Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 15 of 64
Found at i:1961453 original size:18 final size:18
Alignment explanation
Indices: 1961430--1961473 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1961420 CAAGTATAGA
1961430 GCTTTAGAGATTAGAGCG
1 GCTTTAGAGATTAGAGCG
*
1961448 GCTTTAGAGCTTAGAGCG
1 GCTTTAGAGATTAGAGCG
*
1961466 ACTTTAGA
1 GCTTTAGA
1961474 ATGCGCTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (18 bp):
GCTTTAGAGATTAGAGCG
Found at i:1966518 original size:66 final size:65
Alignment explanation
Indices: 1966420--1966564 Score: 165
Period size: 66 Copynumber: 2.2 Consensus size: 65
1966410 GTCATAAATC
* *
1966420 TTTTCG-AAAATT-TGACTTTAGAAAATTCATTTTCAAAAAGGTTTATAATCTTCT-GAAAATTC
1 TTTTCGAAAAATTATGACTTTAGAAAATTCATTTTCAAAAAGGTTTATAA-CTTCTCAAAAATCC
1966482 A
65 A
* * * *
1966483 TTTTCGAAAAATTATGACTTTTTA-AAAATTTATTTTCAGAACGGTTTATAACTTTTCAAAAATC
1 TTTTCGAAAAATTATGAC--TTTAGAAAATTCATTTTCAAAAAGGTTTATAACTTCTCAAAAATC
1966547 CA
64 CA
1966549 TTTTC-AAAAACTTATG
1 TTTTCGAAAAA-TTATG
1966565 TGAAAGAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
63 6 0.09
64 6 0.09
65 13 0.19
66 41 0.59
67 4 0.06
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (65 bp):
TTTTCGAAAAATTATGACTTTAGAAAATTCATTTTCAAAAAGGTTTATAACTTCTCAAAAATCCA
Found at i:1966914 original size:21 final size:21
Alignment explanation
Indices: 1966888--1966927 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1966878 AACCACCTAC
1966888 CAAGCAAATCTAAAACCACAA
1 CAAGCAAATCTAAAACCACAA
*
1966909 CAAGCAAATCTAAAGCCAC
1 CAAGCAAATCTAAAACCAC
1966928 CTACCCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.30, G:0.07, T:0.10
Consensus pattern (21 bp):
CAAGCAAATCTAAAACCACAA
Found at i:1968176 original size:168 final size:169
Alignment explanation
Indices: 1967897--1968245 Score: 655
Period size: 168 Copynumber: 2.1 Consensus size: 169
1967887 GATCAAAGAA
1967897 AATAAAAAAAATTCGGACTCATAATTAAAAATTCATTTAAATTTTTATTTTTTATTGTAATCAAT
1 AATAAAAAAAATTCGGACTCATAATTAAAAATTCATTTAAATTTTTATTTTTTATTGTAATCAAT
1967962 CAATTAATTTTTTTAATATTTATTTAAATTTAATTAAATTTTTATTTGGATAAAAAAATTAACAT
66 CAATTAATTTTTTTAATATTTATTTAAATTTAATTAAATTTTTATTTGGATAAAAAAATTAACAT
*
1968027 CATTAATTTTTTAATTAAAATTAAATTTCATGTGACATT
131 CAATAATTTTTTAATTAAAATTAAATTTCATGTGACATT
*
1968066 -ATAAAAAAAATTCTGACTCATAATTAAAAATTCATTTAAATTTTTATTTTTTATTGTAATCAAT
1 AATAAAAAAAATTCGGACTCATAATTAAAAATTCATTTAAATTTTTATTTTTTATTGTAATCAAT
*
1968130 CAATTAATTTTTTTAATATTTATTTACATTTAATTAAATTTTTATTTGGATAAAAAAATTAACAT
66 CAATTAATTTTTTTAATATTTATTTAAATTTAATTAAATTTTTATTTGGATAAAAAAATTAACAT
1968195 CAATAATTTTTTAATTAAAATTAAATTTCATGTGACATT
131 CAATAATTTTTTAATTAAAATTAAATTTCATGTGACATT
*
1968234 AATAAAATAAAT
1 AATAAAAAAAAT
1968246 AAAAATTTAT
Statistics
Matches: 175, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
168 165 0.94
169 10 0.06
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.47
Consensus pattern (169 bp):
AATAAAAAAAATTCGGACTCATAATTAAAAATTCATTTAAATTTTTATTTTTTATTGTAATCAAT
CAATTAATTTTTTTAATATTTATTTAAATTTAATTAAATTTTTATTTGGATAAAAAAATTAACAT
CAATAATTTTTTAATTAAAATTAAATTTCATGTGACATT
Found at i:1972003 original size:2 final size:2
Alignment explanation
Indices: 1971996--1972036 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1971986 TTTTATTTCT
1971996 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1972037 TGTAGTTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1973211 original size:30 final size:30
Alignment explanation
Indices: 1973136--1973212 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 30
1973126 TTTATTTTGC
*
1973136 ACTAAATAAACTTTTAAATTTTAATTTATA
1 ACTAAATAAACTCTTAAATTTTAATTTATA
* * ** ** **
1973166 TCCATGTAAGTTCTTATCTTTTAATTTATA
1 ACTAAATAAACTCTTAAATTTTAATTTATA
1973196 ACTAAATAAACTCTTAA
1 ACTAAATAAACTCTTAA
1973213 TATAAATCAA
Statistics
Matches: 31, Mismatches: 16, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (30 bp):
ACTAAATAAACTCTTAAATTTTAATTTATA
Found at i:1984982 original size:5 final size:5
Alignment explanation
Indices: 1984974--1985038 Score: 53
Period size: 5 Copynumber: 13.0 Consensus size: 5
1984964 TTTATTTTAG
** * * *
1984974 TATTT TATTT TATTT GCTTT TATTT TAATTT TAATT TA-TT AATTT TCTCTT
1 TATTT TATTT TATTT TATTT TATTT T-ATTT TATTT TATTT TATTT TAT-TT
1985025 TATTT T-TTT TATTT
1 TATTT TATTT TATTT
1985039 ACTTACATAC
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
4 7 0.15
5 31 0.66
6 9 0.19
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:1986399 original size:2 final size:2
Alignment explanation
Indices: 1986355--1986387 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1986345 TTGTAATCTA
1986355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1986388 ACAACATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1993990 original size:167 final size:165
Alignment explanation
Indices: 1993666--1993993 Score: 362
Period size: 167 Copynumber: 2.0 Consensus size: 165
1993656 AGAGAGGTCA
*
1993666 TAACACTCCCAATTTCACATTAAAAGAATGTGTAGATATGGTATGATATATATGAAGAGATCTAA
1 TAACACTCCCAATCTCACATTAAAAGAATGTGTAGATATGGTATGATATATATGAAGAGATCTAA
* * *
1993731 ATCAAAATCTATGGGATACTTTTTGTGGGATAAAACTGTGAGACCTTTAAGTCAAAGTAGATAAT
66 ACCAAAATCTATGGGATACTTTTTGTGGGATAAAACTATGAGACCTTCAAGTCAAAGTAGATAAT
* * *
1993796 ACCTAGTAGGTTAGGTGTGGGTCTCCACAAAATTG
131 ACCTAGCAGGTTAGGTATGGATCTCCACAAAATTG
* ** * * *
1993831 TAACACTCTCAATCTCACATTGGAAGAATGTGTGGATATGGT-TGATATATATATATAGAGATTT
1 TAACACTCCCAATCTCACATTAAAAGAATGTGTAGATATGGTATGATATATAT-GA-AGAGATCT
* * ** *
1993895 AAACCCAAAA-CTTATGAGG-T-GTCTTTTGTGGGATAAAACTAT-ATGATCTTCGGGTTAAAGT
64 AAA-CCAAAATC-TATG-GGATACT-TTTTGTGGGATAAAACTATGA-GACCTTCAAGTCAAAGT
* *
1993956 TGATAATACCTTA-CAGGTTGGGTATGGATCTCCACAAA
124 AGATAATACC-TAGCAGGTTAGGTATGGATCTCCACAAA
1993994 TAATATCGGA
Statistics
Matches: 135, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
164 10 0.07
165 38 0.28
166 13 0.10
167 70 0.52
168 4 0.03
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (165 bp):
TAACACTCCCAATCTCACATTAAAAGAATGTGTAGATATGGTATGATATATATGAAGAGATCTAA
ACCAAAATCTATGGGATACTTTTTGTGGGATAAAACTATGAGACCTTCAAGTCAAAGTAGATAAT
ACCTAGCAGGTTAGGTATGGATCTCCACAAAATTG
Found at i:1995400 original size:21 final size:21
Alignment explanation
Indices: 1995375--1995432 Score: 98
Period size: 21 Copynumber: 2.7 Consensus size: 21
1995365 AAGGAATGTT
1995375 AAGAAGATGAAGGCTAAAGTG
1 AAGAAGATGAAGGCTAAAGTG
1995396 AAGAAGATGAAGGCTAAAGTG
1 AAGAAGATGAAGGCTAAAGTG
*
1995417 AAGAAGGTGGAAGGCT
1 AAGAAGAT-GAAGGCT
1995433 TGAAGGCCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 28 0.80
22 7 0.20
ACGTcount: A:0.45, C:0.05, G:0.36, T:0.14
Consensus pattern (21 bp):
AAGAAGATGAAGGCTAAAGTG
Found at i:1999280 original size:24 final size:24
Alignment explanation
Indices: 1999238--1999297 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
1999228 AGAGTTTGAG
* *
1999238 AGAGAGAGAGGAGGGGTAGTGTGGT
1 AGAGAGAGA-GAGGGGTAGAGGGGT
1999263 AGAGAGAGAGAGGGGTAGAGGGGT
1 AGAGAGAGAGAGGGGTAGAGGGGT
1999287 AGAGAGAGAGA
1 AGAGAGAGAGA
1999298 AAGAAGAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
24 24 0.73
25 9 0.27
ACGTcount: A:0.35, C:0.00, G:0.55, T:0.10
Consensus pattern (24 bp):
AGAGAGAGAGAGGGGTAGAGGGGT
Found at i:1999595 original size:21 final size:20
Alignment explanation
Indices: 1999557--1999606 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1999547 GATTTTTAGA
*
1999557 ATTATT-TTTTAATATTATT
1 ATTATTATTTTAAAATTATT
*
1999576 TTTATTATTTTAAAATTTATT
1 ATTATTATTTTAAAA-TTATT
*
1999597 ATTAGTATTT
1 ATTATTATTT
1999607 ATGCATGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 5 0.20
20 7 0.28
21 13 0.52
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
ATTATTATTTTAAAATTATT
Found at i:1999856 original size:3 final size:3
Alignment explanation
Indices: 1999848--1999892 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1999838 ACCAAAAATG
1999848 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1999893 GTAAAAAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2001703 original size:17 final size:17
Alignment explanation
Indices: 2001661--2001703 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2001651 TGCATGTCAT
**
2001661 TCATTCATAAATCATCA
1 TCATTCATTCATCATCA
2001678 TCATTCATTCATCAT-A
1 TCATTCATTCATCATCA
2001694 TCATTGCATT
1 TCATT-CATT
2001704 ATATAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.33, C:0.23, G:0.02, T:0.42
Consensus pattern (17 bp):
TCATTCATTCATCATCA
Found at i:2005284 original size:15 final size:16
Alignment explanation
Indices: 2005258--2005290 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2005248 AAAAGTTGTG
2005258 AAAACAAGAAGAAAAA
1 AAAACAAGAAGAAAAA
2005274 AAAACAA-AAGAAAAA
1 AAAACAAGAAGAAAAA
2005289 AA
1 AA
2005291 TGTTGATGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAACAAGAAGAAAAA
Found at i:2005740 original size:14 final size:15
Alignment explanation
Indices: 2005707--2005745 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
2005697 AAAAAAAGAT
2005707 AAAAAAGAGGGAAGG
1 AAAAAAGAGGGAAGG
2005722 AAAAAAGAGGGAAGG
1 AAAAAAGAGGGAAGG
2005737 AAAAAAGAG
1 AAAAAAGAG
