Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008284.1 Hibiscus syriacus cultivar Beakdansim tig00110946_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: 665325
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:211171 original size:36 final size:36
Alignment explanation
Indices: 211119--211200 Score: 119
Period size: 36 Copynumber: 2.3 Consensus size: 36
211109 CAAGCGGTCA
*
211119 ATGAAGATGAAGCTGACGATGAAGATGACGATGATG
1 ATGAAGATGAAGCTGACGATGAAGATGACGACGATG
* *
211155 ATGACGATGAAGCTGACGATGAAGATGATGACGATG
1 ATGAAGATGAAGCTGACGATGAAGATGACGACGATG
* *
211191 ACGATGATGA
1 ATGAAGATGA
211201 TGATGATCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.38, C:0.10, G:0.33, T:0.20
Consensus pattern (36 bp):
ATGAAGATGAAGCTGACGATGAAGATGACGACGATG
Found at i:214979 original size:25 final size:25
Alignment explanation
Indices: 214951--215015 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
214941 TTATCATTAA
214951 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
214976 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
215001 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
215016 TCTTTTGAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:215406 original size:22 final size:22
Alignment explanation
Indices: 215357--215428 Score: 99
Period size: 23 Copynumber: 3.2 Consensus size: 22
215347 TATGTAAAAA
* *
215357 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTATCG-TT
215380 ATATAATGTAATAGGTATCGTT
1 ATATAATGTAATAGGTATCGTT
*
215402 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTA-TCGTT
215425 ATAT
1 ATAT
215429 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 19 0.42
23 26 0.58
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (22 bp):
ATATAATGTAATAGGTATCGTT
Found at i:215807 original size:21 final size:21
Alignment explanation
Indices: 215783--215853 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
215773 AAAAAATATG
215783 ATGTAATAGGTAGCGCTTATA
1 ATGTAATAGGTAGCGCTTATA
*
215804 ATGTAATAGGTAGCGTTTATATA
1 ATGTAATAGGTAGCG-CT-TATA
* *
215827 ATGTAATAGGTAGTGGTTATA
1 ATGTAATAGGTAGCGCTTATA
*
215848 TTGTAA
1 ATGTAA
215854 AGTATCTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
21 24 0.55
22 2 0.05
23 18 0.41
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (21 bp):
ATGTAATAGGTAGCGCTTATA
Found at i:215830 original size:23 final size:22
Alignment explanation
Indices: 215778--215848 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
215768 TAGGTAAAAA
* *
215778 ATATGATGTAATAGGTAGCGCT
1 ATATAATGTAATAGGTAGCGTT
215800 -TATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCG-TT
*
215822 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAG-CGTT
215845 ATAT
1 ATAT
215849 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 23 0.53
24 1 0.02
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (22 bp):
ATATAATGTAATAGGTAGCGTT
Found at i:217159 original size:62 final size:62
Alignment explanation
Indices: 217091--217209 Score: 193
Period size: 62 Copynumber: 1.9 Consensus size: 62
217081 CGATTTAACT
*
217091 TTTAATATTTAAAATAATAATTAAGCCGACAACAGATATATTAAAAATTAATTACTATAATA
1 TTTAATAATTAAAATAATAATTAAGCCGACAACAGATATATTAAAAATTAATTACTATAATA
** * *
217153 TTTAATAATTAAAATAATAATTAATTCGACAACAGATATTTTAAAATTTAATTACTA
1 TTTAATAATTAAAATAATAATTAAGCCGACAACAGATATATTAAAAATTAATTACTA
217210 CTATAATATT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 52 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (62 bp):
TTTAATAATTAAAATAATAATTAAGCCGACAACAGATATATTAAAAATTAATTACTATAATA
Found at i:217200 original size:26 final size:26
Alignment explanation
Indices: 217171--217227 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
217161 TTAAAATAAT
217171 AATTAATT-CGACAACAGATATTTTAA
1 AATTAATTACGACAACA-ATATTTTAA
* * *
217197 AATTTAATTACTACTATAATATTTTAA
1 AA-TTAATTACGACAACAATATTTTAA
217224 AATT
1 AATT
217228 TGATGATTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
26 4 0.15
27 17 0.65
28 5 0.19
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.42
Consensus pattern (26 bp):
AATTAATTACGACAACAATATTTTAA
Found at i:222895 original size:25 final size:25
Alignment explanation
Indices: 222867--222914 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
222857 AGGTCTGTAT
*
222867 CCGTCTACTTTGGTAGGTTAGGCGC
1 CCGTCTACTTTGGTAGGCTAGGCGC
222892 CCGTCTACTTTGGTAGGCTAGGC
1 CCGTCTACTTTGGTAGGCTAGGC
222915 CCCTGCCGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.25, G:0.31, T:0.31
Consensus pattern (25 bp):
CCGTCTACTTTGGTAGGCTAGGCGC
Found at i:224313 original size:21 final size:21
Alignment explanation
Indices: 224287--224341 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
224277 CAGATCTTTT
224287 ATTGTCGTTGA-CCGTCTGTTA
1 ATTGTCGTTGATCCGTC-GTTA
*
224308 ATTGTCGTTGATCGGTCGTTA
1 ATTGTCGTTGATCCGTCGTTA
*
224329 ATCGTCGTTGATC
1 ATTGTCGTTGATC
224342 AGTAGTTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.15, C:0.18, G:0.25, T:0.42
Consensus pattern (21 bp):
ATTGTCGTTGATCCGTCGTTA
Found at i:224327 original size:11 final size:11
Alignment explanation
Indices: 224311--224353 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
224301 TCTGTTAATT
224311 GTCGTTGATCG
1 GTCGTTGATCG
*
224322 GTCGTTAATC-
1 GTCGTTGATCG
*
224332 GTCGTTGATCA
1 GTCGTTGATCG
*
224343 GTAGTTGATCG
1 GTCGTTGATCG
224354 TTGTTGACTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.16, C:0.16, G:0.30, T:0.37
Consensus pattern (11 bp):
GTCGTTGATCG
Found at i:224353 original size:21 final size:21
Alignment explanation
Indices: 224304--224360 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
224294 TTGACCGTCT
* * *
224304 GTTAATTGTCGTTGATCGGTC
1 GTTAATCGTCGTTGATCAGTA
224325 GTTAATCGTCGTTGATCAGTA
1 GTTAATCGTCGTTGATCAGTA
* *
224346 GTTGATCGTTGTTGA
1 GTTAATCGTCGTTGA
224361 CTGGTCATTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.18, C:0.12, G:0.28, T:0.42
Consensus pattern (21 bp):
GTTAATCGTCGTTGATCAGTA
Found at i:225895 original size:21 final size:22
Alignment explanation
Indices: 225871--225911 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
225861 GTAGGCTTTT
225871 AAGCCCAATGGG-CCTAAGGTA
1 AAGCCCAATGGGTCCTAAGGTA
**
225892 AAGCCTTATGGGTCCTAAGG
1 AAGCCCAATGGGTCCTAAGG
225912 CATTCCTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (22 bp):
AAGCCCAATGGGTCCTAAGGTA
Found at i:226162 original size:21 final size:22
Alignment explanation
Indices: 226138--226178 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
226128 AGTAGGCTTT
226138 AAGCCCAATGGG-CCTAAGGTA
1 AAGCCCAATGGGTCCTAAGGTA
**
226159 AAGCCTTATGGGTCCTAAGG
1 AAGCCCAATGGGTCCTAAGG
226179 CATTCCTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (22 bp):
AAGCCCAATGGGTCCTAAGGTA
Found at i:226269 original size:263 final size:267
Alignment explanation
Indices: 225792--226328 Score: 1028
Period size: 263 Copynumber: 2.0 Consensus size: 267
225782 TTAAGATCTA
*
225792 ATATAAAGACTCTTTAGGTTCGGTTTTGATCAAGTCGATAATTTCTTATTGACCTAAGGTGACTA
1 ATATGAAGACTCTTTAGGTTCGGTTTTGATCAAGTCGATAATTTCTTATTGACCTAAGGTGACTA
225857 TTTAGTAGGCTTTTAAGCCCAATGGGCCTAAGGTAAAGCCTTATGGGTCCTAAGGCATTCCTTTA
66 TTTAGTAGGCTTTTAAGCCCAATGGGCCTAAGGTAAAGCCTTATGGGTCCTAAGGCATTCCTTTA
225922 GGATACTAATTTGTTTTGTTATAGGGTAAGTTCTTATAGGCCTGAGGCACCCCTTTGGGTGGGCT
131 GGA-ACTAATTTGTTTTGTTATAGGGTAAGTTCTTATAGGCCTGAGGCACCCCTTTGGGTGGGCT
225987 CTTAAGCTTCGACTAGGGTAAGTCCTTGTGAACCCAATGTGCTCCCTTAGTTTGGCATTTATGTC
195 CTTAAGCTTCGACTAGGGTAAGTCCTTGTGAACCCAATGTGCTCCCTTAGTTTGGCATTTATGTC
226052 CAAGGGGC
260 CAAGGGGC
226060 ATATGAAGACTCTTTAGGTTCGGTTTTGATCAAGTCGATAATTTCTTATTGACCTAAGGTGACTA
1 ATATGAAGACTCTTTAGGTTCGGTTTTGATCAAGTCGATAATTTCTTATTGACCTAAGGTGACTA
226125 TTTAGTAGGC-TTTAAGCCCAATGGGCCTAAGGTAAAGCCTTATGGGTCCTAAGGCATTCCTTTA
66 TTTAGTAGGCTTTTAAGCCCAATGGGCCTAAGGTAAAGCCTTATGGGTCCTAAGGCATTCCTTTA
226189 GG-A-TAA-TTGTTTTGTTATAGGGTAAGTTCTTATAGGCCTGAGGCACCCCTTTGGGTGGGCTC
131 GGAACTAATTTGTTTTGTTATAGGGTAAGTTCTTATAGGCCTGAGGCACCCCTTTGGGTGGGCTC
226251 TTAAGCTTCGACTAGGGTAAGTCCTTGTGAACCCAATGTGCTCCCTTAGTTTGGCATTTATGTCC
196 TTAAGCTTCGACTAGGGTAAGTCCTTGTGAACCCAATGTGCTCCCTTAGTTTGGCATTTATGTCC
226316 AAGGGGC
261 AAGGGGC
226323 ATATGA
1 ATATGA
226329 TAAGTCTTTA
Statistics
Matches: 268, Mismatches: 1, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
263 134 0.50
264 3 0.01
265 1 0.00
267 56 0.21
268 74 0.28
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (267 bp):
ATATGAAGACTCTTTAGGTTCGGTTTTGATCAAGTCGATAATTTCTTATTGACCTAAGGTGACTA
TTTAGTAGGCTTTTAAGCCCAATGGGCCTAAGGTAAAGCCTTATGGGTCCTAAGGCATTCCTTTA
GGAACTAATTTGTTTTGTTATAGGGTAAGTTCTTATAGGCCTGAGGCACCCCTTTGGGTGGGCTC
TTAAGCTTCGACTAGGGTAAGTCCTTGTGAACCCAATGTGCTCCCTTAGTTTGGCATTTATGTCC
AAGGGGC
Found at i:227069 original size:5 final size:5
Alignment explanation
Indices: 227059--227096 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
227049 CATATTCTTA
227059 ATTCG ATTCG ATTCG ATTCG A-TCG ATTCG ATTCG ATTC
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTC
227097 TATCGTACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:227085 original size:19 final size:19
Alignment explanation
Indices: 227061--227101 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
227051 TATTCTTAAT
227061 TCGATTCGATTCGATTCGA
1 TCGATTCGATTCGATTCGA
*
227080 TCGATTCGATTCGATTCTA
1 TCGATTCGATTCGATTCGA
227099 TCG
1 TCG
227102 TACAATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.39
Consensus pattern (19 bp):
TCGATTCGATTCGATTCGA
Found at i:233505 original size:18 final size:18
Alignment explanation
Indices: 233482--233519 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
233472 AATGGAGGAA
233482 ATGAGGAACGAATTAGGG
1 ATGAGGAACGAATTAGGG
* *
233500 ATGAGGAATGAATTGGGG
1 ATGAGGAACGAATTAGGG
233518 AT
1 AT
233520 TTAGAAATTA
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:0.37, C:0.03, G:0.39, T:0.21
