Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006655.1 Hibiscus syriacus cultivar Beakdansim tig00016430_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: 456786
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 3
Found at i:167732 original size:26 final size:22
Alignment explanation
Indices: 167682--167725 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
167672 ATTTATTCAG
167682 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
167704 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
167726 AAAATATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:167786 original size:31 final size:31
Alignment explanation
Indices: 167749--167807 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
167739 AGTTGTATGG
*
167749 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTGCAAAACTAAA
167780 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTGCAAAACT
167808 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTGCAAAACTAAA
Found at i:183857 original size:30 final size:29
Alignment explanation
Indices: 183816--183911 Score: 165
Period size: 30 Copynumber: 3.2 Consensus size: 29
183806 AAAGAAAGTC
183816 AAGGTAGCTATGCACATTTTTTCTGTGTTG
1 AAGGT-GCTATGCACATTTTTTCTGTGTTG
183846 AAGGTGTCTATGCACATTTTTTCTGTGTTG
1 AAGGTG-CTATGCACATTTTTTCTGTGTTG
183876 AAGGTAGCTATGCACATTTTTTCTGTGTTG
1 AAGGT-GCTATGCACATTTTTTCTGTGTTG
183906 AAGGTG
1 AAGGTG
183912 GTGGTGTAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
29 2 0.03
30 61 0.95
31 1 0.02
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.43
Consensus pattern (29 bp):
AAGGTGCTATGCACATTTTTTCTGTGTTG
Found at i:187347 original size:19 final size:19
Alignment explanation
Indices: 187323--187373 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
187313 ATAGGATTTA
187323 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
187342 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
187361 TGCATCGATGCAT
1 TGCATCGATGCAT
187374 CCCCATTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCATAAGGAG
Found at i:187353 original size:83 final size:83
Alignment explanation
Indices: 187258--187437 Score: 240
Period size: 83 Copynumber: 2.2 Consensus size: 83
187248 ATTGTTTAAG
* *
187258 GTGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTT
1 GTGCATCGATGCACAAGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTT
187322 ATGCATCGATGCATAAG-G-A
64 ATGCATCGATGCAT-AGTGTA
* * * *
187341 GTGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 GTGCATCGATGCACAAGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTTA
*
187406 TGCATCGATGCATGGTGTA
65 TGCATCGATGCATAGTGTA
187425 GTGCATCGATGCA
1 GTGCATCGATGCA
187438 TACCTTCATT
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
82 1 0.01
83 63 0.73
84 21 0.24
85 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (83 bp):
GTGCATCGATGCACAAGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTAT
GCATCGATGCATAGTGTA
Found at i:189181 original size:149 final size:150
Alignment explanation
Indices: 188912--189225 Score: 461
Period size: 149 Copynumber: 2.1 Consensus size: 150
188902 GTCGAGGGTC
* * * * * * * *
188912 TACGCGGTCCTTCGGGACATATGTATATTCTTTGGAATATTTATGAGGTCTTTGAGGCACATACT
1 TACGCGGCCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATACT
* *
188977 TGGTCCTTAGTATATGTATATGATTCTTAAGGAATAATATGTGGCCCTTATGGACATTA-T-TAT
66 TGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGCCCTTATGGACATTATTATAT
189040 ATGGCACTACGGTGCAATTA
131 ATGGCACTACGGTGCAATTA
* * *
189060 TACGCGGCCCTTTGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATAC
1 TACGCGGCCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACATAC
*
189125 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTATA
65 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGCCCTTATGGACATTATTATA
*
189190 TATGGCACTACGGTGCAATTC
130 TATGGCACTACGGTGCAATTA
*
189211 TACGCGGCACTTCGG
1 TACGCGGCCCTTCGG
189226 TGCAATTCTA
Statistics
Matches: 146, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
148 43 0.29
149 67 0.46
150 1 0.01
151 35 0.24
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (150 bp):
TACGCGGCCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATACT
TGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGCCCTTATGGACATTATTATAT
ATGGCACTACGGTGCAATTA
Found at i:189226 original size:23 final size:23
Alignment explanation
Indices: 189193--189237 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
189183 TATTATATAT
189193 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
189216 GGCACTTCGGTGCAATTCTACG
1 GGCACTACGGTGCAATTCTACG
189238 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:189900 original size:17 final size:17
Alignment explanation
Indices: 189880--189915 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
189870 ACTTCGGACT
189880 CGTATCCGGGTCGGATA
1 CGTATCCGGGTCGGATA
189897 CGTATCCGGGTCGGATA
1 CGTATCCGGGTCGGATA
189914 CG
1 CG
189916 GGTTGGAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.25, G:0.36, T:0.22
Consensus pattern (17 bp):
CGTATCCGGGTCGGATA
Found at i:192581 original size:64 final size:64
Alignment explanation
Indices: 192506--192648 Score: 193
Period size: 64 Copynumber: 2.2 Consensus size: 64
192496 ATTGTTTAAG
*
192506 GTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAG-G
1 GTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTTATGCATCGATGCAT-AGTG
192569 -A
63 TA
* * *
192570 GTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTATGCATCGATGCATGGTGTA
1 GTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTTATGCATCGATGCATAGTGTA
192635 GTGCATCGATGCAT
1 GTGCATCGATGCAT
192649 ACCTTCATTA
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
63 1 0.01
64 47 0.66
65 22 0.31
66 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (64 bp):
GTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTATGCATCGATGCATAGTGTA
Found at i:192648 original size:65 final size:65
Alignment explanation
Indices: 192524--192648 Score: 200
Period size: 64 Copynumber: 1.9 Consensus size: 65
192514 ATGCATGAAT
192524 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA
1 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA
* *
192589 TTAAATA-CAAACATCGAATAGGATTTATGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAG-G-AGTGCATCGATGCAT
192649 ACCTTCATTA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
63 1 0.02
64 33 0.59
65 22 0.39
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (65 bp):
TTAAATAGAAAACATCGAATAGGATTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA
Found at i:194395 original size:149 final size:148
Alignment explanation
Indices: 194123--194436 Score: 479
Period size: 149 Copynumber: 2.1 Consensus size: 148
194113 GAGTCGAGGG
* * * * * *
194123 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* * *
194188 ATTGGTCCTTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGAGACATTATTAT
66 ATTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATACGTGGTCCTTAGAGACATTATTAT
194253 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
* *
194271 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
*
194336 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATACGTGGTCCTTATG-GACATTATT
65 AATTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATACGTGGTCCTTA-GAGACATTATT
194400 ATATGGCACTACGGTGCAAT
129 ATATGGCACTACGGTGCAAT
194420 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
194437 TGCAATTCTA
Statistics
Matches: 151, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
148 49 0.32
149 101 0.67
150 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
ATTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATACGTGGTCCTTAGAGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:194437 original size:23 final size:23
Alignment explanation
Indices: 194404--194448 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
194394 ATTATTATAT
194404 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
194427 GGCACTTCGGTGCAATTCTACG
1 GGCACTACGGTGCAATTCTACG
194449 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:197822 original size:64 final size:63
Alignment explanation
Indices: 197737--197897 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
197727 TTGTTTAAGG
* * * *
197737 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAGGATTTA
* * *
197801 TGCATCGATGCATAAGGAGTGCATCGATACATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAGGATTTA
*
197865 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
197898 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 61 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATAGGATTTA
Found at i:199680 original size:149 final size:148
Alignment explanation
Indices: 199368--199673 Score: 468
Period size: 149 Copynumber: 2.1 Consensus size: 148
199358 GAGTCGAGGG
* * * * * * *
199368 TCTACGCGGTCTTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* * *
