Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007805.1 Hibiscus syriacus cultivar Beakdansim tig00110123_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: 2708727
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:309104 original size:16 final size:17
Alignment explanation
Indices: 309076--309108 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
309066 AATAGCAATC
309076 CTACCCAGACATGCTTT
1 CTACCCAGACATGCTTT
309093 CTACCC-GACATGCTTT
1 CTACCCAGACATGCTTT
309109 TATTTCAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.21, C:0.36, G:0.12, T:0.30
Consensus pattern (17 bp):
CTACCCAGACATGCTTT
Found at i:312245 original size:3 final size:3
Alignment explanation
Indices: 312237--312300 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
312227 TTAACCTGAA
* * * * * *
312237 AAT AAT AAT AAA AAC AAT ATT AGT AGT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
312285 AAT AAT AAT AAAT AAT
1 AAT AAT AAT -AAT AAT
312301 TAATTAAAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:318701 original size:12 final size:12
Alignment explanation
Indices: 318684--318716 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
318674 AGGTGGAGGA
318684 TTTGGAGGTGAG
1 TTTGGAGGTGAG
318696 TTTGGAGGTGAG
1 TTTGGAGGTGAG
318708 TTTGGAGGT
1 TTTGGAGGT
318717 TGGCTAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.48, T:0.36
Consensus pattern (12 bp):
TTTGGAGGTGAG
Found at i:319031 original size:22 final size:22
Alignment explanation
Indices: 319000--319084 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 22
318990 AGAACCCTCA
* **
319000 GGGGGTATCGATTCCCTTGTAG
1 GGGGGAATCGATTCCCTTCAAG
* *
319022 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCCTTCAAG
*
319045 GGGGGAATCGACTCTCCTTCAAG
1 GGGGGAATCGATTC-CCTTCAAG
* *
319068 GAGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
319085 CTGCACCAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
22 15 0.30
23 35 0.70
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.26
Consensus pattern (22 bp):
GGGGGAATCGATTCCCTTCAAG
Found at i:323105 original size:115 final size:116
Alignment explanation
Indices: 322889--323106 Score: 282
Period size: 115 Copynumber: 1.9 Consensus size: 116
322879 TTCAAATCGA
322889 AATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTTCA
1 AATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTTCA
* *
322954 TTTTGATTTTCAAAATCCATTTTTGTTTCTAGAAGAAGTTTGTTTAATTTG
66 TTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
* * * * *
323005 AATTTT-TTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAATATTT
1 AATTTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAAGATTT
* * **
323067 CATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 CATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
323107 ATCATTTTTA
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
114 2 0.02
115 76 0.86
116 10 0.11
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.50
Consensus pattern (116 bp):
AATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTTCA
TTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTG
Found at i:325232 original size:14 final size:14
Alignment explanation
Indices: 325215--325241 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
325205 AATATCTTTT
325215 AAAATAATTTTAAG
1 AAAATAATTTTAAG
325229 AAAATAATTTTAA
1 AAAATAATTTTAA
325242 AAGATAAAAA
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:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
AAAATAATTTTAAG
Found at i:326967 original size:25 final size:27
Alignment explanation
Indices: 326897--326967 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
326887 ATCTGCTAGA
*
326897 CTTCTCGGGTCTGGGCCTCCTGTTTGT
1 CTTCTCGGGTCTGGGCCTCCTGTTTAT
*
326924 CTTCTCGGGTCTGGACCTCCAT-TTTAT
1 CTTCTCGGGTCTGGGCCTCC-TGTTTAT
*
326951 C-T-TCGGGTTTGGGCCTC
1 CTTCTCGGGTCTGGGCCTC
326968 TGGGTTCTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 13 0.33
26 1 0.03
27 24 0.62
28 1 0.03
ACGTcount: A:0.04, C:0.30, G:0.27, T:0.39
Consensus pattern (27 bp):
CTTCTCGGGTCTGGGCCTCCTGTTTAT
Found at i:327011 original size:3 final size:3
Alignment explanation
Indices: 327003--327032 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
326993 TTGTAAAATT
327003 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
327033 ATATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:332381 original size:15 final size:15
Alignment explanation
Indices: 332363--332392 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
332353 CCACGGTGCT
332363 CCCGAAATCCTGCGC
1 CCCGAAATCCTGCGC
*
332378 CCCGGAATCCTGCGC
1 CCCGAAATCCTGCGC
332393 GATTGTGATA
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:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (15 bp):
CCCGAAATCCTGCGC
Found at i:363123 original size:25 final size:25
Alignment explanation
Indices: 363093--363161 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 25
363083 TACAAGAACC
* *
363093 CGGAGGCCCAAACCCGAAGATAAAA
1 CGGAGGCCCAGACCCGAAGACAAAA
* * *
363118 TGGAGGTCCAGACCCGAGAAGACAAAC
1 CGGAGGCCCAGACCC--GAAGACAAAA
363145 CGGAGGCCCAGACCCGA
1 CGGAGGCCCAGACCCGA
363162 GAAGTCCAGT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
25 14 0.40
27 21 0.60
ACGTcount: A:0.36, C:0.30, G:0.29, T:0.04
Consensus pattern (25 bp):
CGGAGGCCCAGACCCGAAGACAAAA
Found at i:371216 original size:23 final size:22
Alignment explanation
Indices: 371184--371268 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 22
371174 TTGGTGCAGA
*
371184 GGGAATCGATACCCTCC-TTGAAG
1 GGGAACCGAT-CCC-CCTTTGAAG
*
371207 GGGAGCCGATCCCCCCTTTGAAG
1 GGGAACCGAT-CCCCCTTTGAAG
371230 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGA-TCCCCCTTTGAAG
371253 GGGAACCGATTCCCCC
1 GGGAACCGA-TCCCCC
371269 CCCACAGGGG
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
22 2 0.04
23 53 0.95
24 1 0.02
ACGTcount: A:0.21, C:0.33, G:0.27, T:0.19
Consensus pattern (22 bp):
GGGAACCGATCCCCCTTTGAAG
Found at i:371277 original size:23 final size:22
Alignment explanation
Indices: 371227--371292 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
371217 CCCCCCTTTG
***
371227 AAGGGGAACCGATTCCCCCTTTG
1 AAGGGGAACCGATTCCCCC-CCC
371250 AAGGGGAACCGATTCCCCCCCC
1 AAGGGGAACCGATTCCCCCCCC
* *
371272 ACAGGGGAATCGATACCCCCC
1 A-AGGGGAACCGATTCCCCCC
371293 TGAGGGTTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.24, C:0.38, G:0.24, T:0.14
Consensus pattern (22 bp):
AAGGGGAACCGATTCCCCCCCC
Found at i:381341 original size:16 final size:17
Alignment explanation
Indices: 381317--381349 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
381307 TCTTGAAATA
381317 AAAGCATGTC-GGGTAG
1 AAAGCATGTCTGGGTAG
*
381333 AAAGTATGTCTGGGTAG
1 AAAGCATGTCTGGGTAG
381350 GATTGCTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.30, C:0.09, G:0.36, T:0.24
Consensus pattern (17 bp):
AAAGCATGTCTGGGTAG
Found at i:395476 original size:23 final size:23
Alignment explanation
Indices: 395433--395506 Score: 55
Period size: 23 Copynumber: 3.2 Consensus size: 23
395423 ATAGAGTTTT
* *
395433 AGTACCAAAAATGATAGAGTTCC
1 AGTACCAAAAACGATAAAGTTCC
*
395456 AGTACC-AAAACGATCAAAGTTTC
1 AGTACCAAAAACGAT-AAAGTTCC
* *
395479 AATA-CAAAAAC-ATACATAGTTTC
1 AGTACCAAAAACGATA-A-AGTTCC
395502 AGTAC
1 AGTAC
395507 TACTAAAAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 1 0.02
22 11 0.27
23 29 0.71
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (23 bp):
AGTACCAAAAACGATAAAGTTCC
Found at i:396764 original size:2 final size:2
Alignment explanation
Indices: 396757--396791 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
396747 ACAAGTGCAT
396757 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
396792 CTAAAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:396854 original size:2 final size:2
Alignment explanation
Indices: 396849--396879 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
396839 AAACACATAC
396849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
396880 ATAGTGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:397033 original size:30 final size:30
Alignment explanation
Indices: 396994--397097 Score: 109
Period size: 30 Copynumber: 3.4 Consensus size: 30
396984 AAAAGAATTG
* *
396994 AAATGTAAATAAAGGAAAATAAAAGTGCTT
1 AAATATAAATAAAGGAAAATAAAAGTGCTA
* * *
397024 AAATATAAATAAAGAAAAATAAAGGTACTA
1 AAATATAAATAAAGGAAAATAAAAGTGCTA
* * * *
397054 AAATTGTAAATAAATGAAAATTAAAGTGCTG
1 AAA-TATAAATAAAGGAAAATAAAAGTGCTA
*
397085 AAATAAAAATAAA
1 AAATATAAATAAA
397098 TAAATAAATA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
30 36 0.61
31 23 0.39
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.23
Consensus pattern (30 bp):
AAATATAAATAAAGGAAAATAAAAGTGCTA
Found at i:400004 original size:431 final size:431
Alignment explanation
Indices: 399194--400058 Score: 1184
Period size: 431 Copynumber: 2.0 Consensus size: 431
399184 TGAATGCATG
* * * *
399194 TAGTGTAGTAAAGTTTTTAGTGAGGCACTGAGCTCGTAAGCTCAACGTTCAAAATGTGTTTCCAT
1 TAGTATAGTAAAGTTTTTAGTGAGACACTAAGCTCGTAAGCTCAACATTCAAAATGTGTTTCCAT
* * *
399259 ACGCAGACTAAGAGATTATTCTTGGGGAGTTTTCATCATCAGATATTCCAGCACAGCAGATCAGA
66 ACGCAGACTAAGAGATCATTCTTGGGGAGTTTTCATCATCAGATATTCCAGCACAACAGATCAAA
* * * *
399324 TCCGGCCAAGTATCTCAGAGTATTTCTTGAGTTACTTGTAAAGGGCATGTACCTTTATGGACCCT
131 TCCAGCCAAGTATCTCAGAGTATGTCTTGAGTCACTTGTAAAGGGCATGTACCTCTATGGACCCT
* * *
399389 TATATTACTTAGTCATAACCTTTGATTTTAAACTCAGTGATGTATTATTATTTTGATGATTTTGG
196 TATATTACTCACTCATAACCTTTGATTTTAAACTCAGTGATGTATTATTATTTTGATGATTTTAG
* * *
399454 GAGCTCCCTCGTATTTGTAAAACTTAATTACTATGCTTTTATTTATTCAATATTGATGGATTTTT
261 GAGCTCCCCCGTATTTGTAAAACTTAATTAATATGCTTTTATTTATTCAATATTGATAGATTTTT
*
399519 ATCCGATTCTTTATAATCAATCTGCTTAAAAAGAAAATTTTTGGGTTAGCCACTTAGGT-GAACC
326 ATCCGATACTTTATAATCAATCTGCTTAAAAAGAAAATTTTTGGGTTAGCCACTTAGGTAG-ACC
* *
399583 CATTTGACATCGTGATTCAGTGATCTTCGGGTCGGACTGGAT
390 CATGTGACATCGTGATTCAGTAATCTTCGGGTCGGACTGGAT
* ** * * *
399625 TAGTATAGTAAAGTTTTTAGTGAGACACTAAGCTTGTAAGCTCAACATTTGACATGTGTTTTCGT
1 TAGTATAGTAAAGTTTTTAGTGAGACACTAAGCTCGTAAGCTCAACATTCAAAATGTGTTTCCAT
* * * * * * * *
399690 GCGCAGGCTAGGAGATCGTT-TGTGGGGAGTTTTCGTTATCAGATATTCTATCACAACAGATCAA
66 ACGCAGACTAAGAGATCATTCT-TGGGGAGTTTTCATCATCAGATATTCCAGCACAACAGATCAA
* * * *
399754 ATCCAGTCGAGTATCTCAGAGTATGTCTTGAGTCACTTGTAGAGGGCATGTA-CTACTATGGACT
130 ATCCAGCCAAGTATCTCAGAGTATGTCTTGAGTCACTTGTAAAGGGCATGTACCT-CTATGGACC
* *
399818 CTTGTATTACTCACTCATAACCTTTTATTTTAAACTCAGTGATGTATTATTATTTTGAAT-ATTT
194 CTTATATTACTCACTCATAACCTTTGATTTTAAACTCAGTGATGTATTATTATTTTG-ATGATTT
*
399882 TAGGAGCTCCCCCGTATTTGTAAAACTTAATTAATATGCTTTTATTTATTCAGTA-TGTATAGAT
258 TAGGAGCTCCCCCGTATTTGTAAAACTTAATTAATATGCTTTTATTTATTCAATATTG-ATAGAT
* * * * *
399946 TTTTATTCGGTACTTTATAATCAGTC-GACTTAAAAAGAAATTTTTTGGGTTTGCCACTTAGGTA
322 TTTTATCCGATACTTTATAATCAATCTG-CTTAAAAAGAAAATTTTTGGGTTAGCCACTTAGGTA
* * * *
400010 GTCTCGTGTGACATCGTGGTTCAGTAATCTTCGGGTCGGACTGGAT
386 GACCCATGTGACATCGTGATTCAGTAATCTTCGGGTCGGACTGGAT
400056 TAG
1 TAG
400059 AGTGTTACAA
Statistics
