Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001978.1 Hibiscus syriacus cultivar Beakdansim tig00004013_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: 2594977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:284841 original size:27 final size:26
Alignment explanation
Indices: 284766--284834 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
284756 ATATTGTAGT
**
284766 AACAATAAAATATTGT-AGCAATAATA
1 AACAATAAAATATCATCA-CAATAATA
* * *
284792 AACAATATAATTTCATCAAAATAATA
1 AACAATAAAATATCATCACAATAATA
284818 ATACAATAAAATATCAT
1 A-ACAATAAAATATCAT
284835 TCCAATATCA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
26 20 0.59
27 14 0.41
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (26 bp):
AACAATAAAATATCATCACAATAATA
Found at i:285255 original size:212 final size:214
Alignment explanation
Indices: 284873--285293 Score: 605
Period size: 212 Copynumber: 2.0 Consensus size: 214
284863 TTGTAGCAGA
* **
284873 AACATAACAGAAACACATCAAAATAAAATTAGAATAAAATTTGTAATCAAACTGAGTTAAATAAA
1 AACATAACAGAAAAACATCAAAATAAAATTAGAATAAAATTTGTAATCAAACAAAGTTAAATAAA
*
284938 CAAAATAATAATTTTTGTTGAGACTTAAATGAACAGTTTCCTTAAGACATATTCATCATCTCATC
66 CAAAAGAATAATTTTTGTTGAGACTTAAATGAACAGTTTCCTTAAGACATATTCATCATCTCATC
* * * * * *
285003 GATATTTTGAGTAGCGTTGGACGCTCGTCTCCCATGATACAACAAAAAACAATCACAATAGTAAG
131 GATACTTTGAGTAACATTGGACGCTAGTCTCCCATGATACAACAAAAAACAATCACAACAGTAAA
*
285068 TACAACAACAATGACTAGT
196 CACAACAACAATGACTAGT
* *
285087 AACATAATA-AAAAACATCAAAATAAAATTAGAATAAAATTTGTAATCAGACAAAGTTAAAT-AA
1 AACATAACAGAAAAACATCAAAATAAAATTAGAATAAAATTTGTAATCAAACAAAGTTAAATAAA
* * *
285150 CAAAAGAATAATTTTTGTTGAGACTTATATGAACAGTTTTCTTAAGACATATTCATCATCTC-CC
66 CAAAAGAATAATTTTTGTTGAGACTTAAATGAACAGTTTCCTTAAGACATATTCATCATCTCATC
* * * * * * *
285214 TGGTGCTTTGATTAACATTGGACGTTAGTCTCCCATGATACAACAACAAACGATCACAGCAGTAA
131 -GATACTTTGAGTAACATTGGACGCTAGTCTCCCATGATACAACAAAAAACAATCACAACAGTAA
285279 ACACAACAACAATGA
195 ACACAACAACAATGA
285294 ACAATTGAAT
Statistics
Matches: 183, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
211 1 0.01
212 126 0.69
213 48 0.26
214 8 0.04
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (214 bp):
AACATAACAGAAAAACATCAAAATAAAATTAGAATAAAATTTGTAATCAAACAAAGTTAAATAAA
CAAAAGAATAATTTTTGTTGAGACTTAAATGAACAGTTTCCTTAAGACATATTCATCATCTCATC
GATACTTTGAGTAACATTGGACGCTAGTCTCCCATGATACAACAAAAAACAATCACAACAGTAAA
CACAACAACAATGACTAGT
Found at i:285581 original size:36 final size:36
Alignment explanation
Indices: 285529--285603 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
285519 ATAATAAATA
*
285529 TATTTATCAAGTGGCA-TAACTTATTATTAACATATC
1 TATTCATCAAGTGGCATTAA-TTATTATTAACATATC
*
285565 TATTCATCAAGTGGCATTGATTATTATTAACATATC
1 TATTCATCAAGTGGCATTAATTATTATTAACATATC
285601 TAT
1 TAT
285604 CACAAATATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 34 0.94
37 2 0.06
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (36 bp):
TATTCATCAAGTGGCATTAATTATTATTAACATATC
Found at i:285849 original size:21 final size:21
Alignment explanation
Indices: 285804--285849 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
285794 AAAGAATGTT
* * **
285804 ATTAAAAGTAGGAAGAAGGTT
1 ATTAAAAATAGAAAGAAGGCC
285825 ATTAAAAATAGAAAGAAGGCC
1 ATTAAAAATAGAAAGAAGGCC
285846 ATTA
1 ATTA
285850 TTAATAATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.22
Consensus pattern (21 bp):
ATTAAAAATAGAAAGAAGGCC
Found at i:285853 original size:24 final size:21
Alignment explanation
Indices: 285794--285843 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
285784 GACTATTAAC
* *
285794 AAAGAATGTTATTAAAAGTAG
1 AAAGAAGGTTATTAAAAATAG
*
285815 GAAGAAGGTTATTAAAAATAG
1 AAAGAAGGTTATTAAAAATAG
285836 AAAGAAGG
1 AAAGAAGG
285844 CCATTATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (21 bp):
AAAGAAGGTTATTAAAAATAG
Found at i:286063 original size:23 final size:23
Alignment explanation
Indices: 286037--286086 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
286027 TCGTCAATTC
*
286037 GAGTTCCAAATAGGTATGGAATA
1 GAGTTCCAAATAGCTATGGAATA
*
286060 GAGTTTCAAATAGCTATGGAATA
1 GAGTTCCAAATAGCTATGGAATA
286083 GAGT
1 GAGT
286087 AGATTCTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (23 bp):
GAGTTCCAAATAGCTATGGAATA
Found at i:288633 original size:34 final size:35
Alignment explanation
Indices: 288579--288648 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 35
288569 CAGTTGATAT
* *
288579 TATTTTAGATTTAAATCTTATT-ATTTATATGATTA
1 TATTTTAGAATTAAAACTTATTAATTT-TATGATTA
*
288614 TATTTTA-AATTAAAACTTATTAATTTTATGTTTA
1 TATTTTAGAATTAAAACTTATTAATTTTATGATTA
288648 T
1 T
288649 CATCCACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 20 0.65
35 11 0.35
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (35 bp):
TATTTTAGAATTAAAACTTATTAATTTTATGATTA
Found at i:288719 original size:15 final size:16
Alignment explanation
Indices: 288695--288732 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
288685 AATTTAGTTA
*
288695 AATTATTATTATA-AT
1 AATTAATATTATATAT
288710 AATTAATATTATATAT
1 AATTAATATTATATAT
288726 ATATTAA
1 A-ATTAA
288733 AATAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 3 0.15
17 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTAATATTATATAT
Found at i:293166 original size:21 final size:21
Alignment explanation
Indices: 293142--293201 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
293132 ATATGTAATC
*
293142 CTTTGGAACATATATGTGGTT
1 CTTTGGAACATATATGTGGTA
293163 CTTTGAGACACATAT-T-TGGTA
1 CTTTG-GA-ACATATATGTGGTA
*
293184 CTTTGGAATATATATGTG
1 CTTTGGAACATATATGTG
293202 ATCCTTAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 5 0.15
20 3 0.09
21 16 0.48
22 3 0.09
23 6 0.18
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.42
Consensus pattern (21 bp):
CTTTGGAACATATATGTGGTA
Found at i:293239 original size:21 final size:22
Alignment explanation
Indices: 293213--293258 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
293203 TCCTTAAGTA
* *
293213 GTGGTCCTTCGGGACATA-TAT
1 GTGGTCATTCGGGACAAATTAT
293234 GTGGTCATTCGGGACAAATTAT
1 GTGGTCATTCGGGACAAATTAT
293256 GTG
1 GTG
293259 TGCCCCTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (22 bp):
GTGGTCATTCGGGACAAATTAT
Found at i:297380 original size:21 final size:21
Alignment explanation
Indices: 297289--297436 Score: 76
Period size: 21 Copynumber: 7.4 Consensus size: 21
297279 TCGAGGGTTT
* * *
297289 TATGTGGTCATTCGGGATATA
1 TATGTGGTCCTTCGGAACATA
** *
297310 TATGTAATCCTTTGGAACATA
1 TATGTGGTCCTTCGGAACATA
* * * *
297331 TATGCGGTTCTTCGGGACACA
1 TATGTGGTCCTTCGGAACATA
* * *
297352 TATTTGGTCCTTTGGAATATA
1 TATGTGGTCCTTCGGAACATA
*
297373 TATGTGGTCCTT----A-A-G
1 TATGTGGTCCTTCGGAACATA
* * *
297388 GA-GTGATCATTCGGAACATA
1 TATGTGGTCCTTCGGAACATA
* *
297408 TATGTGGTCCTTCGGGATATA
1 TATGTGGTCCTTCGGAACATA
297429 TATGTGGT
1 TATGTGGT
297437 ATGATATGAT
Statistics
Matches: 89, Mismatches: 31, Indels: 14
0.66 0.23 0.10
Matches are distributed among these distances:
14 7 0.08
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 1 0.01
20 1 0.01
21 76 0.85
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (21 bp):
TATGTGGTCCTTCGGAACATA
Found at i:303350 original size:17 final size:17
Alignment explanation
Indices: 303328--303380 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
303318 AATTAAGAGT
303328 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
303345 TAGTTTTATGAATGAAC
1 TAGTTTAATAAATGAAC
* * *
303362 AAGTTTATTTAATGAAC
1 TAGTTTAATAAATGAAC
303379 TA
1 TA
303381 ACATTATTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.40
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:303461 original size:36 final size:36
Alignment explanation
Indices: 303390--303473 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
303380 AACATTATTC
* *
303390 AATGAACT--ATATGCATAAATGAAGTAGCTTACTA
1 AATGAACTAAATATGCATAAATAAACTAGCTTACTA
* *
303424 AATGATCTAAATATGCATAAATAAACTA-CTTCCCTA
1 AATGAACTAAATATGCATAAATAAACTAGCTT-ACTA
*
303460 AATGAACTAGATAT
1 AATGAACTAAATAT
303474 TTTAAATGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
34 7 0.17
35 3 0.07
36 31 0.76
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (36 bp):
AATGAACTAAATATGCATAAATAAACTAGCTTACTA
Found at i:305647 original size:28 final size:26
Alignment explanation
Indices: 305609--305661 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 26
305599 TCCTCTTTAA
305609 AGTTTTTATTTTTTTATTATTTTTTT
1 AGTTTTTATTTTTTTATTATTTTTTT
*
305635 AGTTTTTCGATTTTTTTGTTATTTTTT
1 AGTTTTT--ATTTTTTTATTATTTTTT
305662 ACTAACCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 7 0.29
28 17 0.71
ACGTcount: A:0.13, C:0.02, G:0.08, T:0.77
Consensus pattern (26 bp):
AGTTTTTATTTTTTTATTATTTTTTT
Found at i:306997 original size:18 final size:17
Alignment explanation
Indices: 306959--307000 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
306949 TAGTTTGATG
*
306959 AATGAACAAGTTTAATT
1 AATGAACAACTTTAATT
306976 AATGAACAAACTTT-ATT
1 AATGAAC-AACTTTAATT
306993 CAATGAAC
1 -AATGAAC
307001 TAGATGCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (17 bp):
AATGAACAACTTTAATT
Found at i:311972 original size:12 final size:12
Alignment explanation
Indices: 311957--311981 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
311947 TTGACCTGGT
311957 CGTTAACCTTCC
1 CGTTAACCTTCC
311969 CGTTAACCTTCC
1 CGTTAACCTTCC
311981 C
1 C
311982 TTTGACTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.44, G:0.08, T:0.32
Consensus pattern (12 bp):
CGTTAACCTTCC
Found at i:320315 original size:698 final size:696
Alignment explanation
Indices: 318959--320406 Score: 2081
Period size: 698 Copynumber: 2.1 Consensus size: 696
318949 TTCCCTCTGG
* * * *
318959 AGTTGCATATCCTCTTTGGTCTCCCAAGTTGTTTCCTCTGTCCCATGGTTCCTCCATATGACCTT
1 AGTTGCATATCCTCTTTGATCTCCCAAGTTATTTCCTCAGTCCCATGGTTCCTCCACATGACCTT
* *
319024 TACTAACGAATTCTGCGTGTTCCTTAACTCTCTAACCTCTCGATATAAAATCCTTATCGGTTATT
66 CACTAACGAATTCTACGTGTTCCTTAACTCTCTAACCTCTCGATATAAAATCCTTATCGGTTATT
* *
319089 CTTCATAGGTCATATACTGCCTTACTTCAATCTGCTATATTAGAAAGACGAGGAAGGGTCGGAAT
131 CTTCATAGGTCATATACTGCCTTACTTCAATCTGCTATATCAGAAAGACGAGGAAGGGTCAGAAT
* * *
319154 GATACCTCATAAGCATCGATACGTAGAGCACATTATGGATGCCTTCATCTCATGTGGTAAGGCTA
196 GATACCTCATAAGCATCGATACGTAGAACACATTATGGATGCCTCCATCTCAGGTGGTAAGGCTA
** * * * * * *
319219 GTCGATAGTTTAGGGGTCCAAGCCTTTCAAGAATCTCATAAGGTCTAATGAAACATTGAACTAGC
261 GTCGATAGGCTACGGGTCCAAGCCTTTCAAGAATCTCACAAGATCTAATCAAACACTGAACTAAC
* *
319284 TTCCATTTCCTCTAAAACTAAATCACTCTTTTCCAAGGTGATACTTTTAGGAAAAACTTGTCACC
326 TTCCATTTCCTCCAAAACTAAATCACTCTTTTCCAAGGTGAGACTTTTAGGAAAAACTTGTCACC
*
319349 CACTTTAAATTCTATGTCCTTACGCTTCAAATCAAAATATGATTTCTGACGATTGATGGTTTCTT
391 CACTTTAAATTCTATGTCCTTACGCTTCAAATCAAAATATGATTTCTGACGATTGAAGGTTTCTT
* *
319414 GAGTCAATTTTGAATCAATCATACTTTGTCTTTTGTTTAATTTATAAGATTAGGACCAATTCATT
456 GAATCAATTTTGAATCAATCATACTTTGTCTTTTGTTTAATTGATAAGATTAGGACCAATTCATT
* * * * * *
319479 AAGCTCCATCCAACGCAAGGGTTTCCTTCACCTTCGACCGTACAACAACTCAAAATGAATTCCCT
521 AAGCTCCATCAAACACAAGGGTGTCCTTCACCTCCAACCGTAAAACAACTCAAAATGAATTCCCT
* * *
319544 CTCGAGTTTACCCAAAACTAGTAACCCGTAGTTTGGGTCGTTACAACTCTCCCTCCTCGTATGAA
586 CTCGAGTTTACCCAAAACTAGTAACCCGTAGTTTGGGCCGTTACAACTCTCCATCCTCGTAAGAA
* *
319609 ATTTCATCCTTAAAATTTTTCTAAGTATAAGATATGTCGAAACTGA
651 ATTTCATCCTTAAAATTTTCCTAAGTATAAGATATGGCGAAACTGA
* *
319655 AGTTGCATATCCTCCTTT-ATGTCCCAATTTATTTCCTCAGTCCCAT-GTTACCTCCACATGACC
1 AGTTGCATATCCT-CTTTGATCTCCCAAGTTATTTCCTCAGTCCCATGGTT-CCTCCACATGACC
* * ** *
319718 TTCACTAATGGAA-TCTACTTGTTCCTTAGGTCTCTAACCTCTCGATCTAAAATCCTTATCGGTT
64 TTCACTAA-CGAATTCTACGTGTTCCTTAACTCTCTAACCTCTCGATATAAAATCCTTATCGGTT
* * * * *
319782 ATTCTTCATAGGTCATAT-CTTGGCTTACTTTAATTTGCTCTATCAGAACA-ACGTGAGAAGGGT
128 ATTCTTCATAGGTCATATAC-TGCCTTACTTCAATCTGCTATATCAGAA-AGACGAG-GAAGGGT
*
