Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008680.1 Hibiscus syriacus cultivar Beakdansim tig00111701_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: 579941
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:365946 original size:70 final size:70
Alignment explanation
Indices: 365812--365955 Score: 191
Period size: 70 Copynumber: 2.1 Consensus size: 70
365802 TCATAGTTAT
* * *
365812 TTCAGAAACATGTTGTTCAGACATCTCACAAATAATTCAGAAATATATGGTTCGAACGTCTCACA
1 TTCAGAAACATATGGTTCAGACATCTCACAAATAATTCAGAAATATATGGTTCAAACGTCTCACA
365877 -AGTAA
66 GA-TAA
* * * * * *
365882 TTCAGAAATATATGGTTCGGACGTCTCACAAGTAATTCAGAAATATATGGTTCAAATGTGTCACA
1 TTCAGAAACATATGGTTCAGACATCTCACAAATAATTCAGAAATATATGGTTCAAACGTCTCACA
365947 GATAA
66 GATAA
365952 TTCA
1 TTCA
365956 ATGACAAATT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
70 63 0.98
71 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (70 bp):
TTCAGAAACATATGGTTCAGACATCTCACAAATAATTCAGAAATATATGGTTCAAACGTCTCACA
GATAA
Found at i:368728 original size:3 final size:3
Alignment explanation
Indices: 368720--368756 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
368710 CTATGATTGC
368720 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
368757 CGAGTAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:378335 original size:26 final size:25
Alignment explanation
Indices: 378294--378345 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
378284 TCATTCCCCA
*
378294 TATTTTTTTTCTTCACTTTTCTTCT
1 TATTTTTTCTCTTCACTTTTCTTCT
378319 TATTTCTTTCTCTTCACTTTTCTTCT
1 TATTT-TTTCTCTTCACTTTTCTTCT
378345 T
1 T
378346 TTCCTCTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (25 bp):
TATTTTTTCTCTTCACTTTTCTTCT
Found at i:380269 original size:65 final size:65
Alignment explanation
Indices: 380109--380269 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 65
380099 TTGTTTAAGG
* * * ** *
380109 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATATGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
380172 A
65 A
*
380173 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
* *
380237 TGCATCTATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
380270 ACCTTCATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 60 0.71
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:381675 original size:21 final size:21
Alignment explanation
Indices: 381649--381711 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
381639 GTCGAGGGTT
*
381649 TCATAGGTCATTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
*
381670 TCATAGGTCCTTCGGGACAAAT
1 TCATAGGTCCTTCGGGAC-AAC
*
381692 TCACAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
381712 ATTTCATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 19 0.50
22 19 0.50
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:381702 original size:22 final size:22
Alignment explanation
Indices: 381648--381719 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
381638 AGTCGAGGGT
*
381648 TTCATAGGTCATTCGGGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
*
381669 CTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
381691 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
381713 TTTCATA
1 -TTCATA
381720 TGCCACTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 17 0.39
22 22 0.50
23 5 0.11
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:382760 original size:26 final size:26
Alignment explanation
Indices: 382729--382778 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
382719 TTCGATGCGA
*
382729 AAGAAGGAA-AGTGAAGAGAAAGAAAT
1 AAGAA-GAATAGTGAAGAAAAAGAAAT
382755 AAGAAGAATAGTGAAGAAAAAGAA
1 AAGAAGAATAGTGAAGAAAAAGAA
382779 GATGGGGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (26 bp):
AAGAAGAATAGTGAAGAAAAAGAAAT
Found at i:384085 original size:210 final size:211
Alignment explanation
Indices: 383722--384139 Score: 811
Period size: 210 Copynumber: 2.0 Consensus size: 211
383712 TAACAACTTT
383722 TTTCTTAAAACACTCCTGTAAACTCTTCATTGACTAGATTTTTGGGGGGGTAAAGTACACTAAAG
1 TTTCTTAAAACACTCCTGTAAACTCTTCATTGACTAGATTTTTGGGGGGGTAAAGTACACTAAAG
383787 TTTATTAAATTGTGTTAAAATAATTTATTAGTTAACAAACTTTTAAATATTATAAAATAGTCATT
66 TTTATTAAATTGTGTTAAAATAATTTATTAGTTAACAAACTTTTAAATATTATAAAATAGTCATT
383852 AAAGCTCATCAATATGTTATAAAAATGTCATTAAATTTATTAAATTATTATAAAATGATACTTAA
131 AAAGCTCATCAATATGTTATAAAAATGTCATTAAATTTATTAAATTATTATAAAATGATACTTAA
383917 ACTTATCAAAATTGTG
196 ACTTATCAAAATTGTG
* *
383933 TTTCTTAAAACACTCCTTTAAACTCTTCATTGACTAGATTTTT-GGGGGGTAAGGTACACTAAAG
1 TTTCTTAAAACACTCCTGTAAACTCTTCATTGACTAGATTTTTGGGGGGGTAAAGTACACTAAAG
383997 TTTATTAAATTGTGTTAAAATAATTTATTAGTTAACAAACTTTTAAATATTATAAAATAGTCATT
66 TTTATTAAATTGTGTTAAAATAATTTATTAGTTAACAAACTTTTAAATATTATAAAATAGTCATT
384062 AAAGCTCATCAATATGTTATAAAAATGTCATTAAATTTATTAAATTATTATAAAATGATACTTAA
131 AAAGCTCATCAATATGTTATAAAAATGTCATTAAATTTATTAAATTATTATAAAATGATACTTAA
384127 ACTTATCAAAATT
196 ACTTATCAAAATT
384140 TATTACTATT
Statistics
Matches: 205, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
210 163 0.80
211 42 0.20
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (211 bp):
TTTCTTAAAACACTCCTGTAAACTCTTCATTGACTAGATTTTTGGGGGGGTAAAGTACACTAAAG
TTTATTAAATTGTGTTAAAATAATTTATTAGTTAACAAACTTTTAAATATTATAAAATAGTCATT
AAAGCTCATCAATATGTTATAAAAATGTCATTAAATTTATTAAATTATTATAAAATGATACTTAA
ACTTATCAAAATTGTG
Found at i:385685 original size:14 final size:15
Alignment explanation
Indices: 385660--385688 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
385650 AATAATTTAA
385660 CACATGCAAAAATAT
1 CACATGCAAAAATAT
385675 CACAT-CAAAAATAT
1 CACATGCAAAAATAT
385689 GCGTTCAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.21, G:0.03, T:0.21
Consensus pattern (15 bp):
CACATGCAAAAATAT
Found at i:391454 original size:6 final size:6
Alignment explanation
Indices: 391443--391481 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
391433 GCTTAAAGAT
391443 GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAA
1 GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAA
391482 GATTGTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
GAAAGG
Found at i:392712 original size:191 final size:191
Alignment explanation
Indices: 392388--392769 Score: 764
Period size: 191 Copynumber: 2.0 Consensus size: 191
392378 ATAAGCTTGG
392388 TTATTTTTTTTCTTCAAAAACAAATTCAGTTTCGAGTTAAGTTGTGTTGTTTTTTTAAGAAGGGA
1 TTATTTTTTTTCTTCAAAAACAAATTCAGTTTCGAGTTAAGTTGTGTTGTTTTTTTAAGAAGGGA
392453 ATGTCGGGTCGGGTTAGATTTATGGTAAAAAATATCCGACCAAAGAATAATAATATATTCAATCT
66 ATGTCGGGTCGGGTTAGATTTATGGTAAAAAATATCCGACCAAAGAATAATAATATATTCAATCT
392518 ATATATATATATATATGAATAATTATTATAATATTCCTATATATATATATATATATGAATT
131 ATATATATATATATATGAATAATTATTATAATATTCCTATATATATATATATATATGAATT
392579 TTATTTTTTTTCTTCAAAAACAAATTCAGTTTCGAGTTAAGTTGTGTTGTTTTTTTAAGAAGGGA
1 TTATTTTTTTTCTTCAAAAACAAATTCAGTTTCGAGTTAAGTTGTGTTGTTTTTTTAAGAAGGGA
392644 ATGTCGGGTCGGGTTAGATTTATGGTAAAAAATATCCGACCAAAGAATAATAATATATTCAATCT
66 ATGTCGGGTCGGGTTAGATTTATGGTAAAAAATATCCGACCAAAGAATAATAATATATTCAATCT
392709 ATATATATATATATATGAATAATTATTATAATATTCCTATATATATATATATATATGAATT
131 ATATATATATATATATGAATAATTATTATAATATTCCTATATATATATATATATATGAATT
392770 GAAATGGAGG
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
191 191 1.00
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (191 bp):
TTATTTTTTTTCTTCAAAAACAAATTCAGTTTCGAGTTAAGTTGTGTTGTTTTTTTAAGAAGGGA
ATGTCGGGTCGGGTTAGATTTATGGTAAAAAATATCCGACCAAAGAATAATAATATATTCAATCT
ATATATATATATATATGAATAATTATTATAATATTCCTATATATATATATATATATGAATT
Found at i:396927 original size:305 final size:302
Alignment explanation
Indices: 396357--396966 Score: 1044
Period size: 305 Copynumber: 2.0 Consensus size: 302
396347 TTTGAGTTAT
*