199433 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGGGACATTACTAT
*
199498 ATGGCACTATGGTGCAAT
131 ATGGCACTACGGTGCAAT
* *
199516 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
*
199581 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTACTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGGGACATTACTA
*
199646 TATGGCACTCCGGTGCAAT
130 TATGGCACTACGGTGCAAT
199665 TCTACGCGG
1 TCTACGCGG
199674 CACTTCGATG
Statistics
Matches: 142, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
148 47 0.33
149 95 0.67
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTAGGGACATTACTAT
ATGGCACTACGGTGCAAT
Found at i:199685 original size:23 final size:23
Alignment explanation
Indices: 199649--199693 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
199639 ATTACTATAT
*
199649 GGCACTCCGGTGCAATTCTACGC
1 GGCACTCCGATGCAATTCTACGC
*
199672 GGCACTTCGATGCAATTCTACG
1 GGCACTCCGATGCAATTCTACG
199694 AACTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.24
Consensus pattern (23 bp):
GGCACTCCGATGCAATTCTACGC
Found at i:202318 original size:25 final size:25
Alignment explanation
Indices: 202284--202331 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
202274 GGTGTAACCT
202284 CACCAACAACCACGAAAGACCACCA
1 CACCAACAACCACGAAAGACCACCA
*
202309 CACCAACAACGACGAAAGACCAC
1 CACCAACAACCACGAAAGACCAC
202332 AAAGATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.42, G:0.10, T:0.00
Consensus pattern (25 bp):
CACCAACAACCACGAAAGACCACCA
Found at i:209661 original size:42 final size:42
Alignment explanation
Indices: 209615--209744 Score: 206
Period size: 42 Copynumber: 3.1 Consensus size: 42
209605 TGCATCCACC
*
209615 GGTGTAGCCGGTTTCTGTCCTTGATTACCATGTTCAGCCATT
1 GGTGTAGCCGGTTTCTGTCCTTGATTACCATGTGCAGCCATT
209657 GGTGTAGCCGGTTTCTGTCCTTGATTACCATGTGCAGCCATT
1 GGTGTAGCCGGTTTCTGTCCTTGATTACCATGTGCAGCCATT
** * * *
209699 TTTGTAGCCGGTTTCTGTCCTTGATCACCACGTGCAGCCATC
1 GGTGTAGCCGGTTTCTGTCCTTGATTACCATGTGCAGCCATT
209741 GGTG
1 GGTG
209745 GTGATTCGTT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.35
Consensus pattern (42 bp):
GGTGTAGCCGGTTTCTGTCCTTGATTACCATGTGCAGCCATT
Found at i:210099 original size:31 final size:30
Alignment explanation
Indices: 210058--210157 Score: 100
Period size: 30 Copynumber: 3.4 Consensus size: 30
210048 GCACCAATGT
210058 GAACCAAAATTACACAAAGATCAGTCCTTC
1 GAACCAAAATTACACAAAGATCAGTCCTTC
* * **
210088 GAACCGAAAATT--TCAACG-T-AGCTCCTGA
1 GAACC-AAAATTACACAAAGATCAG-TCCTTC
210116 GAACCAAAATTACACAAAGATCAGTCCTTC
1 GAACCAAAATTACACAAAGATCAGTCCTTC
*
210146 AAACCGAAAATT
1 GAACC-AAAATT
210158 TCAACCTCGA
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
27 8 0.15
28 10 0.19
29 8 0.15
30 14 0.26
31 14 0.26
ACGTcount: A:0.43, C:0.25, G:0.12, T:0.20
Consensus pattern (30 bp):
GAACCAAAATTACACAAAGATCAGTCCTTC
Found at i:211536 original size:39 final size:39
Alignment explanation
Indices: 211491--211569 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
211481 TTGAAAGATA
211491 GAAATGGAAATGGAAATGGAGTTTCATTCATGAAATTTG
1 GAAATGGAAATGGAAATGGAGTTTCATTCATGAAATTTG
* *
211530 GAAATGGGAATGGAAATGGGGTTTCATTCATGAAATTTG
1 GAAATGGAAATGGAAATGGAGTTTCATTCATGAAATTTG
211569 G
1 G
211570 CTATGTTGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.30
Consensus pattern (39 bp):
GAAATGGAAATGGAAATGGAGTTTCATTCATGAAATTTG
Found at i:213149 original size:14 final size:14
Alignment explanation
Indices: 213130--213156 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
213120 AATTGACTAT
213130 TTAATTAATATTAA
1 TTAATTAATATTAA
213144 TTAATTAATATTA
1 TTAATTAATATTA
213157 TATATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAATTAATATTAA
Found at i:213401 original size:135 final size:135
Alignment explanation
Indices: 213261--213532 Score: 508
Period size: 135 Copynumber: 2.0 Consensus size: 135
213251 AATAATGTGT
*
213261 AAAAATTAAAAAATTATTAAAATTCGTCAAAAATTTAATTAGTTTTATTCTTTTATTTAACAATT
1 AAAAATTAAAAAATTATTAAAATTCGTCAAAAAATTAATTAGTTTTATTCTTTTATTTAACAATT
* *
213326 TAATTAATTTACTCTGTAAATATTCTTAAAAACGTTATACACCTTTTATATCAAAAAAGATTATC
66 TAATTAATTTACTATGTAAATATTCTTAAAAACGCTATACACCTTTTATATCAAAAAAGATTATC
213391 TTATG
131 TTATG
213396 AAAAATTAAAAAATTATTAAAATTCGTCAAAAAATTAATTAGTTTTATTCTTTTATTTAACAATT
1 AAAAATTAAAAAATTATTAAAATTCGTCAAAAAATTAATTAGTTTTATTCTTTTATTTAACAATT
*
213461 TAATTAATTTACTATGTAAATATTCTTAAAAACGCTATACACCTTTTATATCAAAAAATATTATC
66 TAATTAATTTACTATGTAAATATTCTTAAAAACGCTATACACCTTTTATATCAAAAAAGATTATC
213526 TTATG
131 TTATG
213531 AA
1 AA
213533 CCTAATACAT
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
135 133 1.00
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (135 bp):
AAAAATTAAAAAATTATTAAAATTCGTCAAAAAATTAATTAGTTTTATTCTTTTATTTAACAATT
TAATTAATTTACTATGTAAATATTCTTAAAAACGCTATACACCTTTTATATCAAAAAAGATTATC
TTATG
Found at i:221090 original size:14 final size:15
Alignment explanation
Indices: 221063--221095 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
221053 TTATAATTTT
221063 TTAAAAAATTATAAAA
1 TTAAAAAA-TATAAAA
221079 TTAAAAAA-ATAAAA
1 TTAAAAAATATAAAA
221093 TTA
1 TTA
221096 TATATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TTAAAAAATATAAAA
Found at i:221188 original size:19 final size:19
Alignment explanation
Indices: 221164--221203 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
221154 ACTTTCCTTT
221164 TAACTCCTAAACCCACGTC
1 TAACTCCTAAACCCACGTC
221183 TAACTCCTAAACCCACGTC
1 TAACTCCTAAACCCACGTC
221202 TA
1 TA
221204 CCGCTGCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.40, G:0.05, T:0.23
Consensus pattern (19 bp):
TAACTCCTAAACCCACGTC
Found at i:225363 original size:26 final size:26
Alignment explanation
Indices: 225333--225388 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
225323 CTTCATTTTG
225333 TTTTGTTATT-TTTATATATTTTA-TTA
1 TTTTGTT-TTGTTT-TATATTTTATTTA
*
225359 TTTTGTTTTGTTTTTTATTTTATTTA
1 TTTTGTTTTGTTTTATATTTTATTTA
225385 TTTT
1 TTTT
225389 ACCTTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (26 bp):
TTTTGTTTTGTTTTATATTTTATTTA
Found at i:225369 original size:36 final size:36
Alignment explanation
Indices: 225328--225416 Score: 110
Period size: 36 Copynumber: 2.4 Consensus size: 36
225318 CTTCTCTTCA
*
225328 TTTTGTTTTGTTATTTTTATATATTTTA-TTATTTTG
1 TTTTGTTTT-TTATTTTTATATATTTTACTTATTTTC
*
225364 TTTTGTTTTTTA-TTTTATTTATTTTACCTTATTTTC
1 TTTTGTTTTTTATTTTTATATATTTTA-CTTATTTTC
*
225400 TTTTATTGTTTTATTTT
1 TTTTGTT-TTTTATTTT
225417 ATTTCTTAGC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
34 13 0.28
35 3 0.07
36 22 0.48
37 5 0.11
38 3 0.07
ACGTcount: A:0.15, C:0.03, G:0.06, T:0.76
Consensus pattern (36 bp):
TTTTGTTTTTTATTTTTATATATTTTACTTATTTTC
Found at i:232515 original size:150 final size:151
Alignment explanation
Indices: 232293--232649 Score: 509
Period size: 151 Copynumber: 2.4 Consensus size: 151
232283 GAAAAACCCA
* * * ** * *
232293 ATGTTTATATTCTATTGATATTCAACGAAACAAAACAAATTTGGGTTCTTAATCTCATCTCTGAA
1 ATGTTTATATTTTATTAACATTCAAATAAACAAAACAAATTTGGGTTCTTAATCTTATCTCCGAA
* * * *
232358 CAATAAAGCTTCTTTACTGGGTA-TTATATTCATTTTATTTTCTCGAGAAAATCCGACCAAACGA
66 CAATAAAGCTTCTTTACTGGGTATTTATATTCAATTAATTTTCTCGAGAAAATCCAACCAAACAA
*
232422 ACTACAAGAAGAGAACCCCTT
131 ACTACAAAAAGAGAACCCCTT
*
232443 GTGTTTATATTTTATTAACATTCAAATAAACAAAACAAATTTGGGTTCTTAATCTTATCTCCGAA
1 ATGTTTATATTTTATTAACATTCAAATAAACAAAACAAATTTGGGTTCTTAATCTTATCTCCGAA
* * * * * *
232508 CAATAAAGTTTCTTTCCTGGGTATTTCTTTTCAATTAATTTTCTCGAGAAAATCTAATCAAACAA
66 CAATAAAGCTTCTTTACTGGGTATTTATATTCAATTAATTTTCTCGAGAAAATCCAACCAAACAA
232573 ACTACAAAAAGAGAACCCCTT
131 ACTACAAAAAGAGAACCCCTT
* * *
232594 ATGTTTATATTTTATTAACTTTCAAATAAACAAAACAAATTTGGATTCCTAATCTT
1 ATGTTTATATTTTATTAACATTCAAATAAACAAAACAAATTTGGGTTCTTAATCTT
232650 GTTTGTGTAT
Statistics
Matches: 183, Mismatches: 23, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
150 78 0.43
151 105 0.57
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (151 bp):
ATGTTTATATTTTATTAACATTCAAATAAACAAAACAAATTTGGGTTCTTAATCTTATCTCCGAA
CAATAAAGCTTCTTTACTGGGTATTTATATTCAATTAATTTTCTCGAGAAAATCCAACCAAACAA
ACTACAAAAAGAGAACCCCTT
Found at i:243823 original size:16 final size:16
Alignment explanation
Indices: 243804--243846 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
243794 GATTAAGCGC
*
243804 TGAATGATTTAAATAT
1 TGAATGATTCAAATAT
243820 TGAATGATTCAAATAT
1 TGAATGATTCAAATAT
243836 TGAATGATTCA
1 TGAATGATTCA
243847 GAGGTTCTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.40
Consensus pattern (16 bp):
TGAATGATTCAAATAT
Found at i:244310 original size:3 final size:3
Alignment explanation
Indices: 244304--244340 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
244294 AATTGTAATA
244304 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
244341 GCTTATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:245207 original size:11 final size:11
Alignment explanation