319845 CAGAATGATACCTCATAAGCATCGATACGTAGAACGCATTATGGATGCACTCCATCTCAGGTGGT
190 CAGAATGATACCTCATAAGCATCGATACGTAGAACACATTATGGATGC-CTCCATCTCAGGTGGT
*
319910 AAGGCTAGTCCG-TAGGCTACGGGTCCAAGCCTTTCAAGAATCTCACAAGATCTAATCAAACGCT
254 AAGGCTAGT-CGATAGGCTACGGGTCCAAGCCTTTCAAGAATCTCACAAGATCTAATCAAACACT
*
319974 GAGCTAACTTCTC-TTTCCTCCAAAACTAAATCACTCTTTTCCAAGGTGAGACTTTTAGGAAAAA
318 GAACTAACTTC-CATTTCCTCCAAAACTAAATCACTCTTTTCCAAGGTGAGACTTTTAGGAAAAA
*
320038 CTTGTCACCCACTTTAAATTCTATGTCCTTACGCTTCAAATCAAAATATGTTTTCTGACGATTGA
382 CTTGTCACCCACTTTAAATTCTATGTCCTTACGCTTCAAATCAAAATATGATTTCTGACGATTGA
* * **
320103 AGGTTTCTTGTAAT-GATTTTGAATCAATCATACTTTTTCTTTTGTTTCGTTGATAAGATTAGGA
447 AGGTTTCTTG-AATCAATTTTGAATCAATCATACTTTGTCTTTTGTTTAATTGATAAGATTAGGA
* * * *
320167 CCAACTT-ATTGAGCTCCATCAAACACAAGGGTGTCCTTCACCTCCAATCGTAAAACAGCTCGAA
511 CCAA-TTCATTAAGCTCCATCAAACACAAGGGTGTCCTTCACCTCCAACCGTAAAACAACTCAAA
* ** *
320231 ATGAATTCCCTCTTGAGTTTACCTGAAACTAGTAACCCGTAGTTTGGGCCGTTACAACTCTATCA
575 ATGAATTCCCTCTCGAGTTTACCCAAAACTAGTAACCCGTAGTTTGGGCCGTTACAACTCT-CCA
*
320296 TCCTCGTAAGAAA-TTCATCCTTAAAATTTTCCTAAGTATAAGATATGGGGAAACTGA
639 TCCTCGTAAGAAATTTCATCCTTAAAATTTTCCTAAGTATAAGATATGGCGAAACTGA
* ** *
320353 AGTTGCATATCCTTTTTTTG-TCTCCCAAGTTGCTTCCTTAGTCCCATGGTTCCT
1 AGTTGCATATCC--TCTTTGATCTCCCAAGTTATTTCCTCAGTCCCATGGTTCCT
320407 GATAACTCTG
Statistics
Matches: 666, Mismatches: 70, Indels: 29
0.87 0.09 0.04
Matches are distributed among these distances:
695 4 0.01
696 146 0.22
697 60 0.09
698 404 0.61
699 48 0.07
700 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (696 bp):
AGTTGCATATCCTCTTTGATCTCCCAAGTTATTTCCTCAGTCCCATGGTTCCTCCACATGACCTT
CACTAACGAATTCTACGTGTTCCTTAACTCTCTAACCTCTCGATATAAAATCCTTATCGGTTATT
CTTCATAGGTCATATACTGCCTTACTTCAATCTGCTATATCAGAAAGACGAGGAAGGGTCAGAAT
GATACCTCATAAGCATCGATACGTAGAACACATTATGGATGCCTCCATCTCAGGTGGTAAGGCTA
GTCGATAGGCTACGGGTCCAAGCCTTTCAAGAATCTCACAAGATCTAATCAAACACTGAACTAAC
TTCCATTTCCTCCAAAACTAAATCACTCTTTTCCAAGGTGAGACTTTTAGGAAAAACTTGTCACC
CACTTTAAATTCTATGTCCTTACGCTTCAAATCAAAATATGATTTCTGACGATTGAAGGTTTCTT
GAATCAATTTTGAATCAATCATACTTTGTCTTTTGTTTAATTGATAAGATTAGGACCAATTCATT
AAGCTCCATCAAACACAAGGGTGTCCTTCACCTCCAACCGTAAAACAACTCAAAATGAATTCCCT
CTCGAGTTTACCCAAAACTAGTAACCCGTAGTTTGGGCCGTTACAACTCTCCATCCTCGTAAGAA
ATTTCATCCTTAAAATTTTCCTAAGTATAAGATATGGCGAAACTGA
Found at i:330058 original size:2 final size:2
Alignment explanation
Indices: 330051--330083 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
330041 TGTAAGAACG
330051 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
330084 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:348551 original size:14 final size:14
Alignment explanation
Indices: 348532--348572 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
348522 TAACAGATTC
348532 TTCTTTTTTTATTT
1 TTCTTTTTTTATTT
*
348546 TTC-TTTTCT-TTT
1 TTCTTTTTTTATTT
348558 TTCTTTTTTCTATTT
1 TTCTTTTTT-TATTT
348573 CTTTTCCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 6 0.27
13 9 0.41
14 4 0.18
15 3 0.14
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTTTTTATTT
Found at i:348554 original size:19 final size:20
Alignment explanation
Indices: 348532--348577 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
348522 TAACAGATTC
348532 TTCTTTTTT-TATTTTTCT-T
1 TTCTTTTTTCT-TTTTTCTAT
348551 TTCTTTTTTCTTTTTTCTAT
1 TTCTTTTTTCTTTTTTCTAT
348571 TTCTTTT
1 TTCTTTT
348578 CCTTTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (20 bp):
TTCTTTTTTCTTTTTTCTAT
Found at i:348582 original size:19 final size:19
Alignment explanation
Indices: 348543--348582 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
348533 TCTTTTTTTA
*
348543 TTTTTCTTTTCTTTTTTCT
1 TTTTTCTTTTCTTTTTCCT
348562 TTTTTCTATTTC-TTTTCCT
1 TTTTTCT-TTTCTTTTTCCT
348581 TT
1 TT
348583 CCTTTCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTCTTTTTCCT
Found at i:351934 original size:15 final size:15
Alignment explanation
Indices: 351910--351944 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
351900 TTTGGAAGAT
351910 AAATGAAATGATGGA
1 AAATGAAATGATGGA
* *
351925 AAATGGAATGATTGA
1 AAATGAAATGATGGA
351940 AAATG
1 AAATG
351945 CAAGCAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (15 bp):
AAATGAAATGATGGA
Found at i:357718 original size:2 final size:2
Alignment explanation
Indices: 357711--357741 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
357701 GATACATTAG
357711 AT AT AT 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 AT AT AT A
357742 GGAGTGACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:368974 original size:24 final size:24
Alignment explanation
Indices: 368947--369075 Score: 107
Period size: 24 Copynumber: 5.4 Consensus size: 24
368937 TATATCAAAA
* * *
368947 ATCAAAACATAATTCACGTCAAGT
1 ATCAAATCATAATCCAAGTCAAGT
* * *
368971 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAATCATAATCCAAGTCAAGT
*
368995 ATCAGATCATAATCCAAGTCAAGT
1 ATCAAATCATAATCCAAGTCAAGT
** * *
369019 ATCAGGTCAAAATCCATGTC-AGAT
1 ATCAAATCATAATCCAAGTCAAG-T
* * *
369043 ATCAGATCAGAATCCATGTCAAGT
1 ATCAAATCATAATCCAAGTCAAGT
*
369067 ATCAGATCA
1 ATCAAATCA
369076 GAATTCAAAT
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.02
24 86 0.96
25 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (24 bp):
ATCAAATCATAATCCAAGTCAAGT
Found at i:369079 original size:24 final size:24
Alignment explanation
Indices: 368964--369075 Score: 154
Period size: 24 Copynumber: 4.7 Consensus size: 24
368954 CATAATTCAC
* *
368964 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAAAATCCAT
* *
368988 GTCAAGTATCAGATCATAATCCAA
1 GTCAAGTATCAGATCAAAATCCAT
*
369012 GTCAAGTATCAGGTCAAAATCCAT
1 GTCAAGTATCAGATCAAAATCCAT
*
369036 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAAAATCCAT
369060 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
369076 GAATTCAAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 2 0.03
24 74 0.95
25 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAAAATCCAT
Found at i:369095 original size:48 final size:48
Alignment explanation
Indices: 368964--369097 Score: 128
Period size: 48 Copynumber: 2.8 Consensus size: 48
368954 CATAATTCAC
* ** * *
368964 GTCAAGTATCATATCAAAATCCAGGTCA-AGTATCAGATCATAATCCAA
1 GTCAAGTATCAGATCAAAATCCAAATCAGA-AATCAGATCAGAATCCAA
* ** * *
369012 GTCAAGTATCAGGTCAAAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAAAATCCAAATCAGAAATCAGATCAGAATCCAA
* *
369060 GTCAAGTATCAGATCAGAATTCAAATC-GAAAATCAGAT
1 GTCAAGTATCAGATCAAAATCCAAATCAG-AAATCAGAT
369098 AAAATATTCA
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
47 1 0.01
48 71 0.97
49 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAAAATCCAAATCAGAAATCAGATCAGAATCCAA
Found at i:376541 original size:31 final size:32
Alignment explanation
Indices: 376480--376544 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 32
376470 CCAACCTAAA
*
376480 GGAGTACCTTGGAGCCTTAGAGCCTACCCAAG
1 GGAGTACCTTGGAGCCTAAGAGCCTACCCAAG
* *
376512 GGAGTACCTTTG-GCCTAAGAGTCTACCCAAG
1 GGAGTACCTTGGAGCCTAAGAGCCTACCCAAG
376543 GG
1 GG
376545 TCACATTAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.25, C:0.26, G:0.29, T:0.20
Consensus pattern (32 bp):
GGAGTACCTTGGAGCCTAAGAGCCTACCCAAG
Found at i:377391 original size:20 final size:20
Alignment explanation
Indices: 377362--377399 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
377352 TCAATGGGTT
*
377362 AGACATGTTTGAGTTGACTC
1 AGACAAGTTTGAGTTGACTC
377382 AGACAAGTTTGAGTTGAC
1 AGACAAGTTTGAGTTGAC
377400 ACAATTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (20 bp):
AGACAAGTTTGAGTTGACTC
Found at i:390381 original size:36 final size:36
Alignment explanation
Indices: 390334--390428 Score: 163
Period size: 36 Copynumber: 2.6 Consensus size: 36
390324 CATCAAACAA
390334 AGATAAGTCAGAAACATTAAAAGATACAACAAAAGG
1 AGATAAGTCAGAAACATTAAAAGATACAACAAAAGG
* *
390370 GGATAAGTCAGAAACATTAAAAGATACATCAAAAGG
1 AGATAAGTCAGAAACATTAAAAGATACAACAAAAGG
*
390406 AGATAAGTCATAAACATTAAAAG
1 AGATAAGTCAGAAACATTAAAAG
390429 TGTACTCACG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.56, C:0.11, G:0.17, T:0.17
Consensus pattern (36 bp):
AGATAAGTCAGAAACATTAAAAGATACAACAAAAGG
Found at i:392317 original size:59 final size:59
Alignment explanation
Indices: 392225--392341 Score: 162
Period size: 59 Copynumber: 2.0 Consensus size: 59
392215 CCATGAATGA
* * *
392225 AAACTATATAAATGATAAGAGATAAGGATCAACTCTATTACTTGGTACGCCAAGATAAG
1 AAACTATATAAATGATAAGACATAAAGATCAACTCTATTACTTAGTACGCCAAGATAAG
* * * * *
392284 AAACTATCTAAATGATAAGACCTAAAGCTCAACTCTGTTACTTAGTACGCCACGATAA
1 AAACTATATAAATGATAAGACATAAAGATCAACTCTATTACTTAGTACGCCAAGATAA
392342 AATTCGTATG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.26
Consensus pattern (59 bp):
AAACTATATAAATGATAAGACATAAAGATCAACTCTATTACTTAGTACGCCAAGATAAG
Found at i:393617 original size:74 final size:75
Alignment explanation
Indices: 393534--393699 Score: 199
Period size: 81 Copynumber: 2.1 Consensus size: 75
393524 GTAAGTAATG
* * * * *
393534 TAAAAACTTGACTCCTTTTTAGGTTGCAACTTGATTTATC-AAACCTAATTTTAGTTGCGACCTA
1 TAAAAACTTGACTCATTTTTAGGTTGCAACCTAATTTATCAAAACCTAATTTTAGTTGCAAACTA
393598 AATTATTGTA
66 AATTATTGTA
* *
393608 TAAAAACTTGATTCATTTTTAGGTTGCAACCTAATTTATCAATGAAGAAACCTATTTTTAGTTGC
1 TAAAAACTTGACTCATTTTTAGGTTGCAACCTAATTTATC-----A-AAACCTAATTTTAGTTGC
393673 AAACTAAATTATTGTA
60 AAACTAAATTATTGTA
*
393689 TATAAACTTGA
1 TAAAAACTTGA
393700 TTCCATTTAT
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
74 36 0.47
81 41 0.53
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (75 bp):
TAAAAACTTGACTCATTTTTAGGTTGCAACCTAATTTATCAAAACCTAATTTTAGTTGCAAACTA
AATTATTGTA
Found at i:393640 original size:43 final size:42
Alignment explanation
Indices: 393582--393707 Score: 111
Period size: 43 Copynumber: 3.0 Consensus size: 42
393572 TCAAACCTAA
*
393582 TTTTAGTTGCGACCTAAATTATTGTATAAAAACTTGATTCAT
1 TTTTAGTTGCAACCTAAATTATTGTATAAAAACTTGATTCAT
* ** *
393624 TTTTAGGTTGCAACCTAATTTA-TCAATGAAGAAAC----CT-AT
1 TTTTA-GTTGCAACCTAAATTATTGTAT-AA-AAACTTGATTCAT
* *
393663 TTTTAGTTGCAAACTAAATTATTGTATATAAACTTGATTCCAT
1 TTTTAGTTGCAACCTAAATTATTGTATAAAAACTTGATT-CAT
393706 TT
1 TT
393708 ATTTGTAACT
Statistics
Matches: 63, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
37 4 0.06
38 15 0.24
39 10 0.16
40 1 0.02
41 1 0.02
42 8 0.13
43 20 0.32
44 4 0.06
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (42 bp):
TTTTAGTTGCAACCTAAATTATTGTATAAAAACTTGATTCAT
Found at i:394327 original size:81 final size:80
Alignment explanation
Indices: 394197--394392 Score: 245
Period size: 81 Copynumber: 2.5 Consensus size: 80
394187 TTAATTCATG
* * * * *
394197 TAGAAAATTAACTCCTTTTTAGGTT-CAACCTGATTTATCAATTTAGAAACATGTTTTTAGTTGC
1 TAGAAACTTAATTCC-TTTTAGGTTGCAACCTGATTTAGCAATTAAGAAACATGGTTTTAGTTGC
394261 AACATAAATTATTGTA
65 AACATAAATTATTGTA
** *
394277 TAGAAACTTGTTTCCATTTTAGGTTGCAACCTAATTTAGCAA-TAAGGAAACATGGTTTTAGTTG
1 TAGAAACTTAATTCC-TTTTAGGTTGCAACCTGATTTAGCAATTAA-GAAACATGGTTTTAGTTG
* *
394341 CAACCTAAATTATTTTA
64 CAACATAAATTATTGTA
*
394358 TAGAAACTTAATTCCTTTTA-TTTGCAACCTGATTT
1 TAGAAACTTAATTCCTTTTAGGTTGCAACCTGATTT
394393 TTTTCTTATA
Statistics
Matches: 99, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
79 13 0.13
80 27 0.27
81 59 0.60
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (80 bp):
TAGAAACTTAATTCCTTTTAGGTTGCAACCTGATTTAGCAATTAAGAAACATGGTTTTAGTTGCA
ACATAAATTATTGTA
Found at i:397699 original size:17 final size:17
Alignment explanation
Indices: 397652--397701 Score: 73
Period size: 18 Copynumber: 2.9 Consensus size: 17
397642 CTCAATTTAT
*
397652 TTTTTTAATTAAAATTA
1 TTTTTTATTTAAAATTA
*
397669 TTTATTATTTTAAAATTA
1 TTTTTTA-TTTAAAATTA
397687 TTTTTTATTTAAAAT
1 TTTTTTATTTAAAAT
397702 GACAATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTTATTTAAAATTA
Found at i:399117 original size:21 final size:21
Alignment explanation