2005746 ATGATTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (15 bp):
AAAAAAGAGGGAAGG
Found at i:2007390 original size:42 final size:41
Alignment explanation
Indices: 2007331--2007427 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 41
2007321 AGTATTCAAT
2007331 GGTGATATCCAAGTATTAAAGTATGGAATTGCATTTTCTCGG
1 GGTGATATCCAAGTATTAAAGTAT-GAATTGCATTTTCTCGG
* * *
2007373 GGTGATATTCAAGTATTAAAGTATGAATTTCATTTTCTTGG
1 GGTGATATCCAAGTATTAAAGTATGAATTGCATTTTCTCGG
*
2007414 TGATGATATCCAAG
1 -GGTGATATCCAAG
2007428 ACATTTTCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
41 15 0.31
42 34 0.69
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (41 bp):
GGTGATATCCAAGTATTAAAGTATGAATTGCATTTTCTCGG
Found at i:2007710 original size:81 final size:80
Alignment explanation
Indices: 2007537--2007710 Score: 185
Period size: 81 Copynumber: 2.1 Consensus size: 80
2007527 CTTGGGTGGC
* * * *
2007537 AGTATCTAAAGTCATTTGCATTTTCTCGATGGTGATATCTGAATGTTAAAAATTATTTGCATTTT
1 AGTAT-TAAAGTCATTTGCATATTCTCGACGGTGATATCTCAATGTTAAAAATTAATTGCATTTT
* *
2007602 TTTAGTGATGATATCA
65 GTCAGTGATGATATCA
* *
2007618 AGTATTAAAAGTCATTTGCATATTCTTGGCGGTGATATC-CAAGTGTT-AAAATTGAAATTGCAT
1 AGTATT-AAAGTCATTTGCATATTCTCGACGGTGATATCTCAA-TGTTAAAAATT--AATTGCAT
2007681 TTTGTCAGT-AGTGATATCCA
62 TTTGTCAGTGA-TGATAT-CA
2007701 AGT-TTAAAGT
1 AGTATTAAAGT
2007711 TTGAATTTCC
Statistics
Matches: 79, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
80 9 0.11
81 43 0.54
82 22 0.28
83 5 0.06
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (80 bp):
AGTATTAAAGTCATTTGCATATTCTCGACGGTGATATCTCAATGTTAAAAATTAATTGCATTTTG
TCAGTGATGATATCA
Found at i:2007846 original size:137 final size:137
Alignment explanation
Indices: 2007691--2008037 Score: 468
Period size: 137 Copynumber: 2.5 Consensus size: 137
2007681 TTTGTCAGTA
* * *
2007691 GTGATATCCAAGTTTAAAGTTTGAATTTCCATTCTTTCTCTACATTTACAATTTTTTGGTGGTGA
1 GTGATATCCGAGTTTAAAGTTTGAATTTGCATTCTTTCTCTACATTTACAATTTTTTGATGGTGA
* *
2007756 TATCCGAA-TATTAAAGTATGAATTTCATTTTCTTGGTGGTGATATCTAATG-CATTTTCAAAAT
66 TATCC-AAGTATTAAAATATGAATTTCATTTTCTTGGTGGTGATATCCAA-GACATTTTCAAAAT
*
2007819 CCCTCGATG
129 CACTCGATG
** ** * *
2007828 GTGATATTTGAGTTTAAAGTTTGAATTTGCATTCTTTCTCTACATTTGTATTTTTTTTATGGTGA
1 GTGATATCCGAGTTTAAAGTTTGAATTTGCATTCTTTCTCTACATTTACAATTTTTTGATGGTGA
*
2007893 TATCCAAGTATTAAAATATGAATTTCATTTTCTTGTTGGTGATATCCAAGACATTTTCAAAATCA
66 TATCCAAGTATTAAAATATGAATTTCATTTTCTTGGTGGTGATATCCAAGACATTTTCAAAATCA
* *
2007958 TTTGATG
131 CTCGATG
* * *
2007965 GTGATATCCGAGTTTAAA-TTTGAATTTGCATTCTTTCTTTACATTTGC-ATTTTCCTGATGGTG
1 GTGATATCCGAGTTTAAAGTTTGAATTTGCATTCTTTCTCTACATTTACAATTTT-TTGATGGTG
*
2008028 ATATTCAAGT
65 ATATCCAAGT
2008038 TTCCTTTGGT
Statistics
Matches: 184, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
135 4 0.02
136 47 0.26
137 133 0.72
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.46
Consensus pattern (137 bp):
GTGATATCCGAGTTTAAAGTTTGAATTTGCATTCTTTCTCTACATTTACAATTTTTTGATGGTGA
TATCCAAGTATTAAAATATGAATTTCATTTTCTTGGTGGTGATATCCAAGACATTTTCAAAATCA
CTCGATG
Found at i:2008146 original size:40 final size:42
Alignment explanation
Indices: 2008058--2008157 Score: 109
Period size: 40 Copynumber: 2.5 Consensus size: 42
2008048 GGCAATATCC
* * * *
2008058 AAAGTCATTTGCATTTTCT-TGATGGTGATATCTAAGTGTTG
1 AAAGTCATTTGCATTTTCTCAGATGATGATATCTAAGTATTA
*
2008099 AAA-TCATTTGCATTTTCTCAG-TGATGATATC-GAGTATTA
1 AAAGTCATTTGCATTTTCTCAGATGATGATATCTAAGTATTA
* *
2008138 AAAGTCATTTACATCTTCTC
1 AAAGTCATTTGCATTTTCTC
2008158 GGGGGTGATA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
39 8 0.16
40 38 0.76
41 4 0.08
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (42 bp):
AAAGTCATTTGCATTTTCTCAGATGATGATATCTAAGTATTA
Found at i:2008344 original size:513 final size:515
Alignment explanation
Indices: 2007359--2008408 Score: 1555
Period size: 513 Copynumber: 2.0 Consensus size: 515
2007349 AAGTATGGAA
* * *
2007359 TTGCATTTTCTCG-GGGTGATATTCAAGTATTAAAGTATGAATTTCATTTTCTTGGTGATGATAT
1 TTGCATTTTCTCGATGGTGATATCCAAGTATTAAAATATGAATTTCATTTTCTTGGTGATGATAT
2007423 CCAAGACATTTTCAAAATCTCTTGATGGTGATATCCGAGTTTAAAGTTTAAATTTGCATTCTTTC
66 CCAAGACATTTTCAAAATCTCTTGATGGTGATATCCGAGTTTAAAGTTTAAATTTGCATTCTTTC
* * * *
2007488 TCTACGTTTGAATTTTCTCAGTGGTGATATTCGAGTTTCCTTGGGTGGCAGTATCTAAAGTCATT
131 TCTACATTTGAATTTTCTCAGTGGTGATATTCAAGTTTCCTTGGGTGGCAATATCCAAAGTCATT
* * *
2007553 TGCATTTTCTCGATGGTGATATCTGAATGTTAAAAATTATTTGCATTTTTTTAGTGATGATATCA
196 TGCATTTTCTCGATGGTGATATCTGAATGTTAAAAATCATTTGCATTTTCTCAGTGATGATATCA
* * * *
2007618 AGTATTAAAAGTCATTTGCATATTCTTGGCGGTGATATCCAAGTGTTAAAATTGAAATTGCATTT
261 AGTATTAAAAGTCATTTACATATTCTCGGCGGTGATATCCAAGTGTTAAAATAGAAATTACATTT
*
2007683 TGTCAGTAGTGATATCCAAGTTTAAAGTTTGAATTTCCATTCTTTCTCTACATTTACAATTTTTT
326 TGTCAGTAGTGATATCCAAGTTTAAAGTTTGAATTTCCATTCTTTCTCTACATTGACAATTTTTT
* * *
2007748 GGTGGTGATATCCGAATATTAAAGTATGAATTTCATTTTCTTGGTGGTGATATCTAATGCATTTT
391 GGTGGTGATATACGAATATTAAAGTATGAAATTCATTTTCTTGGTGGTGATATCCAATGCATTTT
* * * *
2007813 CAAAATCCCTCGATGGTGATAT-TTGAGTTTAAAGTTTGAATTTGCATTCTTTCTCTACAT
456 CAAAATCACTCAATGGTGATATCCT-AGTTTAAAGTTTGAATTTGCATTCTTTATCTACAT
* * ** * *
2007873 TTGTATTTTTTTTATGGTGATATCCAAGTATTAAAATATGAATTTCATTTTCTTGTTGGTGATAT
1 TTGCATTTTCTCGATGGTGATATCCAAGTATTAAAATATGAATTTCATTTTCTTGGTGATGATAT
*
2007938 CCAAGACATTTTCAAAATCAT-TTGATGGTGATATCCGAGTTTAAA-TTTGAATTTGCATTCTTT
66 CCAAGACATTTTCAAAATC-TCTTGATGGTGATATCCGAGTTTAAAGTTTAAATTTGCATTCTTT
* * * *
2008001 CTTTACATTTGCATTTTC-CTGATGGTGATATTCAAGTTTCCTTTGGTGGCAATATCCAAAGTCA
130 CTCTACATTTGAATTTTCTCAG-TGGTGATATTCAAGTTTCCTTGGGTGGCAATATCCAAAGTCA
* *
2008065 TTTGCATTTTCTTGATGGTGATATCT-AAGTGTT-GAAATCATTTGCATTTTCTCAGTGATGATA
194 TTTGCATTTTCTCGATGGTGATATCTGAA-TGTTAAAAATCATTTGCATTTTCTCAGTGATGATA
* * *
2008128 TCGAGTATTAAAAGTCATTTACATCTTCTCGGGGGTGATATCCAAGTGTTAAAACTAG-AATTAC
258 TCAAGTATTAAAAGTCATTTACATATTCTCGGCGGTGATATCCAAGTGTTAAAA-TAGAAATTAC
* * * *
2008192 ATTTTCT-TGATAGTGATATCCAAGTTTAAAGTTTGAATTTGCATTCTTTCTCTACATTGGC-AT
322 ATTTTGTCAG-TAGTGATATCCAAGTTTAAAGTTTGAATTTCCATTCTTTCTCTACATTGACAAT
* *
2008255 TTTCTTGGTGGTGATATATGAGTATTAAAGTATGAAATTCATTTTCTTGGTGGTGATATCCAA-G
386 TTT-TTGGTGGTGATATACGAATATTAAAGTATGAAATTCATTTTCTTGGTGGTGATATCCAATG
2008319 ACATTTTCAAAATCACTCAATGGTGATATCCTAGTTTAAAGTTTGAATTTGCATTCTTTATCTAC
450 -CATTTTCAAAATCACTCAATGGTGATATCCTAGTTTAAAGTTTGAATTTGCATTCTTTATCTAC
2008384 AT
514 AT
2008386 TTGCATTTTCTCGATGGTGATAT
1 TTGCATTTTCTCGATGGTGATAT
2008409 TCGAGTTTCC
Statistics
Matches: 479, Mismatches: 48, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
512 7 0.01
513 271 0.57
514 111 0.23
515 89 0.19
516 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (515 bp):
TTGCATTTTCTCGATGGTGATATCCAAGTATTAAAATATGAATTTCATTTTCTTGGTGATGATAT
CCAAGACATTTTCAAAATCTCTTGATGGTGATATCCGAGTTTAAAGTTTAAATTTGCATTCTTTC
TCTACATTTGAATTTTCTCAGTGGTGATATTCAAGTTTCCTTGGGTGGCAATATCCAAAGTCATT
TGCATTTTCTCGATGGTGATATCTGAATGTTAAAAATCATTTGCATTTTCTCAGTGATGATATCA
AGTATTAAAAGTCATTTACATATTCTCGGCGGTGATATCCAAGTGTTAAAATAGAAATTACATTT
TGTCAGTAGTGATATCCAAGTTTAAAGTTTGAATTTCCATTCTTTCTCTACATTGACAATTTTTT
GGTGGTGATATACGAATATTAAAGTATGAAATTCATTTTCTTGGTGGTGATATCCAATGCATTTT
CAAAATCACTCAATGGTGATATCCTAGTTTAAAGTTTGAATTTGCATTCTTTATCTACAT
Found at i:2008538 original size:21 final size:21
Alignment explanation
Indices: 2008477--2008538 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 21
2008467 TTCATAATTC
2008477 AAAGATTTTCATTCAAAAGTT
1 AAAGATTTTCATTCAAAAGTT
** ** *
2008498 TTAGAGATTCATACTGAAAAGTT
1 AAAGATTTTCAT--TCAAAAGTT
2008521 AAAGATTTTCATTCAAAA
1 AAAGATTTTCATTCAAAA
2008539 AATTTAAGGA
Statistics
Matches: 29, Mismatches: 10, Indels: 4
0.67 0.23 0.09
Matches are distributed among these distances:
21 13 0.45
23 16 0.55
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (21 bp):
AAAGATTTTCATTCAAAAGTT
Found at i:2008551 original size:44 final size:45
Alignment explanation
Indices: 2008474--2008630 Score: 133
Period size: 45 Copynumber: 3.5 Consensus size: 45
2008464 ACTTTCATAA
* * *
2008474 TTCAAAGATTTTCATTCAAAAGTTTTAGAGATTCATACTGAAAAG
1 TTCAAAGATTTTCATTCAAAAATTTAAGAGATTCATACTCAAAAG
* *
2008519 TT-AAAGATTTTCATTCAAAAAATTTAAG-GATTCATATTCAAAAT
1 TTCAAAGATTTTCATTC-AAAAATTTAAGAGATTCATACTCAAAAG
* * * * *
2008563 TTCAAAGATTCAT-ATTAAAAATATTTTAGAGATTCACA-TCCAAAG
1 TTCAAAGATT-TTCATTCAAAA-ATTTAAGAGATTCATACTCAAAAG
* **
2008608 TTTCAAAGGTTTTTTTTCAAAAA
1 -TTCAAAGATTTTCATTCAAAAA
2008631 ATTTTTGGCT
Statistics
Matches: 90, Mismatches: 15, Indels: 14
0.76 0.13 0.12
Matches are distributed among these distances:
44 33 0.37
45 34 0.38
46 23 0.26
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.38
Consensus pattern (45 bp):
TTCAAAGATTTTCATTCAAAAATTTAAGAGATTCATACTCAAAAG
Found at i:2008561 original size:21 final size:22
Alignment explanation
Indices: 2008536--2008584 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
2008526 TTTTCATTCA
*
2008536 AAAAATTT-AAGGATTCATATT
1 AAAAATTTCAAAGATTCATATT
*
2008557 CAAAATTTCAAAGATTCATATT
1 AAAAATTTCAAAGATTCATATT
2008579 AAAAAT
1 AAAAAT
2008585 ATTTTAGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.35
Consensus pattern (22 bp):