Indices: 245191--245216 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
245181 CCCTCCCCGA
245191 TGAGGAGAGGT
1 TGAGGAGAGGT
245202 TGAGGAGAGGT
1 TGAGGAGAGGT
245213 TGAG
1 TGAG
245217 AGATTTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.54, T:0.19
Consensus pattern (11 bp):
TGAGGAGAGGT
Found at i:252079 original size:4 final size:4
Alignment explanation
Indices: 252070--252131 Score: 94
Period size: 4 Copynumber: 16.2 Consensus size: 4
252060 GATCGAGAAA
*
252070 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT AC-- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
252116 ACAT ACAT A-AT ACAT A
1 ACAT ACAT ACAT ACAT A
252132 AAATTTGCAT
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 2 0.04
3 3 0.06
4 48 0.91
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:252560 original size:71 final size:72
Alignment explanation
Indices: 252474--252608 Score: 184
Period size: 71 Copynumber: 1.9 Consensus size: 72
252464 TGAGAATTTT
* * ** *
252474 AAAACAAATTTTTGTCTCGCTCGAGACAATTTCTTT-CAAAGCAAATTTTGTCTCGCTTGAGACA
1 AAAACAAATTTTTGTCTCGCTCGAGACAATTT-TTTGAAAAACAAATTCCGTCTCACTTGAGACA
252538 GCTTTCTA
65 GCTTTCTA
* *
252546 AAAACAAA-TTTTGTCTCGTTTGAGACAATTTTTTGAAAAACAAATTCCGTCTCACTTGAGACA
1 AAAACAAATTTTTGTCTCGCTCGAGACAATTTTTTGAAAAACAAATTCCGTCTCACTTGAGACA
252609 TTTTTCCTTG
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
70 3 0.05
71 44 0.80
72 8 0.15
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (72 bp):
AAAACAAATTTTTGTCTCGCTCGAGACAATTTTTTGAAAAACAAATTCCGTCTCACTTGAGACAG
CTTTCTA
Found at i:252561 original size:35 final size:34
Alignment explanation
Indices: 252474--252608 Score: 135
Period size: 36 Copynumber: 3.8 Consensus size: 34
252464 TGAGAATTTT
* *
252474 AAAACAAATTTTTGTCTCGCTCGAGACAATTTCTTTC
1 AAAACAAA-TTTTGTCTCGCTTGAGACAATTTC--TA
* *
252511 AAAGCAAATTTTGTCTCGCTTGAGACAGCTTTCTA
1 AAAACAAATTTTGTCTCGCTTGAGACA-ATTTCTA
* *
252546 AAAACAAATTTTGTCTCGTTTGAGACAATTTTTTGA
1 AAAACAAATTTTGTCTCGCTTGAGACAA-TTTCT-A
** *
252582 AAAACAAATTCCGTCTCACTTGAGACA
1 AAAACAAATTTTGTCTCGCTTGAGACA
252609 TTTTTCCTTG
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
35 30 0.36
36 42 0.51
37 11 0.13
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (34 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTCTA
Found at i:252775 original size:36 final size:36
Alignment explanation
Indices: 252694--252775 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
252684 ATTTTGTTTT
* * *
252694 GCTTGAGACAATTTCTTTAAAAACAAAGTTTGTATC
1 GCTTGAGACAAATTCTTTAAAAACAAACTTCGTATC
* * *
252730 ACTTAAGACAAATTCTCTT-AAAACAAACTTCGTCTC
1 GCTTGAGACAAATTCT-TTAAAAACAAACTTCGTATC
252766 GCTTGAGACA
1 GCTTGAGACA
252776 TTTTTCCTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 35 0.95
37 2 0.05
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (36 bp):
GCTTGAGACAAATTCTTTAAAAACAAACTTCGTATC
Found at i:253054 original size:29 final size:27
Alignment explanation
Indices: 253004--253090 Score: 113
Period size: 29 Copynumber: 3.1 Consensus size: 27
252994 TTGAGACAGT
*
253004 TTCTTTTGAAACAAATCTTTGAGTTTG
1 TTCTTTTGAAAAAAATCTTTGAGTTTG
253031 TTCATTTTGAATAAAAATCTTTGAGTTAT-
1 TTC-TTTTGAA-AAAAATCTTTGAGTT-TG
253060 TTCTTTTGAGAAAAAAATCTTTGAGTTTG
1 TTCTTTT--GAAAAAAATCTTTGAGTTTG
253089 TT
1 TT
253091 TCTCTTAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
27 3 0.06
28 12 0.23
29 34 0.64
30 4 0.08
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.48
Consensus pattern (27 bp):
TTCTTTTGAAAAAAATCTTTGAGTTTG
Found at i:253228 original size:120 final size:121
Alignment explanation
Indices: 252973--253258 Score: 344
Period size: 120 Copynumber: 2.4 Consensus size: 121
252963 TTTGAATATT
* * * * * *
252973 TTAAAACGATTTTTGTCTCTCTTGAGACAGTTTCTTTTGAAACAAATCTTTGAGTTTGTTCATTT
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTATTGAAA-AAATCTTGGAGTCTATTCATTT
** * * *
253038 TGAATAAAAATCTTTGAGTTATTTCTTTTGAGAAAAAAATCTTTGAGTTTGTTTCTC
65 TGAATAAAAATCTTTGAGTTATTTCTACTAACAAAAAAATCTTTGAGTTTATTTCTC
* * * *
253095 TTAAAACATATTTTGTCTCTCTTAAGACAGTTTCTCTTGAAAAAATCTTGGAGTCTATTCCTTTT
1 TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTATTGAAAAAATCTTGGAGTCTATTCATTTT
* ** *
253160 G-A-AAAAATCTTTGAGTTTGTTTCTACTAACAAAATCATCTTTTAGTTTATTTCT-
66 GAATAAAAATCTTTGAG-TTATTTCTACTAACAAAAAAATCTTTGAGTTTATTTCTC
*
253214 TTAAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTAATGAAAAA
1 TT-AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTATTGAAAAA
253259 CCAACCTTTG
Statistics
Matches: 140, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
119 15 0.11
120 68 0.49
121 20 0.14
122 37 0.26
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.44
Consensus pattern (121 bp):
TTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTATTGAAAAAATCTTGGAGTCTATTCATTTT
GAATAAAAATCTTTGAGTTATTTCTACTAACAAAAAAATCTTTGAGTTTATTTCTC
Found at i:253530 original size:31 final size:31
Alignment explanation
Indices: 253495--253555 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 31
253485 CCTTGAGGCA
253495 GTTTCTC-TATAAATACAAA-ATCTTTGAGTTT
1 GTTTCTCTTA-AAATA-AAACATCTTTGAGTTT
253526 GTTTCTCTTAAAATAAAACCATCTTTGAGT
1 GTTTCTCTTAAAATAAAA-CATCTTTGAGT
253556 CGTTTCCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 3 0.11
31 12 0.44
32 12 0.44
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (31 bp):
GTTTCTCTTAAAATAAAACATCTTTGAGTTT
Found at i:254138 original size:28 final size:28
Alignment explanation
Indices: 254107--254170 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
254097 GAAACATATT
254107 ATCTTTGAG-CTTGTTT-TTCATGAAACAA
1 ATCTTTGAGTC-TGTTTCTT-ATGAAACAA
*
254135 ATCTTTGAGTCTGTTTCTTTTGAAACAA
1 ATCTTTGAGTCTGTTTCTTATGAAACAA
254163 ATCTTTGA
1 ATCTTTGA
254171 ATCGATTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 30 0.91
29 3 0.09
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (28 bp):
ATCTTTGAGTCTGTTTCTTATGAAACAA
Found at i:254179 original size:28 final size:28
Alignment explanation
Indices: 254118--254188 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
254108 TCTTTGAGCT
* * *
254118 TGTTTTTCATGAAACAAATCTTTGAGTC
1 TGTTTCTCTTGAAACAAATCTTTGAATC
*
254146 TGTTTCTTTTGAAACAAATCTTTGAATC
1 TGTTTCTCTTGAAACAAATCTTTGAATC
254174 -GATTTCTCTTGAAAC
1 TG-TTTCTCTTGAAAC
254189 CATGATCCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (28 bp):
TGTTTCTCTTGAAACAAATCTTTGAATC
Found at i:254628 original size:3 final size:3
Alignment explanation
Indices: 254620--254668 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
254610 TCTAATTGTA
254620 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
254667 AT
1 AT
254669 GCTTATTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:258426 original size:14 final size:15
Alignment explanation
Indices: 258398--258430 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
258388 TCTATGTCAA
258398 CTGTTCCCAACCTTG
1 CTGTTCCCAACCTTG
258413 CTGTTCCC-ACCTTG
1 CTGTTCCCAACCTTG
258427 CTGT
1 CTGT
258431 ACTCCATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.09, C:0.39, G:0.15, T:0.36
Consensus pattern (15 bp):
CTGTTCCCAACCTTG
Found at i:263164 original size:23 final size:24
Alignment explanation
Indices: 263120--263170 Score: 95
Period size: 23 Copynumber: 2.2 Consensus size: 24
263110 CTGTGACTTG
263120 TTCGTTTCATCTATTTTTTTCTCA
1 TTCGTTTCATCTATTTTTTTCTCA
263144 TTCGTTTCATCTA-TTTTTTCTCA
1 TTCGTTTCATCTATTTTTTTCTCA
263167 TTCG
1 TTCG
263171 CTTCCCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.12, C:0.22, G:0.06, T:0.61
Consensus pattern (24 bp):
TTCGTTTCATCTATTTTTTTCTCA
Found at i:263179 original size:22 final size:23
Alignment explanation
Indices: 263120--263180 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
263110 CTGTGACTTG
* *
263120 TTCGTTTCATCTATTTTTTTCTCA
1 TTCGCTTCACCTA-TTTTTTCTCA
* *
263144 TTCGTTTCATCTATTTTTTCTCA
1 TTCGCTTCACCTATTTTTTCTCA
263167 TTCGCTTC-CCTATT
1 TTCGCTTCACCTATT
263181 GTATCCACGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.14
23 17 0.49
24 13 0.37
ACGTcount: A:0.11, C:0.25, G:0.05, T:0.59
Consensus pattern (23 bp):
TTCGCTTCACCTATTTTTTCTCA
Found at i:267948 original size:31 final size:31
Alignment explanation
Indices: 267912--267971 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
267902 AACTTAAAAG
* *
267912 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
267943 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
267972 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:268595 original size:38 final size:38
Alignment explanation
Indices: 268553--268650 Score: 94
Period size: 38 Copynumber: 2.6 Consensus size: 38
268543 ATAACAAATC
* * *
268553 TAAAA-AAATATTATATTTAAACTTAAATAAAAAATAAT
1 TAAAATAAATATAAAATTTAAA-TAAAATAAAAAATAAT
* *
268591 TAAAATAAATATAAAATTTTAATAAAATATAAAATAAT
1 TAAAATAAATATAAAATTTAAATAAAATAAAAAATAAT
* * *
