Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 131 of 332
Found at i:42667176 original size:43 final size:43
Alignment explanation
Indices: 42667007--42667177 Score: 132
Period size: 43 Copynumber: 4.0 Consensus size: 43
42666997 TAGGATTTCT
* * * **
42667007 GATATGTGATTTCGTGTAAGACCACGTCTGGGATGTTGGCATC
1 GATATTTGATTACATGTAAGACCACGTCTGGGACATTGGCATC
* * * * *
42667050 GAT-TTGAGATTTACATGTAAGACCATGTTTGGGACATCGACATC
1 GATATT-TGA-TTACATGTAAGACCACGTCTGGGACATTGGCATC
* * * * * * *
42667094 G-TATTTAATTTCGTGTAGGACC-CTATTTGGGACAATGGCATC
1 GATATTTGATTACATGTAAGACCAC-GTCTGGGACATTGGCATC
*
42667136 GATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 GATATTTGATTACATGTAAGACCACGTCTGGGACATTGGCAT
42667178 TGTATGAGCT
Statistics
Matches: 94, Mismatches: 28, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
42 27 0.29
43 37 0.39
44 30 0.32
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (43 bp):
GATATTTGATTACATGTAAGACCACGTCTGGGACATTGGCATC
Found at i:42674038 original size:39 final size:39
Alignment explanation
Indices: 42673982--42674113 Score: 167
Period size: 39 Copynumber: 3.4 Consensus size: 39
42673972 TTAAGTGTTG
* *
42673982 TGATATATGCTTGAATGTTATGTGATTATATGAGTATTA
1 TGATATATGCTTAAATGTTATGTGATTATATGAGTACTA
* ** *
42674021 TGATATATGTTTAAATGTTATGTGATTATACAAGTACTG
1 TGATATATGCTTAAATGTTATGTGATTATATGAGTACTA
* *
42674060 TGATATATGCTTAAATGTTATGTGATTATATGTA-TAATG
1 TGATATATGCTTAAATGTTATGTGATTATATG-AGTACTA
*
42674099 TGACATATGCTTAAA
1 TGATATATGCTTAAA
42674114 AGTGAATATG
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 80 0.99
40 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (39 bp):
TGATATATGCTTAAATGTTATGTGATTATATGAGTACTA
Found at i:42675522 original size:30 final size:30
Alignment explanation
Indices: 42675487--42675611 Score: 116
Period size: 30 Copynumber: 4.2 Consensus size: 30
42675477 TAAAGTTACT
* *
42675487 TACATAATGTAACCAATAATATACATAACA
1 TACATAATGTAAACAGTAATATACATAACA
* *
42675517 TACATAATAG-AAATAGTAATAAACATAACA
1 TACATAAT-GTAAACAGTAATATACATAACA
* ** *
42675547 TACATGACATAAATAGTAATATAC-T-ACA
1 TACATAATGTAAACAGTAATATACATAACA
42675575 TAACATACA--TAAACAGTAATATACATAACA
1 T-ACATA-ATGTAAACAGTAATATACATAACA
42675605 TACATAA
1 TACATAA
42675612 AATCCATACT
Statistics
Matches: 79, Mismatches: 10, Indels: 14
0.77 0.10 0.14
Matches are distributed among these distances:
28 19 0.24
29 11 0.14
30 48 0.61
31 1 0.01
ACGTcount: A:0.55, C:0.14, G:0.05, T:0.26
Consensus pattern (30 bp):
TACATAATGTAAACAGTAATATACATAACA
Found at i:42675584 original size:28 final size:28
Alignment explanation
Indices: 42675527--42675612 Score: 99
Period size: 25 Copynumber: 3.1 Consensus size: 28
42675517 TACATAATAG
*
42675527 AAATAGTAATAAACATAACAT-ACATGACAT
1 AAATAGTAATATAC-T-ACATAACAT-ACAT
42675557 AAATAGTAATATACTACATAACATACAT
1 AAATAGTAATATACTACATAACATACAT
*
42675585 AAACAGT-A-ATA-TACATAACATACAT
1 AAATAGTAATATACTACATAACATACAT
42675610 AAA
1 AAA
42675613 ATCCATACTA
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
25 17 0.32
26 3 0.06
27 1 0.02
28 14 0.26
29 5 0.09
30 13 0.25
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.24
Consensus pattern (28 bp):
AAATAGTAATATACTACATAACATACAT
Found at i:42675600 original size:16 final size:16
Alignment explanation
Indices: 42675553--42675602 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
42675543 AACATACATG
*
42675553 ACATAAATAGTAATAT
1 ACATAAACAGTAATAT
*
42675569 AC-T--ACA-TAACAT
1 ACATAAACAGTAATAT
42675581 ACATAAACAGTAATAT
1 ACATAAACAGTAATAT
42675597 ACATAA
1 ACATAA
42675603 CATACATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
12 7 0.26
13 3 0.11
15 4 0.15
16 13 0.48
ACGTcount: A:0.56, C:0.14, G:0.04, T:0.26
Consensus pattern (16 bp):
ACATAAACAGTAATAT
Found at i:42675625 original size:30 final size:30
Alignment explanation
Indices: 42675503--42675635 Score: 139
Period size: 30 Copynumber: 4.5 Consensus size: 30
42675493 ATGTAACCAA
* *
42675503 TAATATACATAACATACATAATAGAAATAG
1 TAATATACATAACATACATAAAATAAATAG
* * *
42675533 TAATAAACATAACATACATGACATAAATAG
1 TAATATACATAACATACATAAAATAAATAG
* *
42675563 TAATATAC-T-ACATAACAT-ACATAAACAG
1 TAATATACATAACAT-ACATAAAATAAATAG
** *
42675591 TAATATACATAACATACATAAAATCCATAC
1 TAATATACATAACATACATAAAATAAATAG
42675621 TAATATACAT-ACATA
1 TAATATACATAACATA
42675636 ATAGACATAC
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
28 21 0.24
29 15 0.17
30 52 0.59
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (30 bp):
TAATATACATAACATACATAAAATAAATAG
Found at i:42675630 original size:25 final size:25
Alignment explanation
Indices: 42675567--42675652 Score: 81
Period size: 25 Copynumber: 3.4 Consensus size: 25
42675557 AAATAGTAAT
42675567 ATACTACATA-ACATACATAAACAGTA-
1 ATACTA-ATATACATACATAAA-AG-AC
**
42675593 ATA-TACATA-ACATACATAAAATCC
1 ATACTA-ATATACATACATAAAAGAC
*
42675617 ATACTAATATACATACATAATAGAC
1 ATACTAATATACATACATAAAAGAC
42675642 ATACTAATATA
1 ATACTAATATA
42675653 GCAATTGACT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
24 7 0.13
25 42 0.81
26 3 0.06
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.27
Consensus pattern (25 bp):
ATACTAATATACATACATAAAAGAC
Found at i:42675637 original size:13 final size:12
Alignment explanation
Indices: 42675602--42675652 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
42675592 AATATACATA
*
42675602 ACATACATAAAAT
1 ACATAC-TAATAT
*
42675615 CCATACTAATAT
1 ACATACTAATAT
*
42675627 ACATACATAATAG
1 ACATAC-TAATAT
42675640 ACATACTAATAT
1 ACATACTAATAT
42675652 A
1 A
42675653 GCAATTGACT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
12 16 0.50
13 16 0.50