AAAAATTTCAAAGATTCATATT
Found at i:2008595 original size:24 final size:23
Alignment explanation
Indices: 2008491--2008598 Score: 71
Period size: 22 Copynumber: 4.8 Consensus size: 23
2008481 ATTTTCATTC
* * * *
2008491 AAAAGTTTTAGAGATTCATACTG
1 AAAAATTTAAGAGATTCATATTA
* * ** *
2008514 AAAAGTTAAAGATTTTCAT-TCA
1 AAAAATTTAAGAGATTCATATTA
2008536 AAAAATTTAAG-GATTCATATT-
1 AAAAATTTAAGAGATTCATATTA
*
2008557 CAAAATTTCAA-AGATTCATATTA
1 AAAAATTT-AAGAGATTCATATTA
*
2008580 AAAATATTTTAGAGATTCA
1 AAAA-ATTTAAGAGATTCA
2008599 CATCCAAAGT
Statistics
Matches: 64, Mismatches: 15, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
21 12 0.19
22 22 0.34
23 19 0.30
24 11 0.17
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.36
Consensus pattern (23 bp):
AAAAATTTAAGAGATTCATATTA
Found at i:2008635 original size:46 final size:45
Alignment explanation
Indices: 2008531--2008654 Score: 124
Period size: 46 Copynumber: 2.7 Consensus size: 45
2008521 AAAGATTTTC
* * *
2008531 ATTCAAAAAATTTAAGGATTCATATTCAAAATTTCAAAGATTCAT
1 ATTCAAAAAATTTTAGGATTCACATCCAAAATTTCAAAGATTCAT
* * **
2008576 ATT-AAAAATATTTTAGAGATTCACATCCAAAGTTTCAAAGGTTTTT
1 ATTCAAAAA-ATTTTAG-GATTCACATCCAAAATTTCAAAGATTCAT
* * * *
2008622 TTTCAAAAAATTTTTGGCTTTACATCCAAAATT
1 ATTCAAAAAATTTTAGGATTCACATCCAAAATT
2008655 GTAAAAATTC
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
44 5 0.08
45 23 0.36
46 31 0.48
47 5 0.08
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (45 bp):
ATTCAAAAAATTTTAGGATTCACATCCAAAATTTCAAAGATTCAT
Found at i:2009803 original size:16 final size:16
Alignment explanation
Indices: 2009770--2009803 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2009760 TCTTTTTCCC
**
2009770 TTTTTTTTTTGCTTTT
1 TTTTTTTTTTGCACTT
2009786 TTTTTTTTTTGCACTT
1 TTTTTTTTTTGCACTT
2009802 TT
1 TT
2009804 CATCATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTTTTTTTGCACTT
Found at i:2012983 original size:24 final size:22
Alignment explanation
Indices: 2012938--2012986 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
2012928 ATTAGTATGC
*
2012938 ACATAATATATACAAAAAAACA
1 ACATAATACATACAAAAAAACA
* *
2012960 ACATAATACATA-TAAAGAACA
1 ACATAATACATACAAAAAAACA
2012981 ACATAA
1 ACATAA
2012987 ATGGTTCGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.65, C:0.14, G:0.02, T:0.18
Consensus pattern (22 bp):
ACATAATACATACAAAAAAACA
Found at i:2014581 original size:25 final size:24
Alignment explanation
Indices: 2014527--2014583 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
2014517 CCAAAAAATT
*
2014527 AAAAATCAAACATAAAAAACAAAA
1 AAAAATCAAACAGAAAAAACAAAA
2014551 AGAAAATCAAAGCAGAAAATAAACAAAA
1 A-AAAATCAAA-CAG-AAA-AAACAAAA
2014579 AAAAA
1 AAAAA
2014584 AGAAAAAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 1 0.04
25 9 0.32
26 2 0.07
27 7 0.25
28 9 0.32
ACGTcount: A:0.77, C:0.11, G:0.05, T:0.07
Consensus pattern (24 bp):
AAAAATCAAACAGAAAAAACAAAA
Found at i:2015717 original size:20 final size:21
Alignment explanation
Indices: 2015692--2015733 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2015682 AAAGAAAATT
2015692 AAAATC-AAAACTAAATTAAA
1 AAAATCTAAAACTAAATTAAA
* *
2015712 AAAATCTAAATCTAATTTAAA
1 AAAATCTAAAACTAAATTAAA
2015733 A
1 A
2015734 TTAATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATCTAAAACTAAATTAAA
Found at i:2015737 original size:6 final size:6
Alignment explanation
Indices: 2015728--2015788 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
2015718 TAAATCTAAT
* * * * *
2015728 TTAAAA TTAATA TTAAAA TCAAAA TCAAGA TTAAAA -TAAAA ATAAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
* *
2015775 TTACAG TTAAAA TT
1 TTAAAA TTAAAA TT
2015789 TTGAGCTTTA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
5 5 0.12
6 38 0.88
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (6 bp):
TTAAAA
Found at i:2019676 original size:12 final size:12
Alignment explanation
Indices: 2019659--2019689 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2019649 AAGAAAACAT
2019659 AAGAAAAACCAA
1 AAGAAAAACCAA
2019671 AAGAAAAACCAA
1 AAGAAAAACCAA
2019683 AAGAAAA
1 AAGAAAA
2019690 GAAAGAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.77, C:0.13, G:0.10, T:0.00
Consensus pattern (12 bp):
AAGAAAAACCAA
Found at i:2020977 original size:20 final size:19
Alignment explanation
Indices: 2020935--2020977 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2020925 TAATTTACAT
**
2020935 TTTTTTTAGCCATTTTGGG
1 TTTTTTTAGCCATTTTGCC
2020954 TTTTTTTAGCCATTTTTGCC
1 TTTTTTTAGCCA-TTTTGCC
2020974 TTTT
1 TTTT
2020978 GTATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (19 bp):
TTTTTTTAGCCATTTTGCC
Found at i:2024233 original size:15 final size:15
Alignment explanation
Indices: 2024189--2024266 Score: 61
Period size: 15 Copynumber: 5.0 Consensus size: 15
2024179 CAAAAAATCA
*
2024189 AATAATAAAATAAAT
1 AATAATATAATAAAT
*
2024204 -AT-ATATGATATAAT
1 AATAATATAATA-AAT
2024218 AATAATATAATAAAT
1 AATAATATAATAAAT
2024233 AAATAAATGATAAATAAAT
1 -AAT-AAT-AT-AATAAAT
* *
2024252 AAAAAAATAATAAAT
1 AATAATATAATAAAT
2024267 GGTAATAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
13 6 0.12
14 5 0.10
15 12 0.24
16 12 0.24
17 5 0.10
18 4 0.08
19 7 0.14
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (15 bp):
AATAATATAATAAAT
Found at i:2024235 original size:4 final size:4
Alignment explanation
Indices: 2024183--2024266 Score: 52
Period size: 4 Copynumber: 21.0 Consensus size: 4
2024173 ATTAAGCAAA
* *
2024183 AAAT CAAAT -AAT AAAAT AAAT ATAT ATGAT ATAAT -AAT -AAT ATAAT
1 AAAT -AAAT AAAT -AAAT AAAT AAAT A-AAT A-AAT AAAT AAAT A-AAT
* *
2024229 AAAT AAAT AAAT -GAT AAAT AAAT AAAA AAAT -AAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
2024267 GGTAATAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
3 14 0.22
4 34 0.52
5 17 0.26
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:2024238 original size:11 final size:11
Alignment explanation
Indices: 2024183--2024266 Score: 59
Period size: 11 Copynumber: 7.4 Consensus size: 11
2024173 ATTAAGCAAA
2024183 AAATCAAATAAT
1 AAAT-AAATAAT
2024195 AAAATAAATATAT
1 -AAATAAATA-AT
*
2024208 ATGATATAATAAT
1 A-AATA-AATAAT
2024221 -AATATAATAAAT
1 AAATA-AAT-AAT
*
2024233 AAATAAATGAT
1 AAATAAATAAT
2024244 AAATAAAT-A-
1 AAATAAATAAT
2024253 AAA-AAATAAT
1 AAATAAATAAT
2024263 AAAT
1 AAAT
2024267 GGTAATAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
8 4 0.07
9 4 0.07
10 4 0.07
11 17 0.28
12 12 0.20
13 15 0.25
14 4 0.07
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:2024245 original size:26 final size:27
Alignment explanation
Indices: 2024189--2024274 Score: 79
Period size: 26 Copynumber: 3.2 Consensus size: 27
2024179 CAAAAAATCA
* * *
2024189 AATAATAAAATAAATATATATGATATAAT
1 AATAATATAATAAATATA-AT-AAATGAT
2024218 AATAATATAATAAATA-AATAAATGAT
1 AATAATATAATAAATATAATAAATGAT
* *
2024244 AAATAA-ATAA-AAAAATAATAAATGGT
1 -AATAATATAATAAATATAATAAATGAT
2024270 AATAA
1 AATAA
2024275 AAAGGAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
25 9 0.18
26 18 0.36
27 7 0.14
28 1 0.02
29 15 0.30
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (27 bp):
AATAATATAATAAATATAATAAATGAT
Found at i:2024248 original size:19 final size:19
Alignment explanation
Indices: 2024218--2024266 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
2024208 ATGATATAAT
*
2024218 AATAATATAATAAATAAATA
1 AATAATA-AATAAATAAAAA
*
2024238 AATGATAAATAAATAAAAA
1 AATAATAAATAAATAAAAA
2024257 AATAATAAAT
1 AATAATAAAT
2024267 GGTAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AATAATAAATAAATAAAAA
Found at i:2024284 original size:26 final size:27
Alignment explanation
Indices: 2024183--2024275 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 27
2024173 ATTAAGCAAA
*
2024183 AAATCAAATAATAAAATAAATATATATGAT
1 AAAT-AAATAAAAAAATAAATA-A-ATGAT
*
2024213 ATAATAATAATATAATAAATAAATAAATGAT
1 A-AAT-A-AATA-AAAAAATAAATAAATGAT
*
2024244 AAATAAATAAAAAAAT-AATAAATGGT
1 AAATAAATAAAAAAATAAATAAATGAT
2024270 -AATAAA
1 AAATAAA
2024276 AAGGAAAAAG
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
25 6 0.11
26 9 0.16
27 6 0.11
28 4 0.07
29 1 0.02
30 4 0.07
31 10 0.18
32 5 0.09
33 10 0.18
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (27 bp):
AAATAAATAAAAAAATAAATAAATGAT
Found at i:2026375 original size:21 final size:20
Alignment explanation
Indices: 2026331--2026380 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2026321 TTATTAATAG
2026331 TTAAATAAAATAATAAAAGA
1 TTAAATAAAATAATAAAAGA
*
2026351 TTAAATAATAATAATAATA-A
1 TTAAATAA-AATAATAAAAGA
*
2026371 TTTAATAAAA
1 TTAAATAAAA
2026381 AGAAAGTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 16 0.59
21 9 0.33
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
TTAAATAAAATAATAAAAGA
Found at i:2026552 original size:27 final size:25
Alignment explanation
Indices: 2026480--2026563 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 25
2026470 AGAGAGGTAT
* * * *
2026480 TAAAACCTTAAAGTGAAACTCTAAA
1 TAAAACTTTAAACTCAAACCCTAAA
**
2026505 TAAAACTTTAAGGTCAGAACCCTAAA
1 TAAAACTTTAAACTCA-AACCCTAAA
2026531 TAAAACTTTTAAAACTCAAACCCTAAA
1 TAAAAC-TTT-AAACTCAAACCCTAAA
2026558 TGAAAA