268629 TTATAT-GATATAAAA-TTAAATA
1 TAAAATAAATATAAAATTTAAATA
268651 TCTATAATAT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
36 6 0.12
37 8 0.16
38 23 0.46
39 13 0.26
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (38 bp):
TAAAATAAATATAAAATTTAAATAAAATAAAAAATAAT
Found at i:268601 original size:20 final size:20
Alignment explanation
Indices: 268576--268629 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 20
268566 TATTTAAACT
*
268576 TAAATAAAAAATAATTAAAA
1 TAAATATAAAATAATTAAAA
* *
268596 TAAATATAAAAT-TTTAATA
1 TAAATATAAAATAATTAAAA
268615 -AAATATAAAATAATT
1 TAAATATAAAATAATT
268630 TATATGATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 11 0.38
19 7 0.24
20 11 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAATATAAAATAATTAAAA
Found at i:268708 original size:14 final size:14
Alignment explanation
Indices: 268660--268744 Score: 67
Period size: 14 Copynumber: 6.5 Consensus size: 14
268650 ATCTATAATA
*
268660 TAATATTAAAAAAG
1 TAATATTAAAAAAT
*
268674 TAATATT---TAAT
1 TAATATTAAAAAAT
*
268685 TTAT-TTAAAAAAT
1 TAATATTAAAAAAT
268698 TAATATT--AAAAT
1 TAATATTAAAAAAT
* *
268710 TAATATCTATAATA-
1 TAATAT-TAAAAAAT
268724 TAATATTAAAAAAT
1 TAATATTAAAAAAT
268738 TAATATT
1 TAATATT
268745 TAATTTATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
10 2 0.04
11 5 0.09
12 11 0.20
13 12 0.22
14 22 0.40
15 3 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (14 bp):
TAATATTAAAAAAT
Found at i:268728 original size:26 final size:27
Alignment explanation
Indices: 268698--268785 Score: 105
Period size: 24 Copynumber: 3.4 Consensus size: 27
268688 TTTAAAAAAT
268698 TAATATT-AAAATTAATATCTATAATA
1 TAATATTAAAAATTAATATCTATAATA
268724 TAATATTAAAAAATTAATAT-T-TAAT-
1 TAATATT-AAAAATTAATATCTATAATA
*
268749 TTAT-TTAAAAAATTAATATCTATAATA
1 TAATATT-AAAAATTAATATCTATAATA
*
268776 TAAAATTAAA
1 TAATATTAAA
268786 TATAAAACCT
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
24 15 0.28
25 4 0.08
26 15 0.28
27 6 0.11
28 13 0.25
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TAATATTAAAAATTAATATCTATAATA
Found at i:268761 original size:24 final size:28
Alignment explanation
Indices: 268698--268785 Score: 116
Period size: 28 Copynumber: 3.4 Consensus size: 28
268688 TTTAAAAAAT
268698 TAATATT--AAAATTAATATCTATAATA
1 TAATATTAAAAAATTAATATCTATAATA
268724 TAATATTAAAAAATTAATAT-T-TAAT-
1 TAATATTAAAAAATTAATATCTATAATA
*
268749 TTAT-TTAAAAAATTAATATCTATAATA
1 TAATATTAAAAAATTAATATCTATAATA
*
268776 TAAAATTAAA
1 TAATATTAAA
268786 TATAAAACCT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
24 15 0.28
25 4 0.08
26 15 0.28
27 3 0.06
28 16 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
TAATATTAAAAAATTAATATCTATAATA
Found at i:268788 original size:64 final size:64
Alignment explanation
Indices: 268639--268790 Score: 236
Period size: 64 Copynumber: 2.4 Consensus size: 64
268629 TTATATGATA
268639 TAAAATTAAATATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAA-ATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
* *
268704 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAAATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
*
268768 CTATAATATAAAAT-TA-AATATAA
1 -TAAAAT-TAAAATCTATAATATAA
268791 AACCTCTTTG
Statistics
Matches: 81, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
64 60 0.74
65 16 0.20
66 5 0.06
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (64 bp):
TAAAATTAAAATCTATAATATAATATTAAAAAAGTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:277505 original size:58 final size:60
Alignment explanation
Indices: 277412--277537 Score: 143
Period size: 58 Copynumber: 2.1 Consensus size: 60
277402 ATTTATCTCT
* ** * *
277412 AAACTATAACTATCATTCTAAATTTCTCTTCAAAC-TTTTGAACGTTTCATTTTC-TCCC
1 AAACTATAACTATCATTCTAAATTTCTCCTCAAACTTTTTGAACAATCCAATTTCATCCC
* *
277470 AAACTATGACTTTCATTCTAAATTGATC-CCT-AAACTTTTTGAACAATCCAATTTCATCCC
1 AAACTATAACTATCATTCTAAATT--TCTCCTCAAACTTTTTGAACAATCCAATTTCATCCC
277530 AAACTATA
1 AAACTATA
277538 CCAAACTATA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
58 26 0.46
59 17 0.30
60 13 0.23
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (60 bp):
AAACTATAACTATCATTCTAAATTTCTCCTCAAACTTTTTGAACAATCCAATTTCATCCC
Found at i:277740 original size:60 final size:60
Alignment explanation
Indices: 277675--277811 Score: 148
Period size: 60 Copynumber: 2.3 Consensus size: 60
277665 TGAATTTGAT
* * * **
277675 GATGAAATTAGAATATTTAAAAGTCCAAGGACTAATTTAAAAAGTGAGTCATAGTTTAAG
1 GATGAAATTAAAATATTAAAAAGTCCAAGGAATAATTTAAAAAGAAAGTCATAGTTTAAG
* * ** * * * *
277735 GATGAAACTAAAATGTTAAAAAGTTTAAGTAATAATTTAGAATGAAAGTCATAGTTTGAG
1 GATGAAATTAAAATATTAAAAAGTCCAAGGAATAATTTAAAAAGAAAGTCATAGTTTAAG
*
277795 GATAAAATTAAAATATT
1 GATGAAATTAAAATATT
277812 CCAAAGTTTA
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.47, C:0.04, G:0.17, T:0.31
Consensus pattern (60 bp):
GATGAAATTAAAATATTAAAAAGTCCAAGGAATAATTTAAAAAGAAAGTCATAGTTTAAG
Found at i:277832 original size:60 final size:60
Alignment explanation
Indices: 277721--277833 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
277711 TTAAAAAGTG
* * *
277721 AGTCATAGTTTAAGGATGAAACTAAAATGTTAAAAAGTTTAAGTAATAATTTAGAATGAA
1 AGTCATAGTTTAAGGATAAAACTAAAATATTAAAAAGTTTAAGAAATAATTTAGAATGAA
* * **
277781 AGTCATAGTTTGAGGATAAAATTAAAATATTCCAAAGTTTAA-AAATCAATTTA
1 AGTCATAGTTTAAGGATAAAACTAAAATATTAAAAAGTTTAAGAAAT-AATTTA
277834 AAATCAGGGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 3 0.07
60 42 0.93
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (60 bp):
AGTCATAGTTTAAGGATAAAACTAAAATATTAAAAAGTTTAAGAAATAATTTAGAATGAA
Found at i:277968 original size:20 final size:18
Alignment explanation
Indices: 277927--277970 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
277917 TAAAAATCAA
*
277927 TTTAAAAATATTTCAAAG
1 TTTAAAAATATTTAAAAG
*
277945 TTTAAAAATCAATTTAAAAT
1 TTTAAAAAT--ATTTAAAAG
277965 TTTAAA
1 TTTAAA
277971 CTCGAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (18 bp):
TTTAAAAATATTTAAAAG
Found at i:278094 original size:23 final size:23
Alignment explanation
Indices: 278053--278096 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
278043 GTAATAAATG
* * *
278053 TAAAATTTTATATATTAAAAAAA
1 TAAAATTTTAGAAAATAAAAAAA
278076 TAAAATTTTAGAAAATAAAAA
1 TAAAATTTTAGAAAATAAAAA
278097 TAAATGGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
TAAAATTTTAGAAAATAAAAAAA
Found at i:278460 original size:18 final size:19
Alignment explanation
Indices: 278426--278461 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
278416 AAATTATACT
*
278426 TAAATTAATATTTAAAATC
1 TAAATTAATAGTTAAAATC
278445 TAAATTAAT-GTTAAAAT
1 TAAATTAATAGTTAAAAT
278462 AATAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (19 bp):
TAAATTAATAGTTAAAATC
Found at i:278467 original size:19 final size:19
Alignment explanation
Indices: 278426--278473 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
278416 AAATTATACT
* *
278426 TAAATTAATATTTAAAATC
1 TAAATTAATAGTTAAAATA
278445 TAAATTAAT-GTTAAAATAA
1 TAAATTAATAGTTAAAAT-A
278464 TAAAATTAAT
1 T-AAATTAAT
278474 TAATTAATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 10 0.40
20 8 0.32
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TAAATTAATAGTTAAAATA
Found at i:279511 original size:60 final size:60
Alignment explanation
Indices: 279393--279576 Score: 150
Period size: 60 Copynumber: 3.1 Consensus size: 60
279383 ATATGTATAG
* ** * *
279393 TTTGGGATGAAATTAGAATGTTCAAAAAGTTTGAGGAGCAATTTAGAATGAAGGTCATAT
1 TTTGGGATGAAATTAAAATGTTCAAAAAGTTCAAGGAGCAATTTAAAATGAAGATCATAT
279453 TTTGGGAATGAAATTAAAATGTTC-AAAAGTTCAAGG-GCTAATTTAAAATGATA-ATCATAGT
1 TTTGGG-ATGAAATTAAAATGTTCAAAAAGTTCAAGGAGC-AATTTAAAATGA-AGATCATA-T
* * * * *
279514 TTAT-GGATAAAATTAGAGCAT-TT--AAAAGTTTAAGGATCAATTTAAAATG-AGAGTTATAT
1 TT-TGGGATGAAATTA-A-AATGTTCAAAAAGTTCAAGGAGCAATTTAAAATGAAGA-TCATAT
279573 TTTG
1 TTTG
279577 AGGACATATC
Statistics
Matches: 103, Mismatches: 10, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
58 2 0.02
59 6 0.06
60 66 0.64
61 26 0.25
62 3 0.03
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (60 bp):
TTTGGGATGAAATTAAAATGTTCAAAAAGTTCAAGGAGCAATTTAAAATGAAGATCATAT
Found at i:280667 original size:242 final size:238
Alignment explanation
Indices: 280208--280670 Score: 624
Period size: 238 Copynumber: 1.9 Consensus size: 238
280198 TAAACTAGTC
* * * * *
280208 GATCTAGCCGAATACACGTCGATTCGAGTTTGTTGAACCTTGAATAGATATGTTTGATCTTCAAA
1 GATCTAGCAGAATAAACATCAATTCGAGCTTGTTGAACCTTGAATAGATATGTTTGATCTTCAAA
* * * *
280273 GAGCAAGCTCTGTACCCGTTGGATTTGGATCAACTCAATTTTGCTCCTACATGGTCTTCTGAGCC
66 AAGCAAGCTCTGTACACGTTGGACTTGGATCAACTCAATTTTGCTCCTACATGGTCTTCTAAGCC
* *
280338 AACCACCTTGTGATTTGTCGGTAGAATGTTGGACTCCTAGTCCCGAGATTATACCCTGGCGATTT
131 AACCACCATGTGATTTGTCGGTAGAATGTTGGACTCCTAGTCCCGAGATTATACCCTGGCAATTT
280403 CAATAGAACCAGAAATGTCTTACTTTGAGTAGCGTGACCAGTT