Consensus pattern (18 bp):
ATGAGGAACGAATTAGGG
Found at i:233776 original size:17 final size:18
Alignment explanation
Indices: 233738--233779 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
233728 TAAGAATTCG
233738 TTTTCTGTAAACCCACCT
1 TTTTCTGTAAACCCACCT
* *
233756 TTTTCTGTAAACTCGCCT
1 TTTTCTGTAAACCCACCT
233774 TTTTCT
1 TTTTCT
233780 TCTTCTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.29, G:0.07, T:0.48
Consensus pattern (18 bp):
TTTTCTGTAAACCCACCT
Found at i:238464 original size:18 final size:18
Alignment explanation
Indices: 238441--238478 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
238431 AATGGGGAAA
238441 ATGAGGAACGAATTAGGG
1 ATGAGGAACGAATTAGGG
* *
238459 ATGAGGAATGAATTGGGG
1 ATGAGGAACGAATTAGGG
238477 AT
1 AT
238479 TTAGAAATTA
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:0.37, C:0.03, G:0.39, T:0.21
Consensus pattern (18 bp):
ATGAGGAACGAATTAGGG
Found at i:245682 original size:26 final size:26
Alignment explanation
Indices: 245642--245691 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
245632 AATGTTAGAT
* *
245642 AAAATAAAAGTAAATATG-TAAAAAGA
1 AAAAAAAAAGAAAATA-GATAAAAAGA
245668 AAAAAAAAAGAAAATAGATAAAAA
1 AAAAAAAAAGAAAATAGATAAAAA
245692 AATAAATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 20 0.95
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (26 bp):
AAAAAAAAAGAAAATAGATAAAAAGA
Found at i:245717 original size:2 final size:2
Alignment explanation
Indices: 245710--245754 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
245700 AAATTTAGTA
245710 AT AT AT AT 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 AT AT AT AT
245752 AT A
1 AT A
245755 AAACAAAAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:246230 original size:93 final size:93
Alignment explanation
Indices: 246071--246256 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
246061 CCAAAGTTTA
*
246071 CTTTCACGTGGGATGAGTTGGTTTCCTGCAAAAGCAATAATAACAAATTTTTTTAATTCATTTGC
1 CTTTCACGTGGGATGAGTTGGTTTCCTGCAAAAGCAATAATAACAAAATTTTTTAATTCATTTGC
246136 AATTCAGAAGCTTTCCCTGTTCCCTTTC
66 AATTCAGAAGCTTTCCCTGTTCCCTTTC
246164 CTTTCACGTGGGATGAGTTGGTTTCCTGCAAAAGCAATAATAACAAAATTTTTTAATTCATTTGC
1 CTTTCACGTGGGATGAGTTGGTTTCCTGCAAAAGCAATAATAACAAAATTTTTTAATTCATTTGC
246229 AATTCAGAAGCTTTCCCTGTTCCCTTTC
66 AATTCAGAAGCTTTCCCTGTTCCCTTTC
246257 TTATACGTTC
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.38
Consensus pattern (93 bp):
CTTTCACGTGGGATGAGTTGGTTTCCTGCAAAAGCAATAATAACAAAATTTTTTAATTCATTTGC
AATTCAGAAGCTTTCCCTGTTCCCTTTC
Found at i:247891 original size:84 final size:83
Alignment explanation
Indices: 247712--248087 Score: 400
Period size: 84 Copynumber: 4.5 Consensus size: 83
247702 TACCTGGGGC
* ** * * * *
247712 TATGCTGTAAATGATGTGCCTAAGAGATGAGCGTAGTCGAACTTGAAGATCTTTGTTGGCAGATA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATA
* * ***
247777 ACCCTCCTAGCCTGGCGT
66 ACCCTTCTAGACTTAAGT
* * * *
247795 TATGCCGCAAATGATGTGCTTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGGTGACAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGGCAGAT
*
247860 AACCCTTCTAGCCTTAAGT
65 AACCCTTCTAGACTTAAGT
* * *
247879 TATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAATCGAAGGTCTTTAGTTGGCAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GGTGGCAGAT
*
247944 AACCCTTCTCGACTTAAGT
65 AACCCTTCTAGACTTAAGT
* * * * ** *
247963 TATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TT--TGGCAGAC
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGAT
* * * *
248025 AATCCTTCTCGATTTAAGC
65 AACCCTTCTAGACTTAAGT
248044 TATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAACTC
1 TATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTC
248088 AAATATCTTT
Statistics
Matches: 249, Mismatches: 40, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
80 20 0.08
81 42 0.17
83 45 0.18
84 116 0.47
85 26 0.10
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (83 bp):
TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGGCAGATA
ACCCTTCTAGACTTAAGT
Found at i:248083 original size:165 final size:166
Alignment explanation
Indices: 247710--248084 Score: 434
Period size: 165 Copynumber: 2.3 Consensus size: 166
247700 CTTACCTGGG
* * * *
247710 GCTATGCTGTAAATGATGTGCCTAAGAGATGAGCGTAGTCGAACTTGAAGATCTTTGTTGGCAGA
1 GCTATGCTGTAAATGATGTGCCT-TGAGCTGAGCGTAGTCGAAATCGAAGATCTTTGTTGGCAGA
* ** * * * *
247775 TAACCCTCCTAGCCTGGCGTTATGCCGCAAATGATGTGCTTTGGAGCTGAACGTAGTCGAACTCG
65 TAACCCTCCTAGACTGAAGTTATGCCGCAAATGATGTGCCTCGAAGCTGAACGTAATCGAACTCG
* *
247840 AAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTAA
130 AAGGTCTTTTGGTGACAGACAACCCTTCTAGACTTAA
* *
247877 GTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAATCGAAGGTCTTTAGTTGGCAG
1 GCTATGCTGTAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAAATCGAAGATCTTT-GTTGGCAG
* * * * **
247942 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
64 ATAACCCTCCTAGACTGAAGTTATGCCGCAAATGATGTG-CCTCGAAGCTGAACGTAATCGAACT
** * * *
248007 CGGGGGTC-TTT-G-G-CAGACAATCCTTCTCGATTTAA
128 CGAAGGTCTTTTGGTGACAGACAACCCTTCTAGACTTAA
*
248042 GCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAA
1 GCTATGCTGTAAATGATGTGCC-TTGAGCTGAGCGTAGTCGAA
248085 CTCAAATATC
Statistics
Matches: 176, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
165 55 0.31
166 3 0.02
167 50 0.28
168 43 0.24
169 25 0.14
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.29
Consensus pattern (166 bp):
GCTATGCTGTAAATGATGTGCCTTGAGCTGAGCGTAGTCGAAATCGAAGATCTTTGTTGGCAGAT
AACCCTCCTAGACTGAAGTTATGCCGCAAATGATGTGCCTCGAAGCTGAACGTAATCGAACTCGA
AGGTCTTTTGGTGACAGACAACCCTTCTAGACTTAA
Found at i:248499 original size:106 final size:106
Alignment explanation
Indices: 248311--249575 Score: 2127
Period size: 106 Copynumber: 11.9 Consensus size: 106
248301 GTGAAGTTGA
* *
248311 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCG
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
248376 ATATCCTTCGCTATGAAGTTGAAATTGACTCTGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
248417 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * *
248482 ATTTCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
248523 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
248588 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
248629 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
248694 TTATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
248735 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
** *
248800 ATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* *
248841 AAGTTGTTTGTTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
248906 ATATCCTTCGATGTGAAGTTGAAATTGGCTCTAAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
248947 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
249012 ATATCCTTCGCCGTGAAGTTGAAATTGGCTCTGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
249053 AAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * *
249118 ATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* * * *
249159 AAGTTGTTTGTTAACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCATTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
249224 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
*
249265 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
249330 ATATCCTTCGCT-TGAAGTTGAAATTGGCTCTGAAATTGGG
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
249370 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * * * *
249435 ATATCCTTCGTTGTGAAATTGAAATTGGCTCTAAAAGTGGA
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
* *
249476 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCA
1 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * * * *
249541 ATTTTCTTCGCTGCGAAGTTGAAATAGACTCTGAA
66 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
249576 TGAAATTGGA
Statistics
Matches: 1090, Mismatches: 68, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
105 103 0.09
106 987 0.91
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
Found at i:253435 original size:2 final size:2
Alignment explanation
Indices: 253428--253458 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
253418 ATTTAGTAAA
253428 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
253459 AACAAAAACA
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:253932 original size:93 final size:93
Alignment explanation
Indices: 253773--253958 Score: 372
Period size: 93 Copynumber: 2.0 Consensus size: 93
253763 CCAAAGTTTA
253773 CTTTCACGTGGGATGAGTTGGTTTCCTGCAAAAGCAATAATAACAAATTTTTTTAATTCATTTGC
1 CTTTCACGTGGGATGAGTTGGTTTCCTGCAAAAGCAATAATAACAAATTTTTTTAATTCATTTGC
253838 AATTCAGAAGCTTTCCCTGTTCCCTTTC
66 AATTCAGAAGCTTTCCCTGTTCCCTTTC
253866 CTTTCACGTGGGATGAGTTGGTTTCCTGCAAAAGCAATAATAACAAATTTTTTTAATTCATTTGC
1 CTTTCACGTGGGATGAGTTGGTTTCCTGCAAAAGCAATAATAACAAATTTTTTTAATTCATTTGC
253931 AATTCAGAAGCTTTCCCTGTTCCCTTTC
66 AATTCAGAAGCTTTCCCTGTTCCCTTTC
253959 TTATACGTTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (93 bp):
CTTTCACGTGGGATGAGTTGGTTTCCTGCAAAAGCAATAATAACAAATTTTTTTAATTCATTTGC
AATTCAGAAGCTTTCCCTGTTCCCTTTC
Found at i:261874 original size:2 final size:2
Alignment explanation
Indices: 261863--261907 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
261853 ATAAAAGAAG
261863 TA TA -A 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
261904 TA TA
1 TA TA
261908 CACACATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:262344 original size:35 final size:35
Alignment explanation
Indices: 262300--262379 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
262290 AATAAAGTCA
*
262300 TCAATTACATTCTAAAC-TCCAAAATCCAAAATGCT
1 TCAATTACATTCTAAACAT-CAAAATCCAAAATACT
* *
262335 TCAAGTACATTCTAAACATCAAATTCCAAAATACT
1 TCAATTACATTCTAAACATCAAAATCCAAAATACT
262370 TCAATTACAT
1 TCAATTACAT
262380 GCCCAACCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 39 0.98
36 1 0.03