1 T-AAAA
2026564 TCCAAGCCTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
25 13 0.27
26 14 0.29
27 13 0.27
28 9 0.18
ACGTcount: A:0.51, C:0.18, G:0.07, T:0.24
Consensus pattern (25 bp):
TAAAACTTTAAACTCAAACCCTAAA
Found at i:2027149 original size:24 final size:24
Alignment explanation
Indices: 2027117--2027162 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2027107 TCATCAATGA
2027117 TTATCA-TTTACAAAGAATGTTATT
1 TTATCATTTTA-AAAGAATGTTATT
* *
2027141 TTATTATTTTAAAGGAATGTTA
1 TTATCATTTTAAAAGAATGTTA
2027163 CGATAATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (24 bp):
TTATCATTTTAAAAGAATGTTATT
Found at i:2031639 original size:10 final size:10
Alignment explanation
Indices: 2031620--2031652 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2031610 AAAGAAATAG
2031620 AAAAAA-AGA
1 AAAAAAGAGA
2031629 AAAAAAGAGA
1 AAAAAAGAGA
*
2031639 AAAAAAGGGA
1 AAAAAAGAGA
2031649 AAAA
1 AAAA
2031653 TTTTTGTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAAGAGA
Found at i:2032379 original size:19 final size:20
Alignment explanation
Indices: 2032355--2032392 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2032345 GGGCCATATC
2032355 AAAAGA-AAAAAAAAAGAAG
1 AAAAGAGAAAAAAAAAGAAG
2032374 AAAAGAGAAAAAAAAAGAA
1 AAAAGAGAAAAAAAAAGAA
2032393 AAGGAAACAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAGAGAAAAAAAAAGAAG
Found at i:2032386 original size:17 final size:16
Alignment explanation
Indices: 2032355--2032399 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
2032345 GGGCCATATC
2032355 AAAAGAAAA--AAAAA
1 AAAAGAAAAGGAAAAA
*
2032369 AGAAGAAAAGAGAAAAA
1 AAAAGAAAAG-GAAAAA
2032386 AAAAGAAAAGGAAA
1 AAAAGAAAAGGAAA
2032400 CAGAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 8 0.31
16 4 0.15
17 14 0.54
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAGGAAAAA
Found at i:2032388 original size:22 final size:22
Alignment explanation
Indices: 2032358--2032409 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
2032348 CCATATCAAA
* *
2032358 AGAAAAAAAAA-AGAAGAAAAG
1 AGAAAAAAAAAGAAAAGAAAAC
*
2032379 AGAAAAAAAAAGAAAAGGAAAC
1 AGAAAAAAAAAGAAAAGAAAAC
2032401 AGAAAAAAA
1 AGAAAAAAA
2032410 TGGTTATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (22 bp):
AGAAAAAAAAAGAAAAGAAAAC
Found at i:2032924 original size:23 final size:24
Alignment explanation
Indices: 2032893--2032966 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 24
2032883 AATGAAAAGG
*
2032893 AAAAGTGAAA-AAAAAAAAAGAAA
1 AAAAATGAAAGAAAAAAAAAGAAA
*
2032916 AAAAATGAAAGAAAAACAAAGGAAA
1 AAAAATGAAAGAAAAA-AAAAGAAA
*
2032941 AGAAGGAA-GAAAGAAAAGAAAAGAAA
1 A-AA--AATGAAAGAAAAAAAAAGAAA
2032967 GGAGTGATTG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
23 9 0.21
24 5 0.12
25 8 0.19
26 9 0.21
27 9 0.21
28 2 0.05
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (24 bp):
AAAAATGAAAGAAAAAAAAAGAAA
Found at i:2032944 original size:16 final size:14
Alignment explanation
Indices: 2032899--2032967 Score: 61
Period size: 14 Copynumber: 4.7 Consensus size: 14
2032889 AAGGAAAAGT
2032899 GAAAAAAAA-AAAA
1 GAAAAAAAAGAAAA
2032912 GAAAAAAAATG-AAA
1 GAAAAAAAA-GAAAA
2032926 GAAAAACAAAGGAAAA
1 GAAAAA-AAA-GAAAA
*
2032942 GAAGGAAGAAAGAAAA
1 GAA--AAAAAAGAAAA
*
2032958 GAAAAGAAAG
1 GAAAAAAAAG
2032968 GAGTGATTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
13 9 0.19
14 16 0.33
15 4 0.08
16 14 0.29
17 3 0.06
18 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.01
Consensus pattern (14 bp):
GAAAAAAAAGAAAA
Found at i:2034061 original size:22 final size:22
Alignment explanation
Indices: 2033991--2034065 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 22
2033981 GTTGGCAAGC
* * *
2033991 AAGCC-AGATTAGCTGGCATAT
1 AAGCCTAGTTTAGCTGGTACAT
* *
2034012 AAGCCCAATTTAGCTGGTACAT
1 AAGCCTAGTTTAGCTGGTACAT
2034034 AAGCCTAGTTTAGCTGGTACAT
1 AAGCCTAGTTTAGCTGGTACAT
2034056 AAGCCTAGTT
1 AAGCCTAGTT
2034066 AGTTGGCATG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 5 0.11
22 42 0.89
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (22 bp):
AAGCCTAGTTTAGCTGGTACAT
Found at i:2034584 original size:26 final size:28
Alignment explanation
Indices: 2034530--2034585 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
2034520 GCCCCGATGA
*
2034530 AAATTTAAGCCCAATTTAGTTGGCATCC
1 AAATTTAAGCCCAATTTAGCTGGCATCC
*
2034558 AAATTTAAG-TCAATTT-GCTGGCATCC
1 AAATTTAAGCCCAATTTAGCTGGCATCC
2034584 AA
1 AA
2034586 TAAAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 11 0.42
27 6 0.23
28 9 0.35
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (28 bp):
AAATTTAAGCCCAATTTAGCTGGCATCC
Found at i:2034706 original size:64 final size:63
Alignment explanation
Indices: 2034529--2034708 Score: 174
Period size: 63 Copynumber: 2.9 Consensus size: 63
2034519 AGCCCCGATG
*
2034529 AAAATTTAAGCCCAATTTAGTTGGCATCC----AAATTTAAGTCAATTT-GCTGGCATCCAATA
1 AAAATTTAAGCCCAATTTAGTTGGCA-CCAATGAAATTTAAGTCAATTTAGTTGGCATCCAATA
* * * * * * * * *
2034588 AAAATTTAAGCCTAGTTTAGCTAGCACCAATGAAATATAGGCCCAATCTAGTTGGCAT-TAATA
1 AAAATTTAAGCCCAATTTAGTTGGCACCAATGAAATTTAAG-TCAATTTAGTTGGCATCCAATA
* *
2034651 AAAATATAAGCCCAATTTAGTTGGCACCTAATGAAATTTAAGTCTAGTTTAGTTGGCA
1 AAAATTTAAGCCCAATTTAGTTGGCACC-AATGAAATTTAAGTC-AATTTAGTTGGCA
2034709 CCTAAATTCA
Statistics
Matches: 93, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
58 2 0.02
59 22 0.24
62 7 0.08
63 33 0.35
64 29 0.31
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (63 bp):
AAAATTTAAGCCCAATTTAGTTGGCACCAATGAAATTTAAGTCAATTTAGTTGGCATCCAATA
Found at i:2034993 original size:32 final size:33
Alignment explanation
Indices: 2034955--2035038 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 33
2034945 CACTATTAAA
*
2034955 AAGATTTAAACTCAGTTTAACTGGCACCTAAT-
1 AAGATTTAAACTCAGTTTAACTGACACCTAATG
* * *
2034987 AAGATTTAAGC-CTAGTTTAATTGACATCTAATG
1 AAGATTTAAACTC-AGTTTAACTGACACCTAATG
* *
2035020 AAGTTTTAAACTCAATTTA
1 AAGATTTAAACTCAGTTTA
2035039 GCTAGCATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
31 1 0.02
32 26 0.62
33 14 0.33
34 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (33 bp):
AAGATTTAAACTCAGTTTAACTGACACCTAATG
Found at i:2035161 original size:22 final size:22
Alignment explanation
Indices: 2035118--2035167 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2035108 GTAAATGCGG
*
2035118 AATTAGCTGGCATCAAAGCCCA
1 AATTAGCTGGCATCAAAACCCA
2035140 AATTAGCTGGCA-CATAAACCCA
1 AATTAGCTGGCATCA-AAACCCA
*
2035162 TATTAG
1 AATTAG
2035168 TGGTCATTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (22 bp):
AATTAGCTGGCATCAAAACCCA
Found at i:2035354 original size:19 final size:19
Alignment explanation
Indices: 2035280--2035344 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
2035270 GTAGTAAGGG
*
2035280 AAAAA-AAAAACCCAAAAA
1 AAAAAGAAAAAACCAAAAA
* *
2035298 CAAAAGGCAAAAA-C-AAAA
1 -AAAAAGAAAAAACCAAAAA
*
2035316 AAAAATAAAAAACCAAAAA
1 AAAAAGAAAAAACCAAAAA
2035335 AAAAAGAAAA
1 AAAAAGAAAA
2035345 GAAGAAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
17 9 0.25
18 5 0.14
19 18 0.50
20 4 0.11
ACGTcount: A:0.82, C:0.12, G:0.05, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAAAACCAAAAA
Found at i:2035768 original size:7 final size:7
Alignment explanation
Indices: 2035704--2035790 Score: 53
Period size: 7 Copynumber: 12.6 Consensus size: 7
2035694 CAAAAAATCG
2035704 AATAATA
1 AATAATA
2035711 AA-AATA
1 AATAATA
2035717 AATAAATA
1 AAT-AATA
2035725 AATAA-A
1 AATAATA
*
2035731 ATATATTTA
1 A-ATA-ATA
2035740 TAAT-ATA
1 -AATAATA
2035747 ATATAA-A
1 A-ATAATA
2035754 AATAATA
1 AATAATA
*
2035761 AATGATA
1 AATAATA
2035768 AATAAGT-
1 AATAA-TA
2035775 AAT-A-A
1 AATAATA
2035780 AATAATA
1 AATAATA
2035787 AATA
1 AATA
2035791 GTAATAAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 26
0.68 0.04 0.28
Matches are distributed among these distances:
5 3 0.05
6 15 0.24
7 32 0.51
8 9 0.14
9 3 0.05
10 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (7 bp):
AATAATA
Found at i:2035796 original size:47 final size:48
Alignment explanation
Indices: 2035704--2035800 Score: 112
Period size: 50 Copynumber: 2.0 Consensus size: 48
2035694 CAAAAAATCG
2035704 AATAATAAAAATAAATAAATAAATAAAATATATTTATAATATAATATAAA
1 AATAATAAAAATAAATAAATAAATAAAATATA-TTATAATATAATA-AAA
* *
2035754 AATAATAAATGATAAATAAGT-AATAAAATA-A-TA-AATAGTAATAAAA
1 AATAATAAA-AATAAATAAATAAATAAAATATATTATAATA-TAATAAAA
2035800 A
1 A
2035801 GGAAAAAGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
46 8 0.19
47 7 0.16
49 1 0.02
50 18 0.42
51 9 0.21
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (48 bp):
AATAATAAAAATAAATAAATAAATAAAATATATTATAATATAATAAAA
Found at i:2035799 original size:18 final size:16
Alignment explanation
Indices: 2035718--2035799 Score: 69
Period size: 16 Copynumber: 4.9 Consensus size: 16
2035708 ATAAAAATAA
2035718 ATAAATA-AATAAAAT
1 ATAAATATAATAAAAT
** *
2035733 ATATTTATAATATAAT
1 ATAAATATAATAAAAT
*
2035749 ATAAAAATAAT-AAAT
1 ATAAATATAATAAAAT
2035764 GATAAATAAGTAATAAAAT
1 -ATAAAT-A-TAATAAAAT
2035783 AATAAATAGTAATAAAA
1 -ATAAATA-TAATAAAA
2035800 AGGAAAAAGG
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
15 8 0.15
16 20 0.38