ACGTcount: A:0.53, C:0.18, G:0.02, T:0.27
Consensus pattern (12 bp):
ACATACTAATAT
Found at i:42675649 original size:12 final size:12
Alignment explanation
Indices: 42675616--42675650 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
42675606 ACATAAAATC
*
42675616 CATACTAATATA
1 CATACTAATAGA
42675628 CATACATAATAGA
1 CATAC-TAATAGA
42675641 CATACTAATA
1 CATACTAATA
42675651 TAGCAATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.29
Consensus pattern (12 bp):
CATACTAATAGA
Found at i:42678477 original size:22 final size:22
Alignment explanation
Indices: 42678464--42678541 Score: 147
Period size: 22 Copynumber: 3.5 Consensus size: 22
42678454 ATGTGTTTAT
42678464 GAGTAAGACCATATCTGTGTGC
1 GAGTAAGACCATATCTGTGTGC
42678486 GAGTAAGACCATATCTGTGTGC
1 GAGTAAGACCATATCTGTGTGC
*
42678508 GAGTAAGACCATATATGTGTGC
1 GAGTAAGACCATATCTGTGTGC
42678530 GAGTAAGACCAT
1 GAGTAAGACCAT
42678542 GGCATCGATA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.26
Consensus pattern (22 bp):
GAGTAAGACCATATCTGTGTGC
Found at i:42680277 original size:98 final size:98
Alignment explanation
Indices: 42680165--42680360 Score: 383
Period size: 98 Copynumber: 2.0 Consensus size: 98
42680155 AAATCATGAA
42680165 ATTGTATGAATTTTTTTTATATGATATACATGTGTTCGGCTGGTTATAGTTAAATGTTATGTAAT
1 ATTGTATGAATTTTTTTTATATGATATACATGTGTTCGGCTGGTTATAGTTAAATGTTATGTAAT
42680230 ATGATAGCTAGTCCCTAAACCATGATTATAAGT
66 ATGATAGCTAGTCCCTAAACCATGATTATAAGT
*
42680263 ATTGTATGACTTTTTTTTATATGATATACATGTGTTCGGCTGGTTATAGTTAAATGTTATGTAAT
1 ATTGTATGAATTTTTTTTATATGATATACATGTGTTCGGCTGGTTATAGTTAAATGTTATGTAAT
42680328 ATGATAGCTAGTCCCTAAACCATGATTATAAGT
66 ATGATAGCTAGTCCCTAAACCATGATTATAAGT
42680361 TGATTAAACA
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 97 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (98 bp):
ATTGTATGAATTTTTTTTATATGATATACATGTGTTCGGCTGGTTATAGTTAAATGTTATGTAAT
ATGATAGCTAGTCCCTAAACCATGATTATAAGT
Found at i:42681166 original size:139 final size:141
Alignment explanation
Indices: 42680870--42681152 Score: 398
Period size: 138 Copynumber: 2.0 Consensus size: 141
42680860 ACGTAGATAA
* *
42680870 AATTAATATATGAATTTGATTCATGCAAAATATTATTAATTGTATATATTTCACCAGATTTTTTA
1 AATTAATATATGAATTTGATTCATACAAAATATTATTAATTGTATATATTTCACCAGATTTATTA
* * * * *
42680935 ATATAACAATTATATTAATTAATTTTTATCAAAATATAAAAAATATGGAAATTAATATTTTTTTT
66 ATATAACAATTATATTAATGAATTTTGATCAAAATATAAAAAACATAGAAATTAATATTTGTTTT
42681000 GGAAAGAATAC
131 GGAAAGAATAC
*
42681011 AATTAATATATGAATTTGATTCATAC-AAA-A-TATTAATTGTATATATTTTACC-GAATTTATT
1 AATTAATATATGAATTTGATTCATACAAAATATTATTAATTGTATATATTTCACCAG-ATTTATT
* *
42681072 AATATAA-ATAGTTATATTAATGAATTTTGGTCAAAATATAAAAGACATAGAAATTAATA-TTGT
65 AATATAACA-A-TTATATTAATGAATTTTGATCAAAATATAAAAAACATAGAAATTAATATTTGT
*
42681135 TTTGGAAAGAATAT
128 TTTGGAAAGAATAC
42681149 AATT
1 AATT
42681153 CCTTTTCCTA
Statistics
Matches: 128, Mismatches: 11, Indels: 9
0.86 0.07 0.06
Matches are distributed among these distances:
137 2 0.02
138 55 0.43
139 43 0.34
140 3 0.02
141 25 0.20
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (141 bp):
AATTAATATATGAATTTGATTCATACAAAATATTATTAATTGTATATATTTCACCAGATTTATTA
ATATAACAATTATATTAATGAATTTTGATCAAAATATAAAAAACATAGAAATTAATATTTGTTTT
GGAAAGAATAC
Found at i:42684204 original size:17 final size:17
Alignment explanation
Indices: 42684182--42684216 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
42684172 TGTGTCCCCT
42684182 GCACCTTAAAATTTTAA
1 GCACCTTAAAATTTTAA
42684199 GCACCTTAAAATTTTAA
1 GCACCTTAAAATTTTAA
42684216 G
1 G
42684217 TCAGTATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (17 bp):
GCACCTTAAAATTTTAA
Found at i:42690156 original size:51 final size:49
Alignment explanation
Indices: 42690098--42690231 Score: 196
Period size: 51 Copynumber: 2.7 Consensus size: 49
42690088 GAAGCTAACT
* * *
42690098 GGTACGCATAGTAGCCTGCACTTAGTACTATACATGCGACCACAGTTTTCG
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCA-A-TTATCC
*
42690149 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATTATCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCC
* *
42690198 GGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACA
42690232 CGTGACCTCA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
49 35 0.46
50 1 0.01
51 40 0.53
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (49 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCC
Found at i:42693481 original size:29 final size:29
Alignment explanation
Indices: 42693446--42693519 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
42693436 GTTGTGAGAT
* *
42693446 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
42693475 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
42693504 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
42693520 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:42708936 original size:25 final size:25
Alignment explanation
Indices: 42708887--42708936 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
42708877 GGGGATAAGA
*
42708887 GAGAAGATTTAGGAGCTGGTAAGGG
1 GAGAAGATTTAGGAGCTGATAAGGG
* *
42708912 GAGAAGTTTTAGGAGCTGATTAGGG
1 GAGAAGATTTAGGAGCTGATAAGGG
42708937 AGGGCAGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.04, G:0.42, T:0.24
Consensus pattern (25 bp):
GAGAAGATTTAGGAGCTGATAAGGG
Found at i:42710373 original size:27 final size:26
Alignment explanation
Indices: 42710333--42710444 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
42710323 AGGAAGCGTC
*
42710333 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
42710360 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
42710387 CTGGTGGCTCTACCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