Indices: 399091--399131 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
399081 TACCAAGGAC
*
399091 GAGAAGACCATTCGTAAAGAT
1 GAGAAGACCATTCATAAAGAT
399112 GAGAAGACCATTCATAAAGA
1 GAGAAGACCATTCATAAAGA
399132 CATGAAGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (21 bp):
GAGAAGACCATTCATAAAGAT
Found at i:399138 original size:21 final size:21
Alignment explanation
Indices: 399092--399142 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
399082 ACCAAGGACG
* *
399092 AGAAGACCATTCGTAAAGATG
1 AGAAGACCATTCATAAAGATC
399113 AGAAGACCATTCATAAAGA-C
1 AGAAGACCATTCATAAAGATC
399133 ATGAAGACCA
1 A-GAAGACCA
399143 CTTTGCATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (21 bp):
AGAAGACCATTCATAAAGATC
Found at i:405322 original size:36 final size:36
Alignment explanation
Indices: 405280--405364 Score: 120
Period size: 36 Copynumber: 2.3 Consensus size: 36
405270 GGGCAAGTCA
405280 ATCTTAAGCCTTCACT-GAAGAGTAGTGAAGCAAAC-C
1 ATCTTAAGCCTTCACTAG-AG-GTAGTGAAGCAAACTC
*
405316 ATCTTAAGCCTTCACTAGAGGTAGTGAAGTAAACTC
1 ATCTTAAGCCTTCACTAGAGGTAGTGAAGCAAACTC
405352 ATCTATAAGCCTT
1 ATCT-TAAGCCTT
405365 TAGGTCAAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
35 13 0.29
36 23 0.51
37 9 0.20
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (36 bp):
ATCTTAAGCCTTCACTAGAGGTAGTGAAGCAAACTC
Found at i:406012 original size:214 final size:211
Alignment explanation
Indices: 405733--406201 Score: 684
Period size: 215 Copynumber: 2.2 Consensus size: 211
405723 CGGGCCATCA
* *
405733 GGTCATCTGTAAGCCTTTTGAGC-A-ATGACAAGTC-TTGCGAGCCATCCATAAAACCTTCGGGT
1 GGTCATCTGTAAGCCTTTTGAGCAAGATGATAAGTCTTTG-G-GCCATCCATAAAACCTTCAGGT
405795 AGGATGTTTTCACATGAATTTGAAAATG-AAAAAGTGATGTTTTAAGAAGATGGAATTTTTGAAA
64 AGGATGTTTTCACATGAATTTGAAAATGAAAAAAGTGATGTTTTAAGAAGATGGAATTTTTGAAA
* * *
405859 ATGAAGAAT-ACGATTTTCAAAATTTTACAATTTATAAGTCCTTCGGGCTATTAGTAAGTCTTTC
129 ATGAAGAATGA-GATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGC---CACTAAGTCTTT-
* *
405923 GAGCATGATGCTTAAA-CTCTTCG
189 GAGCATGATGATGAAATC-CTTCG
*
405946 GGTCATCTGTAAGCCTTTTGAGCAAGATGATAAATCTTTGGGCCATCCATAAAACCTTCAGGTAG
1 GGTCATCTGTAAGCCTTTTGAGCAAGATGATAAGTCTTTGGGCCATCCATAAAACCTTCAGGTAG
*
406011 GATTTTTTCACATGAATTTGAAAATGAAAAAAGTGATGTTTTAAGAAGATGGAATTTTTGAAAAT
66 GATGTTTTCACATGAATTTGAAAATGAAAAAAGTGATGTTTTAAGAAGATGGAATTTTTGAAAAT
*
406076 GAAGAATGAGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCACTAAGTCTTTGTGCATG
131 GAAGAATGAGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCACTAAGTCTTTGAGCATG
406141 ATGATGAAATCCTTCG
196 ATGATGAAATCCTTCG
* * *
406157 GGTCA--TGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGGGCCAT
1 GGTCATCTGTAAGCCTTTTGAGCAAGATGATAAGT-CTTTGGGCCAT
406202 TTAACCTCCT
Statistics
Matches: 235, Mismatches: 14, Indels: 17
0.88 0.05 0.06
Matches are distributed among these distances:
209 25 0.11
210 10 0.04
211 23 0.10
212 11 0.05
213 23 0.10
214 49 0.21
215 90 0.38
216 4 0.02
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.33
Consensus pattern (211 bp):
GGTCATCTGTAAGCCTTTTGAGCAAGATGATAAGTCTTTGGGCCATCCATAAAACCTTCAGGTAG
GATGTTTTCACATGAATTTGAAAATGAAAAAAGTGATGTTTTAAGAAGATGGAATTTTTGAAAAT
GAAGAATGAGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCACTAAGTCTTTGAGCATG
ATGATGAAATCCTTCG
Found at i:406172 original size:39 final size:38
Alignment explanation
Indices: 406107--406200 Score: 109
Period size: 39 Copynumber: 2.4 Consensus size: 38
406097 TTCACAATTT
* * *
406107 ATAAGTCCTTCGGGCCACTAAGTCTTT-GTGCATGATG
1 ATAAATCCTTCGGGCCACTAAGTCTTTAGAGCAAGATG
* *
406144 ATGAAATCCTTCGGGTCATGTAAGTCTTTAGAGCAAGATG
1 AT-AAATCCTTCGGGCCA-CTAAGTCTTTAGAGCAAGATG
*
406184 ATAAGTCCTTCGGGCCA
1 ATAAATCCTTCGGGCCA
406201 TTTAACCTCC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 2 0.04
38 13 0.28
39 22 0.47
40 10 0.21
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (38 bp):
ATAAATCCTTCGGGCCACTAAGTCTTTAGAGCAAGATG
Found at i:406310 original size:55 final size:55
Alignment explanation
Indices: 406207--406339 Score: 162
Period size: 55 Copynumber: 2.4 Consensus size: 55
406197 GCCATTTAAC
* * * * *
406207 CTCCTTGAAAGGAATAGGGACCGAACCCATTTCAGAAGATTTCTTGAGTTCTATA
1 CTCCATGAAAGGAATAGGGAGCAAACCCATTTAAGAAAATTTCTTGAGTTCTATA
* *
406262 CTCTC-TGAAAGGAATATGGAGCAAACCCGTTTTAAGAAAATTTC-TGAGTTCTATA
1 CTC-CATGAAAGGAATAGGGAGCAAACCC-ATTTAAGAAAATTTCTTGAGTTCTATA
*
406317 CTCCATGAAAGGAACAGGGAGCA
1 CTCCATGAAAGGAATAGGGAGCA
406340 CGTTTGCTGA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
54 1 0.01
55 53 0.79
56 13 0.19
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (55 bp):
CTCCATGAAAGGAATAGGGAGCAAACCCATTTAAGAAAATTTCTTGAGTTCTATA
Found at i:408560 original size:17 final size:17
Alignment explanation
Indices: 408533--408578 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
408523 AATTTGTTGG
*
408533 TTTAATTAAAATTAA-T
1 TTTATTTAAAATTAATT
408549 TTTATTTTAAAATTAATT
1 TTTA-TTTAAAATTAATT
408567 TTTATTTAAAAT
1 TTTATTTAAAAT
408579 GATAATGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 4 0.15
17 18 0.67
18 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTATTTAAAATTAATT
Found at i:411783 original size:34 final size:35
Alignment explanation
Indices: 411722--411789 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
411712 AGTATATTGC
*
411722 TTCATTCCATAAAGCTTGTTCACTAATTAAACTAG
1 TTCATTCCATAAAGCTAGTTCACTAATTAAACTAG
*
411757 TTCATT-CATTAAA-CTAGTTCATTAATTAAACTA
1 TTCATTCCA-TAAAGCTAGTTCACTAATTAAACTA
411790 TATCATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 20 0.67
35 10 0.33
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.40
Consensus pattern (35 bp):
TTCATTCCATAAAGCTAGTTCACTAATTAAACTAG
Found at i:411796 original size:17 final size:17
Alignment explanation
Indices: 411739--411789 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
411729 CATAAAGCTT
*
411739 GTTCACTAATTAAACTA
1 GTTCATTAATTAAACTA
*
411756 GTTCATTCATTAAACTA
1 GTTCATTAATTAAACTA
411773 GTTCATTAATTAAACTA
1 GTTCATTAATTAAACTA
411790 TATCATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (17 bp):
GTTCATTAATTAAACTA
Found at i:418563 original size:45 final size:45
Alignment explanation
Indices: 418510--418918 Score: 471
Period size: 45 Copynumber: 9.0 Consensus size: 45
418500 TATACCATTT
* * * *
418510 TTTCATGCCAATAATGCACCAATATGTATTTCAATTATGGCATCT
1 TTTCATGCCGATAATGCACCCATATGTATTTCATTTATGGCATCC
* * * *
418555 TTTTATGCCGATAATGCACCCTTATGTATTTCCTTTATGGAATCC
1 TTTCATGCCGATAATGCACCCATATGTATTTCATTTATGGCATCC
*
418600 TTTCATGCCGATAATGCACCCATATGCATTTCATTTATGGCATCC
1 TTTCATGCCGATAATGCACCCATATGTATTTCATTTATGGCATCC
** *
418645 TTTCATGCCGATAATGCACCCATATCCATTTTC-TTTATGGCATCA
1 TTTCATGCCGATAATGCACCCATATGTA-TTTCATTTATGGCATCC
* * * *
418690 TTTCATGCAGATAATGCACCTATATGTATTTCATTAATGGAATCC
1 TTTCATGCCGATAATGCACCCATATGTATTTCATTTATGGCATCC
* * * * * *
418735 TTTCATGACAATAATGCACTCGTATGCATATTTCATTAATGGTATCC
1 TTTCATGCCGATAATGCACCCATATG--TATTTCATTTATGGCATCC
* *** * *
418782 TTTCATGACGATAATGCACTTGTATGCATTTCATTTATGGAATCC
1 TTTCATGCCGATAATGCACCCATATGTATTTCATTTATGGCATCC
418827 TTTCATGCCGATAATGCACCCATAT-TCATTTCATTTATGGCATCC
1 TTTCATGCCGATAATGCACCCATATGT-ATTTCATTTATGGCATCC
* * * * *
418872 TTTCATGCTGATAATACACCTATATGCATTTCATTTATGTCATCC
1 TTTCATGCCGATAATGCACCCATATGTATTTCATTTATGGCATCC
418917 TT
1 TT
418919 CTATGCCTTT
Statistics
Matches: 313, Mismatches: 45, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
44 4 0.01
45 263 0.84
46 4 0.01
47 42 0.13
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (45 bp):
TTTCATGCCGATAATGCACCCATATGTATTTCATTTATGGCATCC
Found at i:418820 original size:182 final size:179
Alignment explanation
Indices: 418510--418906 Score: 537
Period size: 182 Copynumber: 2.2 Consensus size: 179
418500 TATACCATTT
* * * * * *
418510 TTTCATGCCA-ATAATGCACCAATATGTATTTCAATTATGGCATCTTTTTATGCCGATAATGCAC
1 TTTCATG-CAGATAATGCACCTATATGTATTTC-ATTATGGAATCCTTTCATGACAATAATGCAC
* * * *
418574 CCTTATGTATTTCCTTTATGGAATCCTTTCATGCCGATAATGCACCCATATGCATTTCATTTATG
64 CCGTATGTATTTCATTAATGGAATCCTTTCATGACGATAATGCACCCATATGCATTTCATTTATG
*
418639 GCATCCTTTCATGCCGATAATGCACCCATATCCATTTTC-TTTATGGCATCA
129 GAATCCTTTCATGCCGATAATGCACCCATATCCA-TTTCATTTATGGCATCA
*
418690 TTTCATGCAGATAATGCACCTATATGTATTTCATTAATGGAATCCTTTCATGACAATAATGCACT
1 TTTCATGCAGATAATGCACCTATATGTATTTCATT-ATGGAATCCTTTCATGACAATAATGCACC
* ***
418755 CGTATGCATATTTCATTAATGGTATCCTTTCATGACGATAATGCACTTGTATGCATTTCATTTAT
65 CGTATG--TATTTCATTAATGGAATCCTTTCATGACGATAATGCACCCATATGCATTTCATTTAT
* *
418820 GGAATCCTTTCATGCCGATAATGCACCCATATTCATTTCATTTATGGCATCC
128 GGAATCCTTTCATGCCGATAATGCACCCATATCCATTTCATTTATGGCATCA
* * *
418872 TTTCATGCTGATAATACACCTATATGCATTTCATT
1 TTTCATGCAGATAATGCACCTATATGTATTTCATT
418907 TATGTCATCC
Statistics
Matches: 191, Mismatches: 21, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
179 5 0.03
180 56 0.29
181 4 0.02
182 126 0.66
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (179 bp):
TTTCATGCAGATAATGCACCTATATGTATTTCATTATGGAATCCTTTCATGACAATAATGCACCC
GTATGTATTTCATTAATGGAATCCTTTCATGACGATAATGCACCCATATGCATTTCATTTATGGA
ATCCTTTCATGCCGATAATGCACCCATATCCATTTCATTTATGGCATCA
Found at i:419108 original size:68 final size:68
Alignment explanation
Indices: 419000--419325 Score: 334
Period size: 68 Copynumber: 4.8 Consensus size: 68
418990 TTATGGCATT
** ** * * *
419000 CTTTCATCTAACTGAAACGATTGATACCTTTC-ATTCAAATGCATAGCTAGGCCACAAAGGCACA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTA-TCAAATGCACAGCTAGGCCACAAAGGCACT
*
419064 TAGT
65 TAGC
* * * * * *
419068 CTTTCATCTAACTGGCATTATTGACACCTTTCTGTCAAATGCACAGCTAGGACTCAAAGGAACCT
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAGCTAGGCCACAAAGGCACTT
*
419133 AAC
66 AGC
* * * * *
419136 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAACTGCACA-CCATGG-CATCAGAGGTAC
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAGCTA-GGCCA-CAAAGGCAC
419199 TTAGC
64 TTAGC
* * * * *
419204 CTTTCATCTAACTGACATAATTGACACATTTCTATAAAATGCATAGCTAGGCCTCAAAGGCACTT
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAGCTAGGCCACAAAGGCACTT
*
419269 GGC
66 AGC
* * * *
419272 CTTTTATCTAACTGGCATAGTTGACACCTTTCTATCAAATGCACAACGAGGCCA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAGCTAGGCCA
419326 TTAATCTGTT
Statistics
Matches: 212, Mismatches: 41, Indels: 10
0.81 0.16 0.04
Matches are distributed among these distances:
67 3 0.01
68 206 0.97
69 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (68 bp):
CTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAGCTAGGCCACAAAGGCACTT
AGC
Found at i:419573 original size:57 final size:57
Alignment explanation
Indices: 419530--419805 Score: 410
Period size: 57 Copynumber: 4.8 Consensus size: 57
419520 TAAAGTTATT
* * * *
419530 ATACAAAAATTCATAAACAAATTATTAATTTCTTAACTTTTTGCACCCGAAGTGCCC
1 ATACGAAAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCC
*
419587 ATACTG-AAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACACAAAGTTCCC
1 ATAC-GAAAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCC
* *
419644 ATACGGAAATTCATAAACAAATTATAAATTTCTTAACTTTTTACACACAAAGTGCCC
1 ATACGAAAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * * *
419701 ATTCGAAAATTCATAAACAAATTATAAATTTATTAACTTTTAGTACACAAAGTGCCC
1 ATACGAAAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCC
* * *
419758 ATACGAAAATTCATAAACAAATTATGAATTTCCTAACTTTTTGTACAC
1 ATACGAAAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACAC
419806 TTAGTACCAT
Statistics
Matches: 199, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
56 1 0.01
57 198 0.99
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (57 bp):
ATACGAAAATTCATAAACAAATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCC
Found at i:422070 original size:2 final size:2
Alignment explanation
Indices: 422063--422093 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
422053 CCACAAAAGC