17 1 0.02
18 14 0.26
19 10 0.19
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (16 bp):
ATAAATATAATAAAAT
Found at i:2036197 original size:6 final size:6
Alignment explanation
Indices: 2036181--2036225 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
2036171 AGAAACAGAG
* * * *
2036181 AAAGGA GAAGGA AAAGGA AAAGGA AAAGAA AAAGAA AAAGTA AAA
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAA
2036226 ACGCAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (6 bp):
AAAGGA
Found at i:2038419 original size:14 final size:14
Alignment explanation
Indices: 2038400--2038451 Score: 86
Period size: 14 Copynumber: 3.7 Consensus size: 14
2038390 TAAACTTATT
*
2038400 AAAACCCTAAGGCC
1 AAAACCCTAAGGTC
2038414 AAAACCCTAAGGTC
1 AAAACCCTAAGGTC
*
2038428 AAAACCCTAAGGTT
1 AAAACCCTAAGGTC
2038442 AAAACCCTAA
1 AAAACCCTAA
2038452 ATAAGACCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.46, C:0.29, G:0.12, T:0.13
Consensus pattern (14 bp):
AAAACCCTAAGGTC
Found at i:2038681 original size:9 final size:8
Alignment explanation
Indices: 2038659--2038698 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
2038649 TTTGCTTTGT
2038659 TAAAATAA
1 TAAAATAA
2038667 T-AAAT-A
1 TAAAATAA
2038673 T-AAATAA
1 TAAAATAA
2038680 TAAAATAA
1 TAAAATAA
2038688 TAAAAATAA
1 T-AAAATAA
2038697 TA
1 TA
2038699 GAATTGAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 6 0.21
7 6 0.21
8 9 0.31
9 8 0.28
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
TAAAATAA
Found at i:2039061 original size:24 final size:24
Alignment explanation
Indices: 2039029--2039074 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2039019 TAATTAATCA
2039029 TTATCA-TTTACAAAGAATGTTATT
1 TTATCATTTTA-AAAGAATGTTATT
*
2039053 TTATTATTTTAAAAGAATGTTA
1 TTATCATTTTAAAAGAATGTTA
2039075 AGATAAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (24 bp):
TTATCATTTTAAAAGAATGTTATT
Found at i:2041014 original size:3 final size:3
Alignment explanation
Indices: 2041006--2041113 Score: 94
Period size: 3 Copynumber: 36.7 Consensus size: 3
2040996 TAAAAAATAC
* *
2041006 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAC AAT AAT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * * * *
2041053 AAT AAT -AT TAT AAC AAT AAC AAC AAT AAC AAC AAC AAC AAC AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2041100 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
2041114 ACAAAGAAGA
Statistics
Matches: 92, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
2 4 0.04
3 88 0.96
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:2041050 original size:35 final size:35
Alignment explanation
Indices: 2041004--2041089 Score: 118
Period size: 35 Copynumber: 2.5 Consensus size: 35
2040994 ACTAAAAAAT
* * *
2041004 ACAATAATAATAATAATAATATAATAATAATAATA
1 ACAATAATAATAACAATAATATAATAACAATAACA
*
2041039 ACAATAATAATAACAATAATATTATAACAATAACA
1 ACAATAATAATAACAATAATATAATAACAATAACA
* *
2041074 ACAATAACAACAACAA
1 ACAATAATAATAACAA
2041090 CAACAACAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.24
Consensus pattern (35 bp):
ACAATAATAATAACAATAATATAATAACAATAACA
Found at i:2041990 original size:30 final size:30
Alignment explanation
Indices: 2041955--2042011 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
2041945 ATTCACATAT
* *
2041955 AAAAATTCAAACATTTGCAAATAAATTAAA
1 AAAAATTCAAACATTTACAAAGAAATTAAA
*
2041985 AAAAATTCAAAGATTTACAAAGAAATT
1 AAAAATTCAAACATTTACAAAGAAATT
2042012 TAAAGATTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.60, C:0.09, G:0.05, T:0.26
Consensus pattern (30 bp):
AAAAATTCAAACATTTACAAAGAAATTAAA
Found at i:2042010 original size:20 final size:20
Alignment explanation
Indices: 2041987--2042045 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
2041977 AAATTAAAAA
* *
2041987 AAATTCAAAGATTTACAAAG
1 AAATTTAAAGATTCACAAAG
*
2042007 AAATTTAAAGATTCACAAAT
1 AAATTTAAAGATTCACAAAG
*
2042027 AATTTTAAAGATTCACAAA
1 AAATTTAAAGATTCACAAA
2042046 AGAGTCCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.29
Consensus pattern (20 bp):
AAATTTAAAGATTCACAAAG
Found at i:2042116 original size:42 final size:43
Alignment explanation
Indices: 2042069--2042152 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 43
2042059 GGGCAACATA
* * *
2042069 AGTTCAAATATTTACAAAATAATT-CTAAGATTTACAAAAAAT
1 AGTTCAAAGATTTACAAAAGAATTCCAAAGATTTACAAAAAAT
* * *
2042111 AGTTCAAAGGTTTACAAAAGAGTTCCAAAGATTTGCAAAAAA
1 AGTTCAAAGATTTACAAAAGAATTCCAAAGATTTACAAAAAA
2042153 GGTTTAACAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
42 20 0.57
43 15 0.43
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (43 bp):
AGTTCAAAGATTTACAAAAGAATTCCAAAGATTTACAAAAAAT
Found at i:2042124 original size:22 final size:22
Alignment explanation
Indices: 2042066--2042129 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
2042056 GCTGGGCAAC
*
2042066 ATAAGTTCAAATATTTAC--AAA
1 ATAA-TTCAAAGATTTACAAAAA
*
2042087 ATAATTCTAAGATTTACAAAAA
1 ATAATTCAAAGATTTACAAAAA
* *
2042109 ATAGTTCAAAGGTTTACAAAA
1 ATAATTCAAAGATTTACAAAA
2042130 GAGTTCCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 11 0.31
21 4 0.11
22 21 0.58
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.31
Consensus pattern (22 bp):
ATAATTCAAAGATTTACAAAAA
Found at i:2042134 original size:20 final size:20
Alignment explanation
Indices: 2042069--2042150 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 20
2042059 GGGCAACATA
*
2042069 AGTTCAAATATTTACAAAAT
1 AGTTCAAAGATTTACAAAAT
* *
2042089 AATTCTAAGATTTACAAAAAAT
1 AGTTCAAAGATTTAC--AAAAT
* *
2042111 AGTTCAAAGGTTTACAAAAG
1 AGTTCAAAGATTTACAAAAT
*
2042131 AGTTCCAAAGATTTGCAAAA
1 AGTT-CAAAGATTTACAAAA
2042151 AAGGTTTAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 20 0.40
21 13 0.26
22 17 0.34
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (20 bp):
AGTTCAAAGATTTACAAAAT
Found at i:2042139 original size:21 final size:20
Alignment explanation
Indices: 2041990--2042150 Score: 76
Period size: 20 Copynumber: 7.8 Consensus size: 20
2041980 TTAAAAAAAA
*
2041990 TTCAAAGATTTAC-AAAGAAA
1 TTCAAAGATTTACAAAAG-AG
* * *
2042010 TTTAAAGATTCACAAATA-AT
1 TTCAAAGATTTACAAA-AGAG
* *
2042030 TTTAAAGATTCACAAAAGAG
1 TTCAAAGATTTACAAAAGAG
* * ***
2042050 TCCAAAGCTGGGCAACATA-AG
1 TTCAAAGATTTACAA-A-AGAG
* * *
2042071 TTCAAATATTTACAAAATAA
1 TTCAAAGATTTACAAAAGAG
* *
2042091 TTCTAAGATTTACAAAAAATAG
1 TTCAAAGATTTAC--AAAAGAG
*
2042113 TTCAAAGGTTTACAAAAGAG
1 TTCAAAGATTTACAAAAGAG
*
2042133 TTCCAAAGATTTGCAAAA
1 TT-CAAAGATTTACAAAA
2042151 AAGGTTTAAC
Statistics
Matches: 107, Mismatches: 25, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.02
20 59 0.55
21 27 0.25
22 19 0.18
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (20 bp):
TTCAAAGATTTACAAAAGAG
Found at i:2042258 original size:20 final size:20
Alignment explanation
Indices: 2041983--2042258 Score: 72
Period size: 20 Copynumber: 13.9 Consensus size: 20
2041973 AAATAAATTA
* * *
2041983 AAAAAAATTCAAAGATTTAC
1 AAAAAAGTTTAAAGATTCAC
2042003 AAAGAAA-TTTAAAGATTCAC
1 AAA-AAAGTTTAAAGATTCAC
* *
2042023 AAATAATTTTAAAGATTCAC
1 AAAAAAGTTTAAAGATTCAC
* ** * ***
2042043 AAAAGAGTCCAAAGCTGGGC
1 AAAAAAGTTTAAAGATTCAC
* * * *
2042063 AACATAAGTTCAAATATTTAC
1 AA-AAAAGTTTAAAGATTCAC
*
2042084 AAAATAA-TTCT-AAGATTTAC
1 AAAA-AAGTT-TAAAGATTCAC
* * *
2042104 AAAAAATAGTTCAAAGGTTTAC
1 -AAAAA-AGTTTAAAGATTCAC
* * **
2042126 AAAAGAGTTCCAAAGATTTGC
1 AAAAAAGTT-TAAAGATTCAC
*
2042147 AAAAAAGGTTTAACA-ATTCTC
1 AAAAAA-GTTTAA-AGATTCAC
* * **
2042168 --AAAACTTCAAAGATTTGC
1 AAAAAAGTTTAAAGATTCAC
2042186 --AAAAGTTTAAAGATTC-C
1 AAAAAAGTTTAAAGATTCAC
* *
2042203 -TAGAAGTTTAAAGATTCAC
1 AAAAAAGTTTAAAGATTCAC
* **
2042222 AAAAGA-TTCCAAG-TTCAC
1 AAAAAAGTTTAAAGATTCAC
*
2042240 AAAAAAGTTTGAAGATTCA
1 AAAAAAGTTTAAAGATTCA
2042259 TGAGAGGTTT
Statistics
Matches: 190, Mismatches: 48, Indels: 36
0.69 0.18 0.13
Matches are distributed among these distances:
17 2 0.01
18 46 0.24
19 17 0.09
20 65 0.34
21 46 0.24
22 14 0.07
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (20 bp):
AAAAAAGTTTAAAGATTCAC
Found at i:2043612 original size:15 final size:15
Alignment explanation
Indices: 2043575--2043614 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2043565 TTTTTTCCAC
2043575 CTTTTTTTTTCTCTT
1 CTTTTTTTTTCTCTT
*
2043590 -TTCCTTTTTTCTCTT
1 CTT-TTTTTTTCTCTT
2043605 CTTTTTTTTT
1 CTTTTTTTTT
2043615 TTTCATTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 2 0.10
15 17 0.81
16 2 0.10
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
CTTTTTTTTTCTCTT
Found at i:2043615 original size:18 final size:17
Alignment explanation
Indices: 2043576--2043618 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2043566 TTTTTCCACC
2043576 TTTTTTTT-TCTCTTTT
1 TTTTTTTTCTCTCTTTT
**
2043592 CCTTTTTTCTCTTCTTTT
1 TTTTTTTTCTC-TCTTTT
2043610 TTTTTTTTC
1 TTTTTTTTC
2043619 ATTTCTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 6 0.29
17 2 0.10
18 13 0.62
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTTTCTCTCTTTT
Found at i:2043938 original size:18 final size:18
Alignment explanation
Indices: 2043915--2043955 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2043905 TTTGCCTTTT
