Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008122.1 Hibiscus syriacus cultivar Beakdansim tig00110676_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: 2511854
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:391184 original size:58 final size:59
Alignment explanation
Indices: 391084--391242 Score: 155
Period size: 58 Copynumber: 2.7 Consensus size: 59
391074 TCGAGTGACC
* * * ** *
391084 ATTTTATAACTTTTTATA-GTCAAAAGACTCAAGAAAGTAACACTTTATAATT-AGATGATT
1 ATTTTATAACTTTTAATATGTC-AGA-ACTTAAGAAAACAACACCTTATAATTGAGAT-ATT
* *
391144 ATTTTGTAATTTTTAATA-GTC-GACACTTAAGAAAACAACACCTTATAATTGAGATATT
1 ATTTTATAACTTTTAATATGTCAGA-ACTTAAGAAAACAACACCTTATAATTGAGATATT
* * *
391202 ATTTTATTACTTTTAATATTTCAGAACTTAATAAAACAACA
1 ATTTTATAACTTTTAATATGTCAGAACTTAAGAAAACAACA
391243 TCATATATAT
Statistics
Matches: 82, Mismatches: 14, Indels: 7
0.80 0.14 0.07
Matches are distributed among these distances:
58 41 0.50
59 21 0.26
60 20 0.24
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (59 bp):
ATTTTATAACTTTTAATATGTCAGAACTTAAGAAAACAACACCTTATAATTGAGATATT
Found at i:391581 original size:29 final size:29
Alignment explanation
Indices: 391549--391607 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
391539 TGCACTGAAG
*
391549 AAAATAAGTTTACTATTATACTAAAACTA
1 AAAATAAATTTACTATTATACTAAAACTA
391578 AAAATAAATTTACTATTATACTAAAACTA
1 AAAATAAATTTACTATTATACTAAAACTA
391607 A
1 A
391608 GTAAAATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (29 bp):
AAAATAAATTTACTATTATACTAAAACTA
Found at i:396902 original size:42 final size:42
Alignment explanation
Indices: 396840--396940 Score: 184
Period size: 42 Copynumber: 2.4 Consensus size: 42
396830 TACTCAGTCA
*
396840 TTTTCTTTTCAAAATTATATTTAACGTTATATTATGTTTTTC
1 TTTTCTTTTCAAAATCATATTTAACGTTATATTATGTTTTTC
*
396882 TTTTCTTTTCAAAATCATATTTAACGTTATATTCTGTTTTTC
1 TTTTCTTTTCAAAATCATATTTAACGTTATATTATGTTTTTC
396924 TTTTCTTTTCAAAATCA
1 TTTTCTTTTCAAAATCA
396941 CATCTAACTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.57
Consensus pattern (42 bp):
TTTTCTTTTCAAAATCATATTTAACGTTATATTATGTTTTTC
Found at i:399174 original size:262 final size:261
Alignment explanation
Indices: 398257--399760 Score: 2009
Period size: 262 Copynumber: 5.8 Consensus size: 261
398247 CTAGAAGCAT
* * *
398257 GAATATTATGATTTTAAAAAATATAAAAGTGATTGCGCCTAAAGTATTATGAAAGTTTTAGCCGA
1 GAATATTATCATTTTAAAAAATA-AAAA-CGATTGCACCTAAAGTATTATGAAAGTTTTAGCCGA
*** * * * * *
398322 TGGAGCCTTAAAGTTCCCCACAACAATCAAATAGGTTAAGAGCATAAAGTATTACGATTAGGTAT
64 TGGAGCCTTGGCGTTCCCCACGACAATCAAATAGGTTAAGAGCACAAACTTTTACGATTTGGTAT
* * * * *
398387 ATAGATATGGTTGTGCCCTAGAATATCACGGTTCTAAAGGAAATAGATTACGACTAGTAATGTCA
129 ATAGATACGGTTGCGCCCCA-AATATCACGGTTCTAAAGGAAATAGGTTACGACTTGTAATGTCA
* *
398452 ACTTGTGTATTAATAGAATAGATTGCGCCCAGAATGTCAT-GACCCCAAAGAAAACATGTTGCAA
193 ACTTGTGTATTAATAGAATAGATTGCGCCCAGAATGTCATGGCCCCCAAAGAAAGCATGTTGCAA
*
398516 TATG
258 TCTG
** * *
398520 GAATATTATCATTTTAAAAAATAAAAGTGATTGCGCTTAAAGTATTATGAAAGTTTTAGCCGATG
1 GAATATTATCATTTTAAAAAATAAAAACGATTGCACCTAAAGTATTATGAAAGTTTTAGCCGATG
* * *
398585 AAGCCTTGGCATTCCCCACGACAATCAAATAGGTTAAGAACACAAACTTTTACGATTTGGTATAT
66 GAGCCTTGGCGTTCCCCACGACAATCAAATAGGTTAAGAGCACAAACTTTTACGATTTGGTATAT
* *** **
398650 AGATACGGTTGTGCCCCAAAATATCACAACTCTAAA-GAAAGTAGGTTGTGACTTGTAATGTCAA
131 AGATACGGTTGCGCCCC-AAATATCACGGTTCTAAAGGAAA-TAGGTTACGACTTGTAATGTCAA
* *
398714 CTTATGTATTAATAGAATAGATTGCGCCCAGAATGTAATGGCCCCCCAAAGAAAGCATGTTGCAA
194 CTTGTGTATTAATAGAATAGATTGCGCCCAGAATGTCATGG-CCCCCAAAGAAAGCATGTTGCAA
*
398779 TATG
258 TCTG
* *
398783 GAATATTATCATTTTAAAAAATAAAAGCGATTGCACCTAAAGTATTATGAAAGTTTTAGCTGATG
1 GAATATTATCATTTTAAAAAATAAAAACGATTGCACCTAAAGTATTATGAAAGTTTTAGCCGATG
* * *
398848 GAGCTTTGGCATTCCCCACGATAATCAAATAGGTTAAGAGCACAAACTTTTACGATTT-GTATAT
66 GAGCCTTGGCGTTCCCCACGACAATCAAATAGGTTAAGAGCACAAACTTTTACGATTTGGTATAT
* * *
398912 AGATACAGTTGCGCCCCATAATATCATGGTTCTAAAGGAAATAGGTTACGACTTGTAATGTTAAC
131 AGATACGGTTGCGCCCCA-AATATCACGGTTCTAAAGGAAATAGGTTACGACTTGTAATGTCAAC
* * *
398977 TTGTGTATTAATAGAATAGATTGTGCCCAGAATGTTATGGCCCCCAAAGAAAGCATGTTGTAATC
195 TTGTGTATTAATAGAATAGATTGCGCCCAGAATGTCATGGCCCCCAAAGAAAGCATGTTGCAATC
*
399042 TA
260 TG
*
399044 GAATATTATCATTTTAAAAAGTAAAAACGATTGCACCTAAAGTATTATGAAAGTTTTAGCCGATG
1 GAATATTATCATTTTAAAAAATAAAAACGATTGCACCTAAAGTATTATGAAAGTTTTAGCCGATG
** * *
399109 GAGAATTGGTGTTCCCCACGACAATCAAATAGGTTAAGAGCACAAACTTTTACAATTTGGTATAT
66 GAGCCTTGGCGTTCCCCACGACAATCAAATAGGTTAAGAGCACAAACTTTTACGATTTGGTATAT
* * * *
399174 AGATAAGG-TGTCACCCCAGAATATCACGGTTCAAAAGGAAATAAGTTACGACTTGTAATGTCAA
131 AGATACGGTTG-CGCCCCA-AATATCACGGTTCTAAAGGAAATAGGTTACGACTTGTAATGTCAA
* *
399238 CTTCTGTATTAATAGAATAGATTGCGCCCAGAATGTCATGGCCCCCAAAGAATGCATGTTGCAAT
194 CTTGTGTATTAATAGAATAGATTGCGCCCAGAATGTCATGGCCCCCAAAGAAAGCATGTTGCAAT
399303 CTG
259 CTG
* * ** * ** *
399306 GAATATTATCATTTAAAAAAATAGAAGTGACTGCGTCTAAAGTATTATGAAAGTTTTAGCTGATG
1 GAATATTATCATTTTAAAAAATAAAAACGATTGCACCTAAAGTATTATGAAAGTTTTAGCCGATG
* * *
399371 GAGTCTTGGCGTTCCCCACGAAAATAAAATAGGTTAAGAGCACAAACTTTTACGATTTGGTATAT
66 GAGCCTTGGCGTTCCCCACGACAATCAAATAGGTTAAGAGCACAAACTTTTACGATTTGGTATAT
* * *
399436 AGATACGG-T--G---------TCACGGCTT-TAACA-GAAATAGGTTGCGACTTCTAATGTCTA
131 AGATACGGTTGCGCCCCAAATATCACGG-TTCTAA-AGGAAATAGGTTACGACTTGTAATGTCAA
* *
399487 CTTGTGTATTAATAGAATAGATTGCGTCCAGAATGTCATGGTCCCCAAAGAAAGCATGTTGCAAT
194 CTTGTGTATTAATAGAATAGATTGCGCCCAGAATGTCATGGCCCCCAAAGAAAGCATGTTGCAAT
399552 CTG
259 CTG
* * *
399555 GAATATTATCATTTTAAAAAATAAAAACGATTGCAGCAAAAGTATTATGAAAGTTTTAGCTGATG
1 GAATATTATCATTTTAAAAAATAAAAACGATTGCACCTAAAGTATTATGAAAGTTTTAGCCGATG
* * *
399620 GAGCCTTGGCGTTCCCCACAACAATCAAATAGGTTAAGAGCATAAACTTTTAAGATTTGGTATAT
66 GAGCCTTGGCGTTCCCCACGACAATCAAATAGGTTAAGAGCACAAACTTTTACGATTTGGTATAT
* * * **
399685 ATATATGGTTGCACCCCCAAATATCACGGTTCTAAAGGAAATATATTACGACTTGTAATGTCAAC
131 AGATACGGTTGC-GCCCCAAATATCACGGTTCTAAAGGAAATAGGTTACGACTTGTAATGTCAAC
399750 TTGTGTATTAA
195 TTGTGTATTAA
399761 CATAAAATAG
Statistics
Matches: 1095, Mismatches: 121, Indels: 51
0.86 0.10 0.04
Matches are distributed among these distances:
249 217 0.20
250 4 0.00
260 4 0.00
261 320 0.29
262 384 0.35
263 166 0.15
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (261 bp):
GAATATTATCATTTTAAAAAATAAAAACGATTGCACCTAAAGTATTATGAAAGTTTTAGCCGATG
GAGCCTTGGCGTTCCCCACGACAATCAAATAGGTTAAGAGCACAAACTTTTACGATTTGGTATAT
AGATACGGTTGCGCCCCAAATATCACGGTTCTAAAGGAAATAGGTTACGACTTGTAATGTCAACT
TGTGTATTAATAGAATAGATTGCGCCCAGAATGTCATGGCCCCCAAAGAAAGCATGTTGCAATCT
G
Found at i:402337 original size:49 final size:49
Alignment explanation
Indices: 402263--402365 Score: 188
Period size: 49 Copynumber: 2.1 Consensus size: 49
402253 TCGGTCCTCA
402263 GTTTCGATACTAACCGATAACATAACTTACCCGATTAAGCCATTCTTTT
1 GTTTCGATACTAACCGATAACATAACTTACCCGATTAAGCCATTCTTTT
* *
402312 GTTTCGATACTAACCGGTAATATAACTTACCCGATTAAGCCATTCTTTT
1 GTTTCGATACTAACCGATAACATAACTTACCCGATTAAGCCATTCTTTT
402361 GTTTC
1 GTTTC
402366 CTAGACTACA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (49 bp):
GTTTCGATACTAACCGATAACATAACTTACCCGATTAAGCCATTCTTTT
Found at i:419593 original size:31 final size:31
Alignment explanation
Indices: 419551--419676 Score: 171
Period size: 31 Copynumber: 4.1 Consensus size: 31
419541 ATTTGTACAC
* * *
419551 TTTTGGCCACTTACGTTATCATTTTATTAAG
1 TTTTGGTCACTTATGTTATCGTTTTATTAAG
*
419582 TTTTGGTCACTTATGATATCGTTTTATTAAG
1 TTTTGGTCACTTATGTTATCGTTTTATTAAG
*
419613 TTTTGGTCACTTATGTTATCGTTTTATTATG
1 TTTTGGTCACTTATGTTATCGTTTTATTAAG
** * *
419644 TTTCAGTCACTTTTATTATCGTTTTATTAAG
1 TTTTGGTCACTTATGTTATCGTTTTATTAAG
419675 TT
1 TT
419677 CTTATCACTT
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 84 1.00
ACGTcount: A:0.21, C:0.12, G:0.13, T:0.54
Consensus pattern (31 bp):
TTTTGGTCACTTATGTTATCGTTTTATTAAG
Found at i:420424 original size:31 final size:31
Alignment explanation
Indices: 420389--420462 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
420379 TTCAACGTTC
* *
420389 AAGTGACCAAAGCTTAATAAAACAATAACGT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
* *
420420 AAGTGACCAAAACTTAATAAAACGATAATAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
*
420451 AAGTGATCAAAA
1 AAGTGACCAAAA
420463 GTGTACAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.54, C:0.14, G:0.12, T:0.20
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACAT
Found at i:422611 original size:3 final size:3
Alignment explanation
Indices: 422603--422628 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
422593 TTCTATTCTA
422603 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
422629 AATAAGACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:428366 original size:2 final size:2
Alignment explanation
Indices: 428359--428397 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
428349 TACTAACAAT
428359 TA TA 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 TA TA T
428398 TTTAAATCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:429418 original size:104 final size:102
Alignment explanation
Indices: 429286--429495 Score: 338
Period size: 104 Copynumber: 2.0 Consensus size: 102
429276 CATTTATGGC
429286 AATAATTATTTAATGTACTATATCGTTGAAAG-TGAAACAATGACAAGTTTTTT-AATTGTGTTA
1 AATAATTATTTAATGTACTATATCGTTGAAAGTTGAAACAATGACAAGTTTTTTAAATTGTGTT-
429349 TGGAATTATTTTTTCATGATGGTACATCAAATAA-TACATAA
65 T--AATTA-TTTTTCAT-ATGGTACATCAAATAATTACATAA
429390 AATAATTATTTAATGTA-TATTATCGTTGAAAGTTGAAACAATGACAAGTTTTTTAAATTGTGTT
1 AATAATTATTTAATGTACTA-TATCGTTGAAAGTTGAAACAATGACAAGTTTTTTAAATTGTGTT
429454 TAATTATTTTTCATATGGTACATCAAATAATTACATAA
65 TAATTATTTTTCATATGGTACATCAAATAATTACATAA
429492 AATA
1 AATA
429496 CTTCTAGGTA
Statistics
Matches: 102, Mismatches: 0, Indels: 10
0.91 0.00 0.09
Matches are distributed among these distances:
101 16 0.16
102 19 0.19
103 7 0.07
104 29 0.28
105 22 0.22
106 9 0.09
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (102 bp):
AATAATTATTTAATGTACTATATCGTTGAAAGTTGAAACAATGACAAGTTTTTTAAATTGTGTTT
AATTATTTTTCATATGGTACATCAAATAATTACATAA
Found at i:431019 original size:162 final size:165
Alignment explanation
Indices: 430736--431053 Score: 526
Period size: 162 Copynumber: 1.9 Consensus size: 165
430726 TAACACCTAT
430736 TTAAGCCTTCAAATTGTAGTTTATTTTGATTCTCCCTGTTTTTGTTATTATACTTTACCCCTATT
1 TTAAGCCTTCAAATTGTAGTTTATTTTGATTCTCCCTGTTTTTGTTATTATACTTTACCCCTATT
430801 TTCTATTATTAATTATATTTTACTCCCACTGGATTGGTACTTAGTTCCGTTCCTTGTATACATAT
66 TTCTATTATTAA-TATATTTTACTCCCACTGGATTGGTACTTAGTTCCGTTCCTTGTATACATAT
430866 GTAACCGATCGAAAAAAAACATTAACCTTTATTACCG
130 GTAACCGATCG-AAAAAAACATTAACCTTTATTACCG
430903 TTAAGCCTTCAAATTGTAGTTTA-TTTGATTCTCCC-GTTTTTATGTTAATTATACTTTACCCCT
1 TTAAGCCTTCAAATTGTAGTTTATTTTGATTCTCCCTG-TTTT-TGTT-ATTATACTTTACCCCT
430966 A-TTT-TATTATT-A-AT-TTTTACTCCCACTGGATTGGTATCTTAGTTCCG-TCCTTGTATACA
63 ATTTTCTATTATTAATATATTTTACTCCCACTGGATTGGTA-CTTAGTTCCGTTCCTTGTATACA
431025 TATGTAACCGATCGAAAAAAACATTAACC
127 TATGTAACCGATCGAAAAAAACATTAACC
431054 ATTACCGATA
Statistics
Matches: 147, Mismatches: 0, Indels: 14
0.91 0.00 0.09
Matches are distributed among these distances:
161 15 0.10
162 48 0.33
163 12 0.08
165 2 0.01
166 23 0.16
167 30 0.20
168 17 0.12
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (165 bp):
TTAAGCCTTCAAATTGTAGTTTATTTTGATTCTCCCTGTTTTTGTTATTATACTTTACCCCTATT
TTCTATTATTAATATATTTTACTCCCACTGGATTGGTACTTAGTTCCGTTCCTTGTATACATATG
TAACCGATCGAAAAAAACATTAACCTTTATTACCG
Found at i:432410 original size:13 final size:13
Alignment explanation
Indices: 432392--432416 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
432382 AACGAACGCA
432392 AATGAACATAAAC
1 AATGAACATAAAC
432405 AATGAACATAAA
1 AATGAACATAAA
432417 ATTAATTGTG
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:0.64, C:0.12, G:0.08, T:0.16
Consensus pattern (13 bp):
AATGAACATAAAC
Found at i:435218 original size:28 final size:28
Alignment explanation
Indices: 435160--435225 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
435150 ATATATTTAT
* * * *
435160 TTTTTTTAAAATAAATTAGGATGTAACA
1 TTTTTTAAAAATAAATTAAGATCTAAAA
* *
435188 TTTTTTAAAAATTAATTAAGCTCTAAAA
1 TTTTTTAAAAATAAATTAAGATCTAAAA
435216 TTTTCTTAAA
1 TTTT-TTAAA
435226 GAATCAATCA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
28 26 0.84
29 5 0.16
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (28 bp):
TTTTTTAAAAATAAATTAAGATCTAAAA
Found at i:441023 original size:3 final size:3
Alignment explanation
Indices: 441015--441054 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
441005 TATAAACTAA
441015 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
441055 GAAAAGGGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:441246 original size:2 final size:2
Alignment explanation
Indices: 441239--441277 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
441229 AATTCTTCCT
441239 TA TA 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 TA TA T
441278 TGTACAAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:447712 original size:20 final size:20
Alignment explanation
Indices: 447676--447713 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
447666 ATCATATTCC
**
447676 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
447696 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
447714 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:448490 original size:17 final size:17
Alignment explanation
Indices: 448439--448496 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
448429 TATTTGTATT
448439 TAATAACTATAAAATATC
1 TAATAACTAT-AAATATC
* ** * *
448457 TTATATTTGTAATTATC
1 TAATAACTATAAATATC
*
448474 TGATAACTATAAATATC
1 TAATAACTATAAATATC
448491 TAATAA
1 TAATAA
448497 ATATGCTAGT
Statistics
Matches: 29, Mismatches: 11, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
17 23 0.79
18 6 0.21
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (17 bp):
TAATAACTATAAATATC
Found at i:451189 original size:34 final size:34
Alignment explanation
Indices: 451145--451213 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
451135 GTCTTGATTA
*
451145 TATATATTTTATATTAATTATATATATAATATTT
1 TATATATTTTATATTAATTATATATAAAATATTT
*
451179 TATATTTTTTATATTAATTATATATAAAATATTT
1 TATATATTTTATATTAATTATATATAAAATATTT
451213 T
1 T
451214 CGGGTTCGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TATATATTTTATATTAATTATATATAAAATATTT
Found at i:451201 original size:25 final size:25
Alignment explanation
Indices: 451143--451201 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
451133 CCGTCTTGAT
451143 TATA-TATATTTTATATTAATTATA
1 TATATTATATTTTATATTAATTATA
* **
451167 TATATAATATTTTATATTTTTTATA
1 TATATTATATTTTATATTAATTATA
451192 T-TAATTATAT
1 TAT-ATTATAT
451202 ATAAAATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TATATTATATTTTATATTAATTATA
Found at i:457552 original size:12 final size:12
Alignment explanation
Indices: 457520--457559 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
457510 TCAAAGAACA
457520 TTAAAA-TTA-T
1 TTAAAATTTATT
*
457530 TT-AAATATATT
1 TTAAAATTTATT
457541 TTAAAATTTATT
1 TTAAAATTTATT
457553 TTAAAAT
1 TTAAAAT
457560 ATGGATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 3 0.12
10 4 0.16
11 3 0.12
12 15 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:457561 original size:22 final size:21
Alignment explanation
Indices: 457520--457561 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
457510 TCAAAGAACA
457520 TTAAAATTATTTAAATATATT
1 TTAAAATTATTTAAATATATT
457541 TTAAAATTTATTTTAAA-ATAT
1 TTAAAA-TTA-TTTAAATATAT
457562 GGATTGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTAAAATTATTTAAATATATT
Found at i:457571 original size:22 final size:22
Alignment explanation
Indices: 457546--457862 Score: 435
Period size: 22 Copynumber: 14.6 Consensus size: 22
457536 ATATTTTAAA
457546 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* * *
457568 ATTTATTTTAAAACATGAATGG
1 ATTTATTTTAAAATATGGATTG
*
457590 TTTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
457612 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
457634 ATTTATTTTAAAATAT--A--G
1 ATTTATTTTAAAATATGGATTG
* *
457652 ATTAATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
***
457674 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
457696 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
457718 ATTTATTTTAAAATATTGATTG
1 ATTTATTTTAAAATATGGATTG
457740 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
457762 ATTTATTTTAAAATATGAAAAA
1 ATTTATTTTAAAATATGGATTG
* *
457784 ATTTATTTTTAAATTTGGATTG
1 ATTTATTTTAAAATATGGATTG
457806 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* *
457828 ATTTATTTTAAATTTTGGATTG
1 ATTTATTTTAAAATATGGATTG
*
457850 ATTTATTTAAAAA
1 ATTTATTTTAAAA
457863 ATTATTATTA
Statistics