422063 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
422094 CTGACATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:423902 original size:45 final size:45
Alignment explanation
Indices: 423817--424489 Score: 827
Period size: 45 Copynumber: 15.0 Consensus size: 45
423807 CTTCATACTT
* * ** * *
423817 ATAATGCA-CCATTCTGCATTTTCATTTATGCCATTTTTTCATCCCA
1 ATAATGCACCCA-TATGCA-TTTCATTTATGGCATCCTTTCATGCCG
* **
423863 ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATATCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* * * * * *
423908 ATAATGCACGCATATTCATGTC-TTATATGGCAACTTTTCATACCG
1 ATAATGCACCCATATGCATTTCATT-TATGGCATCCTTTCATGCCG
* * *
423953 ATAATGTTA-TCATATGCATTTCATTTATGGCATCATTTCATGCCG
1 ATAATG-CACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* *
423998 ATAATGCATCCATATGTATTTCATTTATGGCATCCTTTCATGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* *
424043 ATTATGCACCCATATGCATTTCATTTATGGTATCCTTTCATGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
424088 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* * * *
424133 ATAATGCACCCATACGCATTTCATTTATCGAATCCTTTCATGCAG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* * * *
424178 ATAATGCACCCATTTGCATTTCATTTATGGTATCCTATCACGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
*
424223 ATAATGCACCCATATTCATTTCATTTATGGCATCCTTTCATGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* * *
424268 ATAATGCACCCATATTCATTTCATTTATGGCATCATTTCATGTCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* ** *
424313 ATAATGCACCAATATGGTTTTCATTTATGGCATCCTTTCATGCCT
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* *
424358 ATAATGCACCCACATTCATTTCA-TT-TGGCATCCTTTCATGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* *
424401 ATAATGCACCCATATGCATTACATTTATGGCATCCTTTCATGCCT
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
* * * * * *
424446 TTAATACA-CTACTATACATTTCATTTATAGCACCCTTTCATGCC
1 ATAATGCACCCA-TATGCATTTCATTTATGGCATCCTTTCATGCC
424490 TTTTACACAC
Statistics
Matches: 545, Mismatches: 74, Indels: 17
0.86 0.12 0.03
Matches are distributed among these distances:
43 37 0.07
44 8 0.01
45 481 0.88
46 16 0.03
47 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
Found at i:424615 original size:68 final size:68
Alignment explanation
Indices: 424532--424849 Score: 406
Period size: 68 Copynumber: 4.7 Consensus size: 68
424522 ATCCTTTAAA
* * * *
424532 CTAATTGGCATAATTGACACCTCTT-TGTCAAATACACAGCTAGGCCTCAAAGGCAGTTTGTCTT
1 CTAACTGGCATAATTGACACCT-TTCTGTCAAATGCACAGCTAGGCCTCAAAGGCAGTTAGCCTT
*
424596 TAAT
65 TCAT
* * * * * * *
424600 ATATCTGGCATAATTGACACCTTTTTGTTAAATGCATAACTAGGCCTCGAAGGCACG-TAGCCTT
1 CTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCA-GTTAGCCTT
424664 TCAT
65 TCAT
* * *
424668 CTAACAGGTATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCAATTAGCCTTT
1 CTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCAGTTAGCCTTT
424733 CAT
66 CAT
* * **
424736 CTAACTGGCATAATTGTCACCTTTCTGTCAAATGCATAGCTAGGCCTCAAAGGCACCTAGCCTTT
1 CTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCAGTTAGCCTTT
424801 CAT
66 CAT
* * *
424804 CTAACTGGCATAATTGACACATTTCTTTCAAATGCACAACTAGGCC
1 CTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCC
424850 ATTAATCTTT
Statistics
Matches: 215, Mismatches: 32, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
67 2 0.01
68 212 0.99
69 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (68 bp):
CTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCAGTTAGCCTTT
CAT
Found at i:425098 original size:57 final size:57
Alignment explanation
Indices: 425014--425263 Score: 342
Period size: 57 Copynumber: 4.4 Consensus size: 57
425004 CCAATAAAGT
* * * **
425014 AATTCATATAATTTCTT-AGTTTTTGCACATAAAGTTCTTATACGGAAATTCATAAACA
1 AATT-ATA-AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACA
* * *
425072 AATTATGAATTTCTTAACTTTTTGCACCCAAAGTGCCCATACAGAAATTCATAAACA
1 AATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACA
425129 AATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACA
1 AATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACA
* *
425186 AATTATAAATTTCTTAACTTTTTGCACACAATA-TGCCCATATGGAAATTTATAAACA
1 AATTATAAATTTCTTAACTTTTTGCACACAA-AGTGCCCATACGGAAATTCATAAACA
** *
425243 AATTATGGATTTCCTAACTTT
1 AATTATAAATTTCTTAACTTT
425264 ATGTACACTC
Statistics
Matches: 174, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
56 8 0.05
57 161 0.93
58 5 0.03
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.36
Consensus pattern (57 bp):
AATTATAAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACA
Found at i:428686 original size:22 final size:22
Alignment explanation
Indices: 428643--428697 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
428633 GTGGAACCAA
*
428643 GAAGGTAACTG-ACACTAGCTG
1 GAAGGTAGCTGAACACTAGCTG
*
428664 GAAGGTAGCTGAACAGTAGCTG
1 GAAGGTAGCTGAACACTAGCTG
*
428686 GATGGTAGCTGA
1 GAAGGTAGCTGA
428698 GGACTCAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.31, C:0.15, G:0.35, T:0.20
Consensus pattern (22 bp):
GAAGGTAGCTGAACACTAGCTG
Found at i:446858 original size:25 final size:26
Alignment explanation
Indices: 446783--446861 Score: 133
Period size: 26 Copynumber: 3.1 Consensus size: 26
446773 ACTGAAGTGC
* *
446783 TAATACAAATAAGGTCGTGTCCACCA
1 TAATACACATAAGGTCGTGCCCACCA
446809 TAATACACATAAGGTCGTGCCCACCA
1 TAATACACATAAGGTCGTGCCCACCA
446835 TAATACACATAAGG-CGTGCCCACCA
1 TAATACACATAAGGTCGTGCCCACCA
446860 TA
1 TA
446862 TGCACTTAGT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 13 0.25
26 38 0.75
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (26 bp):
TAATACACATAAGGTCGTGCCCACCA
Found at i:470934 original size:10 final size:11
Alignment explanation
Indices: 470919--470947 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
470909 TTCAGATTAT
470919 TTTCAATTTA-
1 TTTCAATTTAG
470929 TTTCAATTTAG
1 TTTCAATTTAG
470940 TTTCAATT
1 TTTCAATT
470948 CATTCTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.59
Consensus pattern (11 bp):
TTTCAATTTAG
Found at i:471954 original size:424 final size:424
Alignment explanation
Indices: 471080--472347 Score: 1861
Period size: 424 Copynumber: 3.0 Consensus size: 424
471070 AAAAATACTA
* * * * * * *
471080 ATGTGACCCTACTTCTACACCTTCTACTTTTCATCTTTCTATCTTCAAGTTTGGAACTCATCATG
1 ATGTGATCCTACTTCTACACCTACTATTTTTCATCTTTCTTTCTTCAAATGTGGAACTCATCAAG
** * *
471145 GATAAGGGAGC-TTTCACTATCTTCTTATTAAATTTC-TT--GTATTTTCATCCACATAACATCA
66 GACCAGGGA-CTTTTCACTATCTTCTTCTTAAATTTCTTTAAGTATTTTCATCAACATAACATCA
* * * * * *
471206 ACTCATATTGTGCTTTGCACCAATATTTTTACATGTTCAACATGTTGTTAGAATACTTCCATTTT
130 ACTCATATTATGCTTTGCACCCATGTTTTCACATGTTAAACATGTTGTTAGAATACTTCCATTTC
* * * * *
471271 AGATTCTTACCCATCATAATTCATCTTATTACATACTTAGTTGAATTCATAACTCTTTTACTTTA
195 AGATTCATGCCCATTATAATTCATCTTAGTACATACTTAGTTGAATTCATAACTCTTATACTTTA
* * *
471336 TATGTTGATATATAGAGACTAACATACTTTACTTAGCATATAACATGCATTTCATATCTTTACAT
260 TATATTGATATATAGAG--TAACATACTTTACTTAGCATATAACATGCATTTCACATCTTTACTT
471401 AGTCTATTTTATGATTGTGCATCATATCTTAGCTCATGTCATTCATACACATTGTATCCTAGCTC
323 AGTCTATTTTATGATTGTGCATCATATCTTAGCTCATGTCATTCATACACATTGTATCCTAGCTC
471466 ATCTTATGTATTTGAAGTTACTACTAGCTCATACCTG
388 ATCTTATGTATTTGAAGTTACTACTAGCTCATACCTG
* * *
471503 ATGTGATCCTACTTCTACACCTACTATTTTTTATCTTGCTTTCTTCAAATGTGAAACTCATCAAG
1 ATGTGATCCTACTTCTACACCTACTATTTTTCATCTTTCTTTCTTCAAATGTGGAACTCATCAAG
* * *
471568 GACCAGGGACTTTTCATTATTTTCTTCTTAAATTTCTTTAAGTATTTTCATCAACATAACATTAA
66 GACCAGGGACTTTTCACTATCTTCTTCTTAAATTTCTTTAAGTATTTTCATCAACATAACATCAA
* * * *
471633 CTCATATTTTTCTATT-CACCCATGCTTTGACATGTTAAACATGTTGTTAGAATACTTCCATTTC
131 CTCATATTATGCT-TTGCACCCATGTTTTCACATGTTAAACATGTTGTTAGAATACTTCCATTTC
*
471697 AGATTCATGCCCATTATAATTCATCTTAGTACATACTTAGTTGAATTTATAACTCTTATACTTTA
195 AGATTCATGCCCATTATAATTCATCTTAGTACATACTTAGTTGAATTCATAACTCTTATACTTTA
471762 TATATTGATATATAGAGTAACATACTTTACTTAGCATATAACATGCATTTCACATCTTTACTTAG
260 TATATTGATATATAGAGTAACATACTTTACTTAGCATATAACATGCATTTCACATCTTTACTTAG
* * *
471827 TATATTTTATGATTGTCCATCATATCTTAGCCCATGTCATTCATACACATTGTATCCTAGCTCAT
325 TCTATTTTATGATTGTGCATCATATCTTAGCTCATGTCATTCATACACATTGTATCCTAGCTCAT
* * *
471892 CTTATGTATTTCAGGTTACTAATAGCTCATACCTG
390 CTTATGTATTTGAAGTTACTACTAGCTCATACCTG
*
471927 ATGTGATCCTACTTCTACACCTACTATTTTTCATCTTTCTTTCTTCAAATGTGGAACTCATAAAG
1 ATGTGATCCTACTTCTACACCTACTATTTTTCATCTTTCTTTCTTCAAATGTGGAACTCATCAAG
* *
471992 GACCAGGGA-TTTTAACTATCTTCTTCTTAAATTTCTTTAAATATTTTCATCAACATAACATCAA
66 GACCAGGGACTTTTCACTATCTTCTTCTTAAATTTCTTTAAGTATTTTCATCAACATAACATCAA
* * *
472056 CTCATATTATGCTTTGCACCCATGTTTTCACATGTTAAACA---TGTTAGATTACTTCCATGTGA
131 CTCATATTATGCTTTGCACCCATGTTTTCACATGTTAAACATGTTGTTAGAATACTTCCATTTCA
* *
472118 GATTCATGCCCATTATAATTCATCTTCGTACATATTTAGTTGAATTCATAACTCTTATACTTTAT
196 GATTCATGCCCATTATAATTCATCTTAGTACATACTTAGTTGAATTCATAACTCTTATACTTTAT
* * * * *
472183 ATATTAATATATGGAGAGTATCATACTTTACTTAGCATATAGCATGCATTTCACATATTTACTCA
261 ATATTGATATAT--AGAGTAACATACTTTACTTAGCATATAACATGCATTTCACATCTTTACTTA
* * * *
472248 GTCTATTTTATGATTGTGCATCATATATTAGCTCATATCATTCATACACATTGTATCATAGTTCA
324 GTCTATTTTATGATTGTGCATCATATCTTAGCTCATGTCATTCATACACATTGTATCCTAGCTCA
* * *
472313 TATTATGTATTTGAAGTCATTACTAGCTCATACCT
389 TCTTATGTATTTGAAGTTACTACTAGCTCATACCT
472348 AGTCAATAAC
Statistics
Matches: 760, Mismatches: 77, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
420 91 0.12
422 137 0.18
423 168 0.22
424 212 0.28
426 150 0.20
427 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.42
Consensus pattern (424 bp):
ATGTGATCCTACTTCTACACCTACTATTTTTCATCTTTCTTTCTTCAAATGTGGAACTCATCAAG
GACCAGGGACTTTTCACTATCTTCTTCTTAAATTTCTTTAAGTATTTTCATCAACATAACATCAA
CTCATATTATGCTTTGCACCCATGTTTTCACATGTTAAACATGTTGTTAGAATACTTCCATTTCA
GATTCATGCCCATTATAATTCATCTTAGTACATACTTAGTTGAATTCATAACTCTTATACTTTAT
ATATTGATATATAGAGTAACATACTTTACTTAGCATATAACATGCATTTCACATCTTTACTTAGT
CTATTTTATGATTGTGCATCATATCTTAGCTCATGTCATTCATACACATTGTATCCTAGCTCATC
TTATGTATTTGAAGTTACTACTAGCTCATACCTG
Found at i:484048 original size:132 final size:132
Alignment explanation
Indices: 483827--484078 Score: 486
Period size: 132 Copynumber: 1.9 Consensus size: 132
483817 CCAAATATTT
483827 ATATTTATATTTATGTTTATGTTAAGTTATTGCATGTATACTTTATGTTATTCATTTTCGCATAT
1 ATATTTATATTTATGTTTATGTTAAGTTATTGCATGTATACTTTATGTTATTCATTTTCGCATAT
483892 AAGTTAGATTGCATTTGCATTCATTCTTTAGACGTGCATCTTACTTAACATATGTTATATGATCC
66 AAGTTAGATTGCATTTGCATTCATTCTTTAGACGTGCATCTTACTTAACATATGTTATATGATCC
483957 AA
131 AA
**
483959 ATATTTATATTTATGTTTATGTTAAGTTATTGTTTGTATACTTTATGTTATTCATTTTCGCATAT
1 ATATTTATATTTATGTTTATGTTAAGTTATTGCATGTATACTTTATGTTATTCATTTTCGCATAT
484024 AAGTTAGATTGCATTTGCATTCATTCTTTAGACGTGCATCTTACTTAACATATGT
66 AAGTTAGATTGCATTTGCATTCATTCTTTAGACGTGCATCTTACTTAACATATGT
484079 AATAAAATTT
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 118 1.00
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (132 bp):
ATATTTATATTTATGTTTATGTTAAGTTATTGCATGTATACTTTATGTTATTCATTTTCGCATAT
AAGTTAGATTGCATTTGCATTCATTCTTTAGACGTGCATCTTACTTAACATATGTTATATGATCC
AA
Found at i:490648 original size:23 final size:25
Alignment explanation
Indices: 490621--490672 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
490611 ATTTTTATAC
490621 AAAACAATT-T-AATATTATTTTAA
1 AAAACAATTATGAATATTATTTTAA
* * *
490644 AAAACAGTTATGACTTTTATTTTAA
1 AAAACAATTATGAATATTATTTTAA
490669 AAAA
1 AAAA
490673 TTGGTGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.33
24 1 0.04
25 15 0.62
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (25 bp):
AAAACAATTATGAATATTATTTTAA
Found at i:491517 original size:59 final size:60
Alignment explanation
Indices: 491394--491566 Score: 143
Period size: 59 Copynumber: 2.9 Consensus size: 60
491384 TACAAGGACC
* ** * * * * * *
491394 AAAATGGGAAAAACATTAACTTAAAGGGCCAAAATAGTACAAACAGGAATTTAGAGGACT