Matches: 378, Mismatches: 50, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
430 6 0.02
431 369 0.98
432 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (431 bp):
TAGTATAGTAAAGTTTTTAGTGAGACACTAAGCTCGTAAGCTCAACATTCAAAATGTGTTTCCAT
ACGCAGACTAAGAGATCATTCTTGGGGAGTTTTCATCATCAGATATTCCAGCACAACAGATCAAA
TCCAGCCAAGTATCTCAGAGTATGTCTTGAGTCACTTGTAAAGGGCATGTACCTCTATGGACCCT
TATATTACTCACTCATAACCTTTGATTTTAAACTCAGTGATGTATTATTATTTTGATGATTTTAG
GAGCTCCCCCGTATTTGTAAAACTTAATTAATATGCTTTTATTTATTCAATATTGATAGATTTTT
ATCCGATACTTTATAATCAATCTGCTTAAAAAGAAAATTTTTGGGTTAGCCACTTAGGTAGACCC
ATGTGACATCGTGATTCAGTAATCTTCGGGTCGGACTGGAT
Found at i:402505 original size:29 final size:31
Alignment explanation
Indices: 402466--402528 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 31
402456 TTTGTATTTT
* *
402466 AAATTCAAATAATTTCTTAAATTTTCTA-AA
1 AAATTCAAATAATTCCTCAAATTTTCTACAA
402496 AAATT-AAATAATTCCTCAAATTTTCTACAA
1 AAATTCAAATAATTCCTCAAATTTTCTACAA
402526 AAA
1 AAA
402529 GCAATTAGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (31 bp):
AAATTCAAATAATTCCTCAAATTTTCTACAA
Found at i:404732 original size:95 final size:94
Alignment explanation
Indices: 404628--404811 Score: 219
Period size: 95 Copynumber: 1.9 Consensus size: 94
404618 ATACTAAAAG
** * * * * *
404628 GAAAGTATCGATACCATGGATTCCAGAATGCCA-AAATGGTATCGATACTGAAAGAGAGTATC-A
1 GAAAGTATCGATACCATAAATTACAAAAT-ACAGAAATGGTATCAATACTAAAAGAGAGTATCGA
*
404691 GTACCATAGTATAGTAGTATCCATACTGAGA
65 -TACCATAGTATAGAAGTATCCATACTGAGA
* * *
404722 GAAAGGTATCGATACCATAAATTACAAAATATAGAAATGGTATCAATACTAAAAGGGGGTATCGA
1 GAAA-GTATCGATACCATAAATTACAAAATACAGAAATGGTATCAATACTAAAAGAGAGTATCGA
*
404787 TACCATAGTATAGAAGTATCGATAC
65 TACCATAGTATAGAAGTATCCATAC
404812 CATGGTAAGG
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
94 5 0.07
95 69 0.92
96 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.24
Consensus pattern (94 bp):
GAAAGTATCGATACCATAAATTACAAAATACAGAAATGGTATCAATACTAAAAGAGAGTATCGAT
ACCATAGTATAGAAGTATCCATACTGAGA
Found at i:405335 original size:45 final size:45
Alignment explanation
Indices: 405176--405364 Score: 271
Period size: 45 Copynumber: 4.3 Consensus size: 45
405166 TGTTTTTATT
*
405176 TCATAAATGAAATGCATAACGGTGCATTAAAGGCATG--A--ATG
1 TCATAAATGAAATGCATGACGGTGCATTAAAGGCATGAAAGGATG
*
405217 CCATAAATGAAATGCATGACGGTGCATTAAAGGCATGAAAGGATG
1 TCATAAATGAAATGCATGACGGTGCATTAAAGGCATGAAAGGATG
* * *
405262 TCATAATTG-AATGCATGACGATGCATTAAAGGTATGAAAGGATG
1 TCATAAATGAAATGCATGACGGTGCATTAAAGGCATGAAAGGATG
*
405306 TCATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATG
1 TCATAAATGAAATGCATGACGGTGCATTAAAGGCATGAAAGGATG
*
405351 ACATAAATGGAAAT
1 TCATAAAT-GAAAT
405365 AATGAATAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
41 35 0.27
43 1 0.01
44 41 0.31
45 49 0.37
46 5 0.04
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.23
Consensus pattern (45 bp):
TCATAAATGAAATGCATGACGGTGCATTAAAGGCATGAAAGGATG
Found at i:407740 original size:31 final size:31
Alignment explanation
Indices: 407674--407733 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
407664 GTCCACATGT
407674 CATGTTTGAGTTACCAATTTAGTCAATCTGA
1 CATGTTTGAGTTACCAATTTAGTCAATCTGA
* *
407705 CATGTTTGAGTTACTAATTTAGTTAATCT
1 CATGTTTGAGTTACCAATTTAGTCAATCT
407734 ACCATGTCAT
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:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (31 bp):
CATGTTTGAGTTACCAATTTAGTCAATCTGA
Found at i:416716 original size:30 final size:30
Alignment explanation
Indices: 416682--416743 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
416672 TGCACTATCT
416682 TGTGCAACGAACACCTCATAATCTTCATTG
1 TGTGCAACGAACACCTCATAATCTTCATTG
* *
416712 TGTGCAATGAACACCTCATGATCTTCATTG
1 TGTGCAACGAACACCTCATAATCTTCATTG
416742 TG
1 TG
416744 CACAAGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (30 bp):
TGTGCAACGAACACCTCATAATCTTCATTG
Found at i:418393 original size:21 final size:21
Alignment explanation
Indices: 418367--418422 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
418357 CCCTTGCAGC
*
418367 TTAACTACCGGCACAGATAGA
1 TTAACTACCGACACAGATAGA
* *
418388 TTAACTAACGACACGGATAGA
1 TTAACTACCGACACAGATAGA
418409 TTAACTACCGACAC
1 TTAACTACCGACAC
418423 TCAAATCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (21 bp):
TTAACTACCGACACAGATAGA
Found at i:419396 original size:25 final size:24
Alignment explanation
Indices: 419363--419410 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
419353 GTACTTGAAG
*
419363 TTCAGTTTGAGCTCAAGTTCAAAC
1 TTCAGTTTGAGCTCAAGTCCAAAC
419387 TTCAGGTTTGAGCTCAAGTCCAAA
1 TTCA-GTTTGAGCTCAAGTCCAAA
419411 ATTAGGTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (24 bp):
TTCAGTTTGAGCTCAAGTCCAAAC
Found at i:421690 original size:28 final size:28
Alignment explanation
Indices: 421655--421732 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
421645 TCAAATTTTA
*
421655 TAAGTAACTTCAAGACTTCAAATATC-T
1 TAAGTAACTTCAATACTTCAAATATCAT
* * *
421682 TAGAGTAACTGCAATACTAT-AGATTTCAT
1 TA-AGTAACTTCAATACT-TCAAATATCAT
421711 TAAGTAACTTCAATACTTCAAA
1 TAAGTAACTTCAATACTTCAAA
421733 GTTGAAGGAC
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
27 3 0.07
28 34 0.83
29 4 0.10
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (28 bp):
TAAGTAACTTCAATACTTCAAATATCAT
Found at i:422064 original size:30 final size:29
Alignment explanation
Indices: 422030--422137 Score: 101
Period size: 30 Copynumber: 3.6 Consensus size: 29
422020 TACCCCTATA
*
422030 TTTGTTTCTTTGTTTTTGTTGTGATGGGCT
1 TTTGTTTCTTTG-TTTTGTTGTGATGGGTT
* *
422060 TTTGTTTCCTTTGCTTCTGCTGTGA-GGGTT
1 TTTGTTT-CTTTG-TTTTGTTGTGATGGGTT
* *
422090 TTTGTTTTCTTTGGTTTGTTGTGGTGGGTT
1 TTTG-TTTCTTTGTTTTGTTGTGATGGGTT
* *
422120 TCTTCTTTCTTTGGTTTG
1 T-TTGTTTCTTTGTTTTG
422138 CTTTCACGGG
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
29 7 0.11
30 39 0.60
31 19 0.29
ACGTcount: A:0.02, C:0.10, G:0.27, T:0.61
Consensus pattern (29 bp):
TTTGTTTCTTTGTTTTGTTGTGATGGGTT
Found at i:423651 original size:29 final size:31
Alignment explanation
Indices: 423618--423677 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
423608 TCTATTTTTC
* *
423618 CACTAAAATT-T-TAAAAGTAACGAAATGGT
1 CACTAAAATTATGGAAAAGTAACAAAATGGT
*
423647 CACTAATATTATGGAAAAGTAACAAAATGGT
1 CACTAAAATTATGGAAAAGTAACAAAATGGT
423678 GATTGTGGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 9 0.35
30 1 0.04
31 16 0.62
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (31 bp):
CACTAAAATTATGGAAAAGTAACAAAATGGT
Found at i:430919 original size:2 final size:2
Alignment explanation
Indices: 430914--430941 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
430904 ATCATTTAGG
430914 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
430942 CTTGAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:433605 original size:25 final size:26
Alignment explanation
Indices: 433568--433621 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
433558 TGCCTATGAA
433568 GGGTACAAGGGGTGAAGCCCCTTGTG
1 GGGTACAAGGGGTGAAGCCCCTTGTG
* * *
433594 GGGT-CAATGGGTGGAGCCCTTTGTG
1 GGGTACAAGGGGTGAAGCCCCTTGTG
433619 GGG
1 GGG
433622 ATCTAACGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.15, C:0.17, G:0.46, T:0.22
Consensus pattern (26 bp):
GGGTACAAGGGGTGAAGCCCCTTGTG
Found at i:440329 original size:20 final size:20
Alignment explanation
Indices: 440300--440358 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
440290 GATATTGAAC
440300 CTTTTAGTATAGATACCAAA
1 CTTTTAGTATAGATACCAAA
* * *
440320 CTTTTGGTATGGATACCAAT
1 CTTTTAGTATAGATACCAAA
* * *
440340 CCTCTAGTATGGATACCAA
1 CTTTTAGTATAGATACCAA
440359 TTCGTCTTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (20 bp):
CTTTTAGTATAGATACCAAA
Found at i:440359 original size:20 final size:21
Alignment explanation
Indices: 440326--440375 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
440316 CAAACTTTTG
440326 GTATGGATACCAA-TCCTCTA
1 GTATGGATACCAATTCCTCTA
* *
440346 GTATGGATACCAATTCGTCTT
1 GTATGGATACCAATTCCTCTA
440367 GTATGGATA
1 GTATGGATA
440376 GTAATCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (21 bp):
GTATGGATACCAATTCCTCTA
Found at i:443026 original size:28 final size:28
Alignment explanation
Indices: 442977--443031 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
442967 CTTTGTTTAC
**
442977 ATTATGTCGTCAAGTTAATGCTTGAAAT
1 ATTATGTCGTCAAGCCAATGCTTGAAAT
*
443005 ATTATGTCGTCAAGCCATTGCTTGAAA
1 ATTATGTCGTCAAGCCAATGCTTGAAA
443032 GCAACGATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (28 bp):
ATTATGTCGTCAAGCCAATGCTTGAAAT
Found at i:446622 original size:21 final size:21
Alignment explanation
Indices: 446585--446630 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
446575 ATCACTGCAA
*
446585 GGTTACATATAGTGCCCACAG
1 GGTTACATATAGAGCCCACAG
*
446606 GGTTACATACT-GAGCCCGCAG
1 GGTTACATA-TAGAGCCCACAG
446627 GGTT
1 GGTT
446631 TTATGGCACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (21 bp):
GGTTACATATAGAGCCCACAG
Found at i:449520 original size:30 final size:31
Alignment explanation
Indices: 449479--449544 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 31
449469 TGAAATGAAA
* *
449479 TGAAAGGTACATGTTATATGATGTGAATATG
1 TGAAAGGTACATGTTACATGAAGTGAATATG
449510 TGAAA-GTACATGTTACATGAAGTGAATATG
1 TGAAAGGTACATGTTACATGAAGTGAATATG
449540 TGAAA
1 TGAAA
449545 AATACAGGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 28 0.85
31 5 0.15
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (31 bp):
TGAAAGGTACATGTTACATGAAGTGAATATG
Found at i:449669 original size:8 final size:8
Alignment explanation
Indices: 449656--449680 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
449646 TTAAGTCAGT
449656 TTTATATA
1 TTTATATA
449664 TTTATATA
1 TTTATATA
449672 TTTATATA
1 TTTATATA
449680 T
1 T
449681 GATAATTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTATATA
Found at i:461887 original size:49 final size:49
Alignment explanation
Indices: 461783--462181 Score: 500
Period size: 49 Copynumber: 8.2 Consensus size: 49
461773 CATTGTTATA
* * *
461783 CATTTAAC-TGTCATTAGTGGCAGCTTTCTGC-CAAAATGCACCATTTGG
1 CATTTAACTTG-CATTAGTGGCACCTTTCTGCAAAAAATGCACCATTTTG
* *
461831 CATTTAACTTTCATTAGTGGCACATTTCTGCAAAAAATGCACCATTTTG
1 CATTTAACTTGCATTAGTGGCACCTTTCTGCAAAAAATGCACCATTTTG
* * * * *
461880 TATTTAACATGCATTAGTGACACCTTTCTTCAAAAAATGCACCATTATG
1 CATTTAACTTGCATTAGTGGCACCTTTCTGCAAAAAATGCACCATTTTG
* *
461929 CATTTAACTTGCATTAGTGGCACCTTTCAGCCAAAAATGCACCATTTTG
1 CATTTAACTTGCATTAGTGGCACCTTTCTGCAAAAAATGCACCATTTTG
* *
461978 CATTTAACTTGAATTAGTGGCACCTTTCTACAAAAAATGCACCATTTT-
1 CATTTAACTTGCATTAGTGGCACCTTTCTGCAAAAAATGCACCATTTTG
* * * *
462026 CATTTAACGTGCATTAGTGGCACATTTCTGCCAAAAATGCCCCATTTTG
1 CATTTAACTTGCATTAGTGGCACCTTTCTGCAAAAAATGCACCATTTTG
* * * * *
462075 CATTTAACTTGCATTAGTGGCACATTTATACAAAAAATGTACCATTTTC
1 CATTTAACTTGCATTAGTGGCACCTTTCTGCAAAAAATGCACCATTTTG
* * * *
462124 CATTTAA-TGTGCTTTAGTGGCACCTTTTTGCAACAAATGCATCATTTTG
1 CATTTAACT-TGCATTAGTGGCACCTTTCTGCAAAAAATGCACCATTTTG
*
462173 CTTTTAACT
1 CATTTAACT
462182 CTCATTATAG
Statistics