2043915 TTTTTTTCAC-TTTTTCA
1 TTTTTTTCACATTTTTCA
2043932 CTTTTTTTCACATTTTTCA
1 -TTTTTTTCACATTTTTCA
2043951 TTTTT
1 TTTTT
2043956 CTTTATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTTCACATTTTTCA
Found at i:2043938 original size:19 final size:19
Alignment explanation
Indices: 2043914--2043955 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
2043904 TTTTGCCTTT
2043914 TTTTTTTTCAC-TTTTTCA
1 TTTTTTTTCACATTTTTCA
*
2043932 CTTTTTTTCACATTTTTCA
1 TTTTTTTTCACATTTTTCA
2043951 TTTTT
1 TTTTT
2043956 CTTTATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTTTTCACATTTTTCA
Found at i:2043964 original size:9 final size:9
Alignment explanation
Indices: 2043952--2043976 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2043942 CATTTTTCAT
2043952 TTTTCTTTA
1 TTTTCTTTA
2043961 TTTTCTTTA
1 TTTTCTTTA
2043970 TTTTCTT
1 TTTTCTT
2043977 CCAACATTTT
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:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTCTTTA
Found at i:2050259 original size:7 final size:7
Alignment explanation
Indices: 2050244--2050280 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
2050234 GTTACACCCC
2050244 TTTGACT
1 TTTGACT
*
2050251 TTGGACT
1 TTTGACT
*
2050258 TTTGATT
1 TTTGACT
2050265 TTTGACT
1 TTTGACT
2050272 TTTGACT
1 TTTGACT
2050279 TT
1 TT
2050281 CAATTTTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.14, C:0.11, G:0.16, T:0.59
Consensus pattern (7 bp):
TTTGACT
Found at i:2050286 original size:21 final size:21
Alignment explanation
Indices: 2050244--2050287 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2050234 GTTACACCCC
**
2050244 TTTGACTTTGGACTTTTGATT
1 TTTGACTTTGGACTTTCAATT
*
2050265 TTTGACTTTTGACTTTCAATT
1 TTTGACTTTGGACTTTCAATT
2050286 TT
1 TT
2050288 AACTTTGACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59
Consensus pattern (21 bp):
TTTGACTTTGGACTTTCAATT
Found at i:2057371 original size:141 final size:141
Alignment explanation
Indices: 2057117--2057397 Score: 519
Period size: 141 Copynumber: 2.0 Consensus size: 141
2057107 CCAGAAAGGG
*
2057117 AATCAAGAACACTAAGATCGAAACTCTAAGAATAATGCCTAAATTGTTTCTCTTTCAAATTGCCC
1 AATCAAGAACACTAAGAACGAAACTCTAAGAATAATGCCTAAATTGTTTCTCTTTCAAATTGCCC
*
2057182 CATTTTCCTTGGGGTAAAAATCCTAGAAAACCTAAACACGCACAAACTCTAAAACCTACATCTCA
66 CATTTTCCTTGGGGTAAAAATCCTAGAAAACCTAAACACGCACAAACTCTAAAACCAACATCTCA
2057247 ACCCCGAAGAA
131 ACCCCGAAGAA
2057258 AATCAAGAACACTAAGAACGAAACTCTAAGAATAATGCCTAAATTGTTTCTCTTTCAAATTGCCC
1 AATCAAGAACACTAAGAACGAAACTCTAAGAATAATGCCTAAATTGTTTCTCTTTCAAATTG-CC
*
2057323 CCA-TTTCCTTGGTGTAAAAATCCTAGAAAACCTAAACACGCACAAACTCTAAAACCAACATCTC
65 CCATTTTCCTTGGGGTAAAAATCCTAGAAAACCTAAACACGCACAAACTCTAAAACCAACATCTC
2057387 AACCCCGAAGA
130 AACCCCGAAGA
2057398 TTGTTTTAAA
Statistics
Matches: 136, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
141 131 0.96
142 5 0.04
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.23
Consensus pattern (141 bp):
AATCAAGAACACTAAGAACGAAACTCTAAGAATAATGCCTAAATTGTTTCTCTTTCAAATTGCCC
CATTTTCCTTGGGGTAAAAATCCTAGAAAACCTAAACACGCACAAACTCTAAAACCAACATCTCA
ACCCCGAAGAA
Found at i:2058501 original size:15 final size:16
Alignment explanation
Indices: 2058474--2058506 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2058464 TAAAAGTAAA
*
2058474 AAGTTACCTAAAATAG
1 AAGTTACCTAAAAAAG
2058490 AAGTTA-CTAAAAAAG
1 AAGTTACCTAAAAAAG
2058505 AA
1 AA
2058507 AGTTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (16 bp):
AAGTTACCTAAAAAAG
Found at i:2058509 original size:16 final size:17
Alignment explanation
Indices: 2058473--2058510 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
2058463 ATAAAAGTAA
*
2058473 AAAGTTACCTAAAATAG
1 AAAGTTACCTAAAAAAG
2058490 -AAGTTA-CTAAAAAAG
1 AAAGTTACCTAAAAAAG
2058505 AAAGTT
1 AAAGTT
2058511 TTTAAACCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.55, C:0.08, G:0.13, T:0.24
Consensus pattern (17 bp):
AAAGTTACCTAAAAAAG
Found at i:2059264 original size:15 final size:16
Alignment explanation
Indices: 2059238--2059281 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
2059228 GTATTTTTTT
* *
2059238 TTTTTTGAAAAATCTA
1 TTTTTTCAAAAATCCA
2059254 TTTTTTCAAAAATCCA
1 TTTTTTCAAAAATCCA
*
2059270 TTTTTTTAAAAA
1 TTTTTTCAAAAA
2059282 ATATTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (16 bp):
TTTTTTCAAAAATCCA
Found at i:2059308 original size:11 final size:10
Alignment explanation
Indices: 2059275--2059304 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
2059265 ATCCATTTTT
2059275 TTAAAAAATA
1 TTAAAAAATA
2059285 TTAAATAAATA
1 TTAAA-AAATA
2059296 TTAAAAAAT
1 TTAAAAAAT
2059305 TATTTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TTAAAAAATA
Found at i:2059330 original size:26 final size:25
Alignment explanation
Indices: 2059301--2059350 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
2059291 AAATATTAAA
2059301 AAATTATTTATTATTAAAATATATTG
1 AAATTATTTATTATTAAAAT-TATTG
* *
2059327 AAATTATTTGTTATTCAAATTATT
1 AAATTATTTATTATTAAAATTATT
2059351 AATATTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (25 bp):
AAATTATTTATTATTAAAATTATTG
Found at i:2059378 original size:24 final size:21
Alignment explanation
Indices: 2059349--2059393 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
2059339 ATTCAAATTA
2059349 TTAATATTCAATAATAATTATATT
1 TTAATATT-AA-AAT-ATTATATT
2059373 TTAATATTAAAATATTATATT
1 TTAATATTAAAATATTATATT
2059394 AATATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.38
22 3 0.14
23 2 0.10
24 8 0.38
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATATTAAAATATTATATT
Found at i:2059512 original size:23 final size:21
Alignment explanation
Indices: 2059468--2059520 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
2059458 ATTACTATTC
* *
2059468 TTAAAATATTATTTTTATTTATA
1 TTAAAATATAATATTTA-TT-TA
2059491 TTAAAATAGTAATATTTA-TTA
1 TTAAAATA-TAATATTTATTTA
2059512 TTAAAATAT
1 TTAAAATAT
2059521 TTATACTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 10 0.37
22 1 0.04
23 8 0.30
24 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTAAAATATAATATTTATTTA
Found at i:2059532 original size:17 final size:16
Alignment explanation
Indices: 2059501--2059543 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 16
2059491 TTAAAATAGT
2059501 AATATTTAT-TATTAA
1 AATATTTATATATTAA
2059516 AATATTTATACTATTAA
1 AATATTTATA-TATTAA
2059533 AATATTTATAT
1 AATATTTATAT
2059544 TTTATATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.35
16 1 0.04
17 16 0.62
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
AATATTTATATATTAA
Found at i:2059769 original size:35 final size:34
Alignment explanation
Indices: 2059730--2059822 Score: 89
Period size: 35 Copynumber: 2.6 Consensus size: 34
2059720 ATTTACATTA
* *
2059730 ATTATTAAAATAATAAAAATATTATTATA-TATGTT
1 ATTATT-AAATATTAAAAATATTATAATACTAT-TT
* * * *
2059765 ATTATTTATTATTAAATTATAATATAATACTATTT
1 ATTATTAAATATTAAA-AATATTATAATACTATTT
2059800 ATTATTGAAATATTAAAAATATT
1 ATTATT-AAATATTAAAAATATT
2059823 TATGTTTAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
34 7 0.16
35 27 0.60
36 11 0.24
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (34 bp):
ATTATTAAATATTAAAAATATTATAATACTATTT
Found at i:2062233 original size:12 final size:12
Alignment explanation
Indices: 2062216--2062241 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2062206 CATAGATTGT
2062216 TTCCAACTTGGC
1 TTCCAACTTGGC
2062228 TTCCAACTTGGC
1 TTCCAACTTGGC
2062240 TT
1 TT
2062242 GGCTCGTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.31, G:0.15, T:0.38
Consensus pattern (12 bp):
TTCCAACTTGGC
Found at i:2063851 original size:19 final size:20
Alignment explanation
Indices: 2063822--2063876 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
2063812 AAGCATATCA
*
2063822 ATTTGCAAAATTTTTGAAAG
1 ATTTTCAAAATTTTTGAAAG
*
2063842 -TTTTCAAAATTTTGGAAAG
1 ATTTTCAAAATTTTTGAAAG
*
2063861 ATTTTTAAAATTTTTG
1 ATTTTCAAAATTTTTG
2063877 GCAAAACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (20 bp):
ATTTTCAAAATTTTTGAAAG
Found at i:2063887 original size:21 final size:21
Alignment explanation
Indices: 2063827--2063887 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 21
2063817 TATCAATTTG
*
2063827 CAAAATTTTTGAAAG--TTTT
1 CAAAATTTTGGAAAGACTTTT
2063846 CAAAATTTTGGAAAGA-TTTT
1 CAAAATTTTGGAAAGACTTTT
*
2063866 TAAAATTTTTGGCAAA-ACTTTT
1 CAAAA-TTTTGG-AAAGACTTTT
2063888 GTCTACCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 14 0.39
20 8 0.22
21 7 0.19
22 7 0.19
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (21 bp):
CAAAATTTTGGAAAGACTTTT
Found at i:2068479 original size:7 final size:7
Alignment explanation
Indices: 2068461--2068750 Score: 77
Period size: 7 Copynumber: 43.7 Consensus size: 7
2068451 GGGTAAAGTT
2068461 GGTTTCAG
1 GGTTT-AG
2068469 GGTTTAG
1 GGTTTAG
2068476 GG-TT--
1 GGTTTAG
*
2068480 GGTTTAA
1 GGTTTAG
*
2068487 GGTCTA-
1 GGTTTAG
*
2068493 GG-TTAA
1 GGTTTAG
2068499 GGTTTAG
1 GGTTTAG
*
2068506 GGTCTA-
1 GGTTTAG
*
2068512 AGTTT--
1 GGTTTAG
*
2068517 GGTTTAA
1 GGTTTAG
*
2068524 GGTTTTG
1 GGTTTAG
2068531 GGTTTATG
1 GGTTTA-G
* *
2068539 GATTTAC
1 GGTTTAG
* *
