Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold329
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: 4121247
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 5938 characters in sequence are not A, C, G, or T
File 3 of 25
Found at i:318315 original size:29 final size:28
Alignment explanation
Indices: 318284--318378 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 28
318274 ATCTAAGGAC
318284 CATTTAGCATTTTTCATGCATATTAGGT
1 CATTTAGCATTTTTCATGCATATTAGGT
* *
318312 CCATTTAG-GTTATTTTAT--ATAATCTAGGGT
1 -CATTTAGCATT-TTTCATGCAT-AT-TA-GGT
*
318342 CATTTTAGCATTTTTCATGCATTTTAAGGT
1 CA-TTTAGCATTTTTCATGCATATT-AGGT
318372 CATTTAG
1 CATTTAG
318379 GTGGTTTTAC
Statistics
Matches: 52, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
27 2 0.04
28 4 0.08
29 21 0.40
30 19 0.37
31 4 0.08
32 2 0.04
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.47
Consensus pattern (28 bp):
CATTTAGCATTTTTCATGCATATTAGGT
Found at i:318387 original size:59 final size:59
Alignment explanation
Indices: 318226--318380 Score: 197
Period size: 59 Copynumber: 2.6 Consensus size: 59
318216 ATTATGGATT
* * * * * *
318226 ATTTAGCAATTTCCATGCTTTTTAGGGTTATTTAGGTTATTTTATGTAATCTAAGGACC
1 ATTTAGCATTTTTCATGCATTTTAAGGTCATTTAGGTTATTTTATATAATCTAAGGACC
* **
318285 ATTTAGCATTTTTCATGCATATT-AGGTCCATTTAGGTTATTTTATATAATCT-AGGGTC
1 ATTTAGCATTTTTCATGCATTTTAAGGT-CATTTAGGTTATTTTATATAATCTAAGGACC
318343 ATTTTAGCATTTTTCATGCATTTTAAGGTCATTTAGGT
1 A-TTTAGCATTTTTCATGCATTTTAAGGTCATTTAGGT
318381 GGTTTTACAT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
58 8 0.10
59 71 0.86
60 4 0.05
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.47
Consensus pattern (59 bp):
ATTTAGCATTTTTCATGCATTTTAAGGTCATTTAGGTTATTTTATATAATCTAAGGACC
Found at i:327266 original size:20 final size:20
Alignment explanation
Indices: 327221--327268 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
327211 ATTCTTTTGT
*
327221 TTTCTCTCACTCTTCCATCT
1 TTTCTCTCACTCTTCCATCA
*
327241 TCTTCTCTC-CTCTTCCTGTCA
1 T-TTCTCTCACTCTTCC-ATCA
327262 TTTCTCT
1 TTTCTCT
327269 TATCTTTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.06, C:0.40, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTCTCTCACTCTTCCATCA
Found at i:328065 original size:9 final size:9
Alignment explanation
Indices: 328051--328075 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
328041 AAACGTTGGT
328051 TTTTTTTAA
1 TTTTTTTAA
328060 TTTTTTTAA
1 TTTTTTTAA
328069 TTTTTTT
1 TTTTTTT
328076 GTATTCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:328089 original size:16 final size:15
Alignment explanation
Indices: 328069--328117 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
328059 ATTTTTTTAA
328069 TTTTTTTGTATTCTT
1 TTTTTTTGTATTCTT
*
328084 TCTTTTT-T-TTCTT
1 TTTTTTTGTATTCTT
*
328097 CTTTTTTTCT-TTCTT
1 -TTTTTTTGTATTCTT
328112 TTTTTT
1 TTTTTT
328118 CAAAAACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 5 0.17
14 13 0.43
15 12 0.40
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (15 bp):
TTTTTTTGTATTCTT
Found at i:328100 original size:12 final size:13
Alignment explanation
Indices: 328079--328118 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
328069 TTTTTTTGTA
328079 TTCTTTCTTTTTT
1 TTCTTTCTTTTTT
328092 TTC-TTC-TTTTT
1 TTCTTTCTTTTTT
328103 TTCTTTCTTTTTT
1 TTCTTTCTTTTTT
328116 TTC
1 TTC
328119 AAAAACTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.32
12 6 0.24
13 11 0.44
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (13 bp):
TTCTTTCTTTTTT
Found at i:328103 original size:11 final size:12
Alignment explanation
Indices: 328079--328116 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
328069 TTTTTTTGTA
328079 TTCTTTCTTTTT
1 TTCTTTCTTTTT
328091 TT-TCTTCTTTTT
1 TTCT-TTCTTTTT
328103 TTCTTTCTTTTT
1 TTCTTTCTTTTT
328115 TT
1 TT
328117 TCAAAAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTCTTTCTTTTT
Found at i:329028 original size:13 final size:13
Alignment explanation
Indices: 329006--329042 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
328996 CATTTGACCA
*
329006 TGTATTGATACAC
1 TGTATCGATACAC
329019 TGTATCGATACAC
1 TGTATCGATACAC
*
329032 TATATCGATAC
1 TGTATCGATAC
329043 TGAGTAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:329873 original size:32 final size:32
Alignment explanation
Indices: 329837--329918 Score: 155
Period size: 32 Copynumber: 2.6 Consensus size: 32
329827 TTTTATTATT
329837 TCCCCCTTTATAAAACATTTCTTTACGAAATC
1 TCCCCCTTTATAAAACATTTCTTTACGAAATC
329869 TCCCCCTTTATAAAACATTTCTTTACGAAATC
1 TCCCCCTTTATAAAACATTTCTTTACGAAATC
*
329901 TCCCCCTTTATAAGACAT
1 TCCCCCTTTATAAAACAT
329919 CTCTCCTTCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.30, C:0.29, G:0.04, T:0.37
Consensus pattern (32 bp):
TCCCCCTTTATAAAACATTTCTTTACGAAATC
Found at i:329965 original size:22 final size:23
Alignment explanation
Indices: 329924--329970 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
329914 GACATCTCTC
*
329924 CTTCTTTTCGTTTTCGAAATAAT
1 CTTCTTTTCGTTTTCAAAATAAT
*
329947 CTTCTTTTTG-TTTCAAAATAAT
1 CTTCTTTTCGTTTTCAAAATAAT
329969 CT
1 CT
329971 CTCCTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.53
Consensus pattern (23 bp):
CTTCTTTTCGTTTTCAAAATAAT
Found at i:333294 original size:79 final size:78
Alignment explanation
Indices: 333194--333388 Score: 246
Period size: 78 Copynumber: 2.5 Consensus size: 78
333184 GGGGTTGGAG
* * * * * *
333194 TATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGATTAGGAAATAA
1 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT-ATTAGGAAATAA
*
333259 AATCGGGATTTAAA
65 AATCGGGATTGAAA
* * *
333273 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTGGAAATAAA
1 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTAGGAAATAAA
* * * *
333338 GTCGGGGTTGGAG
66 ATCGGGATTGAAA
*
333351 TATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGAT
1 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
333389 GAAATAACGA
Statistics
Matches: 100, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
78 56 0.56
79 44 0.44
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (78 bp):
TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTAGGAAATAAA
ATCGGGATTGAAA
Found at i:333362 original size:78 final size:78
Alignment explanation
Indices: 333153--333385 Score: 270
Period size: 79 Copynumber: 2.9 Consensus size: 78
333143 ATATGTCCCG
* * * * *
333153 ATGAGAAATTTAATATTTTGGAGATAATAAT-GGGGTTGGAGTATCCCCTTGAAAATAACGGGGT
1 ATGAGAAA-TCAATA-TTTGGAAATAA-AATCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGT
**
333217 TGGAGTATCCCCGGTT
63 TGGAGTATCCCCAATT
* * * * * ** *
333233 GTGAAAAATCGATGATTAGGAAATAAAATCGGGATTTAAATATCCCCTCGGAAGTAACGGGGTTG
1 ATGAGAAATCAAT-ATTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTG
333298 GAGTATCCCCAATT
65 GAGTATCCCCAATT
* *
333312 ATGAGAAATCAATATTTGGAAATAAAGTCGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGG
1 ATGAGAAATCAATATTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGG
333377 AGTATCCCC
66 AGTATCCCC
333386 GATGAAATAA
Statistics
Matches: 126, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
78 57 0.45
79 62 0.49
80 7 0.06
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (78 bp):
ATGAGAAATCAATATTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGG
AGTATCCCCAATT
Found at i:333396 original size:28 final size:28
Alignment explanation
Indices: 333340--333416 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
333330 GAAATAAAGT
*** **
333340 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
333368 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
333396 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
333417 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:333547 original size:51 final size:51
Alignment explanation
Indices: 333399--333619 Score: 210
Period size: 51 Copynumber: 4.3 Consensus size: 51
333389 GAAATAACGA
* * * * * * *
333399 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCAATTATGGAAAATTAGT-GTTTTGGAAATAAAACCAG
* * * * *
333451 AGTTGGAGTATCCCCAATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCAATT-ATGGAAAATTAGTGTTTTGGAAATAAAACCAG
* * * * *
333503 GGTTGGAATATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCAATTATGGAAAATTAGTGTTTTGGAAATAAAACCAG
* * * * *
333554 GGTTGGAGTATCCTCAATTAT-GAGAAATCAATATTTTGGAAATAAAGCCAG
1 GGTTGGAGTATCCCCAATTATGGA-AAATTAGTGTTTTGGAAATAAAACCAG
333605 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
333620 TCGGAGGTTA
Statistics
Matches: 138, Mismatches: 29, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
50 2 0.01
51 79 0.57
52 47 0.34
53 10 0.07
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCAATTATGGAAAATTAGTGTTTTGGAAATAAAACCAG
Found at i:333754 original size:261 final size:261
Alignment explanation
Indices: 333290--333785 Score: 877
Period size: 261 Copynumber: 1.9 Consensus size: 261
333280 TCGGAAGTAA
* *
333290 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTGGAAATAAAGTCGGGGTTGGAGTATC
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTGGAAATAAAGCCAGGGTTGGAGTATC
333355 CCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
66 CCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
* *
333420 GAAAAATTGGTATTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCAATTAAAGGAAAATTGGTG
131 GAAAAATTGGTATTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCAATTAAAAGAAAATTGGTA
333485 TTTTGAAAATAAAACCGGGGTTGGAATATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAA
196 TTTTGAAAATAAAACCGGGGTTGGAATATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAA
333550 C
261 C
*
333551 CGGGGTTGGAGTATCCTCAATTATGAGAAATCAATATTTTGGAAATAAAGCCAGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA-TTTGGAAATAAAGCCAGGGTTGGAGTAT
* * *
333616 CCCCTCGGAGGTTACGGGGTTGGAGTATCCCTGATGAAATTACGAGGTTGGAGTATCCTCGATTG
65 CCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
* *
333681 TGAAAAATTGGT-TTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAAGAAAATTGGT
130 TGAAAAATTGGTATTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCAATTAAAAGAAAATTGGT
*
333745 ATTTTGAAAATAAAACCGGGGTTGGAATATCCTCGATTGTG
195 ATTTTGAAAATAAAACCGGGGTTGGAATATCCCCGATTGTG
333786 AACAATTGAG
Statistics
Matches: 223, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
261 123 0.55
262 100 0.45
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (261 bp):
CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTGGAAATAAAGCCAGGGTTGGAGTATC
CCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
GAAAAATTGGTATTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCAATTAAAAGAAAATTGGTA
TTTTGAAAATAAAACCGGGGTTGGAATATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAA
C
Found at i:333756 original size:52 final size:51
Alignment explanation
Indices: 333662--333782 Score: 152
Period size: 52 Copynumber: 2.4 Consensus size: 51
333652 AAATTACGAG
*** * * *
333662 GTTGGAGTATCCTCGATTGTGAAAAATTGGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCTCGATTAAAAAAAATTGGTATTTTGAAAATAAAACCGGA
* *
333713 GTTGGAGTATCCCCGATTAAAAGAAAATTGGTATTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCTCGATTAAAA-AAAATTGGTATTTTGAAAATAAAACCGGA
*
333765 GTTGGAATATCCTCGATT
1 GTTGGAGTATCCTCGATT
333783 GTGAACAATT
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
51 18 0.31
52 41 0.69
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCTCGATTAAAAAAAATTGGTATTTTGAAAATAAAACCGGA
Found at i:336160 original size:21 final size:21
Alignment explanation
Indices: 336134--336175 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
336124 GTATCAATAC
336134 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
336155 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
336176 GGCAGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:336210 original size:13 final size:13
Alignment explanation
Indices: 336192--336243 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
336182 AGCTTCATAG
336192 CGATACATTGTAT
1 CGATACATTGTAT
336205 CGATACCAAACTTATGTAT
1 CGATA-C--A-TT--GTAT
336224 CGATACATTGTAT
1 CGATACATTGTAT
336237 CGATACA
1 CGATACA
336244 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 16 0.48
14 1 0.03
15 2 0.06
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.27
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:336233 original size:32 final size:32
Alignment explanation
Indices: 336192--336264 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
336182 AGCTTCATAG
336192 CGATACATTGTATCGATACCAA-ACTTATGTAT
1 CGATACATTGTATCGATA-CAACACTTATGTAT
336224 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
336256 TGATACATT
1 CGATACATT
336265 TACTAAATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
31 3 0.08
32 36 0.92
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:336908 original size:40 final size:42
Alignment explanation
Indices: 336863--336959 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 42
336853 CACTTTTTTG
*
336863 AGGACAAAGGAAAAG-AG-AATGAAATAG-GTCTTATTTCTTA
1 AGGACAAAGGAAAAGAAGAAAAGAAA-AGTGTCTTATTTCTTA
* * *
336903 AGGACAAAGGAAGAGAAGAAAAGGAAAGTGTCTTGTTTCTTA
1 AGGACAAAGGAAAAGAAGAAAAGAAAAGTGTCTTATTTCTTA
*
336945 AGGATAAAGTGAAAA
1 AGGACAAAG-GAAAA
336960 AGAGTACGTC
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
40 14 0.30
41 4 0.09
42 25 0.53
43 4 0.09
ACGTcount: A:0.46, C:0.06, G:0.26, T:0.22