Matches: 301, Mismatches: 45, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
48 69 0.23
49 231 0.77
50 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (49 bp):
CATTTAACTTGCATTAGTGGCACCTTTCTGCAAAAAATGCACCATTTTG
Found at i:462013 original size:146 final size:147
Alignment explanation
Indices: 461778--462180 Score: 503
Period size: 146 Copynumber: 2.8 Consensus size: 147
461768 AAATGCATTG
* * * *
461778 TTATACATTTAAC-TGTCATTAGTGGCAGCTTTCTGCC-AAAATGCACCATTTGGCATTTAACTT
1 TTATGCATTTAACTTG-CATTAGTGGCACCTTTCAGCCAAAAATGCACCATTTTGCATTTAACTT
* * *
461841 TCATTAGTGGCACATTTCTGCAAAAAATGCACCATTTTGTATTTAACATGCATTAGTGACACCTT
65 GCATTAGTGGCACCTTTCTGCAAAAAATGCACCATTTTGTATTTAACATGCATTAGTGACACATT
*
461906 TCTTCAAAAAATGCACCA
130 TCTGCAAAAAATGCACCA
461924 TTATGCATTTAACTTGCATTAGTGGCACCTTTCAGCCAAAAATGCACCATTTTGCATTTAACTTG
1 TTATGCATTTAACTTGCATTAGTGGCACCTTTCAGCCAAAAATGCACCATTTTGCATTTAACTTG
* * * * *
461989 AATTAGTGGCACCTTTCTACAAAAAATGCACCATTTT-CATTTAACGTGCATTAGTGGCACATTT
66 CATTAGTGGCACCTTTCTGCAAAAAATGCACCATTTTGTATTTAACATGCATTAGTGACACATTT
* *
462053 CTGCCAAAAATGCCCCA
131 CTGCAAAAAATGCACCA
* * * * * *
462070 TTTTGCATTTAACTTGCATTAGTGGCACATTT-ATACAAAAAATGTACCATTTTCCATTTAA-TG
1 TTATGCATTTAACTTGCATTAGTGGCACCTTTCA-GCCAAAAATGCACCATTTTGCATTTAACT-
* * * *
462133 TGCTTTAGTGGCACCTTTTTGCAACAAATGCATCATTTTGCT-TTTAAC
64 TGCATTAGTGGCACCTTTCTGCAAAAAATGCACCATTTTG-TATTTAAC
462181 TCTCATTATA
Statistics
Matches: 223, Mismatches: 28, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
145 2 0.01
146 154 0.69
147 67 0.30
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (147 bp):
TTATGCATTTAACTTGCATTAGTGGCACCTTTCAGCCAAAAATGCACCATTTTGCATTTAACTTG
CATTAGTGGCACCTTTCTGCAAAAAATGCACCATTTTGTATTTAACATGCATTAGTGACACATTT
CTGCAAAAAATGCACCA
Found at i:462090 original size:195 final size:195
Alignment explanation
Indices: 461795--462181 Score: 528
Period size: 195 Copynumber: 2.0 Consensus size: 195
461785 TTTAACTGTC
* * * * *
461795 ATTAGTGGCAGCTTTCTGCCAAAATGCACCATTTGGCATTTAACTTTCATTAGTGGCACATTTCT
1 ATTAGTGGCACCTTTCTACAAAAATGCACCATTTGGCATTTAACGTGCATTAGTGGCACATTTCT
* * * *
461860 GCAAAAAATGCACCATTTTGTATTTAACATGCATTAGTGACACCTTTCTTCAAAAAATGCACCAT
66 GCAAAAAATGCACCATTTTGCATTTAACATGCATTAGTGACACATTTATACAAAAAATGCACCAT
*
461925 TATGCATTTAACT-TGCATTAGTGGCACCTTTCAGCCAA-AAATGCACCATTTTGCATTTAACTT
131 TATCCATTTAA-TGTGCATTAGTGGCACCTTTCAG-CAACAAATGCACCATTTTGCATTTAACTT
461988 GA
194 GA
*
461990 ATTAGTGGCACCTTTCTACAAAAAATGCACCATTT-TCATTTAACGTGCATTAGTGGCACATTTC
1 ATTAGTGGCACCTTTCTAC-AAAAATGCACCATTTGGCATTTAACGTGCATTAGTGGCACATTTC
* * * * *
462054 TGCCAAAAATGCCCCATTTTGCATTTAACTTGCATTAGTGGCACATTTATACAAAAAATGTACCA
65 TGCAAAAAATGCACCATTTTGCATTTAACATGCATTAGTGACACATTTATACAAAAAATGCACCA
* * ** * *
462119 TTTTCCATTTAATGTGCTTTAGTGGCACCTTTTTGCAACAAATGCATCATTTTGCTTTTAACT
130 TTATCCATTTAATGTGCATTAGTGGCACCTTTCAGCAACAAATGCACCATTTTGCATTTAACT
462182 CTCATTATAG
Statistics
Matches: 167, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
194 4 0.02
195 149 0.89
196 14 0.08
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (195 bp):
ATTAGTGGCACCTTTCTACAAAAATGCACCATTTGGCATTTAACGTGCATTAGTGGCACATTTCT
GCAAAAAATGCACCATTTTGCATTTAACATGCATTAGTGACACATTTATACAAAAAATGCACCAT
TATCCATTTAATGTGCATTAGTGGCACCTTTCAGCAACAAATGCACCATTTTGCATTTAACTTGA
Found at i:467769 original size:20 final size:22
Alignment explanation
Indices: 467726--467771 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
467716 AGAAGGGGGA
*
467726 ATCGGTACCATAGTATAGATGT
1 ATCGGTACCATAGTATAGAAGT
*
467748 ATCGGTACCA-AG-GTAGAAGT
1 ATCGGTACCATAGTATAGAAGT
467768 ATCG
1 ATCG
467772 ATACTCTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 2 0.09
22 10 0.45
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (22 bp):
ATCGGTACCATAGTATAGAAGT
Found at i:468254 original size:45 final size:42
Alignment explanation
Indices: 468190--468412 Score: 145
Period size: 45 Copynumber: 5.5 Consensus size: 42
468180 TTAAAAGGAT
468190 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATGCC--AGATGA
* * *
468235 AATGCATATGGGTGAATTATCGACAT-AAA-A-G--A-AT--
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCCAGATGA
* * *
468269 AATGCATATGAGTGCGTTATTGGCATGAAATGATGCCTTAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATGCC--AGATGA
**
468314 AATGCATATGGGTGCATTATCAGCAT-AAA-A-G--A-AT--
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCCAGATGA
* * *
468348 AATTCATATGGGTGAATTATTGGCATGAAAGGATGCCAAAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATGCC--AGATGA
*
468393 AATGCATATGAGTGCATTAT
1 AATGCATATGGGTGCATTAT
468413 CAACATAAAA
Statistics
Matches: 134, Mismatches: 22, Indels: 44
0.67 0.11 0.22
Matches are distributed among these distances:
34 43 0.32
35 6 0.04
36 3 0.02
37 4 0.03
38 2 0.01
41 2 0.01
42 4 0.03
43 2 0.01
44 6 0.04
45 62 0.46
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (42 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGATGCCAGATGA
Found at i:468273 original size:79 final size:78
Alignment explanation
Indices: 468181--468423 Score: 351
Period size: 79 Copynumber: 3.1 Consensus size: 78
468171 AACAAATGAT
*
468181 TAAAAGGATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGAAATGCATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGAAATGCATATGG
*
468246 GTGAATTATCGACA
66 GTGCATTATC-ACA
* * * *
468260 TAAAAGAATAATGCATATGAGTGCGTTATTGGCATGAAATGATGCCTTAGCTGAAATGCATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGAAATGCATATGG
468325 GTGCATTATCAGCA
66 GTGCATTATCA-CA
* * ** * *
468339 TAAAAGAATAATTCATATGGGTGAATTATTGGCATGAAAGGATGCCAAAGTTGAAATGCATATGA
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGAAATGCATATGG
468404 GTGCATTATCAACA
66 GTGCATTATC-ACA
468418 TAAAAG
1 TAAAAG
468424 TATGCTATAA
Statistics
Matches: 147, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
78 1 0.01
79 145 0.99
80 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (78 bp):
TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGAAATGCATATGG
GTGCATTATCACA
Found at i:472360 original size:20 final size:18
Alignment explanation
Indices: 472316--472362 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 18
472306 ATAATGATGA
*
472316 TTTGAAGAAATATATTCT
1 TTTGAAGAAATATAGTCT
472334 TTATGAAGCAAATTATAGTCT
1 TT-TGAAG-AAA-TATAGTCT
472355 TTTGAAGA
1 TTTGAAGA
472363 TGCATCCCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 8 0.32
21 9 0.36
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (18 bp):
TTTGAAGAAATATAGTCT
Found at i:474549 original size:93 final size:95
Alignment explanation
Indices: 474382--474581 Score: 287
Period size: 95 Copynumber: 2.1 Consensus size: 95
474372 CCGTTGAGGC
** *
474382 AGTATCGATACCATAGTAAGGGTATCGATACCAACAAAACATTGAATCTAATATTGGTATCGATA
1 AGTATCGATACCATAGTAAGGGTATCGATACCAAC-AAACATCAAACCTAATATTGGTATCGATA
* * * *
474447 CTGTAA-GGGGTATTTGTACCATAGCATTGT
65 CTGGAAGGGGGTATCTGTACCATAGCATAGA
* *
474477 AGTATCGATACCATGGTAAGGGTATCGATACCAGC-AACATCAAACCTAATATTGGTATCGATAC
1 AGTATCGATACCATAGTAAGGGTATCGATACCAACAAACATCAAACCTAATATTGGTATCGATAC
*
474541 TGGAAGGGGGTATCTGTACCATAGTATAGA
66 TGGAAGGGGGTATCTGTACCATAGCATAGA
474571 AGTATCGATAC
1 AGTATCGATAC
474582 TGTGGAGCCA
Statistics
Matches: 94, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
93 30 0.32
94 31 0.33
95 33 0.35
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (95 bp):
AGTATCGATACCATAGTAAGGGTATCGATACCAACAAACATCAAACCTAATATTGGTATCGATAC
TGGAAGGGGGTATCTGTACCATAGCATAGA
Found at i:475060 original size:45 final size:42
Alignment explanation
Indices: 474996--475138 Score: 149
Period size: 34 Copynumber: 3.5 Consensus size: 42
474986 ATAAAAGAAT
474996 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCC--AG-TAA
* *
475041 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A--AT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGTAA
*
475075 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCC-AG-TAA
*
475119 AATGTATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
475139 CAACATAAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
34 26 0.32
35 3 0.04
37 2 0.02
38 1 0.01
41 2 0.02
42 1 0.01
44 22 0.27
45 25 0.30
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (42 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGTAA
Found at i:478273 original size:38 final size:38
Alignment explanation
Indices: 478222--478295 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
478212 AACACAAAAG
478222 ACAAAGATAGTGAGGAACATATTTTCCTTACTGAGGCA
1 ACAAAGATAGTGAGGAACATATTTTCCTTACTGAGGCA
478260 ACAAAGATAGTGAGGAACATATTTTCCTTACTGAGG
1 ACAAAGATAGTGAGGAACATATTTTCCTTACTGAGG
478296 ACAAAAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (38 bp):
ACAAAGATAGTGAGGAACATATTTTCCTTACTGAGGCA
Found at i:503809 original size:17 final size:17
Alignment explanation
Indices: 503787--503822 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
503777 GATTAGTAAA
503787 GATCTTAGGTGGGTCGG
1 GATCTTAGGTGGGTCGG
503804 GATCTTAGGTGGGTCGG
1 GATCTTAGGTGGGTCGG
503821 GA
1 GA
503823 GCTAGGTAGG
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:0.14, C:0.11, G:0.47, T:0.28
Consensus pattern (17 bp):
GATCTTAGGTGGGTCGG
Found at i:518989 original size:20 final size:21
Alignment explanation
Indices: 518922--518991 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
518912 ATATCTAGAG
**
518922 TTAATTAAATATATGTTTTAA
1 TTAATTAAATATATAATTTAA
* *
518943 -TAATCCCAAATATTTAATTTCAA
1 TTAAT--TAAATATATAATTT-AA
518966 TTAATTAAATATAT-ATTTAA
1 TTAATTAAATATATAATTTAA
518986 TTAATT
1 TTAATT
518992 TGAAATAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
20 12 0.31
21 4 0.10
22 17 0.44
23 2 0.05
24 4 0.10
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (21 bp):
TTAATTAAATATATAATTTAA
Found at i:519074 original size:90 final size:89
Alignment explanation
Indices: 518953--519125 Score: 283
Period size: 90 Copynumber: 1.9 Consensus size: 89
518943 TAATCCCAAA
* * * *
518953 TATTTAATTTCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCCTAATATGAA
1 TATTAAATCTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAACATGAA
519018 TAGGGTAACTTGGATATAAGAGGAT
65 TAGGGTAACTTGGATATAAGAGGAT
*
519043 TATTAAATCTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAACATGATT
1 TATTAAATCTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAACATGAAT
*
519108 AGGGTAACTTGGCTATAA
66 AGGGTAACTTGGATATAA
519126 AAGGGTGTGT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 28 0.36
90 49 0.64
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.38
Consensus pattern (89 bp):
TATTAAATCTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAACATGAAT
AGGGTAACTTGGATATAAGAGGAT
Found at i:526862 original size:11 final size:11
Alignment explanation
Indices: 526846--526875 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
526836 TTGGGCGTTA
*
526846 TCATTCAGTTT
1 TCATTCAATTT
526857 TCATTCAATTT
1 TCATTCAATTT
526868 TCATTCAA
1 TCATTCAA
526876 GGTGGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.03, T:0.50
Consensus pattern (11 bp):
TCATTCAATTT