** * * *
42710415 CTGGTAACTTTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
42710441 CTGG
1 CTGG
42710445 CAGATATGCT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 7 0.10
27 51 0.71
28 14 0.19
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:42710437 original size:54 final size:54
Alignment explanation
Indices: 42710333--42710444 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
42710323 AGGAAGCGTC
* **
42710333 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATACCACAATTATCTGATCTGGTAACTCTGCCACATATATCTGTT
* * * *
42710387 CTGGTGGCTCTACCACGATTATCTGTATCTGGTAACTTTGTCACAT-TATCTGTT
1 CTGGTGGCTATACCACAATTATCTG-ATCTGGTAACTCTGCCACATATATCTGTT
42710441 CTGG
1 CTGG
42710445 CAGATATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 34 0.68
55 16 0.32
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATACCACAATTATCTGATCTGGTAACTCTGCCACATATATCTGTT
Found at i:42717164 original size:27 final size:27
Alignment explanation
Indices: 42717124--42717235 Score: 120
Period size: 27 Copynumber: 4.1 Consensus size: 27
42717114 AGGAAGCGTC
*
42717124 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
* *
42717151 CTGGTGGCTCTGCCACATATAAT-TGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
* *
42717178 CTGGTGGCTTTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
42717206 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
42717232 CTGG
1 CTGG
42717236 CAGCTATGCT
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
26 9 0.13
27 44 0.62
28 18 0.25
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:42717232 original size:54 final size:54
Alignment explanation
Indices: 42717124--42717244 Score: 156
Period size: 54 Copynumber: 2.2 Consensus size: 54
42717114 AGGAAGCGTC
*
42717124 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATAATTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATAATTGTT
* * *
42717178 CTGGTGGCTTTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-T-ATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATAAT-TGTT
**
42717232 CTGGCAGCTATGC
1 CTGGTGGCTATGC
42717245 TGCATATTTC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 2 0.03
54 38 0.66
55 18 0.31
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.36
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATAATTGTT
Found at i:42737222 original size:42 final size:42
Alignment explanation
Indices: 42737163--42737244 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
42737153 TGAGATCATG
* *
42737163 TGTAAGACCATATCTAGGATATGGCATCGATATTAGACTTCT
1 TGTAAAACCATATCTAGGATATGGCATCGATATAAGACTTCT
42737205 TGTAAAACCATATCTAGGATATGGCATCGATATAAGACTT
1 TGTAAAACCATATCTAGGATATGGCATCGATATAAGACTT
42737245 AGCGTAAGAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (42 bp):
TGTAAAACCATATCTAGGATATGGCATCGATATAAGACTTCT
Found at i:42737257 original size:42 final size:42
Alignment explanation
Indices: 42737164--42737258 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
42737154 GAGATCATGT
* ***
42737164 GTAAGACCATATCTAGGATATGGCATCGATATTAGACTTCTT
1 GTAAGACCATATCTAGGATATGGCATCGATATAAGACTTAGC
*
42737206 GTAAAACCATATCTAGGATATGGCATCGATATAAGACTTAGC
1 GTAAGACCATATCTAGGATATGGCATCGATATAAGACTTAGC
42737248 GTAAGACCATA
1 GTAAGACCATA
42737259 GTTGGCTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (42 bp):
GTAAGACCATATCTAGGATATGGCATCGATATAAGACTTAGC
Found at i:42740471 original size:19 final size:19
Alignment explanation
Indices: 42740447--42740483 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
42740437 TTACTACCAT
42740447 GCTTTTCAAGATAAAACAA
1 GCTTTTCAAGATAAAACAA
42740466 GCTTTTCAAGATAAAACA
1 GCTTTTCAAGATAAAACA
42740484 CTATAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (19 bp):
GCTTTTCAAGATAAAACAA
Found at i:42741370 original size:49 final size:49
Alignment explanation
Indices: 42741306--42741538 Score: 243
Period size: 49 Copynumber: 4.7 Consensus size: 49
42741296 AAAGCTATCT
* * * *
42741306 GGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCAATTATTC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATTC
* * * *
42741355 AGTACACGTAGTAGCCTGCACTTAGTACTACACACATGACCAATTATCC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATTC
* * **
42741404 GGTACACGTAGTAGTCTGCACTTAGTACTACACACGTGACCTAACCA-TC
1 GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATTC
* * * * * * *
42741453 TGATACACATTGTAGCCTTCACTTAGTACTACATACGTGATCACAGTTTTTG
1 -GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATTC
*
42741505 GGTACGCATAGTAGCCTGCACTTAGTACTACACA
1 GGTACACATAGTAGCCTGCACTTAGTACTACACA
42741539 TGCGACCTCA
Statistics
Matches: 149, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
49 80 0.54
50 36 0.24
51 31 0.21
52 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (49 bp):
GGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATTC
Found at i:42741546 original size:101 final size:99
Alignment explanation
Indices: 42741301--42741546 Score: 280
Period size: 98 Copynumber: 2.5 Consensus size: 99
42741291 TAGCCAAAGC
* * ** *
42741301 TATCTGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-AATTATTCAGTACACGTA
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACCATTCAGTACACATA
42741365 GTAGCCTGCACTTAGTACTACACACATGACCAAT
66 GTAGCCTGCACTTAGTACTACACACATGACCAAT
* * * * * *
42741399 TATCCGGTACACGTAGTAGTCTGCACTTAGTACTACACACGTGACCTAACCA-TCTGATACACAT
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACCATTCAG-TACACAT
* * * * *
42741463 TGTAGCCTTCACTTAGTACTACATACGTGATCACAGT
65 AGTAGCCTGCACTTAGTACTACACACATGA-C-CAAT
* **
42741500 TTTTGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCT
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCT
42741547 CACAATAGAT
Statistics
Matches: 120, Mismatches: 24, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
98 42 0.35
99 35 0.29
100 1 0.01
101 42 0.35
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (99 bp):
TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACCATTCAGTACACATA
GTAGCCTGCACTTAGTACTACACACATGACCAAT
Found at i:42745790 original size:26 final size:25
Alignment explanation
Indices: 42745721--42745790 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 25
42745711 GAGGAAGTGC
* * *
42745721 AAAAGGGCTATGCTCCAG-TTACTG
1 AAAAGGGCTTTGCCCCAGTTTACCG
42745745 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
42745770 AAAAGGGCTTTTGCCCTAGTT
1 AAAAGGGC-TTTGCCCCAGTT
42745791 ATTAAAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 16 0.40
25 13 0.32
26 11 0.28
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:42746057 original size:31 final size:31
Alignment explanation
Indices: 42746010--42746093 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
42746000 CTATTACAGT
* *
42746010 AAAGTCTTTGGCCCAGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
42746041 AAAGGCTTCGGCCCAGTGATATGAATAATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
42746072 AAAGGCTTCGGCCTAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
42746094 CTGAGATTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 5 0.10
31 44 0.90
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:42749701 original size:42 final size:42
Alignment explanation
Indices: 42749655--42749810 Score: 188
Period size: 42 Copynumber: 3.7 Consensus size: 42
42749645 ACTGAGATTA
* *
42749655 CGTGTAAGACCACATCTGGGATATGGCATCGATATTAGACTT
1 CGTGTAAGACCATATCTGGGATATGGCATCGATATAAGACTT
*
42749697 CGTGTAAGACCATATCTAGGATATGGCATCGATATAAGACTT
1 CGTGTAAGACCATATCTGGGATATGGCATCGATATAAGACTT
* * * * **
42749739 TGTGTAAGACCATAGCTGGGCTATTGGCATCGGTACGAGA-TT
1 CGTGTAAGACCATATCTGGGATA-TGGCATCGATATAAGACTT
* *
42749781 ACATGTAATACCATATCTGGGATATGGCAT
1 -CGTGTAAGACCATATCTGGGATATGGCAT
42749811 TGGAACGATA
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
42 66 0.68
43 31 0.32
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGGGATATGGCATCGATATAAGACTT
Found at i:42749788 original size:85 final size:84
Alignment explanation
Indices: 42749656--42749810 Score: 204
Period size: 85 Copynumber: 1.8 Consensus size: 84
42749646 CTGAGATTAC
* ** *
42749656 GTGTAAGACCACATCTGGGATATGGCATCGATATTAGACTTCGTGTAAGACCATATCTAGGATAT
1 GTGTAAGACCACAGCTGGGATATGGCATCGATACGAGACTTCATGTAAGACCATATCTAGGATAT
42749721 GGCATCGATATAAGACTTT
66 GGCATCGATATAAGACTTT
* * * * *
42749740 GTGTAAGACCATAGCTGGGCTATTGGCATCGGTACGAGA-TTACATGTAATACCATATCTGGGAT
1 GTGTAAGACCACAGCTGGGATA-TGGCATCGATACGAGACTT-CATGTAAGACCATATCTAGGAT
42749804 ATGGCAT
64 ATGGCAT
42749811 TGGAACGATA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
84 21 0.35
85 39 0.65
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (84 bp):
GTGTAAGACCACAGCTGGGATATGGCATCGATACGAGACTTCATGTAAGACCATATCTAGGATAT
GGCATCGATATAAGACTTT
Found at i:42752847 original size:39 final size:40
Alignment explanation
Indices: 42752747--42752930 Score: 180
Period size: 39 Copynumber: 4.7 Consensus size: 40
42752737 TCGAATGATG
* * *
42752747 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* ** *
42752786 ATCTGAACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
42752827 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
42752866 TCCGAGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
** *
42752905 AACGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42752931 AATGAGTAGC
Statistics
Matches: 117, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
39 55 0.47
40 52 0.44
41 10 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:42752948 original size:79 final size:78
Alignment explanation
Indices: 42752800--42752963 Score: 188
Period size: 79 Copynumber: 2.1 Consensus size: 78
42752790 GAACTAAGAT
** **
42752800 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATAACGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
42752865 ATCCGAGTTAAGTC
66 ATCCG-GTTAAATC
* * * *
42752879 CCGAAGGCATTTGTGCGAGTTACT-ATAACGGGCTATGTCCCGAAGGCATTTGAATGAG-TAGCT
1 CCGAAGGCATTTGTGCGAGATACTAATAACGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CT
* *
42752942 ATATCCGGTTAAATT
64 AAATCCGGTTAAATC
42752957 CCGAAGG
1 CCGAAGG
42752964 TACGTGATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
78 25 0.35
79 47 0.65
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (78 bp):
CCGAAGGCATTTGTGCGAGATACTAATAACGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGTTAAATC
Found at i:42755572 original size:25 final size:25
Alignment explanation
Indices: 42755508--42755561 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
42755498 TTAGTTTCAA
42755508 TTGAACTTAGACTTTGATCTAAAAT
1 TTGAACTTAGACTTTGATCTAAAAT
42755533 TTGAACTTAGACTTTGATCTAAAAT
1 TTGAACTTAGACTTTGATCTAAAAT
42755558 TTGA
1 TTGA
42755562 GCTTCATCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (25 bp):
TTGAACTTAGACTTTGATCTAAAAT
Found at i:42755796 original size:29 final size:29
Alignment explanation
Indices: 42755762--42755857 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 29
42755752 GATTTTATTT
42755762 TTAATTAGGGTTTTAGGCAAGTTTTAAAA
1 TTAATTAGGGTTTTAGGCAAGTTTTAAAA
* * * * ***
42755791 TTAATTATGGATATATAGAC-CGATTTTATTT
1 TTAATTA-GGGT-TTTAGGCAAG-TTTTAAAA
42755822 TTAATTAGGGTTTTAGGCAAGTTTTAAAA
1 TTAATTAGGGTTTTAGGCAAGTTTTAAAA
42755851 TTAATTA
1 TTAATTA
42755858 TGGATATAGG
Statistics
Matches: 49, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