Consensus pattern (42 bp):
AGGACAAAGGAAAAGAAGAAAAGAAAAGTGTCTTATTTCTTA
Found at i:337025 original size:42 final size:43
Alignment explanation
Indices: 336966--337154 Score: 174
Period size: 42 Copynumber: 4.4 Consensus size: 43
336956 AAAAAGAGTA
*
336966 CGTCTTGCT-TTTCGAGGA-AAAAGGAAAAAAGAAAACGAAA-TG
1 CGTCCTGCTCTTT-GAGGACAAAAGGAAAAAAGAAAA-GAAAGTG
* * * *
337008 TGTCCTGCTCTTTGAGGACTAAAAGGGAAAAAAAGGAAATAAAGAG
1 CGTCCTGCTCTTTGAGGAC-AAAA-GG-AAAAAAGAAAAGAAAGTG
*
337054 CGTCCTGCTCTTTGAGGAC-AAAGGAGAAAAGGAAAACGAAA-TG
1 CGTCCTGCTCTTTGAGGACAAAAGGA-AAAAAGAAAA-GAAAGTG
* * * *
337097 CGTCATGCTCTTTGAGGACAAAA-GAAAGAGGAAAATAAAGTG
1 CGTCCTGCTCTTTGAGGACAAAAGGAAAAAAGAAAAGAAAGTG
*
337139 CGTCCCGCTCTTTGAG
1 CGTCCTGCTCTTTGAG
337155 AACTACAAAG
Statistics
Matches: 122, Mismatches: 15, Indels: 20
0.78 0.10 0.13
Matches are distributed among these distances:
41 3 0.02
42 38 0.31
43 34 0.28
44 13 0.11
45 5 0.04
46 29 0.24
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.20
Consensus pattern (43 bp):
CGTCCTGCTCTTTGAGGACAAAAGGAAAAAAGAAAAGAAAGTG
Found at i:337110 original size:89 final size:84
Alignment explanation
Indices: 336966--337154 Score: 229
Period size: 89 Copynumber: 2.2 Consensus size: 84
336956 AAAAAGAGTA
* * *
336966 CGTCTTGCT-TTTCGAGGAAAAAGGAAAAAAGAAAACGAAATGTGTCCTGCTCTTTGAGGACTAA
1 CGTCCTGCTCTTT-GAGGAAAAAGGAAAAAAGAAAACGAAATGCGTCATGCTCTTTGAGGAC-AA
337030 AAGGGAAAAAAAGG-AAATAAAGAG
64 AA--G--AAAAAGGAAAATAAAGAG
* *
337054 CGTCCTGCTCTTTGAGGACAAAGGAGAAAAGGAAAACGAAATGCGTCATGCTCTTTGAGGACAAA
1 CGTCCTGCTCTTTGAGGAAAAAGGA-AAAAAGAAAACGAAATGCGTCATGCTCTTTGAGGACAAA
* *
337119 AGAAAGAGGAAAATAAAGTG
65 AGAAAAAGGAAAATAAAGAG
*
337139 CGTCCCGCTCTTTGAG
1 CGTCCTGCTCTTTGAG
337155 AACTACAAAG
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
84 6 0.07
85 24 0.27
86 1 0.01
88 23 0.26
89 36 0.40
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.20
Consensus pattern (84 bp):
CGTCCTGCTCTTTGAGGAAAAAGGAAAAAAGAAAACGAAATGCGTCATGCTCTTTGAGGACAAAA
GAAAAAGGAAAATAAAGAG
Found at i:337286 original size:55 final size:56
Alignment explanation
Indices: 337140--337691 Score: 429
Period size: 55 Copynumber: 9.4 Consensus size: 56
337130 AATAAAGTGC
* * * *
337140 GTCCCGCTCTTTGAGAACTACAAA-GTGCCACCAACTTGAGTGGGCTTTCAAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTT--AAA-G---AGGT
* ** * *
337202 GTCCTGCTCCTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTT-AAGAGGT
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGT
** * *
337257 GTCCTATTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGT
* * *
337312 GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAGCTCGTGTGGGCTTTGAAAAGAAAAGGT
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT--AAAG---AGGT
* * * *
337373 GTCATGCTCTTTGAGGACTGGAAAA--TGCCTCCAACTTGTGTGGGCTTTGAA-AGGC
1 GTCCTGCTCTTTGAGGACT--AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGT
* * * *
337428 ATCCTGCTCTTTGAAGACTGAAAA-ATGCCACCGACTTGTGTGGGCTTTAAAAGGAAAAGGT
1 GTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTT-AAA-G---AGGT
* * *
337489 GTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGGGGGCTTTAAA-AGGCA
1 GTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGG-T
* **
337546 GTCCTGCTTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAGAC
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT--AAA-G---AGGT
** *
337608 GTCCTGCTCTTTGAGGACT-GGAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAAAGT
1 GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT--AAAG-----AGGT
337670 GTCCTGCTCTTTGAGGACTAAA
1 GTCCTGCTCTTTGAGGACTAAA
337692 GGGCTAAAAG
Statistics
Matches: 402, Mismatches: 58, Indels: 59
0.77 0.11 0.11
Matches are distributed among these distances:
54 5 0.01
55 130 0.32
56 33 0.08
57 21 0.05
58 4 0.01
59 4 0.01
60 2 0.00
61 98 0.24
62 100 0.25
63 5 0.01
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (56 bp):
GTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAGGT
Found at i:337425 original size:116 final size:117
Alignment explanation
Indices: 337196--337658 Score: 599
Period size: 116 Copynumber: 4.0 Consensus size: 117
337186 TTCAAAAGGA
* * *
337196 AAAGGCGTCCTGCTCCTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTT--AA-G---AG
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAAAAG
**
337255 GTGTCCTATTCTTTGAGGACT--AAAAGGTGCCACCAACTTGTGTGGGCTTTG
66 GTGTCCTGCTCTTTGAGGACTGGAAAA-GTGCCACCAACTTGTGTGGGCTTTG
*
337306 AAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAGCTCGTGTGGGCTTTGAAAA-GAAAA
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAGGAAAA
* *
337370 GGTGTCATGCTCTTTGAGGACTGGAAAA-TGCCTCCAACTTGTGTGGGCTTTG
65 GGTGTCCTGCTCTTTGAGGACTGGAAAAGTGCCACCAACTTGTGTGGGCTTTG
* * ** * *
337422 AAAGGCATCCTGCTCTTTGAAGACTGAAAAATGCCACCGACTTGTGTGGGCTTTAAAAGGAAAAG
1 AAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAAAAG
* * *
337487 GTGTCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGGGGGCTTTA
66 GTGTCCTGCTCTTTGAGGACTGGAAAAGTGCCACCAACTTGTGTGGGCTTTG
* * *
337539 AAAGGCAGTCCTGCTTTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGGAAA
1 AAAGGC-GTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAGGAAA
** *
337604 AGACGTCCTGCTCTTTGAGGACTGG--AGGTGCCACCAACTTGTGTGGGCTTTG
64 AGGTGTCCTGCTCTTTGAGGACTGGAAAAGTGCCACCAACTTGTGTGGGCTTTG
337656 AAA
1 AAA
337659 AGAAAAAAAG
Statistics
Matches: 308, Mismatches: 33, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
110 50 0.16
113 3 0.01
115 4 0.01
116 121 0.39
117 54 0.18
118 45 0.15
119 31 0.10
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (117 bp):
AAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAAAAG
GTGTCCTGCTCTTTGAGGACTGGAAAAGTGCCACCAACTTGTGTGGGCTTTG
Found at i:343316 original size:79 final size:78
Alignment explanation
Indices: 343192--343417 Score: 224
Period size: 79 Copynumber: 2.9 Consensus size: 78
343182 TGAGAAATTT
* * * *
343192 AATATTTTGGAGATAATAACGGGGTTGGAGTATCCCCT-TGAAAATAACGAGGTTGGAGTATCCC
1 AATATTTAGGAAATAA-AACCGGGTTGGAGTATCCCCTCAG-AAATAACGAGGTTGGAGTATCCC
* *
343256 CGGTTGTGAAAAATC
64 CGATTATGAAAAATC
* * * *
343271 GATGA-TTAGGAAATAAAATCGGGATTGGAATATCCCCTCAGAAATAACGGGGTTGGAGTATCCC
1 AAT-ATTTAGGAAATAAAACCGGG-TTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCC
* *
343335 CAATTATGAGAAATC
64 CGATTATGAAAAATC
* * * **
343350 AATATTTTGGAAATAAAGCCAGGGTTGGAGTATCCCCTCGGAGGTAAC-AGGGTTGGAGTATCCC
1 AATATTTAGGAAATAAAACC-GGGTTGGAGTATCCCCTCAGAAATAACGA-GGTTGGAGTATCCC
343414 CGAT
64 CGAT
343418 GAAATAACGA
Statistics
Matches: 119, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
78 6 0.05
79 108 0.91
80 5 0.04
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (78 bp):
AATATTTAGGAAATAAAACCGGGTTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCCG
ATTATGAAAAATC
Found at i:343425 original size:28 final size:28
Alignment explanation
Indices: 343369--343445 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 28
343359 GAAATAAAGC
*** **
343369 CAGGGTTGGAGTATCCCCTCGGAGGTAA
1 CAGGGTTGGAGTATCCCCGATGAAATAA
343397 CAGGGTTGGAGTATCCCCGATGAAATAA
1 CAGGGTTGGAGTATCCCCGATGAAATAA
*
343425 C-GAGGTTGGAGTATCCTCGAT
1 CAG-GGTTGGAGTATCCCCGAT
343446 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 1 0.02
28 41 0.98
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.23
Consensus pattern (28 bp):
CAGGGTTGGAGTATCCCCGATGAAATAA
Found at i:343498 original size:52 final size:51
Alignment explanation
Indices: 343429--343823 Score: 249
Period size: 52 Copynumber: 7.6 Consensus size: 51
343419 AAATAACGAG
* *
343429 GTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTG-TTTTGGAAATAAAATCGGA
* * * *
343481 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGGG
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTGGAAATAAAATCGGA
* * * * * *
343533 GTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAATCGGA
* *** * * **
343584 GTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAAT-AAAGCCAA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAATCGGA
* *** * * ***** *
343634 GCTTGGAGTATCCCTTCAGAGGTAATG--GGGTTGGAGTGTCCCCGATGAAATAAC-GA
1 G-TTGGAGTATCCC--C-GA--TTATGAAAAATTGGTGTTTTGGAAAT-AAA-ATCGGA
* * *
343690 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGAAAATAAAATCGGA
1 -GTTGGAGTATCCCCGATTATGAAAAATTGGTG-TTTTGGAAATAAAATCGGA
* * * * * *
343743 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATGAAACCGGG
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTGGAAATAAAATCGGA
* * *
343795 GTTAGAATATCCCCGATTATGAACAATTG
1 GTTGGAGTATCCCCGATTATGAAAAATTG
343824 AGAAACTTAA
Statistics
Matches: 261, Mismatches: 66, Indels: 33
0.73 0.18 0.09
Matches are distributed among these distances:
50 5 0.02
51 85 0.33
52 103 0.39
53 35 0.13
54 12 0.05
56 18 0.07
57 3 0.01
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGGAAATAAAATCGGA
Found at i:343631 original size:262 final size:262
Alignment explanation
Indices: 343318--343812 Score: 873
Period size: 262 Copynumber: 1.9 Consensus size: 262
343308 TCAGAAATAA
* *
343318 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCAGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCAAGCTTGGAGTAT
*
343383 CCCCTCGGAGGTAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
66 CCCCTCAGAGGTAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
*
343448 TGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
131 TGAAAAATTGGTGTTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
* * *
343513 GTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAA
196 GTTTTGAAAATAAAACCGGGGTTAGAATATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAA
343578 AC
261 AC
*
343580 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCAAGCTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCAAGCTTGGAGTAT
* ** *
343645 CCCTTCAGAGGTAATGGGGTTGGAGTGTCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
66 CCCCTCAGAGGTAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
343710 TGAAAAATTGGTGTTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
131 TGAAAAATTGGTGTTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
*
343775 GTTTTGAAAATGAAACCGGGGTTAGAATATCCCCGATT
196 GTTTTGAAAATAAAACCGGGGTTAGAATATCCCCGATT
343813 ATGAACAATT
Statistics
Matches: 220, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
262 220 1.00
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (262 bp):
CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCAAGCTTGGAGTAT
CCCCTCAGAGGTAACAGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
TGAAAAATTGGTGTTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
GTTTTGAAAATAAAACCGGGGTTAGAATATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAA
AC
Found at i:346255 original size:13 final size:13
Alignment explanation
Indices: 346237--346288 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
346227 AGCTTCGTAG
346237 CGATACATTGTAT
1 CGATACATTGTAT
346250 CGATACCAAACTTATGTAT
1 CGATA-C--A-TT--GTAT
346269 CGATACATTGTAT
1 CGATACATTGTAT
346282 CGATACA
1 CGATACA
346289 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 16 0.48
14 1 0.03
15 2 0.06
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.27
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:346269 original size:19 final size:18
Alignment explanation
Indices: 346245--346313 Score: 78
Period size: 19 Copynumber: 4.1 Consensus size: 18
346235 AGCGATACAT
346245 TGTATCGATACCAAACTTA
1 TGTATCGATA-CAAACTTA
346264 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
346277 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
346296 TGTATCGATACAAA-TTA
1 TGTATCGATACAAACTTA
346313 T
1 T
346314 TGAAATTCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.25
14 1 0.02
16 2 0.05
17 4 0.09
18 3 0.07
19 23 0.52
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:346278 original size:32 final size:32
Alignment explanation
Indices: 346237--346307 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
346227 AGCTTCGTAG
346237 CGATACATTGTATCGATACCAA-ACTTATGTAT
1 CGATACATTGTATCGATA-CAACACTTATGTAT
346269 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
346301 CGATACA
1 CGATACA
346308 AATTATTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 3 0.08
32 35 0.92
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:351575 original size:13 final size:13
Alignment explanation
Indices: 351557--351581 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
351547 TACCAAGAAC
351557 ATGTATCGATACA
1 ATGTATCGATACA
351570 ATGTATCGATAC
1 ATGTATCGATAC
351582 TAAGCAATAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:363653 original size:20 final size:20
Alignment explanation
Indices: 363628--363677 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
363618 CTAGGTAATG
363628 TATCGATACATTGAATC-ATA
1 TATCGATACA-TGAATCAATA
* *
363648 TATCGATACATGATTCAATG
1 TATCGATACATGAATCAATA
363668 TATCGATACA
1 TATCGATACA
363678 AAACTTATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (20 bp):
TATCGATACATGAATCAATA
Found at i:363703 original size:13 final size:13
Alignment explanation
Indices: 363685--363709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
363675 ACAAAACTTA
363685 TGTATCGATACAT
1 TGTATCGATACAT
363698 TGTATCGATACA
1 TGTATCGATACA
363710 AATTATAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:364665 original size:101 final size:103
Alignment explanation
Indices: 364536--364733 Score: 247