1 AAAATGGAAAAAACAAAAACTTAAAGGGCCAAAACAATAAAAACAGAAATTTAAAGAACT
* * *
491454 AAAATGGAAAAAACAAAAACTTAAA-GGCTAAAACAATAAAAACTGAAATTTAAAGAATT
1 AAAATGGAAAAAACAAAAACTTAAAGGGCCAAAACAATAAAAACAGAAATTTAAAGAACT
* * * * * * * * *
491513 AAAATGG-CAAAATAGAAATTTAAAGGGCCAATATAGTAAAAATAGAAACTTAAA
1 AAAATGGAAAAAACAAAAACTTAAAGGGCCAAAACAATAAAAACAGAAATTTAAA
491567 TGTCTAAATA
Statistics
Matches: 89, Mismatches: 23, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
58 13 0.15
59 54 0.61
60 22 0.25
ACGTcount: A:0.57, C:0.09, G:0.15, T:0.19
Consensus pattern (60 bp):
AAAATGGAAAAAACAAAAACTTAAAGGGCCAAAACAATAAAAACAGAAATTTAAAGAACT
Found at i:491557 original size:30 final size:29
Alignment explanation
Indices: 491521--491634 Score: 122
Period size: 30 Copynumber: 3.9 Consensus size: 29
491511 TTAAAATGGC
* * *
491521 AAAATAGAAATTTAAAGGGCCAATATAGTA
1 AAAATAGAAACTTAAAGGACTAA-ATAGTA
* *
491551 AAAATAGAAACTTAAATGTCTAAATAGTA
1 AAAATAGAAACTTAAAGGACTAAATAGTA
* * *
491580 AATACAGACAA-TTAAAGGACTAAAATAGCA
1 AAAATAGA-AACTTAAAGGACT-AAATAGTA
491610 AAAATAGAAACTTAAAGGACTAAAT
1 AAAATAGAAACTTAAAGGACTAAAT
491635 TTGTAAATAC
Statistics
Matches: 70, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
29 26 0.37
30 44 0.63
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (29 bp):
AAAATAGAAACTTAAAGGACTAAATAGTA
Found at i:491595 original size:59 final size:60
Alignment explanation
Indices: 491532--491645 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 60
491522 AAATAGAAAT
* * * * *
491532 TTAAAGGGCCAATATAGTAAAAATAGAAACTTAAATGTCTAAA-TAGTAAATACAGACAA
1 TTAAAGGACCAAAATAGCAAAAATAGAAACTTAAAGGACTAAATTAGTAAATACAGACAA
* *
491591 TTAAAGGACTAAAATAGCAAAAATAGAAACTTAAAGGACTAAATTTGTAAATACA
1 TTAAAGGACCAAAATAGCAAAAATAGAAACTTAAAGGACTAAATTAGTAAATACA
491646 AAAAAAAACA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 37 0.79
60 10 0.21
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.24
Consensus pattern (60 bp):
TTAAAGGACCAAAATAGCAAAAATAGAAACTTAAAGGACTAAATTAGTAAATACAGACAA
Found at i:492427 original size:17 final size:17
Alignment explanation
Indices: 492405--492438 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
492395 TTCTTTTTCC
492405 TTTGGTTATCTCTCTCT
1 TTTGGTTATCTCTCTCT
492422 TTTGGTTATCTCTCTCT
1 TTTGGTTATCTCTCTCT
492439 CTAATCCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.12, T:0.59
Consensus pattern (17 bp):
TTTGGTTATCTCTCTCT
Found at i:493516 original size:26 final size:26
Alignment explanation
Indices: 493487--493542 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
493477 CTGAGCTCGA
*
493487 CTCGACTCGAAAACTCTGAAATGGAG
1 CTCGACTCGAAAACTCTGAAATGAAG
493513 CTCGACTCGAAAACTCTGAAATGAAG
1 CTCGACTCGAAAACTCTGAAATGAAG
493539 CTCG
1 CTCG
493543 TGAGCAACTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (26 bp):
CTCGACTCGAAAACTCTGAAATGAAG
Found at i:494605 original size:2 final size:2
Alignment explanation
Indices: 494598--494624 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
494588 TGTTGGCTGC
494598 AT 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 AT A
494625 CACTGTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:494830 original size:2 final size:2
Alignment explanation
Indices: 494823--494850 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
494813 TAATTTATGG
494823 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
494851 GTAAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:495702 original size:19 final size:19
Alignment explanation
Indices: 495678--495724 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
495668 AAAGGCCAAT
495678 GGAGCAGATGAGAACGTGA
1 GGAGCAGATGAGAACGTGA
495697 GGAGCAGATGAGAACGTGA
1 GGAGCAGATGAGAACGTGA
495716 GGAGCAGAT
1 GGAGCAGAT
495725 TTATCTCGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.43, T:0.11
Consensus pattern (19 bp):
GGAGCAGATGAGAACGTGA
Found at i:507421 original size:53 final size:53
Alignment explanation
Indices: 507332--507588 Score: 397
Period size: 53 Copynumber: 4.8 Consensus size: 53
507322 AGAATTCTAC
* * *
507332 CAGAAAATTGTTCGAGTTCTACTCCCTGAAGAAAGAGGGAGCGAACCTGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
** * *
507385 TGGAAGATTGTTCAAGTTCTACTCCCTGAAGTAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
507438 CAGAAGATTGTCCGAGTTCTACTCCCTGAAGCAAGAGGGAGGGAACCCATAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
507491 CAGAAGATTGTTTGAGTTCTACACCCTGAAGCAAGAGGGAGTGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
507544 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAA
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAA
507589 TGCACTGAAG
Statistics
Matches: 183, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 183 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:508914 original size:19 final size:19
Alignment explanation
Indices: 508890--508939 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
508880 TATTTATTTC
508890 ATTTGTTTGTTTCTTTGCA
1 ATTTGTTTGTTTCTTTGCA
*
508909 ATTTGTTTGTTGCTTTGCA
1 ATTTGTTTGTTTCTTTGCA
508928 ATTTGTTTGTTT
1 ATTTGTTTGTTT
508940 GTCTTTAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.10, C:0.08, G:0.18, T:0.64
Consensus pattern (19 bp):
ATTTGTTTGTTTCTTTGCA
Found at i:508917 original size:23 final size:21
Alignment explanation
Indices: 508890--508945 Score: 84
Period size: 19 Copynumber: 2.9 Consensus size: 21
508880 TATTTATTTC
508890 ATTTGTTTG-TT-TCTTTGCA
1 ATTTGTTTGTTTGTCTTTGCA
508909 ATTTGTTTG-TTG-CTTTGCA
1 ATTTGTTTGTTTGTCTTTGCA
508928 ATTTGTTTGTTTGTCTTT
1 ATTTGTTTGTTTGTCTTT
508946 AACATTTGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 27 0.79
20 3 0.09
21 4 0.12
ACGTcount: A:0.09, C:0.09, G:0.18, T:0.64
Consensus pattern (21 bp):
ATTTGTTTGTTTGTCTTTGCA
Found at i:510847 original size:131 final size:129
Alignment explanation
Indices: 510444--510849 Score: 508
Period size: 130 Copynumber: 3.1 Consensus size: 129
510434 AAGAGTTTTG
* ** *
510444 GCCATCTTTAGGAAGGGCAATAACATGGTTCCTACGCGATGAGGACGACTGGTTATCTAGGGGGT
1 GCCATCTTTAGG-AGTG--ATAACACAGTTCCTACGTGATGAGGACG-CTGGTTATCTA-GGGGT
* * *
510509 GACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGCGATGAGGAT
61 GATACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGCGATGAGGAC
**
510574 GGGA
126 GACA
* * *
510578 GACCATCTTTAGGAATGATAACACAGTTCCTACATGATGAGGACGATCGGTTATC-AGGGGTGAT
1 G-CCATCTTTAGGAGTGATAACACAGTTCCTACGTGATGAGGACGCT-GGTTATCTAGGGGTGAT
* * * *
510642 ACGACTCCTACGTGATGAGGAGGTCTGGTCAGGGGCTGACACGGTTCCTACGCGATGAGGACAAC
64 ACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGCGATGAGGACGAC
510707 AA
129 -A
* * *
510709 GCAATCTTTAGGAGTGATAACACAGTTCCTACGTGATAAGGACAGCTGGTTATCTAGGGTTGATA
1 GCCATCTTTAGGAGTGATAACACAGTTCCTACGTGATGAGGAC-GCTGGTTATCTAGGGGTGATA
* * * *
510774 CGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGAAACGGTTTCTACTCGATGAGGACGATA
65 CGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGCGATGAGGACGACA
510839 TGCCATCTTTA
1 -GCCATCTTTA
510850 AGGATAATGT
Statistics
Matches: 235, Mismatches: 31, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
130 110 0.47
131 80 0.34
132 31 0.13
134 3 0.01
135 11 0.05
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (129 bp):
GCCATCTTTAGGAGTGATAACACAGTTCCTACGTGATGAGGACGCTGGTTATCTAGGGGTGATAC
GGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGCGATGAGGACGACA
Found at i:510963 original size:34 final size:34
Alignment explanation
Indices: 510924--511029 Score: 173
Period size: 34 Copynumber: 3.2 Consensus size: 34
510914 ACCAAATTCA
510924 TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
1 TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
510958 TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
1 TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
*
510992 TTTCAAGGGAAACTGACACAAAGAT--G-GTTTTG
1 TTTCAAGGGAAA-TGACTCAAAGATAGGTGTTTTG
511024 TTTCAA
1 TTTCAA
511030 AAAAAACATA
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
32 12 0.17
33 1 0.01
34 46 0.66
35 11 0.16
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (34 bp):
TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
Found at i:511136 original size:67 final size:66
Alignment explanation
Indices: 511042--511241 Score: 245
Period size: 67 Copynumber: 3.1 Consensus size: 66
511032 AAAACATACC
511042 CAAAGATTTTGTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAAATTTGTTTTC-AGAGAAATA
1 CAAAGATTTT-TTT-TCAAAAGAAATTGTCTCAAGAGAGACAAAAATTTG-TTTCAAGAGAAATA
511106 GACT
63 GACT
* * * *
511110 CAAATATTTTTTTATCAAAATAAATTGTCTCAAGAGAGACAAAACTTTGTTTCTAGAGAAACT-G
1 CAAAGATTTTTTT-TCAAAAGAAATTGTCTCAAGAGAGACAAAAATTTGTTTCAAGAGAAA-TAG
511174 ACT
64 ACT
* *
511177 CAAAGATTTTTTTT--AAAGAAACTGTCTC--GAGAGAC-AAAATTTGTTTCAAGAGAAACA-AC
1 CAAAGATTTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAAATTTGTTTCAAGAGAAATAGAC
511236 T
66 T
511237 CAAAG
1 CAAAG
511242 GATACTGATA
Statistics
Matches: 119, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
60 8 0.07
61 18 0.15
62 7 0.06
64 12 0.10
66 5 0.04
67 59 0.50
68 10 0.08
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (66 bp):
CAAAGATTTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAAATTTGTTTCAAGAGAAATAGAC
T
Found at i:511361 original size:32 final size:32
Alignment explanation
Indices: 511312--511380 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
511302 TCACATCAGG
* *
511312 ATGTTGAATCCCAAAAGATACTCCAATATTCA
1 ATGTTGAATCCCAAAAGATACCCCAACATTCA
* *
511344 ATGTTGAATCTCC-AAAGATGCCCCAACATTCG
1 ATGTTGAATC-CCAAAAGATACCCCAACATTCA
511376 ATGTT
1 ATGTT
511381 TCTTGCTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (32 bp):
ATGTTGAATCCCAAAAGATACCCCAACATTCA
Found at i:517067 original size:59 final size:59
Alignment explanation
Indices: 516962--517086 Score: 136
Period size: 59 Copynumber: 2.1 Consensus size: 59
516952 TACAAATAGG
516962 AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCTAAAACAATAAAAACCA-A
1 AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCTAAAACAAT-AAAACCATA
* *
517021 AATTTAAA-GAATTAAAATGGCAAAACA-A-AAA-TATAAAGGGGC-AAAACAGTAACACCATA
1 AATTTAAAGGAA-TAAAATGGCAAAA-ATAGAAACT-TAAA--GGCTAAAACAATAAAACCATA
517080 AATTTAA
1 AATTTAA
517087 GGGTCTAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
57 1 0.02
58 16 0.28
59 37 0.64
60 4 0.07
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.18
Consensus pattern (59 bp):
AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCTAAAACAATAAAACCATA
Found at i:517115 original size:29 final size:30
Alignment explanation
Indices: 517083--517166 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
517073 CACCATAAAT
*
517083 TTAAGGGTCT-AAATAGAAAATACAGACAA-
1 TTAAGGGACTAAAATAGAAAATACAGA-AAC
*
517112 TTAAAGGACTAAAATAGAAAA-ACTAGAAAC
1 TTAAGGGACTAAAATAGAAAATAC-AGAAAC
*
517142 ATAAGGGACTAAAATAGAAAATACA
1 TTAAGGGACTAAAATAGAAAATACA
517167 AAAAAATAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 12 0.26
30 33 0.70
31 2 0.04
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.18
Consensus pattern (30 bp):
TTAAGGGACTAAAATAGAAAATACAGAAAC
Found at i:519489 original size:59 final size:59
Alignment explanation
Indices: 519384--519508 Score: 143
Period size: 59 Copynumber: 2.1 Consensus size: 59
519374 TACAAAATGG
*
519384 AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCTAAAACAATAAAAACCA-A
1 AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCCAAAACAAT-AAAACCATA
* *
519443 AATTTAAA-GAATTAAAATGGCAAAACA-A-AAA-TATAAAGGGCCAAAACAGTAACACCATA
1 AATTTAAAGGAA-TAAAATGGCAAAA-ATAGAAACT-TAAA-GGCCAAAACAATAAAACCATA
519502 AATTTAA
1 AATTTAA
519509 GGGTCTAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
57 1 0.02
58 16 0.28
59 40 0.69
60 1 0.02
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.18
Consensus pattern (59 bp):
AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCCAAAACAATAAAACCATA
Found at i:519537 original size:29 final size:30
Alignment explanation
Indices: 519505--519588 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
519495 CACCATAAAT
*
519505 TTAAGGGTCT-AAATAGAAAATACAGACAA-
1 TTAAGGGACTAAAATAGAAAATACAGA-AAC
*
519534 TTAAAGGACTAAAATAGAAAA-ACTAGAAAC
1 TTAAGGGACTAAAATAGAAAATAC-AGAAAC
*
519564 ATAAGGGACTAAAATAGAAAATACA
1 TTAAGGGACTAAAATAGAAAATACA
519589 AATAAAATAG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 12 0.26
30 33 0.70
31 2 0.04
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.18
Consensus pattern (30 bp):
TTAAGGGACTAAAATAGAAAATACAGAAAC
Found at i:519810 original size:24 final size:28
Alignment explanation
Indices: 519783--519842 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
519773 CATCAAACAT
519783 AAATAAAAT-A-T-AAACTAAAGACT-G
1 AAATAAAATCATTAAAACTAAAGACTCG
* *
519807 AAATGAAATCATTGAAAACTAAAGGCTCG
1 AAATAAAATCATT-AAAACTAAAGACTCG
519836 AAATAAA
1 AAATAAA
519843 TCAACAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 8 0.29
25 1 0.04
26 1 0.04
28 11 0.39
29 7 0.25
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.20
Consensus pattern (28 bp):
AAATAAAATCATTAAAACTAAAGACTCG
Found at i:522008 original size:19 final size:21
Alignment explanation
Indices: 521970--522017 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
521960 TAAAGAAAAA
521970 TATAATATTGTATATATATTT
1 TATAATATTGTATATATATTT
*
521991 TATAATTTTG-AT-TATATTT
1 TATAATATTGTATATATATTT
*
522010 GAT-ATATT
1 TATAATATT
522018 AAATAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 9 0.38
20 2 0.08
21 9 0.38
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (21 bp):
TATAATATTGTATATATATTT
Found at i:522015 original size:21 final size:22
Alignment explanation
Indices: 521969--522015 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
521959 ATAAAGAAAA
521969 ATATAATATTGTATATATATTT
1 ATATAATATTGTATATATATTT
*
521991 -TATAATTTTG-AT-TATATTT
1 ATATAATATTGTATATATATTT
522010 GATATA
1 -ATATA
522016 TTAAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 7 0.32
20 2 0.09
21 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (22 bp):
ATATAATATTGTATATATATTT
Found at i:522574 original size:31 final size:30
Alignment explanation
Indices: 522539--522604 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
522529 TGATTACATC
* *
522539 AAAAAAAAGTTAGGTACCTAACTGTACCAT
1 AAAAAAAAGTTAGGCACCTAAATGTACCAT
*
522569 AAAAAAACGTTAGGCACCTAAATGTACCAT
1 AAAAAAAAGTTAGGCACCTAAATGTACCAT
*
522599 TAAAAA
1 AAAAAA
522605 TTAGATACCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (30 bp):
AAAAAAAAGTTAGGCACCTAAATGTACCAT
Found at i:522616 original size:27 final size:29
Alignment explanation
Indices: 522540--522616 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
522530 GATTACATCA
*
522540 AAAAAAAGTTAGGTACCTAACTGTACCAT
1 AAAAAAAGTTAGGTACCTAAATGTACCAT
*
522569 AAAAAAACGTTAGGCACCTAAATGTACCAT
1 AAAAAAA-GTTAGGTACCTAAATGTACCAT
* *
522599 -TAAAAA-TTAGATACCTAA
1 AAAAAAAGTTAGGTACCTAA
522617 TTACAACAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 10 0.24
29 12 0.29
30 20 0.48
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (29 bp):
AAAAAAAGTTAGGTACCTAAATGTACCAT
Found at i:523916 original size:17 final size:18
Alignment explanation
Indices: 523886--523922 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
523876 AGATAATATC
523886 TTTTTAAAATAATATAAT
1 TTTTTAAAATAATATAAT
*
523904 TTTTTATAA-AATATAAT
1 TTTTTAAAATAATATAAT
523921 TT
1 TT
523923 AATTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTTAAAATAATATAAT
Found at i:524874 original size:36 final size:36
Alignment explanation
Indices: 524795--524879 Score: 84
Period size: 36 Copynumber: 2.4 Consensus size: 36
524785 ATTATAATCT
*
524795 TTATATTATAA-AACTTAATTATAATCATTAAATTAA
1 TTATATTA-AATAACTTAATTATAAACATTAAATTAA
* * * *
524831 TTTTATTAAATAACTTATTTATTAAACATT-ATTTTA
1 TTATATTAAATAACTTAATTA-TAAACATTAAATTAA
*
524867 TTATATTATATAA
1 TTATATTAAATAA
524880 AATTAATTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
35 2 0.05
36 31 0.77
37 7 0.17
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.51
Consensus pattern (36 bp):
TTATATTAAATAACTTAATTATAAACATTAAATTAA
Found at i:524875 original size:23 final size:22
Alignment explanation
Indices: 524845--524898 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
524835 ATTAAATAAC
*
524845 TTATTTAT-TAAACATTATTTTA
1 TTATTTATATAAA-ATTAATTTA
524867 TTATATTATATAAAATTAATTTAA
1 TTAT-TTATATAAAATTAATTT-A
*
524891 ATATTTAT
1 TTATTTAT
524899 GAGTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 4 0.15
23 15 0.56
24 8 0.30
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATTTATATAAAATTAATTTA
Found at i:527970 original size:14 final size:15
Alignment explanation
Indices: 527944--527975 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
527934 AAATAATTAA
527944 AATAATATAATTTAT
1 AATAATATAATTTAT
527959 AATAATAT-ATTTAT
1 AATAATATAATTTAT
527973 AAT
1 AAT
527976 TATTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAATATAATTTAT
Found at i:528064 original size:21 final size:21
Alignment explanation
Indices: 527950--528055 Score: 75
Period size: 21 Copynumber: 5.2 Consensus size: 21
527940 TTAAAATAAT
527950 ATAATTTATAATAATATA-TTT-
1 ATAA-TTA-AATAATATATTTTA
** * *
527971 ATAATTATTTATTATATTTAA
1 ATAATTAAATAATATATTTTA
*
527992 ACAATTAAATTAATATATTTT-
1 ATAATTAAA-TAATATATTTTA
528013 ATATATT---T-ATA-ATTTTA
1 ATA-ATTAAATAATATATTTTA
528030 ATAATTAAATAATATATTTTA
1 ATAATTAAATAATATATTTTA
528051 ATAAT
1 ATAAT
528056 ATTAAAATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
16 8 0.12
17 6 0.09
18 1 0.02
19 7 0.11
20 8 0.12
21 23 0.35
22 12 0.18
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (21 bp):
ATAATTAAATAATATATTTTA
Found at i:529589 original size:20 final size:19
Alignment explanation
Indices: 529566--529619 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
529556 AATAAAGTAT
529566 TATTACTTTATATAATT-TAA
1 TATTA-TTTATAT-ATTATAA
529586 TATTTATTTATATATTATAA
1 TA-TTATTTATATATTATAA
529606 TATT-TTTATA-ATTA
1 TATTATTTATATATTA
529620 GGTACATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.12
18 6 0.19
19 5 0.16
20 14 0.44
21 3 0.09
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTATTTATATATTATAA
Found at i:545712 original size:27 final size:27
Alignment explanation
Indices: 545674--545728 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
545664 CATGTCTATG
545674 TATGCAACTACTTAATTGAAAACCTCT
1 TATGCAACTACTTAATTGAAAACCTCT
* *
545701 TATGCAACTACTTGATTGAAAACTTCT
1 TATGCAACTACTTAATTGAAAACCTCT
545728 T
1 T
545729 TCTCCTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (27 bp):
TATGCAACTACTTAATTGAAAACCTCT
Found at i:552406 original size:19 final size:19
Alignment explanation
Indices: 552357--552409 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
552347 TTAATTCAAG
*
552357 CATTGACTTTGACCAAGAT
1 CATTGACTTTGACCAAGAC
* *
552376 CGTTGACCTTGACCAAGAC
1 CATTGACTTTGACCAAGAC
*
552395 CATTAACTTTGACCA
1 CATTGACTTTGACCA
552410 GAGTTGACTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (19 bp):
CATTGACTTTGACCAAGAC
Found at i:572899 original size:20 final size:20
Alignment explanation
Indices: 572874--572919 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
572864 AACTAAATTC
*
572874 TTTCATCCCTTAATGCATCA
1 TTTCATCCCTTAATGAATCA
* *
572894 TTTCATGCCTTAATGAATCC
1 TTTCATCCCTTAATGAATCA
572914 TTTCAT
1 TTTCAT
572920 ACTAACGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.26, G:0.07, T:0.43
Consensus pattern (20 bp):
TTTCATCCCTTAATGAATCA
Found at i:573370 original size:68 final size:68
Alignment explanation
Indices: 573129--573626 Score: 767
Period size: 68 Copynumber: 7.4 Consensus size: 68
573119 GCATAATTGG
* * *
573129 ACCTTTATGTCAATTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTT-ATCTAACTAGCATAAAT
1 ACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAAAT
573193 GAC
66 GAC
* *
573196 ACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAACCTTTCATCTAACTGGCATACAT
1 ACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAAAT
573261 GA-
66 GAC
*
573263 ACCTTTCTTTCATTTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAAAT
1 ACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAAAT
573328 GAC
66 GAC
* *
573331 ACATTTCTGTCATTTGCACAGTTAGGCCTTAAAGACACTTAGCCTTTCATCTAACTGGCATAAAT
1 ACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAAAT
573396 GAC
66 GAC
* * *
573399 ACCTTTCTGTCATTTGCACACTTAGGCCTTAAAGGCACCTAACCTTTCATCTAACTGGCATAAAT
1 ACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAAAT
573464 GAC
66 GAC
* * *
573467 ACATTTCTGTCA-TTGCACACTTAGGCCTTAAAGGCACTTAGCC-TTCATTTAACTGGCATAAAT
1 ACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAAAT
573530 GAC
66 GAC
* * *
573533 A-CATTCTGTCATGTGCACAGTTAGG-CTTAAAGGCACTTAGCCTTTCATCTAA-TGTCATAAAT
1 ACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAAAT
573595 GAC
66 GAC
* * *
573598 GCCTTTCAGTCATTTGCATAGTTAGGCCT
1 ACCTTTCTGTCATTTGCACAGTTAGGCCT
573627 ATCCTTTATT
Statistics
Matches: 394, Mismatches: 31, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
65 37 0.09
66 62 0.16
67 139 0.35
68 156 0.40
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (68 bp):
ACCTTTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAAAT
GAC
Found at i:573493 original size:203 final size:201
Alignment explanation
Indices: 573136--573626 Score: 792
Period size: 203 Copynumber: 2.4 Consensus size: 201
573126 TGGACCTTTA
* *
573136 TGTCAATTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTT-ATCTAACTAGCATAAATGACACCT
1 TGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCT
* *
573200 TTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAACCTTTCATCTAACTGGCATACATGAAC
66 TTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACCTAACCTTTCATCTAACTGGCATAAATGAAC
* * *
573265 CTTTCTTTCATTTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGA
131 ATTTCTGTCATTTGCACACTTAGGCCTTAAAGGCACTTAGCC-TTCATCTAACTGGCATAAATGA
573330 CACATTTC
195 CACA-TTC
*
573338 TGTCATTTGCACAGTTAGGCCTTAAAGACACTTAGCCTTTCATCTAACTGGCATAAATGACACCT
1 TGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCT
*
573403 TTCTGTCATTTGCACACTTAGGCCTTAAAGGCACCTAACCTTTCATCTAACTGGCATAAATGACA
66 TTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACCTAACCTTTCATCTAACTGGCATAAATGA-A
*
573468 CATTTCTGTCA-TTGCACACTTAGGCCTTAAAGGCACTTAGCCTTCATTTAACTGGCATAAATGA
130 CATTTCTGTCATTTGCACACTTAGGCCTTAAAGGCACTTAGCCTTCATCTAACTGGCATAAATGA
573532 CACATTC
195 CACATTC
* * *
573539 TGTCATGTGCACAGTTAGG-CTTAAAGGCACTTAGCCTTTCATCTAA-TGTCATAAATGACGCCT
1 TGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCT
* *
573602 TTCAGTCATTTGCATAGTTAGGCCT
66 TTCTGTCATTTGCACAGTTAGGCCT
573627 ATCCTTTATT
Statistics
Matches: 270, Mismatches: 17, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
199 37 0.14
200 26 0.10
201 21 0.08
202 63 0.23
203 113 0.42
204 10 0.04
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (201 bp):
TGTCATTTGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCT
TTCTGTCATTTGCACAGTTAGGCCTTAAAGGCACCTAACCTTTCATCTAACTGGCATAAATGAAC
ATTTCTGTCATTTGCACACTTAGGCCTTAAAGGCACTTAGCCTTCATCTAACTGGCATAAATGAC
ACATTC
Found at i:573895 original size:55 final size:55
Alignment explanation
Indices: 573827--573937 Score: 170
Period size: 55 Copynumber: 2.0 Consensus size: 55
573817 ACATCTATTT
*
573827 CCCATACAGAAATTCATACACTTAGTATGAATTTCTT-ATTTTTGCACACAAAGTG
1 CCCATACAGAAATTCATACACTTAGTATGAA-TTCTTAATTTTTACACACAAAGTG
* *
573882 CCCATACATAAATTCATACACTTAGTATGAATTCTTAAATTTTTACACACATAGTG
1 CCCATACAGAAATTCATACACTTAGTATGAATTCTT-AATTTTTACACACAAAGTG
573938 TCATTTGGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
54 5 0.10
55 30 0.59
56 16 0.31
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (55 bp):