Matches: 256, Mismatches: 35, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
18 16 0.06
20 2 0.01
22 238 0.93
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:458571 original size:24 final size:24
Alignment explanation
Indices: 458525--458577 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
458515 TAATGGAATA
* ***
458525 TTTATATTTAAATTTTTTGATATT
1 TTTATATTTAAAATTTAAAATATT
458549 TTTATATTTAAAATTTAAAATATT
1 TTTATATTTAAAATTTAAAATATT
458573 TTTAT
1 TTTAT
458578 TAAAAAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTATATTTAAAATTTAAAATATT
Found at i:466553 original size:2 final size:2
Alignment explanation
Indices: 466548--466594 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
466538 CTTGACTTAT
466548 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
466590 TA TA T
1 TA TA T
466595 GTCCCTCCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:467240 original size:22 final size:22
Alignment explanation
Indices: 467215--467275 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
467205 TCTCCCGTCC
* * *
467215 TCATCTTTATTTTAGAGTATCT
1 TCATCTTTACTCTAGAGTATAT
*
467237 TCATCTCTACTCTAGAGTATAT
1 TCATCTTTACTCTAGAGTATAT
*
467259 TTATCTTTACTCTAGAG
1 TCATCTTTACTCTAGAG
467276 ATGAAACAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.48
Consensus pattern (22 bp):
TCATCTTTACTCTAGAGTATAT
Found at i:467724 original size:17 final size:17
Alignment explanation
Indices: 467685--467726 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
467675 TCTAAAATTC
*
467685 AAAATTTTTTTATATTA
1 AAAATTTTTTTATATGA
*
467702 ATAATTTATTTTAT-TGA
1 AAAATTT-TTTTATATGA
467719 AAAATTTT
1 AAAATTTT
467727 ATCGAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 14 0.67
18 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
AAAATTTTTTTATATGA
Found at i:467725 original size:13 final size:13
Alignment explanation
Indices: 467709--467742 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
467699 TTAATAATTT
467709 ATTTTATTGAAAA
1 ATTTTATTGAAAA
*
467722 ATTTTATCGAAAA
1 ATTTTATTGAAAA
467735 ATTTTATT
1 ATTTTATT
467743 TATATCTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (13 bp):
ATTTTATTGAAAA
Found at i:474198 original size:36 final size:36
Alignment explanation
Indices: 474127--474265 Score: 187
Period size: 36 Copynumber: 3.9 Consensus size: 36
474117 AAAAATGAAC
* * *
474127 ACTTGAATC-GAAA-GTGCGACGCCTCATTCCGTTCG
1 ACTTGAATCGGAAATGT-CGATGCTTCCTTCCGTTCG
474162 ACTTGAATCGGAAATGTCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAATGTCGATGCTTCCTTCCGTTCG
*
474198 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTC-
1 ACTTGAATCGGAAATGTCGATGCTTCCTTCCGTTCG
* *
474233 ACTTGAATCGGAAGTG-CGATACTTCCTTCCGTT
1 ACTTGAATCGGAAATGTCGATGCTTCCTTCCGTT
474266 ATTCTTGTTC
Statistics
Matches: 97, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
34 16 0.16
35 25 0.26
36 54 0.56
37 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (36 bp):
ACTTGAATCGGAAATGTCGATGCTTCCTTCCGTTCG
Found at i:474243 original size:71 final size:70
Alignment explanation
Indices: 474127--474265 Score: 199
Period size: 71 Copynumber: 2.0 Consensus size: 70
474117 AAAAATGAAC
*
474127 ACTTGAATCGAAAGTGCGACGCCTCATTCCGTTCGACTTGAATCGGAAATGTCGATGCTTCCTTC
1 ACTTGAATCGAAAGTGCGACGCCTCATTCCGTTCGACTTGAATCGGAAATG-CGATACTTCCTTC
474192 CGTTCG
65 CGTTCG
* * * * *
474198 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTC-ACTTGAATCGGAAGTGCGATACTTCCTTC
1 ACTTGAATCGAAAGTG-CGACGCCTCATTCCGTTCGACTTGAATCGGAAATGCGATACTTCCTTC
474262 CGTT
65 CGTT
474266 ATTCTTGTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
70 16 0.26
71 30 0.49
72 15 0.25
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (70 bp):
ACTTGAATCGAAAGTGCGACGCCTCATTCCGTTCGACTTGAATCGGAAATGCGATACTTCCTTCC
GTTCG
Found at i:481914 original size:14 final size:14
Alignment explanation
Indices: 481895--481936 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
481885 ACAATTTCGG
481895 TATTTTATTTATTT
1 TATTTTATTTATTT
*
481909 TATTTTA-TTAATT
1 TATTTTATTTATTT
*
481922 AATTTTTATTTATTT
1 TA-TTTTATTTATTT
481937 AGATAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 6 0.26
14 12 0.52
15 5 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTATTTATTT
Found at i:482760 original size:30 final size:32
Alignment explanation
Indices: 482702--482761 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
482692 ATTAATAATA
* *
482702 AAATATATTTTTTAAAATTATTATAATTTATT
1 AAATATATTTTTTAAAATGATCATAATTTATT
482734 AAAT-TATTTTTTAAAATGATCA-AATTTA
1 AAATATATTTTTTAAAATGATCATAATTTA
482762 AATATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 6 0.23
31 16 0.62
32 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (32 bp):
AAATATATTTTTTAAAATGATCATAATTTATT
Found at i:483953 original size:13 final size:13
Alignment explanation
Indices: 483935--483963 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
483925 AACTGAATAA
483935 AGTTCAATTAATC
1 AGTTCAATTAATC
483948 AGTTCAATTAATC
1 AGTTCAATTAATC
483961 AGT
1 AGT
483964 CGGTTAACCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (13 bp):
AGTTCAATTAATC
Found at i:486163 original size:6 final size:6
Alignment explanation
Indices: 486152--486181 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
486142 CAATTGAGAT
486152 GGGATG GGGATG GGGATG GGGATG GGGATG
1 GGGATG GGGATG GGGATG GGGATG GGGATG
486182 TATATAAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.67, T:0.17
Consensus pattern (6 bp):
GGGATG
Found at i:489931 original size:14 final size:14
Alignment explanation
Indices: 489912--489953 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
489902 ACAATTTCGG
489912 TATTTTATTTATTT
1 TATTTTATTTATTT
*
489926 TATTTTA-TTAATT
1 TATTTTATTTATTT
*
489939 GATTTTTATTTATTT
1 TA-TTTTATTTATTT
489954 AGATAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 6 0.26
14 12 0.52
15 5 0.22
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (14 bp):
TATTTTATTTATTT
Found at i:494007 original size:7 final size:7
Alignment explanation
Indices: 493995--494019 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
493985 CATACCCGCC
493995 GTGGGTA
1 GTGGGTA
494002 GTGGGTA
1 GTGGGTA
494009 GTGGGTA
1 GTGGGTA
494016 GTGG
1 GTGG
494020 ATATGTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.60, T:0.28
Consensus pattern (7 bp):
GTGGGTA
Found at i:508081 original size:7 final size:7
Alignment explanation
Indices: 508069--508111 Score: 86
Period size: 7 Copynumber: 6.1 Consensus size: 7
508059 ACTTTCTCTG
508069 CTATTTT
1 CTATTTT
508076 CTATTTT
1 CTATTTT
508083 CTATTTT
1 CTATTTT
508090 CTATTTT
1 CTATTTT
508097 CTATTTT
1 CTATTTT
508104 CTATTTT
1 CTATTTT
508111 C
1 C
508112 CTCCTCCCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (7 bp):
CTATTTT
Found at i:512815 original size:2 final size:2
Alignment explanation
Indices: 512808--512846 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
512798 TTCCATGTTT
512808 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
512847 GTTATTTAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:513854 original size:18 final size:18
Alignment explanation
Indices: 513831--513866 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
513821 AACAAGAACA
513831 TTAAAA-AAATGAGAAAAT
1 TTAAAAGAAATG-GAAAAT
513849 TTAAAAGAAATGGAAAAT
1 TTAAAAGAAATGGAAAAT
513867 CTAATAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.22
Consensus pattern (18 bp):
TTAAAAGAAATGGAAAAT
Found at i:514158 original size:18 final size:18
Alignment explanation
Indices: 514135--514172 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
514125 CCGGAATTAT
*
514135 ATAAATAAACAAGAATAA
1 ATAAATAAACAAAAATAA
*
514153 ATAAATAAATAAAAATAA
1 ATAAATAAACAAAAATAA
514171 AT
1 AT
514173 TGTATGGCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
ATAAATAAACAAAAATAA
Found at i:521294 original size:65 final size:66
Alignment explanation
Indices: 521171--521304 Score: 198
Period size: 65 Copynumber: 2.0 Consensus size: 66
521161 AGAAAATTAG
* * *
521171 ATATACTTGTTCAAACACATATAGAAACCCAATATTTAATATAATAAAAAATATATGATAATTTA
1 ATATACTTATTCAAACACA-ATAGAAACCCAATATTCAATAGAATAAAAAATATATGATAATTTA
521236 AA
65 AA
* * *
521238 ATATACTTATTCAAACAC-ATAGAAACTCATTATTCAATAGAATACAAAATATATGATAATTTAA
1 ATATACTTATTCAAACACAATAGAAACCCAATATTCAATAGAATAAAAAATATATGATAATTTAA
521302 A
66 A
521303 AT
1 AT