Found at i:527324 original size:19 final size:18
Alignment explanation
Indices: 527297--527340 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
527287 ATTTCATTTT
527297 TATTAAATTTAATATTAAA
1 TATTAAATTTAAT-TTAAA
*
527316 TATTTAATTTAATTT-AA
1 TATTAAATTTAATTTAAA
527333 T-TTAAATT
1 TATTAAATT
527341 AAGCGATGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 3 0.13
18 2 0.09
19 12 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTAAATTTAATTTAAA
Found at i:532431 original size:134 final size:134
Alignment explanation
Indices: 532191--532456 Score: 442
Period size: 134 Copynumber: 2.0 Consensus size: 134
532181 CCTCAATCTA
* * * * *
532191 GAGTTTGTTTCTAATGCTATAGACCATTATCAATTGATTTCAAACTTATTATTAATGGGACCTCT
1 GAGTTTGTTTCCAAAGCTATAGACCATTATCAATTGACTTAAAACTTACTATTAATGGGACCTCT
* *
532256 TGTGGATATTTCTGTTTCGAAAACATAGTTGCAAAGGAAACTAGGCTGAGTTTTGTTATTCTTTA
66 TGTGGATATTTCTGTTTCGAAAACATAGTTGCAAAAGAAACTAGGCTGAATTTTGTTATTCTTTA
532321 GGCC
131 GGCC
* *
532325 GAGTTTGTTTCCAAAGCTGTAGTCCATTATCAATTGACTTAAAACTTACTATTAATGGGACCTCT
1 GAGTTTGTTTCCAAAGCTATAGACCATTATCAATTGACTTAAAACTTACTATTAATGGGACCTCT
*
532390 TGTGGATATTTCTGTTTCGAAAACATAGTTGGAAAAGAAACTAGGCTGAATTTTGTTATTCTTTA
66 TGTGGATATTTCTGTTTCGAAAACATAGTTGCAAAAGAAACTAGGCTGAATTTTGTTATTCTTTA
532455 GG
131 GG
532457 GAAGAGACCC
Statistics
Matches: 122, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
134 122 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.39
Consensus pattern (134 bp):
GAGTTTGTTTCCAAAGCTATAGACCATTATCAATTGACTTAAAACTTACTATTAATGGGACCTCT
TGTGGATATTTCTGTTTCGAAAACATAGTTGCAAAAGAAACTAGGCTGAATTTTGTTATTCTTTA
GGCC
Found at i:535388 original size:20 final size:20
Alignment explanation
Indices: 535346--535391 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
535336 AATTTATGTG
*
535346 TTTTTAATTATAATTATAAT
1 TTTTTAATTATAAATATAAT
* *
535366 TTTTTAATTTTAAATA-AAG
1 TTTTTAATTATAAATATAAT
535385 TTTTTAA
1 TTTTTAA
535392 AATTATCAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTTAATTATAAATATAAT
Found at i:538595 original size:54 final size:54
Alignment explanation
Indices: 537844--538581 Score: 886
Period size: 54 Copynumber: 13.7 Consensus size: 54
537834 TTGTGTAACA
* * * *
537844 ATATGTTGATGAACAACC-ATTCGGTACTAAGTGTGC-AATTCACAGAATTCATC
1 ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGT-ACAGAATTCATC
** * * *
537897 ATATGTTGATGAATAATTGTTTCGACACTAAGTGTGCAAAATACAAAATTCATC
1 ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTACAGAATTCATC
* *
537951 ATATGTTGATGAATAACCGTTTCGGCACTAAGTTTGTAAAGTAC-GAAATTCATC
1 ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTACAG-AATTCATC
* ** *
538005 ATATGTTAATGAATAACCGTTTCAACACTAAGTGTGCAAAGTACGGAATTCATC
1 ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTACAGAATTCATC
*
538059 ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGC-AATTCACAGAATTCATC
1 ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGT-ACAGAATTCATC
** *
538113 ATATGTTGATGAATAAATGTTTCGGCACTAAGTGTGCAAAGTACATAATTCATC
1 ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTACAGAATTCATC
* *
538167 ATATGTTAATGAATAACCGTTTCGGCACTAAGTGTGC-AATTCACAGAATTCATC
1 ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGT-ACAGAATTCATC
* *
538221 ATATGTTGATGAAAAACCGTTTCGGCACTAAGTGTGCAAAGTAC-GAAATTCAGC
1 ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTACAG-AATTCATC
* * **
538275 ATATGTTGATGAATAACCGTTTCGACATTAAGTGTGCAATTTACAGAATTCATC
1 ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTACAGAATTCATC
* * * *
538329 ATATGTT-ATTGAAAAACCGTTTCGGCACTAAGTGTACAAAGTATAGAATTCATT
1 ATATGTTGA-TGAATAACCGTTTCGGCACTAAGTGTGCAAAGTACAGAATTCATC
* * * * *
538383 ATATGTTGATGAATAATCATTTCGGCACTAAGTGTACAAAGTGCGGAATTCATC
1 ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTACAGAATTCATC
* * **
538437 ATATGTTGATGAATAACCATTTCGGCACTAAGTGTGC-AATTCACAGAATTTGTC
1 ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGT-ACAGAATTCATC
* * * * * *
538491 ATATATTGAT--ATAACCATTTCGACACTTAGTGTGC-AATTCACGGAATTCATC
1 ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGT-ACAGAATTCATC
* **
538543 ATATGTTGATGAATAACCGTTTTGGCACTTTGTGTGCAA
1 ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAA
538582 CCCACAAAAT
Statistics
Matches: 592, Mismatches: 77, Indels: 30
0.85 0.11 0.04
Matches are distributed among these distances:
52 46 0.08
53 26 0.04
54 507 0.86
55 13 0.02
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (54 bp):
ATATGTTGATGAATAACCGTTTCGGCACTAAGTGTGCAAAGTACAGAATTCATC
Found at i:541317 original size:32 final size:32
Alignment explanation
Indices: 541247--541320 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
541237 CCTAAGGTGA
*
541247 CCCTTGGGTAGGCTCTAAGGCCCCGAGAAACT
1 CCCTTGGGTAGGCTCTAAGGCCCCAAGAAACT
** * * **
541279 TTCTTGGGTAGGCTTTCAGGCCCCAAGGCACT
1 CCCTTGGGTAGGCTCTAAGGCCCCAAGAAACT
541311 CCCTTGGGTA
1 CCCTTGGGTA
541321 AATCATGGGA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.24
Consensus pattern (32 bp):
CCCTTGGGTAGGCTCTAAGGCCCCAAGAAACT
Found at i:545871 original size:60 final size:60
Alignment explanation
Indices: 545769--546381 Score: 850
Period size: 60 Copynumber: 10.2 Consensus size: 60
545759 AACTGCTCTA
** * *
545769 AGATGAAAAGTTAAGCACCTAACTATGCATTTTCGCAGAAAGGTTCCACTAATGCAAGTT
1 AGATGAAAAGTTAAGTGCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * *
545829 AGATGAAAAGTTAAGTGCCTAACTATGCTTTTTGGTAAAAAGGTGCCACTAATGCAAGTT
1 AGATGAAAAGTTAAGTGCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * * * *
545889 ATATGAAAAGTTAAGTACCTAGCTGTGCATTTTGGCAGAAAGGTACCACTAATGCAAGTT
1 AGATGAAAAGTTAAGTGCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * *
545949 AGATGAAAAGTTAAGTGCCTAACTATGAATTTTGGTAGAAAGGTGTCACTAATGCAAGTT
1 AGATGAAAAGTTAAGTGCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * * ** **
546009 ATATGAAAAGTTAAATTCCTAACGGTGCATTTTGGCAGAAAAATGCCACTAATGCAAGTT
1 AGATGAAAAGTTAAGTGCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * *
546069 AGATGAAAAGTTAAGTGCCTAACTATGCATTTTGGTAGAAAGGTACCACTAATGAAAGTT
1 AGATGAAAAGTTAAGTGCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * * * * *
546129 AGATGAAAATTTAAGTACATAAATGTGCATTTTGGCATAAAGGTGCCACTAATGCAAGTT
1 AGATGAAAAGTTAAGTGCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * *
546189 AGATGAAAAATTTAGTGCCTAACTGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
1 AGATGAAAAGTTAAGTGCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* *
546249 AGATGAAAAGTTAAATGCCTAACGATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
1 AGATGAAAAGTTAAGTGCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * *
546309 AAATGAAAAGTTAAATGCCTAAC-AGTGCATTTTGGTAGAAAGGTGCCACTAATGCAAGTT
1 AGATGAAAAGTTAAGTGCCTAACTA-TGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
*
546369 ATATGAAAAGTTA
1 AGATGAAAAGTTA
546382 GAACCGTGCA
Statistics
Matches: 486, Mismatches: 66, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
59 1 0.00
60 485 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (60 bp):
AGATGAAAAGTTAAGTGCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
Found at i:547681 original size:214 final size:215
Alignment explanation
Indices: 547311--547739 Score: 851
Period size: 214 Copynumber: 2.0 Consensus size: 215
547301 CAAGGATGTT
547311 GATCCCAAAGGATTTGAAGAGTTTGGGAGCTCCAGAATTATGGGGAGAAGAGGATGAAGGTCCTA
1 GATCCCAAAGGATTTGAAGAGTTTGGGAGCTCCAGAATTATGGGGAGAAGAGGATGAAGGTCCTA
547376 CAAAGGTTGACTTATGGCTAAATGATGTAATGTTAATGCTTGAAAGTCTCCACTGCTCGGATTCA
66 CAAAGGTTGACTTATGGCTAAATGATGTAATGTTAATGCTTGAAAGTCTCCACTGCTCGGATTCA
547441 AAAAATGGGTGGAGCTATATCGTTACTAAGGGAATCAACTCGAGTGTGGTGGTCAAATACTACAA
131 AAAAATGGGTGGAGCTATATCGTTACTAAGGGAATCAACTCGAGTGTGGTGGTCAAATACTACAA
547506 TGTATGCACCACTGGAACAA
196 TGTATGCACCACTGGAACAA
547526 GATCCCAAAGGATTTGAAGAGTTTGGGAGCTCCAGAATTATGGGGA-AAGAGGATGAAGGTCCTA
1 GATCCCAAAGGATTTGAAGAGTTTGGGAGCTCCAGAATTATGGGGAGAAGAGGATGAAGGTCCTA
547590 CAAAGGTTGACTTATGGCTAAATGATGTAATGTTAATGCTTGAAAGTCTCCACTGCTCGGATTCA
66 CAAAGGTTGACTTATGGCTAAATGATGTAATGTTAATGCTTGAAAGTCTCCACTGCTCGGATTCA
547655 AAAAATGGGTGGAGCTATATCGTTACTAAGGGAATCAACTCGAGTGTGGTGGTCAAATACTACAA
131 AAAAATGGGTGGAGCTATATCGTTACTAAGGGAATCAACTCGAGTGTGGTGGTCAAATACTACAA
547720 TGTATGCACCACTGGAACAA
196 TGTATGCACCACTGGAACAA
547740 TTGACCTGTT
Statistics
Matches: 214, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
214 168 0.79
215 46 0.21
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (215 bp):
GATCCCAAAGGATTTGAAGAGTTTGGGAGCTCCAGAATTATGGGGAGAAGAGGATGAAGGTCCTA
CAAAGGTTGACTTATGGCTAAATGATGTAATGTTAATGCTTGAAAGTCTCCACTGCTCGGATTCA
AAAAATGGGTGGAGCTATATCGTTACTAAGGGAATCAACTCGAGTGTGGTGGTCAAATACTACAA
TGTATGCACCACTGGAACAA
Found at i:548539 original size:28 final size:28
Alignment explanation
Indices: 548477--548570 Score: 116
Period size: 28 Copynumber: 3.4 Consensus size: 28
548467 TGAAGAGGTT
* * *
548477 TTAATGGAGAGTAAAGCAAAGCAATGTA
1 TTAATGGAGAGTAAAGTAAAGCAAAGTC
* *
548505 TAAATGGAGAATAAAGTAAAGCAAAGTC
1 TTAATGGAGAGTAAAGTAAAGCAAAGTC
* *
548533 TTGATGGAGAGTAAAGTAAAGCGAAGTC
1 TTAATGGAGAGTAAAGTAAAGCAAAGTC
*
548561 TTTATGGAGA
1 TTAATGGAGA
548571 TGGCATGCCG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 56 1.00
ACGTcount: A:0.45, C:0.06, G:0.27, T:0.22
Consensus pattern (28 bp):
TTAATGGAGAGTAAAGTAAAGCAAAGTC
Found at i:554300 original size:60 final size:60
Alignment explanation
Indices: 554207--554563 Score: 520
Period size: 60 Copynumber: 6.0 Consensus size: 60
554197 AGATGAAAAG
* * *
554207 GCCTAACTATGCATTTTTGCATAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTTAAGT
1 GCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTTAAAT
* * * ** *
554267 GCCTAATTATGCATTTTGGCAGAAAGGTTCCACTAATGTAAGTTAGATGAAAAACTAATT
1 GCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTTAAAT
*
554327 GCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTTAAGT
1 GCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTTAAAT
* *
554387 GCCTAACTGTGCATTTTGGCAGAAAGGTGCCAATAATGCAAGTTAGATGAAAAGTTAAAT
1 GCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTTAAAT
* ** *
554447 GTCTAAC-AGTGCATTTTCACAGAAAGGTGCCACTAATGCAAGTTAGTTGAAAAGTTAAAT
1 GCCTAACTA-TGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTTAAAT
* *
554507 GCCTAAC-AGTGCATTTTGGCATAAAGGTGCCACTAATGCAAGTTACATGAAAAGTTA
1 GCCTAACTA-TGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTTA
554564 GAACCGTGCA
Statistics
Matches: 267, Mismatches: 29, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
60 267 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (60 bp):
GCCTAACTATGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAGATGAAAAGTTAAAT
Found at i:557164 original size:8 final size:8
Alignment explanation
Indices: 557151--557176 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
557141 TATTGAAGAT
557151 TTAAAATA
1 TTAAAATA
557159 TTAAAATA
1 TTAAAATA
557167 TTAAAATA
1 TTAAAATA
557175 TT
1 TT
557177 TTAGAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TTAAAATA
Found at i:557204 original size:40 final size:36
Alignment explanation
Indices: 557151--557250 Score: 101