29 24 0.49
30 8 0.16
31 17 0.35
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (29 bp):
TTAATTAGGGTTTTAGGCAAGTTTTAAAA
Found at i:42755812 original size:60 final size:60
Alignment explanation
Indices: 42755743--42755865 Score: 246
Period size: 60 Copynumber: 2.0 Consensus size: 60
42755733 AAAATAAGGC
42755743 ATATAGACCGATTTTATTTTTAATTAGGGTTTTAGGCAAGTTTTAAAATTAATTATGGAT
1 ATATAGACCGATTTTATTTTTAATTAGGGTTTTAGGCAAGTTTTAAAATTAATTATGGAT
42755803 ATATAGACCGATTTTATTTTTAATTAGGGTTTTAGGCAAGTTTTAAAATTAATTATGGAT
1 ATATAGACCGATTTTATTTTTAATTAGGGTTTTAGGCAAGTTTTAAAATTAATTATGGAT
42755863 ATA
1 ATA
42755866 GGTTGACTTA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (60 bp):
ATATAGACCGATTTTATTTTTAATTAGGGTTTTAGGCAAGTTTTAAAATTAATTATGGAT
Found at i:42755826 original size:31 final size:30
Alignment explanation
Indices: 42755743--42755830 Score: 81
Period size: 29 Copynumber: 2.9 Consensus size: 30
42755733 AAAATAAGGC
*
42755743 ATATAGACCGATTTTATTTTTAATTAGGGT
1 ATATAGACCGATTTTATTTTTAATTAGGAT
* * * ***
42755773 -TTTAG-GCAAGTTTTAAAATTAATTATGGAT
1 ATATAGACCGA-TTTTATTTTTAATTA-GGAT
42755803 ATATAGACCGATTTTATTTTTAATTAGG
1 ATATAGACCGATTTTATTTTTAATTAGG
42755831 GTTTTAGGCA
Statistics
Matches: 41, Mismatches: 13, Indels: 8
0.66 0.21 0.13
Matches are distributed among these distances:
28 2 0.05
29 16 0.39
30 5 0.12
31 16 0.39
32 2 0.05
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (30 bp):
ATATAGACCGATTTTATTTTTAATTAGGAT
Found at i:42755867 original size:29 final size:29
Alignment explanation
Indices: 42755775--42755867 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
42755765 ATTAGGGTTT
42755775 TAGGCAAGTTTTAAAATTAATTATGGATA
1 TAGGCAAGTTTTAAAATTAATTATGGATA
* * *** * * *
42755804 TATAG-ACCGATTTTATTTTTAATTAGGGTTT
1 TA-GGCA-AG-TTTTAAAATTAATTATGGATA
42755835 TAGGCAAGTTTTAAAATTAATTATGGATA
1 TAGGCAAGTTTTAAAATTAATTATGGATA
42755864 TAGG
1 TAGG
42755868 TTGACTTAAC
Statistics
Matches: 44, Mismatches: 16, Indels: 8
0.65 0.24 0.12
Matches are distributed among these distances:
29 22 0.50
30 4 0.09
31 18 0.41
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.42
Consensus pattern (29 bp):
TAGGCAAGTTTTAAAATTAATTATGGATA
Found at i:42756073 original size:9 final size:10
Alignment explanation
Indices: 42756038--42756081 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
42756028 TTCACATCTT
42756038 TCTCTCAAAC
1 TCTCTCAAAC
*
42756048 TCTCTTAAAC
1 TCTCTCAAAC
*
42756058 CCTCTCAAA-
1 TCTCTCAAAC
42756067 TCTCTC-AAC
1 TCTCTCAAAC
42756076 TCTCTC
1 TCTCTC
42756082 GTTTTTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 2 0.07
9 11 0.38
10 16 0.55
ACGTcount: A:0.25, C:0.41, G:0.00, T:0.34
Consensus pattern (10 bp):
TCTCTCAAAC
Found at i:42762557 original size:39 final size:39
Alignment explanation
Indices: 42762503--42762700 Score: 342
Period size: 39 Copynumber: 5.1 Consensus size: 39
42762493 AATTTTATTA
*
42762503 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
42762542 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
* * *
42762581 CCAGCACGAAGCCTGCGGGTCTTTGGCCCGGATATATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
*
42762620 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
*
42762659 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATATATTT
1 CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
42762698 CCA
1 CCA
42762701 TACACATTTC
Statistics
Matches: 149, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 149 1.00
ACGTcount: A:0.23, C:0.30, G:0.24, T:0.23
Consensus pattern (39 bp):
CCAGCACAAAGCCTGCGGGTCTTTAGCCCGGATACATTT
Found at i:42764437 original size:14 final size:15
Alignment explanation
Indices: 42764413--42764443 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
42764403 ATCAAAACAC
42764413 AATATTTTCACATAT
1 AATATTTTCACATAT
42764428 AATA-TTTCACATAT
1 AATATTTTCACATAT
42764442 AA
1 AA
42764444 CAAACATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATTTTCACATAT
Found at i:42764841 original size:23 final size:23
Alignment explanation
Indices: 42764815--42764908 Score: 127
Period size: 23 Copynumber: 4.1 Consensus size: 23
42764805 AAGTTAGAAG
42764815 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
42764838 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
42764861 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
*
42764884 AGTTAAGATG-CTTGAATATGAAA
1 AGTGAAGA-GACTTGAATATGAAA
42764907 AG
1 AG
42764909 ATACACACAT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 60 0.98
24 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.23
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:42769347 original size:23 final size:23
Alignment explanation
Indices: 42769321--42769414 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
42769311 AAGTTAGAAG
42769321 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
42769344 AGTGAAAAAACTTGAATATGAAT
1 AGTGAAGAGACTTGAATATGAAA
*
42769367 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
42769390 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
42769413 AG
1 AG
42769415 ATACACACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.48, C:0.04, G:0.26, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:42769587 original size:48 final size:48
Alignment explanation
Indices: 42769505--42769598 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
42769495 TTTCTTGGCT
* *
42769505 TAAAAACGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
42769553 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
42769599 AGAATTCCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 4 0.10
48 38 0.90