CCCATACAGAAATTCATACACTTAGTATGAATTCTTAATTTTTACACACAAAGTG
Found at i:579770 original size:26 final size:26
Alignment explanation
Indices: 579741--579796 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
579731 ATTCGGGTTT
579741 CAGGTTGGATGAAATTATCATAAACC
1 CAGGTTGGATGAAATTATCATAAACC
*
579767 CAGGTTGGATGAATTTATCATAAACC
1 CAGGTTGGATGAAATTATCATAAACC
579793 CAGG
1 CAGG
579797 CTGGGTCAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (26 bp):
CAGGTTGGATGAAATTATCATAAACC
Found at i:579991 original size:19 final size:22
Alignment explanation
Indices: 579964--580015 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 22
579954 TTACACACAA
*
579964 ATAAGATATTTAG-TTA-A-AT
1 ATAATATATTTAGTTTATACAT
*
579983 ATAATATATGTAGTTTATACAT
1 ATAATATATTTAGTTTATACAT
580005 ATAATAT-TTTA
1 ATAATATATTTA
580016 ACTAAAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 11 0.41
20 3 0.11
21 4 0.15
22 9 0.33
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (22 bp):
ATAATATATTTAGTTTATACAT
Found at i:580144 original size:2 final size:2
Alignment explanation
Indices: 580137--580205 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
580127 AAATTGTAAT
580137 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
580179 TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
580206 TAAAAAGGAG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:580163 original size:101 final size:102
Alignment explanation
Indices: 579969--580177 Score: 239
Period size: 101 Copynumber: 2.0 Consensus size: 102
579959 CACAAATAAG
* *
579969 ATATTTAGTTAAATATAATATATGTAGTTTATACATATAATATTTTAACTAAAATCAAATTATTA
1 ATATTTAATTAAATATAATATATGTAGTTTATACATATAATATTTTAACTAAAATCAAATAATTA
* * * *
580034 TAATTATTGTAATTTAAAATAATTTATATATGTATA-
66 TAATTATTATAATATAAAATAATATATATATATATAT
* *
580070 ATATTTAATTAAA-ATTAATTTGTGTA-TTTGATACATATAATATTTTAACTAAAAT-AAA-AAT
1 ATATTTAATTAAATA-TAATATATGTAGTTT-ATACATATAATATTTTAACTAAAATCAAATAAT
* *
580131 TGTAATTATATATATATATATATATATATATATATATATATAT
64 TATAATTAT-TATA-ATATA-AAATA-ATATATATATATATAT
580174 ATAT
1 ATAT
580178 ATATATATAT
Statistics
Matches: 91, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
99 10 0.11
100 10 0.11
101 50 0.55
102 4 0.04
103 13 0.14
104 4 0.04
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.47
Consensus pattern (102 bp):
ATATTTAATTAAATATAATATATGTAGTTTATACATATAATATTTTAACTAAAATCAAATAATTA
TAATTATTATAATATAAAATAATATATATATATATAT
Found at i:580300 original size:92 final size:90
Alignment explanation
Indices: 580202--580438 Score: 259
Period size: 92 Copynumber: 2.6 Consensus size: 90
580192 ATATATATTT
* *
580202 ATATTAAAAAGGAGATAATTTTTGTAATCATCAAACTTTATTAAATATATATTTATCAT-ATAAA
1 ATATT-AAAAGGAGATAATTATTGTAATTATCAAACTTTATTAAATATATATTTAT-ATGATAAA
* *
580266 A-CTTAATCTCAA-TTGAAATA-GATTTAT
64 ACCTT-AT-TCAAGCTGAAATATG-TTTAA
*
580293 ATAATTAAAAGAGAGATAATTATTGTAATTATCAAATTTTATTAAAAGTATATATTTATATGATA
1 AT-ATTAAAAG-GAGATAATTATTGTAATTATCAAACTTTATT-AAA-TATATATTTATATGATA
*
580358 AAACCTTATTTAAGCTGAAATATGTTTAA
62 AAACCTTATTCAAGCTGAAATATGTTTAA
* * *
580387 ATATTTAAAA-GAGATACTTATTATAATTATCAAACTTTATCAAAATATATAT
1 ATA-TTAAAAGGAGATAATTATTGTAATTATCAAACTTTAT-TAAATATATAT
580439 AAGTTTATAT
Statistics
Matches: 126, Mismatches: 10, Indels: 20
0.81 0.06 0.13
Matches are distributed among these distances:
91 14 0.11
92 61 0.48
93 9 0.07
94 38 0.30
95 4 0.03
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (90 bp):
ATATTAAAAGGAGATAATTATTGTAATTATCAAACTTTATTAAATATATATTTATATGATAAAAC
CTTATTCAAGCTGAAATATGTTTAA
Found at i:580540 original size:149 final size:153
Alignment explanation
Indices: 580308--580596 Score: 345
Period size: 150 Copynumber: 1.9 Consensus size: 153
580298 TAAAAGAGAG
* * * *
580308 ATAATTATTGTAATTATCAAATTTTATTAAAAGTATATATTTATATGATAAAACCTTATTTAAGC
1 ATAATTATTGTAATTATCAAACTCTATTAAAAGTATATATTTATATGATAAAACCTAATCTAAGC
* * **
580373 TGAAATATGTTTAAATATTT-AAAAGAGATACTTATTATAATTATCAAACT-TTATCAAAATAT-
66 TGAAATAGGTTTAAATATTTAAAAAAAGATAAGTATTATAATTATCAAACTCTT-TCAAAATATA
580435 ATA-TAAGTTTATATATATTTAAA
130 ATATTAAGTTTATATATATTTAAA
* * * * * * *
580458 ATAATTATTTTAATTATTAAACTCTATTAAAA-TATATATTTATTTGTTAGAACCTAATCTGAGT
1 ATAATTATTGTAATTATCAAACTCTATTAAAAGTATATATTTATATGATAAAACCTAATCTAAGC
* ** * * *
580522 TGAGATAGGTTTTTATATTTAAAAAAAGATAAGTATTTTAATTATTAAACTCTTTTAAAATATAA
66 TGAAATAGGTTTAAATATTTAAAAAAAGATAAGTATTATAATTATCAAACTCTTTCAAAATATAA
580587 TATTAAGTTT
131 TATTAAGTTT
580597 GACATAATAT
Statistics
Matches: 114, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
149 41 0.36
150 61 0.54
151 5 0.04
152 7 0.06
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (153 bp):
ATAATTATTGTAATTATCAAACTCTATTAAAAGTATATATTTATATGATAAAACCTAATCTAAGC
TGAAATAGGTTTAAATATTTAAAAAAAGATAAGTATTATAATTATCAAACTCTTTCAAAATATAA
TATTAAGTTTATATATATTTAAA
Found at i:588168 original size:74 final size:75
Alignment explanation
Indices: 588026--588190 Score: 278
Period size: 74 Copynumber: 2.2 Consensus size: 75
588016 AATAAAATAA
* * *
588026 AATGTTAGCAAGTTAGTAAGAACAATAAAAATAATAAAGTTAGTATGTTAATATGAACAATACAA
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAATAAAGTTAGAATGTTAATATGAACAATAAAA
588091 TAAAAGTTAG
66 TAAAAGTTAG
* *
588101 AATGTTTGTAAGTTAGTAAGAACAATAAAAATAA-AAAGTTAGAATGTTAGTATGAACAATAAAA
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAATAAAGTTAGAATGTTAATATGAACAATAAAA
588165 TAAAAGTTAG
66 TAAAAGTTAG
588175 AATGTTAGTAAGTTAG
1 AATGTTAGTAAGTTAG
588191 AAAAGTTAGA
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
74 52 0.62
75 32 0.38
ACGTcount: A:0.51, C:0.04, G:0.16, T:0.29
Consensus pattern (75 bp):
AATGTTAGTAAGTTAGTAAGAACAATAAAAATAATAAAGTTAGAATGTTAATATGAACAATAAAA
TAAAAGTTAG
Found at i:588182 original size:32 final size:32
Alignment explanation
Indices: 588015--588184 Score: 162
Period size: 32 Copynumber: 4.9 Consensus size: 32
588005 TTAGTTTGTG
*
588015 CAATAAAATAAAATGTTAGCAA-GTTAGTAAGAA
1 CAATAAAATAAAA-GTTAG-AATGTTAGTATGAA
* *
588048 CAATAAAAATAATAAAGTTAGTATGTTAATATGAA
1 CAAT-AAAAT-A-AAAGTTAGAATGTTAGTATGAA
*
588083 CAATACAATAAAAGTTAGAATGTTTGTAAGTTAGTAAGAA
1 CAATAAAATAAAAGTTAGAATG--T-T-AG-TA-T--GAA
588123 CAATAAAAATAAAAAGTTAGAATGTTAGTATGAA
1 CAAT-AAAAT-AAAAGTTAGAATGTTAGTATGAA
588157 CAATAAAATAAAAGTTAGAATGTTAGTA
1 CAATAAAATAAAAGTTAGAATGTTAGTA
588185 AGTTAGAAAA
Statistics
Matches: 116, Mismatches: 7, Indels: 29
0.76 0.05 0.19
Matches are distributed among these distances:
32 30 0.26
33 10 0.09
34 18 0.16
35 20 0.17
36 5 0.04
37 4 0.03
38 3 0.03
39 1 0.01
40 8 0.07
41 4 0.03
42 13 0.11
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGAATGTTAGTATGAA
Found at i:588190 original size:40 final size:36
Alignment explanation
Indices: 588019--588190 Score: 145
Period size: 40 Copynumber: 4.6 Consensus size: 36
588009 TTTGTGCAAT
*
588019 AAAATAAAATGTTAGCAAGTTAGTAAGAACAATAAAA
1 AAAAT-AAATGTTAGTAAGTTAGTAAGAACAATAAAA
* * * *
588056 ATAATAAA-GTTAGTATGTTAATATGAACAATACAATA
1 AAAATAAATGTTAGTAAGTTAGTAAGAACAATA-AA-A
* *
588093 AAAGTTAGAATGTTTGTAAGTTAGTAAGAACAATAAAA
1 AAA-ATA-AATGTTAGTAAGTTAGTAAGAACAATAAAA
* *
588131 ATAA-AAA-GTTAG-AATGTTAGTATGAACAATAAAA
1 AAAATAAATGTTAGTAA-GTTAGTAAGAACAATAAAA
588165 TAAAAGTTAGAATGTTAGTAAGTTAG
1 -AAAA--TA-AATGTTAGTAAGTTAG
588191 AAAAGTTAGA
Statistics
Matches: 106, Mismatches: 16, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
33 2 0.02
34 22 0.21
35 25 0.24
36 6 0.06
37 7 0.07
38 6 0.06
39 6 0.06
40 30 0.28
41 2 0.02
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.28
Consensus pattern (36 bp):
AAAATAAATGTTAGTAAGTTAGTAAGAACAATAAAA
Found at i:588417 original size:121 final size:125
Alignment explanation
Indices: 588203--588531 Score: 427
Period size: 121 Copynumber: 2.6 Consensus size: 125
588193 AAGTTAGAGA
* * * *
588203 TTAGTGGTTAGCAAGGTTCGAACCATAATAATGTGGATTATA-TCCCGAATCAGGTCACCACAAA
1 TTAGTGGTTAGCAA-GTTCGAACCATAATAATGTGGATCATACTCCAG-ATCTGGTCACCACAAG
588267 GTCGAATCGAATAATTCAAACAAATATAT-A-AAAAT-A-AAATAAAATAAAATAAAAAA-G
64 GTCGAATCGAATAATTCAAACAAATATATAATAAAATAATAAATAAAATAAAATAAAAAAGG
* * * *
588324 TTAGTGGTTAGTAGAGTTTGAACCATAATAATATGGATCATACTTCAGATCTGGTCACCACAAGG
1 TTAGTGGTTAGCA-AGTTCGAACCATAATAATGTGGATCATACTCCAGATCTGGTCACCACAAGG
*
588389 CCGAATCGAATAATTCAAACAAATATATAAAAATAAAATGAAATAAATAAAATAAAATAAAAAAG
65 TCGAATCGAATAATTCAAACAAATATAT---AATAAAAT--AATAAATAAAATAAAATAAAAAAG
588454 G
125 G
* * *
588455 TTAATGGTTAGGAAAGTTCGAACCATAATAATGTGGATCATACCCCAGATCTGGTCACCACAAGG
1 TTAGTGGTTA-GCAAGTTCGAACCATAATAATGTGGATCATACTCCAGATCTGGTCACCACAAGG
588520 TCGAATCGAATA
65 TCGAATCGAATA
588532 TTAGAAACAA
Statistics
Matches: 179, Mismatches: 16, Indels: 16
0.85 0.08 0.08
Matches are distributed among these distances:
121 78 0.44
122 4 0.02
125 1 0.01
126 5 0.03
129 1 0.01
130 20 0.11
131 68 0.38
132 2 0.01
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.25
Consensus pattern (125 bp):
TTAGTGGTTAGCAAGTTCGAACCATAATAATGTGGATCATACTCCAGATCTGGTCACCACAAGGT
CGAATCGAATAATTCAAACAAATATATAATAAAATAATAAATAAAATAAAATAAAAAAGG
Found at i:588432 original size:5 final size:5
Alignment explanation
Indices: 588418--588450 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
588408 CAAATATATA
*
588418 AAAAT AAAAT GAAAT -AAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
588451 AAGGTTAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:588438 original size:14 final size:14
Alignment explanation
Indices: 588419--588449 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
588409 AAATATATAA
*
588419 AAATAAAATGAAAT
1 AAATAAAATAAAAT
588433 AAATAAAATAAAAT
1 AAATAAAATAAAAT
588447 AAA
1 AAA
588450 AAAGGTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:588540 original size:131 final size:130
Alignment explanation
Indices: 588298--588549 Score: 373
Period size: 131 Copynumber: 1.9 Consensus size: 130
588288 AAATATATAA
* * * *
588298 AAATAAAATAAAATAAAATAAAAAAGTTAGTGGTTAGTAGAGTTTGAACCATAATAATATGGATC
1 AAATAAAATAAAATAAAATAAAAAAGTTAATGGTTAGGAAAGTTCGAACCATAATAATATGGATC
** *
588363 ATACTTCAGATCTGGTCACCACAAGGCCGAATCGAATAATTCAAACAAATATATAAAAATAAAAT
66 ATACCCCAGATCTGGTCACCACAAGGCCGAATCGAATAATTCAAAC-AATAAATAAAAATAAAAT
588428 G
130 G
*
588429 AAAT-AAATAAAATAAAATAAAAAAGGTTAATGGTTAGGAAAGTTCGAACCATAATAATGTGGAT
1 AAATAAAATAAAATAAAATAAAAAA-GTTAATGGTTAGGAAAGTTCGAACCATAATAATATGGAT
* *
588493 CATACCCCAGATCTGGTCACCACAAGGTCGAATCGAAT-ATTAGAAACAATAAATAAA
65 CATACCCCAGATCTGGTCACCACAAGGCCGAATCGAATAATT-CAAACAATAAATAAA
588550 TAAATAACAA
Statistics
Matches: 109, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
130 32 0.29
131 77 0.71
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.24
Consensus pattern (130 bp):
AAATAAAATAAAATAAAATAAAAAAGTTAATGGTTAGGAAAGTTCGAACCATAATAATATGGATC
ATACCCCAGATCTGGTCACCACAAGGCCGAATCGAATAATTCAAACAATAAATAAAAATAAAATG
Found at i:590458 original size:15 final size:15
Alignment explanation
Indices: 590438--590486 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
590428 TTTATAATAA
*
590438 TAAATTGATTTGTTT
1 TAAATTGATATGTTT
590453 TAAATTGATATGTTT
1 TAAATTGATATGTTT
* *
590468 TAAATTAATATATTT
1 TAAATTGATATGTTT
590483 TAAA
1 TAAA
590487 CTTTATAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (15 bp):
TAAATTGATATGTTT
Found at i:591047 original size:2 final size:2
Alignment explanation
Indices: 591042--591076 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
591032 GTTACATGCA
591042 AT AT AT AT AT 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 AT AT AT AT AT A
591077 AATAAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:596818 original size:88 final size:85
Alignment explanation
Indices: 596550--596947 Score: 315
Period size: 85 Copynumber: 4.7 Consensus size: 85
596540 TCGCTAAAGT
* * * * * * *
596550 TAGCGGCGTTTGTGGAAAAAAAATGCTGCAATAGGTCTAAATCTATAGCGGCGTTTTTTTAGAAA