Period size: 41 Copynumber: 2.6 Consensus size: 36
557141 TATTGAAGAT
*
557151 TTAAAATATTAAAATATTAAAATATTTTAGAAAATTAAA
1 TTAAAATATAAAAATATT-AAATATTTTA-AAAA-TAAA
*
557190 TATAAAATTATAAAAAATATTAATTATTTTAAAAATAAA
1 T-TAAAA-TAT-AAAAATATTAAATATTTTAAAAATAAA
* * *
557229 TGAAAATATGAAAATATGAAAT
1 TTAAAATATAAAAATATTAAAT
557251 TATACAATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
36 10 0.19
37 3 0.06
38 4 0.08
39 6 0.12
40 9 0.17
41 12 0.23
42 8 0.15
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (36 bp):
TTAAAATATAAAAATATTAAATATTTTAAAAATAAA
Found at i:561485 original size:56 final size:56
Alignment explanation
Indices: 561418--561532 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
561408 AAATCAAAGG
561418 AGGGTGCGTGTTCTCCAATATAGATTTGAGATCGGGGTACTATCAGTTAAAGATTA
1 AGGGTGCGTGTTCTCCAATATAGATTTGAGATCGGGGTACTATCAGTTAAAGATTA
561474 AGGGTGCGTGTTCTCCAATATAGATTTGAGATCGGGGTACTATCAGTTAAAGATTA
1 AGGGTGCGTGTTCTCCAATATAGATTTGAGATCGGGGTACTATCAGTTAAAGATTA
561530 AGG
1 AGG
561533 ATGCCGTCAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.31
Consensus pattern (56 bp):
AGGGTGCGTGTTCTCCAATATAGATTTGAGATCGGGGTACTATCAGTTAAAGATTA
Found at i:564703 original size:49 final size:50
Alignment explanation
Indices: 564630--564728 Score: 128
Period size: 49 Copynumber: 2.0 Consensus size: 50
564620 TTTATTTAAG
*
564630 ATAGTTTCCAGCAACTAGGAAACTAAG-TAACACATCCACAACTCTTTCA
1 ATAGTTTCCAACAACTAGGAAACTAAGTTAACACATCCACAACTCTTTCA
* * * * * *
564679 ATAGTTTTCAACATCTATGAAACTAAGTTAACAGATTCATAACTCTTTCA
1 ATAGTTTCCAACAACTAGGAAACTAAGTTAACACATCCACAACTCTTTCA
564729 TACCATTTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 23 0.55
50 19 0.45
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.30
Consensus pattern (50 bp):
ATAGTTTCCAACAACTAGGAAACTAAGTTAACACATCCACAACTCTTTCA
Found at i:566305 original size:101 final size:102
Alignment explanation
Indices: 566130--566333 Score: 401
Period size: 101 Copynumber: 2.0 Consensus size: 102
566120 CCCATGCGGA
566130 GGTGAAAACCATCACGATGGAGTAGCTTCTCAGTTCCACTTAAATGGGATGGAGTGGGGTTTTAA
1 GGTGAAAACCATCACGATGGAGTAGCTTCTCAGTTCCACTTAAATGGGATGGAGTGGGGTTTTAA
566195 CTTAATGCCATGAAAA-GCAACTATGTAGTGTGTGAG
66 CTTAATGCCATGAAAATGCAACTATGTAGTGTGTGAG
566231 GGTGAAAACCATCACGATGGAGTAGCTTCTCAGTTCCACTTAAATGGGATGGAGTGGGGTTTTAA
1 GGTGAAAACCATCACGATGGAGTAGCTTCTCAGTTCCACTTAAATGGGATGGAGTGGGGTTTTAA
566296 CTTAATGCCATGAAAATGCAACTATGTAGTGTGTGAG
66 CTTAATGCCATGAAAATGCAACTATGTAGTGTGTGAG
566333 G
1 G
566334 AAAAAAGAAC
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 81 0.79
102 21 0.21
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (102 bp):
GGTGAAAACCATCACGATGGAGTAGCTTCTCAGTTCCACTTAAATGGGATGGAGTGGGGTTTTAA
CTTAATGCCATGAAAATGCAACTATGTAGTGTGTGAG
Found at i:567560 original size:2 final size:2
Alignment explanation
Indices: 567553--567578 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
567543 CATTATACTA
567553 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
567579 GGTTAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:572860 original size:26 final size:26
Alignment explanation
Indices: 572824--572880 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
572814 AACCCATTTC
* *
572824 ATTTCATTTCATTTTATTTCTAGTAA
1 ATTTTATTTCATTTAATTTCTAGTAA
*
572850 ATTTTATTTCATTTAATTTTTAGTAA
1 ATTTTATTTCATTTAATTTCTAGTAA
572876 ATTTT
1 ATTTT
572881 TTTATTAGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (26 bp):
ATTTTATTTCATTTAATTTCTAGTAA
Found at i:572871 original size:16 final size:15
Alignment explanation
Indices: 572819--572869 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
572809 GAGGCAACCC
* *
572819 ATTTCATTTCATTTC
1 ATTTTATTTCATTTA
* *
572834 ATTTTATTTCTAGTAA
1 ATTTTATTTC-ATTTA
572850 ATTTTATTTCATTTA
1 ATTTTATTTCATTTA
572865 ATTTT
1 ATTTT
572870 TAGTAAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.63
Consensus pattern (15 bp):
ATTTTATTTCATTTA
Found at i:580437 original size:42 final size:42
Alignment explanation
Indices: 580371--580461 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
580361 CTTGTATTAT
* *
580371 ATAGTAATATCAGTACGAGAAATAGTCATACC-AGTATTAGAA
1 ATAGTAATATCAGTACGAGAAATAGTAATACCGA-TACTAGAA
**
580413 ATAGTAATATCAGTACTG-TTAATAGTAATACCGATACTAGAA
1 ATAGTAATATCAGTAC-GAGAAATAGTAATACCGATACTAGAA
580455 ATAGTAA
1 ATAGTAA
580462 AATCGATACT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 41 0.95
43 2 0.05
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (42 bp):
ATAGTAATATCAGTACGAGAAATAGTAATACCGATACTAGAA
Found at i:580457 original size:21 final size:21
Alignment explanation
Indices: 580371--580461 Score: 96
Period size: 21 Copynumber: 4.3 Consensus size: 21
580361 CTTGTATTAT
*
580371 ATAGTAATATCAGTACGAGAA
1 ATAGTAATATCAGTACTAGAA
* * *
580392 ATAGTCATACCAGTATTAGAA
1 ATAGTAATATCAGTACTAGAA
*
580413 ATAGTAATATCAGTACT-GTTA
1 ATAGTAATATCAGTACTAG-AA
*
580434 ATAGTAATA-CCGATACTAGAA
1 ATAGTAATATCAG-TACTAGAA
580455 ATAGTAA
1 ATAGTAA
580462 AATCGATACT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 3 0.05
21 53 0.93
22 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (21 bp):
ATAGTAATATCAGTACTAGAA
Found at i:580468 original size:21 final size:21
Alignment explanation
Indices: 580371--580473 Score: 79
Period size: 21 Copynumber: 4.9 Consensus size: 21
580361 CTTGTATTAT
*
580371 ATAGTAATATC-AGTACGAGAA
1 ATAGTAATATCGA-TACTAGAA
* * *
580392 ATAGTCATA-CCAGTATTAGAA
1 ATAGTAATATCGA-TACTAGAA
*
580413 ATAGTAATATC-AGTACT-GTTA
1 ATAGTAATATCGA-TACTAG-AA
*
580434 ATAGTAATACCGATACTAGAA
1 ATAGTAATATCGATACTAGAA
*
580455 ATAGTAAAATCGATACTAG
1 ATAGTAATATCGATACTAG
580474 GTAATTTTTG
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
20 2 0.03
21 62 0.93
22 3 0.04
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.28
Consensus pattern (21 bp):
ATAGTAATATCGATACTAGAA
Found at i:602932 original size:21 final size:23
Alignment explanation
Indices: 602908--602961 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
602898 CCCCTTGCTA
602908 TGTATTC-ATACA-CCTTGAATG
1 TGTATTCGATACATCCTTGAATG
602929 TGTA-TCGATACATTCCTTGAATG
1 TGTATTCGATACA-TCCTTGAATG
602952 TGTA-TCGATA
1 TGTATTCGATA
602962 ACCCTAGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 2 0.07
21 9 0.30
23 19 0.63
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (23 bp):
TGTATTCGATACATCCTTGAATG
Found at i:605074 original size:13 final size:13
Alignment explanation
Indices: 605056--605080 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
605046 CAATTTACAA
605056 ATTGTTTATGAAT
1 ATTGTTTATGAAT
605069 ATTGTTTATGAA
1 ATTGTTTATGAA
605081 CTGATGGCTA
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
ATTGTTTATGAAT
Found at i:610300 original size:20 final size:20
Alignment explanation
Indices: 610275--610346 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
610265 TTTGAGTTTG
610275 AGTATCGATACTAGATGAAT
1 AGTATCGATACTAGATGAAT
*
610295 AGTATCGATACTTA-ATGAAC
1 AGTATCGATAC-TAGATGAAT
* * *
610315 AATA-CTGATACTAGTTGCAT
1 AGTATC-GATACTAGATGAAT
*
610335 AGTACCGATACT
1 AGTATCGATACT
610347 GGTATTTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (20 bp):
AGTATCGATACTAGATGAAT
Found at i:613304 original size:25 final size:24
Alignment explanation
Indices: 613276--613325 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
613266 TAACAAAAAA
* *
613276 TTTAGATGTACAATAATATATATTT
1 TTTAGAGGTACAACAAT-TATATTT
613301 TTTAGAGGTACAACAATTATATTT
1 TTTAGAGGTACAACAATTATATTT
613325 T
1 T
613326 ACTCATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (24 bp):
TTTAGAGGTACAACAATTATATTT
Found at i:618719 original size:54 final size:54
Alignment explanation
Indices: 618650--618774 Score: 169
Period size: 54 Copynumber: 2.3 Consensus size: 54
618640 CTTTGGGGTA
* * * * * *
618650 CACACGTAGTTCCGATACAGTAATTCATAAGCATATTATGAATTTCTTGGGTTG
1 CACACTTAGTGCCGATACAGTAATTCAAAAACATATTATGAATTCCGTGGGTTG
* *
618704 CACACTTAGTGCCGATACGGTCATTCAAAAACATATTATGAATTCCGTGGGTTG
1 CACACTTAGTGCCGATACAGTAATTCAAAAACATATTATGAATTCCGTGGGTTG
*
618758 CACACTTAGTGCTGATA
1 CACACTTAGTGCCGATA
618775 GTACACATAG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (54 bp):
CACACTTAGTGCCGATACAGTAATTCAAAAACATATTATGAATTCCGTGGGTTG
Found at i:625258 original size:54 final size:54
Alignment explanation
Indices: 625143--625297 Score: 197
Period size: 54 Copynumber: 2.9 Consensus size: 54
625133 AGGCGATACG
* * *
625143 GTCATTCATAAACATTTTATGAATTT-TTGGGTTGCACACTTAGTGCCAAAATG
1 GTCATTCATAAACATATTATGAATTTCGTGGGTTGCACACTTAGTGCCAAAATA
* * ** * *
625196 GTCGTTCATAAATATATTATGAATTTCGTGGGTTGCACACTTAGTTTCGATATA
1 GTCATTCATAAACATATTATGAATTTCGTGGGTTGCACACTTAGTGCCAAAATA
*
625250 GTCATTCATAAACATATTATGAA-TTCAGTGGGTTGTACACTTAGTGCC
1 GTCATTCATAAACATATTATGAATTTC-GTGGGTTGCACACTTAGTGCC
625298 GCTAGTACAC
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
53 26 0.30
54 60 0.70
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (54 bp):
GTCATTCATAAACATATTATGAATTTCGTGGGTTGCACACTTAGTGCCAAAATA
Found at i:637450 original size:174 final size:177
Alignment explanation
Indices: 637160--637510 Score: 681
Period size: 174 Copynumber: 2.0 Consensus size: 177
637150 ATATCAGTCA
637160 ATGCTGTGATTTGTGAAGCCATTGAATTGATGATGTCATTATACACTGTTGTAACATTACGTCTT
1 ATGCTGTGATTTGTGAAGCCATTGAATTGATGATGTCATTATACACTGTTGTAACATTACGTCTT
637225 CCAAACATATTCCTCGTATTGGGGTATTGATAATCATTGTTGGATATCCTCTCCAAAATGTCGTA
66 CCAAACATATTCCTCGTATTGGGGTATTGATAATCATTGTTGGATATCCTCTCCAAAATGTCGTA
637290 AGCTTCA-T-TCGGATTTATCCAACAA-GCTTCACTGGTAGAAACAC
131 AGCTTCATTGTCGGATTTATCCAACAATGCTTCACTGGTAGAAACAC
637334 ATGCTGTGATTTGTGAAGCCATTGAATTGATGATGTCATTATACACTGTTGTAACATTACGTCTT
1 ATGCTGTGATTTGTGAAGCCATTGAATTGATGATGTCATTATACACTGTTGTAACATTACGTCTT
637399 CCAAACATATTCCTCGTATTGGGGTATTGATAATCATTGTTGGATATCCTCTCCAAAATGTCGTA
66 CCAAACATATTCCTCGTATTGGGGTATTGATAATCATTGTTGGATATCCTCTCCAAAATGTCGTA
637464 AGCTTCATTGTCGGATTTATCCAACAATGCTTCACTGGTAGAAACAC
131 AGCTTCATTGTCGGATTTATCCAACAATGCTTCACTGGTAGAAACAC
637511 CATTAACCAT
Statistics
Matches: 174, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
174 137 0.79
175 1 0.01
176 17 0.10
177 19 0.11
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (177 bp):
ATGCTGTGATTTGTGAAGCCATTGAATTGATGATGTCATTATACACTGTTGTAACATTACGTCTT
CCAAACATATTCCTCGTATTGGGGTATTGATAATCATTGTTGGATATCCTCTCCAAAATGTCGTA
AGCTTCATTGTCGGATTTATCCAACAATGCTTCACTGGTAGAAACAC
Found at i:649959 original size:41 final size:45
Alignment explanation
Indices: 649861--650005 Score: 115
Period size: 47 Copynumber: 3.3 Consensus size: 45
649851 TCAGTTAAGG
* * *
649861 TTTAGGGTTAGAGAAGATAAATAGAAGAAGAAAAGGCTCGGTTAGTG
1 TTTAAGGTTAGAGAAGATAAATAGAAGAAG--AACGCTCGGTTAGTA
* *
649908 TTTAAAGTTAGAGAAGATGAATAGAAGAAG-ACG-T-GGTTAG-A
1 TTTAAGGTTAGAGAAGATAAATAGAAGAAGAACGCTCGGTTAGTA
* * * * * *
649949 TTTAAGGTTAGATATGA-AGA-AGATGAATAATGCTCGGTTAG-A
1 TTTAAGGTTAGAGAAGATAAATAGAAGAAGAACGCTCGGTTAGTA
*
649991 TTTAGGGTTAGAGAA
1 TTTAAGGTTAGAGAA
650006 AGAAAAGGTT
Statistics
Matches: 79, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