521305 TTTTAAGAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 44 0.72
67 17 0.28
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.33
Consensus pattern (66 bp):
ATATACTTATTCAAACACAATAGAAACCCAATATTCAATAGAATAAAAAATATATGATAATTTAA
A
Found at i:531803 original size:27 final size:27
Alignment explanation
Indices: 531773--531837 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
531763 CCTGTGCCTG
*
531773 TGGATGGTAACATGCCAAAGCTAGGCA
1 TGGATGGTAACATGCCAAAGCCAGGCA
* *
531800 TGGATGGTAAAATGCCAATGCCAGGCA
1 TGGATGGTAACATGCCAAAGCCAGGCA
* *
531827 AGGATGATAAC
1 TGGATGGTAAC
531838 TTACTGATGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.18
Consensus pattern (27 bp):
TGGATGGTAACATGCCAAAGCCAGGCA
Found at i:531899 original size:33 final size:33
Alignment explanation
Indices: 531810--531900 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 33
531800 TGGATGGTAA
* * * * *
531810 AATGCCAATGCCAGGCAAGGATGATAACTTACT
1 AATGCCGATGCCGGGAAAGGATGGTAACTTACC
* * * *
531843 GATGCTGGTGCCGGCAAAGGATGGTAACTTACC
1 AATGCCGATGCCGGGAAAGGATGGTAACTTACC
531876 AATGCCGATGCCGGGAAAGGATGGT
1 AATGCCGATGCCGGGAAAGGATGGT
531901 CATATGCCGG
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.30, C:0.20, G:0.31, T:0.20
Consensus pattern (33 bp):
AATGCCGATGCCGGGAAAGGATGGTAACTTACC
Found at i:534233 original size:33 final size:33
Alignment explanation
Indices: 534196--534264 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
534186 TCGAAAGTAT
*
534196 ACCAAAGGGACCGATATGGTGCAAGCCGAAACA
1 ACCAAAGGGACCGATACGGTGCAAGCCGAAACA
*
534229 ACCAAAGGGACCGATACGGTGCAAGCTGAAACA
1 ACCAAAGGGACCGATACGGTGCAAGCCGAAACA
534262 ACC
1 ACC
534265 CATGAAGACC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.39, C:0.26, G:0.26, T:0.09
Consensus pattern (33 bp):
ACCAAAGGGACCGATACGGTGCAAGCCGAAACA
Found at i:539944 original size:29 final size:32
Alignment explanation
Indices: 539873--539945 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 32
539863 TCCATTGTTT
*
539873 CTCACTGAA-TTTTATTCTCTCTCCTATTTTA
1 CTCACTGAACTTTCATTCTCTCTCCTATTTTA
* *
539904 CTCAC-CATACTTTCATT-TCT-T-CTATTTTG
1 CTCACTGA-ACTTTCATTCTCTCTCCTATTTTA
539933 CTCACTGAACTTT
1 CTCACTGAACTTT
539946 ATAGATTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
29 17 0.49
30 3 0.09
31 9 0.26
32 6 0.17
ACGTcount: A:0.19, C:0.27, G:0.04, T:0.49
Consensus pattern (32 bp):
CTCACTGAACTTTCATTCTCTCTCCTATTTTA
Found at i:544648 original size:13 final size:13
Alignment explanation
Indices: 544630--544655 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
544620 CGGATGCAAC
544630 ACAAAGTAACGAT
1 ACAAAGTAACGAT
544643 ACAAAGTAACGAT
1 ACAAAGTAACGAT
544656 TGCATCGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
ACAAAGTAACGAT
Found at i:547130 original size:22 final size:22
Alignment explanation
Indices: 547102--547146 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
547092 TTATCAAGAG
547102 TGAACTATTAAATATAATGAAA
1 TGAACTATTAAATATAATGAAA
*
547124 TGAACTATTAAATTTAATGAAA
1 TGAACTATTAAATATAATGAAA
547146 T
1 T
547147 TAGTATACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (22 bp):
TGAACTATTAAATATAATGAAA
Found at i:555879 original size:21 final size:21
Alignment explanation
Indices: 555853--555898 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
555843 TTTCCATTTA
555853 GCACCATAAACTAACTAATAT
1 GCACCATAAACTAACTAATAT
555874 GCACCATAAACTAACTAATAT
1 GCACCATAAACTAACTAATAT
555895 GCAC
1 GCAC
555899 TCACTTTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.26, G:0.07, T:0.22
Consensus pattern (21 bp):
GCACCATAAACTAACTAATAT
Found at i:563279 original size:21 final size:21
Alignment explanation
Indices: 563253--563297 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
563243 GATTTCTGGG
* *
563253 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
563274 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
563295 CAA
1 CAA
563298 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:565169 original size:23 final size:23
Alignment explanation
Indices: 565125--565169 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
565115 ATCATTATAT
*
565125 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
565148 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
565170 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:568602 original size:16 final size:16
Alignment explanation
Indices: 568567--568603 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
568557 TGTTTAGGAG
*
568567 GAATTAGAATATGTAA
1 GAATTAGAATATATAA
*
568583 GAATTAGAATATATAT
1 GAATTAGAATATATAA
568599 GAATT
1 GAATT
568604 GAAATTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (16 bp):
GAATTAGAATATATAA
Found at i:568703 original size:14 final size:15
Alignment explanation
Indices: 568684--568717 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
568674 GAATTATCTT
568684 TTTTATATTT-TTTA
1 TTTTATATTTATTTA
568698 TTTTATATTTATTTA
1 TTTTATATTTATTTA
568713 TTTTA
1 TTTTA
568718 CAAATTACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATATTTATTTA
Found at i:569620 original size:37 final size:38
Alignment explanation
Indices: 569535--569622 Score: 142
Period size: 38 Copynumber: 2.3 Consensus size: 38
569525 TTTTCACCCT
*
569535 AAACTCGAACCGACCCGACCCGAATATCACACTTAAAA
1 AAACTCGACCCGACCCGACCCGAATATCACACTTAAAA
*
569573 AAACTCGACCCGACTCGACCCGAATATCACACTT-AAA
1 AAACTCGACCCGACCCGACCCGAATATCACACTTAAAA
*
569610 AAACCCGACCCGA
1 AAACTCGACCCGA
569623 ACAAAATAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
37 15 0.32
38 32 0.68
ACGTcount: A:0.40, C:0.36, G:0.11, T:0.12
Consensus pattern (38 bp):
AAACTCGACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:571195 original size:2 final size:2
Alignment explanation
Indices: 571188--571221 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
571178 TGGAAAATTA
571188 AT AT AT 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 AT AT AT
571222 GAATTTTGTG
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):
AT
Found at i:576121 original size:23 final size:23
Alignment explanation
Indices: 576075--576142 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 23
576065 TAAATACTTA
576075 AAATATAATTTATTGATTTA-AA-TT
1 AAATATAATTT-TT--TTTATAATTT
576099 AATATATAATTTTTTTTATAATTT
1 AA-ATATAATTTTTTTTATAATTT
*
576123 AAATA-AATTATTTATTATAA
1 AAATATAATT-TTTTTTATAA
576143 GTATTCTTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 8 0.21
23 14 0.36
24 8 0.21
25 9 0.23
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (23 bp):
AAATATAATTTTTTTTATAATTT
Found at i:577802 original size:22 final size:21
Alignment explanation
Indices: 577774--577818 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
577764 AAAGTTTTTA
* *
577774 ATTTAAAATGTTATCATATCTT
1 ATTTAAAAAGTTAT-ATAACTT
577796 ATTTAAAAAGTTATATAACTT
1 ATTTAAAAAGTTATATAACTT
577817 AT
1 AT
577819 AATATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (21 bp):
ATTTAAAAAGTTATATAACTT
Found at i:578629 original size:16 final size:16
Alignment explanation
Indices: 578605--578697 Score: 73
Period size: 16 Copynumber: 5.8 Consensus size: 16
578595 CAACTTGAAT
*
578605 CAAAATCAATCCGAAC
1 CAAAATCAACCCGAAC
*
578621 CAAAGTCAACCCGAAC
1 CAAAATCAACCCGAAC
* *
578637 CAAAAGT-AACTCGAAT
1 CAAAA-TCAACCCGAAC
* **
578653 CGAAATCAACTTGAAC
1 CAAAATCAACCCGAAC
578669 CGAAAAT-AACCCGAAC
1 C-AAAATCAACCCGAAC
* *
578685 CGAAAGCAACCCG
1 CAAAATCAACCCG
578698 GATTTAATTT
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
15 4 0.07
16 51 0.85
17 5 0.08
ACGTcount: A:0.46, C:0.30, G:0.13, T:0.11
Consensus pattern (16 bp):
CAAAATCAACCCGAAC
Found at i:578662 original size:32 final size:32
Alignment explanation
Indices: 578606--578697 Score: 89
Period size: 32 Copynumber: 2.8 Consensus size: 32
578596 AACTTGAATC
*
578606 AAAATCAATCCGAACC-AAAGTCAACCCGAACC-
1 AAAAT-AACCCGAACCGAAA-TCAACCCGAACCG
* * **
578638 AAAAGTAACTCGAATCGAAATCAACTTGAACCG
1 AAAA-TAACCCGAACCGAAATCAACCCGAACCG
*
578671 AAAATAACCCGAACCGAAAGCAACCCG
1 AAAATAACCCGAACCGAAATCAACCCG
578698 GATTTAATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
32 39 0.83
33 8 0.17
ACGTcount: A:0.47, C:0.29, G:0.13, T:0.11
Consensus pattern (32 bp):
AAAATAACCCGAACCGAAATCAACCCGAACCG
Found at i:581764 original size:9 final size:9
Alignment explanation
Indices: 581750--581775 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