Period size: 101 Copynumber: 1.9 Consensus size: 103
364526 AGAAAAATGG
* * * * * ** * * *
364536 CAATGTGCTGATTCAAGGCTAGTGACATTGGGCTTAGGAATGTTAAAGA-TGCCAATATGCTGAT
1 CAATGTGCTAATTCAAGGCCAGTAACATTAGACTTAAAAAAGATAAAGAGTGCCAACATGCTGAT
** *
364600 TGAAGGCCAATGATATTGGAC-TTAAAGATGATGGTGC
66 TGAAGGCCAACAACATTGGACTTTAAAGATGATGGTGC
*
364637 CAATGTGCTAATTCAAGTCCAGTAACATTAGACTTAAAAAAGATAAAGAGTGCCAACATGCTGAT
1 CAATGTGCTAATTCAAGGCCAGTAACATTAGACTTAAAAAAGATAAAGAGTGCCAACATGCTGAT
*
364702 TTAAGGCCAACAACATTGGACTTTAAAGATGA
66 TGAAGGCCAACAACATTGGACTTTAAAGATGA
364734 CAAAGGCGTC
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
101 39 0.49
102 31 0.39
103 10 0.12
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (103 bp):
CAATGTGCTAATTCAAGGCCAGTAACATTAGACTTAAAAAAGATAAAGAGTGCCAACATGCTGAT
TGAAGGCCAACAACATTGGACTTTAAAGATGATGGTGC
Found at i:364866 original size:32 final size:31
Alignment explanation
Indices: 364830--365081 Score: 312
Period size: 32 Copynumber: 7.9 Consensus size: 31
364820 TAGAAGGAAA
*
364830 TGCCACTAACTTGTGTGGGCTTTTGAAAGGGT
1 TGCCACCAACTTGTGTGGGC-TTTGAAAGGGT
*
364862 TGCCACCGACTTGTGTGGGCTTT-AAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAAG--GGT
364894 TGCCACCAACTTGTGTGGGCTTT-AAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAAG--GGT
* *
364926 TGCCACTAACTTGTGTGGGCTTTAGAAAGGGC
1 TGCCACCAACTTGTGTGGGCTTT-GAAAGGGT
* *
364958 TGCCACCAACTTATGTGGGCTTTTGAAAAGGT
1 TGCCACCAACTTGTGTGGGC-TTTGAAAGGGT
* * *
364990 TGCCACCTATTTGTGTAGGCTTTAGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTT-GAAAGGGT
365022 TGCCACCAACTTGTGTGGGCTTTG-AAGAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAAG-GGT
*
365053 TGCCACCTACTTGTGTGGGCTTTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGG
365082 TTTCTCTACT
Statistics
Matches: 194, Mismatches: 18, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
30 7 0.04
31 34 0.18
32 146 0.75
33 3 0.02
34 4 0.02
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (31 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGGGT
Found at i:366674 original size:15 final size:13
Alignment explanation
Indices: 366654--366696 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
366644 CCTTTTCTTG
366654 TTTGTTGTTTTATT
1 TTTGTTGTTTT-TT
366668 TTGTGTT-TTTTTT
1 TT-TGTTGTTTTTT
366681 GTTTGTTGTTTTTT
1 -TTTGTTGTTTTTT
366695 TT
1 TT
366697 ACAGAGGACG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.31
14 14 0.54
15 4 0.15
ACGTcount: A:0.02, C:0.00, G:0.16, T:0.81
Consensus pattern (13 bp):
TTTGTTGTTTTTT
Found at i:366690 original size:16 final size:16
Alignment explanation
Indices: 366646--366696 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
366636 TTCTTCCCCC
*
366646 TTTTCTTGTTTGTTG-
1 TTTTTTTGTTTGTTGT
*
366661 -TTTTAT-TTTG-TGT
1 TTTTTTTGTTTGTTGT
366674 TTTTTTTGTTTGTTGT
1 TTTTTTTGTTTGTTGT
366690 TTTTTTT
1 TTTTTTT
366697 ACAGAGGACG
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
12 2 0.07
13 4 0.14
14 9 0.31
15 4 0.14
16 10 0.34
ACGTcount: A:0.02, C:0.02, G:0.16, T:0.80
Consensus pattern (16 bp):
TTTTTTTGTTTGTTGT
Found at i:371694 original size:52 final size:52
Alignment explanation
Indices: 371616--371766 Score: 239
Period size: 52 Copynumber: 2.9 Consensus size: 52
371606 TGAAATATGA
* *
371616 AAATTTGCCTACATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCAGGGC
*
371668 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCAGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCAGGGC
** *
371720 AAATTTGCCTGCATGTATCGATACATTTGGGTAGTTTATCGATACAT
1 AAATTTGCCTGCATGTATCGATACATTT-AATAGTGTATCGATACAT
371767 TTTTTGGCAG
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
52 77 0.84
53 15 0.16
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCAGGGC
Found at i:372493 original size:67 final size:68
Alignment explanation
Indices: 372367--372493 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 68
372357 ATTGGGTTTT
* * * *
372367 AAAGATGATGAAGGTGCCAATATATTGATTCAAGGCCAGCAATATTGGACTTAATGATGAAGATG
1 AAAGATGATAAAGATGCCAATATATTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
372432 AGA
66 AGA
* * * *
372435 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATATTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
372494 GAAAAAGGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
67 47 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATATTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:372616 original size:43 final size:43
Alignment explanation
Indices: 372555--372783 Score: 269
Period size: 43 Copynumber: 5.0 Consensus size: 43
372545 ATGGAAAATG
*
372555 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
* * *
372598 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
*
372641 TGAAGGCACCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGG
1 T----G--CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
* * *
372690 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGA
*
372739 TGCCAACATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
372782 TG
1 TG
372784 AGAAAAAGGA
Statistics
Matches: 160, Mismatches: 14, Indels: 24
0.81 0.07 0.12
Matches are distributed among these distances:
43 81 0.51
45 2 0.01
47 2 0.01
49 75 0.47
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (43 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
Found at i:372694 original size:92 final size:92
Alignment explanation
Indices: 372497--373254 Score: 1149
Period size: 92 Copynumber: 8.0 Consensus size: 92
372487 AAGATGAGAA
* * *
372497 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAAT
*
372562 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCGATATTGGACTT
* **
372593 AAAGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGCACCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
372658 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* *
372685 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAACATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
372750 TGATTCAAGGCCAGCGATATTGGACTTAAAGAT
66 TGATTCAAGGCCAGCGATATTGGAC-T-----T
* *
372783 GAGAAAAAGGATGTCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGATGACA-GTGCC
1 -----AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGA-AGGTGCC
*
372847 AATATGCTGATTCAAGGCCAACGATATTGGACTT
59 AATATGCTGATTCAAGGCCAGCGATATTGGACTT
*
372881 AAAGGTGCCAATGTGCTGATTCAAGGCCTGCTACATTGGACTTAAAGATGACAAAGGTGCCAATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG---AAGGTGCCAATA
372946 TGCTGATTCAAGGCCAGCGATATTGGACTT
63 TGCTGATTCAAGGCCAGCGATATTGGACTT
* *
372976 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
373041 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
** *
373068 GGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
373133 TGATTCAAGGCCAGCGATATTAGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
373160 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
373225 TGATTCAAGGCCAGCGATATTGGGCTT
66 TGATTCAAGGCCAGCGATATTGGACTT
373252 AAA
1 AAA
373255 AGCGTTGCCA
Statistics
Matches: 610, Mismatches: 35, Indels: 38
0.89 0.05 0.06
Matches are distributed among these distances:
92 382 0.63
93 6 0.01
94 2 0.00
95 129 0.21
96 4 0.01
98 2 0.00
103 6 0.01
104 78 0.13
105 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:372831 original size:55 final size:53
Alignment explanation
Indices: 372685--373254 Score: 427
Period size: 49 Copynumber: 11.9 Consensus size: 53
372675 TATTGGACTT
372685 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT--G
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAG
** * *
372735 -AA-GATGCCAACATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAG
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAG
* *
372786 AAAAAGGATGTCAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGAT--G
1 --AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAG
* * * * *
372839 ACA-G-TGCCAATATGCTGATTCAAGGCCAACGATATTGGAC-T-----T---
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAG
* *
372881 AAAGG-TGCCAATGTGCTGATTCAAGGCCTGCTACATTGGACTTAAAGATGAC
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAG
* * *
372933 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAG
*
372976 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT--G
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAG
* * *
373026 -AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----TG-G
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAG
373070 --AGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT--G
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAG
* * * * *
373118 -ATGG-TGCCAATATGCTGATTCAAGGCCAGCGATATTAGAC-T-----T---
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAG
373160 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT--G
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAG
* * * *
373210 -AAGG-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAA
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
373255 AGCGTTGCCA
Statistics
Matches: 430, Mismatches: 48, Indels: 85
0.76 0.09 0.15
Matches are distributed among these distances:
42 2 0.00
43 143 0.33
44 6 0.01
46 1 0.00
48 6 0.01
49 187 0.43
50 1 0.00
51 4 0.01
52 37 0.09
53 1 0.00
54 2 0.00
55 40 0.09
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (53 bp):
AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAG
Found at i:372903 original size:43 final size:44
Alignment explanation
Indices: 372787--373256 Score: 453
Period size: 43 Copynumber: 10.1 Consensus size: 44
372777 AAAGATGAGA
* * * *
372787 AAAAGGATGTCAATGTGCTGATTCAAGGCTAGCTACATTGGACTT
1 AAAAGG-TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* *
372832 AAAGATGACAGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTT
1 AAA-A-G---GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* * *
372881 -AAAGGTGCCAATGTGCTGATTCAAGGCCTGCTACATTGGACTTAAAGAT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-T-----T
*
372930 GACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
*
372976 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
*
373019 AAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
** * *
373068 -GGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* *
373111 AAAGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTT
1 -AA-A--A-GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* *
373160 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* *
373203 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
1 --A-A--AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
373252 AAAAG
1 AAAAG
373257 CGTTGCCACC
Statistics
Matches: 355, Mismatches: 38, Indels: 65
0.78 0.08 0.14
Matches are distributed among these distances:
43 144 0.41
44 8 0.02
45 4 0.01
46 7 0.02
47 6 0.02
48 4 0.01
49 143 0.40
50 1 0.00
51 1 0.00
52 37 0.10
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (44 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
Found at i:373297 original size:33 final size:33
Alignment explanation
Indices: 373258--373488 Score: 344
Period size: 33 Copynumber: 7.1 Consensus size: 33
373248 GCTTAAAAGC
*
373258 GTTGCCACCGACTTGTGTGGGCTTTAGAGAATG
1 GTTGCCACCGACTTGTGTGGGCTTTAGAGAAGG
* *
373291 GTTGCCACCAACTTGTGTGGGCTTTTGAAGAA-G
1 GTTGCCACCGACTTGTGTGGGCTTTAG-AGAAGG
373324 GTTGCCACCGACTTGTGTGGGCTTT-GAGAAGG
1 GTTGCCACCGACTTGTGTGGGCTTTAGAGAAGG
373356 GTTGCCACCGACTTGTGTGGGCTTTAGAGAAGG
1 GTTGCCACCGACTTGTGTGGGCTTTAGAGAAGG
**
373389 GTTGCCATTGACTTGTGTGGGCTTTAGAAGAA-G
1 GTTGCCACCGACTTGTGTGGGCTTTAG-AGAAGG
*
373422 GTTGCCACCGACTTGTGTAGGCTTTAGAGAAGG
1 GTTGCCACCGACTTGTGTGGGCTTTAGAGAAGG
* *
373455 GTTACCACCGACTTGTGTGGGCTTTA-AAAAGG
1 GTTGCCACCGACTTGTGTGGGCTTTAGAGAAGG
373487 GT
1 GT
373489 GAAAGATTCC
Statistics
Matches: 182, Mismatches: 11, Indels: 11
0.89 0.05 0.05
Matches are distributed among these distances:
31 4 0.02
32 38 0.21
33 132 0.73
34 8 0.04
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.29
Consensus pattern (33 bp):
GTTGCCACCGACTTGTGTGGGCTTTAGAGAAGG
Found at i:373427 original size:98 final size:99
Alignment explanation
Indices: 373258--373488 Score: 376
Period size: 98 Copynumber: 2.4 Consensus size: 99
373248 GCTTAAAAGC
* *
373258 GTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTGTGGGCTTTTGAAGAA
1 GTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAAGAA
*
373323 GGTTGCCACCGACTTGTGTGGGCTTT-GAGAAGG
66 GGTTGCCACCGACTTGTGTAGGCTTTAGAGAAGG
***
373356 GTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCATTGACTTGTGTGGGCTTTAGAAGAA
1 GTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAAGAA
373421 GGTTGCCACCGACTTGTGTAGGCTTTAGAGAAGG
66 GGTTGCCACCGACTTGTGTAGGCTTTAGAGAAGG
* *
373455 GTTACCACCGACTTGTGTGGGCTTTA-AAAAGGGT
1 GTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGT
373489 GAAAGATTCC
Statistics
Matches: 124, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
98 92 0.74
99 32 0.26
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.29
Consensus pattern (99 bp):
GTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAAGAA
GGTTGCCACCGACTTGTGTAGGCTTTAGAGAAGG
Found at i:373571 original size:36 final size:37
Alignment explanation
Indices: 373470--373590 Score: 128
Period size: 36 Copynumber: 3.4 Consensus size: 37
373460 CACCGACTTG
* * *
373470 TGTGGGCTTTAAAAAGGGTGAAAGA-TTCCACGAAGT
1 TGTGGGCTTTAAAAAGGGAGAAAGAGTGCCACGGAGT
* * *