396357 TTGCATAAAACATCCTTGATTTATTGTTTAGATTCTAAATTATATGATAAACTTCAAAACATTCT
1 TTGCATAAAACATCCTTGATTTATGGTTTAGATTCTAAATTATATGATAAACTTCAAAACATTCT
396422 AACCGAGTACTCAAACTATCAAAATTCTTTCAATGAGATCCTTCCATTAGTTTAGTATGTAAGCC
66 AACC-AG-A-TCAAACTATCAAAATTCTTTCAATGAGATCCTTCCATTAGTTTAGTATGTAAGCC
* * *
396487 GGATATGACAATACATATTTAAAACTCTTGAAATAAATTAGGCTTAATGGTATCTAAGGCCCTCA
128 AGATATGACAATACATATTTAAAACTCCTGAAATAAATTAGGCTTAATGGTATCTAAGCCCCTCA
* *
396552 AACTTTTTAAAAAATTAATATAGCCCTCGAATTATTTGTGTATTCATTGTGACCCTTAAACTCGA
193 AAATTTTTAAAAAATTAATATAGCCCTCGAATCATTTGTGTATTCATTGTGACCCTTAAACTCGA
*
396617 AAAAAAACTCAATGTGACCTTTTGATCAACGGTTTTCGTCGTTGA
258 AAAAAAACTCAATGTGACCTTTTGACCAACGGTTTTCGTCGTTGA
396662 TTGCATAAAACATCCTTGATTTATGGTTTAGATTCTAAATTATATGATAAACTTCAAAACATTCT
1 TTGCATAAAACATCCTTGATTTATGGTTTAGATTCTAAATTATATGATAAACTTCAAAACATTCT
*
396727 AACC-G-TCAAACTATCAATATTCTTTCAATGAGATCCTTCCATTAGTTTAGTATGTAAGCCAGA
66 AACCAGATCAAACTATCAAAATTCTTTCAATGAGATCCTTCCATTAGTTTAGTATGTAAGCCAGA
396790 TATGACACAATACATATTTAAAACTCCTGAAATAAATTAGGCTTAATGGTATCTAAGCCCCTCAA
131 TATG--ACAATACATATTTAAAACTCCTGAAATAAATTAGGCTTAATGGTATCTAAGCCCCTCAA
396855 AATTTTTAAAAAAATTAATATAGCCCTCGAATCATTTGTGTATTCATTGTGACCCTTAAACTCGA
194 AATTTTT-AAAAAATTAATATAGCCCTCGAATCATTTGTGTATTCATTGTGACCCTTAAACTCG-
* *
396920 AAAAAAAAACTCAATGTGCCCTTTTGACCAACGGTTTTCTTCGTTGA
257 -AAAAAAAACTCAATGTGACCTTTTGACCAACGGTTTTCGTCGTTGA
396967 CCATTACAAT
Statistics
Matches: 290, Mismatches: 10, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
300 60 0.21
302 63 0.22
303 56 0.19
305 111 0.38
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (302 bp):
TTGCATAAAACATCCTTGATTTATGGTTTAGATTCTAAATTATATGATAAACTTCAAAACATTCT
AACCAGATCAAACTATCAAAATTCTTTCAATGAGATCCTTCCATTAGTTTAGTATGTAAGCCAGA
TATGACAATACATATTTAAAACTCCTGAAATAAATTAGGCTTAATGGTATCTAAGCCCCTCAAAA
TTTTTAAAAAATTAATATAGCCCTCGAATCATTTGTGTATTCATTGTGACCCTTAAACTCGAAAA
AAAACTCAATGTGACCTTTTGACCAACGGTTTTCGTCGTTGA
Found at i:399762 original size:14 final size:14
Alignment explanation
Indices: 399743--399770 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
399733 GAAAATCGGT
399743 ATCACTTCAATCGA
1 ATCACTTCAATCGA
399757 ATCACTTCAATCGA
1 ATCACTTCAATCGA
399771 GTCCATAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
ATCACTTCAATCGA
Found at i:406090 original size:3 final size:3
Alignment explanation
Indices: 406082--406114 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
406072 ATTAAATTAA
*
406082 AAT AAT AAT AAT AAT AAT AA- AAT AAT AAA AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
406115 GAAATCTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:407511 original size:17 final size:18
Alignment explanation
Indices: 407483--407521 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
407473 AAAAATAATT
407483 ATAAACTAATAAAATAAA
1 ATAAACTAATAAAATAAA
* *
407501 ATAAA-TAATAATATAAT
1 ATAAACTAATAAAATAAA
407518 ATAA
1 ATAA
407522 TGTTTTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAACTAATAAAATAAA
Found at i:413640 original size:15 final size:15
Alignment explanation
Indices: 413620--413649 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
413610 CAAACTATGT
413620 CTCTAAATTAGGAAA
1 CTCTAAATTAGGAAA
*
413635 CTCTAAGTTAGGAAA
1 CTCTAAATTAGGAAA
413650 GATACTAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (15 bp):
CTCTAAATTAGGAAA
Found at i:424296 original size:2 final size:2
Alignment explanation
Indices: 424289--424319 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
424279 GGATTCCTTG
*
424289 TA TA TA TA AA 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
424320 GATAAACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:426250 original size:213 final size:215
Alignment explanation
Indices: 425897--426389 Score: 694
Period size: 213 Copynumber: 2.3 Consensus size: 215
425887 CAGAATAAAG
* * *
425897 AAAGGGCAAATCGGAACTCGGCATTTATGGCAAGTTCAACACTAATTGGCAGGCCCCATCTCTTC
1 AAAGGGCAAACCGGAATTCAGCATTTATGGCAAGTTCAACACTAATTGGCAGG-CCCA-CTCTTC
*
425962 TAACCTCATCACTTGAGAGGTAACATAAACCACCATGGAAAAGAACTTTATAGGTATCACCCTTT
64 TAACCTCATCACTTGAGAGGTAACATAAACCACCATGGAAAAGAACTTTAGAGGTATCACCCTTT
* * ** *
426027 CTTTCTTCCCCCAATAAAACTGAACACCATACCGTTCCTCTTCTGTGCTCTTGC-CTTT-CCACA
129 CTTTCTTCCCCCAATAAAACTGAACAACATACCCTTCCTCTTCCATGATC-T-CACTTTCCCACA
* *
426090 GGAGCGGCACTCTTAGAAATAACA
192 GGAGCGACACTCTTAAAAATAACA
*
426114 AAAGGGCAAACCGGAATTCAGTATTTATGGCAAGTTCAACACTAATTGGCAGGCCC-C-CTTCTA
1 AAAGGGCAAACCGGAATTCAGCATTTATGGCAAGTTCAACACTAATTGGCAGGCCCACTCTTCTA
* ** *
426177 ACCAT-ATCACTTGAGAGGTAATATAAACCACCATGGGGAAGAACTTTAGAGGTATCGCCCTTTC
66 ACC-TCATCACTTGAGAGGTAACATAAACCACCATGGAAAAGAACTTTAGAGGTATCACCCTTTC
426241 TTTCTTCCCCCAATAAAACTGAACAACATACCCTTCCTCTTCCATGATCTCACTTTCCCACAGGA
130 TTTCTTCCCCCAATAAAACTGAACAACATACCCTTCCTCTTCCATGATCTCACTTTCCCACAGGA
426306 GCGACACTCTTAAAAATAACA
195 GCGACACTCTTAAAAATAACA
* * * *
426327 AAA-GGC-ATCCAGAATTCAGCATTTATGACAAGTTCAACACTAATTGGCAAGGCCTATCTCTTC
1 AAAGGGCAAACCGGAATTCAGCATTTATGGCAAGTTCAACACTAATTGGC-AGGCCCA-CTCTTC
426390 CATGGAAGAG
Statistics
Matches: 248, Mismatches: 21, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
211 39 0.16
212 13 0.05
213 137 0.55
214 3 0.01
215 4 0.02
216 3 0.01
217 49 0.20
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.26
Consensus pattern (215 bp):
AAAGGGCAAACCGGAATTCAGCATTTATGGCAAGTTCAACACTAATTGGCAGGCCCACTCTTCTA
ACCTCATCACTTGAGAGGTAACATAAACCACCATGGAAAAGAACTTTAGAGGTATCACCCTTTCT
TTCTTCCCCCAATAAAACTGAACAACATACCCTTCCTCTTCCATGATCTCACTTTCCCACAGGAG
CGACACTCTTAAAAATAACA
Found at i:427450 original size:24 final size:24
Alignment explanation
Indices: 427418--427490 Score: 146
Period size: 24 Copynumber: 3.0 Consensus size: 24
427408 TGAAGAAGAG
427418 ATGACTGCGATACGCCTATAAACA
1 ATGACTGCGATACGCCTATAAACA
427442 ATGACTGCGATACGCCTATAAACA
1 ATGACTGCGATACGCCTATAAACA
427466 ATGACTGCGATACGCCTATAAACA
1 ATGACTGCGATACGCCTATAAACA
427490 A
1 A
427491 ATCAGTCATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (24 bp):
ATGACTGCGATACGCCTATAAACA
Found at i:430251 original size:29 final size:30
Alignment explanation
Indices: 430209--430275 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
430199 ATAATTGTTT
430209 TAATTATTAAATTT-TTAAAAT-TTATAGAA
1 TAATTATTAAATTTATTAAAATATTATA-AA
* *
430238 TTATTATTAAATTTATTAAAGTATTATAAA
1 TAATTATTAAATTTATTAAAATATTATAAA
430268 TAATTATT
1 TAATTATT
430276 GTAACATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 13 0.39
30 15 0.45
31 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (30 bp):
TAATTATTAAATTTATTAAAATATTATAAA
Found at i:430262 original size:20 final size:19
Alignment explanation
Indices: 430226--430268 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
430216 TAAATTTTTA
*
430226 AAATTTATAGAATTATTATT
1 AAATTTATAGAAGTATTA-T
430246 AAATTTATTA-AAGTATTAT
1 AAATTTA-TAGAAGTATTAT
430265 AAAT
1 AAAT
430269 AATTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 14 0.67
21 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
AAATTTATAGAAGTATTAT
Found at i:432486 original size:2 final size:2
Alignment explanation
Indices: 432481--432528 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
432471 CACACACGTG
432481 TA TA TA -A 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
432522 TA TA TA T
1 TA TA TA T
432529 GTGTGTGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:437282 original size:26 final size:28
Alignment explanation
Indices: 437252--437313 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
437242 GAAAATTTTA
437252 AGCTC-GC-GAGTTTTCGAGTCGAGTCG
1 AGCTCTGCAGAGTTTTCGAGTCGAGTCG
*
437278 AGCTCCATTTCAGAGTTTTCGAGTCGAGTCG
1 AGCT-C--TGCAGAGTTTTCGAGTCGAGTCG
437309 AGCTC
1 AGCTC