581740 GAAATCGGTT
581750 AATTAACCG
1 AATTAACCG
581759 AATTAACCG
1 AATTAACCG
581768 AATTAACC
1 AATTAACC
581776 TTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:589161 original size:132 final size:132
Alignment explanation
Indices: 588924--589176 Score: 346
Period size: 132 Copynumber: 1.9 Consensus size: 132
588914 CTTTACTTGC
* *
588924 TTGGTTTCTGGAGCACTAGCCTCCTCTGATGCCTGTGTATTCTCCCTAGGAGGCTTCATAACATT
1 TTGGTTTCTGGAGCACTAGCCTCCTCTGATGCCTGTGTATTCTCCATAGGAAGCTTCATAACATT
* * * * *
588989 CATAGGTAAGTTGGTATCATCTTTATCATAGAAGTCATCAGGAAGATATCCTTTCATTTGCTTAG
66 CATAGGTAACTTGGTATCATCCTTATCAAAGAAGCCATCAGGAAGAGATCCTTTCATTTGCTTAG
589054 TT
131 TT
* * * * * *
589056 TTGGTTTCTGGAGCACTAGCCTGCTTTGGT-TCTGGTTTATTTTCCATAGGAAGCTTCATAACAT
1 TTGGTTTCTGGAGCACTAGCCTCCTCTGATGCCT-GTGTATTCTCCATAGGAAGCTTCATAACAT
* * *
589120 TGATTGGTAACTTGGTTTCATCCTTATCAAAGAAGCCATCAGGAAGAGATCCTTTCA
65 TCATAGGTAACTTGGTATCATCCTTATCAAAGAAGCCATCAGGAAGAGATCCTTTCA
589177 CTTTCTTGCT
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
131 2 0.02
132 102 0.98
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (132 bp):
TTGGTTTCTGGAGCACTAGCCTCCTCTGATGCCTGTGTATTCTCCATAGGAAGCTTCATAACATT
CATAGGTAACTTGGTATCATCCTTATCAAAGAAGCCATCAGGAAGAGATCCTTTCATTTGCTTAG
TT
Found at i:602805 original size:2 final size:2
Alignment explanation
Indices: 602798--602823 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
602788 TTAATATTAA
602798 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
602824 TTTTTGAAAA
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:608732 original size:59 final size:59
Alignment explanation
Indices: 608636--608747 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
608626 TTATGATTTG
* * * *
608636 TGTGATTATGAGATATATGTTTACACATACATATGGTATGTGACCGAAGAGAATGAATA
1 TGTGATTATAAGATATATGATTACACATACATATGGTACGTGACCGAAAAGAATGAATA
* * *
608695 TGTGATTATAAGATCA-ATGATTACACGTACATTTGGTACGTGACTGAAAAGAA
1 TGTGATTATAAGAT-ATATGATTACACATACATATGGTACGTGACCGAAAAGAA
608748 AAGATATATG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 44 0.98
60 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (59 bp):
TGTGATTATAAGATATATGATTACACATACATATGGTACGTGACCGAAAAGAATGAATA
Found at i:608959 original size:31 final size:31
Alignment explanation
Indices: 608866--608948 Score: 148
Period size: 31 Copynumber: 2.7 Consensus size: 31
608856 AAGGTCGAGG
*
608866 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
608897 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
608928 GTTTACCTAGGTTCTTCGGGA
1 GTTTACCTATGTTCTTCGGGA
608949 TCTATAGACT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:610419 original size:24 final size:20
Alignment explanation
Indices: 610362--610402 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
610352 TTCCCATTGA
*
610362 AGTGCATCGGTGCATTCTTT
1 AGTGCATCGATGCATTCTTT
610382 AGTGCATCGATGCATTCTTT
1 AGTGCATCGATGCATTCTTT
610402 A
1 A
610403 ACATGTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTT
Found at i:613195 original size:15 final size:16
Alignment explanation
Indices: 613175--613207 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
613165 CAAAGAGGTT
613175 TTATATTT-AATTTAA
1 TTATATTTGAATTTAA
*
613190 TTATATTTGATTTTAA
1 TTATATTTGAATTTAA
613206 TT
1 TT
613208 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TTATATTTGAATTTAA
Found at i:613250 original size:13 final size:12
Alignment explanation
Indices: 613202--613274 Score: 51
Period size: 14 Copynumber: 5.8 Consensus size: 12
613192 ATATTTGATT
613202 TTAATTTTAATA
1 TTAATTTTAATA
613214 TTAATTTTTTAA-A
1 TTAA--TTTTAATA
* *
613227 -TAAATTAAATA
1 TTAATTTTAATA
613238 TTAATTTTTAATA
1 TTAA-TTTTAATA
*
613251 TTATATTATAGATA
1 TTA-ATTTTA-ATA
613265 TTTAATTTTA
1 -TTAATTTTA
613275 TATCATATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
10 4 0.09
11 1 0.02
12 10 0.21
13 14 0.30
14 15 0.32
15 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (12 bp):
TTAATTTTAATA
Found at i:613835 original size:31 final size:31
Alignment explanation
Indices: 613776--613836 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
613766 GTAGTTTTAT
* * * **
613776 AAATTATTTAAATTTTAGTATTGTAAAACTA
1 AAATTATTTAAATCTCAATATTACAAAACTA
613807 AAATTATTTAAATCTCAATATTACAAAACT
1 AAATTATTTAAATCTCAATATTACAAAACT
613837 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (31 bp):
AAATTATTTAAATCTCAATATTACAAAACTA
Found at i:621043 original size:13 final size:13
Alignment explanation
Indices: 621025--621050 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
621015 TGTGTCTTAT
621025 CTCTCTTTTTTTC
1 CTCTCTTTTTTTC
621038 CTCTCTTTTTTTC
1 CTCTCTTTTTTTC
621051 TTAATGCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
CTCTCTTTTTTTC
Found at i:621113 original size:17 final size:17
Alignment explanation
Indices: 621091--621123 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
621081 TGTTCAGTCA
621091 ATGTTTTTCACATGGTC
1 ATGTTTTTCACATGGTC
621108 ATGTTTTTCACATGGT
1 ATGTTTTTCACATGGT
621124 TTTAGAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.48
Consensus pattern (17 bp):
ATGTTTTTCACATGGTC
Found at i:631368 original size:15 final size:15
Alignment explanation
Indices: 631348--631379 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
631338 CCCCCAACGA
631348 AGCTCCTCCGCCGCC
1 AGCTCCTCCGCCGCC
631363 AGCTCCTCCGCCGCC
1 AGCTCCTCCGCCGCC
631378 AG
1 AG
631380 TAGTCATGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.56, G:0.22, T:0.12
Consensus pattern (15 bp):
AGCTCCTCCGCCGCC
Found at i:632267 original size:2 final size:2
Alignment explanation
Indices: 632260--632347 Score: 79
Period size: 2 Copynumber: 43.5 Consensus size: 2
632250 TTTCAAAAAC
* * * * * *
632260 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TG TG TG TG TT TCA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* *
632303 AA AA CTA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
632345 TA T
1 TA T
632348 CAAAACATTT
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
1 1 0.01
2 76 0.97
3 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (2 bp):
TA
Found at i:632392 original size:34 final size:35
Alignment explanation
Indices: 632331--632416 Score: 129
Period size: 34 Copynumber: 2.5 Consensus size: 35
632321 TATATATATA
*
632331 TATATATATATATATATCAAAACATTTTTAAAAAC
1 TATATATATATATATATCAAAACATTTTCAAAAAC
* * *
632366 TATATTTATATAT-TTTCAAAATATTTTCAAAAAC
1 TATATATATATATATATCAAAACATTTTCAAAAAC
632400 TATATATATATATATAT
1 TATATATATATATATAT
632417 ATATATATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
34 30 0.68
35 14 0.32
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (35 bp):
TATATATATATATATATCAAAACATTTTCAAAAAC
Found at i:632407 original size:2 final size:2
Alignment explanation
Indices: 632400--632436 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
632390 TTTCAAAAAC
632400 TA 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 TA T
632437 TCAAATGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:632413 original size:81 final size:90
Alignment explanation
Indices: 632313--632508 Score: 292
Period size: 89 Copynumber: 2.2 Consensus size: 90
632303 AAAACTATAT
** *
632313 TATATATATATATATATATATATATATATATATATCAAAACATTTTTAAAAAC-TATATT-TATA
1 TATATATATATATATATATATATATATATATATATC--AATGTTTTCAAAAACATATATTATATA
632376 TATTTTCAAAATATTTTC-AAAAACTA
64 TATTTTCAAAATATTTTCAAAAAACTA
632402 TATATATATATATATATATATATATATATATATATTCAAATGTTTTCAAAAACTATATATTATAT
1 TATATATATATATATATATATATATATATATATA-TC-AATGTTTTCAAAAAC-ATATATTATAT
632467 ATATTTTCAAAATATTTTCAAAAAACTA
63 ATATTTTCAAAATATTTTCAAAAAACTA
632495 TATAT-TATATATAT
1 TATATATATATATAT
632509 TTTCTCAAAA
Statistics
Matches: 99, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
89 47 0.47
90 2 0.02
91 6 0.06
92 31 0.31
93 13 0.13
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (90 bp):
TATATATATATATATATATATATATATATATATATCAATGTTTTCAAAAACATATATTATATATA
TTTTCAAAATATTTTCAAAAAACTA
Found at i:632529 original size:38 final size:38
Alignment explanation
Indices: 632416--632536 Score: 149
Period size: 38 Copynumber: 3.1 Consensus size: 38
632406 TATATATATA
*
632416 TATATATATATATATATATATTC-AAATGTTTTCAAAAAC
1 TATATAT-TATATATAT-TTTTCAAAATGTTTTCAAAAAC
*
632455 TATATATTATATATA-TTTTCAAAATATTTTCAAAAAAC
1 TATATATTATATATATTTTTCAAAATGTTTTC-AAAAAC
*