373506 TAT-GGATTT-AAAA-GGAGCAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAAGGGAGAAAGAGTGCCACGGAGT
*
373539 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAAGGGAGAAAGAGTGCCACGGAGT
*
373575 TGTGGGCTTTGAAAAG
1 TGTGGGCTTTAAAAAG
373591 AAAGTGCCAC
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
33 17 0.24
34 13 0.19
35 11 0.16
36 24 0.34
37 5 0.07
ACGTcount: A:0.32, C:0.11, G:0.34, T:0.23
Consensus pattern (37 bp):
TGTGGGCTTTAAAAAGGGAGAAAGAGTGCCACGGAGT
Found at i:373644 original size:31 final size:31
Alignment explanation
Indices: 373524--373653 Score: 129
Period size: 31 Copynumber: 4.1 Consensus size: 31
373514 TAAAAGGAGC
* *
373524 AAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
1 AAGGTGCCACGGAGTCGTGGACTTTAAAA-GG
* *
373556 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA-G
1 ---AAG-GTGCCACGGAGTCGTGGACTTT-AAAAGG
* * *
373591 AAAGTGCCACGGAGTCGCGGACTTTGAAAGG
1 AAGGTGCCACGGAGTCGTGGACTTTAAAAGG
373622 AAGGTGCCACGGAGTCGTGGAC-TTAAAAGG
1 AAGGTGCCACGGAGTCGTGGACTTTAAAAGG
373652 AA
1 AA
373654 CAAGGTCTAC
Statistics
Matches: 84, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
30 12 0.14
31 40 0.48
32 2 0.02
35 4 0.05
36 22 0.26
37 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.36, T:0.18
Consensus pattern (31 bp):
AAGGTGCCACGGAGTCGTGGACTTTAAAAGG
Found at i:385851 original size:20 final size:20
Alignment explanation
Indices: 385826--385900 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
385816 ATTTGCTTAT
385826 ATGTATCGATACATTAAATA
1 ATGTATCGATACATTAAATA
**
385846 ATGTATCGATACATCTAGGTA
1 ATGTATCGATACAT-TAAATA
* *
385867 ATGTATCGATACATTGAATC
1 ATGTATCGATACATTAAATA
385887 ATGTATCGATACAT
1 ATGTATCGATACAT
385901 CTAGGTAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 30 0.62
21 18 0.38
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTAAATA
Found at i:385871 original size:41 final size:41
Alignment explanation
Indices: 385826--385908 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
385816 ATTTGCTTAT
385826 ATGTATCGATACATTAAATAATGTATCGATACATCTAGGTA
1 ATGTATCGATACATTAAATAATGTATCGATACATCTAGGTA
* *
385867 ATGTATCGATACATTGAATCATGTATCGATACATCTAGGTA
1 ATGTATCGATACATTAAATAATGTATCGATACATCTAGGTA
385908 A
1 A
385909 AATACCTAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (41 bp):
ATGTATCGATACATTAAATAATGTATCGATACATCTAGGTA
Found at i:392143 original size:52 final size:52
Alignment explanation
Indices: 392065--392195 Score: 199
Period size: 52 Copynumber: 2.5 Consensus size: 52
392055 CCCGAAATAT
*
392065 GAAAATTTGCCTGCATATATCGATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
** * *
392117 GAAAATTTGCCTATATGTATCGATACATTTTATAGTGTATCGATACATTTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
* *
392169 GAAAATTTACCTGCATGTATCAATACA
1 GAAAATTTGCCTGCATGTATCGATACA
392196 AAGATTAGTG
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
Found at i:392157 original size:20 final size:19
Alignment explanation
Indices: 392128--392166 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
392118 AAAATTTGCC
392128 TATATGTATCGATACATTT
1 TATATGTATCGATACATTT
392147 TATAGTGTATCGATACATTT
1 TATA-TGTATCGATACATTT
392167 GGGAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (19 bp):
TATATGTATCGATACATTT
Found at i:392205 original size:52 final size:52
Alignment explanation
Indices: 392096--392215 Score: 152
Period size: 52 Copynumber: 2.3 Consensus size: 52
392086 GATACATTTC
* * * ***
392096 ATAGTGTATCGATACATCTGGGAAAATTTGCCTATATGTATCGATACATTTT
1 ATAGTGTATCGATACATCTGGGAAAATTTACCTACATGTATCAATACAAGAT
* *
392148 ATAGTGTATCGATACATTTGGGAAAATTTACCTGCATGTATCAATACAAAGAT
1 ATAGTGTATCGATACATCTGGGAAAATTTACCTACATGTATCAATAC-AAGAT
392201 -TAGTGTATCGATACA
1 ATAGTGTATCGATACA
392216 CTTTTTGGCA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
52 57 0.97
53 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35
Consensus pattern (52 bp):
ATAGTGTATCGATACATCTGGGAAAATTTACCTACATGTATCAATACAAGAT
Found at i:392273 original size:32 final size:33
Alignment explanation
Indices: 392232--392300 Score: 131
Period size: 32 Copynumber: 2.1 Consensus size: 33
392222 GGCAGTAGCT
392232 TACATTGTATCGATACAACAC-TTATGTATCGA
1 TACATTGTATCGATACAACACTTTATGTATCGA
392264 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACACTTTATGTATCGA
392297 TACA
1 TACA
392301 AATCATTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 21 0.58
33 15 0.42
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (33 bp):
TACATTGTATCGATACAACACTTTATGTATCGA
Found at i:392274 original size:13 final size:13
Alignment explanation
Indices: 392256--392280 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
392246 ACAACACTTA
392256 TGTATCGATACAT
1 TGTATCGATACAT
392269 TGTATCGATACA
1 TGTATCGATACA
392281 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:392802 original size:16 final size:16
Alignment explanation
Indices: 392754--392794 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
392744 GAATGAAACC
*
392754 CAAAAGAAACAAAAAAA
1 CAAAA-AAATAAAAAAA
*
392771 TAAAAAAATAAAAAAA
1 CAAAAAAATAAAAAAA
392787 CAAAAAAA
1 CAAAAAAA
392795 AGAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.85, C:0.07, G:0.02, T:0.05
Consensus pattern (16 bp):
CAAAAAAATAAAAAAA
Found at i:392803 original size:8 final size:8
Alignment explanation
Indices: 392764--392794 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
392754 CAAAAGAAAC
392764 AAAAAAAT
1 AAAAAAAT
392772 AAAAAAAT
1 AAAAAAAT
*
392780 AAAAAAAC
1 AAAAAAAT
392788 AAAAAAA
1 AAAAAAA
392795 AGAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.06
Consensus pattern (8 bp):
AAAAAAAT
Found at i:392805 original size:9 final size:9
Alignment explanation
Indices: 392755--392807 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
392745 AATGAAACCC
392755 AAAAGAAACA
1 AAAAGAAA-A
392765 AAAA-AATAA
1 AAAAGAA-AA
392774 AAAA-ATAAA
1 AAAAGA-AAA
*
392783 AAAACAAAA
1 AAAAGAAAA
392792 AAAAGAAAA
1 AAAAGAAAA
392801 AAAAGAA
1 AAAAGAA
392808 CCAACTTAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
9 32 0.82
10 7 0.18
ACGTcount: A:0.87, C:0.04, G:0.06, T:0.04
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:393828 original size:71 final size:71
Alignment explanation
Indices: 393752--393883 Score: 178
Period size: 71 Copynumber: 1.9 Consensus size: 71
393742 TTAAACCTTT
* * * *
393752 TTTTTAGTCCTTAAATAA-CATGATACC-TTTTCTTTTTAAAGCCCATACAAGTTGGTGGCACAC
1 TTTTTAATCCTTAAA-AAGCAGGATACCTTTTTC-TTTTAAAGCCCACACAACTTGGTGGCACAC
393815 ATTTTATC
64 ATTTTATC
* *
393823 TTTTTAATCTTTAAAAAGCAGGATGCCTTTTTCTTTTAAAGCCCACACAACTTGGTGGCAC
1 TTTTTAATCCTTAAAAAGCAGGATACCTTTTTCTTTTAAAGCCCACACAACTTGGTGGCAC
393884 TCTTTTTAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
70 2 0.04
71 46 0.87
72 5 0.09
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (71 bp):
TTTTTAATCCTTAAAAAGCAGGATACCTTTTTCTTTTAAAGCCCACACAACTTGGTGGCACACAT
TTTATC
Found at i:397173 original size:28 final size:28
Alignment explanation
Indices: 397141--397203 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
397131 TTTCACCGTT
*
397141 GGGGATACTCCATCACC-ATAATTTCTGA
1 GGGGATACTCCAAC-CCTATAATTTCTGA
*
397169 GGGGATACTCCAACCCTATCATTTCTGA
1 GGGGATACTCCAACCCTATAATTTCTGA
397197 GGGGATA
1 GGGGATA
397204 TTTTAACCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 2 0.06
28 30 0.94
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (28 bp):
GGGGATACTCCAACCCTATAATTTCTGA
Found at i:397283 original size:81 final size:81
Alignment explanation
Indices: 397172--397380 Score: 228
Period size: 81 Copynumber: 2.6 Consensus size: 81
397162 TTTCTGAGGG
* * * * * *
397172 GATACTCCAACCCTATCATTTCTGAGGGGATATTTTAACCTCGTTTTTACTTCTAAAGGCATCAA
1 GATACTCTAACCTTATTATTTCTGAGGGGATATTTCAACCTCGTTTTTACTTCCAAAAGCAT-AA
*
397237 AATTTT-TACCATCGAA
65 AATTTTCCACCATCGAA
* * *
397253 GATACTCTAACCTTATTATTTTCT-AGGGGATACTCCAACAC-CGTTTTTACTTCCAAAAGCATT
1 GATACTCTAACCTTATTA-TTTCTGAGGGGATATTTCAAC-CTCGTTTTTACTTCCAAAAGCATA
**
397316 AAATTTTCCACCATCGGG
64 AAATTTTCCACCATCGAA
* *
397334 GATACT-TCAACCTCATTATTTCTGAGAGGATATTTCAACCTCGTTTT
1 GATACTCT-AACCTTATTATTTCTGAGGGGATATTTCAACCTCGTTTT
397381 AATTTTTAAA
Statistics
Matches: 106, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
80 14 0.13
81 86 0.81
82 6 0.06
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (81 bp):
GATACTCTAACCTTATTATTTCTGAGGGGATATTTCAACCTCGTTTTTACTTCCAAAAGCATAAA
ATTTTCCACCATCGAA
Found at i:398374 original size:26 final size:26
Alignment explanation
Indices: 398345--398399 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
398335 AATAGACATT
*
398345 TGATCATGCCTAGCCAAAATAATCGG
1 TGATCATGCCTAGCCAAAACAATCGG
*
398371 TGATCATGCCTAGCCAAAACGATCGG
1 TGATCATGCCTAGCCAAAACAATCGG
398397 TGA
1 TGA
398400 CGACTCCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (26 bp):
TGATCATGCCTAGCCAAAACAATCGG
Found at i:399005 original size:24 final size:24
Alignment explanation
Indices: 398978--399028 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
398968 TCCATTTTTC
398978 TTTT-CTCTCTTTTTCTTTCTA-TTA
1 TTTTCCTCTC-TTTTCTTT-TATTTA
*
399002 TTTTCCTTTCTTTTCTTTTATTTA
1 TTTTCCTCTCTTTTCTTTTATTTA
399026 TTT
1 TTT
399029 CATTTTCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 2 0.08
24 18 0.75
25 4 0.17
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTCCTCTCTTTTCTTTTATTTA
Found at i:399833 original size:19 final size:20
Alignment explanation
Indices: 399809--399846 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
399799 CAAATAGAAA
399809 AGAAAAAAGAGAA-AAAAAT
1 AGAAAAAAGAGAAGAAAAAT
*
399828 AGAAAAAATAGAAGAAAAA
1 AGAAAAAAGAGAAGAAAAA
399847 GGGCAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (20 bp):
AGAAAAAAGAGAAGAAAAAT
Found at i:399842 original size:24 final size:23
Alignment explanation
Indices: 399800--399846 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
399790 AACACTAAAC
399800 AAATAGAAAAGAAAAAAGAGAAAA
1 AAATAGAAAAGAAAAAAGA-AAAA
*
399824 AAATAGAAAA-AATAGAAGAAAAA
1 AAATAGAAAAGAA-AAAAGAAAAA
399847 GGGCAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (23 bp):
AAATAGAAAAGAAAAAAGAAAAA
Found at i:400633 original size:29 final size:28
Alignment explanation
Indices: 400593--400693 Score: 78
Period size: 29 Copynumber: 3.5 Consensus size: 28
400583 TTTTATGCAT
400593 TTTA-GGTCCATTTAGGTTATTTTATATAA
1 TTTAGGGT-CATTTAGGTT-TTTTATATAA
* * * ** *
400622 TCTAGGGTCATTTTAAGATTTTTCATGCAT
1 TTTAGGGTCA-TTT-AGGTTTTTTATATAA
*
400652 TTTAGGGTCATTTAGGTTGTTTTACATAA
1 TTTAGGGTCATTTAGGTT-TTTTATATAA
*
400681 TTTAAGGTCATTT
1 TTTAGGGTCATTT
400694 TAGTAATTTT
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
28 4 0.07
29 25 0.46
30 21 0.39
31 4 0.07
ACGTcount: A:0.25, C:0.09, G:0.17, T:0.50
Consensus pattern (28 bp):
TTTAGGGTCATTTAGGTTTTTTATATAA
Found at i:400690 original size:59 final size:59
Alignment explanation
Indices: 400527--400704 Score: 207
Period size: 59 Copynumber: 3.0 Consensus size: 59
400517 TAGCAATTTC
* * * **
400527 CATGCTTTTTAGGGTTATTTAGGTTATTTTATGTAATCTAATGACCA-TTTAAAATTTTT
1 CATGCATTTTAGGGTCATTTAGGTTATTTTATATAATCTAA-GGTCATTTTAAAATTTTT
* * *
400586 TATGCATTTTA-GGTCCATTTAGGTTATTTTATATAATCTAGGGTCATTTTAAGATTTTT
1 CATGCATTTTAGGGT-CATTTAGGTTATTTTATATAATCTAAGGTCATTTTAAAATTTTT
* * * *
400645 CATGCATTTTAGGGTCATTTAGGTTGTTTTACATAATTTAAGGTCATTTTAGTAATTTTT
1 CATGCATTTTAGGGTCATTTAGGTTATTTTATATAATCTAAGGTCATTTTA-AAATTTTT
400705 TTAACCTTAA
Statistics
Matches: 100, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
58 6 0.06
59 85 0.85
60 9 0.09
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (59 bp):
CATGCATTTTAGGGTCATTTAGGTTATTTTATATAATCTAAGGTCATTTTAAAATTTTT
Found at i:401367 original size:21 final size:21
Alignment explanation
Indices: 401341--401380 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
401331 TTTTTGCCTA
*
401341 CATGTATCGATACATGCAAGG
1 CATGTATCAATACATGCAAGG
*
401362 CATGTATCAATGCATGCAA
1 CATGTATCAATACATGCAA
401381 AAGGTCCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (21 bp):
CATGTATCAATACATGCAAGG
Found at i:401443 original size:21 final size:20
Alignment explanation
Indices: 401419--401469 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
401409 TTATACAATT
*
401419 TGTATCGATACAACAAGTTAA
1 TGTATCGATAC-ACAAGTGAA
* *
401440 TGTATCAATACATAAGTGAA
1 TGTATCGATACACAAGTGAA
401460 TGTATCGATA
1 TGTATCGATA
401470 TTGGACCTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (20 bp):
TGTATCGATACACAAGTGAA
Found at i:404609 original size:80 final size:79
Alignment explanation
Indices: 404444--404670 Score: 238
Period size: 80 Copynumber: 2.9 Consensus size: 79
404434 CTTCATCTCA
* * * * *
404444 GGGATACTCCAACTCCGGTTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAATC
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTTCACAATCAGGGATACTCCAACC
*
404509 CCGTTATTTCCGAG
66 CCGTCATTTCCGAG
* * * * *
404523 GGGATACTCCAACCCCGATTTTATTCCCAAAACACCAGTTTTTTCACAATTAGGGATATTCCAAC
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACCA-ATTTTTCACAATCAGGGATACTCCAAC
**
404588 CCCGTCATTTTTGAG
65 CCCGTCATTTCCGAG
* * * *** * * * *
404603 GGGATACTCCAACCTCGGCTTTATTTCCAAAATATTGATTTCTCATAATCGGGGATACTTCAACC
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTTCACAATCAGGGATACTCCAACC
404668 CCG
66 CCG
404671 GCCTTATTTC
Statistics
Matches: 119, Mismatches: 28, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