196 CAATAGAACCAGAAATGTCTTACTTTGAGTAGCGTGACCAGTT
*
280446 GATCTAGCAGAATAAACATCAATTTGAGCTTGTTGAACCTTGAAT-GCATATGTTTGATCTTCAA
1 GATCTAGCAGAATAAACATCAATTCGAGCTTGTTGAACCTTGAATAG-ATATGTTTGATCTTCAA
* * * * ** *
280510 AAAGCAAGCTTTGTACACTTTTGACTTGGATCGACTCGGTTTTGCTCCTATATGGTGTTACTTCT
65 AAAGCAAGCTCTGTACACGTTGGACTTGGATCAACTCAATTTTGCTCCTACAT-G-G-T-CTTCT
** * *
280575 AAGCCAACGGCCATGTGATTTGTTGGTAGAATGTTGGACTCCTAGTCTCGAGATTATACCCTGGC
126 AAGCCAACCACCATGTGATTTGTCGGTAGAATGTTGGACTCCTAGTCCCGAGATTATACCCTGGC
* * *
280640 AATTTCGATCGTACC-GAAAATGTCTTACTTT
191 AATTTCAATAGAACCAG-AAATGTCTTACTTT
280671 TGAGCTGTGT
Statistics
Matches: 193, Mismatches: 26, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
237 1 0.01
238 99 0.51
239 1 0.01
240 1 0.01
241 2 0.01
242 89 0.46
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (238 bp):
GATCTAGCAGAATAAACATCAATTCGAGCTTGTTGAACCTTGAATAGATATGTTTGATCTTCAAA
AAGCAAGCTCTGTACACGTTGGACTTGGATCAACTCAATTTTGCTCCTACATGGTCTTCTAAGCC
AACCACCATGTGATTTGTCGGTAGAATGTTGGACTCCTAGTCCCGAGATTATACCCTGGCAATTT
CAATAGAACCAGAAATGTCTTACTTTGAGTAGCGTGACCAGTT
Found at i:282092 original size:44 final size:44
Alignment explanation
Indices: 282037--282171 Score: 175
Period size: 44 Copynumber: 3.1 Consensus size: 44
282027 AATTTTGATT
* *
282037 CTATCCGTGTTTGTTACTATCTTTATTTTATGATTTCGATTCGA
1 CTATCCGTGTTTGTTACGATCATTATTTTATGATTTCGATTCGA
* * * * *
282081 CTATCTGTGTTTGTCACGAACGTTATTTTATGATTTCAAATT--A
1 CTATCCGTGTTTGTTACGATCATTATTTTATGATTTC-GATTCGA
*
282124 CTATCCGTGTTTGTTACGATCATTATTTTAGGATTTCGATTCGA
1 CTATCCGTGTTTGTTACGATCATTATTTTATGATTTCGATTCGA
282168 CTAT
1 CTAT
282172 GGAAGTATTG
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
42 3 0.04
43 33 0.43
44 37 0.49
45 3 0.04
ACGTcount: A:0.21, C:0.16, G:0.15, T:0.48
Consensus pattern (44 bp):
CTATCCGTGTTTGTTACGATCATTATTTTATGATTTCGATTCGA
Found at i:285697 original size:38 final size:38
Alignment explanation
Indices: 285646--285719 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
285636 CGTTATTGAG
* * * *
285646 TTATTTCATAAATGAAATGACAATCAACTTTGATATGT
1 TTATCTCACAAATGAAATAACAATCAACTTTAATATGT
* *
285684 TTATCTCACAAATGAATTAACAATCGACTTTAATAT
1 TTATCTCACAAATGAAATAACAATCAACTTTAATAT
285720 ATTTCGATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (38 bp):
TTATCTCACAAATGAAATAACAATCAACTTTAATATGT
Found at i:286535 original size:21 final size:21
Alignment explanation
Indices: 286496--286535 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
286486 ACGCGTTTAA
**
286496 TACCTAAACTATCCGTTTTGG
1 TACCTAAACTATCAATTTTGG
*
286517 TACCTAAACTTTCAATTTT
1 TACCTAAACTATCAATTTT
286536 TTCAAAACCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.23, G:0.07, T:0.42
Consensus pattern (21 bp):
TACCTAAACTATCAATTTTGG
Found at i:288029 original size:30 final size:31
Alignment explanation
Indices: 287975--288051 Score: 120
Period size: 30 Copynumber: 2.5 Consensus size: 31
287965 TAAAAATTAA
*
287975 AGTTTAGGTACTAAAATTGAGTAAATTTGAT
1 AGTTTAGGTACTAAAATGGAGTAAATTTGAT
288006 AGTTTAGGTACTAAAA-GGAGTAAATTTGAT
1 AGTTTAGGTACTAAAATGGAGTAAATTTGAT
*
288036 AGTTTGGGTACATAAA
1 AGTTTAGGTAC-TAAA
288052 GGCACGGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 23 0.53
31 20 0.47
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (31 bp):
AGTTTAGGTACTAAAATGGAGTAAATTTGAT
Found at i:288325 original size:23 final size:23
Alignment explanation
Indices: 288299--288367 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
288289 ACACAATAAT
288299 AACACTGGGAATCATTACATTGA
1 AACACTGGGAATCATTACATTGA
* * *
288322 AACA-T---AATCA-CACAATAA
1 AACACTGGGAATCATTACATTGA
288340 TAACACTGGGAATCATTACATTGA
1 -AACACTGGGAATCATTACATTGA
288364 AACA
1 AACA
288368 TAATCACACA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 5 0.15
19 9 0.26
20 1 0.03
22 1 0.03
23 13 0.38
24 5 0.15
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (23 bp):
AACACTGGGAATCATTACATTGA
Found at i:288332 original size:42 final size:42
Alignment explanation
Indices: 288273--288415 Score: 242
Period size: 42 Copynumber: 3.5 Consensus size: 42
288263 TCTTAAATTG
*
288273 ACATTCAAACATAATCACACAATAATAACACTGGGAATCATT
1 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
288315 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
1 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
288357 ACATTGAAACATAATCACAC---AAT-A-ACTGGGAATCATT
1 ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
288394 ACATTGAAACATAATCACACAA
1 ACATTGAAACATAATCACACAA
288416 ATCCATTAAT
Statistics
Matches: 98, Mismatches: 1, Indels: 7
0.92 0.01 0.07
Matches are distributed among these distances:
37 33 0.34
38 1 0.01
39 3 0.03
42 61 0.62
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.23
Consensus pattern (42 bp):
ACATTGAAACATAATCACACAATAATAACACTGGGAATCATT
Found at i:288344 original size:19 final size:19
Alignment explanation
Indices: 288280--288344 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 19
288270 TTGACATTCA
288280 AACATAATCACACAATAAT
1 AACATAATCACACAATAAT
* * *
288299 AACACTGGGAATCATTACATTGA-
1 AACA-T---AATCA-CACAATAAT
288322 AACATAATCACACAATAAT
1 AACATAATCACACAATAAT
288341 AACA
1 AACA
288345 CTGGGAATCA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 5 0.15
19 13 0.38
20 1 0.03
22 1 0.03
23 9 0.26
24 5 0.15
ACGTcount: A:0.52, C:0.20, G:0.06, T:0.22
Consensus pattern (19 bp):
AACATAATCACACAATAAT
Found at i:290903 original size:24 final size:23
Alignment explanation
Indices: 290874--290927 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
290864 TCAATTATAA
*
290874 TTACAAATATCTTAAAGTGTAAAT
1 TTACAAATATCTTAAAGAGT-AAT
290898 TTACAAATATCTTAAAGAGTAAT
1 TTACAAATATCTTAAAGAGTAAT
*
290921 TAACAAA
1 TTACAAA
290928 GAAATTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.33
Consensus pattern (23 bp):
TTACAAATATCTTAAAGAGTAAT
Found at i:291656 original size:23 final size:23
Alignment explanation
Indices: 291626--291671 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
291616 ATTTTCAATA
* *
291626 ATCTACCTGTATGAGACGTTTTC
1 ATCTACCTGTATGACACATTTTC
*
291649 ATCTACCTTTATGACACATTTTC
1 ATCTACCTGTATGACACATTTTC
291672 TCATGTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (23 bp):
ATCTACCTGTATGACACATTTTC
Found at i:295548 original size:28 final size:29
Alignment explanation
Indices: 295517--295600 Score: 75
Period size: 28 Copynumber: 2.9 Consensus size: 29
295507 GCTAAAATAT
295517 AACTTTTAAAAATTATATTTTTAGTC-TA
1 AACTTTTAAAAATTATATTTTTAGTCATA
* * * *
295545 AACTTTTTAAAGTT-TATACTTTAGTCATTT
1 AACTTTTAAAAATTATAT-TTTTAGTCA-TA
* *
295575 AACTTTCAAAAATTAGA-TTTTAGTCA
1 AACTTTTAAAAATTATATTTTTAGTCA
295601 CTAGCCAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
27 3 0.07
28 19 0.44
29 8 0.19
30 12 0.28
31 1 0.02
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (29 bp):
AACTTTTAAAAATTATATTTTTAGTCATA
Found at i:296394 original size:13 final size:13
Alignment explanation
Indices: 296376--296400 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
296366 GCCTTTGAAG
296376 AGGAAAAAGAAAA
1 AGGAAAAAGAAAA
296389 AGGAAAAAGAAA
1 AGGAAAAAGAAA
296401 TGGAGAGGAG
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AGGAAAAAGAAAA
Found at i:301181 original size:24 final size:24
Alignment explanation
Indices: 301149--301198 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
301139 AATGCAATGC
* *
301149 GAAGAACATGTTACTGGACGGATT
1 GAAGAACATGTTACAGGACAGATT
*
301173 GAAGAACATGTTGCAGGACAGATT
1 GAAGAACATGTTACAGGACAGATT
301197 GA
1 GA
301199 TTTCGATCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.22
Consensus pattern (24 bp):
GAAGAACATGTTACAGGACAGATT
Found at i:303081 original size:37 final size:36
Alignment explanation
Indices: 303030--303104 Score: 123
Period size: 37 Copynumber: 2.1 Consensus size: 36
303020 ATAAAAATTC
303030 AAGGTTTTGACATGAAACACAGAATACTCGAGTGCTG
1 AAGGTTTTGACATGAAACACAGAATACT-GAGTGCTG
* *
303067 AAGGTTTTGTCATGAAACTCAGAATACTGAGTGCTG
1 AAGGTTTTGACATGAAACACAGAATACTGAGTGCTG
303103 AA
1 AA
303105 AGTATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 10 0.28
37 26 0.72
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (36 bp):
AAGGTTTTGACATGAAACACAGAATACTGAGTGCTG
Found at i:305989 original size:18 final size:18
Alignment explanation
Indices: 305960--306011 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
305950 AGTATTTCAG
305960 AATTTTTGTTTTTAAATAT
1 AATTTTT-TTTTTAAATAT
* *
305979 AATTTTTTTTTTAATTTT
1 AATTTTTTTTTTAAATAT
* *
305997 AAATGTTTTTTTAAA
1 AATTTTTTTTTTAAA
306012 ATTACCAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 21 0.75
19 7 0.25
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (18 bp):
AATTTTTTTTTTAAATAT
Found at i:307056 original size:20 final size:20
Alignment explanation
Indices: 307033--307077 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
307023 AATTAGCGTT
*
307033 GCGAAAATAAAATTTGCAAC