632493 TATATATTATATATATTTTCTCAAAACGTTTT-AAAAATC
1 TATATATTATATATATTTT-TCAAAATGTTTTCAAAAA-C
632532 TATAT
1 TATAT
632537 CAAAATTTTA
Statistics
Matches: 73, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
36 4 0.05
37 9 0.12
38 34 0.47
39 16 0.22
40 10 0.14
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (38 bp):
TATATATTATATATATTTTTCAAAATGTTTTCAAAAAC
Found at i:637990 original size:60 final size:59
Alignment explanation
Indices: 637910--638085 Score: 155
Period size: 60 Copynumber: 2.9 Consensus size: 59
637900 CGTCCCCAAT
* *
637910 CTATGA-CTCTCATT-TAAAATTGGCCCCTAAACTTTTAAACATTTTAATTTTATCCTTAAA
1 CTATGATCT-TCATTCT-AAATTGG-CCCTAAACTTTTGAATATTTTAATTTTATCCTTAAA
* * * * *
637970 CTATGAT-TATCATTCTAAATTAGTCCTCAAACTTTTGAATA-TTTCATTTCCATCCCTAAA
1 CTATGATCT-TCATTCTAAATTGGCCCT-AAACTTTTGAATATTTTAATTT-TATCCTTAAA
* * *
638030 TTGTGATCTTCATTCTAAATTGGTCCC-AAACTTTTTGAATATTTCAATTTTATCCT
1 CTATGATCTTCATTCTAAATTGG-CCCTAAAC-TTTTGAATATTTTAATTTTATCCT
638086 AAATTAAATG
Statistics
Matches: 92, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
59 14 0.15
60 68 0.74
61 10 0.11
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.44
Consensus pattern (59 bp):
CTATGATCTTCATTCTAAATTGGCCCTAAACTTTTGAATATTTTAATTTTATCCTTAAA
Found at i:642610 original size:9 final size:9
Alignment explanation
Indices: 642585--642618 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
642575 CGGTTCTTCT
*
642585 GACCGGTCG
1 GACCGGTTG
642594 GACCGGTTG
1 GACCGGTTG
642603 GACCGGTTG
1 GACCGGTTG
*
642612 AACCGGT
1 GACCGGT
642619 GAACCAGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.15, C:0.26, G:0.41, T:0.18
Consensus pattern (9 bp):
GACCGGTTG
Found at i:644785 original size:29 final size:30
Alignment explanation
Indices: 644752--644809 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
644742 GCTTTGGTTC
*
644752 CAGTTTAGTGCCTAACGTTT-ATTTCGTTT
1 CAGTTTAGTGCCTAACGTTTCATTCCGTTT
*
644781 CAGTTTGGTGCCTAACGTTTCATTCCGTT
1 CAGTTTAGTGCCTAACGTTTCATTCCGTT
644810 ACTCATTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.45
Consensus pattern (30 bp):
CAGTTTAGTGCCTAACGTTTCATTCCGTTT
Found at i:644912 original size:14 final size:16
Alignment explanation
Indices: 644883--644929 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
644873 CATGGTAATT
644883 TTAAAAATATTTAAAA
1 TTAAAAATATTTAAAA
644899 TTAAAAA-A-TTAAAA
1 TTAAAAATATTTAAAA
* *
644913 TTATATATATATTAAAA
1 TTAAAAATAT-TTAAAA
644930 AGAAACCGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 11 0.42
15 2 0.08
16 7 0.27
17 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAAATATTTAAAA
Found at i:663544 original size:21 final size:21
Alignment explanation
Indices: 663527--663615 Score: 178
Period size: 21 Copynumber: 4.2 Consensus size: 21
663517 AATGAGAAGT
663527 AGAAGGATATTGAAGAGAGAG
1 AGAAGGATATTGAAGAGAGAG
663548 AGAAGGATATTGAAGAGAGAG
1 AGAAGGATATTGAAGAGAGAG
663569 AGAAGGATATTGAAGAGAGAG
1 AGAAGGATATTGAAGAGAGAG
663590 AGAAGGATATTGAAGAGAGAG
1 AGAAGGATATTGAAGAGAGAG
663611 AGAAG
1 AGAAG
663616 AATGGGAAGG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 68 1.00
ACGTcount: A:0.48, C:0.00, G:0.38, T:0.13
Consensus pattern (21 bp):
AGAAGGATATTGAAGAGAGAG
Found at i:665489 original size:4 final size:4
Alignment explanation
Indices: 665456--665495 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
665446 GCATGTACGC
* * *
665456 ATGT ATGC ATGT ATGC ATGT ATGC ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
665496 GGGTTGCATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.42
Consensus pattern (4 bp):
ATGT
Found at i:665495 original size:8 final size:8
Alignment explanation
Indices: 665444--665494 Score: 84
Period size: 8 Copynumber: 6.4 Consensus size: 8
665434 TTTGCTTTGC
665444 ATGCATGT
1 ATGCATGT
*
665452 ACGCATGT
1 ATGCATGT
665460 ATGCATGT
1 ATGCATGT
665468 ATGCATGT
1 ATGCATGT
665476 ATGCATGT
1 ATGCATGT
*
665484 ATGTATGT
1 ATGCATGT
665492 ATG
1 ATG
665495 TGGGTTGCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 40 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.37
Consensus pattern (8 bp):
ATGCATGT
Found at i:675655 original size:21 final size:21
Alignment explanation
Indices: 675629--675671 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
675619 TTTCTGGGTT
* *
675629 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
675650 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
675671 A
1 A
675672 CAAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:675747 original size:68 final size:69
Alignment explanation
Indices: 675651--675804 Score: 202
Period size: 69 Copynumber: 2.2 Consensus size: 69
675641 ACCCATTCAA
* * *
675651 GGGGAACCGATACCCCTTCAACAAATATG-ATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
*
675715 GGGG
66 AGGG
* ** * * *
675719 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGACTGCTTGAGGGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
675784 AGGG
66 AGGG
*
675788 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
675805 ATGAGAAAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
68 25 0.34
69 49 0.66
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
AGGG
Found at i:676141 original size:29 final size:29
Alignment explanation
Indices: 676107--676178 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
676097 CATATTATGA
** *
676107 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAACGTAT
*
676136 TACATGACATGAATTCATATTATACGTAT
1 TACATGACATGAATTCATATTAAACGTAT
*
676165 TACTTGACATGAAT
1 TACATGACATGAAT
676179 ATGCAGAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAACGTAT
Found at i:676235 original size:30 final size:29
Alignment explanation
Indices: 676192--676269 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
676182 CAGAAAAAGT
*
676192 TATATGCACTATGTGATAAAGGTATGTAAA
1 TATATGC-CTATGTGATAAAGGTATGGAAA
* *
676222 TGATATGCCTATGTGTTAAAGTTATGGAAA
1 T-ATATGCCTATGTGATAAAGGTATGGAAA
* *
676252 TACTATGTCTACGTGATA
1 TA-TATGCCTATGTGATA
676270 TGAACTACGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.36
Consensus pattern (29 bp):
TATATGCCTATGTGATAAAGGTATGGAAA
Found at i:676544 original size:22 final size:22
Alignment explanation
Indices: 676470--676536 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
676460 TTATGGACAT
676470 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
676492 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
676514 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
676536 A
1 A
676537 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:682598 original size:21 final size:21
Alignment explanation
Indices: 682572--682614 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
682562 TTTCTGGGTT
* *
682572 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
682593 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
682614 A
1 A
682615 CAAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:682665 original size:67 final size:69
Alignment explanation
Indices: 682594--682745 Score: 200
Period size: 68 Copynumber: 2.2 Consensus size: 69
682584 ACCCATTCAA
* * * *
682594 GGGGAACCGATACCCCTTCAACAAATATG-ATTTCCAGAATGCTAGAGGGGAATCGGTACCCC-C
1 GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCTA
682657 AGGG
66 AGGG
* ** * *
682661 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGACTGCTTGAGGGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCTA
682726 AGGG
66 AGGG
*
682730 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
682746 ATGAGAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
67 25 0.34
68 29 0.40
69 19 0.26
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCAACAAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCTA
AGGG
Found at i:683082 original size:29 final size:29
Alignment explanation
Indices: 683048--683119 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
683038 CATATTATGA
** *
683048 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAACGTAT
*
683077 TACATGACATGAATTCATATTATACGTAT
1 TACATGACATGAATTCATATTAAACGTAT
*
683106 TACTTGACATGAAT
1 TACATGACATGAAT
683120 ATGCAGAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAACGTAT
Found at i:683176 original size:30 final size:29
Alignment explanation
Indices: 683133--683210 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
683123 CAGAAAAAGT
*
683133 TATATGCACTATGTGATAAAGGTATGTAAA