79 57 0.48
80 62 0.52
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (79 bp):
GGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTTCACAATCAGGGATACTCCAACC
CCGTCATTTCCGAG
Found at i:404661 original size:51 final size:51
Alignment explanation
Indices: 404602--404721 Score: 143
Period size: 51 Copynumber: 2.4 Consensus size: 51
404592 TCATTTTTGA
* * ** *
404602 GGGGATACTCCAACCTCGGCTTTATTTCCAAAAT-ATTGATTTCTCATAATC
1 GGGGATACTCCAACCCCGGCCTTATTT-CAAAATCATCAATTTCTCACAATC
* * *
404653 GGGGATACTTCAACCCCGGCCTTATTTCTAAATCATCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGGCCTTATTTCAAAATCATCAATTTCTCACAATC
*
404704 AGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
404722 TTATTTTCGA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 5 0.09
51 53 0.91
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGCCTTATTTCAAAATCATCAATTTCTCACAATC
Found at i:404747 original size:79 final size:79
Alignment explanation
Indices: 404653--404881 Score: 284
Period size: 79 Copynumber: 2.9 Consensus size: 79
404643 TCTCATAATC
* *** * *
404653 GGGGATACTTCAACCCCGGCCTTATTTCTAAATCATCAATTTTTCACAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAATCACCAATTTTTCATAATCAGGGATACTCCAAC
404718 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
* * *
404732 GGGGATACTCCAACCCTGATTTTATTTTCAAAAT-ACCAA-TTTTCTATAATCAGGGATACCCCA
1 GGGGATACTCCAACCCCGATTTTA-TTTCTAAATCACCAATTTTTC-ATAATCAGGGATACTCCA
*
404795 ACCCTGTTATTTTCGA
64 ACCCCGTTATTTTCGA
* * * *
404811 GGGGATACTCCAACCCCGATTTTATTTTTAGAA-CACCGATTTTTCATAATCACGGATACTCCAG
1 GGGGATACTCCAACCCCGATTTTATTTCTA-AATCACCAATTTTTCATAATCAGGGATACTCCAA
404875 CCCCGTT
65 CCCCGTT
404882 CTTATCTCCA
Statistics
Matches: 127, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
78 9 0.07
79 105 0.83
80 13 0.10
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAATCACCAATTTTTCATAATCAGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:404797 original size:130 final size:130
Alignment explanation
Indices: 404562--404798 Score: 325
Period size: 130 Copynumber: 1.8 Consensus size: 130
404552 AAACACCAGT
* * * *
404562 TTTTTCACAATTAGGGATATTCCAACCCCGTCATTTTTGAGGGGATACTCCAACCTCGGCTTTAT
1 TTTTTCACAATCAGGGATACTCCAACCCCGTCATTTTCGAGGGGATACTCCAACCTCGACTTTAT
*** * **
404627 TTCCAAAATATTGATTTCTCATAATCGGGGATACTTCAACCCCGGCCTTATTTCTAAATCATCAA
66 TTCCAAAATACCAATTTCTCATAATCAGGGATACCCCAACCCCGGCCTTATTTCTAAATCATCAA
* *
404692 TTTTTCACAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACC-CTGATTTTA
1 TTTTTCACAATCAGGGATACTCCAACCCCGTCATTTTCGAGGGGATACTCCAACCTC-GACTTTA
*
404756 TTTTCAAAATACCAATTT-TCTATAATCAGGGATACCCCAACCC
65 TTTCCAAAATACCAATTTCTC-ATAATCAGGGATACCCCAACCC
404799 TGTTATTTTC
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
129 3 0.03
130 89 0.97
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (130 bp):
TTTTTCACAATCAGGGATACTCCAACCCCGTCATTTTCGAGGGGATACTCCAACCTCGACTTTAT
TTCCAAAATACCAATTTCTCATAATCAGGGATACCCCAACCCCGGCCTTATTTCTAAATCATCAA
Found at i:404906 original size:210 final size:209
Alignment explanation
Indices: 404445--404907 Score: 525
Period size: 210 Copynumber: 2.2 Consensus size: 209
404435 TTCATCTCAG
* * * * *
404445 GGATACTCCAACTCCGGTT-TTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAATC
1 GGATACTCCAAC-CCCGTTCTTA-TTCCAAAATATCAATTTTTCACAATCAGGGATACTCCAACC
* * *
404509 CCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTCCCAAAACACCAGTTTTTTCACAATT
64 CCGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTCCCAAAACACCAATTTTCTCACAATC
** * * * * **
404574 AGGGATATTCCAACCCCGTCATTTTTGAGGGGATACTCCAACCTCGGCTTTATTTCCAAAATATT
129 AGGGATACCCCAACCCCGTCATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAACACC
**
404639 GATTTCTCATAATCGG
194 GATTTCTCATAATCAC
* ** * *
404655 GGATACTTCAACCCCGGCCTTATTTCTAAATCATCAATTTTTCACAATCAGGGATACTCCAACCC
1 GGATACTCCAACCCCGTTCTTATTCCAAAAT-ATCAATTTTTCACAATCAGGGATACTCCAACCC
* * ** * *
404720 CGTTATTTTCGAGGGGATACTCCAACCCTGATTTTATTTTCAAAATACCAATTTTCT-ATAATCA
65 CGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTCCCAAAACACCAATTTTCTCACAATCA
* * * ** *
404784 GGGATACCCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTTTAGAACACCG
130 GGGATACCCCAACCCCGTCATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAACACCG
*
404849 ATTTTTCATAATCAC
195 ATTTCTCATAATCAC
* *
404864 GGATACTCCAGCCCCGTTCTTATCTCCAAAATATTAAATTTTTC
1 GGATACTCCAACCCCGTTCTTAT-TCCAAAATA-TCAATTTTTC
404908 GTCGGGAGAT
Statistics
Matches: 206, Mismatches: 43, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
209 97 0.47
210 109 0.53
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (209 bp):
GGATACTCCAACCCCGTTCTTATTCCAAAATATCAATTTTTCACAATCAGGGATACTCCAACCCC
GTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTCCCAAAACACCAATTTTCTCACAATCAG
GGATACCCCAACCCCGTCATTTTCGAGGGGATACTCCAACCCCGACTTTATTTCCAAAACACCGA
TTTCTCATAATCAC
Found at i:405875 original size:21 final size:20
Alignment explanation
Indices: 405845--405890 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
405835 CGTTGCGACA
* *
405845 GTATCGATACAACAAGTTAAT
1 GTATCAATAC-ACAAGTGAAT
*
405866 GTATCAATACATAAGTGAAT
1 GTATCAATACACAAGTGAAT
405886 GTATC
1 GTATC
405891 GATATTGGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.30
Consensus pattern (20 bp):
GTATCAATACACAAGTGAAT
Found at i:406010 original size:32 final size:33
Alignment explanation
Indices: 405937--406013 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 33
405927 GAAAAATTGT
*
405937 TTGATACATT-TTGGGTTTTTGACCCAAATGTA
1 TTGATACATTCTTGGGTTTTTGACCCAAATATA
*
405969 TCGATACATTCTT-GGTTTTTGACCCAAATATA
1 TTGATACATTCTTGGGTTTTTGACCCAAATATA
*
406001 TTGACACATTCTT
1 TTGATACATTCTT
406014 TAATGTATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 38 0.95
33 2 0.05
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (33 bp):
TTGATACATTCTTGGGTTTTTGACCCAAATATA
Found at i:413259 original size:27 final size:26
Alignment explanation
Indices: 413204--413253 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
413194 CATCGTCGGG
* *
413204 GATACTCCAGCCCTATTCCTTTGAAAA
1 GATACTCAAGCCCTATT-CTTTCAAAA
413231 GATACTCAAGCCCTATT-TTTCAA
1 GATACTCAAGCCCTATTCTTTCAA
413254 CTAAGAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
27 16 0.76
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.32
Consensus pattern (26 bp):
GATACTCAAGCCCTATTCTTTCAAAA
Found at i:416554 original size:12 final size:12
Alignment explanation
Indices: 416537--416565 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
416527 GCGTCAAAGC
416537 CTCATTCTCTGG
1 CTCATTCTCTGG
416549 CTCATTCTCTGG
1 CTCATTCTCTGG
416561 CTCAT
1 CTCAT
416566 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.34, G:0.14, T:0.41
Consensus pattern (12 bp):
CTCATTCTCTGG
Found at i:418852 original size:19 final size:20
Alignment explanation
Indices: 418815--418858 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
418805 ATTTTTTTAA
*
418815 TTTTATATTAAAAATTATAT
1 TTTTAAATTAAAAATTATAT
*
418835 TTTTAAATTAAATA-TATAT
1 TTTTAAATTAAAAATTATAT
418854 TTTTA
1 TTTTA
418859 TTAATTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTAAATTAAAAATTATAT
Found at i:418861 original size:17 final size:18
Alignment explanation
Indices: 418814--418862 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
418804 AATTTTTTTA
418814 ATTTTATATTAAAAATTAT
1 ATTTT-TATTAAAAATTAT
*
418833 ATTTTTAAATTAAATA-TAT
1 ATTTTT--ATTAAAAATTAT
418852 ATTTTTATTAA
1 ATTTTTATTAA
418863 TTATTTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 14 0.52
20 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTTATTAAAAATTAT
Found at i:418906 original size:20 final size:20
Alignment explanation
Indices: 418878--418925 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
418868 TATTATATTT
418878 ATTTTTATTTAATA-TTAAA
1 ATTTTTATTTAATATTTAAA
418897 ATTATTTATTTAATATTTAAA
1 ATT-TTTATTTAATATTTAAA
418918 ATTTTTAT
1 ATTTTTAT
418926 CATTAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.11
20 16 0.59
21 8 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTATTTAATATTTAAA
Found at i:420285 original size:32 final size:31
Alignment explanation
Indices: 420191--420295 Score: 106
Period size: 32 Copynumber: 3.4 Consensus size: 31
420181 TTTTTTATGA
420191 TTATCAAATTTACAAGTAATTAT-TTTAATAT
1 TTATCAAATTTACAAGTAATTATGTTTAAT-T
* * * * * *
420222 TCATTAAATTTATAAGTACTTTTGTTCAATTT
1 TTATCAAATTTACAAGTAATTATGTTTAA-TT
* *
420254 TTATCAAATTTACGAGAAATTATGTTTAA-T
1 TTATCAAATTTACAAGTAATTATGTTTAATT
420284 TTATCAAATTTA
1 TTATCAAATTTA
420296 TGATTCATAT
Statistics
Matches: 58, Mismatches: 14, Indels: 5
0.75 0.18 0.06
Matches are distributed among these distances:
30 13 0.22
31 18 0.31
32 26 0.45
33 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.49
Consensus pattern (31 bp):
TTATCAAATTTACAAGTAATTATGTTTAATT
Found at i:421964 original size:19 final size:19
Alignment explanation
Indices: 421952--421990 Score: 69
Period size: 19 Copynumber: 2.0 Consensus size: 19
421942 TATTATTTAT
421952 TTATTATTATATTAAATTA
1 TTATTATTATATTAAATTA
421971 TTATTATTATAATTAAATTA
1 TTATTATTAT-ATTAAATTA
421991 AATAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTATTATATTAAATTA
Found at i:422001 original size:26 final size:26
Alignment explanation
Indices: 421972--422033 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
421962 ATTAAATTAT
421972 TATTATTATAAT-TAAATT-AAATAAAA
1 TATTATT-TAATAT-AATTAAAATAAAA
421998 TATT-TTTAATATAATTAAAAATAAAA
1 TATTATTTAATATAATT-AAAATAAAA
422024 TATTATTTAA
1 TATTATTTAA
422034 ATTATAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
24 8 0.25
25 3 0.09
26 16 0.50
27 5 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TATTATTTAATATAATTAAAATAAAA
Found at i:422030 original size:29 final size:29
Alignment explanation
Indices: 421964--422031 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
421954 ATTATTATAT
* * *
421964 TAAATTATTATTATTATAATTAAATTAAA
1 TAAATTATTTTTAATATAATTAAAATAAA
*
421993 TAAAATATTTTTAATATAATTAAAAATAAA
1 TAAATTATTTTTAATATAATT-AAAATAAA
*
422023 -ATATTATTT
1 TAAATTATTT
422032 AAATTATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 25 0.78
30 7 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TAAATTATTTTTAATATAATTAAAATAAA
Found at i:422049 original size:26 final size:26
Alignment explanation
Indices: 421990--422056 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
421980 TAATTAAATT
421990 AAATAAAATATTTTTAATATAATTAA
1 AAATAAAATATTTTTAATATAATTAA
*
422016 AAATAAAATATTATTTAA-ATTA-TAA
1 AAATAAAATATT-TTTAATATAATTAA
*
422041 AATTAAAAATATTTTT
1 AAAT-AAAATATTTTT
422057 GAATGAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
25 9 0.24
26 23 0.62
27 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AAATAAAATATTTTTAATATAATTAA
Found at i:430082 original size:20 final size:20
Alignment explanation
Indices: 430051--430125 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
430041 TTTTACCTAG
430051 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * * *
430071 ATATATCAATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
430091 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
430111 ATGTATCGATACATT
1 ATGTATCGATACATT
430126 ATATCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:431088 original size:22 final size:22
Alignment explanation
Indices: 431035--431089 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
431025 AGCCTTTGAC
*
431035 CATGCATTTCTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
431057 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
431079 CATGCATTTTT
1 CATGCATTTTT
431090 AACTTGTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.18, C:0.13, G:0.09, T:0.60
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:444175 original size:9 final size:10
Alignment explanation
Indices: 444152--444220 Score: 61
Period size: 10 Copynumber: 6.6 Consensus size: 10
444142 TTACACCAAA
444152 AAAAAAAAAC
1 AAAAAAAAAC
*
444162 AAAAAGAAAC
1 AAAAAAAAAC
444172 AAAAAAAAA-
1 AAAAAAAAAC
*
444181 AACACAAAAAAT
1 AA-A-AAAAAAC
444193 AAAAAAAAA-
1 AAAAAAAAAC
444202 AAGAAAAAATAGC
1 AA-AAAAAA-A-C
444215 AAAAAA
1 AAAAAA
444221 TAGAAGGGTA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
9 4 0.08
10 30 0.60
11 8 0.16
12 6 0.12
13 2 0.04
ACGTcount: A:0.86, C:0.07, G:0.04, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:444175 original size:22 final size:21
Alignment explanation
Indices: 444150--444220 Score: 88
Period size: 22 Copynumber: 3.3 Consensus size: 21
444140 CTTTACACCA
444150 AAAAAAAAAAACAAAAAGAAAC
1 AAAAAAAAAAACAAAAA-AAAC
* *
444172 AAAAAAAAAAACACAAAAAAT
1 AAAAAAAAAAACAAAAAAAAC
* *
444193 AAAAAAAAAAAGAAAAAATAGC
1 AAAAAAAAAAACAAAAAA-AAC
444215 AAAAAA
1 AAAAAA
444221 TAGAAGGGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 19 0.45
22 23 0.55
ACGTcount: A:0.86, C:0.07, G:0.04, T:0.03
Consensus pattern (21 bp):
AAAAAAAAAAACAAAAAAAAC
Found at i:444220 original size:1 final size:1
Alignment explanation
Indices: 444149--444210 Score: 61
Period size: 1 Copynumber: 62.0 Consensus size: 1
444139 CCTTTACACC
* * * * * * *
444149 AAAAAAAAAAAACAAAAAGAAACAAAAAAAAAAACACAAAAAATAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
444211 TAGCAAAAAA
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.89, C:0.06, G:0.03, T:0.02
Consensus pattern (1 bp):
A
Found at i:444225 original size:19 final size:19