ACGTcount: A:0.44, C:0.24, G:0.03, T:0.30
Consensus pattern (35 bp):
TCAATTACATTCTAAACATCAAAATCCAAAATACT
Found at i:262740 original size:143 final size:143
Alignment explanation
Indices: 262547--262831 Score: 471
Period size: 143 Copynumber: 2.0 Consensus size: 143
262537 CCTAAATACT
*** * *
262547 CAATTCAGTTTATAAAATAGTTGACTCGGTTTTTTTTCGATTTGATTTTATAAAATTTAAATCAA
1 CAATTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAA
* * *
262612 GTCGAATTAAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATAATATTA
66 GTCGAATTAAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTA
*
262677 TTTTATTCTAATC
131 TTTGATTCTAATC
262690 CAATTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAA
1 CAATTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAA
* *
262755 GTTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTA
66 GTCGAATTAAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTA
262820 TTTGATTCTAAT
131 TTTGATTCTAAT
262832 TTAAATAGTT
Statistics
Matches: 131, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
143 131 1.00
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (143 bp):
CAATTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCAATTTGAGTTTATAAAATTTAAATCAA
GTCGAATTAAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTA
TTTGATTCTAATC
Found at i:263410 original size:16 final size:16
Alignment explanation
Indices: 263385--263435 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
263375 ATTTATACAG
*
263385 AGCATCTGAATCATTC
1 AGCATTTGAATCATTC
*
263401 AGCATTTGAATCATTA
1 AGCATTTGAATCATTC
*
263417 AGCATTTGAATTATTC
1 AGCATTTGAATCATTC
263433 AGC
1 AGC
263436 GCTTAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (16 bp):
AGCATTTGAATCATTC
Found at i:263649 original size:35 final size:35
Alignment explanation
Indices: 263610--263686 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
263600 GTTGGGCATG
263610 TAATTGAAGTATTTTTGG-ATTTGAAG-TTTAGAATA
1 TAATTGAAGTA-TTTTGGAATTTG-AGTTTTAGAATA
* *
263645 TAATTGAAGTATTTTGGAATTTGGGTTTTAGAATG
1 TAATTGAAGTATTTTGGAATTTGAGTTTTAGAATA
263680 TAATTGA
1 TAATTGA
263687 TGATTATGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 7 0.18
35 31 0.82
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.45
Consensus pattern (35 bp):
TAATTGAAGTATTTTGGAATTTGAGTTTTAGAATA
Found at i:268267 original size:44 final size:44
Alignment explanation
Indices: 268202--268290 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
268192 CCGGACCAAG
* *
268202 TCTTATTGTTTCTTCATGAGGATAGTGATGTTTTAGGCCAACTT
1 TCTTATTGTTTCTTCACGAGGATAGTAATGTTTTAGGCCAACTT
268246 TCTTATTGTTTCTTCACGAGGATAGTAATGTTTTAGGCCAACTT
1 TCTTATTGTTTCTTCACGAGGATAGTAATGTTTTAGGCCAACTT
268290 T
1 T
268291 TAATATAGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.45
Consensus pattern (44 bp):
TCTTATTGTTTCTTCACGAGGATAGTAATGTTTTAGGCCAACTT
Found at i:269107 original size:32 final size:32
Alignment explanation
Indices: 269062--269148 Score: 122
Period size: 32 Copynumber: 2.7 Consensus size: 32
269052 TTAGAAATTT
* *
269062 AATTATTATTTAATTTAATTCTAAACTGA-TA
1 AATTATTAGTTAATTTGATTCTAAACTGATTA
* *
269093 CACTTATTAGTTAATTTGATTATAAACTGATTA
1 -AATTATTAGTTAATTTGATTCTAAACTGATTA
269126 AATTATTAGTTAATTTGATTCTA
1 AATTATTAGTTAATTTGATTCTA
269149 GATTGATAGA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
32 46 0.96
33 2 0.04
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (32 bp):
AATTATTAGTTAATTTGATTCTAAACTGATTA
Found at i:271973 original size:17 final size:17
Alignment explanation
Indices: 271936--271969 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
271926 TGAGGTTACT
271936 ATTTATATGAATAGTAA
1 ATTTATATGAATAGTAA
271953 ATTT-TATGAATAGTAA
1 ATTTATATGAATAGTAA
271969 A
1 A
271970 ATTTGGTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (17 bp):
ATTTATATGAATAGTAA
Found at i:276049 original size:23 final size:23
Alignment explanation
Indices: 276004--276052 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
275994 ATAAAGAACC
*
276004 AAAATAAACTTAAATATATCATT
1 AAAATAAACTTAAATAGATCATT
*
276027 AAAATAAAGTTAAA-AGATCCATT
1 AAAATAAACTTAAATAGAT-CATT
276050 AAA
1 AAA
276053 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.59, C:0.08, G:0.04, T:0.29
Consensus pattern (23 bp):
AAAATAAACTTAAATAGATCATT
Found at i:277177 original size:8 final size:9
Alignment explanation
Indices: 277145--277190 Score: 56
Period size: 9 Copynumber: 4.7 Consensus size: 9
277135 ACTACACATC
277145 TTTTTTCTT
1 TTTTTTCTT
277154 ATTGTTTTCACTT
1 -TT-TTTT--CTT
277167 TTTTTTCTT
1 TTTTTTCTT
277176 TTTTTTCTT
1 TTTTTTCTT
277185 TTTTTT
1 TTTTTT
277191 ACGCTGCTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
9 18 0.55
10 2 0.06
11 8 0.24
12 2 0.06
13 3 0.09
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:281608 original size:23 final size:23
Alignment explanation
Indices: 281563--281611 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
281553 ATAAAGAACC
*
281563 AAAATAAACTTAAATATATCATT
1 AAAATAAACTTAAATACATCATT
*
281586 AAAATAAAGTTAAA-ACATCCATT
1 AAAATAAACTTAAATACAT-CATT
281609 AAA
1 AAA
281612 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAACTTAAATACATCATT
Found at i:284926 original size:12 final size:10
Alignment explanation
Indices: 284886--284926 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
284876 TTTATCACAC
284886 CAAATTCTCT
1 CAAATTCTCT
284896 CAAATTCTCT
1 CAAATTCTCT
284906 -AAATTTCTCT
1 CAAA-TTCTCT
*
284916 CAAATACTCT
1 CAAATTCTCT
284926 C
1 C
284927 CCTTTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:285003 original size:17 final size:18
Alignment explanation
Indices: 284973--285008 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
284963 ATGTATATAA
*
284973 TTTATTTATGTATTTTAC
1 TTTATTTATATATTTTAC
284991 TTTATTTA-ATATTTTAC
1 TTTATTTATATATTTTAC
285008 T
1 T
285009 AAATTGCGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.67
Consensus pattern (18 bp):
TTTATTTATATATTTTAC
Found at i:286573 original size:29 final size:29
Alignment explanation
Indices: 286531--286609 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
286521 TACTGCTACG
286531 GGTGTTAGATCGGAAAATATAATCTGACC
1 GGTGTTAGATCGGAAAATATAATCTGACC
286560 GGTGTTAGATCGGAAAATATAATCTGACC
1 GGTGTTAGATCGGAAAATATAATCTGACC
*
286589 GGTGTTAGATCGGTAAATATA
1 GGTGTTAGATCGGAAAATATA
286610 CCGATCACCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGGAAAATATAATCTGACC
Found at i:286901 original size:17 final size:15
Alignment explanation
Indices: 286860--286907 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 15
286850 AAAGTAAATT
*
286860 TATAAATTATA-AAA
1 TATAAATAATATAAA
286874 TATAAATAATATAAA
1 TATAAATAATATAAA
286889 TATAACTATAATATAAA
1 TATAA--ATAATATAAA
286906 TA
1 TA
286908 GTAATATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 10 0.33
15 8 0.27
17 12 0.40
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
TATAAATAATATAAA
Found at i:286907 original size:23 final size:21
Alignment explanation
Indices: 286860--286904 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
286850 AAAGTAAATT
286860 TATAAATTATAAAATATAAATAA
1 TATAAA-TAT-AAATATAAATAA
*
286883 TATAAATATAACTATAATATAA
1 TATAAATATAAATATAA-ATAA
286905 ATAGTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TATAAATATAAATATAAATAA
Found at i:286912 original size:12 final size:11
Alignment explanation
Indices: 286860--286915 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
286850 AAAGTAAATT
286860 TATAAAT-T-A
1 TATAAATATAA
286869 TA-AAATATAA
1 TATAAATATAA
286879 -AT-AATATAAA
1 TATAAATAT-AA
*
286889 TATAACTATAA
1 TATAAATATAA
286900 TATAAATAGTAA
1 TATAAATA-TAA
286912 TATA
1 TATA
286916 CAAATGCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
8 4 0.11
9 9 0.24
10 3 0.08
11 11 0.29
12 11 0.29
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (11 bp):
TATAAATATAA
Found at i:286915 original size:17 final size:16
Alignment explanation
Indices: 286871--286915 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
286861 ATAAATTATA
286871 AAATATAA-ATAATAT
1 AAATATAATATAATAT
286886 AAATATAACTATAATAT
1 AAATATAA-TATAATAT
286903 AAATAGTAATATA
1 AAATA-TAATATA
286916 CAAATGCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.30
17 16 0.59
18 3 0.11
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (16 bp):
AAATATAATATAATAT
Found at i:287905 original size:4 final size:4
Alignment explanation
Indices: 287896--287929 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
287886 ATAAAAGGAA
287896 AAAT AAAT AAAT AAAT AAAT AAAT AAAT GAAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A
287930 TTAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:287940 original size:2 final size:2
Alignment explanation
Indices: 287933--287973 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
287923 TGAAATATTA
287933 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
287974 AATGAGTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:288040 original size:18 final size:18
Alignment explanation
Indices: 287991--288044 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 18
287981 AAAATAGAAA
*
287991 AATAATAATCATAACAATAAT
1 AATAGTAAT-ATAA-AAT-AT
288012 AATAGTAATATGAAAATAT
1 AATAGTAATAT-AAAATAT
288031 AATA-TAATATAAAA
1 AATAGTAATATAAAA
288045 AAACCAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 4 0.13
18 6 0.19
19 6 0.19
20 5 0.16
21 10 0.32
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.30
Consensus pattern (18 bp):
AATAGTAATATAAAATAT
Found at i:288045 original size:18 final size:19
Alignment explanation
Indices: 287995--288045 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
287985 TAGAAAAATA
*
287995 ATAATCATAACAATAATAAT
1 ATAAT-ATAAAAATAATAAT
*
288015 AGTAATATGAAAAT-ATAAT
1 A-TAATATAAAAATAATAAT
288034 ATAATATAAAAA
1 ATAATATAAAAA
288046 AACCAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 6 0.22