39 6 0.08
40 3 0.04
41 15 0.19
42 25 0.32
43 1 0.01
44 2 0.03
47 27 0.34
ACGTcount: A:0.40, C:0.03, G:0.30, T:0.27
Consensus pattern (45 bp):
TTTAAGGTTAGAGAAGATAAATAGAAGAAGAACGCTCGGTTAGTA
Found at i:650236 original size:99 final size:102
Alignment explanation
Indices: 650045--650250 Score: 258
Period size: 100 Copynumber: 2.0 Consensus size: 102
650035 ATTATATATT
* * *
650045 AAAAAAAAGGTTGGATTTTGGTTTCGGGTGTTTATAAGGATAAAATAAGAGTTTGGGGGATAAAC
1 AAAAAAAAGGTTGGACTTTGGTTTCGGGTGTTTATAAGGATAAAAGAAGAGTTTGAGGGATAAAC
*
650110 ATGGATAAATAATGGTTGAGTTTGGGGT-TTT-ATAG
66 ATGGATAAATAAGGGTTGAGTTTGGGGTGTTTGATAG
* * * * * * *
650145 AAAAAATAGGTTGGGCTTTGGTTTTGGGTGTTTGTAAGGATCAAAGAATAGTTT-AGGGATTAAC
1 AAAAAAAAGGTTGGACTTTGGTTTCGGGTGTTTATAAGGATAAAAGAAGAGTTTGAGGGATAAAC
* *
650209 ATGGATGAATAAGGGTTG-GATTTGGGGTGTTTGATCG
66 ATGGATAAATAAGGGTTGAG-TTTGGGGTGTTTGATAG
650246 AAAAA
1 AAAAA
650251 TATGATAGGT
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
98 1 0.01
99 32 0.36
100 49 0.54
101 8 0.09
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (102 bp):
AAAAAAAAGGTTGGACTTTGGTTTCGGGTGTTTATAAGGATAAAAGAAGAGTTTGAGGGATAAAC
ATGGATAAATAAGGGTTGAGTTTGGGGTGTTTGATAG
Found at i:650265 original size:100 final size:100
Alignment explanation
Indices: 650060--650292 Score: 249
Period size: 100 Copynumber: 2.3 Consensus size: 100
650050 AAAGGTTGGA
* * * *
650060 TTTTGGTTTCGGGTGTTTATAAGGATAAAATAAGAGTTTGGGGGATAAACATGGATAAATAATGG
1 TTTTGGTTTTGGGTGTTTATAAGGATAAAAGAAGAGTTTGAGGGATAAACATGGATAAATAAGGG
* *
650125 TTGAGTTTGGGGTTTTATAGAAAAAATAGGTTGGG
66 TTGAGTTTGGGGTTTTATAGAAAAAATAGGATAGG
* * * * * *
650160 CTTTGGTTTTGGGTGTTTGTAAGGATCAAAGAATAGTTT-AGGGATTAACATGGATGAATAAGGG
1 TTTTGGTTTTGGGTGTTTATAAGGATAAAAGAAGAGTTTGAGGGATAAACATGGATAAATAAGGG
* *
650224 TTG-GATTTGGGGTGTTTGATCG-AAAAATATGATAGG
66 TTGAG-TTTGGGGT-TTT-ATAGAAAAAATAGGATAGG
* *
650260 TTTTGGGTTTT-TGTGTTTATAAAGATTAAAAGA
1 TTTT-GGTTTTGGGTGTTTATAAGGA-TAAAAGA
650293 GGGTTTTTAA
Statistics
Matches: 109, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
98 1 0.01
99 32 0.29
100 61 0.56
101 15 0.14
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.37
Consensus pattern (100 bp):
TTTTGGTTTTGGGTGTTTATAAGGATAAAAGAAGAGTTTGAGGGATAAACATGGATAAATAAGGG
TTGAGTTTGGGGTTTTATAGAAAAAATAGGATAGG
Found at i:650465 original size:17 final size:18
Alignment explanation
Indices: 650436--650477 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
650426 GAGTGTAGAG
*
650436 AAAAA-GAGCAAAA-TCA
1 AAAAATGAGAAAAATTCA
*
650452 AAAAATGAGAAAAATTGA
1 AAAAATGAGAAAAATTCA
650470 AAAAATGA
1 AAAAATGA
650478 CCGAAATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 5 0.23
17 7 0.32
18 10 0.45
ACGTcount: A:0.69, C:0.05, G:0.14, T:0.12
Consensus pattern (18 bp):
AAAAATGAGAAAAATTCA
Found at i:650716 original size:22 final size:21
Alignment explanation
Indices: 650683--650773 Score: 98
Period size: 20 Copynumber: 4.3 Consensus size: 21
650673 TTAATTAATA
*
650683 TTATATGT-ATAAACTCTATACT
1 TTATAT-TAATAAA-TCTATAGT
650705 TTATATTAATAAA-CTATAGT
1 TTATATTAATAAATCTATAGT
* *
650725 TTATATTAATAAACTATATAAT
1 TTATATTAATAAA-TCTATAGT
*
650747 TCATATTAATAAAT-TATAGT
1 TTATATTAATAAATCTATAGT
650767 TTATATT
1 TTATATT
650774 GTTTATATTA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
20 30 0.50
21 2 0.03
22 28 0.47
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (21 bp):
TTATATTAATAAATCTATAGT
Found at i:650730 original size:42 final size:42
Alignment explanation
Indices: 650683--650907 Score: 152
Period size: 42 Copynumber: 5.1 Consensus size: 42
650673 TTAATTAATA
* * *
650683 TTATATGT-ATAAACTCTATACTTTATATTAATAAACTATAGT
1 TTATAT-TAATAAACTATATAATTCATATTAATAAACTATAGT
*
650725 TTATATTAATAAACTATATAATTCATATTAATAAATTATAGT
1 TTATATTAATAAACTATATAATTCATATTAATAAACTATAGT
* * * *
650767 TTATATTGTTTATATTAATA-AAAATAATTTATATTAATAAACTACAGT
1 TTATA----TTA-A-TAA-ACTATATAATTCATATTAATAAACTATAGT
* * * * *
650815 TTATTTTAATAAATTATATAGTTTATATTAA-AAGTTCATATAGT
1 TTATATTAATAAACTATATAATTCATATTAATAA--AC-TATAGT
* * *
650859 TTATATTAATGAACT-TCATAATTTATATTAATAAATTATATAGT
1 TTATATTAATAAACTAT-ATAATTCATATTAATAAA--CTATAGT
650903 TTATA
1 TTATA
650908 AAGTTTATAT
Statistics
Matches: 146, Mismatches: 21, Indels: 30
0.74 0.11 0.15
Matches are distributed among these distances:
41 4 0.03
42 58 0.40
43 3 0.02
44 44 0.30
45 2 0.01
46 3 0.02
47 1 0.01
48 30 0.21
49 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (42 bp):
TTATATTAATAAACTATATAATTCATATTAATAAACTATAGT
Found at i:650805 original size:48 final size:50
Alignment explanation
Indices: 650723--650818 Score: 142
Period size: 48 Copynumber: 1.9 Consensus size: 50
650713 ATAAACTATA
* *
650723 GTTTATATTAATAAACTATATAATTCATATTAATAAATTATAGTTTATATT
1 GTTTATATTAATAAAC-ATATAATTCATATTAATAAACTACAGTTTATATT
*
650774 GTTTATATTAATAAA-A-ATAATTTATATTAATAAACTACAGTTTAT
1 GTTTATATTAATAAACATATAATTCATATTAATAAACTACAGTTTAT
650819 TTTAATAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
48 26 0.62
49 1 0.02
51 15 0.36
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (50 bp):
GTTTATATTAATAAACATATAATTCATATTAATAAACTACAGTTTATATT
Found at i:650840 original size:22 final size:22
Alignment explanation
Indices: 650767--650907 Score: 136
Period size: 22 Copynumber: 6.6 Consensus size: 22
650757 AAATTATAGT
*
650767 TTATATTGTTTATATTAATAAA
1 TTATATAGTTTATATTAATAAA
*
650789 --A-ATAATTTATATTAATAAA
1 TTATATAGTTTATATTAATAAA
* * *
650808 --CTACAGTTTATTTTAATAAA
1 TTATATAGTTTATATTAATAAA
*
650828 TTATATAGTTTATATTAA-AAG
1 TTATATAGTTTATATTAATAAA
*
650849 TTCATATAGTTTATATTAATGAAC
1 TT-ATATAGTTTATATTAAT-AAA
650873 TTCATA-A-TTTATATTAATAAA
1 TT-ATATAGTTTATATTAATAAA
650894 TTATATAGTTTATA
1 TTATATAGTTTATA
650908 AAGTTTATAT
Statistics
Matches: 99, Mismatches: 12, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
19 16 0.16
20 19 0.19
21 9 0.09
22 46 0.46
23 1 0.01
24 8 0.08
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (22 bp):
TTATATAGTTTATATTAATAAA
Found at i:650916 original size:31 final size:33
Alignment explanation
Indices: 650880--650948 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 33
650870 AACTTCATAA
* *
650880 TTTATATTAATAAATTATATAGTTTATA-A-AG
1 TTTATATTAATAAACTATATACTTTATATATAG
650911 TTTATATTAATAAACTATATACTTTATATATAG
1 TTTATATTAATAAACTATATACTTTATATATAG
650944 TTTAT
1 TTTAT
650949 TAGTTTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 26 0.76
32 1 0.03
33 7 0.21
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (33 bp):
TTTATATTAATAAACTATATACTTTATATATAG
Found at i:650931 original size:15 final size:15
Alignment explanation
Indices: 650882--650931 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
650872 CTTCATAATT
*
650882 TATATTAATAAATTA
1 TATATTAATAAACTA
* * *
650897 TATAGTTTATAAAGTT
1 TATA-TTAATAAACTA
650913 TATATTAATAAACTA
1 TATATTAATAAACTA
650928 TATA
1 TATA
650932 CTTTATATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (15 bp):
TATATTAATAAACTA
Found at i:650977 original size:50 final size:52
Alignment explanation
Indices: 650854--650990 Score: 165
Period size: 50 Copynumber: 2.7 Consensus size: 52
650844 AAAAGTTCAT
650854 ATAGTTTATATTAATGAACT-TCATAATTTATATTAATAAATTATATAGTTTATA
1 ATAGTTTATATTAATGAACTAT-ATAATTTATA-T-ATAAATTATATAGTTTATA
* * **
650908 A-AGTTTATATTAATAAACTATATACTTTATATATAGTTTAT-TAGTTTA-A
1 ATAGTTTATATTAATGAACTATATAATTTATATATAAATTATATAGTTTATA
* *
650957 ATAGTTTATAGTAATGAACTATATAATTCATATA
1 ATAGTTTATATTAATGAACTATATAATTTATATA
650991 ATTTTATGTT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
49 2 0.03
50 35 0.48
51 7 0.10
52 1 0.01
53 26 0.36
54 2 0.03
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (52 bp):
ATAGTTTATATTAATGAACTATATAATTTATATATAAATTATATAGTTTATA
Found at i:651009 original size:32 final size:33
Alignment explanation
Indices: 650961--651032 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 33
650951 GTTTAAATAG
*
650961 TTTATA-G-TAATGAACTATATAATTCATATAA
1 TTTATATGTTAATAAACTATATAATTCATATAA
* * *
650992 TTT-TATGTTAATAAACTATATAGTTTATATAG
1 TTTATATGTTAATAAACTATATAATTCATATAA
651024 TTTATATGT
1 TTTATATGT
651033 ATAGCTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
30 2 0.06
31 4 0.12
32 23 0.68
33 5 0.15
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (33 bp):
TTTATATGTTAATAAACTATATAATTCATATAA
Found at i:651035 original size:22 final size:22
Alignment explanation
Indices: 651008--651220 Score: 133
Period size: 22 Copynumber: 9.6 Consensus size: 22
650998 GTTAATAAAC
651008 TATATAGTTTATATAGTTTATA
1 TATATAGTTTATATAGTTTATA
* *
651030 TGTATAGCTTATATAGTTTATA
1 TATATAGTTTATATAGTTTATA
* *
651052 TATGTAGTTTATATAATTTATA
1 TATATAGTTTATATAGTTTATA
*
651074 TAGT-T-TTTATATATAGTTTATTAA
1 TA-TATAGTT-TATATAGTTTA-T-A
* * *
651098 TTTATTCAGTTT-TATA-TATAGTT
1 TATA-T-AGTTTATATAGTTTA-TA
*
651121 TATATAGTTTAT-TA---AAT-
1 TATATAGTTTATATAGTTTATA
*
651138 TATATAGTTTATATAGATTATA
1 TATATAGTTTATATAGTTTATA
*
651160 TATATAGTTTATACATATAGTTTA-C
1 TATATAG-TT-T--ATATAGTTTATA
*
651185 TATATAGTTTATATACG-TAATA
1 TATATAGTTTATATA-GTTTATA
651207 TATATAGTTTATAT
1 TATATAGTTTATAT
651221 GTAGTATATA
Statistics
Matches: 151, Mismatches: 20, Indels: 40
0.72 0.09 0.19
Matches are distributed among these distances:
17 12 0.08
18 3 0.02
19 1 0.01
21 18 0.12
22 75 0.50
23 9 0.06
24 9 0.06
25 12 0.08
26 10 0.07
27 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (22 bp):
TATATAGTTTATATAGTTTATA
Found at i:651134 original size:38 final size:39
Alignment explanation
Indices: 651060--651171 Score: 131
Period size: 38 Copynumber: 2.9 Consensus size: 39
651050 TATATGTAGT
* * * *
651060 TTATATAATTTATATAGTTTTTATATATAGTTTATTAAT
1 TTATATAGTTTATATAGATTATATATATAGTTTATTAAA
* *
651099 TTAT-TCAGTTT-TATATA-TAGTTTATATAGTTTATTAAA
1 TTATAT-AGTTTATATAGATTA-TATATATAGTTTATTAAA
651137 TTATATAGTTTATATAGATTATATATATAGTTTAT
1 TTATATAGTTTATATAGATTATATATATAGTTTAT
651172 ACATATAGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
37 1 0.02
38 30 0.50
39 27 0.45
40 2 0.03
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.56
Consensus pattern (39 bp):
TTATATAGTTTATATAGATTATATATATAGTTTATTAAA
Found at i:651172 original size:9 final size:9
Alignment explanation
Indices: 651008--651161 Score: 91
Period size: 9 Copynumber: 17.7 Consensus size: 9
650998 GTTAATAAAC
651008 TATATAGTT
1 TATATAGTT
651017 TATATAGTT
1 TATATAGTT
651026 TATAT-G--
1 TATATAGTT
*
651032 --TATAGCT
1 TATATAGTT
651039 TATATAGTTT
1 TATATAG-TT
651049 ATATATGTAGTT
1 -TATA--TAGTT
*
651061 TATATAATT
1 TATATAGTT
651070 TATATAGTT
1 TATATAGTT
651079 T-T-TA---
1 TATATAGTT
651083 TATATAGTT
1 TATATAGTT
*
651092 TAT-TAATT
1 TATATAGTT
651100 TAT-TCAGTTTT
1 TATAT-AG--TT
651111 ATATATAGTT
1 -TATATAGTT
651121 TATATAGTT
1 TATATAGTT
**
651130 TAT-TAAAT
1 TATATAGTT
651138 TATATAGTT
1 TATATAGTT
*
651147 TATATAGAT
1 TATATAGTT
651156 TATATA
1 TATATA
651162 TATAGTTTAT
Statistics
Matches: 115, Mismatches: 10, Indels: 40
0.70 0.06 0.24
Matches are distributed among these distances:
4 4 0.03
5 2 0.02
6 2 0.02
7 2 0.02