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:42772102 original size:48 final size:48
Alignment explanation
Indices: 42772020--42772113 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
42772010 TTTCTTGGCT
* *
42772020 TAAAAACGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAACCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
42772068 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAAC
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAAC
42772114 AGAATTCCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 4 0.10
48 38 0.90
ACGTcount: A:0.40, C:0.28, G:0.13, T:0.19
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACCG
Found at i:42775380 original size:18 final size:18
Alignment explanation
Indices: 42775357--42775407 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
42775347 TTTATACAAA
*
42775357 TAATTCAGTTAATTCGAG
1 TAATTCGGTTAATTCGAG
* *
42775375 TAATTCGGGTAATTCGAT
1 TAATTCGGTTAATTCGAG
42775393 TAATTCGGTTAATTC
1 TAATTCGGTTAATTC
42775408 TATATTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (18 bp):
TAATTCGGTTAATTCGAG
Found at i:42775678 original size:75 final size:75
Alignment explanation
Indices: 42775555--42775704 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
42775545 GTTAACCGGT
*
42775555 CGGTTAACCGACTGAACACCCTTACTTGTATGATAATAACATTTTATAAAATTTTTATTCCTCAA
1 CGGTTAACCGACTGAACACCCATACTTGTATGATAATAACATTTTATAAAATTTTTATTCCTCAA
42775620 AATTTTCTAC
66 AATTTTCTAC
42775630 CGGTTAACCGACTGAACACCCATACTTGTATGATAATAACATTTTATAAAATTTTTATTCCTCAA
1 CGGTTAACCGACTGAACACCCATACTTGTATGATAATAACATTTTATAAAATTTTTATTCCTCAA
42775695 AATTTTCTAC
66 AATTTTCTAC
42775705 TTTCTTACTC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (75 bp):
CGGTTAACCGACTGAACACCCATACTTGTATGATAATAACATTTTATAAAATTTTTATTCCTCAA
AATTTTCTAC
Found at i:42777553 original size:46 final size:47
Alignment explanation
Indices: 42777374--42777637 Score: 192
Period size: 47 Copynumber: 5.7 Consensus size: 47
42777364 TTTGTATGCT
* * * **
42777374 AGTGTAAGA-TATGTCTGGGACAT-GCATCAGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTACAAGATGA-AGCC
* * * ** * *
42777420 AGTGTAATACCATGTTTGGGACATGGTATCGGC-ATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTA-CAAGATGA-AGCC
* *
42777468 AGTGTAAGA-AATGTCTGGGACATGTGC--CGGCCT-CGAGATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATG-GCATCGG-CTACAAGATG-AAGCC
* *
42777514 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACAAGATG-TGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTACAAGATGAAGCC
* * **
42777558 AGTGTAAGACCATGTCTGGGGCATGGCATCGAGTTGA-TGGATG-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCG-GCT-ACAAGATGAAGCC
42777605 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
42777638 ATTATACCCT
Statistics
Matches: 174, Mismatches: 30, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
44 13 0.07
45 15 0.09
46 57 0.33
47 66 0.38
48 23 0.13
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCTACAAGATGAAGCC
Found at i:42782265 original size:127 final size:126
Alignment explanation
Indices: 42781948--42782266 Score: 460
Period size: 126 Copynumber: 2.5 Consensus size: 126
42781938 GGATATTCAA
* * * * * ** *
42781948 TTATTTGGTCCAACGAAAAACCCAAACCCAACACGTTAGGGCATAATTTCTCGGATTTCCAAACA
1 TTATTTGGACAAACGAAAAACCGAATCCCAGCACGTTAGGGCACGATTTCTCGAATTTCCAAACA
42782013 TAGAACATTGCCTTGTTTTGAAGTTTTGAAAACACAGACGAAATTTTAAAGGGATATTTGG
66 TAGAACATTGCCTTGTTTTGAAGTTTTGAAAACACAGACGAAATTTTAAAGGGATATTTGG
* * * *
42782074 TTATTTAGACAAAC-AGAAAATCGAATCCCAGCACGTTAGGGCACGATTTCTCAAATTTCTAAAC
1 TTATTTGGACAAACGA-AAAACCGAATCCCAGCACGTTAGGGCACGATTTCTCGAATTTCCAAAC
* * * *
42782138 ATAGAACATTGCCTTGTTTTGAAGTTTTGAAGACACAGACGAGATTTTAATGGGGGTATTTGG
65 ATAGAACATTGCCTTGTTTTGAAGTTTTGAAAACACAGACGAAATTTTAA-AGGGATATTTGG
*
42782201 TTATTTGGACAAACGAAAAACCGAATCCCAGCGCGTTAGGGCACGATTTCTCGAATTTCCAAACA
1 TTATTTGGACAAACGAAAAACCGAATCCCAGCACGTTAGGGCACGATTTCTCGAATTTCCAAACA
42782266 T
66 T
42782267 CAAACAATAT
Statistics
Matches: 169, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
125 1 0.01
126 98 0.58
127 69 0.41
128 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (126 bp):
TTATTTGGACAAACGAAAAACCGAATCCCAGCACGTTAGGGCACGATTTCTCGAATTTCCAAACA
TAGAACATTGCCTTGTTTTGAAGTTTTGAAAACACAGACGAAATTTTAAAGGGATATTTGG
Found at i:42782362 original size:18 final size:20
Alignment explanation
Indices: 42782339--42782376 Score: 53
Period size: 18 Copynumber: 1.9 Consensus size: 20
42782329 AATTCCATTT
42782339 AGAAAA-CTTTAC-TAAAAA
1 AGAAAATCTTTACATAAAAA
42782357 AGAAAATTCTTTACATAAAA
1 AGAAAA-TCTTTACATAAAA
42782377 TGGGCTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.58, C:0.11, G:0.05, T:0.26
Consensus pattern (20 bp):
AGAAAATCTTTACATAAAAA
Found at i:42785731 original size:126 final size:126
Alignment explanation
Indices: 42785538--42785841 Score: 448
Period size: 126 Copynumber: 2.4 Consensus size: 126
42785528 TTTGTCCAAT
* * * * * *
42785538 GAAAAATCGAAA-CCCAACATGTTAGGGCACAATTTCTCGGATTTTCAAACATAGAACATTGCTT
1 GAAAAATC-AAATCCCAACACGTTAGGGCACAATTTCTCGAATTTCCAAACATAGAAAATTACCT
42785602 TGTTTAAAAGTTTTGAAAACACGGATGAAATTTTAAAGGGATATTTGGTTATTTGGACAAAC
65 TGTTTAAAAGTTTTGAAAACACGGATGAAATTTTAAAGGGATATTTGGTTATTTGGACAAAC
* * *
42785664 GGAAAATCAAATCCCAGCACGTTAGGGCACAATTTCTCAAATTTCCAAACATAGAAAATTACCTT
1 GAAAAATCAAATCCCAACACGTTAGGGCACAATTTCTCGAATTTCCAAACATAGAAAATTACCTT
** * *
42785729 GTTTTGAAGTTTTGAAAGCACGGATGAAATTTTAAAGGGGTATTTGGTTATTTGGACAAAC
66 GTTTAAAAGTTTTGAAAACACGGATGAAATTTTAAAGGGATATTTGGTTATTTGGACAAAC
** *
42785790 GAAAAATTGAATCCCAACACGTTAGGGCACGATTTCTCGAATTTCCAAACAT
1 GAAAAATCAAATCCCAACACGTTAGGGCACAATTTCTCGAATTTCCAAACAT