437314 AGCAATACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
30 2 0.07
31 23 0.77
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCTCTGCAGAGTTTTCGAGTCGAGTCG
Found at i:445685 original size:37 final size:37
Alignment explanation
Indices: 445616--445772 Score: 190
Period size: 37 Copynumber: 4.3 Consensus size: 37
445606 CCTTGTTAGC
* * *
445616 TTAAAAGC-TCGATTCGTTCCCGCATGCATAACATAG
1 TTAAAAACATCGATACGTTCCAGCATGCATAACATAG
* * *
445652 TTCAAAACATCGATACGTTCCAGAATGCGTAACATAG
1 TTAAAAACATCGATACGTTCCAGCATGCATAACATAG
* * *
445689 TTAAAAACATCGATACATTCCAGCATGTATAACATAC
1 TTAAAAACATCGATACGTTCCAGCATGCATAACATAG
* * *
445726 TTAAAAACATCGATACTTTCCTGCATGCATAACATAC
1 TTAAAAACATCGATACGTTCCAGCATGCATAACATAG
*
445763 CTAAAAACAT
1 TTAAAAACAT
445773 TAAAATATTC
Statistics
Matches: 104, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
36 6 0.06
37 98 0.94
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (37 bp):
TTAAAAACATCGATACGTTCCAGCATGCATAACATAG
Found at i:448037 original size:13 final size:13
Alignment explanation
Indices: 448019--448044 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
448009 GTTGCGAAAT
448019 TTTAAAATTTAAA
1 TTTAAAATTTAAA
448032 TTTAAAATTTAAA
1 TTTAAAATTTAAA
448045 AATTCGATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAAAATTTAAA
Found at i:448166 original size:1 final size:1
Alignment explanation
Indices: 448157--448191 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
448147 AATATAAATT
* *
448157 AAAACAAAAAAAAACAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
448192 TTAAACAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:448170 original size:10 final size:10
Alignment explanation
Indices: 448157--448189 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
448147 AATATAAATT
448157 AAAACAAAAA
1 AAAACAAAAA
448167 AAAACAAAAA
1 AAAACAAAAA
448177 AAAA-AAAAA
1 AAAACAAAAA
448186 AAAA
1 AAAA
448190 AATTAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAACAAAAA
Found at i:449814 original size:122 final size:124
Alignment explanation
Indices: 449648--449884 Score: 460
Period size: 122 Copynumber: 1.9 Consensus size: 124
449638 TATATATTAT
449648 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
449713 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATA-TATATTTTCAAAAA
66 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATTTTCAAAAA
449771 ATATA-TTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
449835 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATAT
66 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATAT
449885 AATTTTCAAA
Statistics
Matches: 113, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
122 103 0.91
123 10 0.09
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.45
Consensus pattern (124 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATTTTCAAAAA
Found at i:449840 original size:36 final size:36
Alignment explanation
Indices: 449788--449955 Score: 117
Period size: 36 Copynumber: 4.6 Consensus size: 36
449778 TCAAAATGGT
* * * * *
449788 TTTTAAAAATTATATATTATATAAATGTTTTCATAACG
1 TTTTCAAAAGTATATA-T-TATAAATATTTTAAAAACG
*
449826 TTTTCAAAAGTATATATTATATATATTTTAAAAACG
1 TTTTCAAAAGTATATATTATAAATATTTTAAAAACG
* * **
449862 TTTTCAAAAACTATATATTATATAAT-TTTCAAAAATA
1 TTTTC-AAAAGTATATATTATA-AATATTTTAAAAACG
* * * * *
449899 TTTTAAAAACTATATAATATACATATTTTCAAAAAATG
1 TTTTCAAAAGTATATATTATAAATATTTT--AAAAACG
*
449937 TTTT--AAACTATATATTATA
1 TTTTCAAAAGTATATATTATA
449956 TATGTATTTT
Statistics
Matches: 108, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
35 2 0.02
36 52 0.48
37 28 0.26
38 26 0.24
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (36 bp):
TTTTCAAAAGTATATATTATAAATATTTTAAAAACG
Found at i:449934 original size:75 final size:72
Alignment explanation
Indices: 449788--449994 Score: 204
Period size: 75 Copynumber: 2.8 Consensus size: 72
449778 TCAAAATGGT
* * * * * * *
449788 TTTTAAAAATTATATATTATATAAATGTTTTC-ATAACGTTTTCAAAAGTATATATTATATATAT
1 TTTTAAAAACTATATATTATAT-AA--TTTTCAAAAACATTTTAAAAACTATATAATATACATAT
449852 TTTAAAAACG
63 TTTAAAAACG
*
449862 TTTTCAAAAACTATATATTATATAATTTTCAAAAATATTTTAAAAACTATATAATATACATATTT
1 TTTT-AAAAACTATATATTATATAATTTTCAAAAACATTTTAAAAACTATATAATATACATATTT
*
449927 TCAAAAAATG
65 T--AAAAACG
* **
449937 TTTT--AAACTATATATTATATATGTATTTTCAAAAACAATTTGCAAACTATATAATATA
1 TTTTAAAAACTATATATTATATA---ATTTTCAAAAACATTTTAAAAACTATATAATATA
449995 TATGTGTATA
Statistics
Matches: 113, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
72 22 0.19
73 28 0.25
74 6 0.05
75 57 0.50
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (72 bp):
TTTTAAAAACTATATATTATATAATTTTCAAAAACATTTTAAAAACTATATAATATACATATTTT
AAAAACG
Found at i:449936 original size:122 final size:122
Alignment explanation
Indices: 449669--449940 Score: 358
Period size: 122 Copynumber: 2.2 Consensus size: 122
449659 AAATGGTTTT
* *
449669 TAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAAGTATATATTATATATATTTTA
1 TAAAAATCATATATTATAAAAATGTTTTCATAACGTTTTCAAAAGTATATATTATATATATTTTA
** * *
449734 AAAACGTTTTCAAAAACTATATATATATTTTCAAAAAATATATTTCAAAATGGTTTT
66 AAAACGTTTTCAAAAACTATATATATATTTTCAAAAAATATATTTCAAAATACTATA
* *
449791 TAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAAGTATATATTATATATATTTTA
1 TAAAAATCATATATTATAAAAATGTTTTCATAACGTTTTCAAAAGTATATATTATATATATTTTA
449856 AAAACGTTTTCAAAAACTATATATTATATAATTTTC-AAAAATAT-TTT-AAAA-ACTATA
66 AAAACGTTTTCAAAAAC--TATA-TATAT-ATTTTCAAAAAATATATTTCAAAATACTATA
* *
449913 T-AATATACATATTTTCA-AAAAATGTTTT
1 TAAAAAT-CATATATT-ATAAAAATGTTTT
449941 AAACTATATA
Statistics
Matches: 136, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
121 4 0.03
122 101 0.74
123 5 0.04
124 7 0.05
125 13 0.10
126 6 0.04
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (122 bp):
TAAAAATCATATATTATAAAAATGTTTTCATAACGTTTTCAAAAGTATATATTATATATATTTTA
AAAACGTTTTCAAAAACTATATATATATTTTCAAAAAATATATTTCAAAATACTATA
Found at i:451109 original size:249 final size:248
Alignment explanation
Indices: 450645--451910 Score: 1451
Period size: 249 Copynumber: 5.1 Consensus size: 248
450635 GAGTCTTTGG
* * * * * * * * * * *
450645 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGA
* * * ** * * * * *
450709 ACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
66 ACTTAAGGGTC-TTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCT
* * * * * * * *
450774 CCGAAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTT
130 TCGAAGCTGAGCGTAGTCGAACTCG-AGG--GTTT-TTGGCAGATAGCCCTTCTCGACTTAAGTT
* * * *
450839 GTGCCGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGA
191 ATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGA
*
450897 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGTTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGA
*
450962 ACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCT
66 ACTTAAGGGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCT
* * *
451027 TCGAAGCTGAACGTAGTCGAACTCGAGGGTTTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTC
130 TCGAAGCTGAGCGTAGTCGAACTCGAGGGTTTTTGGCAGATAGCCCTTCTCGACTTAAGTTATAC
*
451092 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGA
195 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGA
*
451146 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTATAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGA
*
451211 ACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCT
66 ACTTAAGGGTCTTT-GTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCT
* * * *
451276 TCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTC
130 TCGAAGCTGAGCGTAGTCGAACTCGAGGGTTTTTGGCAGATAGCCCTTCTCGACTTAAGTTATAC
* * * * * *
451341 TGTAAATGATGTGCCTTGGAACTGAGCGTAGCCGAACTCAAAGGTCTTTGCTAA