1 TATATGC-CTATGTGATAAAGGTATGGAAA
* *
683163 TGATATGCCTATGTGTTAAAGTTATGGAAA
1 T-ATATGCCTATGTGATAAAGGTATGGAAA
* *
683193 TACTATGTCTACGTGATA
1 TA-TATGCCTATGTGATA
683211 TGAACTACGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.36
Consensus pattern (29 bp):
TATATGCCTATGTGATAAAGGTATGGAAA
Found at i:683487 original size:22 final size:22
Alignment explanation
Indices: 683413--683479 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
683403 TTATGGACAT
683413 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
683435 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
683457 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
683479 A
1 A
683480 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:685892 original size:15 final size:16
Alignment explanation
Indices: 685860--685892 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
685850 AAAATCTTTC
*
685860 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTAGATT
685876 TTTCCCG-TCTAGATT
1 TTTCCCGTTCTAGATT
685891 TT
1 TT
685893 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:687116 original size:16 final size:16
Alignment explanation
Indices: 687095--687170 Score: 152
Period size: 16 Copynumber: 4.8 Consensus size: 16
687085 TCAACCGGCT
687095 GCCATCTAGAATGGCA
1 GCCATCTAGAATGGCA
687111 GCCATCTAGAATGGCA
1 GCCATCTAGAATGGCA
687127 GCCATCTAGAATGGCA
1 GCCATCTAGAATGGCA
687143 GCCATCTAGAATGGCA
1 GCCATCTAGAATGGCA
687159 GCCATCTAGAAT
1 GCCATCTAGAAT
687171 TTCAACAGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 60 1.00
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.20
Consensus pattern (16 bp):
GCCATCTAGAATGGCA
Found at i:689507 original size:13 final size:14
Alignment explanation
Indices: 689478--689703 Score: 59
Period size: 13 Copynumber: 16.4 Consensus size: 14
689468 ATTAAAAAAA
*
689478 TATAATATATACA-
1 TATAATATATAAAT
689491 TATAATATA-AAAT
1 TATAATATATAAAT
*
689504 TAT-ATATA-AACT
1 TATAATATATAAAT
*
689516 ATATTTATATTATAAAT
1 -TA-TAATA-TATAAAT
689533 TAT-ATATATAAAT
1 TATAATATATAAAT
* * * *
689546 TATATTTATGTGAAC
1 TATA-ATATATAAAT
*
689561 TAT-ATATATAAAC
1 TATAATATATAAAT
*
689574 TAT-GTATATAAAAT
1 TATAATATAT-AAAT
689588 TATAACTATAT---T
1 TATAA-TATATAAAT
689600 TAT-AT-TATAAACT
1 TATAATATATAAA-T
**
689613 ATATAATTATTATAAGC
1 -TATAA-TA-TATAAAT
689630 TAT-ATATATAAAT
1 TATAATATATAAAT
** * * *
689643 TATGTTTATGTGAAC
1 TAT-AATATATAAAT
689658 TAT-ATATATAAAT
1 TATAATATATAAAT
* *
689671 TAT-GTATATAAAC
1 TATAATATATAAAT
* *
689684 TATATATGTATAAAC
1 TATA-ATATATAAAT
689699 TATAA
1 TATAA
689704 AAAGTATATA
Statistics
Matches: 160, Mismatches: 29, Indels: 47
0.68 0.12 0.20
Matches are distributed among these distances:
9 3 0.02
10 1 0.01
11 1 0.01
12 14 0.09
13 68 0.43
14 16 0.10
15 36 0.22
16 13 0.08
17 3 0.02
18 5 0.03
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (14 bp):
TATAATATATAAAT
Found at i:689542 original size:31 final size:30
Alignment explanation
Indices: 689491--689554 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
689481 AATATATACA
689491 TATAATATAAAATTATATATAAACTATATT
1 TATAATATAAAATTATATATAAACTATATT
* * *
689521 TATATTATAAATTATATATATAAATTATATT
1 TATAATATAAAAT-TATATATAAACTATATT
689552 TAT
1 TAT
689555 GTGAACTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (30 bp):
TATAATATAAAATTATATATAAACTATATT
Found at i:689592 original size:97 final size:97
Alignment explanation
Indices: 689501--689682 Score: 287
Period size: 97 Copynumber: 1.9 Consensus size: 97
689491 TATAATATAA
* *
689501 AATTATA-TATAAACTATAT-TTATATTATAAATTATATATATAAATTATATTTATGTGAACTAT
1 AATTATATTATAAACTATATAAT-TATTATAAACTATATATATAAATTATATTTATGTGAACTAT
689564 ATATATAAACTATGTATATAAAATTATAACTAT
65 ATATATAAACTATGTATATAAAATTATAACTAT
* * *
689597 ATTTATATTATAAACTATATAATTATTATAAGCTATATATATAAATTATGTTTATGTGAACTATA
1 AATTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTATGTGAACTATA
*
689662 TATATAAATTATGTATATAAA
66 TATATAAACTATGTATATAAA
689683 CTATATATGT
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
96 6 0.08
97 71 0.91
98 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (97 bp):
AATTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTATGTGAACTATA
TATATAAACTATGTATATAAAATTATAACTAT
Found at i:689644 original size:20 final size:20
Alignment explanation
Indices: 689508--689645 Score: 87
Period size: 18 Copynumber: 7.2 Consensus size: 20
689498 TAAAATTATA
*
689508 TATAAACTATAT-T-TATAT
1 TATAAACTATATATATAAAT
*
689526 TATAAATTATATATATAAAT
1 TATAAACTATATATATAAAT
** * *
689546 TAT-ATTTATGTGA-ACTATAT
1 TATAAACTATAT-ATA-TAAAT
*
689566 ATATAAACTATGTATATAAAAT
1 -TATAAACTATATATAT-AAAT
*
689588 TAT-AACTATAT-T-TATAT
1 TATAAACTATATATATAAAT
*
689605 TATAAACTATATA-AT-TAT
1 TATAAACTATATATATAAAT
*
689623 TATAAGCTATATATATAAAT
1 TATAAACTATATATATAAAT
689643 TAT
1 TAT
689646 GTTTATGTGA
Statistics
Matches: 95, Mismatches: 12, Indels: 24
0.73 0.09 0.18
Matches are distributed among these distances:
17 6 0.06
18 35 0.37
19 12 0.13
20 24 0.25
21 8 0.08
22 10 0.11
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (20 bp):
TATAAACTATATATATAAAT
Found at i:689684 original size:26 final size:27
Alignment explanation
Indices: 689623--689690 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 27
689613 ATATAATTAT
*
689623 TATAAGCTATATATATAAATTATGTTTA
1 TATAAACTATATATATAAATTATG-TTA
* *
689651 TGTGAACTATATATATAAATTATG-TA
1 TATAAACTATATATATAAATTATGTTA
689677 TATAAACTATATAT
1 TATAAACTATATAT
689691 GTATAAACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 14 0.40
28 21 0.60
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (27 bp):
TATAAACTATATATATAAATTATGTTA
Found at i:689735 original size:97 final size:99
Alignment explanation
Indices: 689523--689771 Score: 234
Period size: 97 Copynumber: 2.6 Consensus size: 99
689513 ACTATATTTA
*
689523 TATTATAAATTA-TA-TATATAAATTATATTTATGTGAACTATATATATAAACTATGTATATAAA
1 TATTATAAAATATTATTATATAAATTATATTTATGTGAACTATATATATAAACTATGTATATAAA
** * *
689586 ATTATAACTATATTTATATTATAAACTATATAAT
66 ATTATAACTATATAAATATTAAAAACTATATAAG
** * *
689620 TATTATAAGCTA-TA-TATATAAATTATGTTTATGTGAACTATATATATAAATTATGTATAT-AA
1 TATTATAAAATATTATTATATAAATTATATTTATGTGAACTATATATATAAACTATGTATATAAA
* * *
689682 ACTATATA-TGTATAAACTA-TAAAAAGTATAT-AG
66 ATTATA-ACTATATAAA-TATTAAAAACTATATAAG
*
689715 T-TTATAAAATATTATT-TAT-ATTTATATTAATATAGTGTATA-TATATATATAAACTAT
1 TATTATAAAATATTATTATATAAATTATATT--TAT-GTG-A-ACTATATATATAAACTAT
689772 ATATGTATAA
Statistics
Matches: 127, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
94 15 0.12
95 7 0.06
96 26 0.20
97 62 0.49
98 16 0.13
99 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (99 bp):
TATTATAAAATATTATTATATAAATTATATTTATGTGAACTATATATATAAACTATGTATATAAA
ATTATAACTATATAAATATTAAAAACTATATAAG
Found at i:689772 original size:15 final size:15
Alignment explanation
Indices: 689754--689789 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
689744 ATATAGTGTA
689754 TATATATATATAAAC
1 TATATATATATAAAC
*
689769 TATATATGTATAAAC
1 TATATATATATAAAC
689784 TATATA
1 TATATA
689790 AAACATATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:689958 original size:2 final size:2
Alignment explanation
Indices: 689953--690006 Score: 63
Period size: 2 Copynumber: 26.0 Consensus size: 2
689943 TTATATAGTT
** *
689953 TA TA TA TA TA TA TA TA GG TA TA TA TA TA TA TA TA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
689996 TA TA TA CTA TA
1 TA TA TA -TA TA
690007 CATGGTTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
2 41 0.93
3 3 0.07
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:690006 original size:20 final size:20
Alignment explanation
Indices: 689939--690022 Score: 91
Period size: 20 Copynumber: 4.2 Consensus size: 20
689929 ATAAGTAATT
*
689939 TACTTTATATAGTTTATATA
1 TACTATATATAGTTTATATA
689959 TA-TATATATAGGTATATATATA
1 TACTATATATA-GT-T-TATATA
689981 TA-TATATATAGTTTATATA
1 TACTATATATAGTTTATATA
* * *
690000 TACTATACATGGTTTATACA
1 TACTATATATAGTTTATATA
690020 TAC
1 TAC
690023 ATTAAGGTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
19 15 0.27
20 22 0.39
21 3 0.05
22 16 0.29
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (20 bp):
TACTATATATAGTTTATATA
Found at i:690445 original size:2 final size:2
Alignment explanation
Indices: 690438--690488 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