42785842 CAAACATTGC
Statistics
Matches: 158, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
125 3 0.02
126 155 0.98
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (126 bp):
GAAAAATCAAATCCCAACACGTTAGGGCACAATTTCTCGAATTTCCAAACATAGAAAATTACCTT
GTTTAAAAGTTTTGAAAACACGGATGAAATTTTAAAGGGATATTTGGTTATTTGGACAAAC
Found at i:42788580 original size:44 final size:45
Alignment explanation
Indices: 42788417--42788866 Score: 220
Period size: 45 Copynumber: 9.9 Consensus size: 45
42788407 AAGAGATTTG
* * * * * * *
42788417 TAGCTTCGATCTACTCCGCTGGAACTTAAAGGAGAT-AGGAACTGG
1 TAGCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGG-ACTGC
** * *
42788462 TAATTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTA-TG-
1 TAGCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGG---ACTGC
* ** * ** *
42788508 TA-TTTTTATCTTGCTCTACTGCAACTTTAGAAAGATAAGGA-TGG
1 TAGCTTCAATC-TGCTCCACTGCAACTTTAGGGAGATAAGGACTGC
** *
42788552 TAGCTTTGATCTGCTCCACTGTAACTTTAGGGAGATAA-GATCTGC
1 TAGCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGGA-CTGC
* *
42788597 TATCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAA-GATCTGT
1 TAGCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGGA-CTGC
* * * *
42788642 TATCTTCAATCTACTCCACTGCAATTTTAGAGAGATAA-GATCTGC
1 TAGCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGGA-CTGC
* * * * ** *
42788687 TATCTTCAATCTGCTCCAGTGCAAATTCAAAGAGATAA-GATCTGTTTATTTA
1 TAGCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGGA-CTG-------C
* * * * *
42788739 TAGCTTCAATCTGTTCCACTGTAACTTCAGGGAAATAA-GATTCGC
1 TAGCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGGACT-GC
* * * ** * * **
42788784 TATCTTTAGTCTGCTCTGCTTCAACTTCAGGGAGATAA-GACTTA
1 TAGCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGGACTGC
* *
42788828 TGGCTTCAATCTGCTCCACTGCCACTTTAGGGAGATAAG
1 TAGCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAG
42788867 ATTTTCCATG
Statistics
Matches: 318, Mismatches: 70, Indels: 34
0.75 0.17 0.08
Matches are distributed among these distances:
43 5 0.02
44 54 0.17
45 192 0.60
46 30 0.09
47 2 0.01
48 1 0.00
51 1 0.00
52 33 0.10
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (45 bp):
TAGCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGGACTGC
Found at i:42788623 original size:45 final size:45
Alignment explanation
Indices: 42788466--42788868 Score: 309
Period size: 45 Copynumber: 8.8 Consensus size: 45
42788456 AACTGGTAAT
* * * *
42788466 TTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATG-TAT-
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAA-G-ATCTGCTATC
** * ** * *
42788511 TTTTATCTTGCTCTACTGCAACTTTAGAAAGATAAGGA--TGGTAGC
1 TTCAATC-TGCTCCACTGCAACTTTAGGGAGATAA-GATCTGCTATC
** *
42788556 TTTGATCTGCTCCACTGTAACTTTAGGGAGATAAGATCTGCTATC
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGCTATC
*
42788601 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGTTATC
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGCTATC
* * *
42788646 TTCAATCTACTCCACTGCAATTTTAGAGAGATAAGATCTGCTATC
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGCTATC
* * * ** *
42788691 TTCAATCTGCTCCAGTGCAAATTCAAAGAGATAAGATCTGTTTATTTATAGC
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTG-----CTAT--C
* * * *
42788743 TTCAATCTGTTCCACTGTAACTTCAGGGAAATAAGAT-TCGCTATC
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCT-GCTATC
* * ** * *
42788788 TTTAGTCTGCTCTGCTTCAACTTCAGGGAGATAAGA-CT--TATGGC
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGCTAT--C
*
42788832 TTCAATCTGCTCCACTGCCACTTTAGGGAGATAAGAT
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
42788869 TTTCCATGAT
Statistics
Matches: 288, Mismatches: 53, Indels: 34
0.77 0.14 0.09
Matches are distributed among these distances:
42 3 0.01
43 4 0.01
44 55 0.19
45 162 0.56
46 25 0.09
47 3 0.01
50 3 0.01
51 1 0.00
52 32 0.11
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (45 bp):
TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGCTATC
Found at i:42788659 original size:90 final size:91
Alignment explanation
Indices: 42788466--42788868 Score: 340
Period size: 90 Copynumber: 4.4 Consensus size: 91
42788456 AACTGGTAAT
* * * * ** *
42788466 TTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATG-TAT-TTTTATCTTGCTCTACTG
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAA-G-ATCTGCTATCTTCAATC-TGCTCCACTG
* ** *
42788529 CAACTTTAGAAAGATAAGGA--TGGTA-GC
63 CAACTTCAGGGAGATAA-GATCTGTTATGC
** *
42788556 TTTGATCTGCTCCACTGTAACTTTAGGGAGATAAGATCTGCTATCTTCAATCTGCTCCACTGCAA
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGCTATCTTCAATCTGCTCCACTGCAA
*
42788621 CTTTAGGGAGATAAGATCTGTTAT-C
66 CTTCAGGGAGATAAGATCTGTTATGC
* * * *
42788646 TTCAATCTACTCCACTGCAATTTTAGAGAGATAAGATCTGCTATCTTCAATCTGCTCCAGTGCAA
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGCTATCTTCAATCTGCTCCACTGCAA
* **
42788711 ATTCAAAGAGATAAGATCTGTTTATTTATAGC
66 CTTCAGGGAGATAAGATCTG-----TTAT-GC
* * * * * * ** *
42788743 TTCAATCTGTTCCACTGTAACTTCAGGGAAATAAGAT-TCGCTATCTTTAGTCTGCTCTGCTTCA
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCT-GCTATCTTCAATCTGCTCCACTGCA
42788807 ACTTCAGGGAGATAAGA-C--TTATGGC
65 ACTTCAGGGAGATAAGATCTGTTAT-GC
*
42788832 TTCAATCTGCTCCACTGCCACTTTAGGGAGATAAGAT
1 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
42788869 TTTCCATGAT
Statistics
Matches: 254, Mismatches: 46, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
88 5 0.02
89 66 0.26
90 113 0.44
95 4 0.02
96 2 0.01
97 64 0.25
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (91 bp):
TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGCTATCTTCAATCTGCTCCACTGCAA
CTTCAGGGAGATAAGATCTGTTATGC