195 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGA
*
451395 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGA
* * *
451460 ACTTAAGGGTC--T-TTGGCAGATAGCTCTTCTCA-ACTTAAGCTATACTGCAAATGATGTGCCT
66 ACTTAAGGGTCTTTGTTGGCAGATAACCCTTCT-AGACTTAAGTTATACTGCAAATGATGTGCCT
* * * * *
451521 T-GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTT
130 TCGAAGCTGAGCGTAGTCGAACTCGAGGGT-TTTTG---GCAGATAGCCCTTCTCGACTTAAGTT
* * *
451585 ATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTT-G-G-
191 ATACTGCAAATGATGTGCCTT-GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGA
* * * * * * * * *
451641 CAGATAGCCCTTCTCGACTTAAGCTATTCTGTAAATGATGTG-CCTTGGAA-CTGAGCGTAGTCG
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTT-GAAGCTGAGTGTAATCG
* * * ** * * * * * *
451704 AACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCC
65 AACTTAAGGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTG-CC
* * ** * * *
451769 TT-GAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCTCTTCTCAACTTAAGTTATA
129 TTCGAAGCTGAGCGTAGTCGAACTCGAGGGTTTTTGGCAGATAGCCCTTCTCGACTTAAGTTATA
* *
451833 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC-TTGGTGGG
194 CTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT-GA
* *
451888 CAGATAGCCCTTCTGGCCTTGAG
1 CAGATAACCCTTCTAGCCTTGAG
451911 CTAAGCTGCA
Statistics
Matches: 885, Mismatches: 111, Indels: 41
0.85 0.11 0.04
Matches are distributed among these distances:
243 2 0.00
244 50 0.06
245 117 0.13
246 38 0.04
247 23 0.03
248 78 0.09
249 446 0.50
250 3 0.00
252 40 0.05
253 88 0.10
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (248 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGA
ACTTAAGGGTCTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATACTGCAAATGATGTGCCTT
CGAAGCTGAGCGTAGTCGAACTCGAGGGTTTTTGGCAGATAGCCCTTCTCGACTTAAGTTATACT
GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGA
Found at i:451184 original size:164 final size:162
Alignment explanation
Indices: 450567--451910 Score: 1349
Period size: 164 Copynumber: 8.1 Consensus size: 162
450557 TTATTGACAA
* * * * * * * *
450567 ATAACCTTTCTCGCCATGAGTTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACT
* * * * *
450632 C-GGGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGC
66 CAAGG-GTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCTTGAAGC
450696 TGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAG
130 TGAGCGTAGTCGAACTCAAAGGTCTTTTGG---CAG
** *
450732 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCCCGAAGCTGAGTGTAATCAAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACT
* * * * * * *
450797 CGAA-GGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCCGCAAATGATATGCCTTG
66 C-AAGGGTC---T-TTGGCAGATAGCCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCTTG
* * *
450861 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
126 AAGCTGAGCGTAGTCGAACTCAAAGGTCTTT--TGGCAG
* *
450900 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGTTGAGTGTAATCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACT
* * * *
450965 TAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCG
66 CAAGGGTC--T--TTGGCAGATAGCCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCTT-G
* * *
451030 AAGCTGAACGTAGTCGAACTCGAGGGT-TTTTGGCAG
126 AAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGCAG
* * * * * * * * * *
451066 ATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACT
* * * * * * * *
451130 CAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGA
66 CAAGGGTCTTT-G-G-CAGATAGCCCTTCTAGACTTAAGCTATACTGCAAATGATGTG-CCTTGA
** * * *
451195 AGCTGAGTATAATCGAACTTAAGGGTCTTTAGTTGGCAG
127 AGCTGAGCGTAGTCGAACTCAAAGGTC-TT--TTGGCAG
* * * * * ** *
451234 ATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTG-CCTTCGAAGCTGAACGTAGTCGAAC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTT-GAAGCTGAGTGTAATCGAAC
* * * *
451298 TCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGTAAATGATGTGCCTTGGAA-
65 TCAAGGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCTT-GAAG
* **
451362 CTGAGCGTAGCCGAACTCAAAGGTCTTTGCTAACAG
129 CTGAGCGTAGTCGAACTCAAAGGTCTTT--TGGCAG
* *
451398 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACT
* * *
451463 TAAGGGTCTTTGGCAGATAGCTCTTCTCA-ACTTAAGCTATACTGCAAATGATGTGCCTTGGAGC
66 CAAGGGTCTTTGGCAGATAGCCCTTCT-AGACTTAAGCTATACTGCAAATGATGTGCCTTGAAGC
451527 TGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAG
130 TGAGCGTAGTCGAACTCAAAGGTCTTTTG---GCAG
* * * * * ** *
451563 ATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTG-CCTTCGAAGCTGAACGTAGTCGAAC
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTT-GAAGCTGAGTGTAATCGAAC
* * * *
451627 TCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGTAAATGATGTGCCTTGGAA-
65 TCAAGGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCTT-GAAG
**
451691 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAG
129 CTGAGCGTAGTCGAACTCAAAGGTCTTT--TGGCAG
* *
451727 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACT
1 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACT
* * * *
451792 TAAGGGTCTTTGGCAGATAGCTCTTCTCA-ACTTAAGTTATACTGCAAATGATGTGCCTTGGAGC
66 CAAGGGTCTTTGGCAGATAGCCCTTCT-AGACTTAAGCTATACTGCAAATGATGTGCCTTGAAGC
* * *
451856 TGAGCGTAGTCAAACTCGAAGGTCTTGGTGGGCAG
130 TGAGCGTAGTCGAACTCAAAGGTCTT--TTGGCAG
* *
451891 ATAGCCCTTCTGGCCTTGAG
1 ATAACCCTTCTAGCCTTGAG
451911 CTAAGCTGCA
Statistics
Matches: 991, Mismatches: 149, Indels: 79
0.81 0.12 0.06
Matches are distributed among these distances:
161 2 0.00
162 3 0.00
163 6 0.01
164 347 0.35
165 255 0.26
166 80 0.08
167 7 0.01
168 163 0.16
169 126 0.13
171 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (162 bp):
ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACT
CAAGGGTCTTTGGCAGATAGCCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCTTGAAGCT
GAGCGTAGTCGAACTCAAAGGTCTTTTGGCAG
Found at i:451576 original size:329 final size:329
Alignment explanation
Indices: 450625--451881 Score: 1571
Period size: 329 Copynumber: 3.8 Consensus size: 329
450615 TTGAGTGTAA
* *
450625 TCGAACTCG-GGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCC
1 TCGAACTCGAGG-GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCC
* * *
450689 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTT
65 TTGGAACTGAGCGTAGTCGAACTCAAAGGTC-TTTGCTAACAGATAACCCTTCTAGCCTTGAGTT
* ** * *
450754 ATGCTGTAAATGATGTGCCCCCGAAGCTGAGTGTAATCAAACTCGAA-GGTCTTTTGTTGGCAGA
129 ATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACT-TAAGGGTC---T-TTGGCAGA
* * * * *
450818 CAACCCTTCTAGACTTAAGTTGTGCCGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCG
189 TAACCCTTCTAGACTTAAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCA
* * * * * * * *
450883 AAGGTCTTTGGTGA-CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTT-GA
254 AAGGTCTTTAGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTG-CCTTCGA
* ** *
450946 AGTTGAGTGTAA
318 AGCTGAACGTAG
** * * * *
450958 TCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGT
1 TCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGT
* * * * ** * * * *
451023 GCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGT-TTT--TGGCAGATAGCCCTTCTCGACTTAA
62 GCCTTGGAA-CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGA
* * * * * * * * *
451085 GCTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAG
126 GTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTT-G-G-CAG
* * * * * ** *
451149 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTATAATCGAACT
188 ATAACCCTTCTAGACTTAAGTTATACTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACT
* * *
451214 TAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCG
252 CAAAGGTCTTTAGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCG
451279 AAGCTGAACGTAG
317 AAGCTGAACGTAG
*
451292 TCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGTAAATGATGTGCCT
1 TCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCT
*
451357 TGGAACTGAGCGTAGCCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTAT
66 TGGAACTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTAT
* * *
451422 GCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCTCT
131 GCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAACCCT
* *
451487 TCTCA-ACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
196 TCT-AGACTTAAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
*
451551 TTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAA
260 TTTAGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAA
451616 CGTAG
325 CGTAG
*
451621 TCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGTAAATGATGTGCCT
1 TCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCT
451686 TGGAACTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTAT
66 TGGAACTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTAT
* * *
451751 GCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCTCT
131 GCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAACCCT
* * *
451816 TCTCA-ACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTC
196 TCT-AGACTTAAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
451880 TT
260 TT
451882 GGTGGGCAGA
Statistics
Matches: 804, Mismatches: 102, Indels: 40
0.85 0.11 0.04
Matches are distributed among these distances:
329 374 0.47
330 85 0.11
331 3 0.00
332 74 0.09
333 99 0.12
334 97 0.12
335 1 0.00
336 3 0.00
337 47 0.06
338 21 0.03
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (329 bp):
TCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCT
TGGAACTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTAT
GCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAACCCT
TCTAGACTTAAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCT
TTAGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAAC
GTAG
Found at i:455170 original size:18 final size:19
Alignment explanation
Indices: 455129--455173 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
455119 AGTTAATGTG
455129 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
455148 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
455166 AATGCAAA
1 AATGCAAA
455174 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:457054 original size:2 final size:2
Alignment explanation
Indices: 457049--457095 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
457039 AATAAAGTTA
457049 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
457090 AT AT AT
1 AT AT AT
457096 GAACGAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:458339 original size:11 final size:11
Alignment explanation
Indices: 458307--458341 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
458297 CCCTGCACAA
* *
458307 AAATAAATGAG
1 AAATAAATAAT
458318 AAATAAATAAT
1 AAATAAATAAT
458329 AAATAAATAAT
1 AAATAAATAAT
458340 AA
1 AA
458342 TAATATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:458434 original size:38 final size:36
Alignment explanation
Indices: 458361--458747 Score: 219
Period size: 38 Copynumber: 10.0 Consensus size: 36
458351 ATATATAAAC
* *
458361 GTTTTCAAAAACGTATA-A-TATATAAATTTTTAAAAT
1 GTTTT-AAAAAC-TATATATTATATATATTTTCAAAAT
458397 GTTTTAAAAAAACTATATATTATATATATTTTCAAAAT
1 GTTTT--AAAAACTATATATTATATATATTTTCAAAAT
* * * *
458435 GGTTTTTAAAAATTATATATTATATAAATGTTTTCATAAC
1 -G-TTTTAAAAACTATATATTATAT--ATATTTTCAAAAT
* * * *
458475 GTTTTCAAAAGTATATATTATATATATTTTTAAAAC
1 GTTTTAAAAACTATATATTATATATATTTTCAAAAT
458511 GTTTTCAAAAACTATATATTATATA-ATTTTCAAAAAATATATT
1 GTTTT-AAAAACTATATATTATATATATTTTC----AA-A-A-T
* * * * * *
458554 TTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAAC
1 GT----------TTTAAAAACTATATATTATATATATTTT--CAAAAT
* * * *
458602 GTTTTCAAAAGTATATATTATATATATTTTAAAAAC
1 GTTTTAAAAACTATATATTATATATATTTTCAAAAT
458638 GTTTTCAAAAACTATATATTATATA-ATTTTCAAAAAT
1 GTTTT-AAAAACTATATATTATATATATTTTC-AAAAT
* * *
458675 ATTTTAAAAACTATATAATATACATATTTTCAAAAAAT
1 GTTTTAAAAACTATATATTATATATATTTTC--AAAAT
458713 GTTTT--AAACTATATATTATATATGTATTTTCAAAA
1 GTTTTAAAAACTATATATTATATA--TATTTTCAAAA
458748 ACAATTTGCA
Statistics
Matches: 279, Mismatches: 38, Indels: 68
0.72 0.10 0.18
Matches are distributed among these distances:
36 79 0.28
37 55 0.20
38 94 0.34
39 2 0.01
40 16 0.06
41 1 0.00
42 1 0.00
43 1 0.00
48 1 0.00
49 1 0.00
50 1 0.00
51 1 0.00
52 18 0.06
53 7 0.03
55 1 0.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
GTTTTAAAAACTATATATTATATATATTTTCAAAAT
Found at i:458544 original size:25 final size:25
Alignment explanation
Indices: 458512--458588 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
458502 TTTTAAAACG
*
458512 TTTTCAAAAACTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
* * **
458537 TTTTCAAAAAATATATTTTCAAAATGG
1 TTTTCAAAAAATATATATT--ATATAA
* *
458564 TTTTTAAAAATTATATATTATATAA
1 TTTTCAAAAAATATATATTATATAA
458589 ATGTTTTCAT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
25 20 0.51
27 19 0.49
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (25 bp):
TTTTCAAAAAATATATATTATATAA
Found at i:458556 original size:15 final size:16
Alignment explanation
Indices: 458531--458560 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
458521 ACTATATATT
458531 ATATAATTTTCAAAAA
1 ATATAATTTTCAAAAA
458547 ATAT-ATTTTCAAAA
1 ATATAATTTTCAAAA
458561 TGGTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATTTTCAAAAA
Found at i:458569 original size:127 final size:127
Alignment explanation
Indices: 458420--458673 Score: 499
Period size: 127 Copynumber: 2.0 Consensus size: 127
458410 TATATATTAT
458420 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
*
458485 GTATATATTATATATATTTTTAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
458547 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
458612 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
66 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
458674 TATTTTAAAA
Statistics
Matches: 126, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 126 1.00
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (127 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAA
Found at i:458595 original size:27 final size:26
Alignment explanation
Indices: 458494--458595 Score: 70
Period size: 27 Copynumber: 3.8 Consensus size: 26
458484 AGTATATATT
* *
458494 ATATATATT-TTTAAAACGTTTTCAAAA
1 ATATATATTATAT-AAATGTTTT-AAAA
*
458521 ACTATATATTATAT-AAT-TTTCAAAA
1 A-TATATATTATATAAATGTTTTAAAA
*
458546 A-ATATATTTTCA-AAATGGTTTTTAAAA
1 ATATATATTAT-ATAAAT-G-TTTTAAAA
458573 ATTATATATTATATAAATGTTTT
1 A-TATATATTATATAAATGTTTT
458596 CATAACGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
23 8 0.14
24 4 0.07
25 5 0.08
26 3 0.05
27 15 0.25
28 10 0.17
29 14 0.24
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (26 bp):
ATATATATTATATAAATGTTTTAAAA
Found at i:460522 original size:2 final size:2
Alignment explanation
Indices: 460515--460548 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
460505 AAATAAATAA
*
460515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
460549 TTAAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:462741 original size:4 final size:4
Alignment explanation
Indices: 462732--462867 Score: 254
Period size: 4 Copynumber: 34.0 Consensus size: 4
462722 TTAACTAATA
462732 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
462780 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