Alignment explanation
Indices: 444149--444212 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
444139 CCTTTACACC
444149 AAAAAA-AAAAAACAAAAAG
1 AAAAAATAAAAAA-AAAAAG
* * *
444168 AAACAA-AAAAAAAAACAC
1 AAAAAATAAAAAAAAAAAG
444186 AAAAAATAAAAAAAAAAAG
1 AAAAAATAAAAAAAAAAAG
444205 AAAAAATA
1 AAAAAATA
444213 GCAAAAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 9 0.24
19 29 0.76
ACGTcount: A:0.88, C:0.06, G:0.03, T:0.03
Consensus pattern (19 bp):
AAAAAATAAAAAAAAAAAG
Found at i:445476 original size:29 final size:29
Alignment explanation
Indices: 445438--445664 Score: 274
Period size: 29 Copynumber: 8.0 Consensus size: 29
445428 TGTTCATCCC
* *
445438 TTTCAAAGCCCACGAGTCAGTGGCACCTT
1 TTTCAAAGCCCACAAGTTAGTGGCACCTT
* * *
445467 TTTCAAAGCCCACATGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTTAGTGGCACCTT
* *
445496 TTTCAAAACCCATAAGTTAGTGGCA-CTCT
1 TTTCAAAGCCCACAAGTTAGTGGCACCT-T
445525 TTTCAAAGCCCACAAGTTAGTGGCATCC--
1 TTTCAAAGCCCACAAGTTAGTGGCA-CCTT
*
445553 TTTCAAAGCCCACAAGTTAGTGGCA-CTC
1 TTTCAAAGCCCACAAGTTAGTGGCACCTT
445581 TTTCAAAGCCCACAAGTTAGTGGCATCC--
1 TTTCAAAGCCCACAAGTTAGTGGCA-CCTT
* *
445609 TTTC-AAG-CCACAAGTCAGTGGCA-CTC
1 TTTCAAAGCCCACAAGTTAGTGGCACCTT
445635 TTTCAAAGCCCACAAGTTAGTGGCACCTT
1 TTTCAAAGCCCACAAGTTAGTGGCACCTT
445664 T
1 T
445665 CAGCCAAGTC
Statistics
Matches: 173, Mismatches: 13, Indels: 24
0.82 0.06 0.11
Matches are distributed among these distances:
24 1 0.01
26 20 0.12
27 6 0.03
28 70 0.40
29 74 0.43
30 1 0.01
31 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTTAGTGGCACCTT
Found at i:445643 original size:27 final size:28
Alignment explanation
Indices: 445437--446063 Score: 370
Period size: 28 Copynumber: 23.6 Consensus size: 28
445427 CTGTTCATCC
*
445437 CTTTCAAAGCCCACGAGTCAGTGGCACCT
1 CTTTCAAAGCCCACAAGTCAGTGGCA-CT
* * *
445466 TTTTCAAAGCCCACATGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
445494 CTTTTCAAAACCCATAAGTTAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
445523 CTTTTCAAAGCCCACAAGTTAGTGGCA-T
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
445551 CCTTTCAAAGCCCACAAGTTAGTGGCACT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
*
445580 CTTTCAAAGCCCACAAGTTAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
445607 CCTTTC-AAG-CCACAAGTCAGTGGCACT
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
*
445634 CTTTCAAAGCCCACAAGTTAGTGGCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
445661 CTTTC--AG--C-CAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
445684 CTTTCAACAGTGGGCCCACACAAGTCAGTGGCAC-
1 CTTTCAA-A----G-CC-CACAAGTCAGTGGCACT
* * *
445718 CTTTC-AA--CCAC-TGGCACT--C-CT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
445739 -TCT-AGAGCCCACAAGTAAGTGG-ACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
445764 CTTTCGAAGCCCACAAGTCGGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
445792 CTTGCGAAGCCCACAATTCAGTGGCTCT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
445820 CTTTCAAAGCCCAC-AGTCAGT-GCAC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
445845 C-TTC--AGCACAC-A-CCAGTTGC-CT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
445867 CTTT-AAAGCCCAC-A--CATTAGG-A--
1 CTTTCAAAGCCCACAAGTCAGT-GGCACT
* *
445889 CTTTC-AAGCCC-CGAGTCAGT-GCTC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
445913 CTTTTAAAGCCCAGCAAGTTAGTGGCAC-
1 CTTTCAAAGCCCA-CAAGTCAGTGGCACT
*
445941 CTTTCAAAGCCCACGAGTCAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
445968 CCTTCAAAG-CCA-AA-TCA-TCGGTACT
1 CTTTCAAAGCCCACAAGTCAGT-GGCACT
445993 CTTTCAAAGCCCA-AAGCTCAGTGGCAC-
1 CTTTCAAAGCCCACAAG-TCAGTGGCACT
* *
446020 CTTTC-AAG-CC-CTATTC-GTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
446044 CTTTGCCAAAGTCCCACAAG
1 CTTT--CAAAG-CCCACAAG
446064 CTTGGCAAAG
Statistics
Matches: 473, Mismatches: 62, Indels: 125
0.72 0.09 0.19
Matches are distributed among these distances:
20 4 0.01
21 7 0.01
22 39 0.08
23 26 0.05
24 33 0.07
25 24 0.05
26 38 0.08
27 68 0.14
28 134 0.28
29 75 0.16
30 3 0.01
32 1 0.00
33 1 0.00
34 6 0.01
35 14 0.03
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:446383 original size:29 final size:28
Alignment explanation
Indices: 446342--447996 Score: 1497
Period size: 28 Copynumber: 58.6 Consensus size: 28
446332 GAATGTTCAT
*
446342 CCCTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
** *
446370 CTTTTTTCAAAGCCCACATGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
446399 CCCTTTTCAAAACCCATAAGTTAGTGGCA
1 CCC-TTTCAAAGCCCACAAGTCAGTGGCA
* *
446428 CTCTTTTCAAAGCCCACAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
446457 TCCTTTCAAAGCCCTCAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
446485 CTCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
446513 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
446541 CTCTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
446569 CCTTTTC-AAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
446596 CTCTTTTAAAACCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
446624 CTCC-TTCTATAGCCCACAAGTCAGTGGCA
1 C-CCTTTC-AAAGCCCACAAGTCAGTGGCA
* *
446653 CCCTTTCGAAGCCCACAAGTCGGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* ** *
446681 CCC-TT--AAGCCAATTAGCCTCA--GCCA
1 CCCTTTCAAAGCCCACAAG--TCAGTGGCA
** ** * *** **
446706 CAATTT-AGTG-GCACTCTTTCA-AAGC-
1 CCCTTTCAAAGCCCAC-AAGTCAGTGGCA
** * * ***
446731 CCACAAGTCAATGGCACCCTATCAAAGCCCCAGGCA
1 CC-C-TTTCAA-AG--CCC-A-C-AAGTCAGTGGCA
446767 --C-TT--AAG--C-C-AGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
446786 CTCCTTTTAAAGCCCACGCAAGTTAGTGGCA
1 C-CCTTTCAAAGCCCA--CAAGTCAGTGGCA
* *
446817 CCTTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
446845 TCCTTTCAAAGCCCATAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
446873 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
446901 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
446929 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
446957 CCTTTTC-AAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
**
446984 CTATTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*** *
447012 CTCCTTTTGGAGCCCATAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
447041 CCCTTTCGAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
447069 CCCTTTCGAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
447097 CCCTTGCGAAGCCCACGATTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
447125 CTCTTTCAAAGCACACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
447153 CCCTTTCAAAGCCCACACAAGTTAGTGGCA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
* *
447183 CTCCTTTTAGAGCCCACAAGTCAGTGGCA
1 C-CCTTTCAAAGCCCACAAGTCAGTGGCA
*
447212 CCCTTTCGAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
447240 -CTTTTGCGAAGCCCAAAATTTAGTGGCA
1 CCCTTT-CAAAGCCCACAAGTCAGTGGCA
* *
447268 CTCTTTTAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
447296 CCCTTTCAAAGCCCACACAAGTTAGTGGCA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
* *
447326 CTCCTTTTAAAGCCCACGTTAGTCAGTGGCA
1 C-CCTTTCAAAGCCCAC--AAGTCAGTGGCA
* * * **
447357 CCTTTTCAAAGCCCACGAGTCAATAACA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
447385 CCTTTTCAAAGCCCACGAGTCTGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
** *
447413 CTTTTTCAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
447441 CCCTTTC-AAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
447468 CCCTTTC-AAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
447495 CCTTTTCAAAGCCCACGACTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
447523 CTCTTTCAAAGCCCACAAGTCAGTAGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
447551 TCCTTTCAAAGCCCACGCAAGTCAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
*
447581 CCCTTTTAAAGCCCACCCAAGTCAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* * *
447611 CCTTTTCAAAGCCCACGAGTCAGTAGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
** *
447639 CATTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
447667 CTCTTTCAAAGCCCACAAGTTAATGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* *
447695 CCCTTTC-AAGCACACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
** *
447722 CATTTTCAAAGCGCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
447750 CTCTTTTAAAGCCCACAAGTTAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*
447778 TCCTTTCAAAGCCCACGCAAGTCAGTGGCA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* * * *
447808 CCCTTTTAAAGCCCATGCAAATTAGTGACA
1 CCCTTTCAAAGCCCA--CAAGTCAGTGGCA
* *
447838 CCTTTTCAAAGCCCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* **
447866 CCTTTTTCAAAGCCCATGAGTCAGTGGCA
1 CC-CTTTCAAAGCCCACAAGTCAGTGGCA
*
447895 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
447923 TCCTTTCAAAGCTCACGAGTCAGTGGCA
1 CCCTTTCAAAGCCCACAAGTCAGTGGCA
*** *
447951 TTTTTTCAAAGCCCGCGCAAGTCAGTGGCA
1 CCCTTTCAAAG-CC-CACAAGTCAGTGGCA
*
447981 CCCTTTTAAAGCCCAC
1 CCCTTTCAAAGCCCAC
447997 GCAAGTCAAT
Statistics
Matches: 1335, Mismatches: 235, Indels: 114
0.79 0.14 0.07
Matches are distributed among these distances:
19 7 0.01
21 1 0.00
22 1 0.00
23 2 0.00
24 1 0.00
25 19 0.01
26 4 0.00
27 131 0.10
28 768 0.58
29 170 0.13
30 183 0.14
31 40 0.03
32 1 0.00
33 2 0.00
34 2 0.00
35 3 0.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (28 bp):
CCCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:447481 original size:227 final size:227
Alignment explanation
Indices: 446342--447996 Score: 1438
Period size: 227 Copynumber: 7.2 Consensus size: 227
446332 GAATGTTCAT
* * *
446342 CCCTTTCAAAGCCCACGAGTCAGTGGCACTTTTTTCAAAGCCCACATGTCAGTGGCACCCTTTTC
1 CCCTTTC-AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCC-TTTC
* * * * *
446407 AAAACCCATAAGTTAGTGGCACTCTTTTCAAAGCCCAC-AAGTTAGTGGCATCC-TTTCAAAGCC
64 AAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACGAAGTCAGTGGCACCCTTTTCAAAGCC
* * * * *
446470 CTCAAGTTAGTGGCA-CTCTTTCAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCCCACAAGT
129 CACAAGTCAGTGGCACCT-TTTCAAAGCCCACGAGTCAGTGGCACT-TTTTCAAAGCCCACAAGT
*
446533 CAGTGGCACTCTTTCAAAGCCCACAAGTTAGTGGCA
192 CAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA
* *
446569 CCTTTTCAAGCCCACAAGTCAGTGGCACTCTTTT-AAAACCCACAAGTCAGTGGCACTCC-TTCT
1 CCCTTTCAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTC-
* * * * **
446632 ATAGCCCACAAGTCAGTGGCAC-CCTTTCGAAGCCCAC-AAGTCGGTGGCACCCTTAAGCCAATT
64 AAAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACGAAGTCAGTGGCACCCTT--TTCAA--
* * * * ** *
446695 AGCCTCAGCCACAATTTAGTGGCA-CTCTTTCAAAGCCCACAAGTCAATGGCACCCTATCAAAGC
125 AG---C--CCACAAGTCAGTGGCACCT-TTTCAAAGCCCACGAGTCAGTGGCACTTTTTCAAAG-
* *
446759 CCCAGGCACTTAAGCCAGTCAGTGGCACTCCTTTTAAAGCCCACGCAAGTTAGTGGCA
183 -CC---CAC---A---AGTCAGTGGCACT-CTTTCAAAGCCCA--CAAGTCAGTGGCA
* * * * * *
446817 CCTTTTCAAAGCCCACGAGTCAGTGGCA-TCCTTTCAAAGCCCATAAGTTAGTGGCACTCTTTCA
1 CCCTTTC-AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
* *
446881 AAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCAC-AAGTCAGTGGCACTC-TTTCAAAGCCC
65 AAGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACGAAGTCAGTGGCACCCTTTTCAAAGCCC
* *
446943 ACAAGTCAGTGGCACCTTTTC-AAGCCCACAAGTCAGTGGCACTATTTCAAAGCCCACAAGTCAG
130 ACAAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTTTTTCAAAGCCCACAAGTCAG
*** *
447007 TGGCACTCCTTTTGGAGCCCATAAGTCAGTGGCA
195 TGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
447041 CCCTTTCGAAGCCCACAAGTTAGTGGCAC-CCTTTCGAAGCCCACAAGTCAGTGGCACCCTTGCG
1 CCCTTTC-AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
* * *
447105 AAGCCCACGA-TTCAGTGGCACT-CTTTCAAAGCACAC-AAGTTAGTGGCACCC-TTTCAAAGCC
65 AAGCCCACAAGTT-AGTGGCACTCCTTTCAAAGCCCACGAAGTCAGTGGCACCCTTTTCAAAG-C
* * * ** *
447166 CACACAAGTTAGTGGCACTCCTTTT-AGAGCCCACAAGTCAGTGGCACCCTTTCGAAGCCCACAA
128 C-CACAAGTCAGTGGCA--CCTTTTCAAAGCCCACGAGTCAGTGGCACTTTTTCAAAGCCCACAA
* * * *
447230 GTCAGTGGCACT-TTTGCGAAGCCCAAAATTTAGTGGCA
190 GTCAGTGGCACTCTTT-CAAAGCCCACAAGTCAGTGGCA
* * * *
447268 CTCTTTTAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACACAAGTTAGTGGCACTCCTT
1 C-CCTTTCAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG-CC-CACAAGTCAGTGGCAC-CCTT
* * * * * **
447332 TTAAAGCCCACGTTAGTCAGTGGCAC-CTTTTCAAAGCCCACG-AGTCAATAACA-CCTTTTCAA
62 TCAAAGCCCAC--AAGTTAGTGGCACTCCTTTCAAAGCCCACGAAGTCAGTGGCACCCTTTTCAA
* * * * * ** *
447394 AGCCCACGAGTCTGTGGCACTTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTC-AAGCCCACGA
125 AGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTTTTTCAAAGCCCACAA
* *
447458 GTCAGTGGCACCCTTTC-AAGCCCACGAGTCAGTGGCA
190 GTCAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
447495 CCTTTTCAAAGCCCACGACTCAGTGGCACTC-TTTCAAAGCCCACAAGTCAGTAGCATCCTTTCA
1 CCCTTTC-AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
* * *
447559 AAGCCCACGCAAGTCAGTGGCAC-CCTTTTAAAGCCCACCCAAGTCAGTGGCA-CCTTTTCAAAG
65 AAGCCCA--CAAGTTAGTGGCACTCCTTTCAAAGCCCA-CGAAGTCAGTGGCACCCTTTTCAAAG
* * * *
447622 CCCACGAGTCAGTAGCACATTTTCAAAGCCCACGAGTCAGTGGCACTCTTTCAAAGCCCACAAGT
127 CCCACAAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTTTTTCAAAGCCCACAAGT
* * * * *
447687 TAATGGCACCCTTTC-AAGCACACGAGTCAGTGGCA
192 CAGTGGCACTCTTTCAAAGCCCACAAGTCAGTGGCA
** * * *
447722 CATTTTCAAAGCGCACAAGTCAGTGGCACTCTTTT-AAAGCCCACAAGTTAGTGGCATCCTTTCA
1 CCCTTTC-AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCA
* * * * * *
447786 AAGCCCACGCAAGTCAGTGGCAC-CCTTTTAAAGCCCATGCAAATTAGTGACA-CCTTTTCAAAG