20 7 0.26
21 4 0.15
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (19 bp):
ATAATATAAAAATAATAAT
Found at i:288847 original size:37 final size:37
Alignment explanation
Indices: 288793--288894 Score: 131
Period size: 34 Copynumber: 2.8 Consensus size: 37
288783 ATGCTTGTGA
* * *
288793 ATCCTATCTTTAAGAGTTTAAATCATAGTAGAACTT-T
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAA-TTCT
*
288830 ATCCTATTTTTAGGAGTTTGAATCCTA--A-AATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAATTCT
288864 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
288895 GACGAAAATG
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
33 2 0.04
34 29 0.52
35 1 0.02
36 1 0.02
37 23 0.41
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAATTCT
Found at i:289833 original size:106 final size:106
Alignment explanation
Indices: 289641--290691 Score: 1437
Period size: 106 Copynumber: 10.0 Consensus size: 106
289631 AGGATTGTTC
* * *
289641 CGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAA-T-CGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
* * *
289703 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCT
65 AACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
* *
289745 CGAGTCCAATATCCTTCGCTGTGAAGTTGATATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * *
289810 ACCAGCGGTCCCTTAGTTTTGAAGTTGAACTTGCATCGTCT
66 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
* *
289851 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGGGAAGTTGTTTGTTGAC-
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
289915 A--A---GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
* * * * *
289951 -GGGTCCAATATCCTCCG-TCATGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
* * *
290014 AACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
* * *
290056 CGAGTCCAATATCCTTCGCTGTGAAGTTGATATTGGCTCCGAAATTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * *
290121 ACCAGCGGTCCCTTCGTTTTGAAGTTGAACTTGCATCGTCT
66 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
* * * *
290162 CGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
290227 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
*
290268 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT-TCGAAATTGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAATTGTTTGTTGAC
* *
290332 AACTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 AACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
* * * *
290374 GGAGTCCAATATCTTTCGCTGTGAAGTTTAAATTGGCTCTGAAAAT-GGAAAGTTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGAC
*
290438 AACCAGCGGTCCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 AACCAGCGGTCCC-TTCGTTGTGAAGTTGAACTTGCGTTGTCT
* *
290481 CGA-TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
** * * * * * *
290545 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
* *
290586 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * *
290651 ACCAGCGATCCCTTCATCGTGAAGTTAAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
290692 GGAGAGAAAC
Statistics
Matches: 834, Mismatches: 95, Indels: 34
0.87 0.10 0.04
Matches are distributed among these distances:
98 1 0.00
99 54 0.06
100 30 0.04
102 1 0.00
103 1 0.00
104 38 0.05
105 67 0.08
106 606 0.73
107 36 0.04
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCT
Found at i:290746 original size:35 final size:37
Alignment explanation
Indices: 290700--290832 Score: 137
Period size: 37 Copynumber: 3.6 Consensus size: 37
290690 CTGGAGAGAA
* *
290700 ACTGTCTCAAG-GAGATAAAATTTG-TTTCAAGGAAG
1 ACTGTCTCAAGCGAGACAAAATTTGTTTTAAAGGAAG
* * * *
290735 ACTGTCTCAAGGGAGACGAAATTTGTTTTAAAGAAAA
1 ACTGTCTCAAGCGAGACAAAATTTGTTTTAAAGGAAG
* * * *
290772 ACTATCTTAAGCGAGATAAAATCTTGTTTTAAATG-AG
1 ACTGTCTCAAGCGAGACAAAAT-TTGTTTTAAAGGAAG
*
290809 AATGTCTCAAGCGAGACAAAATTT
1 ACTGTCTCAAGCGAGACAAAATTT
290833 ATATTGGAAA
Statistics
Matches: 78, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
35 11 0.14
36 13 0.17
37 44 0.56
38 10 0.13
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (37 bp):
ACTGTCTCAAGCGAGACAAAATTTGTTTTAAAGGAAG
Found at i:291606 original size:22 final size:22
Alignment explanation
Indices: 291580--291678 Score: 153
Period size: 22 Copynumber: 4.5 Consensus size: 22
291570 TTATGTTTGG
*
291580 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
291602 TCAAAGGTTTTGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* *
291624 TCATAGGTTTGGCATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
*
291646 TCAAAGGTTTGTCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
291668 TCAAAGGTTTG
1 TCAAAGGTTTG
291679 ATGGGGTAGC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 69 1.00
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.41
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:292281 original size:19 final size:18
Alignment explanation
Indices: 292255--292302 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
292245 TTTTTGTCCC
292255 TTTTTCTTTTTGATTTTG
1 TTTTTCTTTTTGATTTTG
**
292273 TTCTTTCTTTTTTCTTTTG
1 TT-TTTCTTTTTGATTTTG
*
292292 TTTCTCTTTTT
1 TTTTTCTTTTT
292303 TCTTTGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.79
Consensus pattern (18 bp):
TTTTTCTTTTTGATTTTG
Found at i:292308 original size:17 final size:18
Alignment explanation
Indices: 292268--292311 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
292258 TTCTTTTTGA
*
292268 TTTTGTTCTTTCTTTTTTC
1 TTTTGTT-TCTCTTTTTTC
292287 TTTTGTTTCTCTTTTTTC
1 TTTTGTTTCTCTTTTTTC
292305 -TTTGTTT
1 TTTTGTTT
292312 TTAATTGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 7 0.29
18 10 0.42
19 7 0.29
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (18 bp):
TTTTGTTTCTCTTTTTTC
Found at i:294587 original size:23 final size:22
Alignment explanation
Indices: 294560--294626 Score: 55
Period size: 25 Copynumber: 2.8 Consensus size: 22
294550 GTGTTAGAGG
294560 AAAAAAATGAAAAAATGAA-GAA
1 AAAAAAAT-AAAAAATGAATGAA
*
294582 TAAAAATAAGTAAAAAAATAAATGAA
1 -AAAAA-AA-T-AAAAAATGAATGAA
*
294608 AAATAAATAAATAAATGAA
1 AAAAAAATAAA-AAATGAA
294627 ATATTAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
22 3 0.08
23 12 0.33
24 4 0.11
25 14 0.39
26 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (22 bp):
AAAAAAATAAAAAATGAATGAA
Found at i:295060 original size:66 final size:65
Alignment explanation
Indices: 294899--295069 Score: 154
Period size: 66 Copynumber: 2.6 Consensus size: 65
294889 GCTTATAAGT
*
294899 AAAATATTTAAAAAAAGAGTA-TATATATATATAATAATAAATATAGTATTAAAAAATAATCAAA
1 AAAATATTTAAAAAAA-A-TATTATATATATATAATAATAAATATAGTAGTAAAAAATAATCAAA
294963 TG
64 TG
* ** * *
294965 AATATAAATAAATAAAAA-ATATATGTATATATAATAATAATATATAGT-GT-AAAAA-AATTAA
1 AAAATATTTAAA-AAAAATAT-TATATATATATAATAATAA-ATATAGTAGTAAAAAATAATCAA
*
295026 TTG
63 ATG
*
295029 AAAATCATTTAAAAAAACATATGTATATATATTTATATAAT
1 AAAAT-ATTTAAAAAAA-ATAT-TATATATATATA-ATAAT
295070 GACAATAATG
Statistics
Matches: 84, Mismatches: 13, Indels: 15
0.75 0.12 0.13
Matches are distributed among these distances:
64 16 0.19
65 11 0.13
66 41 0.49
67 16 0.19
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (65 bp):
AAAATATTTAAAAAAAATATTATATATATATAATAATAAATATAGTAGTAAAAAATAATCAAATG
Found at i:297200 original size:23 final size:23
Alignment explanation
Indices: 297147--297208 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
297137 CCAAACAACC
* * *
297147 GAAAACATGGCATAAAGACATAA
1 GAAAACGTGTCATAAAGACAGAA
*
297170 -AAAACGTGTCATAATGACAGAA
1 GAAAACGTGTCATAAAGACAGAA
297192 GAAAACGTGTCATAAAG
1 GAAAACGTGTCATAAAG
297209 TATAATTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 18 0.55
23 15 0.45
ACGTcount: A:0.52, C:0.13, G:0.19, T:0.16
Consensus pattern (23 bp):
GAAAACGTGTCATAAAGACAGAA
Found at i:298324 original size:28 final size:27
Alignment explanation
Indices: 298287--298341 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
298277 ACGTATGCCC
298287 TTTTTTCCAGTTAAGTGCCTAACGTTT
1 TTTTTTCCAGTTAAGTGCCTAACGTTT
** *
298314 TTTTGTTCCAGTTTGGTGCCTCACGTTT
1 TTTT-TTCCAGTTAAGTGCCTAACGTTT
298342 CATTCCGTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.13, C:0.20, G:0.18, T:0.49
Consensus pattern (27 bp):
TTTTTTCCAGTTAAGTGCCTAACGTTT
Found at i:299082 original size:14 final size:13
Alignment explanation
Indices: 299063--299113 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
299053 ATTTGTGTTT
299063 ATTTTAAATATGTA
1 ATTTTAAATAT-TA
**
299077 ATTTTATTTATTA
1 ATTTTAAATATTA
299090 ATTTTAAATA-TA
1 ATTTTAAATATTA
*
299102 TTTTTAAA-ATTA
1 ATTTTAAATATTA
299114 TCATATTGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
11 1 0.03
12 11 0.35
13 10 0.32
14 9 0.29
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
ATTTTAAATATTA
Found at i:301112 original size:8 final size:8
Alignment explanation
Indices: 301099--301126 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
301089 TATCGTAAGG
301099 ATATTTTT
1 ATATTTTT
301107 ATATTTTT
1 ATATTTTT
301115 ATATTTTT
1 ATATTTTT
301123 ATAT
1 ATAT
301127 AATTTTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
ATATTTTT
Found at i:302425 original size:16 final size:16
Alignment explanation
Indices: 302404--302435 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
302394 TTGGTTGAGG
302404 AGAACTGAATAAATAA
1 AGAACTGAATAAATAA
302420 AGAACTGAATAAATAA
1 AGAACTGAATAAATAA
302436 GAAATCAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.19
Consensus pattern (16 bp):
AGAACTGAATAAATAA
Found at i:307412 original size:21 final size:21
Alignment explanation
Indices: 307388--307428 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
307378 CGCTGTAAAG
307388 GGAACAAAAAGAAATTGAAGC
1 GGAACAAAAAGAAATTGAAGC
*
307409 GGAACAAAAGGAAATTGAAG
1 GGAACAAAAAGAAATTGAAG
307429 AATACTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.07, G:0.27, T:0.10
Consensus pattern (21 bp):