2068546 AGCTTAG
1 GGTTTAG
*
2068553 TGT-TAG
1 GGTTTAG
2068559 G-TTTAG
1 GGTTTAG
*
2068565 GATTTAG
1 GGTTTAG
2068572 GGTTT--
1 GGTTTAG
*
2068577 TGTTTAG
1 GGTTTAG
2068584 GGTTTAG
1 GGTTTAG
2068591 GGTTT-G
1 GGTTTAG
2068597 GAGTTTAG
1 G-GTTTAG
2068605 GGTTTAAG
1 GGTTT-AG
**
2068613 ATTTTA-
1 GGTTTAG
2068619 GGTTTA-
1 GGTTTAG
*
2068625 GGTTTAA
1 GGTTTAG
2068632 GGTCTT--
1 GGT-TTAG
2068638 GGTTTAG
1 GGTTTAG
*
2068645 AGG-GTAG
1 -GGTTTAG
2068652 GGTTTAG
1 GGTTTAG
* *
2068659 GG-TGAA
1 GGTTTAG
* *
2068665 AGTTTAA
1 GGTTTAG
2068672 GGTTTA-
1 GGTTTAG
*
2068678 GGTTTTG
1 GGTTTAG
* *
2068685 AGTTTAA
1 GGTTTAG
*
2068692 GG-TTAA
1 GGTTTAG
*
2068698 GGTTTAA
1 GGTTTAG
*
2068705 GGTTCCA-
1 GGTT-TAG
2068712 GGTTTAG
1 GGTTTAG
* *
2068719 GATTTAA
1 GGTTTAG
*
2068726 GGTTTAA
1 GGTTTAG
2068733 GG-TTAG
1 GGTTTAG
2068739 GGTTTAG
1 GGTTTAG
2068746 GGTTT
1 GGTTT
2068751 TAAAAAGATA
Statistics
Matches: 211, Mismatches: 44, Indels: 55
0.68 0.14 0.18
Matches are distributed among these distances:
4 2 0.01
5 15 0.07
6 53 0.25
7 118 0.56
8 23 0.11
ACGTcount: A:0.20, C:0.03, G:0.34, T:0.43
Consensus pattern (7 bp):
GGTTTAG
Found at i:2068502 original size:19 final size:18
Alignment explanation
Indices: 2068480--2068526 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
2068470 GTTTAGGGTT
*
2068480 GGTTTAAGGTCTAGGTTAA
1 GGTTTAAGGTCTAAGTT-A
* *
2068499 GGTTTAGGGTCTAAGTTT
1 GGTTTAAGGTCTAAGTTA
2068517 GGTTTAAGGT
1 GGTTTAAGGT
2068527 TTTGGGTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.40
Consensus pattern (18 bp):
GGTTTAAGGTCTAAGTTA
Found at i:2068643 original size:19 final size:20
Alignment explanation
Indices: 2068480--2068735 Score: 84
Period size: 20 Copynumber: 12.5 Consensus size: 20
2068470 GTTTAGGGTT
*
2068480 GGTTTAAGGTC-TAGGTTAA
1 GGTTTAAGGTCTTAGGTTTA
* *
2068499 GGTTTAGGGTC-TAAGTTT-
1 GGTTTAAGGTCTTAGGTTTA
* *
2068517 GGTTTAAGGTTTTGGGTTTA
1 GGTTTAAGGTCTTAGGTTTA
*
2068537 TGGATTTACAGCTTAGTGTTAGGTTTA
1 -GG-TTTA-AG----GTCTTAGGTTTA
* *
2068564 GGATTTAGGGT-TT-TGTTTA
1 GG-TTTAAGGTCTTAGGTTTA
* *
2068583 GGGTTTAGGGT-TTGGAGTTTA
1 -GGTTTAAGGTCTTAG-GTTTA
* *
2068604 GGGTTTAAGATTTTAGGTTTA
1 -GGTTTAAGGTCTTAGGTTTA
2068625 GGTTTAAGGTCTT-GGTTTA
1 GGTTTAAGGTCTTAGGTTTA
** * **
2068644 GAGGGTAGGGT-TTAGGGTGAA
1 G-GTTTAAGGTCTTA-GGTTTA
* *
2068665 AGTTTAAGGT-TTAGGTTTT
1 GGTTTAAGGTCTTAGGTTTA
*
2068684 GAGTTTAAGGT-TAAGGTTTAA
1 G-GTTTAAGGTCTTAGGTTT-A
**
2068705 GGTTCCAGGT-TTAGGATTTAA
1 GGTTTAAGGTCTTAGG-TTT-A
2068726 GGTTTAAGGT
1 GGTTTAAGGT
2068736 TAGGGTTTAG
Statistics
Matches: 181, Mismatches: 37, Indels: 36
0.71 0.15 0.14
Matches are distributed among these distances:
18 9 0.05
19 47 0.26
20 57 0.31
21 41 0.23
22 7 0.04
23 2 0.01
25 1 0.01
26 7 0.04
27 10 0.06
ACGTcount: A:0.21, C:0.03, G:0.33, T:0.43
Consensus pattern (20 bp):
GGTTTAAGGTCTTAGGTTTA
Found at i:2068714 original size:20 final size:20
Alignment explanation
Indices: 2068690--2068749 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
2068680 TTTTGAGTTT
2068690 AAGGTTAAGGTTTAAGGTTC
1 AAGGTTAAGGTTTAAGGTTC
* * *
2068710 CAGGTTTAGGATTTAAGGTTT
1 AAGGTTAAGG-TTTAAGGTTC
* *
2068731 AAGGTTAGGGTTTAGGGTT
1 AAGGTTAAGGTTTAAGGTT
2068750 TTAAAAAGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.25, C:0.03, G:0.33, T:0.38
Consensus pattern (20 bp):
AAGGTTAAGGTTTAAGGTTC
Found at i:2068749 original size:13 final size:13
Alignment explanation
Indices: 2068668--2068749 Score: 69
Period size: 13 Copynumber: 6.2 Consensus size: 13
2068658 GGGTGAAAGT
2068668 TTAAGGTTT-AGG
1 TTAAGGTTTAAGG
**
2068680 TTTTGAGTTTAAGG
1 TTAAG-GTTTAAGG
2068694 TTAAGGTTTAAGG
1 TTAAGGTTTAAGG
*
2068707 TTCCAGGTTT-AGG
1 TT-AAGGTTTAAGG
2068720 ATTTAAGGTTTAAGG
1 --TTAAGGTTTAAGG
* *
2068735 TTAGGGTTTAGGG
1 TTAAGGTTTAAGG
2068748 TT
1 TT
2068750 TTAAAAAGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
12 3 0.05
13 30 0.54
14 18 0.32
15 5 0.09
ACGTcount: A:0.23, C:0.02, G:0.32, T:0.43
Consensus pattern (13 bp):
TTAAGGTTTAAGG
Found at i:2077009 original size:25 final size:25
Alignment explanation
Indices: 2076950--2077015 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
2076940 AATAATAGGT
* *
2076950 TATTTTATA-TTTTTTAAATTCACA
1 TATTTTATATTTTTTTTAATCCACA
* *
2076974 AATTTGA-ATTTTTTTTAATCCACA
1 TATTTTATATTTTTTTTAATCCACA
2076998 TATTTTATATTTATTTTT
1 TATTTTATATTT-TTTTT
2077016 TAAAATTCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
23 1 0.03
24 23 0.70
25 4 0.12
26 5 0.15
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.61
Consensus pattern (25 bp):
TATTTTATATTTTTTTTAATCCACA
Found at i:2077733 original size:17 final size:17
Alignment explanation
Indices: 2077711--2077743 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2077701 CAAATGAATA
2077711 AAAAT-ATTCATATTATT
1 AAAATAATT-ATATTATT
2077728 AAAATAATTATATTAT
1 AAAATAATTATATTAT
2077744 AACATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATAATTATATTATT
Found at i:2081096 original size:43 final size:43
Alignment explanation
Indices: 2081035--2081160 Score: 252
Period size: 43 Copynumber: 2.9 Consensus size: 43
2081025 TTTAGTTGTT
2081035 TTTCTTACTTCAAATAAAATGTATGTGTGATTGTGATGATATA
1 TTTCTTACTTCAAATAAAATGTATGTGTGATTGTGATGATATA
2081078 TTTCTTACTTCAAATAAAATGTATGTGTGATTGTGATGATATA
1 TTTCTTACTTCAAATAAAATGTATGTGTGATTGTGATGATATA
2081121 TTTCTTACTTCAAATAAAATGTATGTGTGATTGTGATGAT
1 TTTCTTACTTCAAATAAAATGTATGTGTGATTGTGATGAT
2081161 GTAATAGGTG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (43 bp):
TTTCTTACTTCAAATAAAATGTATGTGTGATTGTGATGATATA
Found at i:2081888 original size:20 final size:20
Alignment explanation
Indices: 2081863--2081911 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2081853 CTTAAATCTC
* *
2081863 AAATCCTACATTCAAACCCT
1 AAATCCTAAATTCAAACCAT
*
2081883 AAATCCCAAATTCAAACCAT
1 AAATCCTAAATTCAAACCAT
2081903 AAA-CCTAAA
1 AAATCCTAAA
2081912 CCCTCAAACC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (20 bp):
AAATCCTAAATTCAAACCAT
Found at i:2081906 original size:7 final size:6
Alignment explanation
Indices: 2081896--2082044 Score: 52
Period size: 7 Copynumber: 22.5 Consensus size: 6
2081886 TCCCAAATTC
* * *
2081896 AAACCAT AAACCT AAACCCT CAAACCC AAACCAT AAACCCC AAACCCA
1 AAACC-T AAACCT AAA-CCT -AAACCT AAACC-T AAA-CCT AAA-CCT
* * *
2081944 AAACCT AAACGCC AAA-TT GAAACCTT AAATCCC AAACACT AAACCT AAACCTT
1 AAACCT AAAC-CT AAACCT -AAACC-T AAA-CCT AAAC-CT AAACCT AAACC-T
* *
2081997 AAACCCT AAATC- AAA-CT ATAACCAT AAACCCT AACCCT AAACCCT AAA
1 AAA-CCT AAACCT AAACCT A-AACC-T AAA-CCT AAACCT AAA-CCT AAA
2082045 ACCAAAGCCC
Statistics
Matches: 110, Mismatches: 14, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
4 1 0.01
5 4 0.04
6 34 0.31
7 57 0.52
8 14 0.13
ACGTcount: A:0.49, C:0.35, G:0.01, T:0.15
Consensus pattern (6 bp):
AAACCT
Found at i:2081906 original size:27 final size:26
Alignment explanation
Indices: 2081876--2081945 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
2081866 TCCTACATTC
**
2081876 AAACCCTAAATCCCAAATTCAAACCAT
1 AAACCCTAAA-CCCAAACCCAAACCAT
2081903 AAA-CCTAAACCCTCAAACCCAAACCAT
1 AAACCCTAAA-CC-CAAACCCAAACCAT
*
2081930 AAACCCCAAACCCAAA
1 AAACCCTAAACCCAAA
2081946 ACCTAAACGC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 12 0.32
27 20 0.54
28 5 0.14
ACGTcount: A:0.50, C:0.39, G:0.00, T:0.11
Consensus pattern (26 bp):
AAACCCTAAACCCAAACCCAAACCAT
Found at i:2081926 original size:14 final size:13
Alignment explanation
Indices: 2081895--2082071 Score: 72
Period size: 13 Copynumber: 12.9 Consensus size: 13
2081885 ATCCCAAATT
*
2081895 CAAACCATAAACC
1 CAAACCCTAAACC
*
2081908 TAAACCCTCAAACC
1 CAAACCCT-AAACC
*
2081922 CAAACCATAAACCC
1 CAAACCCTAAA-CC
*
2081936 CAAACCCAAAACC
1 CAAACCCTAAACC
* **
2081949 TAAACGCC-AAATT
1 CAAAC-CCTAAACC
* *
2081962 GAAACCTTAAATCC
1 CAAACCCTAAA-CC
*
2081976 CAAACACTAAACC
1 CAAACCCTAAACC
* *
2081989 TAAACCTTAAACC
1 CAAACCCTAAACC
*
2082002 CTAAATCAAACTATAACC
1 C-AAA-C--CCTA-AACC
*
2082020 ATAAACCCT-AACC
1 -CAAACCCTAAACC
*
2082033 CTAAACCCTAAAAC
1 C-AAACCCTAAACC
2082047 CAAAGCCCT-AACC
1 CAAA-CCCTAAACC
* *
2082060 TAGACCCTAAAC
1 CAAACCCTAAAC
2082072 AAATCCCAAG
Statistics
Matches: 120, Mismatches: 29, Indels: 30
0.67 0.16 0.17
Matches are distributed among these distances:
12 5 0.04
13 59 0.49
14 43 0.36
15 3 0.03
17 3 0.03
18 7 0.06
ACGTcount: A:0.47, C:0.36, G:0.02, T:0.14
Consensus pattern (13 bp):
CAAACCCTAAACC
Found at i:2081939 original size:20 final size:20
Alignment explanation
Indices: 2081903--2081959 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
2081893 TTCAAACCAT
2081903 AAACCTAAACCCTCAAACCC-
1 AAACCTAAACCC-CAAACCCA
2081923 AAACCATAAACCCCAAACCCA
1 AAACC-TAAACCCCAAACCCA
*
2081944 AAACCTAAACGCCAAA
1 AAACCTAAACCCCAAA
2081960 TTGAAACCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.51, C:0.40, G:0.02, T:0.07
Consensus pattern (20 bp):
AAACCTAAACCCCAAACCCA
Found at i:2081947 original size:27 final size:27
Alignment explanation
Indices: 2081895--2081953 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
2081885 ATCCCAAATT
* *
2081895 CAAACCATAAACCTAAACCCTCAAACC
1 CAAACCATAAACCCAAACCCTAAAACC