462828 TATG TATG TATG TATG TATG TATA TATG TATG AATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
462868 CTGTTTCAAC
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 128 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:464803 original size:3 final size:3
Alignment explanation
Indices: 464795--464820 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
464785 CGATTATTGT
464795 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
464821 TTTCTAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:467167 original size:13 final size:13
Alignment explanation
Indices: 467149--467173 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
467139 TTCTTATATC
467149 TTTTCATAGTCGT
1 TTTTCATAGTCGT
467162 TTTTCATAGTCG
1 TTTTCATAGTCG
467174 GGAGACTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (13 bp):
TTTTCATAGTCGT
Found at i:467512 original size:60 final size:59
Alignment explanation
Indices: 467349--467518 Score: 198
Period size: 60 Copynumber: 2.8 Consensus size: 59
467339 GATCTAATTT
* * *
467349 TAAATTGGTCCCTAAACTTTTAAATATTTCAATTACATCCCTATACTATGACTATCATTC
1 TAAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATCCC-AAACTATAACTATCATTC
* * * * * *
467409 TAAAATAGT-CCTCAAACTTTTGAACATTTCAATCTCATCCCCAAACTATAACTTTCATTC
1 TAAATTGGTCCCT-AAACTTTTAAATATTTCAATTTCAT-CCCAAACTATAACTATCATTC
* *
467469 TAAATTGGTCCCTAAAATTTTTAAATATTCCAATTTCATCCCAAACTATA
1 TAAATTGGTCCCT-AAACTTTTAAATATTTCAATTTCATCCCAAACTATA
467519 CGTATATTAT
Statistics
Matches: 90, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
59 3 0.03
60 61 0.68
61 26 0.29
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (59 bp):
TAAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATCCCAAACTATAACTATCATTC
Found at i:483716 original size:10 final size:10
Alignment explanation
Indices: 483688--483722 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
483678 AGAGAGAACT
*
483688 GAGAAAGACA
1 GAGAAAGAGA
483698 GAGAAAGAGA
1 GAGAAAGAGA
483708 GAGAAAGAGA
1 GAGAAAGAGA
483718 G-GAAA
1 GAGAAA
483723 AATTATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.17
10 20 0.83
ACGTcount: A:0.60, C:0.03, G:0.37, T:0.00
Consensus pattern (10 bp):
GAGAAAGAGA
Found at i:484679 original size:3 final size:3
Alignment explanation
Indices: 484671--484712 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
484661 TGTCAACCCC
484671 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
484713 TCATCCCACC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:486652 original size:25 final size:25
Alignment explanation
Indices: 486598--486653 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
486588 TTTAACCAAA
*
486598 ATTTTATTTTTTATTTTTATTTTTT
1 ATTTTATTTTTTATTTTTATTTTAT
486623 ATTTTATTTTTTATTTTTATATTTAT
1 ATTTTATTTTTTATTTTTAT-TTTAT
*
486649 TTTTT
1 ATTTT
486654 TATATTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 20 0.71
26 8 0.29
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (25 bp):
ATTTTATTTTTTATTTTTATTTTAT
Found at i:486653 original size:13 final size:13
Alignment explanation
Indices: 486599--486652 Score: 85
Period size: 12 Copynumber: 4.3 Consensus size: 13
486589 TTAACCAAAA
486599 TTTTATTTTTTAT
1 TTTTATTTTTTAT
486612 TTTTATTTTTTA-
1 TTTTATTTTTTAT
486624 TTTTATTTTTTAT
1 TTTTATTTTTTAT
*
486637 TTTTA-TATTTAT
1 TTTTATTTTTTAT
486649 TTTT
1 TTTT
486653 TTATATTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
12 22 0.56
13 17 0.44
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:490269 original size:38 final size:38
Alignment explanation
Indices: 490227--490344 Score: 227
Period size: 38 Copynumber: 3.1 Consensus size: 38
490217 AACTGATAGC
*
490227 TTTAAACCTTCGTGGGAAATTCGACAAGGGGATCTGCT
1 TTTAAACCTTCGTGGGGAATTCGACAAGGGGATCTGCT
490265 TTTAAACCTTCGTGGGGAATTCGACAAGGGGATCTGCT
1 TTTAAACCTTCGTGGGGAATTCGACAAGGGGATCTGCT
490303 TTTAAACCTTCGTGGGGAATTCGACAAGGGGATCTGCT
1 TTTAAACCTTCGTGGGGAATTCGACAAGGGGATCTGCT
490341 TTTA
1 TTTA
490345 CCTTATCTGT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 79 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (38 bp):
TTTAAACCTTCGTGGGGAATTCGACAAGGGGATCTGCT
Found at i:499591 original size:17 final size:17
Alignment explanation
Indices: 499569--499606 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
499559 AAATTATTAC
499569 TCGACCACTCATATATT
1 TCGACCACTCATATATT
499586 TCGACCACTCATATATT
1 TCGACCACTCATATATT
499603 TCGA
1 TCGA
499607 AATTATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (17 bp):
TCGACCACTCATATATT
Found at i:500591 original size:141 final size:141
Alignment explanation
Indices: 500337--500616 Score: 488
Period size: 141 Copynumber: 2.0 Consensus size: 141
500327 CCACCGAAAA
*
500337 GGCGGGAGAGCAGGCGGCCGGTTTCAATATCTCTGTTTCTCTCTCACTTCCTCCTTGCACCCAAA
1 GGCGGGAGAGCAGGCGACCGGTTTCAATATCTCTGTTTCTCTCTCACTTCCTCCTTGCACCCAAA
* *
500402 TGTACGGATTTTATTGGTTTCATTTATGAATCCATCACAGGCTTCCAAAGACTTACTTCAAAGAT
66 TGTACGGATTTTATTGCTTTCATTTAGGAATCCATCACAGGCTTCCAAAGACTTACTTCAAAGAT
500467 AAATTTTAAAT
131 AAATTTTAAAT
* *
500478 GGCGGGAGAGCAGGCGATCGGTTTCAATATCTCTGTTTCTCTCTCACTTCCTCCTTGTACCCAAA
1 GGCGGGAGAGCAGGCGACCGGTTTCAATATCTCTGTTTCTCTCTCACTTCCTCCTTGCACCCAAA
* *
500543 TGTACGGATTTTATTGCTTTCATTTAGGAATCCATCACAGTCTTCCAAAGACTTACTTCAAAGCT
66 TGTACGGATTTTATTGCTTTCATTTAGGAATCCATCACAGGCTTCCAAAGACTTACTTCAAAGAT
*
500608 AACTTTTAA
131 AAATTTTAA
500617 GCTATTATTT
Statistics
Matches: 131, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
141 131 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (141 bp):
GGCGGGAGAGCAGGCGACCGGTTTCAATATCTCTGTTTCTCTCTCACTTCCTCCTTGCACCCAAA
TGTACGGATTTTATTGCTTTCATTTAGGAATCCATCACAGGCTTCCAAAGACTTACTTCAAAGAT
AAATTTTAAAT
Found at i:528449 original size:24 final size:25
Alignment explanation
Indices: 528397--528450 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
528387 ATAATCGCGG
*
528397 TTGATGCTATGAGTTTCCTTCCGGGT
1 TTGATGC-ATGAGTTTCCTTCCGGAT
*
528423 TTGATGC-TGAGTTTCCTTCCGTAT
1 TTGATGCATGAGTTTCCTTCCGGAT
528447 TTGA
1 TTGA
528451 ATCTTGTGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 19 0.73
26 7 0.27
ACGTcount: A:0.13, C:0.19, G:0.24, T:0.44
Consensus pattern (25 bp):
TTGATGCATGAGTTTCCTTCCGGAT
Found at i:539377 original size:16 final size:16
Alignment explanation
Indices: 539356--539388 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
539346 TCGATCATAT
539356 ATGTAAGAATAGACTG
1 ATGTAAGAATAGACTG
539372 ATGTAAGAATAGACTG
1 ATGTAAGAATAGACTG
539388 A
1 A
539389 GGGAAAGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.06, G:0.24, T:0.24
Consensus pattern (16 bp):
ATGTAAGAATAGACTG
Found at i:540978 original size:23 final size:23
Alignment explanation
Indices: 540952--540999 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
540942 ATAAAGTACA
*
540952 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
540975 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
540998 AT
1 AT
541000 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:541750 original size:18 final size:18
Alignment explanation
Indices: 541727--541763 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
541717 CGAAATATAT
541727 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
541745 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
541763 A
1 A
541764 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:541999 original size:22 final size:23
Alignment explanation
Indices: 541967--542030 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
541957 ATGCGAGATA
541967 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
541990 GATACC-ATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
542012 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