8 16 0.14
9 65 0.57
10 3 0.03
11 10 0.09
12 7 0.06
13 4 0.03
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.55
Consensus pattern (9 bp):
TATATAGTT
Found at i:651220 original size:13 final size:13
Alignment explanation
Indices: 651039--651199 Score: 95
Period size: 13 Copynumber: 12.2 Consensus size: 13
651029 ATGTATAGCT
651039 TATATAGTTTATA
1 TATATAGTTTATA
*
651052 TATGTAGTTTATATAA
1 TATATAG-TT-TAT-A
*
651068 TTTATATAGTTTTTA
1 --TATATAGTTTATA
651083 TATATAGTTTATTAA
1 TATATAGTTTA-T-A
*
651098 TTTATTCAGTTT-TA
1 TATA-T-AGTTTATA
651112 TATATAGTTTATA
1 TATATAGTTTATA
* *
651125 TAGTTTA--TTAAA
1 TA-TATAGTTTATA
651137 TTATATAG--T-T-
1 -TATATAGTTTATA
*
651147 TATATAGATTATA
1 TATATAGTTTATA
651160 TATATAGTTTATA
1 TATATAGTTTATA
* *
651173 CATATAGTTTA-C
1 TATATAGTTTATA
651185 TATATAGTTTATA
1 TATATAGTTTATA
651198 TA
1 TA
651200 CGTAATATAT
Statistics
Matches: 115, Mismatches: 15, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
9 7 0.06
11 1 0.01
12 24 0.21
13 47 0.41
14 10 0.09
15 9 0.08
16 4 0.03
17 7 0.06
18 6 0.05
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:651229 original size:22 final size:22
Alignment explanation
Indices: 651138--651230 Score: 84
Period size: 22 Copynumber: 4.1 Consensus size: 22
651128 TTTATTAAAT
*
651138 TATATAGTTTATATAG-ATTATA
1 TATATAGTTTATAT-GTAGTATA
* *
651160 TATATAGTTTATACATATAGTTTA
1 TATATAGTTTAT--ATGTAGTATA
651184 CTATATAGTTTATA--TACGTAATA
1 -TATATAGTTTATATGTA-GT-ATA
651207 TATATAGTTTATATGTAGTATA
1 TATATAGTTTATATGTAGTATA
651229 TA
1 TA
651231 AATATAAATT
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
21 2 0.03
22 32 0.54
23 5 0.08
24 8 0.14
25 12 0.20
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.48
Consensus pattern (22 bp):
TATATAGTTTATATGTAGTATA
Found at i:651290 original size:16 final size:17
Alignment explanation
Indices: 651269--651311 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
651259 ATAATTTTTG
651269 TATAGTTTATACTA-TA
1 TATAGTTTATACTATTA
*
651285 TATAGTTTA-CCTATTA
1 TATAGTTTATACTATTA
*
651301 TATAATTTATA
1 TATAGTTTATA
651312 GATAGTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (17 bp):
TATAGTTTATACTATTA
Found at i:651304 original size:2 final size:2
Alignment explanation
Indices: 651299--651376 Score: 56
Period size: 2 Copynumber: 40.0 Consensus size: 2
651289 GTTTACCTAT
* * * * *
651299 TA TA TA -A TT TA TA GA TA GTA TA TA AA TA TA AA T- TA TA TA GTT
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA
*
651341 TA TA TA CA T- TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
651377 ATTGTTTCAA
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
1 4 0.07
2 51 0.88
3 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:651335 original size:33 final size:33
Alignment explanation
Indices: 651297--651371 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
651287 TAGTTTACCT
*
651297 ATTATATAATTTATAGATAGTATATAAATATAA
1 ATTATATAATTTATAGACAGTATATAAATATAA
* * * * *
651330 ATTATATAGTTTATATACATTATATATATATAT
1 ATTATATAATTTATAGACAGTATATAAATATAA
651363 ATATATATA
1 AT-TATATA
651372 TTATAATTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
33 29 0.83
34 6 0.17
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (33 bp):
ATTATATAATTTATAGACAGTATATAAATATAA
Found at i:655462 original size:21 final size:20
Alignment explanation
Indices: 655438--655486 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
655428 CTCAAAAACA
* *
655438 TTTTTCAAAATGTCATTTTG
1 TTTTTCAAAATCTAATTTTG
655458 TTTTTCAAAATCTAATTTTG
1 TTTTTCAAAATCTAATTTTG
*
655478 -CTTTCAAAA
1 TTTTTCAAAA
655487 GAAAATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:658765 original size:15 final size:15
Alignment explanation
Indices: 658742--658776 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
658732 ACGAACGAAT
*
658742 ATTACCCTTAGTCAA
1 ATTATCCTTAGTCAA
658757 ATTATCCTTAGTCAA
1 ATTATCCTTAGTCAA
658772 ATTAT
1 ATTAT
658777 TTTGATTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (15 bp):
ATTATCCTTAGTCAA
Found at i:660583 original size:20 final size:20
Alignment explanation
Indices: 660558--660624 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
660548 TTATCTTGCT
660558 CGAAAGGCTTATAGATGACC
1 CGAAAGGCTTATAGATGACC
* *
660578 CGAAAGAG-TTAGTCATCATG-CT
1 CGAAAG-GCTTA-T-A-GATGACC
660600 CGAAAGGCTTATAGATGACC
1 CGAAAGGCTTATAGATGACC
660620 CGAAA
1 CGAAA
660625 AAGTTAATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
19 3 0.08
20 16 0.43
21 4 0.11
22 11 0.30
23 3 0.08
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (20 bp):
CGAAAGGCTTATAGATGACC
Found at i:660606 original size:42 final size:41
Alignment explanation
Indices: 660519--660652 Score: 160
Period size: 42 Copynumber: 3.2 Consensus size: 41
660509 ATCTTACCCG
* * * * * *
660519 AAGGTCTTATGGATGGCCCGAATGACTTATTATCTTGCTCGA
1 AAGG-CTTATAGATGACCCGAAAGAGTTATCATCATGCTCGA
660561 AAGGCTTATAGATGACCCGAAAGAGTTAGTCATCATGCTCGA
1 AAGGCTTATAGATGACCCGAAAGAGTTA-TCATCATGCTCGA
* *
660603 AAGGCTTATAGATGACCCGAAAAAGTTAATCATAATGCTCGA
1 AAGGCTTATAGATGACCCGAAAGAGTT-ATCATCATGCTCGA
*
660645 AAGACTTA
1 AAGGCTTA
660653 CTGATGGCCA
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
41 20 0.25
42 60 0.74
43 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (41 bp):
AAGGCTTATAGATGACCCGAAAGAGTTATCATCATGCTCGA
Found at i:663232 original size:22 final size:21
Alignment explanation
Indices: 663206--663265 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
663196 TTTTTCTCCT
663206 TTTCTTTTTCTTTTTATTTTAAC
1 TTTCTTTTTCTTTTTATTTT--C
*
663229 -TTCTTTTTC-TTTTCTTTTC
1 TTTCTTTTTCTTTTTATTTTC
663248 TTTCTTTTCTCTTTTTAT
1 TTTCTTTT-TCTTTTTAT
663266 CTATTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 1 0.03
20 7 0.22
21 10 0.31
22 14 0.44
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTCTTTTTCTTTTTATTTTC
Found at i:667557 original size:81 final size:81
Alignment explanation
Indices: 667464--667627 Score: 301
Period size: 81 Copynumber: 2.0 Consensus size: 81
667454 AAAACAAGTT
667464 AGTACAAATAAGATAAAAAAATGACAAGAATTATTATAAAAGAAATAATAACAAAATAAATTAAT
1 AGTACAAATAAGATAAAAAAATGACAAGAATTATTATAAAAGAAATAATAACAAAATAAATTAAT
667529 AAGATAATGCAAAACC
66 AAGATAATGCAAAACC
* *
667545 AGTACAAATAAGATAACAAAATGACATGAATTATTATAAAAGAAATAATAACAAAATAAATTAAT
1 AGTACAAATAAGATAAAAAAATGACAAGAATTATTATAAAAGAAATAATAACAAAATAAATTAAT
*
667610 AAGCTAATGCAAAACC
66 AAGATAATGCAAAACC
667626 AG
1 AG
667628 AATGCAAATG
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.21
Consensus pattern (81 bp):
AGTACAAATAAGATAAAAAAATGACAAGAATTATTATAAAAGAAATAATAACAAAATAAATTAAT
AAGATAATGCAAAACC
Found at i:670893 original size:20 final size:21
Alignment explanation
Indices: 670849--670893 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
670839 TTAGTTATGA
*
670849 TTTTTTTATGTTTTTTTCTTT
1 TTTTTTTATGTTTTTTCCTTT
670870 TTTTTTT-TG-TTTTTCCTTT
1 TTTTTTTATGTTTTTTCCTTT
*
670889 GTTTT
1 TTTTT
670894 CTGAACTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
20 2 0.09
21 7 0.32
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.84
Consensus pattern (21 bp):
TTTTTTTATGTTTTTTCCTTT
Found at i:670980 original size:22 final size:22
Alignment explanation
Indices: 670948--670989 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
670938 TTTTTCTTTT
670948 TTCCTCCAAAACCGAATGATTG
1 TTCCTCCAAAACCGAATGATTG
*
670970 TTCCTCTAAAACCGAATGAT
1 TTCCTCCAAAACCGAATGAT
670990 CCTCCTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (22 bp):
TTCCTCCAAAACCGAATGATTG
Found at i:676642 original size:21 final size:21
Alignment explanation
Indices: 676618--676681 Score: 128
Period size: 21 Copynumber: 3.0 Consensus size: 21
676608 TGGAATATTA
676618 CTTTTTAGCCCTTATATGCTT
1 CTTTTTAGCCCTTATATGCTT
676639 CTTTTTAGCCCTTATATGCTT
1 CTTTTTAGCCCTTATATGCTT
676660 CTTTTTAGCCCTTATATGCTT
1 CTTTTTAGCCCTTATATGCTT
676681 C
1 C
676682 ATATTGAACC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.14, C:0.25, G:0.09, T:0.52
Consensus pattern (21 bp):
CTTTTTAGCCCTTATATGCTT
Found at i:677734 original size:27 final size:28
Alignment explanation
Indices: 677688--677745 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
677678 ATAAATATGA
*
677688 AAAAATATTAAATTTAATTTATAATTAT
1 AAAAATATCAAATTTAATTTATAATTAT
* *
677716 AAAAATATCAAATTT-ATTTTTAATTTT
1 AAAAATATCAAATTTAATTTATAATTAT
677743 AAA
1 AAA
677746 TCTTACATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
AAAAATATCAAATTTAATTTATAATTAT
Found at i:691950 original size:35 final size:34
Alignment explanation
Indices: 691865--691951 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 34
691855 AAAATGATTT
691865 TAAATACAACAAAATTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
691899 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
691937 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
691952 ACTGAAATAC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
34 5 0.11
35 25 0.54
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:703361 original size:29 final size:29
Alignment explanation
Indices: 703183--703361 Score: 134
Period size: 29 Copynumber: 6.2 Consensus size: 29
703173 TATACCTCTA
* *
703183 AAAATATATTTTATTTTTATCTTAACTTATT
1 AAAATATATTTTATTATTATATTAA-TT-TT
* *
703214 -AAATATATTTTATTATTA-ATTTATGTT
1 AAAATATATTTTATTATTATATTAATTTT
* *
703241 AATA-ATATTTTATTATTATTTTAA-TTT
1 AAAATATATTTTATTATTATATTAATTTT
* * **
703268 AAAATTATATTTTATTTTTATCTT-AGCTT
1 AAAA-TATATTTTATTATTATATTAATTTT
* * * *
703297 AAATATATATTTTATTCTTATTTTAACTTC
1 AAA-ATATATTTTATTATTATATTAATTTT
* * *
703327 AGAATATATTTTATTCTTAGATTAATTTT
1 AAAATATATTTTATTATTATATTAATTTT
703356 AAAATA
1 AAAATA
703362 GTCAAAATAT
Statistics
Matches: 118, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
27 21 0.18
28 7 0.06
29 68 0.58
30 22 0.19
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (29 bp):
AAAATATATTTTATTATTATATTAATTTT
Found at i:703426 original size:31 final size:30
Alignment explanation
Indices: 703370--703436 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 30
703360 TAGTCAAAAT
703370 ATATATTTTATTCTTACATTAACTTATTAA
1 ATATATTTTATTCTTACATTAACTTATTAA
* *
703400 ATATATTTTACTTTTTACTTTAACTTATTAA
1 ATATATTTTA-TTCTTACATTAACTTATTAA
703431 ATATAT
1 ATATAT
703437 GTTAAAGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 10 0.29
31 24 0.71
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (30 bp):
ATATATTTTATTCTTACATTAACTTATTAA
Found at i:703486 original size:29 final size:29
Alignment explanation
Indices: 703453--703637 Score: 104
Period size: 29 Copynumber: 6.7 Consensus size: 29
703443 GTATTTGTTC
* *
703453 ATTAAGATAAGAATAAAATTTTTATTTAA
1 ATTAAGATAAGAATAAAATATATATTTAA
703482 ATTAAGATAAGAATAAAATATATATTTAA
1 ATTAAGATAAGAATAAAATATATATTTAA
* * *
703511 ATT---TTAA-AATAAATTAT-TTTTCTAA
1 ATTAAGATAAGAATAAAATATATATT-TAA
* * * *
703536 GTTAAAATATGAATAAAAAATATA-TTAA
1 ATTAAGATAAGAATAAAATATATATTTAA
*** * *
703564 GCAAATATAAGAAT---ATATATATAT-A
1 ATTAAGATAAGAATAAAATATATATTTAA
* *
703589 ATTAAAATAATAATAAAATATAT-TTAATAA