65 AAGCCCA--CAAGTTAGTGGCACTCCTTTCAAAGCCCACG-AAGTCAGTGGCACCCTTTTCAAAG
* * *
447849 CCCACGAGTCAGTGGCACCTTTTTCAAAGCCCATGAGTCAGTGGCACTCTTTCAAAGCCCACAAG
127 CCCACAAGTCAGTGGCACC-TTTTCAAAGCCCACGAGTCAGTGGCACTTTTTCAAAGCCCACAAG
* *
447914 TCAGTGGCA-TCCTTTCAAAGCTCACGAGTCAGTGGCA
191 TCAGTGGCACT-CTTTCAAAGCCCACAAGTCAGTGGCA
*** * *
447951 TTTTTTCAAAGCCCGCGCAAGTCAGTGGCACCCTTTT-AAAGCCCAC
1 CCCTTTC-AAG-CC-CACAAGTCAGTGGCACTCTTTTCAAAGCCCAC
447997 GCAAGTCAAT
Statistics
Matches: 1216, Mismatches: 145, Indels: 130
0.82 0.10 0.09
Matches are distributed among these distances:
223 1 0.00
224 179 0.15
225 56 0.05
226 142 0.12
227 271 0.22
228 144 0.12
229 75 0.06
230 25 0.02
231 33 0.03
232 40 0.03
233 1 0.00
234 48 0.04
235 2 0.00
236 2 0.00
237 27 0.02
238 18 0.01
239 5 0.00
240 1 0.00
242 1 0.00
243 2 0.00
245 16 0.01
246 12 0.01
247 1 0.00
248 73 0.06
249 41 0.03
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (227 bp):
CCCTTTCAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAA
AGCCCACAAGTTAGTGGCACTCCTTTCAAAGCCCACGAAGTCAGTGGCACCCTTTTCAAAGCCCA
CAAGTCAGTGGCACCTTTTCAAAGCCCACGAGTCAGTGGCACTTTTTCAAAGCCCACAAGTCAGT
GGCACTCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:448665 original size:20 final size:20
Alignment explanation
Indices: 448615--448688 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 20
448605 TTTTACCCAG
* *
448615 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATCA
* * *
448635 ATATATTGATACATGTATGA
1 ATGTATCGATACATGTATCA
* *
448655 ATGTATCGATATAT-TCTTCA
1 ATGTATCGATACATGT-ATCA
*
448675 CTGTATCGATACAT
1 ATGTATCGATACAT
448689 TATGTCTTTT
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
19 1 0.02
20 40 0.98
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:448686 original size:40 final size:39
Alignment explanation
Indices: 448615--448692 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
448605 TTTTACCCAG
* *
448615 ATGTATCGATACATTTTTCAATATATTGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* * *
448655 ATGTATCGATATATTCTTCACTGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
448693 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:449636 original size:23 final size:23
Alignment explanation
Indices: 449600--449655 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
449590 AGCCTTTGAC
*
449600 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTCT
449622 CATGCATTTTTTTTATTATGTCT
1 CATGCATTTTTTTTATTATGTCT
449645 CATGCATTTTT
1 CATGCATTTTT
449656 AACATGTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 6 0.19
23 26 0.81
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTCT
Found at i:450471 original size:51 final size:51
Alignment explanation
Indices: 450404--450522 Score: 222
Period size: 51 Copynumber: 2.4 Consensus size: 51
450394 ACAATTTTTG
450404 ATGTATCGATACATATTTGAAAATATAGCCGTTTCTAGCCGTTACAAGCCA
1 ATGTATCGATACATATTTGAAAATATAGCCGTTTCTAGCCGTTACAAGCCA
*
450455 ATGTATCGATACATATTTGAAAATATAGCCGTTTCTTGCCGTTACAAGCCA
1 ATGTATCGATACATATTTGAAAATATAGCCGTTTCTAGCCGTTACAAGCCA
450506 ATGTATCGATACA-ATTT
1 ATGTATCGATACATATTT
450523 TTTGTGTATC
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
50 4 0.06
51 63 0.94
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (51 bp):
ATGTATCGATACATATTTGAAAATATAGCCGTTTCTAGCCGTTACAAGCCA
Found at i:450545 original size:13 final size:13
Alignment explanation
Indices: 450527--450552 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
450517 CAATTTTTTG
450527 TGTATCGATACAT
1 TGTATCGATACAT
450540 TGTATCGATACAT
1 TGTATCGATACAT
450553 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:450567 original size:32 final size:33
Alignment explanation
Indices: 450507--450570 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
450497 TACAAGCCAA
** *
450507 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
450540 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
450571 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:452605 original size:148 final size:150
Alignment explanation
Indices: 452452--452740 Score: 483
Period size: 150 Copynumber: 1.9 Consensus size: 150
452442 AAAAAAAATC
* *
452452 AAATTTATCCCGAAAGTATTAATTCAA-TT-ATTTTATTTATTTTTGAAAATACCATTTCATACC
1 AAATTTATCCCAAAAGTATTAATTCAATTTAATTGTATTTATTTTTGAAAATACCATTTCATACC
**
452515 CTAATGGAAGCCTGAAAGGATACGAAATGTTTTTGAAATCTTTTATACCCCCACGGATACCCATA
66 CTAATGGAAGCCTGAAAGGATACGAAACATTTTTGAAATCTTTTATACCCCCACGGATACCCATA
452580 AAAATATAAAAAAATAATTA
131 AAAATATAAAAAAATAATTA
*
452600 AAATTTATCCCAAAAGTATTAATTCAATTTAATTGTATTTATTTTTGAAAATACCATTTCATATC
1 AAATTTATCCCAAAAGTATTAATTCAATTTAATTGTATTTATTTTTGAAAATACCATTTCATACC
* *
452665 CTAATGGAAGCCTGAAAGGATACGAAACATTTTTGAAATCTTTTATACCCCTACGGATGCCCATA
66 CTAATGGAAGCCTGAAAGGATACGAAACATTTTTGAAATCTTTTATACCCCCACGGATACCCATA
**
452730 GGAATATAAAA
131 AAAATATAAAA
452741 GATTAAAAAA
Statistics
Matches: 130, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
148 26 0.20
149 2 0.02
150 102 0.78
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (150 bp):
AAATTTATCCCAAAAGTATTAATTCAATTTAATTGTATTTATTTTTGAAAATACCATTTCATACC
CTAATGGAAGCCTGAAAGGATACGAAACATTTTTGAAATCTTTTATACCCCCACGGATACCCATA
AAAATATAAAAAAATAATTA
Found at i:454625 original size:166 final size:163
Alignment explanation
Indices: 454247--454941 Score: 583
Period size: 167 Copynumber: 4.2 Consensus size: 163
454237 ATAGGAGTTT
* * ** ** * *
454247 AATAACAATATTAGATGAATTTTAAAAATTTTAAACTGAGAAAAATCCCCTTTAAAAAATTTACA
1 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCACTTGAAAAAATTTACA
* * * *
454312 AAGTAGAAAACTCGGT-TTCTCTAAAAAAGGGAAAATTTCAAAGAAAAAA-TCCAAAACTCATGG
66 GAGTAGAAAACTC-ATATT-T-TAAAAAA-GG-AAATTTCAAAGAAAAAATTCAAAAACTCATGA
* * * *
454375 AAATGAATTAATTTTTTTAAAAAAATTTAATATGAATCA
126 AAATGAATGAA-TTTTTTAAACAGATTTAATATGAATTA
* * * * ** *
454414 AATGATGATATTTTATGAATTTTAAAAATTGAAAACCGGGAAAAATCCACTTGAAAAAATTTACG
1 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCACTTGAAAAAATTTACA
* * * * * * *
454479 GAGTAGAAAACATCATATTTTAAGAAATGGGAGTTTCAAGGAAAAAATTTAAAAATTTATGAAAA
66 GAGTAGAAAAC-TCATATTTTAA-AAAAGGAAATTTCAAAGAAAAAATTCAAAAACTCATGAAAA
454544 TGAATGAATTTTTTAGAACAGATTTAATATGAATTA
129 TGAATGAATTTTTTA-AACAGATTTAATATGAATTA
** * * ** * **
454580 AATAATAATATTTGATGAATTTTAAAAATTAAAAATTAAGAAAAATTCTCCCGAAAATATTTATG
1 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCACTTGAAAAAATTTACA
* *
454645 GAGTAGAAAACTCCATATTTTGAAAAAAGAAATATTTCAAAGAAAAAAATCAAAAACTCATGAAA
66 GAGTAGAAAACT-CATATTTT-AAAAAAGGAA-ATTTCAAAGAAAAAATTCAAAAACTCATGAAA
* * * ** *
454710 ATGGATGTATTTTTGCAAATTGACTTAATATGGAA-TA
128 ATGAATGAATTTTT-TAAACAGATTTAATAT-GAATTA
* * * *
454747 AATAATAATATTCGATGAATTTTAAAAATTAAAAACCAAG-AAAA-CTAGTTCCAAAAAAATTTA
1 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCACTT--GAAAAAATTTA
* * ** * *
454810 CAGAGTACAAAACTTCGTATTTTAAAAATAAATAAATTT-AAAGGGAAAAATTCAAAAACTAATG
64 CAGAGTAGAAAAC-TCATATTTT-AAAA-AAGGAAATTTCAAA-GAAAAAATTCAAAAACTCATG
* ** * *
454874 AAAATGAATGAATTTTTGAAAACTTATTTAATATAAAATA
125 AAAATGAATGAATTTTT-TAAACAGATTTAATATGAATTA
*
454914 AATAATAATATTTTATGAATTTCTAAAA
1 AATAATAATATTTGATGAATTT-TAAAA
454942 TTTTAAACCC
Statistics
Matches: 425, Mismatches: 86, Indels: 33
0.78 0.16 0.06
Matches are distributed among these distances:
165 22 0.05
166 125 0.29
167 260 0.61
168 18 0.04
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (163 bp):
AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCACTTGAAAAAATTTACA
GAGTAGAAAACTCATATTTTAAAAAAGGAAATTTCAAAGAAAAAATTCAAAAACTCATGAAAATG
AATGAATTTTTTAAACAGATTTAATATGAATTA
Found at i:454833 original size:333 final size:332
Alignment explanation
Indices: 454342--454941 Score: 735
Period size: 333 Copynumber: 1.8 Consensus size: 332
454332 CTAAAAAAGG
* * ** *
454342 GAAAATTTCAAAGAAAAAATCCAAAACTCATGGAAATGAATTAATTTTTTTAAAAAAATTTAATA
1 GAAAATTTCAAAGAAAAAATCAAAAACTCATGAAAATGAATTAATTTTTGCAAAAAAACTTAATA
* * ** * ** *
454407 TGAATCAAATGATGATATTTTATGAATTTTAAAAATTGAAAACCGGGAAAAATCCACTTGAAAAA
66 TGAATCAAATAATAATATTCGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCACTTAAAAAA
* * * * * * * *
454472 ATTTACGGAGTAGAAAACATCATATTTTAAGAAAT-GGGAGTTTCAAGGAAAAAATTTAAAAATT
131 ATTTACAGAGTACAAAACATCATATTTTAA-AAATAAGAAATTTAAAGGAAAAAATTCAAAAACT
* * * * *
454536 TATGAAAATGAATGAATTTTTTAGAACAGATTTAATATGAATTAAATAATAATATTTGATGAATT
195 AATGAAAATGAATGAATTTTTGAAAACAGATTTAATATAAAATAAATAATAATATTTGATGAATT
454601 T-TAAAAATTAAAAATTAAGAAAAATTCTCCCGAAAATATTTATGGAGTAGAAAACTCCATATTT
260 TCTAAAAATTAAAAATTAAGAAAAATTCTCCCGAAAATATTTATGGAGTAGAAAACTCCATATTT
454665 TGAAAAAA
325 TGAAAAAA
* ***
454673 GAAATATTTCAAAGAAAAAAATCAAAAACTCATGAAAATGGATGT-ATTTTTGCAAATTGACTTA
1 GAAA-ATTTCAAAG-AAAAAATCAAAAACTCATGAAAATGAAT-TAATTTTTGCAAAAAAACTTA
* *
454737 ATATGGAAT-AAATAATAATATTCGATGAATTTTAAAAATTAAAAACCAAG-AAAA-CTAGTTCC
63 ATAT-GAATCAAATAATAATATTCGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCACTT--
* * * *
454799 AAAAAAATTTACAGAGTACAAAACTTCGTATTTTAAAAATAAATAAATTTAAAGGGAAAAATTCA
125 AAAAAAATTTACAGAGTACAAAACATCATATTTTAAAAAT-AAGAAATTTAAAGGAAAAAATTCA
** *
454864 AAAACTAATGAAAATGAATGAATTTTTGAAAACTTATTTAATATAAAATAAATAATAATATTTTA
189 AAAACTAATGAAAATGAATGAATTTTTGAAAACAGATTTAATATAAAATAAATAATAATATTTGA
454929 TGAATTTCTAAAA
254 TGAATTTCTAAAA
454942 TTTTAAACCC
Statistics
Matches: 221, Mismatches: 39, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
331 8 0.04
332 17 0.08
333 107 0.48
334 84 0.38
335 5 0.02
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.32
Consensus pattern (332 bp):
GAAAATTTCAAAGAAAAAATCAAAAACTCATGAAAATGAATTAATTTTTGCAAAAAAACTTAATA
TGAATCAAATAATAATATTCGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCACTTAAAAAA
ATTTACAGAGTACAAAACATCATATTTTAAAAATAAGAAATTTAAAGGAAAAAATTCAAAAACTA
ATGAAAATGAATGAATTTTTGAAAACAGATTTAATATAAAATAAATAATAATATTTGATGAATTT
CTAAAAATTAAAAATTAAGAAAAATTCTCCCGAAAATATTTATGGAGTAGAAAACTCCATATTTT
GAAAAAA
Found at i:456415 original size:44 final size:44
Alignment explanation
Indices: 456364--457095 Score: 418
Period size: 44 Copynumber: 16.8 Consensus size: 44
456354 AAGAAGGTAG
* *
456364 ATTTGACCAAGGTGATAACCATACATCAAATCAAAATGAAAAGA
1 ATTTGACCAAGGTGGTAACCATACGTCAAATCAAAATGAAAAGA
* * * * **
456408 ATCTGACCAAGGTGGTAACCATACGTTAGA-CAAGAAAGAGGCAG-
1 ATTTGACCAAGGTGGTAACCATACGTCAAATCAA-AATGA-AAAGA
* * * *
456452 ATTTGACC-AGAGTGGTAGCCATATGTCAAATTAGAATGAAAAGA
1 ATTTGACCAAG-GTGGTAACCATACGTCAAATCAAAATGAAAAGA
* * * * * *
456496 ATCTAACCAAGGTGGTAACCATATGTTAGA-CAGGAAA-GAGACAG-
1 ATTTGACCAAGGTGGTAACCATACGTCAAATCA--AAATGA-AAAGA
* * * * *
456540 ATTTGACCATA-GTGGTAGCCATATGCCAAATCAGAATGAAAATA
1 ATTTGACCA-AGGTGGTAACCATACGTCAAATCAAAATGAAAAGA
* * * * * *
456584 ATCTAACCAGGGTGGTAACCATACATCAGACCTAAAAT-AAGAAGA
1 ATTTGACCAAGGTGGTAACCATACGTCAAATC-AAAATGAA-AAGA
* * * * * *
456629 GTTTGATCAGGGTGGTAACCATACATTAAA-CAGAAGA-GAGGAA-A
1 ATTTGACCAAGGTGGTAACCATACGTCAAATCA-AA-ATGA-AAAGA
* * * *
456673 ATTTGACCAAGATGGCAACCATACATCAAATCATAATGAAAAGA
1 ATTTGACCAAGGTGGTAACCATACGTCAAATCAAAATGAAAAGA
* *
456717 ATCTGACCAAGGTGGTAACCATACGTC-AATCCTAAAATGAGAAGA
1 ATTTGACCAAGGTGGTAACCATACGTCAAAT-C-AAAATGAAAAGA
* *
456762 GTTTGA-CAAGGGTGGTAACCATACGTCAAA-CAAAAAAGAGAAA-A
1 ATTTGACCAA-GGTGGTAACCATACGTCAAATC-AAAATGA-AAAGA
* * *
456806 ATTTGACCAGGGTGGTAACCATACGTCAAAT-AGAA--AAGAGAA
1 ATTTGACCAAGGTGGTAACCATACGTCAAATCAAAATGAAAAG-A
* * * *
456848 ATTTGACTAGGGTGGTAACCATACGTCAAAT-AGAA--AAGAGAA
1 ATTTGACCAAGGTGGTAACCATACGTCAAATCAAAATGAAAAG-A
* * *
456890 ATTTGACCAGGGTGGTAACCATTCGTCAAATCAGAATGAAAAGA
1 ATTTGACCAAGGTGGTAACCATACGTCAAATCAAAATGAAAAGA
** * * * * * * *
456934 ATCAGACTAGGGTGGTAACCATACATCAGA-CGGAAA-GGAAA-T
1 ATTTGACCAAGGTGGTAACCATACGTCAAATC-AAAATGAAAAGA
* * *
456976 ACTTGACCAAGGTGTTAACCATACGTCAAATCATAATGAAAAGA
1 ATTTGACCAAGGTGGTAACCATACGTCAAATCAAAATGAAAAGA
* * * * * * * *
457020 ATCTGACTAGGGTGGTAACCATATGTTAGAT-AGAAAGGAAAA-T
1 ATTTGACCAAGGTGGTAACCATACGTCAAATCA-AAATGAAAAGA
* *
457063 ATTTGACCAGGGTGATAACCATACGTCAAATCA
1 ATTTGACCAAGGTGGTAACCATACGTCAAATCA
457096 TAAGGGAAAA
Statistics
Matches: 528, Mismatches: 119, Indels: 82
0.72 0.16 0.11
Matches are distributed among these distances:
40 2 0.00
41 1 0.00
42 95 0.18
43 62 0.12
44 277 0.52
45 89 0.17
46 2 0.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (44 bp):
ATTTGACCAAGGTGGTAACCATACGTCAAATCAAAATGAAAAGA
Found at i:456430 original size:88 final size:86
Alignment explanation
Indices: 456328--457095 Score: 544
Period size: 88 Copynumber: 8.8 Consensus size: 86
456318 TTGTTTGATG
* * * * *
456328 AAGGTGATAACCATATGTCAAACAGGAAGAAGGTAGATTTGACCAAGGTGATAACCATACATCAA
1 AAGGTGGTAACCATACGTCAAACA-GAA-AAGGAAGATTTGACCAAGGTGGTAACCATACGTCAA
*
456393 ATCAAAATGAAAAGAATCTGACC
64 ATCAGAATGAAAAGAATCTGACC
* * * * *
456416 AAGGTGGTAACCATACGTTAGACAAGAAAGAGGCAGATTTGACC-AGAGTGGTAGCCATATGTCA
1 AAGGTGGTAACCATACGTCAAAC-AGAAA-AGGAAGATTTGACCAAG-GTGGTAACCATACGTCA
* *
456480 AATTAGAATGAAAAGAATCTAACC
63 AATCAGAATGAAAAGAATCTGACC
* * * * * * *
456504 AAGGTGGTAACCATATGTTAGACAGGAAAGAGACAGATTTGACCATA-GTGGTAGCCATATGCCA
1 AAGGTGGTAACCATACGTCAAACAGAAAAG-GA-AGATTTGACCA-AGGTGGTAACCATACGTCA
* *
456568 AATCAGAATGAAAATAATCTAACC
63 AATCAGAATGAAAAGAATCTGACC
* * * * * * * *
456592 AGGGTGGTAACCATACATCAGACCTA-AAATAAGAAGAGTTTGATCAGGGTGGTAACCATACATT
1 AAGGTGGTAACCATACGTCA-AAC-AGAAA-AGGAAGA-TTTGACCAAGGTGGTAACCATACGTC
*
456656 AAA-CAGAA-GAGAGGAA-AATTTGACC