1 GCGAAAATAAAATTCGCAAC
* *
307053 GCGAAAGTCAAATTCGCAAC
1 GCGAAAATAAAATTCGCAAC
307073 GCGAA
1 GCGAA
307078 TAGTTAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.16
Consensus pattern (20 bp):
GCGAAAATAAAATTCGCAAC
Found at i:307057 original size:49 final size:49
Alignment explanation
Indices: 306958--307057 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 49
306948 GCGAATAGTT
* * * ****
306958 AATTACCTATATAGGTAATTAGCGTTGTGAAAATGAAATTCGGTTTGCG
1 AATTACCTAAATAGGTAATTAGCGTTGCGAAAATAAAATTCGCAACGCG
*
307007 AATTACCTAAATAGGTAATTAGCGTTGCGAAAATAAAATTTGCAACGCG
1 AATTACCTAAATAGGTAATTAGCGTTGCGAAAATAAAATTCGCAACGCG
307056 AA
1 AA
307058 AGTCAAATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (49 bp):
AATTACCTAAATAGGTAATTAGCGTTGCGAAAATAAAATTCGCAACGCG
Found at i:307133 original size:19 final size:20
Alignment explanation
Indices: 307109--307152 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
307099 GATTAGCGTT
307109 GCGAAAAG-AAATTCGCAAC
1 GCGAAAAGCAAATTCGCAAC
307128 GCG-AAAGTCAAATTCGCAAC
1 GCGAAAAG-CAAATTCGCAAC
307148 GCGAA
1 GCGAA
307153 TAGTTAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 3 0.14
20 14 0.64
21 1 0.05
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (20 bp):
GCGAAAAGCAAATTCGCAAC
Found at i:307142 original size:20 final size:21
Alignment explanation
Indices: 307117--307247 Score: 98
Period size: 20 Copynumber: 6.4 Consensus size: 21
307107 TTGCGAAAAG
307117 AAATTCGCAACGCGAA-AGTC
1 AAATTCGCAACGCGAATAGTC
*
307137 AAATTCGCAACGCGAATAGTT
1 AAATTCGCAACGCGAATAGTC
**
307158 AAA-TCGCAACGATAATATGT-
1 AAATTCGCAACGCGAATA-GTC
*
307178 -AATTCTCAACGCGAATAGGT-
1 AAATTCGCAACGCGAATA-GTC
**
307198 AAA-TCGCAACGATAATATGT-
1 AAATTCGCAACGCGAATA-GTC
**
307218 AAA-TCGCAACGCGAATTCTCC
1 AAATTCGCAACGCGAATAGT-C
307239 AAATTCGCA
1 AAATTCGCA
307248 TCTTGAATTT
Statistics
Matches: 89, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.03
20 68 0.76
21 13 0.15
22 5 0.06
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (21 bp):
AAATTCGCAACGCGAATAGTC
Found at i:307148 original size:75 final size:76
Alignment explanation
Indices: 307007--307159 Score: 263
Period size: 75 Copynumber: 2.0 Consensus size: 76
306997 TCGGTTTGCG
*
307007 AATTACCTAAATAGGTAATTAGCGTTGCGAAAATAAAATTTGCAACGCGAAAGTCAAATTCGCAA
1 AATTACCTAAATAGGTAATTAGCGTTGCGAAAATAAAATTCGCAACGCGAAAGTCAAATTCGCAA
307072 CGCGAATAGTT
66 CGCGAATAGTT
* * *
307083 AATTACCTATATAGGTGATTAGCGTTGCGAAAA-GAAATTCGCAACGCGAAAGTCAAATTCGCAA
1 AATTACCTAAATAGGTAATTAGCGTTGCGAAAATAAAATTCGCAACGCGAAAGTCAAATTCGCAA
307147 CGCGAATAGTT
66 CGCGAATAGTT
307158 AA
1 AA
307160 ATCGCAACGA
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
75 42 0.58
76 31 0.42
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (76 bp):
AATTACCTAAATAGGTAATTAGCGTTGCGAAAATAAAATTCGCAACGCGAAAGTCAAATTCGCAA
CGCGAATAGTT
Found at i:307165 original size:40 final size:41
Alignment explanation
Indices: 307137--307233 Score: 162
Period size: 40 Copynumber: 2.4 Consensus size: 41
307127 CGCGAAAGTC
*
307137 AAATTCGCAACGCGAATAGTTAAATCGCAACGATAATATGT
1 AAATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
*
307178 -AATTCTCAACGCGAATAGGTAAATCGCAACGATAATATGT
1 AAATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
307218 AAA-TCGCAACGCGAAT
1 AAATTCGCAACGCGAAT
307234 TCTCCAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
40 50 0.96
41 2 0.04
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.23
Consensus pattern (41 bp):
AAATTCGCAACGCGAATAGGTAAATCGCAACGATAATATGT
Found at i:307583 original size:20 final size:20
Alignment explanation
Indices: 307528--307603 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
307518 AATTTGGAGA
307528 ATTCGCGTTGCGATTTATAT
1 ATTCGCGTTGCGATTTATAT
** *
307548 ATTATCGTTGCGATTTA-CT
1 ATTCGCGTTGCGATTTATAT
** *
307567 ATTCGCGTTGCGAATTTGGAA
1 ATTCGCGTTGCG-ATTTATAT
*
307588 AATCGCGTTGCGATTT
1 ATTCGCGTTGCGATTT
307604 GGAACCTGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 11 0.24
20 23 0.51
21 11 0.24
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTATAT
Found at i:307605 original size:20 final size:21
Alignment explanation
Indices: 307569--307644 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 21
307559 GATTTACTAT
307569 TCGCGTTGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAAAA
**
307590 TCGCGTTGCG-ATTTGGAACC
1 TCGCGTTGCGAATTTGGAAAA
* * **
307610 T-GTGTTGCGAAATTGG-AGT
1 TCGCGTTGCGAATTTGGAAAA
307629 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
307645 TTGGTCATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
19 9 0.20
20 26 0.58
21 10 0.22
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGGAAAA
Found at i:308044 original size:20 final size:20
Alignment explanation
Indices: 308018--308069 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
308008 TGGAGAATTC
308018 GCGTTGCGATTTATA-TATTA
1 GCGTTGCGATTTA-ACTATTA
* *
308038 TCGTTGCGATTTAACTATTC
1 GCGTTGCGATTTAACTATTA
308058 GCGTTGCGATTT
1 GCGTTGCGATTT
308070 TGGAACCTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.44
Consensus pattern (20 bp):
GCGTTGCGATTTAACTATTA
Found at i:311080 original size:18 final size:18
Alignment explanation
Indices: 311057--311095 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
311047 CTCTTGAAAA
311057 TTTAAAATTATCATATAT
1 TTTAAAATTATCATATAT
* * *
311075 TTTAAATTTTTTATATAT
1 TTTAAAATTATCATATAT
311093 TTT
1 TTT
311096 TCTATTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAAAATTATCATATAT
Found at i:311698 original size:17 final size:18
Alignment explanation
Indices: 311676--311712 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
311666 TAATAATGTA
311676 ATCTCCTTT-AAAAAATT
1 ATCTCCTTTAAAAAAATT
311693 ATCTCCTTTAAAAAAATT
1 ATCTCCTTTAAAAAAATT
311711 AT
1 AT
311713 TATTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (18 bp):
ATCTCCTTTAAAAAAATT
Found at i:314948 original size:30 final size:29
Alignment explanation
Indices: 314914--314987 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 29
314904 CTGATTGAAT
*
314914 TGAATTAATTCGGTTAATTCGGTCGATTA
1 TGAATTAATTCGGTTAATTCGGTCGATCA
* * *
314943 CTGAATTAATTCAGTTAATTTGGTCGGTCA
1 -TGAATTAATTCGGTTAATTCGGTCGATCA
314973 TCGAATTAATTCGGT
1 T-GAATTAATTCGGT
314988 CGGAAAACAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 1 0.03
30 37 0.97
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (29 bp):
TGAATTAATTCGGTTAATTCGGTCGATCA
Found at i:315202 original size:17 final size:17
Alignment explanation
Indices: 315180--315218 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
315170 TGAATCAGAT
315180 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
315197 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
315214 -AATTA
1 TAATTA
315219 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:316418 original size:19 final size:20
Alignment explanation
Indices: 316394--316458 Score: 80
Period size: 19 Copynumber: 3.3 Consensus size: 20
316384 ACATATTATT
316394 TTTTTTGTA-ATTTTTCTGA
1 TTTTTTGTATATTTTTCTGA
*
316413 TTTTTTGTATTTTTTTCTGA
1 TTTTTTGTATATTTTTCTGA
* *
316433 TTTTTTTTTGTATTTTT-TGA
1 -TTTTTTGTATATTTTTCTGA
316453 TTTTTT
1 TTTTTT
316459 TAAAAATTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
19 15 0.38
20 12 0.30
21 13 0.32
ACGTcount: A:0.11, C:0.03, G:0.09, T:0.77
Consensus pattern (20 bp):
TTTTTTGTATATTTTTCTGA
Found at i:316418 original size:20 final size:20
Alignment explanation
Indices: 316393--316459 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
316383 AACATATTAT
316393 TTTTTTTGTAATTTTTCTGA
1 TTTTTTTGTAATTTTTCTGA
*
316413 -TTTTTTGTATTTTTTTCTGA
1 TTTTTTTGTA-ATTTTTCTGA
316433 TTTTTTTTTGT-ATTTTT-TGA
1 --TTTTTTTGTAATTTTTCTGA
316453 TTTTTTT
1 TTTTTTT
316460 AAAAATTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
18 7 0.17
19 9 0.22
20 12 0.29
21 5 0.12
23 8 0.20
ACGTcount: A:0.10, C:0.03, G:0.09, T:0.78
Consensus pattern (20 bp):
TTTTTTTGTAATTTTTCTGA
Found at i:316495 original size:136 final size:136
Alignment explanation
Indices: 316327--316574 Score: 336
Period size: 136 Copynumber: 1.8 Consensus size: 136
316317 AATTTATTTT
** * * *
316327 AATTCAAATAGATTAAATTAAAAGATAGATAAAAATACATTAAAATTAGATATATGAACATATTA
1 AATTCAAATAGATTAAATTAAAAGATAGATAAAAATACAGGAAAATTAGATAAATAAACATACTA
* *
316392 TTTTTTTTGTAATTTTTCTG-ATTTTTTGTATTTTTTTCTGATTTTTTTTTGTATTTTTTGATTT
66 ATTTTTTTGTAATTATTCTGTATTTTTTGTA-TTTTTTCTGATTTTTTTTTGTATTTTTTGATTT
316456 TTTTAAA
130 TTTTAAA
* ** * ** **
316463 AATTCAAATAGATTAATTTGCAAGATATATAAAAATATGGGGTAATTAGATAAATAAACATACTA
1 AATTCAAATAGATTAAATTAAAAGATAGATAAAAATACAGGAAAATTAGATAAATAAACATACTA
*
316528 ATTTTTTTGTAATTATTCTGTTTTTTTTGTATTTTTTCTGATTTTTT
66 ATTTTTTTGTAATTATTCTGTATTTTTTGTATTTTTTCTGATTTTTT
316575 AAAATTCAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
136 86 0.91
137 9 0.09
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.52