GGAACAAAAAGAAATTGAAGC
Found at i:327697 original size:18 final size:18
Alignment explanation
Indices: 327676--327718 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
327666 ATCTGAAACC
327676 TATTCAAAATAATATTTT
1 TATTCAAAATAATATTTT
*
327694 TATTAAAAATAATATTTT
1 TATTCAAAATAATATTTT
327712 TATTCAA
1 TATTCAA
327719 TAAAAATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTCAAAATAATATTTT
Found at i:327726 original size:19 final size:18
Alignment explanation
Indices: 327676--327727 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 18
327666 ATCTGAAACC
*
327676 TATTCAAAATAATATTTT
1 TATTCAAAAAAATATTTT
327694 TATT-AAAAATAATATTTT
1 TATTCAAAAA-AATATTTT
327712 TATTCAATAAAAATAT
1 TATTCAA-AAAAATAT
327728 GAATTTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.13
18 16 0.53
19 7 0.23
20 3 0.10
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (18 bp):
TATTCAAAAAAATATTTT
Found at i:329118 original size:11 final size:11
Alignment explanation
Indices: 329101--329130 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
329091 AAATAAAAAG
329101 AAATAAAGTAA
1 AAATAAAGTAA
*
329112 CAATAAAGTAA
1 AAATAAAGTAA
329123 AAATAAAG
1 AAATAAAG
329131 ATGTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.70, C:0.03, G:0.10, T:0.17
Consensus pattern (11 bp):
AAATAAAGTAA
Found at i:330088 original size:11 final size:11
Alignment explanation
Indices: 330071--330100 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
330061 AAATAAAAAG
330071 AAATAAAGTAA
1 AAATAAAGTAA
*
330082 CAATAAAGTAA
1 AAATAAAGTAA
330093 AAATAAAG
1 AAATAAAG
330101 ATGTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.70, C:0.03, G:0.10, T:0.17
Consensus pattern (11 bp):
AAATAAAGTAA
Found at i:330510 original size:979 final size:979
Alignment explanation
Indices: 328596--331506 Score: 5095
Period size: 979 Copynumber: 3.0 Consensus size: 979
328586 TTGGGTCCGG
* *
328596 AATTGGGTTTCGACTTGAAATGA-TGGGTTAGAGTCGCCACCGACCACTTTAAAATAAATTTAGG
1 AATTGGGCTTCGACTTGAAATGATTGGGTTAGAGTCGCCACCGACCACTTTAAAACAAATTTAGG
* * * *
328660 TGAGTCGGACACCATCTTACCTGATCTGCATTGTACCA-GAAATGTGTCGGGTTCGGGAGTCGGT
66 TGAGTCGGATACCATCTTAACTGTTCTGCGTTGTA-CAGGAAATGTGTCGGGTTCGGGAGTCGGT
* * * * * * * *
328724 TACGGTCAAAGAAGGATTAGTACCATTGAACCACCCTTTCGGTACCAATTAATTTTCCGGTTATC
130 TATGGTCAATGAAGGATTAGCACCCTTGAACCGCCATTTCGGTACCAATTAATTTTCTGGTTGTC
* *
328789 TTTATTTGCAAAAATTAAGAATTTAAATTAAAATTTAAGAATTCGATTCAACTACTTACCTTTGA
195 TTTATTTGCGAAAATTAAGAATTTAAATTAAATTTTAAGAATTCGATTCAACTACTTACCTTTGA
328854 TTAGTTTGAAATTTCTAAAAAAAATAGGTCGAAAATGTTAGAGGAAAAAAATTATTTAAATAAAT
260 TTAGTTTGAAATTTCTAAAAAAAATAGGTCGAAAATGTTAGAGGAAAAAAATTATTTAAA-AAAT
* *
328919 -AAAAAAGGAAAAAAATTGATAATAAAAAC-------A-ATAAAGAAATAAAGAAAATAAATTGA
324 AAAAAAAGG-AAAAAA-TGATAATAAAAACAATAAATATATAAACAAATAAATAAAATAAATTGA
*
328975 AAGGGAAAACAAAAAAA-ATTAAATAAATCAAAAAAAGAAAAGAAAATATATTTATAAATAAATA
387 AAGGGAAAACAAAAAAACATTAAATAAATC-AAAAAAG----GAAAATATATTTATAAAGAAATA
* * *
329039 ATAAAAGGACAAATCAAAAGAAAAAAATAGAAAATAACAAACATAAAATAATAAATAAAAAGAAA
447 ATAAAAGTACAAATCAAAAGAAAAAAATAGAAAATAACAAACAGAACATAATAAATAAAAAGAAA
* *
329104 TAAAGTAACAATAAAGTAAAAATAAAGATG-TTT-AA-AATAAT-TTAA-AAAAACCCAGAAAAA
512 TAAAGTAACAATAAAGTAAAAATAAAGATGTTTTAAATAATAATAATAATAAAAACCCATAAAAA
** *
329164 ATATAATAAAATAAAATGTGTAAGAACATGAAGGACTAAAAATATAGTTAACCCTAAGCATACAT
577 ATATGGTAAAATAAAATGTGTAAGAACATGAAGGACTAAAAATATAGTTAACCATAAGCATACAT
* * * *
329229 GCCAAATTAGTGA-TAAAA-AAAATATATGAAAATGTAAGGGTCAAATTTGAATATTAACACAAA
642 GCCAAATTAGTGACCAAAACAGAAGATATGAAAATGTAAGGGTCAAATTCGAATATTAACACAAA
* **
329292 AAACATGTAATAT-AAAAAAGGGCTAAAATATAAATTATGGAAATTTAATGCTCAAAATAAAATG
707 AAACATGTAATATAAAAAAAGGGATAAAATATAAATCCTGGAAATTTAATGCTCAAAATAAAATG
329356 AATGAAAAGTTCAATGTATGGCCAGAAAGCAACATTACAAGGGACGAGGGACCCATGCTGTGATA
772 AATGAAAAGTTCAATGTATGGCCAGAAAGCAACATTACAAGGGACGAGGGACCCATGCTGTGATA
329421 AACCCCTAAGCAAAATTACGAGCCACTTCCCCATCGAAACTACATCGTTTCATCAGCATTATAAA
837 AACCCCTAAGCAAAATTACGAGCCACTTCCCCATCGAAACTACATCGTTTCATCAGCATTATAAA
*
329486 AAGGCCATATGAGAGTGAAATAATACCAAACCCTCTCATTTTACTCTCCACACTCTCTCTCTAAA
902 AAGGCCATATGAGAGTGAAATAACACCAAACCCTCTCATTTTACTCTCCACACTCTCTCTCTAAA
329551 ATGTTGGGCCCAA
967 ATGTTGGGCCCAA
329564 AATTGGGCTTCGACTTGAAATGATTGGGTTAGAGTCGCCACCGACCACTTTAAAACAAATTTAGG
1 AATTGGGCTTCGACTTGAAATGATTGGGTTAGAGTCGCCACCGACCACTTTAAAACAAATTTAGG
329629 TGAGTCGGATACCATCTTAACTGTTCTGCGTTGTACAGGAAATGTGTCGGGTTCGGGAGTCGGTT
66 TGAGTCGGATACCATCTTAACTGTTCTGCGTTGTACAGGAAATGTGTCGGGTTCGGGAGTCGGTT
*
329694 ATGGTCAATGAAGGATTAGCACCCTTGAACCGTCATTTCGGTACCAATTAATTTTCTGGTTGTCT
131 ATGGTCAATGAAGGATTAGCACCCTTGAACCGCCATTTCGGTACCAATTAATTTTCTGGTTGTCT
329759 TTATTTGCGAAAATTAAGAATTTAAATTAAATTTTAAGAATTCGATTCAACTACTTACCTTTGAT
196 TTATTTGCGAAAATTAAGAATTTAAATTAAATTTTAAGAATTCGATTCAACTACTTACCTTTGAT
*
329824 TAGTTTGAAATTTCT-AAAAAAATAGGTCGAAAATGTTAGAGGAAAAAAAGTATTTAAAAAATAA
261 TAGTTTGAAATTTCTAAAAAAAATAGGTCGAAAATGTTAGAGGAAAAAAATTATTTAAAAAATAA
329888 AAAAAGGAAAAAATGATAATAAAAACAATAAATATATAAACAAATAAATAAAATAAATTGAAAGG
326 AAAAAGGAAAAAATGATAATAAAAACAATAAATATATAAACAAATAAATAAAATAAATTGAAAGG
329953 GAAAACAAAAAAACATTAAATAAATCAAAAAAGGAAAATATATTTATAAAGAAATAATAAAAGTA
391 GAAAACAAAAAAACATTAAATAAATCAAAAAAGGAAAATATATTTATAAAGAAATAATAAAAGTA
*
330018 CAAATCAAAAGAAAAAAATAGAAAATAACAAACAGATCATAATAAATAAAAAGAAATAAAGTAAC
456 CAAATCAAAAGAAAAAAATAGAAAATAACAAACAGAACATAATAAATAAAAAGAAATAAAGTAAC
330083 AATAAAGTAAAAATAAAGATGTTTTAAATAATAATAATAATAATAAACCCATAAAAAATATGGTA
521 AATAAAGTAAAAATAAAGATGTTTTAAATAATAATAATAATAA-AAACCCATAAAAAATATGGTA
330148 AAATAAAATGTGTAAGAACATGAAGGACTAAAAATATAGTTAACCATAAGCATACATGCCAAATT
585 AAATAAAATGTGTAAGAACATGAAGGACTAAAAATATAGTTAACCATAAGCATACATGCCAAATT
330213 AGTGACCAAAACAGAAGATATGAAAATGTAAGGGTCAAATTCGAATATTAACACAAAAAACATGT
650 AGTGACCAAAACAGAAGATATGAAAATGTAAGGGTCAAATTCGAATATTAACACAAAAAACATGT
* *
330278 AATATAAAAAAAGGGATAAAATATAAATCCTGGAAATTTAATGCTTAGAATAAAATGAATGAAAA
715 AATATAAAAAAAGGGATAAAATATAAATCCTGGAAATTTAATGCTCAAAATAAAATGAATGAAAA
330343 GTTCAATGTATGGCCAGAAAGCAACATTACAAGGGACGAGGGACCCATGCTGTGATAAACCCCTA
780 GTTCAATGTATGGCCAGAAAGCAACATTACAAGGGACGAGGGACCCATGCTGTGATAAACCCCTA
*
330408 AGCAAAATTACGAGCCACTTCCCCATCGAAACTACATCGTTTCATTAGCATTATAAAAAGGCCAT
845 AGCAAAATTACGAGCCACTTCCCCATCGAAACTACATCGTTTCATCAGCATTATAAAAAGGCCAT
330473 ATGAGAGTGAAATAACACCAAACCCTCTCATTTTACTCTCCACACTCTCTCTCTAAAATGTTGGG
910 ATGAGAGTGAAATAACACCAAACCCTCTCATTTTACTCTCCACACTCTCTCTCTAAAATGTTGGG
*
330538 CCCGA
975 CCCAA
330543 AATTGGGCTTCGACTTGAAATGATTGGGTTAGAGTCGCCACCGACCACTTTAAAACAAATTTAGG
1 AATTGGGCTTCGACTTGAAATGATTGGGTTAGAGTCGCCACCGACCACTTTAAAACAAATTTAGG
330608 TGAGTCGGATACCATCTTAACTGTTCTGCGTTGTACAGGAAATGTGTCGGGTTCGGGAGTCGGTT
66 TGAGTCGGATACCATCTTAACTGTTCTGCGTTGTACAGGAAATGTGTCGGGTTCGGGAGTCGGTT
330673 ATGGTCAATGAAGGATTAGCACCCTTGAACCGCCATTTCGGTACCAATTAATTTTCTGGTTGTCT
131 ATGGTCAATGAAGGATTAGCACCCTTGAACCGCCATTTCGGTACCAATTAATTTTCTGGTTGTCT
330738 TTATTTGCGAAAATTAAGAATTTAAATTAAATTTTAAGAATTCGATTCAACTACTTACCTTTGAT
196 TTATTTGCGAAAATTAAGAATTTAAATTAAATTTTAAGAATTCGATTCAACTACTTACCTTTGAT
330803 TAGTTTGAAATTTCTAAAAAAAATAGGTCGAAAATGTTAGAGG-AAAAAATTATTTAAAAAATAA
261 TAGTTTGAAATTTCTAAAAAAAATAGGTCGAAAATGTTAGAGGAAAAAAATTATTTAAAAAATAA
330867 AAAAAGGAAAAAATGATAATAAAAACAATAAATATATAAACAAATAAATAAAATAAATTGAAAGG
326 AAAAAGGAAAAAATGATAATAAAAACAATAAATATATAAACAAATAAATAAAATAAATTGAAAGG
330932 GAAAACAAAAAAACATTAAATAAATCAAAAAAGGAAAATATATTTATAAAGAAAT-A-AAAAGTA
391 GAAAACAAAAAAACATTAAATAAATCAAAAAAGGAAAATATATTTATAAAGAAATAATAAAAGTA
330995 CAAATCAAAAG-AAAAAATAGAAAATAACAAACAGAACATAATAAAT-AAAAGAAATAAAGTAAC
456 CAAATCAAAAGAAAAAAATAGAAAATAACAAACAGAACATAATAAATAAAAAGAAATAAAGTAAC
331058 AATAAAGT-AAAATAAAGATGTTTTAAATAATAATAATAATAAAAAAACCCATAAAAAATATGGT
521 AATAAAGTAAAAATAAAGATGTTTTAAATAATAATAATAAT--AAAAACCCATAAAAAATATGGT
331122 AAAATAAAATGTGTAAGAACATGAAGGACTAAAAATATAGTTAACCATAAGCATACATGCCAAAT
584 AAAATAAAATGTGTAAGAACATGAAGGACTAAAAATATAGTTAACCATAAGCATACATGCCAAAT
331187 TAGTGACCAAAACAGAAGATATGAAAATGTAAGGGTCAAATTCGAATATTAACACAAAAAACATG
649 TAGTGACCAAAACAGAAGATATGAAAATGTAAGGGTCAAATTCGAATATTAACACAAAAAACATG
331252 TAATATAAAAAAAGGGATAAAATATAAATCCTGGAAATTTAATGCTCAAAATAAAATGAATGAAA
714 TAATATAAAAAAAGGGATAAAATATAAATCCTGGAAATTTAATGCTCAAAATAAAATGAATGAAA
*
331317 AGTTCAATGTATGGCCAGAAAGCAACATTACAAGGGACGAGGGACCCATGCTGCGATAAACCCCT
779 AGTTCAATGTATGGCCAGAAAGCAACATTACAAGGGACGAGGGACCCATGCTGTGATAAACCCCT
* *
331382 AAGCAAAATTACGAGCCACTCCCCCATCGAAACTACGTCGTTTCATCAGCATTAT-AAAAGGCCA
844 AAGCAAAATTACGAGCCACTTCCCCATCGAAACTACATCGTTTCATCAGCATTATAAAAAGGCCA
**
331446 TATGAGAGTGAAATAACACCAAACCCTCTCATTTTACTCTTTACACTCTCTCTCTAAAATG
909 TATGAGAGTGAAATAACACCAAACCCTCTCATTTTACTCTCCACACTCTCTCTCTAAAATG
331507 ATATATCTCC
Statistics
Matches: 1866, Mismatches: 53, Indels: 42
0.95 0.03 0.02
Matches are distributed among these distances:
966 13 0.01
967 10 0.01
968 74 0.04
969 232 0.12
970 113 0.06
971 3 0.00
972 2 0.00
973 7 0.00
974 151 0.08
975 368 0.20
976 123 0.07
977 22 0.01
978 56 0.03
979 665 0.36
980 27 0.01
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (979 bp):
AATTGGGCTTCGACTTGAAATGATTGGGTTAGAGTCGCCACCGACCACTTTAAAACAAATTTAGG
TGAGTCGGATACCATCTTAACTGTTCTGCGTTGTACAGGAAATGTGTCGGGTTCGGGAGTCGGTT
ATGGTCAATGAAGGATTAGCACCCTTGAACCGCCATTTCGGTACCAATTAATTTTCTGGTTGTCT
TTATTTGCGAAAATTAAGAATTTAAATTAAATTTTAAGAATTCGATTCAACTACTTACCTTTGAT
TAGTTTGAAATTTCTAAAAAAAATAGGTCGAAAATGTTAGAGGAAAAAAATTATTTAAAAAATAA
AAAAAGGAAAAAATGATAATAAAAACAATAAATATATAAACAAATAAATAAAATAAATTGAAAGG
GAAAACAAAAAAACATTAAATAAATCAAAAAAGGAAAATATATTTATAAAGAAATAATAAAAGTA
CAAATCAAAAGAAAAAAATAGAAAATAACAAACAGAACATAATAAATAAAAAGAAATAAAGTAAC
AATAAAGTAAAAATAAAGATGTTTTAAATAATAATAATAATAAAAACCCATAAAAAATATGGTAA
AATAAAATGTGTAAGAACATGAAGGACTAAAAATATAGTTAACCATAAGCATACATGCCAAATTA
GTGACCAAAACAGAAGATATGAAAATGTAAGGGTCAAATTCGAATATTAACACAAAAAACATGTA
