTAGTAATAATG-AATTATTATTAATTTT--T-A-ATG--ATT--T
*
238855 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
*
238920 ACTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTTAGTAA
66 AGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTTAGTAA
238985 TGATTAGTAATAATGAATTATTATTAATTTTTAATGATTT
131 TGATTAGTAATAATGAATTATTATTAATTTTTAATGATTT
* *
239025 GA--TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
239087 AGTAATGATT
66 AGTAATGATT
239097 TGATAGTAAT
Statistics
Matches: 231, Mismatches: 9, Indels: 16
0.90 0.04 0.06
Matches are distributed among these distances:
167 46 0.20
168 20 0.09
170 3 0.01
172 3 0.01
174 2 0.01
175 1 0.00
176 1 0.00
178 16 0.07
179 137 0.59
181 2 0.01
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (170 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTT
AGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTTAGTAA
TGATTAGTAATAATGAATTATTATTAATTTTTAATGATTT
Found at i:239035 original size:48 final size:48
Alignment explanation
Indices: 238979--239092 Score: 185
Period size: 48 Copynumber: 2.4 Consensus size: 48
238969 AGTAATGATT
*
238979 TAGTAATGATTAGTAATAATGAA-TTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGA
239027 TAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGA
*
239075 TATTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
239093 GATTTGATAG
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
47 2 0.03
48 52 0.84
49 8 0.13
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.48
Consensus pattern (48 bp):
TAGTAATGATTAGTAATAATAATTTATTATTAATATTTAATGATTTGA
Found at i:239080 original size:14 final size:14
Alignment explanation
Indices: 239064--239111 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
239054 TATTAATATT
*
239064 TAATGATTTGATAT
1 TAATGATTTGATAG
239078 TAATGA-TT--TAG
1 TAATGATTTGATAG
239089 TAATGATTTGATAG
1 TAATGATTTGATAG
239103 TAATGATTT
1 TAATGATTT
239112 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:240130 original size:23 final size:21
Alignment explanation
Indices: 240104--240156 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
240094 ATACAAAAAC
*
240104 AATAAAATTTATTTAAATCAAAT
1 AATAAAATTAATTTAAAT--AAT
* *
240127 AATATAGTTAATTTAAATAAT
1 AATAAAATTAATTTAAATAAT
240148 AATTAAAAT
1 AA-TAAAAT
240157 AACAGATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 5 0.21
22 4 0.17
23 15 0.62
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AATAAAATTAATTTAAATAAT
Done.