Consensus pattern (136 bp):
AATTCAAATAGATTAAATTAAAAGATAGATAAAAATACAGGAAAATTAGATAAATAAACATACTA
ATTTTTTTGTAATTATTCTGTATTTTTTGTATTTTTTCTGATTTTTTTTTGTATTTTTTGATTTT
TTTAAA
Found at i:316554 original size:20 final size:21
Alignment explanation
Indices: 316529--316574 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
316519 AACATACTAA
316529 TTTTTTTGTAATTATTCTG-T
1 TTTTTTTGTAATTATTCTGAT
* *
316549 TTTTTTTGTATTTTTTCTGAT
1 TTTTTTTGTAATTATTCTGAT
316570 TTTTT
1 TTTTT
316575 AAAATTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.11, C:0.04, G:0.09, T:0.76
Consensus pattern (21 bp):
TTTTTTTGTAATTATTCTGAT
Found at i:320613 original size:6 final size:6
Alignment explanation
Indices: 320602--320626 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
320592 AATCCACCAG
320602 AAATCA AAATCA AAATCA AAATCA A
1 AAATCA AAATCA AAATCA AAATCA A
320627 GCAAGAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATCA
Found at i:322706 original size:22 final size:22
Alignment explanation
Indices: 322664--322706 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
322654 AGGTATGATT
**
322664 TAAAACAAATAAGTTTAGATAC
1 TAAAACAAATAAAATTAGATAC
322686 TAAAACAAACTAAAATT-GATA
1 TAAAACAAA-TAAAATTAGATA
322707 GTTTAGGTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (22 bp):
TAAAACAAATAAAATTAGATAC
Found at i:322869 original size:36 final size:36
Alignment explanation
Indices: 322822--322891 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
322812 GAAATATTCT
*
322822 TAAATTGACATTCAAATCA-AATCATACAAATCCAAA
1 TAAATTGACATTCAAA-CATAATCACACAAATCCAAA
*
322858 TAAATTGACATTGAAACATAATCACACAAATCCA
1 TAAATTGACATTCAAACATAATCACACAAATCCA
322892 TTAATCACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 2 0.06
36 29 0.94
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.24
Consensus pattern (36 bp):
TAAATTGACATTCAAACATAATCACACAAATCCAAA
Found at i:327453 original size:60 final size:60
Alignment explanation
Indices: 327374--327560 Score: 238
Period size: 60 Copynumber: 3.1 Consensus size: 60
327364 TGCATCATAT
*
327374 ATCCCCAAACTATGACTCTCATT-TCAAATTAGTCCTTAAACTTTTAAACATTCCAATTAC
1 ATCCCCAAACTATGACTCTCATTCT-AAATTAGTCCTTAAACTTTTAAACATTCCAATTTC
** * * *
327434 ATCCTTAAACTATGACTCTCATTCTAAATTAGTCCTTAAATTTTTTAACATTCCAATTTT
1 ATCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCCAATTTC
* * * *
327494 ATCCCCAAACTATGA--ATCATTCTAAATTAGTCCCTATACTTTTAGATC-TTCCAATTTC
1 ATCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTA-AACATTCCAATTTC
327552 ATCCCCAAA
1 ATCCCCAAA
327561 TTCATCCAAA
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
58 42 0.38
59 2 0.02
60 65 0.59
61 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (60 bp):
ATCCCCAAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTTTAAACATTCCAATTTC
Found at i:327470 original size:31 final size:31
Alignment explanation
Indices: 327380--327473 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 31
327370 ATATATCCCC
327380 AAACTATGACTCTCATT-TCAAATTAGTCCTT
1 AAACTATGACTCTCATTCT-AAATTAGTCCTT
* * ** * *
327411 AAACTTTTA--AACATTC-CAATTACATCCTT
1 AAACTATGACTCTCATTCTAAATTA-GTCCTT
327440 AAACTATGACTCTCATTCTAAATTAGTCCTT
1 AAACTATGACTCTCATTCTAAATTAGTCCTT
327471 AAA
1 AAA
327474 TTTTTTAACA
Statistics
Matches: 46, Mismatches: 12, Indels: 10
0.68 0.18 0.15
Matches are distributed among these distances:
28 5 0.11
29 16 0.35
31 20 0.43
32 5 0.11
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.37
Consensus pattern (31 bp):
AAACTATGACTCTCATTCTAAATTAGTCCTT
Found at i:333907 original size:32 final size:32
Alignment explanation
Indices: 333834--333925 Score: 114
Period size: 31 Copynumber: 2.9 Consensus size: 32
333824 CCATACCTAA
* * *
333834 TGTTTACTTTTTATTTTATTTTAGTA-CCCAT
1 TGTTAACTTTTTATTTCATTTTAGTACCCCAC
*
333865 TGTTAACTTTTTATTTCATTTTAATACCCCAC
1 TGTTAACTTTTTATTTCATTTTAGTACCCCAC
* *
333897 TGTTACCTTTTTTGTTTCATTTTAGTACC
1 TGTTAAC-TTTTTATTTCATTTTAGTACC
333926 TAATTTTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
31 23 0.44
32 10 0.19
33 19 0.37
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.57
Consensus pattern (32 bp):
TGTTAACTTTTTATTTCATTTTAGTACCCCAC
Found at i:335627 original size:16 final size:18
Alignment explanation
Indices: 335608--335645 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
335598 TTAAGTTTTT
335608 AAAA-AATT-ATATATAA
1 AAAACAATTGATATATAA
335624 AAAACAATTGATATATAA
1 AAAACAATTGATATATAA
335642 AAAA
1 AAAA
335646 TTGTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.20
17 4 0.20
18 12 0.60
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAACAATTGATATATAA
Found at i:341654 original size:35 final size:35
Alignment explanation
Indices: 341606--341681 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
341596 AATAATACGA
* *
341606 ATCAAATATTGTAGAGGCAAAGACGACTAATCCAG
1 ATCAAATACTGTAGAGGCAAAGAAGACTAATCCAG
* *
341641 ATCAAATACTGTAGAGGCAAAGAAGTCTAATCCGG
1 ATCAAATACTGTAGAGGCAAAGAAGACTAATCCAG
341676 ATCAAA
1 ATCAAA
341682 CACCGATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (35 bp):
ATCAAATACTGTAGAGGCAAAGAAGACTAATCCAG
Found at i:343364 original size:33 final size:32
Alignment explanation
Indices: 343290--343375 Score: 115
Period size: 30 Copynumber: 2.7 Consensus size: 32
343280 CCTAATGTTT
343290 ACTTTTTGTTTCATTTTAGTA--CCGTCGTTG
1 ACTTTTTGTTTCATTTTAGTACCCCGTCGTTG
* *
343320 ACTTTTTGTTTCATTTTAATACCCCGTTGTT-
1 ACTTTTTGTTTCATTTTAGTACCCCGTCGTTG
343351 ACCTTTTTTGTTTCATTTTAGTACC
1 A-C-TTTTTGTTTCATTTTAGTACC
343376 TAAAATTTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
30 20 0.41
31 1 0.02
32 8 0.16
33 20 0.41
ACGTcount: A:0.15, C:0.19, G:0.12, T:0.55
Consensus pattern (32 bp):
ACTTTTTGTTTCATTTTAGTACCCCGTCGTTG
Found at i:344633 original size:13 final size:13
Alignment explanation
Indices: 344617--344648 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
344607 AACAGTTCTG
344617 ATATGCAGTCCTC
1 ATATGCAGTCCTC
*
344630 ATATGCAGTCTTC
1 ATATGCAGTCCTC
344643 ATATGC
1 ATATGC
344649 GCTTCTCCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (13 bp):
ATATGCAGTCCTC
Found at i:348918 original size:35 final size:35
Alignment explanation
Indices: 348870--348945 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
348860 AATAATACGA
* *
348870 ATCAAATATTGTAGAGGCAAAGACGACTAATCCAG
1 ATCAAATACTGTAGAGGCAAAGAAGACTAATCCAG
* *
348905 ATCAAATACTGTAGAGGCAAAGAAGTCTAATCCGG
1 ATCAAATACTGTAGAGGCAAAGAAGACTAATCCAG
348940 ATCAAA
1 ATCAAA
348946 CACCGATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (35 bp):
ATCAAATACTGTAGAGGCAAAGAAGACTAATCCAG
Found at i:352636 original size:153 final size:156
Alignment explanation
Indices: 352422--352741 Score: 528
Period size: 153 Copynumber: 2.1 Consensus size: 156
352412 TAAAGTTTAA
352422 GGACTAAATAAAAGAGAGAACATTTTTAGTAAAAAAGTGAGAACTGAAGTTATATATGTATTTTA
1 GGACTAAATAAAAGAGAGAACATTTTTAGTAAAAAAGTGAGAACTGAAGTTATATATGTATTTTA
*
352487 TTGTGGTATATGAGCATGTT-TTTTAATTTGGT-AAAAC-TACTTAAAATAAATG-GAACT-GAA
66 TTGTGGTATATGAGCATGTTGTTTAAATTTGGTAAAAACATACTTAAAATAAATGAGAACTGGAA
352547 G-AAAAACGAAATCATGAAAAATTGAG
131 GAAAAAACGAAATCATG-AAAATTGAG
352573 GGACTAAATAAAAAGAGAGAGAACATTTTTAGTAAAAAAGTGAG-ACTGAAGTTATATATGTATT
1 GGACTAAAT--AAA-AGAGAGAACATTTTTAGTAAAAAAGTGAGAACTGAAGTTATATATGTATT
352637 TTATTGTGGTATATGAGCATGTTGTTTAAATTTGGTAAAAACATACTTAAAATAAATGATGAACT
63 TTATTGTGGTATATGAGCATGTTGTTTAAATTTGGTAAAAACATACTTAAAATAAATGA-GAACT
352702 GGAAGAAAAAAACGAAATCATGAAAATTGAG
127 GGAAG-AAAAAACGAAATCATGAAAATTGAG
352733 GGACTAAAT
1 GGACTAAAT
352742 TGAAAAAAAA
Statistics
Matches: 157, Mismatches: 1, Indels: 13
0.92 0.01 0.08
Matches are distributed among these distances:
151 9 0.06
153 46 0.29
154 40 0.25
155 5 0.03
156 15 0.10
158 5 0.03
159 4 0.03
160 18 0.11
161 15 0.10
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.30
Consensus pattern (156 bp):
GGACTAAATAAAAGAGAGAACATTTTTAGTAAAAAAGTGAGAACTGAAGTTATATATGTATTTTA
TTGTGGTATATGAGCATGTTGTTTAAATTTGGTAAAAACATACTTAAAATAAATGAGAACTGGAA
GAAAAAACGAAATCATGAAAATTGAG
Found at i:353470 original size:23 final size:23
Alignment explanation
Indices: 353444--353512 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
353434 ACACAATAAT
353444 AACACTGGGAATCATTACATTGA
1 AACACTGGGAATCATTACATTGA
* * *
353467 AACA-T---AATCA-CACAATAA
1 AACACTGGGAATCATTACATTGA
*
353485 TAACACTGGGAATAATTACATTGA
1 -AACACTGGGAATCATTACATTGA
353509 AACA
1 AACA
353513 TAATCACACA
Statistics
Matches: 33, Mismatches: 7, Indels: 12
0.63 0.13 0.23
Matches are distributed among these distances:
18 5 0.15
19 9 0.27
20 1 0.03
22 1 0.03
23 12 0.36
24 5 0.15
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (23 bp):
AACACTGGGAATCATTACATTGA
Found at i:353477 original size:42 final size:42
Alignment explanation
Indices: 353413--353523 Score: 195
Period size: 42 Copynumber: 2.6 Consensus size: 42
353403 AAATATCTTA
*