ATATAAAAAAAGGGATAAAATATAAATCCTGGAAATTTAATGCTCAAAATAAAATGAATGAAAAG
TTCAATGTATGGCCAGAAAGCAACATTACAAGGGACGAGGGACCCATGCTGTGATAAACCCCTAA
GCAAAATTACGAGCCACTTCCCCATCGAAACTACATCGTTTCATCAGCATTATAAAAAGGCCATA
TGAGAGTGAAATAACACCAAACCCTCTCATTTTACTCTCCACACTCTCTCTCTAAAATGTTGGGC
CCAA
Found at i:332442 original size:3 final size:3
Alignment explanation
Indices: 332428--332471 Score: 52
Period size: 3 Copynumber: 13.7 Consensus size: 3
332418 AAAGAGAAAA
*
332428 AAT AAA AAT AAT AAT AAGT AAT AAT AAT AAAT AAAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT -AAT -AAT AAT AAT AA
332472 AAAATATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 27 0.73
4 10 0.27
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:332466 original size:17 final size:17
Alignment explanation
Indices: 332427--332477 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
332417 TAAAGAGAAA
*
332427 AAATAAAAATAAT-AAT
1 AAATAATAATAATAAAT
*
332443 AAGTAATAATAATAAAT
1 AAATAATAATAATAAAT
*
332460 AAATAATAATAAAAAAT
1 AAATAATAATAATAAAT
332477 A
1 A
332478 TAAAAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 11 0.37
17 19 0.63
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (17 bp):
AAATAATAATAATAAAT
Found at i:332472 original size:10 final size:10
Alignment explanation
Indices: 332428--332486 Score: 56
Period size: 10 Copynumber: 6.4 Consensus size: 10
332418 AAAGAGAAAA
332428 AATAA-AAAT
1 AATAATAAAT
*
332437 AATAATAAGT
1 AATAATAAAT
332447 AATAAT-AAT
1 AATAATAAAT
332456 -A-AATAAAT
1 AATAATAAAT
*
332464 AATAATAAAA
1 AATAATAAAT
*
332474 AAT-ATAAAA
1 AATAATAAAT
332483 AATA
1 AATA
332487 TTTTTTAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
7 3 0.07
8 4 0.10
9 17 0.40
10 18 0.43
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (10 bp):
AATAATAAAT
Found at i:332571 original size:29 final size:30
Alignment explanation
Indices: 332538--332595 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
332528 TTTTTTTAAC
*
332538 TATATAATTTTTAAAAAT-GTTTTAAAAAT
1 TATATAATTTTCAAAAATAGTTTTAAAAAT
*
332567 TATATAATTTTCAAAAATATTTTTAAAAA
1 TATATAATTTTCAAAAATAGTTTTAAAAA
332596 AAATATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
TATATAATTTTCAAAAATAGTTTTAAAAAT
Found at i:332624 original size:40 final size:38
Alignment explanation
Indices: 332565--332776 Score: 178
Period size: 36 Copynumber: 5.7 Consensus size: 38
332555 TGTTTTAAAA
332565 ATTATATAA-TTTTCAAAAATATTTTTAAAAAAAATAT
1 ATTATATAAGTTTTCAAAAATATTTTTAAAAAAAATAT
*
332602 ATTACATATAAGTTTTCAAAAATGTTTTTAAAAAAACTATAT
1 ATT--ATATAAGTTTTCAAAAATATTTTTAAAAAAA--ATAT
**
332644 ATTATATAAGTTTTC-AAAATGA-TTTTAAAAATTATAT
1 ATTATATAAGTTTTCAAAAAT-ATTTTTAAAAAAAATAT
* **
332681 A-TATAT-A-TTTTCTAAAAATGTTTTT-AAAACTATAT
1 ATTATATAAGTTTTC-AAAAATATTTTTAAAAAAAATAT
** **
332716 ATTATAT-AGTTTTCAAAGGT-TTTTTAAAAACTATAT
1 ATTATATAAGTTTTCAAAAATATTTTTAAAAAAAATAT
*
332752 A-TATATACA-TTTT-AAAAATGTTTTT
1 ATTATATA-AGTTTTCAAAAATATTTTT
332777 TTTTTAAAAA
Statistics
Matches: 150, Mismatches: 10, Indels: 31
0.79 0.05 0.16
Matches are distributed among these distances:
34 5 0.03
35 25 0.17
36 44 0.29
37 14 0.09
39 20 0.13
40 35 0.23
42 7 0.05
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (38 bp):
ATTATATAAGTTTTCAAAAATATTTTTAAAAAAAATAT
Found at i:332740 original size:35 final size:35
Alignment explanation
Indices: 332607--332777 Score: 145
Period size: 35 Copynumber: 4.7 Consensus size: 35
332597 AATATATTAC
*
332607 ATATA-AGTTTTCAAAAATGTTTTTAAAAAAACTATAT
1 ATATATAGTTTTCAAAAA-GTTTTT--TAAAACTATAT
* * * *
332644 ATTATATAAGTTTTCAAAATGATTTTAAAAATTATAT
1 A-TATAT-AGTTTTCAAAAAGTTTTTTAAAACTATAT
332681 ATATATA-TTTTCTAAAAA-TGTTTTTAAAACTATAT
1 ATATATAGTTTTC-AAAAAGT-TTTTTAAAACTATAT
*
332716 ATTATATAGTTTTC-AAAGGTTTTTTAAAAACTATAT
1 A-TATATAGTTTTCAAAAAGTTTTTT-AAAACTATAT
*
332752 ATATATACATTTT-AAAAATGTTTTTT
1 ATATATA-GTTTTCAAAAA-GTTTTTT
332778 TTTTAAAAAC
Statistics
Matches: 112, Mismatches: 10, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
34 5 0.04
35 33 0.29
36 30 0.27
37 24 0.21
38 4 0.04
39 5 0.04
40 11 0.10
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (35 bp):
ATATATAGTTTTCAAAAAGTTTTTTAAAACTATAT
Found at i:332751 original size:71 final size:74
Alignment explanation
Indices: 332565--332776 Score: 224
Period size: 71 Copynumber: 2.9 Consensus size: 74
332555 TGTTTTAAAA
* * *
332565 ATTATATAA-TTTTCAAAAAT-ATTTTTAAAAAAAATATATTACATATAAGTTTTC-AAAAATGT
1 ATTATATAAGTTTTC-AAAATGA-TTTT--AAAAACTATA-TATATAT-ACTTTTCTAAAAATGT
332627 TTTTAAAAAAACTATAT
60 TTTT--AAAAACTATAT
*
332644 ATTATATAAGTTTTCAAAATGATTTTAAAAATTATATATATATA-TTTTCTAAAAATGTTTTT-A
1 ATTATATAAGTTTTCAAAATGATTTTAAAAACTATATATATATACTTTTCTAAAAATGTTTTTAA
332707 AAACTATAT
66 AAACTATAT
* * *
332716 ATTATAT-AGTTTTC-AAAGGTTTTTTAAAAACTATATATATATACATTT-TAAAAATGTTTTT
1 ATTATATAAGTTTTCAAAATG-ATTTTAAAAACTATATATATATACTTTTCTAAAAATGTTTTT
332777 TTTTTAAAAA
Statistics
Matches: 122, Mismatches: 6, Indels: 18
0.84 0.04 0.12
Matches are distributed among these distances:
70 4 0.03
71 41 0.34
72 20 0.16
74 5 0.04
75 13 0.11
76 6 0.05
77 9 0.07
79 18 0.15
80 6 0.05
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (74 bp):
ATTATATAAGTTTTCAAAATGATTTTAAAAACTATATATATATACTTTTCTAAAAATGTTTTTAA
AAACTATAT
Found at i:337914 original size:26 final size:26
Alignment explanation
Indices: 337837--337902 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
337827 ATAAGTTCGG
337837 CCTCACTT-AAATTTTATATATTTGT
1 CCTCACTTAAAATTTTATATATTTGT
337862 CCTCACTTAAAATTTTATATATTTGT
1 CCTCACTTAAAATTTTATATATTTGT
337888 CCTCACTTAAAATTT
1 CCTCACTTAAAATTT
337903 AATAAGTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 8 0.20
26 32 0.80
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.48
Consensus pattern (26 bp):
CCTCACTTAAAATTTTATATATTTGT
Found at i:337922 original size:25 final size:26
Alignment explanation
Indices: 337837--337914 Score: 115
Period size: 26 Copynumber: 3.0 Consensus size: 26
337827 ATAAGTTCGG
*
337837 CCTCACTT-AAATTTTATATATTTGT
1 CCTCACTTAAAATTTAATATATTTGT
*
337862 CCTCACTTAAAATTTTATATATTTGT
1 CCTCACTTAAAATTTAATATATTTGT
337888 CCTCACTTAAAATTTAATA-AGTTTGT
1 CCTCACTTAAAATTTAATATA-TTTGT
337914 C
1 C
337915 TCTTTTAACA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
25 9 0.18
26 41 0.82
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.47
Consensus pattern (26 bp):
CCTCACTTAAAATTTAATATATTTGT
Found at i:338901 original size:26 final size:26
Alignment explanation
Indices: 338872--338925 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
338862 TACACTAAAC
* *
338872 AAATCATAGTCCAGTAAATATCATAA
1 AAATCATACTCCAGTAAATACCATAA
* * *
338898 AAATTATACTGCAGTAAATCCCATAA
1 AAATCATACTCCAGTAAATACCATAA
338924 AA
1 AA
338926 GAGTTACCCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (26 bp):
AAATCATACTCCAGTAAATACCATAA
Found at i:339993 original size:29 final size:29
Alignment explanation
Indices: 339952--340084 Score: 180
Period size: 29 Copynumber: 4.6 Consensus size: 29
339942 CACATTCGAA
339952 AATTCCCAAAATGTCACCATTTTT-AAAAT
1 AATTCCCAAAATGTCACC-TTTTTCAAAAT
* *
339981 AATTCCCAGAATGTTA-CTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
340009 AATTCCCAAAATATCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
* * *
340038 AATTCCCAGAATGACACATTTTTCAAAAT
1 AATTCCCAAAATGTCACCTTTTTCAAAAT
*
340067 AATTCTCAAAATGTCACC
1 AATTCCCAAAATGTCACC
340085 GGGTCGGGTC
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
27 5 0.06
28 19 0.21
29 65 0.73
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.34
Consensus pattern (29 bp):
AATTCCCAAAATGTCACCTTTTTCAAAAT
Found at i:340040 original size:57 final size:58
Alignment explanation
Indices: 339952--340084 Score: 207
Period size: 57 Copynumber: 2.3 Consensus size: 58
339942 CACATTCGAA
**
339952 AATTCCCAAAATGTCACCATTTTTAAAATAATTCCCAGAATGTTAC-TTTTTCAAAAT
1 AATTCCCAAAATGTCACCATTTTTAAAATAATTCCCAGAATGACACATTTTTCAAAAT
*
340009 AATTCCCAAAATATCACC-TTTTTCAAAATAATTCCCAGAATGACACATTTTTCAAAAT
1 AATTCCCAAAATGTCACCATTTTT-AAAATAATTCCCAGAATGACACATTTTTCAAAAT
*
340067 AATTCTCAAAATGTCACC
1 AATTCCCAAAATGTCACC
340085 GGGTCGGGTC
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
56 5 0.07
57 37 0.54
58 27 0.39
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.34
Consensus pattern (58 bp):
AATTCCCAAAATGTCACCATTTTTAAAATAATTCCCAGAATGACACATTTTTCAAAAT
Found at i:340124 original size:19 final size:19
Alignment explanation
Indices: 340102--340173 Score: 108
Period size: 19 Copynumber: 3.8 Consensus size: 19
340092 GTCGGACCGG
* *
340102 TCAACCCGGTTCAGACCAA
1 TCAAACCGGGTCAGACCAA
*
340121 TCAAACCGGGTCAGACCAG
1 TCAAACCGGGTCAGACCAA
*
340140 TCAAACCGGGTCAGACCGA
1 TCAAACCGGGTCAGACCAA
340159 TCAAACCGGGTCAGA
1 TCAAACCGGGTCAGA
340174 ACGGTTTGGA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.32, C:0.32, G:0.24, T:0.12
Consensus pattern (19 bp):
TCAAACCGGGTCAGACCAA
Found at i:340143 original size:38 final size:38
Alignment explanation
Indices: 340089--340173 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
340079 GTCACCGGGT
* * * *
340089 CGGGTCGGACCGGTCAACCCGGTTCAGACCAATCAAAC
1 CGGGTCAGACCAGTCAAACCGGGTCAGACCAATCAAAC
*
340127 CGGGTCAGACCAGTCAAACCGGGTCAGACCGATCAAAC
1 CGGGTCAGACCAGTCAAACCGGGTCAGACCAATCAAAC
340165 CGGGTCAGA
1 CGGGTCAGA
340174 ACGGTTTGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.28, C:0.32, G:0.28, T:0.12
Consensus pattern (38 bp):
CGGGTCAGACCAGTCAAACCGGGTCAGACCAATCAAAC
Found at i:347407 original size:29 final size:29
Alignment explanation
Indices: 347366--347557 Score: 249
Period size: 29 Copynumber: 6.6 Consensus size: 29
347356 CACATTCGAA
*
347366 AATTCCCAAAATGTCTCATTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* * *
347395 AATTCTCAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* * *
347424 AATTCCCAACATATCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* * *