542031 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 19 0.53
23 17 0.47
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:542215 original size:31 final size:30
Alignment explanation
Indices: 542175--542241 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
542165 TCATTTGCAC
* *
542175 AAAA-ATTATTT-GATTGTTTTTATATTTTAT
1 AAAATATTATTTAGAAT-TTTTTA-ATTTAAT
542205 AAAATATTATTTAGAATTTTTTAATTTAAT
1 AAAATATTATTTAGAATTTTTTAATTTAAT
*
542235 AATATAT
1 AAAATAT
542242 ACCGTAACGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 16 0.50
31 13 0.41
32 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (30 bp):
AAAATATTATTTAGAATTTTTTAATTTAAT
Found at i:542421 original size:23 final size:23
Alignment explanation
Indices: 542393--542451 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
542383 TATAACCATT
542393 TATTACATTATATAAACGATACC
1 TATTACATTATATAAACGATACC
** *
542416 TATTACATTATATAAGGGCTACC
1 TATTACATTATATAAACGATACC
*
542439 TATTACATCATAT
1 TATTACATTATAT
542452 GTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACC
Found at i:545685 original size:183 final size:184
Alignment explanation
Indices: 545266--545800 Score: 1015
Period size: 181 Copynumber: 2.9 Consensus size: 184
545256 ACTTATATTA
545266 TGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATATGGACATAAAGTA
1 TGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATATGGACATAAAGTA
545331 CCGACACAATATTAAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATAT
66 CCGACACAATATT-AAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATAT
545396 TTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
130 TTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
545451 TGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATATGGACATAAAGTA
1 TGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATATGGACATAAAGTA
545516 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATT
66 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATT
545581 TATACCGGTTATATTACAAAA-TATCTATTACATTATAATTATGGGTTCCGATG
131 TATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
*
545634 TGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGAC--AAAGTA
1 TGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATATGGACATAAAGTA
545697 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATT
66 CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATT
*
545762 TATACCGGTTATATTACAAAATTATCTATT-TATTATAAT
131 TATACCGGTTATATTACAAAATTATCTATTACATTATAAT
545801 ATGTTGAAAG
Statistics
Matches: 347, Mismatches: 2, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
181 100 0.29
182 8 0.02
183 88 0.25
184 73 0.21
185 78 0.22
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAATATGGACATAAAGTA
CCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAGACCGGTATATT
TATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATG
Found at i:547157 original size:3 final size:3
Alignment explanation
Indices: 547149--547232 Score: 71
Period size: 3 Copynumber: 28.0 Consensus size: 3
547139 ACTTGTTTGG
* * * **
547149 ATC ATC ATC TTC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGT-
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A-TC
* * * *
547197 TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
547233 GTCAGCTTCA
Statistics
Matches: 61, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
2 1 0.02
3 60 0.98
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:547166 original size:12 final size:12
Alignment explanation
Indices: 547149--547247 Score: 65
Period size: 12 Copynumber: 8.0 Consensus size: 12
547139 ACTTGTTTGG
547149 ATCATCATCTTC
1 ATCATCATCTTC
547161 ATCATCATCATCATC
1 ATCATCATC-T--TC
*
547176 GTCATCATCTTC
1 ATCATCATCTTC
**
547188 ATCGCCAGT-TTC
1 ATCATCA-TCTTC
* *
547200 ATCGTCATCATC
1 ATCATCATCTTC
*
547212 ATCATCATCGTC
1 ATCATCATCTTC
* *
547224 ATCTTCATCGTC
1 ATCATCATCTTC
* *
547236 AGCTTCATCTTC
1 ATCATCATCTTC
547248 TGCGACCGAT
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
11 1 0.01
12 57 0.80
13 2 0.03
14 1 0.01
15 10 0.14
ACGTcount: A:0.22, C:0.33, G:0.07, T:0.37
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:547247 original size:6 final size:6
Alignment explanation
Indices: 547153--547247 Score: 57
Period size: 6 Copynumber: 15.3 Consensus size: 6
547143 GTTTGGATCA
* * * * *
547153 TCATCT TCATCA TCATCA TCATCGT CATCATCT TCATCG CCAGT-T TCATCG
1 TCATCT TCATCT TCATCT TCATC-T --TCATCT TCATCT TCA-TCT TCATCT
* * * * *
547204 TCATCA TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
547248 TGCGACCGAT
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
5 1 0.01
6 62 0.89
7 1 0.01
8 1 0.01
9 5 0.07
ACGTcount: A:0.21, C:0.34, G:0.07, T:0.38
Consensus pattern (6 bp):
TCATCT
Found at i:549162 original size:198 final size:199
Alignment explanation
Indices: 548708--550102 Score: 2500
Period size: 198 Copynumber: 7.1 Consensus size: 199
548698 TTTAAATTAG
* *
548708 TATCGACACAAA-TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
548772 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
548837 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC-GGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
548899 AAAA
196 AAAA
*
548903 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
548968 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
549033 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTT-ATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
549097 AAAA
196 AAAA
*
549101 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTTATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
549166 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
549230 CGACACTTTTTATAT-TGGATCGACACTTTATTGATGCACCTTG--TTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
549292 AAAA
196 AAAA
549296 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
549361 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
549425 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
549490 AAAA
196 AAAA
549494 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
549558 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
549623 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGG-A
549688 AAAAAA
194 AAAAAA
549694 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
549759 ATTGTACCGGTTAGATTGAAAAA-TACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
549822 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTTAATTCATTCTGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TTTTTAATTCATTCTGGGAA
549887 AAAAA
195 AAAAA
549892 TATCGACACAAAC--TATTAGTGTCGACACATTATTTAGACTT-TTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
549954 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
550019 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCT-GGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
550083 AAAA
196 AAAA
550087 TATCGACACAAACTAT
1 TATCGACACAAACTAT
550103 TAGTATCGAC
Statistics
Matches: 1165, Mismatches: 17, Indels: 34
0.96 0.01 0.03
Matches are distributed among these distances:
194 41 0.04
195 198 0.17
196 251 0.22
197 116 0.10
198 350 0.30
199 84 0.07
200 92 0.08
201 33 0.03
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGGAAA
AAAA
Found at i:549485 original size:393 final size:397
Alignment explanation
Indices: 548708--550102 Score: 2507
Period size: 393 Copynumber: 3.5 Consensus size: 397
548698 TTTAAATTAG
* *
548708 TATCGACACAAA-TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATT
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
548772 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
548837 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTC-GGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTG-TTTTAATTCATTCTGGAAAA