1 TAGCGGCGTTTTTGG--AACAAACGCCGCAATAGGTCGAGATCTATAGCGGCTTTTTTTTAGAAA
* * *
596615 ACGCCGCAACAGGTCGGATTTA
64 ACGCCACAAAAGGTCGGATCTA
* * * * **
596637 TAGCGGCGTTTTTCGGAACAAATGCCGCAATAAGTCGAGCTCTATAGCGGC---GTTTCCGAAAA
1 TAGCGGCGTTTTT-GGAACAAACGCCGCAATAGGTCGAGATCTATAGCGGCTTTTTTTTAGAAAA
*
596699 CGCCACAAAAGGTCAGATCTA
65 CGCCACAAAAGGTCGGATCTA
*
596720 TAGCGGCGTTTTTGGAACACACGCCGCAATAGGTCGAGATCTATAGCGGCTTTTTTTTTATAGAA
1 TAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTCGAGATCTATAGCGGC--TTTTTTT-TAGAA
*
596785 AACGCCACAAAATGTCGGATCTA
63 AACGCCACAAAAGGTCGGATCTA
* * * * * * **
596808 TAGCGGCGTTTTGGGAGA-AAACACTGCAAAAGGT-TAGATCTATAGCGGCGTTTTTGGA-ACAA
1 TAGCGGCGTTTTTGGA-ACAAACGCCGCAATAGGTCGAGATCTATAGCGGCTTTTTTTTAGA-AA
** * * *
596870 ACGCTGCAGAAGGTCAAGATATA
64 ACGCCACAAAAGGTC-GGATCTA
* * * * ** *
596893 TAGCGACGTTTTTGGAATAAACGCCGTAAAATTTC-AGATCTATAGCGGCGTTTTT
1 TAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTCGAGATCTATAGCGGCTTTTTT
596948 GGATGCAAAC
Statistics
Matches: 254, Mismatches: 45, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
82 33 0.13
83 39 0.15
84 15 0.06
85 55 0.22
86 29 0.11
87 29 0.11
88 53 0.21
89 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (85 bp):
TAGCGGCGTTTTTGGAACAAACGCCGCAATAGGTCGAGATCTATAGCGGCTTTTTTTTAGAAAAC
GCCACAAAAGGTCGGATCTA
Found at i:596950 original size:42 final size:41
Alignment explanation
Indices: 596590--596950 Score: 305
Period size: 42 Copynumber: 8.5 Consensus size: 41
596580 ATAGGTCTAA
** * *
596590 ATCTATAGCGGCGTTTTTTTAGAAAACGCCGCAACAGGTCGG
1 ATCTATAGCGGCGTTTTTGGA-AAAACGCCGCAAAAGGTCAG
* *
596632 ATTTATAGCGGCGTTTTTCGGAACAAATGCCGCAATAA-GTCGAG
1 ATCTATAGCGGCGTTTTT-GGAA-AAACGCCGCAA-AAGGTC-AG
* ** *
596676 CTCTATAGCGGCG-TTTCCG-AAAACGCCACAAAAGGTCAG
1 ATCTATAGCGGCGTTTTTGGAAAAACGCCGCAAAAGGTCAG
* *
596715 ATCTATAGCGGCGTTTTTGGAACACACGCCGCAATAGGTCGAG
1 ATCTATAGCGGCGTTTTTGGAA-AAACGCCGCAAAAGGTC-AG
* ** * * *
596758 ATCTATAGCGGCTTTTTTTTTATAGAAAACGCCACAAAATGTCGG
1 ATCTATAGCGGC---GTTTTTGGA-AAAACGCCGCAAAAGGTCAG
* * * *
596803 ATCTATAGCGGCGTTTTGGGAGAAAACACTGCAAAAGGTTAG
1 ATCTATAGCGGCGTTTTTGGA-AAAACGCCGCAAAAGGTCAG
* *
596845 ATCTATAGCGGCGTTTTTGGAACAAACGCTGCAGAAGGTCAAG
1 ATCTATAGCGGCGTTTTTGGAA-AAACGCCGCAAAAGGTC-AG
* * * **
596888 ATATATAGCGACGTTTTTGGAATAAACGCCGTAAAATTTCAG
1 ATCTATAGCGGCGTTTTTGGAA-AAACGCCGCAAAAGGTCAG
596930 ATCTATAGCGGCGTTTTTGGA
1 ATCTATAGCGGCGTTTTTGGA
596951 TGCAAACGCC
Statistics
Matches: 254, Mismatches: 50, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
39 16 0.06
40 16 0.06
41 3 0.01
42 108 0.43
43 65 0.26
44 13 0.05
45 13 0.05
46 19 0.07
47 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (41 bp):
ATCTATAGCGGCGTTTTTGGAAAAACGCCGCAAAAGGTCAG
Found at i:600713 original size:41 final size:41
Alignment explanation
Indices: 600659--601048 Score: 251
Period size: 41 Copynumber: 9.5 Consensus size: 41
600649 TTGTAAACAC
* *
600659 AAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCGCTAAAGTACTACTCTATAGCGGCGTTTGTATAA
* * * * *
600700 AAATGCCGCTAAAGAATGTA-TTTATAGCGGCGTTTGAATAA
1 AAACGCCGCTAAAGTA-CTACTCTATAGCGGCGTTTGTATAA
* * * *
600741 AAACGCCACTAAAGTACGT-GTCTATAGCGACTTTTGTATAA
1 AAACGCCGCTAAAGTAC-TACTCTATAGCGGCGTTTGTATAA
* * *
600782 AAACGCCGCTAAAGTACTACTCTTTTGCGGTGTTTGTATAAA
1 AAACGCCGCTAAAGTACTACTCTATAGCGGCGTTTGTAT-AA
* * * * *
600824 AAACCCCGCTAAAGTACCACTCTGTTGCGGCGTTTGT-TGA
1 AAACGCCGCTAAAGTACTACTCTATAGCGGCGTTTGTATAA
* * * * * *
600864 TAATGCC-ATAATA-TA-TGAACCCTATTGCGGCGTTTTTATAA
1 AAACGCCGCTAA-AGTACT--ACTCTATAGCGGCGTTTGTATAA
* * * *
600905 AAACGCCGCTAAAGTACTACTATGTCA-CGTCGTTTGTTTAAA
1 AAACGCCGCTAAAGTACTACTCTAT-AGCGGCGTTTGTAT-AA
* * * *
600947 AAACGCCACT-ATGGA-TGAAC-CTATTGCGGCGTTTGTATAA
1 AAACGCCGCTAAAGTACT--ACTCTATAGCGGCGTTTGTATAA
* * * *
600987 AAACGCCACTAAAGTACTACTCTGTTGCGGCGTTTTGCATAA
1 AAACGCCGCTAAAGTACTACTCTATAGCGGCG-TTTGTATAA
**
601029 AAACGCTACTAAAGTTACTA
1 AAACGCCGCTAAAG-TACTA
601049 TTTTGTGGCG
Statistics
Matches: 269, Mismatches: 58, Indels: 42
0.73 0.16 0.11
Matches are distributed among these distances:
39 5 0.02
40 38 0.14
41 143 0.53
42 77 0.29
43 6 0.02
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (41 bp):
AAACGCCGCTAAAGTACTACTCTATAGCGGCGTTTGTATAA
Found at i:601015 original size:123 final size:124
Alignment explanation
Indices: 600726--601048 Score: 297
Period size: 123 Copynumber: 2.6 Consensus size: 124
600716 TGTATTTATA
* * * *
600726 GCGGCGTTTGAATAAAAACGCCACTAAAGTACGT-GTCTATAGCGAC-TTTTGTATAAAAACGCC
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTAC-TACTCTATTGCGGCGTTTTGTATAAAAACGCC
* * ** * *
600789 GCTAAAGTACTACTCTTTTGCGGTGTTTGTATAAAAAACCCCGCTAAAGTACCACTCTGTT
65 GCTAAAGTACTACTATGTCACGGTGTTTGTATAAAAAACCCCACTAAAGTA-CACTCTATT
* * * *
600850 GCGGCGTTTGT-TGATAATGCCA-TAATA-TA-TGAACCCTATTGCGGCGTTTT-TATAAAAACG
1 GCGGCGTTTGTATAAAAACGCCACTAA-AGTACT--ACTCTATTGCGGCGTTTTGTATAAAAACG
* * **
600910 CCGCTAAAGTACTACTATGTCAC-GTCGTTTGTTTAAAAAACGCCACTATGGATGA-AC-CTATT
63 CCGCTAAAGTACTACTATGTCACGGT-GTTTGTATAAAAAACCCCACTAAAG-T-ACACTCTATT
* * **
600972 GCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTGTTGCGGCGTTTTGCATAAAAACGCTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTTGTATAAAAACGCCG
601037 CTAAAGTTACTA
66 CTAAAG-TACTA
601049 TTTTGTGGCG
Statistics
Matches: 159, Mismatches: 26, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
120 1 0.01
122 22 0.14
123 93 0.58
124 36 0.23
125 7 0.04
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (124 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACTACTCTATTGCGGCGTTTTGTATAAAAACGCCG
CTAAAGTACTACTATGTCACGGTGTTTGTATAAAAAACCCCACTAAAGTACACTCTATT
Found at i:601031 original size:82 final size:81
Alignment explanation
Indices: 600659--601042 Score: 321
Period size: 82 Copynumber: 4.7 Consensus size: 81
600649 TTGTAAACAC
* * * * * **
600659 AAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTATAAAAATGCCGCTAAAGAATGTATTTA
1 AAACGCCACTAAAGTACTACTCTGTAGCGGCGTTTGTATAAAAACGCCACTAAAG-ATGAACCTA
* *
600724 TAGCGGCGTTTGAATAA
65 TTGCGGCGTTTGTATAA
* * * * *
600741 AAACGCCACTAAAGTACGT-GTCTATAGCGACTTTTGTATAAAAACGCCGCTAAAG-T-ACTACT
1 AAACGCCACTAAAGTAC-TACTCTGTAGCGGCGTTTGTATAAAAACGCCACTAAAGATGA--AC-
* *
600803 CTTTTGCGGTGTTTGTATAAA
62 CTATTGCGGCGTTTGTAT-AA
* * * * * * * *
600824 AAACCCCGCTAAAGTACCACTCTGTTGCGGCGTTTGT-TGATAATGCCA-TAATATATGAACCCT
1 AAACGCCACTAAAGTACTACTCTGTAGCGGCGTTTGTATAAAAACGCCACTAA-AGATGAA-CCT
*
600887 ATTGCGGCGTTTTTATAA
64 ATTGCGGCGTTTGTATAA
* * * * **
600905 AAACGCCGCTAAAGTACTACTATGTCA-CGTCGTTTGTTTAAAAAACGCCACTATGGATGAACCT
1 AAACGCCACTAAAGTACTACTCTGT-AGCGGCGTTTGTAT-AAAAACGCCACTAAAGATGAACCT
600969 ATTGCGGCGTTTGTATAA
64 ATTGCGGCGTTTGTATAA
* * *
600987 AAACGCCACTAAAGTACTACTCTGTTGCGGCGTTTTGCATAAAAACGCTACTAAAG
1 AAACGCCACTAAAGTACTACTCTGTAGCGGCG-TTTGTATAAAAACGCCACTAAAG
601043 TTACTATTTT
Statistics
Matches: 239, Mismatches: 47, Indels: 32
0.75 0.15 0.10
Matches are distributed among these distances:
80 1 0.00
81 37 0.15
82 148 0.62
83 50 0.21
84 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (81 bp):
AAACGCCACTAAAGTACTACTCTGTAGCGGCGTTTGTATAAAAACGCCACTAAAGATGAACCTAT
TGCGGCGTTTGTATAA
Found at i:614982 original size:131 final size:132
Alignment explanation
Indices: 614748--615105 Score: 402
Period size: 131 Copynumber: 2.7 Consensus size: 132
614738 ATTTTAAGCG
* * * * * *
614748 TGAAAACCATAATATCTAATTATTTCCAATCGTGAATAAATGACCTTTCGTGCATTGAAA-CATT
1 TGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTT-AAAGCAGT
* * * * * * * *
614812 CATTTATTACCCCAATTGAAAT-AAAGATATATTACTATTTCGTCTTAAAATTCAATATCGATTC
65 CATTTATTACTCCAATCGAAATGAAA-AGATATCACTATTTCATCTAAAAAATCAATATCAATTC
614876 -AAA
129 GAAA
* * * *
614879 TGAAAACGATAATATCTAATGATTTCCAATCAAGAATAAATGACATCTCATACCTTAAAGCAGTC
1 TGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
* * * *
614944 ATTTATTGCTCCAATCGAAATGAAAAGATATCATTATTTCATCTAAAAAATCGATATTAATTCGA
66 ATTTATTACTCCAATCGAAATGAAAAGATATCACTATTTCATCTAAAAAATCAATATCAATTCGA
*
615009 GA
131 AA
* * * * *
615011 -GAAAATGACAATATCAAATTATTTCCAATCGAGAATAAATGACCTCTCACGCCTTAGAGCAGTC
1 TGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
615075 ATTTATTACTCCAA-CTGAAATGAAAAGATAT
66 ATTTATTACTCCAATC-GAAATGAAAAGATAT
615106 TACCATTCTC
Statistics
Matches: 190, Mismatches: 33, Indels: 8
0.82 0.14 0.03
Matches are distributed among these distances:
130 4 0.02
131 181 0.95
132 5 0.03
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (132 bp):
TGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
ATTTATTACTCCAATCGAAATGAAAAGATATCACTATTTCATCTAAAAAATCAATATCAATTCGA
AA
Found at i:617218 original size:3 final size:3
Alignment explanation
Indices: 617210--617252 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
617200 ATTAATTAAT
*
617210 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
617253 ATAACCAGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 35 0.95
4 2 0.05
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:618112 original size:19 final size:20
Alignment explanation
Indices: 618077--618125 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
618067 TTAGTTATCG
618077 AATT-ATATT-TAATTATAT
1 AATTAATATTATAATTATAT
**
618095 TCTTAATATTATAA-TATAT
1 AATTAATATTATAATTATAT
618114 AATTAATATTAT
1 AATTAATATTAT
618126 TTATTAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 2 0.08
19 20 0.80
20 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTAATATTATAATTATAT
Found at i:618302 original size:42 final size:42
Alignment explanation
Indices: 618238--618326 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
618228 ATCTTAATAA
* *
618238 TATTATTATTTTAATAAGTAATTAATATAGTTAATAATATAT
1 TATTATTATTTTAATAAATAATTAATATAATTAATAATATAT
* *
618280 TATTCTTATTTTAATAAATAATTAATATAATTTATAATA-AT
1 TATTATTATTTTAATAAATAATTAATATAATTAATAATATAT
618321 T-TTATT
1 TATTATT
618327 TTCATAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 4 0.10
41 3 0.07
42 35 0.83
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (42 bp):
TATTATTATTTTAATAAATAATTAATATAATTAATAATATAT
Found at i:618317 original size:23 final size:22
Alignment explanation
Indices: 618245--618319 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
618235 TAATATTATT
*
618245 ATTTTAATAAGTAATTAATAT-
1 ATTTTAATAAATAATTAATATA
* * * *
618266 A-GTTAAT-AATATATTATTCTT
1 ATTTTAATAAATA-ATTAATATA
618287 ATTTTAATAAATAATTAATATA
1 ATTTTAATAAATAATTAATATA
618309 ATTTATAATAA
1 ATTT-TAATAA
618320 TTTTATTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
19 3 0.07
20 11 0.27
21 2 0.05
22 15 0.37
23 10 0.24
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (22 bp):
ATTTTAATAAATAATTAATATA
Found at i:618334 original size:37 final size:39
Alignment explanation
Indices: 618232--618350 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 39
618222 TTTAATATCT
* *
618232 TAATAATATTATTATTTTAATAAGTAATTAATATAGTTAA
1 TAATAATATTATTATTTTAATAAATAATTAATATAATT-A
*
618272 TAATATATTATTCTTATTTTAATAAATAATTAATATAATT-
1 TAATA-A-TATTATTATTTTAATAAATAATTAATATAATTA
*
618312 T-ATAATAATT-TTATTTTCATAAAATATATTAATCATAAT
1 TAATAAT-ATTATTATTTTAAT-AAATA-ATTAAT-ATAAT
618351 ATTTTTATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
37 10 0.14
38 9 0.13
39 9 0.13
40 11 0.16
41 1 0.01
42 29 0.42
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.50
Consensus pattern (39 bp):
TAATAATATTATTATTTTAATAAATAATTAATATAATTA
Found at i:618466 original size:27 final size:28
Alignment explanation
Indices: 618399--618466 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
618389 TAATATTGAC
*
618399 ATAAATAATATTA-AATTATTTTAATAT
1 ATAAATAATATTATTATTATTTTAATAT
* * *
618426 TTAAA-AAAATTATTATTATTTTAGTA-
1 ATAAATAATATTATTATTATTTTAATAT
618452 ATAAATAATATTATT
1 ATAAATAATATTATT
618467 TATTGTATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
ATAAATAATATTATTATTATTTTAATAT
Done.