347453 AATTCCCAGAATGTCACCTTTTTTAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
* *
347482 AATTCCCATAATGTCACATTTTTCAAAAAA
1 AATTCCCAAAATGTCACATTTTTC-AAAAT
*
347512 AAATCCCAAAATGTCACATTTTTCAAAAT
1 AATTCCCAAAATGTCACATTTTTCAAAAT
*
347541 AATTTCCAAAATGTCAC
1 AATTCCCAAAATGTCAC
347558 CGGTTCGGGT
Statistics
Matches: 141, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
29 115 0.82
30 26 0.18
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (29 bp):
AATTCCCAAAATGTCACATTTTTCAAAAT
Found at i:351294 original size:20 final size:20
Alignment explanation
Indices: 351269--351313 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
351259 ATCATCTAAT
* *
351269 TTTTTAAACCTCAGACCGGA
1 TTTTTAAACCCCAAACCGGA
351289 TTTTTAAACCCCAAACCGGA
1 TTTTTAAACCCCAAACCGGA
351309 TTTTT
1 TTTTT
351314 TTCCGGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (20 bp):
TTTTTAAACCCCAAACCGGA
Found at i:359421 original size:19 final size:19
Alignment explanation
Indices: 359397--359436 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
359387 TAATAAAGAA
359397 AGTAGTGTCAGGATATGGT
1 AGTAGTGTCAGGATATGGT
359416 AGTAGTGTCAGGATATGGT
1 AGTAGTGTCAGGATATGGT
359435 AG
1 AG
359437 AAAACCTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.05, G:0.38, T:0.30
Consensus pattern (19 bp):
AGTAGTGTCAGGATATGGT
Found at i:360204 original size:12 final size:12
Alignment explanation
Indices: 360187--360212 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
360177 GATGCTTGAA
360187 CAGTTCTTATAT
1 CAGTTCTTATAT
360199 CAGTTCTTATAT
1 CAGTTCTTATAT
360211 CA
1 CA
360213 AAGTTTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (12 bp):
CAGTTCTTATAT
Found at i:365035 original size:21 final size:21
Alignment explanation
Indices: 364984--365036 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
364974 ATTATTACTA
364984 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* *
365005 TCGTATTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
365026 TCGCAATGCGA
1 TCGCAATGCGA
365037 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:365056 original size:41 final size:42
Alignment explanation
Indices: 365011--365099 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 42
365001 AATTTCGTAT
* * *
365011 TGCGATTTTCCCAATTCGCAATGCGAA-TAAGTAAATCGCAA
1 TGCGATTTTCCAAAATCGCAATGCGAATTAAGAAAATCGCAA
* ** **
365052 TGCGAATTTGGAAAATCGCAATGCGAATTTGGAAAATCGCAA
1 TGCGATTTTCCAAAATCGCAATGCGAATTAAGAAAATCGCAA
365094 TGCGAT
1 TGCGAT
365100 ACTGACTATC
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
41 22 0.58
42 16 0.42
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (42 bp):
TGCGATTTTCCAAAATCGCAATGCGAATTAAGAAAATCGCAA
Found at i:365069 original size:21 final size:21
Alignment explanation
Indices: 365026--365098 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
365016 TTTTCCCAAT
** *
365026 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
365046 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
365067 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
365088 TCGCAATGCGA
1 TCGCAATGCGA
365099 TACTGACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 12 0.24
21 37 0.76
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:365112 original size:20 final size:20
Alignment explanation
Indices: 365087--365160 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
365077 AATTTGGAAA
365087 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
365107 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
365128 ATCGCAATGCGA-ATCTGACT
1 ATCGCAATGCGATA-CTGACT
365148 ATCGCAATGCGAT
1 ATCGCAATGCGAT
365161 TTACATAGCG
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
19 2 0.05
20 27 0.63
21 12 0.28
22 2 0.05
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:365160 original size:41 final size:42
Alignment explanation
Indices: 365026--365160 Score: 136
Period size: 41 Copynumber: 3.3 Consensus size: 42
365016 TTTTCCCAAT
** * **
365026 TCGCAATGCGA-ATA-AGTAAATCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGATATATACAAAATCGCAATGCGAATCT-GACTA
* **
365067 TCGCAATGCGA-ATTTGGAAAATCGCAATGCG-ATACTGACTA
1 TCGCAATGCGATATATACAAAATCGCAATGCGAAT-CTGACTA
*
365108 TCGCAACGCGATA-ATACAAAATCGCAATGCGAATCTGACTA
1 TCGCAATGCGATATATACAAAATCGCAATGCGAATCTGACTA
365149 TCGCAATGCGAT
1 TCGCAATGCGAT
365161 TTACATAGCG
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
41 61 0.77
42 18 0.23
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (42 bp):
TCGCAATGCGATATATACAAAATCGCAATGCGAATCTGACTA
Found at i:365713 original size:20 final size:20
Alignment explanation
Indices: 365688--365725 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
365678 TAGTTTCGAG
365688 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGCGGA
365708 AATGAAAATCGCAACGCG
1 AATGAAAATCGCAACGCG
365726 AAACTAAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGGA
Found at i:366268 original size:34 final size:34
Alignment explanation
Indices: 366225--366331 Score: 115
Period size: 40 Copynumber: 3.0 Consensus size: 34
366215 GACATTCATT
*
366225 TGACTATCGCAACGGGGAAATCGCAACACGAAAA
1 TGACTATCGCAACGGGGAAATCGCAACGCGAAAA
**
366259 TGACTATCGCAACGCGAAAATGGCTATCGCAACGCGAAAA
1 TGACTATCGCAACG-G-----GGAAATCGCAACGCGAAAA
* *
366299 TGACTATCGCAACGAGAAAATCGCAACGCGAAA
1 TGACTATCGCAACGGGGAAATCGCAACGCGAAA
366332 TGAAAATCGT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
34 29 0.48
35 1 0.02
40 30 0.50
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.13
Consensus pattern (34 bp):
TGACTATCGCAACGGGGAAATCGCAACGCGAAAA
Found at i:366269 original size:20 final size:20
Alignment explanation
Indices: 366244--366319 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
366234 CAACGGGGAA
*
366244 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
366264 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
366284 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
366304 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
366320 CGCAACGCGA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:366379 original size:19 final size:19
Alignment explanation
Indices: 366357--366402 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
366347 AATTTTCTAG
366357 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCACA
*
366376 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCACA
366395 TTGCGATT
1 TTGCGATT
366403 CTCTCGTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.17, C:0.20, G:0.15, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCACA
Found at i:368440 original size:20 final size:19
Alignment explanation
Indices: 368415--368494 Score: 70
Period size: 20 Copynumber: 4.1 Consensus size: 19
368405 AAGAATAGTT
368415 TACTTTCGCAACACGAAACA
1 TACTTTCGCAACACGAAA-A
*
368435 TACTTTCGCAACGCGAAAA
1 TACTTTCGCAACACGAAAA
* * *
368454 TGACTATCGCAACGCGGAAA
1 T-ACTTTCGCAACACGAAAA
* * *
368474 TGGCTATCGCAACACGGAAA
1 T-ACTTTCGCAACACGAAAA
368494 T
1 T
368495 GGCTATCGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 2 0.04
20 52 0.96
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (19 bp):
TACTTTCGCAACACGAAAA
Found at i:368465 original size:40 final size:40
Alignment explanation
Indices: 368420--368526 Score: 99
Period size: 40 Copynumber: 2.7 Consensus size: 40
368410 TAGTTTACTT
* *
368420 TCGCAACACGAAACAT-ACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGAAA-ATGACTATCGCAACACGAAAATGACTA
* * * * *
368460 TCGCAACGCGGAAATGGCTATCGCAACACGGAAATGGCTA
1 TCGCAACACGAAAATGACTATCGCAACACGAAAATGACTA
* * **
368500 TCGCAACGCGGAAATGAAAATCGCAAC
1 TCGCAACACGAAAATGACTATCGCAAC
368527 GACAAGATCA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 2 0.04
40 54 0.96
ACGTcount: A:0.37, C:0.26, G:0.21, T:0.15
Consensus pattern (40 bp):
TCGCAACACGAAAATGACTATCGCAACACGAAAATGACTA
Found at i:368495 original size:20 final size:20
Alignment explanation
Indices: 368440--368515 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
368430 AAACATACTT
* *
368440 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGGCTA
368460 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
*
368480 TCGCAACACGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
368500 TCGCAACGCGGAAATG
1 TCGCAACGCGGAAATG
368516 AAAATCGCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.34, C:0.25, G:0.26, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGGAAATGGCTA
Found at i:368522 original size:20 final size:20
Alignment explanation
Indices: 368440--368527 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
368430 AAACATACTT
*
368440 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
368460 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* *
368480 TCGCAACACGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
**
368500 TCGCAACGCGGAAATGAAAA
1 TCGCAACGCGGAAATGACTA
368520 TCGCAACG
1 TCGCAACG
368528 ACAAGATCAC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.36, C:0.25, G:0.25, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:368552 original size:33 final size:33
Alignment explanation
Indices: 368503--368579 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
368493 ATGGCTATCG
*
368503 CAACGCGGAAATGAAAATCGCAACGACAAGATCA
1 CAACGC-GAAATGAAAATCGCAACGACAAAATCA
* *
368537 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAACGCGAAATGAAAATCGCAACGACAAAATCA
368570 CAACGCGAAA
1 CAACGCGAAA
368580 CATAAATCGC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 34 0.87
34 5 0.13
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.09
Consensus pattern (33 bp):
CAACGCGAAATGAAAATCGCAACGACAAAATCA
Found at i:368587 original size:33 final size:32
Alignment explanation
Indices: 368499--368590 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 32
368489 GGAAATGGCT
* *
368499 ATCGCAACGCGGAAATGAAAATCGCAACGACAAG
1 ATCGCAACGCGAAAAT--AAATCGCAACGACAAA
* *