62 AAATCAGAATGA-A--AAGAATCTGACC
* * * * *
456681 AAGATGGCAACCATACATCAAATCATAATGAA--AAGAATCTGACCAAGGTGGTAACCATACGTC
1 AAGGTGGTAACCATACGTCAAA-CAGAA--AAGGAAG-ATTTGACCAAGGTGGTAACCATACGTC
* * * *
456744 -AATCCTAAAATGAGAAGAGTTTGA-C
62 AAAT-C-AGAATGAAAAGAATCTGACC
* * *
456769 AAGGGTGGTAACCATACGTCAAACAAAAAAGAGAAAAATTTGACCAGGGTGGTAACCATACGTCA
1 AA-GGTGGTAACCATACGTCAAACAGAAAAG-G-AAGATTTGACCAAGGTGGTAACCATACGTCA
* * *
456834 AAT-AGAA--AAGAGAAATTTGACT
63 AATCAGAATGAAAAG-AATCTGACC
* * * *
456856 AGGGTGGTAACCATACGTCAAATAGAAAAGAGAA-ATTTGACCAGGGTGGTAACCATTCGTCAAA
1 AAGGTGGTAACCATACGTCAAACAGAAAAG-GAAGATTTGACCAAGGTGGTAACCATACGTCAAA
* *
456920 TCAGAATGAAAAGAATCAGACT
65 TCAGAATGAAAAGAATCTGACC
* * * * *
456942 AGGGTGGTAACCATACATCAGAC-GGAAAGGAA-ATACTTGACCAAGGTGTTAACCATACGTCAA
1 AAGGTGGTAACCATACGTCAAACAGAAAAGGAAGAT--TTGACCAAGGTGGTAACCATACGTCAA
* *
457005 ATCATAATGAAAAGAATCTGACT
64 ATCAGAATGAAAAGAATCTGACC
* * * * * * * *
457028 AGGGTGGTAACCATATGTTAGATAG-AAAGGAAAATATTTGACCAGGGTGATAACCATACGTCAA
1 AAGGTGGTAACCATACGTCAAACAGAAAAGG--AAGATTTGACCAAGGTGGTAACCATACGTCAA
457092 ATCA
64 ATCA
457096 TAAGGGAAAA
Statistics
Matches: 557, Mismatches: 81, Indels: 85
0.77 0.11 0.12
Matches are distributed among these distances:
84 35 0.06
85 14 0.03
86 134 0.24
87 50 0.09
88 201 0.36
89 106 0.19
90 14 0.03
91 3 0.01
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.20
Consensus pattern (86 bp):
AAGGTGGTAACCATACGTCAAACAGAAAAGGAAGATTTGACCAAGGTGGTAACCATACGTCAAAT
CAGAATGAAAAGAATCTGACC
Found at i:456703 original size:133 final size:133
Alignment explanation
Indices: 456566--456840 Score: 376
Period size: 133 Copynumber: 2.1 Consensus size: 133
456556 AGCCATATGC
* *
456566 CAAATCAGAATGAAAATAATCTAACCAGGGTGGTAACCATACATCAGA-CCTAAAATAAGAAGAG
1 CAAATCAGAATGAAAAGAATCTAACCAAGGTGGTAACCATACATCA-ATCCTAAAATAAGAAGAG
* * * *
456630 TTTGATC-AGGGTGGTAACCATACATTAAACAGAAGAGAGGAAAATTTGACCAAGATGGCAACCA
65 TTTGA-CAAGGGTGGTAACCATACATCAAACAAAAAAGAGAAAAATTTGACCAAGATGGCAACCA
456694 TACAT
129 TACAT
* * * *
456699 CAAATCATAATGAAAAGAATCTGACCAAGGTGGTAACCATACGTCAATCCTAAAATGAGAAGAGT
1 CAAATCAGAATGAAAAGAATCTAACCAAGGTGGTAACCATACATCAATCCTAAAATAAGAAGAGT
* * * *
456764 TTGACAAGGGTGGTAACCATACGTCAAACAAAAAAGAGAAAAATTTGACCAGGGTGGTAACCATA
66 TTGACAAGGGTGGTAACCATACATCAAACAAAAAAGAGAAAAATTTGACCAAGATGGCAACCATA
*
456829 CGT
131 CAT
456832 CAAAT-AGAA
1 CAAATCAGAA
456841 AAGAGAAATT
Statistics
Matches: 124, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
132 5 0.04
133 119 0.96
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.19
Consensus pattern (133 bp):
CAAATCAGAATGAAAAGAATCTAACCAAGGTGGTAACCATACATCAATCCTAAAATAAGAAGAGT
TTGACAAGGGTGGTAACCATACATCAAACAAAAAAGAGAAAAATTTGACCAAGATGGCAACCATA
CAT
Found at i:456885 original size:86 final size:86
Alignment explanation
Indices: 456630--457093 Score: 374
Period size: 86 Copynumber: 5.3 Consensus size: 86
456620 ATAAGAAGAG
* * * * * * * * *
456630 TTTGATCAGGGTGGTAACCATACATTAAACAGAAGAGAGGAAAATTTGACCAAGATGGCAACCAT
1 TTTGACCAGGGTGGTAACCATACGTCAAATAGAAAAGA-G-AAATTTGACTAGGGTGGTAACCAT
* * *
456695 ACATCAAATCA-TAATGA-AAAGAA
64 ACGTCAAAT-AGAAAAGAGAAA-AA
* * * * *
456718 TCTGACCAAGGTGGTAACCATACGTCAATCCTA-AAATGAGAAGAGTTTGACAAGGGTGGTAACC
1 TTTGACCAGGGTGGTAACCATACGTCAA--ATAGAAAAGAGAA-A-TTTGACTAGGGTGGTAACC
* *
456782 ATACGTCAAACAAAAAAGAGAAAAA
62 ATACGTCAAATAGAAAAGAGAAAAA
456807 TTTGACCAGGGTGGTAACCATACGTCAAATAGAAAAGAGAAATTTGACTAGGGTGGTAACCATAC
1 TTTGACCAGGGTGGTAACCATACGTCAAATAGAAAAGAGAAATTTGACTAGGGTGGTAACCATAC
456872 GTCAAATAGAAAAGAG--AAA
66 GTCAAATAGAAAAGAGAAAAA
* * **
456891 TTTGACCAGGGTGGTAACCATTCGTCAAATCAGAATGAAAAG-AATCAGACTAGGGTGGTAACCA
1 TTTGACCAGGGTGGTAACCATACGTCAAAT-AGAA--AAGAGAAATTTGACTAGGGTGGTAACCA
* * * * *
456955 TACATCAGA-CGGAAAG-GAAATA
63 TACGTCAAATAGAAAAGAGAAAAA
* * * * * *
456977 CTTGACCAAGGTGTTAACCATACGTCAAATCATAATGAAAAG-AATCTGACTAGGGTGGTAACCA
1 TTTGACCAGGGTGGTAACCATACGTCAAAT-AGAA--AAGAGAAATTTGACTAGGGTGGTAACCA
* * *
457041 TATGTTAGATAG-AAAG-GAAAATA
63 TACGTCAAATAGAAAAGAGAAAA-A
*
457064 TTTGACCAGGGTGATAACCATACGTCAAAT
1 TTTGACCAGGGTGGTAACCATACGTCAAAT
457094 CATAAGGGAA
Statistics
Matches: 315, Mismatches: 47, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
84 33 0.10
85 9 0.03
86 137 0.43
87 38 0.12
88 34 0.11
89 60 0.19
90 4 0.01
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (86 bp):
TTTGACCAGGGTGGTAACCATACGTCAAATAGAAAAGAGAAATTTGACTAGGGTGGTAACCATAC
GTCAAATAGAAAAGAGAAAAA
Found at i:457393 original size:3 final size:3
Alignment explanation
Indices: 457380--457419 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
457370 TTTTTATGTC
457380 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
457420 TATTTATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:470550 original size:149 final size:149
Alignment explanation
Indices: 470279--470581 Score: 466
Period size: 149 Copynumber: 2.0 Consensus size: 149
470269 AGAAGATTAG
**
470279 AAAAAAAAT-ATTTAAATTTATCCCGAAAGTATTAATTCAATTTAATTTTATTTACTTTCAAAAA
1 AAAAAAAATAATAAAAATTTATCCCGAAAGTATTAATTCAATTTAATTTTATTTACTTTCAAAAA
* *
470343 TACTATTTCATACCCTAATAGAAGCCCAAAAGGATATGAAACGTTTTTGAAATCTTTTATACCCC
66 TACCATTTCATACCCTAATAGAAGCCCAAAAGGATAAGAAACGTTTTTGAAATCTTTTATACCCC
*
470408 TACGGATGCCCATAGGAAT
131 TACGAATGCCCATAGGAAT
**
470427 ATAAAAAAATAATAAAAATTTATCCCGAAAGTATTAATTCAATTT-ATTTTATTTGTTTTCAAAA
1 A-AAAAAAATAATAAAAATTTATCCCGAAAGTATTAATTCAATTTAATTTTATTTACTTTCAAAA
* * * *
470491 ATACCATTTCATACCCTAATGGAAGCCCGAAATGATAAGAAATGTTTTTGAAATCTTTTATACCC
65 ATACCATTTCATACCCTAATAGAAGCCCAAAAGGATAAGAAACGTTTTTGAAATCTTTTATACCC
* *
470556 CTATGAATGCTCATAGGAAT
130 CTACGAATGCCCATAGGAAT
470576 AAAAAA
1 AAAAAA
470582 GATTAAAAAA
Statistics
Matches: 140, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
148 6 0.04
149 102 0.73
150 32 0.23
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (149 bp):
AAAAAAAATAATAAAAATTTATCCCGAAAGTATTAATTCAATTTAATTTTATTTACTTTCAAAAA
TACCATTTCATACCCTAATAGAAGCCCAAAAGGATAAGAAACGTTTTTGAAATCTTTTATACCCC
TACGAATGCCCATAGGAAT
Found at i:472430 original size:159 final size:159
Alignment explanation
Indices: 472105--472522 Score: 423
Period size: 159 Copynumber: 2.6 Consensus size: 159
472095 ATATTATATG
* * ** * * *
472105 AATTTTAAAAATTTTAAACCAAGAAAAATCCCCTTGAAAAAATTTACGAAGTAGAAAACTCC--G
1 AATTTTAAAAATTATAAATCAAGAAAAATCCCCTCAAAAAAATTTACGGAGTAGAAAACACCATA
* * * * * * *
472168 TTTCTAAAAAAA-AAAAATTCAAAGAAAAATATAAAACTCATGAAAATGAATTAATTTTTTAAAA
66 TTTCGAAAAAAAGAGAATTTCAAGGAAAAA-AT-----TTATGAAAATGAATGAATTTTTGAAAA
* * * *
472232 ATGATTTAATATGAATCAAATGATGATATTTTATG
125 ATGATTTAATATGAATCAAATAATAATATTTGATA
* * *
472267 AATTTTAAAAATTGA-AAATCAAGAAAAATCCCTTTAAAAAAATTTACGGAGTAGGAAAACACCG
1 AATTTTAAAAATT-ATAAATCAAGAAAAATCCCCTCAAAAAAATTTACGGAGTA-GAAAACACCA
* * * * *
472331 TATTTCGAGAAAGAG-GAGTTTCAAGGAAAAAATTTATGAAAATGAATGAATTTTTGAGAAATTA
64 TATTTCGAAAAAAAGAGAATTTCAAGGAAAAAATTTATGAAAATGAATGAATTTTTGAAAAATGA
* *
472395 TTTACTATGAATTAAATAATAATATTTGATA
129 TTTAATATGAATCAAATAATAATATTTGATA
** * * * *
472426 AATTTTAAAAATTATAAATTGAGAAAAATCCCCTCAAAAACATTTATGGAGTAGAAAACTCTATA
1 AATTTTAAAAATTATAAATCAAGAAAAATCCCCTCAAAAAAATTTACGGAGTAGAAAACACCATA
472491 TTTCGAAAAAAAGAGAATTTCAAGGAAAAAAT
66 TTTCGAAAAAAAGAGAATTTCAAGGAAAAAAT
472523 CAAAAACTCA
Statistics
Matches: 212, Mismatches: 37, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
158 21 0.10
159 113 0.53
162 47 0.22
163 8 0.04
164 2 0.01
165 21 0.10
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (159 bp):
AATTTTAAAAATTATAAATCAAGAAAAATCCCCTCAAAAAAATTTACGGAGTAGAAAACACCATA
TTTCGAAAAAAAGAGAATTTCAAGGAAAAAATTTATGAAAATGAATGAATTTTTGAAAAATGATT
TAATATGAATCAAATAATAATATTTGATA
Found at i:475936 original size:20 final size:20
Alignment explanation
Indices: 475913--475987 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
475903 AAGTACCCAG
475913 ATGTATCAATACATTTTTCA
1 ATGTATCAATACATTTTTCA
* * *
475933 ATGTATCAATACATGTATGA
1 ATGTATCAATACATTTTTCA
* *
475953 ATGTATCGATACATTCTTCA
1 ATGTATCAATACATTTTTCA
*
475973 ATGTATCGATACATT
1 ATGTATCAATACATT
475988 CTATCTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCAATACATTTTTCA
Found at i:477253 original size:4 final size:4
Alignment explanation
Indices: 477246--477324 Score: 53
Period size: 4 Copynumber: 20.8 Consensus size: 4
477236 TCCACAAAAA
* * *
477246 AAAC AAAC AAAC AAAC AAAC AAAA AGAAG AAA- AAAA AAAC -AAC -AAC
1 AAAC AAAC AAAC AAAC AAAC AAAC A-AAC AAAC AAAC AAAC AAAC AAAC
* *
477292 AAAAA AAAC AAA- AAAC AAA- AAAC CAA- AAAC AAA
1 -AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
477325 GAAAAAAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
3 17 0.28
4 39 0.64
5 5 0.08
ACGTcount: A:0.81, C:0.16, G:0.03, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:477259 original size:8 final size:8
Alignment explanation
Indices: 477246--477324 Score: 53
Period size: 7 Copynumber: 10.4 Consensus size: 8
477236 TCCACAAAAA
477246 AAACAAAC
1 AAACAAAC
477254 AAACAAAC
1 AAACAAAC
*
477262 AAACAAAA
1 AAACAAAC
*
477270 AGAAGAAA-
1 A-AACAAAC
*
477278 AAAAAAAC
1 AAACAAAC
477286 -AAC-AAC
1 AAACAAAC
*
477292 AAAAAAAAC
1 -AAACAAAC
477301 AAA-AAAC
1 AAACAAAC
477308 AAA-AAAC
1 AAACAAAC
*
477315 CAA-AAAC
1 AAACAAAC
477322 AAA
1 AAA
477325 GAAAAAAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
6 3 0.05
7 26 0.44
8 22 0.37
9 8 0.14
ACGTcount: A:0.81, C:0.16, G:0.03, T:0.00
Consensus pattern (8 bp):
AAACAAAC
Found at i:477326 original size:54 final size:55
Alignment explanation
Indices: 477240--477362 Score: 148
Period size: 54 Copynumber: 2.2 Consensus size: 55
477230 GCGTCCTCCA
* *
477240 CAAAAAA-AACAAACAAACAAACAAACAAAAAGAAGAAAAAA-AAAACAACAACAA
1 CAAAAAACAAAAAACAAACAAACAAACAAAAAGAA-AAAAAATAAAAAAACAACAA
477294 -AAAAAACAAAAAACAAA-AAACCAAA-AACAAAGAAAAAAAATAAAAAAACAACAA
1 CAAAAAACAAAAAACAAACAAA-CAAACAA-AAAGAAAAAAAATAAAAAAACAACAA
477348 CAACAACAACAAAAA
1 CAA-AA-AACAAAAA
477363 GGGTCCGGAT
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
53 17 0.28
54 31 0.52
55 2 0.03
56 2 0.03
57 8 0.13
ACGTcount: A:0.80, C:0.16, G:0.02, T:0.01
Consensus pattern (55 bp):
CAAAAAACAAAAAACAAACAAACAAACAAAAAGAAAAAAAATAAAAAAACAACAA
Found at i:477330 original size:60 final size:60
Alignment explanation
Indices: 477239--477353 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
477229 GGCGTCCTCC
* *
477239 ACAAAAAAAACAAACAAACAAACAAACAAAAAGAAGAAAAAAAAAACAACAACAAAAAAA
1 ACAAAAAAAAAAAACAAACAAACAAACAAAAAAAAGAAAAAAAAAACAACAACAAAAAAA
* * * *
477299 ACAAAAAACAAAAAACCAA-AAACAAAGAAAAAAAATAAAAAAACAACAACAACAA
1 ACAAAAAA-AAAAAACAAACAAACAAACAAAAAAAAGAAAAAAAAAACAACAACAA
477354 CAACAAAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 40 0.83
61 8 0.17
ACGTcount: A:0.81, C:0.16, G:0.03, T:0.01
Consensus pattern (60 bp):
ACAAAAAAAAAAAACAAACAAACAAACAAAAAAAAGAAAAAAAAAACAACAACAAAAAAA
Found at i:477344 original size:51 final size:49
Alignment explanation
Indices: 477239--477362 Score: 144
Period size: 51 Copynumber: 2.5 Consensus size: 49
477229 GGCGTCCTCC
* *
477239 ACAAAAAAAACAAACAAACAAACAAACAAAAAGAAGAAAAAAAAAACAACA
1 ACAAAAAAAACAAA-AAACAAA-AAACAAAAAAAAGAAAAAAAAAACAAAA
477290 ACAAAAAAAACAAAAAACAAAAAACCAAAAACAAAGAAAAAAAATAA-AAAA
1 ACAAAAAAAACAAAAAACAAAAAA-CAAAAA-AAAGAAAAAAAA-AACAAAA
* * *
477341 ACAACAACAAC-AACAACAAAAA
1 ACAAAAAAAACAAAAAACAAAAA
477363 GGGTCCGGAT
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
49 3 0.05
50 23 0.35
51 37 0.57
52 2 0.03
ACGTcount: A:0.81, C:0.16, G:0.02, T:0.01
Consensus pattern (49 bp):
ACAAAAAAAACAAAAAACAAAAAACAAAAAAAAGAAAAAAAAAACAAAA
Found at i:477347 original size:57 final size:58
Alignment explanation
Indices: 477243--477362 Score: 165
Period size: 57 Copynumber: 2.1 Consensus size: 58
477233 TCCTCCACAA
*
477243 AAAAAACAAACAAACAAACAAACAAAAAGAAGAAAAAAAAAACAACAACAAAAAAAAC
1 AAAAAACAAACAAACAAACAAACAAAAAGAAAAAAAAAAAAACAACAACAAAAAAAAC
* * *
477301 AAAAAACAAA-AAACCAA-AAACAAAGAA-AAAAAATAAAAAAACAACAACAACAACAAC
1 AAAAAACAAACAAACAAACAAACAAA-AAGAAAAAA-AAAAAAACAACAACAAAAAAAAC
477358 AAAAA
1 AAAAA
477363 GGGTCCGGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
56 12 0.21
57 34 0.61
58 10 0.18
ACGTcount: A:0.81, C:0.16, G:0.03, T:0.01
Consensus pattern (58 bp):
AAAAAACAAACAAACAAACAAACAAAAAGAAAAAAAAAAAAACAACAACAAAAAAAAC
Found at i:478835 original size:28 final size:28
Alignment explanation
Indices: 478762--479037 Score: 318
Period size: 28 Copynumber: 9.6 Consensus size: 28
478752 CCTCACCCTA
*
478762 TCAAAAGCCCACAAGTCAGTGGCACCCTTT
1 TCAAAAGCCCACAAGTCAGTGGCAACC--T
* *
478792 TCCAAAGCCCATAAGTCAGTGGCAACCT
1 TCAAAAGCCCACAAGTCAGTGGCAACCT
* * *
478820 TCAAAAGCCCACAAGTTACTGGCACCCTTT
1 TCAAAAGCCCACAAGTCAGTGGCAACC--T
* *
478850 TCCAAAGCCCACAAGTTAGTGGCAACCT
1 TCAAAAGCCCACAAGTCAGTGGCAACCT
* *
478878 TCAAAAGCCCACAAGTTAGTGGCACCCTTT
1 TCAAAAGCCCACAAGTCAGTGGCAACC--T
*
478908 TCCAAAGCCCACAAGTCAGTGGCAACCT
1 TCAAAAGCCCACAAGTCAGTGGCAACCT
* *
478936 TCCAAAGCCTACAAGTCAGTGGCAACCT
1 TCAAAAGCCCACAAGTCAGTGGCAACCT
* *
478964 TCAAAAGCCCACACGTCAGTGGCACCCTTT
1 TCAAAAGCCCACAAGTCAGTGGCAACC--T
* * *
478994 TCCAAAGCCCATAAGTTAGTGGCAACCT
1 TCAAAAGCCCACAAGTCAGTGGCAACCT
479022 TCAAAAGCCCACAAGT
1 TCAAAAGCCCACAAGT
479038 TAATAGTATC
Statistics
Matches: 212, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
28 115 0.54
30 97 0.46
ACGTcount: A:0.32, C:0.33, G:0.17, T:0.19
Consensus pattern (28 bp):
TCAAAAGCCCACAAGTCAGTGGCAACCT
Done.