1 ATTAAGATAAGAATAAAATATATATT--TAA
* *
703619 GTTAAGATAAAAATAAAAT
1 ATTAAGATAAGAATAAAAT
703638 TTATTGGTAG
Statistics
Matches: 117, Mismatches: 26, Indels: 25
0.70 0.15 0.15
Matches are distributed among these distances:
24 3 0.03
25 30 0.26
26 4 0.03
27 1 0.01
28 21 0.18
29 40 0.34
30 18 0.15
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (29 bp):
ATTAAGATAAGAATAAAATATATATTTAA
Found at i:703609 original size:30 final size:30
Alignment explanation
Indices: 703570--703637 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
703560 TTAAGCAAAT
*
703570 ATAAGAATATATATATATAA-TTAAAATAATA
1 ATAA-AATATATATA-ATAAGTTAAAATAAAA
* *
703601 ATAAAATATATTTAATAAGTTAAGATAAAA
1 ATAAAATATATATAATAAGTTAAAATAAAA
703631 ATAAAAT
1 ATAAAAT
703638 TTATTGGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 4 0.12
30 25 0.76
31 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (30 bp):
ATAAAATATATATAATAAGTTAAAATAAAA
Found at i:705675 original size:20 final size:21
Alignment explanation
Indices: 705639--705678 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
705629 ATGGTACTGA
*
705639 TACTAAGCCCTTTAGTATCAG
1 TACTAAGCCCTTCAGTATCAG
705660 TACTAA-CCCTTCAGTATCA
1 TACTAAGCCCTTCAGTATCA
705679 ATACCCACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.33
Consensus pattern (21 bp):
TACTAAGCCCTTCAGTATCAG
Found at i:721639 original size:2 final size:2
Alignment explanation
Indices: 721632--721665 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
721622 AAGTATTATG
721632 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
721666 ATAGAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:722089 original size:147 final size:142
Alignment explanation
Indices: 721748--722188 Score: 381
Period size: 144 Copynumber: 3.0 Consensus size: 142
721738 AATATTTTTT
* * * * *
721748 AATATCATTTTGTGAGGGGAATACATAGAAACGCACATTGACTGATAAGAAGTGTGTTTTCGATG
1 AATATTATTTTGTGAGGGGAAT-CCTAGAAACGCGCATTGACT-AAAAGGAGTGTGTTTT-GATG
* * * * *
721813 ATTGTTCATATAAAATAATATTATTTTTGTATTCGAGTTTTTTTAATATATTAAATATATAATTT
63 ATTGTTCGTACAAAATAATATTATTTCTATATTCGAGTTTTTTGAATATATTAAATATATAATTT
*
721878 ACTAAAAATTAAGAT
128 ACTAAAAATTAAGAC
* * * * * * *
721893 AATATTA-TTTGAGAGAGAAATCC-ACGGAAACACGCCTTGACTGAAAAGGAGTATGTTTATGAG
1 AATATTATTTTGTGAGGGGAATCCTA--GAAACGCGCATTGACT-AAAAGGAGTGTGTTT-TGAT
* ** * *
721956 GATTGTTTGTACAAAATTGTATTCTTTCTATATTCGAGTTATTCTTGAATGTATTAAGTATATAT
62 GATTGTTCGTACAAAATAATATTATTTCTATATTCGAGTT-TT-TTGAATATATTAA--ATATAT
*
722021 AATTTATTAAAAA-TAAGAC
123 AATTTACTAAAAATTAAGAC
* * *
722040 AATATTATTTTGTGAGGGGAATCCTAGAAACGTGTATTGACTAACAAGGAGTGTGTTTTTTATGA
1 AATATTATTTTGTGAGGGGAATCCTAGAAACGCGCATTGACTAA-AAGGAGTGTG-TTTTGATGA
* * *
722105 TTGTTCGTACAAAATAATATCA-TT-TATATTTGAATGATTTTT-AATATATTAAATATTTATAA
64 TTGTTCGTACAAAATAATATTATTTCTATATTCG-A-GTTTTTTGAATATATTAAATA--TATAA
** *
722167 TTTGTTAAAAACTTAAGGC
125 TTTACTAAAAA-TTAAGAC
722186 AAT
1 AAT
722189 GATCTTTTAA
Statistics
Matches: 235, Mismatches: 44, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
142 4 0.02
143 1 0.00
144 95 0.40
145 18 0.08
146 26 0.11
147 56 0.24
148 34 0.14
149 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.40
Consensus pattern (142 bp):
AATATTATTTTGTGAGGGGAATCCTAGAAACGCGCATTGACTAAAAGGAGTGTGTTTTGATGATT
GTTCGTACAAAATAATATTATTTCTATATTCGAGTTTTTTGAATATATTAAATATATAATTTACT
AAAAATTAAGAC
Found at i:723170 original size:22 final size:21
Alignment explanation
Indices: 723142--723202 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
723132 TCATATAACT
*
723142 AAAGTGCCTCAGCACTGATACG
1 AAAGTGCCT-AGCACTAATACG
* *
723164 AAAGTGCACTACCACTAATACT
1 AAAGTGC-CTAGCACTAATACG
723186 AAAGTGCCATAGCACTA
1 AAAGTGCC-TAGCACTA
723203 GAGGGAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 30 0.91
23 2 0.06
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.20
Consensus pattern (21 bp):
AAAGTGCCTAGCACTAATACG
Found at i:729872 original size:81 final size:81
Alignment explanation
Indices: 729664--730129 Score: 544
Period size: 81 Copynumber: 5.8 Consensus size: 81
729654 TTATTTCAAA
* *
729664 TAAAAGATTATTGGCCTAGTTGTGCATTTAACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
729729 GTTAAATA-ATTTGAG
66 GTTAAATACCTTTGAG
* * * * *
729744 TAAAAGATTAATGGCCTAGTGGTGCATTCGACAGAAAGGTGTAAATTATGCCCGTTAGACGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
729809 ATTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * ** * *
729825 TAAAAGATTAATGGCCTAGCTATAAATTTGACAGAAAGATGTCAATTATACCAGTTAGATG-AA-
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
729888 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* ** * * *** *
729904 TAAAAGATTAATGACCTAGCCGTGCATTTGATAGAAATGTGTCAATTATGGTTGTTATATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
729969 GTTAAATACCTTGGAG
66 GTTAAATACCTTTGAG
* ** * * * * *
729985 TAACAGAAAAATTGTCTAGTTGTGCATTTGACAGGAAGGTGTCAATTATTCCAATTAGATGAAAG
1 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
730050 GCTAAATGCCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
730066 TTAAAGATTAAAT-GCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
1 TAAAAGATT-AATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
730130 AGCTAAATGT
Statistics
Matches: 316, Mismatches: 66, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
79 63 0.20
80 69 0.22
81 181 0.57
82 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:730016 original size:160 final size:161
Alignment explanation
Indices: 729675--730116 Score: 521
Period size: 160 Copynumber: 2.7 Consensus size: 161
729665 AAAAGATTAT
* * *
729675 TGGCCTAGTTGTGCATTTAACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATA-AT
1 TGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATACCAGTTAGATGAAAGGTTAAATACCT
* * *
729739 TTGAGTAAAAGATTAATGGCCTAGTGGTGCATTCGACAGAAAGGTGTAAATTATGCCCGTTAGAC
66 TTGAGTAAAAGATTAAT-GCCTAGTCGTGCATTTGACAGAAAGGTGTCAATTATGCCCGTTAGAC
* **
729804 GAAAGATTAAATACCTTTGAGTAAAAGATTAA
130 GAAAGATTAAATACCTTGGAGTAAAAGAAAAA
* * ** *
729836 TGGCCTAGCTATAAATTTGACAGAAAGATGTCAATTATACCAGTTAGATG-AA-GTTAAATACCT
1 TGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATACCAGTTAGATGAAAGGTTAAATACCT
* * * *** * *
729899 TTGAGTAAAAGATTAATGACCTAGCCGTGCATTTGATAGAAATGTGTCAATTATGGTTGTTATAT
66 TTGAGTAAAAGATTAATG-CCTAGTCGTGCATTTGACAGAAAGGTGTCAATTATGCCCGTTAGAC
* *
729964 GAAAGGTTAAATACCTTGGAGTAACAGAAAAA
130 GAAAGATTAAATACCTTGGAGTAAAAGAAAAA
* * * * * * *
729996 TTGTCTAGTTGTGCATTTGACAGGAAGGTGTCAATTATTCCAATTAGATGAAAGGCTAAATGCCT
1 TGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATACCAGTTAGATGAAAGGTTAAATACCT
* * * *
730061 TTGAGTTAAAGATTAAATGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATAATGC
66 TTGAGTAAAAGATT-AATGCCTAGTCGTGCATTTGACAGAAAGGTGTCAATTATGC
730117 AAGTTAGATG
Statistics
Matches: 232, Mismatches: 44, Indels: 9
0.81 0.15 0.03
Matches are distributed among these distances:
159 9 0.04
160 122 0.53
161 45 0.19
162 52 0.22
163 4 0.02
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (161 bp):
TGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATACCAGTTAGATGAAAGGTTAAATACCT
TTGAGTAAAAGATTAATGCCTAGTCGTGCATTTGACAGAAAGGTGTCAATTATGCCCGTTAGACG
AAAGATTAAATACCTTGGAGTAAAAGAAAAA
Found at i:730111 original size:241 final size:240
Alignment explanation
Indices: 729664--730128 Score: 554
Period size: 241 Copynumber: 1.9 Consensus size: 240
729654 TTATTTCAAA
* * **
729664 TAAAAGATTATTGGCCTAGTTGTGCATTTAACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGACCTAGCCGTGCATTTAACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* **
729729 GTTAAATAATTTGAGTAAAAGATTAATGGCCTAGTGGTGCATTCGACAGAAAGGTGTAAATTATG
66 GTTAAATAATTGGAGTAAAAGAAAAATGGCCTAGTGGTGCATTCGACAGAAAGGTGTAAATTATG
** *
729794 CCCGTTAGACGAAAGATTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTATAAATTTGACAG
131 CCAATTAGACGAAAGACTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTATAAATTTGACAG
* *
729859 AAAGATGTCAATTATACCAGTTAGATGAAGTTAAATACCTTTGAG
196 AAAGATGTCAATAATACAAGTTAGATGAAGTTAAATACCTTTGAG
* * * *** *
729904 TAAAAGATTAATGACCTAGCCGTGCATTTGATAGAAATGTGTCAATTATGGTTGTTATATGAAAG
1 TAAAAGATTAATGACCTAGCCGTGCATTTAACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * * * * * * *
729969 GTTAAATACCTTGGAGTAACAGAAAAATTGTCTAGTTGTGCATTTGACAGGAAGGTGTCAATTAT
66 GTTAAATA-ATTGGAGTAAAAGAAAAATGGCCTAGTGGTGCATTCGACAGAAAGGTGTAAATTAT
* * * * * * * ** *
730034 TCCAATTAGATGAAAGGCTAAATGCCTTTGAGTTAAAGATTAAAT-GCCTAGTTGTGCATTTGGC
130 GCCAATTAGACGAAAGACTAAATACCTTTGAGTAAAAGATT-AATGGCCTAGCTATAAATTTGAC
* *
730098 AGAAAGGTGTCAATAATGCAAGTTAGATGAA
194 AGAAAGATGTCAATAATACAAGTTAGATGAA
730129 AAGCTAAATG
Statistics
Matches: 184, Mismatches: 39, Indels: 3
0.81 0.17 0.01
Matches are distributed among these distances:
240 62 0.34
241 119 0.65
242 3 0.02
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (240 bp):
TAAAAGATTAATGACCTAGCCGTGCATTTAACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATAATTGGAGTAAAAGAAAAATGGCCTAGTGGTGCATTCGACAGAAAGGTGTAAATTATG
CCAATTAGACGAAAGACTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTATAAATTTGACAG
AAAGATGTCAATAATACAAGTTAGATGAAGTTAAATACCTTTGAG
Found at i:730175 original size:81 final size:81
Alignment explanation
Indices: 729688--730196 Score: 229
Period size: 81 Copynumber: 6.3 Consensus size: 81
729678 CCTAGTTGTG
* * * * **
729688 CATTTAACAGAAAGGTGTCAATT-ATGCCAGTTAGATGAAAGGTTAAAT-AATTTGAGTAAAAGA
1 CATTTGACAGAAAGGTGTCAATTAAT-CCAATTAGATGAAAAGCTAAATGCCTTTGAGTAAAAGA
* *** *
729751 -TTAATGGCCTAGTGGTG
65 CTAAAT-GCCTAACAGTA
* * ** * * *
729768 CATTCGACAGAAAGGTGTAAATT-ATGCCCGTTAGACG-AAAGATTAAATACCTTTGAGTAAAAG
1 CATTTGACAGAAAGGTGTCAATTAAT-CCAATTAGATGAAAAG-CTAAATGCCTTTGAGTAAAAG
* *
729831 A-TTAATGGCCTAGCTA-TA
64 ACTAAAT-GCCTAAC-AGTA
* * * * *
729849 AATTTGACAGAAAGATGTCAATT-ATACCAGTTAGATG--AAGTTAAATACCTTTGAGTAAAAGA
1 CATTTGACAGAAAGGTGTCAATTAAT-CCAATTAGATGAAAAGCTAAATGCCTTTGAGTAAAAGA
* * * *
729911 -TTAATGACCTAGCCGTG
65 CTAAATG-CCTAACAGTA
* * **** * * * * * *
729928 CATTTGATAGAAATGTGTCAATT-ATGGTTGTTATATGAAAGGTTAAATACCTTGGAGTAACAGA
1 CATTTGACAGAAAGGTGTCAATTAAT-CCAATTAGATGAAAAGCTAAATGCCTTTGAGTAAAAGA
* * *** *
729992 -AAAATTGTCTAGTTGTG
65 CTAAA-TGCCTAACAGTA
* * * * *
730009 CATTTGACAGGAAGGTGTCAATTATTCCAATTAGATGAAAGGCTAAATGCCTTTGAGTTAAAGAT
1 CATTTGACAGAAAGGTGTCAATTAATCCAATTAGATGAAAAGCTAAATGCCTTTGAGTAAAAGAC
*** *
730074 TAAATGCCTAGTTGTG
66 TAAATGCCTAACAGTA
* * *
730090 CATTTGGCAGAAAGGTGTCAA-TAATGCAAGTTAGATGAAAAGCTAAATGTCTTT-AGGTAAAAG
1 CATTTGACAGAAAGGTGTCAATTAATCCAA-TTAGATGAAAAGCTAAATGCCTTTGA-GTAAAAG
*
730153 ACTAAATGCTTAACAGTA
64 ACTAAATGCCTAACAGTA
* *
730171 CATTTTGACATAAACGATGTCAATTA
1 CA-TTTGACAGAAA-GGTGTCAATTA
730197 TTGATTTGAC
Statistics
Matches: 345, Mismatches: 69, Indels: 26
0.78 0.16 0.06
Matches are distributed among these distances:
78 1 0.00
79 65 0.19
80 48 0.14
81 207 0.60
82 15 0.04
83 7 0.02
84 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.30
Consensus pattern (81 bp):
CATTTGACAGAAAGGTGTCAATTAATCCAATTAGATGAAAAGCTAAATGCCTTTGAGTAAAAGAC
TAAATGCCTAACAGTA
Done.