368533 ATCACAATGCG-AAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAAAT--AAATCGCAACGACAAA
368566 ATCGCAACGCGAAACATAAATCGCA
1 ATCGCAACGCGAAA-ATAAATCGCA
368591 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 38 0.75
34 11 0.22
35 2 0.04
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAAATAAATCGCAACGACAAA
Found at i:368608 original size:19 final size:19
Alignment explanation
Indices: 368586--368682 Score: 83
Period size: 19 Copynumber: 5.6 Consensus size: 19
368576 GAAACATAAA
368586 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
368605 TCGCGTTGCGA---TC-TT
1 TCGCATTGCGATTTTCATT
368620 GTCG--TTGCGATTTTCATT
1 -TCGCATTGCGATTTTCATT
368638 TCGCATTGCGA---TC-TT
1 TCGCATTGCGATTTTCATT
368653 GTCG--TTGCGATTTTCATT
1 -TCGCATTGCGATTTTCATT
368671 TCGCATTGCGAT
1 TCGCATTGCGAT
368683 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 1, Indels: 28
0.68 0.01 0.30
Matches are distributed among these distances:
14 12 0.19
15 4 0.06
16 10 0.16
17 10 0.16
18 4 0.06
19 23 0.37
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:368627 original size:14 final size:14
Alignment explanation
Indices: 368608--368663 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 14
368598 TTTCATTTCG
368608 CGTTGCGATCTTGT
1 CGTTGCGATCTTGT
368622 CGTTGCGATTTTCATT-T
1 CGTTGCGA---TC-TTGT
368639 CGCATTGCGATCTTGT
1 CG--TTGCGATCTTGT
368655 CGTTGCGAT
1 CGTTGCGAT
368664 TTTCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
14 15 0.43
15 2 0.06
16 5 0.14
17 5 0.14
18 2 0.06
19 6 0.17
ACGTcount: A:0.11, C:0.21, G:0.25, T:0.43
Consensus pattern (14 bp):
CGTTGCGATCTTGT
Found at i:368633 original size:33 final size:33
Alignment explanation
Indices: 368591--368682 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
368581 ATAAATCGCA
*
368591 TTGCGATTTTCATTTCGCGTTGCGATCTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATCTTGTCG
368624 TTGCGATTTTCATTTCGCATTGCGATCTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATCTTGTCG
368657 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
368683 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATCTTGTCG
Found at i:368701 original size:20 final size:19
Alignment explanation
Indices: 368667--368721 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
368657 TTGCGATTTT
*
368667 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
368686 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
368706 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
368722 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:369285 original size:18 final size:18
Alignment explanation
Indices: 369256--369303 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
369246 CGGGTCGATT
369256 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
* *
369274 ATGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
369292 AGGTGATGGCTC
1 AGGTGATGGCTC
369304 CCGAAGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.15, C:0.12, G:0.44, T:0.29
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:370956 original size:22 final size:22
Alignment explanation
Indices: 370931--370974 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
370921 GATGGAGCTA
370931 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
370953 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
370975 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:371190 original size:20 final size:20
Alignment explanation
Indices: 371161--371224 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
371151 GATTATGTAT
*
371161 TATCTCGTTGCGAAAGTCAG
1 TATCTCGTTGTGAAAGTCAG
* *
371181 TATCTAGTTGTGAAAGTAAG
1 TATCTCGTTGTGAAAGTCAG
*
371201 TATCGCGTTGTGAAAGTCAG
1 TATCTCGTTGTGAAAGTCAG
371221 TATC
1 TATC
371225 GCATTACGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (20 bp):
TATCTCGTTGTGAAAGTCAG
Found at i:371260 original size:41 final size:41
Alignment explanation
Indices: 371141--371278 Score: 129
Period size: 41 Copynumber: 3.4 Consensus size: 41
371131 CGCTTTGAAA
* * *
371141 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTACGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** ** * *
371182 ATC-TAGTTGTGA--AAGTAAGTATCGCGTTGTGAAAGTCAGT
1 ATCGCA-TTACGATTTTGT-ATTATCGCGTTGCGAAAGTCAGT
*
371222 ATCGCATTACGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTACGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
371263 ATCGCATTGCGATTTT
1 ATCGCATTACGATTTT
371279 CCAAATTCGC
Statistics
Matches: 77, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
39 3 0.04
40 28 0.36
41 44 0.57
42 2 0.03
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (41 bp):
ATCGCATTACGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:371267 original size:20 final size:20
Alignment explanation
Indices: 371161--371274 Score: 86
Period size: 20 Copynumber: 5.7 Consensus size: 20
371151 GATTATGTAT
*
371161 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** * *
371181 TATCTAGTTGTGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
371201 TATCGCGTTGTGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * ** *
371221 TATCGCATTACGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
371242 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
371262 TATCGCATTGCGA
1 TATCGCGTTGCGA
371275 TTTTCCAAAT
Statistics
Matches: 74, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
19 3 0.04
20 57 0.77
21 12 0.16
22 2 0.03
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:371275 original size:20 final size:20
Alignment explanation
Indices: 371141--371275 Score: 69
Period size: 20 Copynumber: 6.7 Consensus size: 20
371131 CGCTTTGAAA
*
371141 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
371162 ATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
371182 ATC-TAGTTGTGAAAGTAAGT
1 ATCGCA-TTGCGATAGTCAGT
* * *
371202 ATCGCGTTGTGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
371222 ATCGCATTACGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
371243 ATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
371263 ATCGCATTGCGAT
1 ATCGCATTGCGAT
371276 TTTCCAAATT
Statistics
Matches: 86, Mismatches: 22, Indels: 13
0.71 0.18 0.11
Matches are distributed among these distances:
19 5 0.06
20 57 0.66
21 22 0.26
22 2 0.02
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:371294 original size:41 final size:41
Alignment explanation
Indices: 371201--371296 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
371191 TGAAAGTAAG
* * * ** *
371201 TATCGCGTTGTGAAAGTCAGTATCGCATTACGATTTTGTAT
1 TATCGCATTGCGATAGTCAGTATCGCATTACGATTTTCAAA
* *
371242 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAA
1 TATCGCATTGCGATAGTCAGTATCGCATTACGATTTT-CAAA
371284 T-TCGCATTGCGAT
1 TATCGCATTGCGAT
371297 TTACTTAATC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (41 bp):
TATCGCATTGCGATAGTCAGTATCGCATTACGATTTTCAAA
Found at i:371329 original size:21 final size:20
Alignment explanation
Indices: 371303--371357 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
371293 CGATTTACTT
*
371303 AATCGCAATGCGAATTGGGAA
1 AATCGCAATGCGAATT-AGAA
*
371324 AATCGCAACGCGAAATTAGAA
1 AATCGCAATGCG-AATTAGAA
*
371345 AATCGCATTGCGA
1 AATCGCAATGCGA
371358 TAGTAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 24 0.83
22 4 0.14
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
AATCGCAATGCGAATTAGAA
Found at i:376182 original size:2 final size:2
Alignment explanation
Indices: 376171--376199 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
376161 ACTTAACAGC
376171 AT AT -T 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
376200 TAAATTATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:376756 original size:3 final size:3
Alignment explanation
Indices: 376748--376773 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
376738 GGGTGTTGGA
376748 TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TG
376774 ATGATGGCTT
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:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:379762 original size:22 final size:23
Alignment explanation
Indices: 379711--379754 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
379701 ACGTATAATT
*
379711 ATAAATTAGTTAAAAATCTAAAG
1 ATAAATTAGTTAAAAATCAAAAG
*
379734 ATAAATTATTTAAAAAT-AAAA
1 ATAAATTAGTTAAAAATCAAAA
379755 TATTAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (23 bp):
ATAAATTAGTTAAAAATCAAAAG
Found at i:382592 original size:2 final size:2
Alignment explanation
Indices: 382585--382625 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
382575 AATAGTATGA
382585 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
382626 AACAAATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:383163 original size:19 final size:19
Alignment explanation
Indices: 383139--383177 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
383129 AATATTCACA
* *
383139 TATTAATTAGTTATAATAT
1 TATTAATCAATTATAATAT
383158 TATTAATCAATTATAATAT
1 TATTAATCAATTATAATAT
383177 T
1 T
383178 TGTGTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (19 bp):
TATTAATCAATTATAATAT
Found at i:383945 original size:22 final size:22
Alignment explanation
Indices: 383915--383957 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
383905 TTTTCAATTA
383915 ATTAATATATTCTTAAATTAAT
1 ATTAATATATTCTTAAATTAAT
*
383937 ATTAGTATATTCTTAAATTAA
1 ATTAATATATTCTTAAATTAA
383958 GGTAAATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTAATATATTCTTAAATTAAT
Found at i:384944 original size:26 final size:26
Alignment explanation
Indices: 384896--384945 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
384886 CCAATACATG
*
384896 ATTTTTAATTATTATTATTATTATAA
1 ATTTTTAATTATTATTATGATTATAA
*
384922 ATTTTTAA-TATTTTTACTGATTAT
1 ATTTTTAATTATTATTA-TGATTAT
384946 TTATAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
ATTTTTAATTATTATTATGATTATAA
Done.