2081922 CAAACCATAAACCCCAAACCC-AAAACC
1 CAAACCATAAA-CCCAAACCCTAAAACC
*
2081949 TAAAC
1 CAAAC
2081954 GCCAAATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.51, C:0.41, G:0.00, T:0.08
Consensus pattern (27 bp):
CAAACCATAAACCCAAACCCTAAAACC
Found at i:2081992 original size:20 final size:20
Alignment explanation
Indices: 2081902--2081994 Score: 75
Period size: 20 Copynumber: 4.6 Consensus size: 20
2081892 ATTCAAACCA
2081902 TAAACCTAAACCCTCAAAC-C
1 TAAACCTAAACCC-CAAACAC
* *
2081922 CAAACCATAAACCCCAAACCC
1 TAAACC-TAAACCCCAAACAC
* * *
2081943 AAAACCTAAACGCC-AA-AT
1 TAAACCTAAACCCCAAACAC
*
2081961 TGAAACCTTAAATCCCAAACAC
1 T-AAACC-TAAACCCCAAACAC
2081983 TAAACCTAAACC
1 TAAACCTAAACC
2081995 TTAAACCCTA
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
19 7 0.12
20 28 0.49
21 20 0.35
22 2 0.04
ACGTcount: A:0.48, C:0.37, G:0.02, T:0.13
Consensus pattern (20 bp):
TAAACCTAAACCCCAAACAC
Found at i:2082044 original size:20 final size:20
Alignment explanation
Indices: 2081896--2082044 Score: 59
Period size: 20 Copynumber: 7.2 Consensus size: 20
2081886 TCCCAAATTC
* *
2081896 AAACCATAAACCTAAACCCT
1 AAACCCTAACCCTAAACCCT
* * *
2081916 CAAACCCAAACCATAAACCCC
1 -AAACCCTAACCCTAAACCCT
* *
2081937 AAACCCAAAACCTAAACGCC-
1 AAACCCTAACCCTAAAC-CCT
**** *
2081957 AAATTGAAACCTTAAATCCC-
1 AAACCCTAACCCTAAA-CCCT
* * *
2081977 AAACACTAAACCTAAACCTT
1 AAACCCTAACCCTAAACCCT
* *
2081997 AAACCCTAAATCAAACTATAACCAT
1 AAACCCT-AA-C--CCTA-AACCCT
2082022 AAACCCTAACCCTAAACCCT
1 AAACCCTAACCCTAAACCCT
2082042 AAA
1 AAA
2082045 ACCAAAGCCC
Statistics
Matches: 95, Mismatches: 25, Indels: 17
0.69 0.18 0.12
Matches are distributed among these distances:
19 2 0.02
20 52 0.55
21 23 0.24
23 1 0.01
24 5 0.05
25 12 0.13
ACGTcount: A:0.49, C:0.35, G:0.01, T:0.15
Consensus pattern (20 bp):
AAACCCTAACCCTAAACCCT
Found at i:2082180 original size:18 final size:20
Alignment explanation
Indices: 2082143--2082183 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2082133 CATTTGCATT
*
2082143 TTCTTTTGTTGTTACATGCA
1 TTCTTTAGTTGTTACATGCA
2082163 TTCTTTAGTTG-T-CATGCA
1 TTCTTTAGTTGTTACATGCA
2082181 TTC
1 TTC
2082184 ATATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 1 0.05
20 10 0.50
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.54
Consensus pattern (20 bp):
TTCTTTAGTTGTTACATGCA
Found at i:2083060 original size:21 final size:21
Alignment explanation
Indices: 2083035--2083104 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
2083025 AGAAAAATAT
* *
2083035 AAAAATTTTAAAAATTTTCGAA
1 AAAAATTCTAAAAATTTTTG-A
* **
2083057 AAAAATTCTAAAATTTTTTTT
1 AAAAATTCTAAAAATTTTTGA
*
2083078 AAAAATTCAAAAAATTTTTGA
1 AAAAATTCTAAAAATTTTTGA
2083099 AAAAAT
1 AAAAAT
2083105 AAAAAATAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 23 0.59
22 16 0.41
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (21 bp):
AAAAATTCTAAAAATTTTTGA
Found at i:2083095 original size:20 final size:20
Alignment explanation
Indices: 2083057--2083111 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
2083047 AATTTTCGAA
** *
2083057 AAAAATTCTAAAATTTTTTTT
1 AAAAATTC-AAAAAATTTTTG
2083078 AAAAATTCAAAAAATTTTTG
1 AAAAATTCAAAAAATTTTTG
*
2083098 AAAAAAT-AAAAAAT
1 AAAAATTCAAAAAAT
2083112 AAAAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 7 0.23
20 15 0.50
21 8 0.27
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAATTCAAAAAATTTTTG
Found at i:2083108 original size:19 final size:20
Alignment explanation
Indices: 2083044--2083111 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
2083034 TAAAAATTTT
*
2083044 AAAAATTTTCGAAAAAAATTCTA
1 AAAAATTTTTG-AAAAAA-TC-A
** * *
2083067 AAATTTTTTTTAAAAATTCA
1 AAAAATTTTTGAAAAAATCA
2083087 AAAAATTTTTGAAAAAAT-A
1 AAAAATTTTTGAAAAAATCA
2083106 AAAAAT
1 AAAAAT
2083112 AAAAAATTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
19 7 0.19
20 15 0.42
21 2 0.06
22 5 0.14
23 7 0.19
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.35
Consensus pattern (20 bp):
AAAAATTTTTGAAAAAATCA
Found at i:2083429 original size:39 final size:39
Alignment explanation
Indices: 2083386--2083460 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
2083376 AAAAAAAAAA
* * *
2083386 AAAAATAAATCCTAACAAA-TTCCAAAAATATGAAAAATT
1 AAAAAGAAATCCCAA-AAATTTCAAAAAATATGAAAAATT
* *
2083425 AAAAAGAATTCCCAAAAATTTCAAAAAATCTGAAAA
1 AAAAAGAAATCCCAAAAATTTCAAAAAATATGAAAA
2083461 TTTTTAGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 3 0.10
39 27 0.90
ACGTcount: A:0.61, C:0.13, G:0.04, T:0.21
Consensus pattern (39 bp):
AAAAAGAAATCCCAAAAATTTCAAAAAATATGAAAAATT
Found at i:2083907 original size:10 final size:10
Alignment explanation
Indices: 2083892--2083916 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2083882 TTAATTTTAG
2083892 TTTTTTAAAT
1 TTTTTTAAAT
2083902 TTTTTTAAAT
1 TTTTTTAAAT
2083912 TTTTT
1 TTTTT
2083917 GTCTTTTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTAAAT
Found at i:2084708 original size:49 final size:48
Alignment explanation
Indices: 2084645--2084768 Score: 131
Period size: 48 Copynumber: 2.6 Consensus size: 48
2084635 TTTTGGTTTC
** *
2084645 AATTTTAAAATTTCAATGCCTTTATTAGGGAAAAGCTTTTCAGTTTCAA
1 AATTTTAAAATTTCAACACCTTTATT-GGGAAAAGCTTTTCAATTTCAA
* ** *
2084694 AATTTTAAACTTTCAACACCTTTATTGGGATGAGCTTTTCAATTTCAG
1 AATTTTAAAATTTCAACACCTTTATTGGGAAAAGCTTTTCAATTTCAA
* * * * *
2084742 ATTTTTTAAATTTGAATACCTCTATTG
1 AATTTTAAAATTTCAACACCTTTATTG
2084769 AGGAGGAGTC
Statistics
Matches: 62, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
48 39 0.63
49 23 0.37
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (48 bp):
AATTTTAAAATTTCAACACCTTTATTGGGAAAAGCTTTTCAATTTCAA
Found at i:2084768 original size:48 final size:49
Alignment explanation
Indices: 2084678--2084788 Score: 118
Period size: 48 Copynumber: 2.3 Consensus size: 49
2084668 ATTAGGGAAA
* * *
2084678 AGCTTTTCAGTTTCAAAATTTTAAACTTTCAACACCTTTATTG-GGATG
1 AGCTTTTCAATTTCAAAATTTTAAACTTTCAACACCTCTATTGAGGAGG
** * *
2084726 AGCTTTTCAATTTCAGATTTTTTAAA-TTTGAATACCTCTATTGAGGAGG
1 AGCTTTTCAATTTCA-AAATTTTAAACTTTCAACACCTCTATTGAGGAGG
*
2084775 AGTCTTTTAAATTT
1 AG-CTTTTCAATTT
2084789 TCCTTGAGGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
48 28 0.54
49 14 0.27
50 10 0.19
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (49 bp):
AGCTTTTCAATTTCAAAATTTTAAACTTTCAACACCTCTATTGAGGAGG
Found at i:2085051 original size:17 final size:17
Alignment explanation
Indices: 2085014--2085052 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2085004 CCCAAAAGTC
*
2085014 TTTTTATTTATTGATAT
1 TTTTTATTTATTGATAA
**
2085031 TTTTTATTTATTTTTAA
1 TTTTTATTTATTGATAA
2085048 TTTTT
1 TTTTT
2085053 TGTTATATGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTTATTTATTGATAA
Found at i:2085058 original size:21 final size:21
Alignment explanation
Indices: 2085016--2085053 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2085006 CAAAAGTCTT
*
2085016 TTTATTTATTGATATTTTTTA
1 TTTATTTATTAATATTTTTTA
2085037 TTTATTT-TTAAT-TTTTT
1 TTTATTTATTAATATTTTT
2085054 GTTATATGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 4 0.25
21 7 0.44
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (21 bp):
TTTATTTATTAATATTTTTTA
Found at i:2087487 original size:14 final size:14
Alignment explanation
Indices: 2087468--2087514 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2087458 ATAAAAAACT
2087468 TTATTATAATAATA
1 TTATTATAATAATA
*
2087482 TTATTATTATAATAA
1 TTATTATAATAAT-A
*
2087497 TTA-AATAATAATA
1 TTATTATAATAATA
2087510 TTATT
1 TTATT
2087515 TTACCCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 4 0.15
14 19 0.70
15 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTATTATAATAATA
Found at i:2087533 original size:3 final size:3
Alignment explanation
Indices: 2087527--2087564 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2087517 ACCCTTTTAT
2087527 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2087565 TCTCATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2088151 original size:2 final size:2
Alignment explanation
Indices: 2088144--2088214 Score: 57
Period size: 2 Copynumber: 39.0 Consensus size: 2
2088134 ATCCCTACTC
* *
2088144 AT AT AT AT A- AT AT AT -T AT AT AT AT AT AT GT TT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2088183 AT -T AT AT AT A- AT GT A- AT AT CT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2088215 GCAAAATCTC
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
1 7 0.13
2 48 0.87
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2088158 original size:7 final size:7
Alignment explanation
Indices: 2088145--2088212 Score: 61
Period size: 7 Copynumber: 10.0 Consensus size: 7
2088135 TCCCTACTCA
2088145 TATATAT
1 TATATAT
*
2088152 AATATAT
1 TATATAT
2088159 TATATA-
1 TATATAT
2088165 TATATAT
1 TATATAT
2088172 GT-T-TAT
1 -TATATAT
2088178 TATATAT
1 TATATAT
2088185 TATATAT
1 TATATAT
* * *
2088192 AATGTAA
1 TATATAT
*
2088199 TATCTAT
1 TATATAT
2088206 TATATAT
1 TATATAT
2088213 ATGCAAAATC
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
5 1 0.02
6 10 0.21
7 36 0.75
8 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (7 bp):
TATATAT
Done.