690428 CACTTGAATA
* * *
690438 AT AT AT AT AT AT AT AT AT AT AT A- AGT GT AT AC AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
690480 AT AT AT AT A
1 AT AT AT AT A
690489 ATTAAACATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:690901 original size:19 final size:19
Alignment explanation
Indices: 690879--690922 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
690869 TTGAGAATAT
690879 AGGGAAATT-AGGAATTTAG
1 AGGGAAATTGA-GAATTTAG
690898 AGGGAAATTGAGAATTTAG
1 AGGGAAATTGAGAATTTAG
690917 AGGGAA
1 AGGGAA
690923 TAGAAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.34, T:0.23
Consensus pattern (19 bp):
AGGGAAATTGAGAATTTAG
Found at i:690933 original size:19 final size:19
Alignment explanation
Indices: 690891--690929 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
690881 GGAAATTAGG
* *
690891 AATTTAGAGGGAAATTGAG
1 AATTTAGAGGGAAATAGAA
690910 AATTTAGAGGG-AATAGAA
1 AATTTAGAGGGAAATAGAA
690928 AA
1 AA
690930 ATTTGGGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (19 bp):
AATTTAGAGGGAAATAGAA
Found at i:691149 original size:8 final size:9
Alignment explanation
Indices: 691124--691156 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
691114 GCATAAACTA
*
691124 TATATAAAC
1 TATATAAAG
691133 TATATAAAG
1 TATATAAAG
691142 TA-ATAAAG
1 TATATAAAG
691150 TATATAA
1 TATATAA
691157 TTTATTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (9 bp):
TATATAAAG
Found at i:691485 original size:25 final size:22
Alignment explanation
Indices: 691455--691507 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
691445 ATTAATAATG
691455 TTTTATCTAATTTACATTTAAATAA
1 TTTTAT-TAATTT-CA-TTAAATAA
*
691480 TTTTATTAATTTTATTAAATAA
1 TTTTATTAATTTCATTAAATAA
691502 TTTTAT
1 TTTTAT
691508 ATTATAGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 14 0.52
23 1 0.04
24 6 0.22
25 6 0.22
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATTAATTTCATTAAATAA
Found at i:706836 original size:57 final size:57
Alignment explanation
Indices: 706768--706913 Score: 159
Period size: 58 Copynumber: 2.5 Consensus size: 57
706758 GTGAATATGA
* * * *
706768 TCTATGAGAATAAATGATAAGTTGAATAATGCTATATGAAATGCTATGAGTA-ATTGT
1 TCTATGTGAATAAATGATAATTTGAATAATGCTACATGAAATACTATGAGTACA-TGT
* ** * *
706825 TCTATGTGAATAAATAATAAATTTGTGTAATTCTACGTGAAATACTATGAGTACATGT
1 TCTATGTGAATAAATGAT-AATTTGAATAATGCTACATGAAATACTATGAGTACATGT
* * *
706883 TTTATGTGAGTAAATGATACTTTGAATAATG
1 TCTATGTGAATAAATGATAATTTGAATAATG
706914 TAATGTGAAA
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
57 25 0.35
58 45 0.63
59 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (57 bp):
TCTATGTGAATAAATGATAATTTGAATAATGCTACATGAAATACTATGAGTACATGT
Found at i:707055 original size:24 final size:23
Alignment explanation
Indices: 706997--707060 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
706987 ATATCGAGGG
**
706997 TTCTACGCGGTCCTTCATGATAA
1 TTCTACGCGGTCCTTCGGGATAA
* * *
707020 TTCTATGTGGTCATTCGGGATAAA
1 TTCTACGCGGTCCTTCGGGAT-AA
707044 TTCTACGCGGTCCTTCG
1 TTCTACGCGGTCCTTCG
707061 AGACAAATCT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 16 0.50
24 16 0.50
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGATAA
Found at i:707068 original size:24 final size:23
Alignment explanation
Indices: 706997--707068 Score: 65
Period size: 24 Copynumber: 3.0 Consensus size: 23
706987 ATATCGAGGG
*
706997 TTCTACGCGGTCCTTC-ATGATAA
1 TTCTACGCGGTCCTTCGA-GAAAA
* * * *
707020 TTCTATGTGGTCATTCGGGATAAA
1 TTCTACGCGGTCCTTCGAGA-AAA
707044 TTCTACGCGGTCCTTCGAGACAAA
1 TTCTACGCGGTCCTTCGAGA-AAA
707068 T
1 T
707069 CTATTTGGCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
23 15 0.41
24 22 0.59
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGAGAAAA
Found at i:707072 original size:47 final size:47
Alignment explanation
Indices: 706997--707098 Score: 120
Period size: 47 Copynumber: 2.2 Consensus size: 47
706987 ATATCGAGGG
* * *
706997 TTCTACGCGGTCCTTCATGATAATTCTATGTGGTCA-TTCGG-GATAAA
1 TTCTACGCGGTCCTTCATGACAAATCTATGTGG-CACTTCGGTG-CAAA
*
707044 TTCTACGCGGTCCTTCGA-GACAAATCTATTTGGCACTTCGGTGCAAA
1 TTCTACGCGGTCCTTC-ATGACAAATCTATGTGGCACTTCGGTGCAAA
707091 TTCTACGC
1 TTCTACGC
707099 AGCAATTTCG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
46 2 0.04
47 44 0.92
48 2 0.04
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.33
Consensus pattern (47 bp):
TTCTACGCGGTCCTTCATGACAAATCTATGTGGCACTTCGGTGCAAA
Found at i:712900 original size:22 final size:22
Alignment explanation
Indices: 712872--712932 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 22
712862 TATTTTTTTA
712872 TATATTAACTTAAAAAACATTT
1 TATATTAACTTAAAAAACATTT
* *
712894 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA--AAAAACATTT
712918 TATTATTAACTTAAA
1 TA-TATTAACTTAAA
712933 TTAAAGATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 12 0.35
23 2 0.06
24 10 0.29
25 10 0.29
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (22 bp):
TATATTAACTTAAAAAACATTT
Found at i:712909 original size:25 final size:25
Alignment explanation
Indices: 712867--712930 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 25
712857 CATAATATTT
712867 TTTTATATATTAACTTA--AAAAACA
1 TTTTAT-TATTAACTTATTAAAAACA
* *
712891 TTTTA-TATTAACTTATTAAATATA
1 TTTTATTATTAACTTATTAAAAACA
712915 TTTTATTATTAACTTA
1 TTTTATTATTAACTTA
712931 AATTAAAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 10 0.29
24 15 0.43
25 10 0.29
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTTATTATTAACTTATTAAAAACA
Found at i:713136 original size:31 final size:31
Alignment explanation
Indices: 713101--713171 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
713091 TCGTGATGAT
*
713101 CACATCTTAATTAAATAAAAACGAAAGTAAC
1 CACATCTTAATTAAACAAAAACGAAAGTAAC
* *
713132 CACATCTTAATTAAACAGAAACGAAAGTGAC
1 CACATCTTAATTAAACAAAAACGAAAGTAAC
*
713163 CATATCTTA
1 CACATCTTA
713172 TGTTTTTTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.49, C:0.18, G:0.08, T:0.24
Consensus pattern (31 bp):
CACATCTTAATTAAACAAAAACGAAAGTAAC
Found at i:714455 original size:36 final size:36
Alignment explanation
Indices: 714414--714489 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
714404 ATTTTCGGGA
*
714414 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
714450 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
714486 TTTT
1 TTTT
714490 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:714932 original size:15 final size:15
Alignment explanation
Indices: 714912--714941 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
714902 TATCACAATC
714912 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
714927 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
714942 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:719376 original size:36 final size:36
Alignment explanation
Indices: 719335--719410 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
719325 ATTTTCGGGA
*
719335 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
719371 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
719407 TTTT
1 TTTT
719411 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:720859 original size:24 final size:24
Alignment explanation
Indices: 720813--720861 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
720803 AGTGGATTGA
* * * *
720813 TCTGCATCTTCTTTTTCATCCTCT
1 TCTGCAACTTCTTGTACAGCCTCT
720837 TCTGCAACTTCTTGTACAGCCTCT
1 TCTGCAACTTCTTGTACAGCCTCT
720861 T
1 T
720862 GTTTCTGATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.12, C:0.33, G:0.08, T:0.47
Consensus pattern (24 bp):
TCTGCAACTTCTTGTACAGCCTCT
Found at i:722209 original size:17 final size:18
Alignment explanation
Indices: 722187--722224 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
722177 TTTATGTTTA
722187 AATTTTATAT-TAAATAT
1 AATTTTATATATAAATAT
*
722204 AATTTTATATATATATAT
1 AATTTTATATATAAATAT
722222 AAT
1 AAT
722225 AAAATTTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTTATATATAAATAT
Found at i:723839 original size:35 final size:35
Alignment explanation
Indices: 723793--723868 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
723783 AAAACAGTCA
* *
723793 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
723828 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
723863 TCAATT
1 TCAATT
723869 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Done.