353413 AATTGACATTCAAACATAATCACACAATAATAACACTGGGAAT
1 AATT-ACATTGAAACATAATCACACAATAATAACACTGGGAAT
*
353456 CATTACATTGAAACATAATCACACAATAATAACACTGGGAAT
1 AATTACATTGAAACATAATCACACAATAATAACACTGGGAAT
353498 AATTACATTGAAACATAATCACACAA
1 AATTACATTGAAACATAATCACACAA
353524 ATCCATTAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
42 62 0.95
43 3 0.05
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (42 bp):
AATTACATTGAAACATAATCACACAATAATAACACTGGGAAT
Found at i:353489 original size:19 final size:19
Alignment explanation
Indices: 353425--353489 Score: 51
Period size: 19 Copynumber: 3.2 Consensus size: 19
353415 TTGACATTCA
353425 AACATAATCACACAATAAT
1 AACATAATCACACAATAAT
* * *
353444 AACACTGGGAATCATTACATTGA-
1 AACA-T---AATCA-CACAATAAT
353467 AACATAATCACACAATAAT
1 AACATAATCACACAATAAT
353486 AACA
1 AACA
353490 CTGGGAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 5 0.15
19 13 0.38
20 1 0.03
22 1 0.03
23 9 0.26
24 5 0.15
ACGTcount: A:0.52, C:0.20, G:0.06, T:0.22
Consensus pattern (19 bp):
AACATAATCACACAATAAT
Found at i:356055 original size:24 final size:24
Alignment explanation
Indices: 356023--356077 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
356013 TGTATACATA
356023 TAAATTATATATGATTTTAGAAAC
1 TAAATTATATATGATTTTAGAAAC
356047 TAAATTATATATGATTTTAGAAAC
1 TAAATTATATATGATTTTAGAAAC
356071 TAAATTA
1 TAAATTA
356078 CAATAATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (24 bp):
TAAATTATATATGATTTTAGAAAC
Found at i:359034 original size:60 final size:60
Alignment explanation
Indices: 358934--359055 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 60
358924 AGCTGCTCTT
* *
358934 AACCTAGTGTTAGGGGCAGCCTACTATCTTATCTCTCCTTACCTCATTACATATGGGAAC
1 AACCTAGTGTTAGGGGCAGCCTACTATCTTACCTCCCCTTACCTCATTACATATGGGAAC
358994 AACCTAGTGTTAGGGGCAGCCTACTATCTTACCTCCCCTTACCTCATTACATATGGGAAC
1 AACCTAGTGTTAGGGGCAGCCTACTATCTTACCTCCCCTTACCTCATTACATATGGGAAC
359054 AA
1 AA
359056 GGGACATCCA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (60 bp):
AACCTAGTGTTAGGGGCAGCCTACTATCTTACCTCCCCTTACCTCATTACATATGGGAAC
Found at i:364789 original size:33 final size:32
Alignment explanation
Indices: 364713--364799 Score: 108
Period size: 31 Copynumber: 2.7 Consensus size: 32
364703 CCTAATGTTT
364713 ACTTTTTGTTTCATTTTAGTA-CCCGTCGTTA
1 ACTTTTTGTTTCATTTTAGTACCCCGTCGTTA
* *
364744 ACGTTTTGTTTCATTTTAATACCCCG-CTGTT-
1 ACTTTTTGTTTCATTTTAGTACCCCGTC-GTTA
364775 ACTTTTTTTGTTTCATTTTAGTACC
1 AC--TTTTTGTTTCATTTTAGTACC
364800 TAAATTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
31 22 0.46
32 7 0.15
33 19 0.40
ACGTcount: A:0.16, C:0.20, G:0.11, T:0.53
Consensus pattern (32 bp):
ACTTTTTGTTTCATTTTAGTACCCCGTCGTTA
Found at i:368097 original size:13 final size:13
Alignment explanation
Indices: 368050--368086 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
368040 AACCCGACCC
368050 GACCCGACCCGTT
1 GACCCGACCCGTT
*
368063 TACCCGACCCGTT
1 GACCCGACCCGTT
368076 GACCCGACCCG
1 GACCCGACCCG
368087 ACCCGTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:368101 original size:7 final size:7
Alignment explanation
Indices: 368089--368120 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
368079 CCGACCCGAC
368089 CCGTTGA
1 CCGTTGA
368096 CCGTTGA
1 CCGTTGA
368103 CCCGTTGA
1 -CCGTTGA
368111 CCGTTGA
1 CCGTTGA
368118 CCG
1 CCG
368121 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:368106 original size:15 final size:15
Alignment explanation
Indices: 368086--368119 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
368076 GACCCGACCC
368086 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
368101 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
368116 GACC
1 GACC
368120 GGAGTTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:369455 original size:18 final size:18
Alignment explanation
Indices: 369429--369464 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
369419 TCGAAAGGAC
*
369429 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
369447 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
369465 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:370600 original size:24 final size:24
Alignment explanation
Indices: 370573--370687 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
370563 TCGATTTGAT
370573 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
370597 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
370621 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
370645 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
* *
370668 TTTATGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
370688 CTGATTTATA
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
23 3 0.04
24 78 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:370688 original size:24 final size:24
Alignment explanation
Indices: 370569--370696 Score: 111
Period size: 24 Copynumber: 5.3 Consensus size: 24
370559 ATTTTCGATT
* *
370569 TGATTTCTGATCTGATACTTGACA
1 TGATTTATGATCTGATACTTGACC
* *
370593 TGGA-TTCTGATCTGATA-TCTGACA
1 T-GATTTATGATCTGATACT-TGACC
* *
370617 TGGA-TTCTGATCTGATACTTGACT
1 T-GATTTATGATCTGATACTTGACC
* *
370641 TGGA-TTCTGATCTGTTACTTGACC
1 T-GATTTATGATCTGATACTTGACC
*
370665 TGATTTATGATATGATACTTGACC
1 TGATTTATGATCTGATACTTGACC
370689 TGATTTAT
1 TGATTTAT
370697 ATTTTGATTT
Statistics
Matches: 94, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
23 3 0.03
24 88 0.94
25 3 0.03
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (24 bp):
TGATTTATGATCTGATACTTGACC
Found at i:372890 original size:13 final size:13
Alignment explanation
Indices: 372871--372913 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
372861 AACCCGACCC
372871 GACCCGACCCATT
1 GACCCGACCCATT
* *
372884 TACCCGACCCGTT
1 GACCCGACCCATT
*
372897 GACCCGACCCGTT
1 GACCCGACCCATT
372910 GACC
1 GACC
372914 GTTGACCCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.19, C:0.47, G:0.19, T:0.16
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:372900 original size:8 final size:8
Alignment explanation
Indices: 372889--372935 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
372879 CCATTTACCC
372889 GACCCGTT
1 GACCCGTT
372897 GACCC---
1 GACCCGTT
372902 GACCCGTT
1 GACCCGTT
372910 GA-CCGTT
1 GACCCGTT
372917 GACCCGTT
1 GACCCGTT
372925 GA-CCGTT
1 GACCCGTT
372932 GACC
1 GACC
372936 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:372917 original size:7 final size:7
Alignment explanation
Indices: 372905--372936 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
372895 TTGACCCGAC
372905 CCGTTGA
1 CCGTTGA
372912 CCGTTGA
1 CCGTTGA
372919 CCCGTTGA
1 -CCGTTGA
372927 CCGTTGA
1 CCGTTGA
372934 CCG
1 CCG
372937 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:372922 original size:15 final size:15
Alignment explanation
Indices: 372889--372935 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
372879 CCATTTACCC
*
372889 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
372902 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
372917 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
372932 GACC
1 GACC
372936 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:374270 original size:18 final size:18
Alignment explanation
Indices: 374244--374279 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
374234 TCGAAAGGAC
*
374244 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
374262 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
374280 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:375414 original size:24 final size:24
Alignment explanation
Indices: 375387--375501 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
375377 TCGATTTGAT
375387 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
375411 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
375435 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
375459 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
* *
375482 TTTATGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
375502 CTGATTTATA
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
23 3 0.04
24 78 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:375502 original size:24 final size:24
Alignment explanation
Indices: 375383--375510 Score: 111
Period size: 24 Copynumber: 5.3 Consensus size: 24
375373 ATTTTCGATT
* *
375383 TGATTTCTGATCTGATACTTGACA
1 TGATTTATGATCTGATACTTGACC
* *
375407 TGGA-TTCTGATCTGATA-TCTGACA
1 T-GATTTATGATCTGATACT-TGACC
* *
375431 TGGA-TTCTGATCTGATACTTGACT
1 T-GATTTATGATCTGATACTTGACC
* *
375455 TGGA-TTCTGATCTGTTACTTGACC
1 T-GATTTATGATCTGATACTTGACC
*
375479 TGATTTATGATATGATACTTGACC
1 TGATTTATGATCTGATACTTGACC
375503 TGATTTAT
1 TGATTTAT
375511 ATTTTGATTT
Statistics
Matches: 94, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
23 3 0.03
24 88 0.94
25 3 0.03
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (24 bp):
TGATTTATGATCTGATACTTGACC
Done.