*
548899 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGG
548964 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
* *
549029 GGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTT-ATTCATTCTGG
325 GGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG
*
549093 GAAAAAAA
390 AAAAAAAA
*
549101 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTTATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
549166 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
549230 CGACACTTTTTATAT-TGGATCGACACTTTATTGATGCACCTTG-TTTAATTCATTCTGGAAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTAATTCATTCTGGAAAAA
549293 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
196 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
549358 ATAATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
261 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
549422 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGA
326 GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGA
549487 AAAAAAA
391 AAAAAAA
549494 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
549558 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
549623 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATGGATGCACCTTG-TTTTAATTCATTCT-GGAA
549688 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
193 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC
549753 GGTATAATTGTACCGGTTAGATTGAAAAA-TACATATTACATTATACTTTTGGGTTCGATGA-TT
258 GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
549816 TGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTTAATTCATTC
323 TGGGATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TTTTTAATTCATTC
549881 TGGAAAAAAAA
387 TGGAAAAAAAA
549892 TATCGACACAAAC--TATTAGTGTCGACACATTATTTAGACTT-TTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
549954 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
550019 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTG-TTTTAATTCATTCTGGAAAA
550083 AAAATATCGACACAAACTAT
195 AAAATATCGACACAAACTAT
550103 TAGTATCGAC
Statistics
Matches: 972, Mismatches: 16, Indels: 28
0.96 0.02 0.03
Matches are distributed among these distances:
392 173 0.18
393 223 0.23
394 145 0.15
395 89 0.09
396 110 0.11
397 65 0.07
398 162 0.17
399 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (397 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGATGCACCTTGTTTTAATTCATTCTGGAAAAA
AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGT
ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
GATCGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGA
AAAAAAA
Found at i:550222 original size:19 final size:19
Alignment explanation
Indices: 550195--550235 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
550185 ATTCACATAA
550195 AAAAATATAAATCGTATAC
1 AAAAATATAAATCGTATAC
* *
550214 AAAATTATAAATCTTATAC
1 AAAAATATAAATCGTATAC
550233 AAA
1 AAA
550236 TTAACTCGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAATATAAATCGTATAC
Found at i:552061 original size:33 final size:33
Alignment explanation
Indices: 552024--552089 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
552014 CATCTTAATA
*
552024 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
552057 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
552090 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:554233 original size:24 final size:24
Alignment explanation
Indices: 554196--554248 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
554186 CCGTTCTATC
554196 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
554220 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
554244 TATTT
1 TATTT
554249 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:554439 original size:20 final size:19
Alignment explanation
Indices: 554393--554439 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
554383 TCTGGTATCA
*
554393 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
554412 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
554433 TTTTACC
1 TTTTACC
554440 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:554585 original size:20 final size:20
Alignment explanation
Indices: 554558--554604 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
554548 ACACTTTTAA
554558 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
554577 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
554598 TTTTACC
1 TTTTACC
554605 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:555087 original size:229 final size:227
Alignment explanation
Indices: 554670--555118 Score: 783
Period size: 229 Copynumber: 2.0 Consensus size: 227
554660 TTAAAACTGC
554670 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTATGTTTTCCACCTACAATAT
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTATGTTTTCCACCTACAATAT
**
554735 TAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTATT
66 TAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
* *
554800 TAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAG
131 TAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
*
554865 TATGGACACTTTTATAAAAATGATATATACTT
196 TATGGACACTTTTATAAAAAGGATATATACTT
*
554897 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTT-ATGTTTTCCACCTACAAT
*
554962 ATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTTATAAAATATT
64 ATTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATA-TTTTATAAAATATT
* *
555027 ATTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAAT
128 ATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAAT
555091 AAGTATGGACACTTTTATAAAAAGGATA
193 AAGTATGGACACTTTTATAAAAAGGATA
555119 GATAATTTAC
Statistics
Matches: 210, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
227 4 0.02
228 40 0.19
229 102 0.49
230 64 0.30
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (227 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTATGTTTTCCACCTACAATAT
TAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATT
TAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
TATGGACACTTTTATAAAAAGGATATATACTT
Found at i:556047 original size:11 final size:12
Alignment explanation
Indices: 556030--556059 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
556020 CATTTAATAG
556030 TTTATTATTTAA
1 TTTATTATTTAA
556042 -TTATTATTTAA
1 TTTATTATTTAA
556053 TTTATTA
1 TTTATTA
556060 ATTTTCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTATTATTTAA
Found at i:559586 original size:26 final size:26
Alignment explanation
Indices: 559557--559607 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
559547 TTGAAGAGTA
559557 TGATAAATTTTTCCAACATAAAATTG
1 TGATAAATTTTTCCAACATAAAATTG
559583 TGATAAATTTTTCCAACATAAAATT
1 TGATAAATTTTTCCAACATAAAATT
559608 CTCTAGAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (26 bp):
TGATAAATTTTTCCAACATAAAATTG
Found at i:571767 original size:28 final size:28
Alignment explanation
Indices: 571736--571794 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
571726 TAGTTGGGTT
*
571736 ACTATTTTGTAACCTTGATAGTCGAGTG
1 ACTATTTTGTAACCTTGATAGTCGAGAG
571764 ACTATTTTGTAACCTTGATAGTCGAGAG
1 ACTATTTTGTAACCTTGATAGTCGAGAG
571792 ACT
1 ACT
571795 CAACAAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.37
Consensus pattern (28 bp):
ACTATTTTGTAACCTTGATAGTCGAGAG
Found at i:572548 original size:16 final size:18
Alignment explanation
Indices: 572511--572547 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
572501 AAAACTATAG
572511 AAATTAGTTATAATTAAA
1 AAATTAGTTATAATTAAA
*
572529 AAATT-GTTGTAATTAAA
1 AAATTAGTTATAATTAAA
572546 AA
1 AA
572548 TATAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (18 bp):
AAATTAGTTATAATTAAA
Done.