Found at i:42788699 original size:135 final size:134
Alignment explanation
Indices: 42788466--42788868 Score: 357
Period size: 135 Copynumber: 2.9 Consensus size: 134
42788456 AACTGGTAAT
* * * *
42788466 TTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTATGTAT-TTTTATCTTGCTCTACTGC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAA-GATTGT-TATCTTTAATC-TGCTCTACTGC
* * ** *
42788530 AACTTTAGAAAGATAAGGA-TGGTAGCTTTGATCTGCTCCACTGTAACTTTAGGGAGATAAGATC
63 AACTTTAGAGAGATAA-GACT-GTATCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATC
42788594 TG-CTAT-C
126 TGTCTATAC
* * * *
42788601 TTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGTTATCTTCAATCTACTCCACTGCAA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGTTATCTTTAATCTGCTCTACTGCAA
* * * * **
42788666 TTTTAGAGAGATAAGATCTGCTATCTTCAATCTGCTCCAGTGCAAATTCAAAGAGATAAGATCTG
65 CTTTAGAGAGATAAGA-CTG-TATCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTG
*
42788731 TTTATTTATAGC
128 ----TCTATA-C
* * * * * * *
42788743 TTCAATCTGTTCCACTGTAACTTCAGGGAAATAAGATTCGCTATCTTTAGTCTGCTCTGCTTCAA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTTATCTTTAATCTGCTCTACTGCAA
* * *
42788808 CTTCAGGGAGATAAGACT-TATGGCTTCAATCTGCTCCACTGCCACTTTAGGGAGATAAGAT
65 CTTTAGAGAGATAAGACTGTAT--CTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGAT
42788869 TTTCCATGAT
Statistics
Matches: 213, Mismatches: 40, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
133 2 0.01
134 29 0.14
135 75 0.35
139 3 0.01
140 3 0.01
141 35 0.16
142 66 0.31
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (134 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTTATCTTTAATCTGCTCTACTGCAAC
TTTAGAGAGATAAGACTGTATCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATCTGTCT
ATAC
Found at i:42790709 original size:47 final size:46
Alignment explanation
Indices: 42790635--42790950 Score: 213
Period size: 47 Copynumber: 6.7 Consensus size: 46
42790625 GATTTCTTGT
*
42790635 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGACCACATTATGA
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGACCACATGATGA
* * * * *
42790681 GTGCTAGTATAAGACCATGTCTGGGACATGGTATCG-GCACAGAGACGA
1 GTGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCACA-TGATGA
* * * *
42790729 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACGATGA
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGACCAC-ATGATGA
* * * * *
42790776 -TAGCTAGTGTAAGACGTGTCTGGGACACGCATCGGCTA-A-GA-GTT
1 GT-GCTAGTGTAAGACATGTCTGGGACATGCATCGACCACATGATG-A
42790820 GTGCTAGTGTAAGACAT-TCTGGGACATGCATC-A--ACATGTATATACGA
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGACCACATG---AT--GA
* * * * *
42790867 GAGCTAGTATAAGACCAT-TCTAGGACATGGCATCAACCTCGATGATGA
1 GTGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCAC-ATGATGA
*
42790915 -TAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GT-GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCG
42790951 GCAACTTATC
Statistics
Matches: 214, Mismatches: 32, Indels: 45
0.74 0.11 0.15
Matches are distributed among these distances:
40 1 0.00
41 1 0.00
42 1 0.00
43 15 0.07
44 16 0.07
45 3 0.01
46 19 0.09
47 81 0.38
48 50 0.23
49 20 0.09
50 3 0.01
52 1 0.00
53 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (46 bp):
GTGCTAGTGTAAGACATGTCTGGGACATGCATCGACCACATGATGA
Found at i:42790801 original size:94 final size:91
Alignment explanation
Indices: 42790635--42790851 Score: 253
Period size: 94 Copynumber: 2.4 Consensus size: 91
42790625 GATTTCTTGT
**
42790635 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGACCACATTATGAGTGCTAGTATAAGACCATG
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGACCACACGATGAGTGCTAGTATAAGACCATG
* *
42790700 TCTGGGACATGGTATCGGC-ACAGAGACGA
66 TCTGGGACA-CGCATCGGCTA-AGAG--GA
* * * * *
42790729 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACGATGA-TAGCTAGTGTAAGA-CG
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGACCAC-ACGATGAGT-GCTAGTATAAGACCA
**
42790792 TGTCTGGGACACGCATCGGCTAAGAGTT
64 TGTCTGGGACACGCATCGGCTAAGAGGA
42790820 GTGCTAGTGTAAGACAT-TCTGGGACATGCATC
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATC
42790852 AACATGTATA
Statistics
Matches: 108, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
90 15 0.14
91 16 0.15
93 11 0.10
94 50 0.46
95 16 0.15
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (91 bp):
GTGCTAGTGTAAGACATGTCTGGGACATGCATCGACCACACGATGAGTGCTAGTATAAGACCATG
TCTGGGACACGCATCGGCTAAGAGGA
Found at i:42790893 original size:91 final size:93
Alignment explanation
Indices: 42790633--42790900 Score: 250
Period size: 94 Copynumber: 2.9 Consensus size: 93
42790623 CAGATTTCTT
*
42790633 GTGTGCTAGTGTAAGACATGTCTGGGACATGCATCGACCACAT--TAT-GAGTGCTAGTATAAGA
1 GTGTGCTAGTGTAAGACATGTCTGGGACATGCATC-A--ACATGATATAGAGAGCTAGTATAAGA
* *
42790695 CCATGTCTGGGACATGGTATCGGCACAGAGA
63 CCATGTCTGGGACATCGCATCGGCACAGAGA
* * ** * * * *
42790726 CGAGTGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGACGAT-GATAGCTAGTGTAAGA
1 -GTGTGCTAGTGTAAGACATGTCTGGGACATGCATCAACAT-GA-TATAGAGAGCTAGTATAAGA
*
42790790 -CGTGTCTGGGACA-CGCATCGGCTA-AGAG-
63 CCATGTCTGGGACATCGCATCGGC-ACAGAGA
*
42790818 TTGTGCTAGTGTAAGACAT-TCTGGGACATGCATCAACATGTATATACGAGAGCTAGTATAAGAC
1 GTGTGCTAGTGTAAGACATGTCTGGGACATGCATCAACATG-ATATA-GAGAGCTAGTATAAGAC
* *
42790882 CAT-TCTAGGACATGGCATC
64 CATGTCTGGGACATCGCATC
42790901 AACCTCGATG
Statistics
Matches: 140, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
89 3 0.02
90 18 0.13
91 40 0.29
92 7 0.05
93 11 0.08
94 46 0.33
95 15 0.11
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (93 bp):
GTGTGCTAGTGTAAGACATGTCTGGGACATGCATCAACATGATATAGAGAGCTAGTATAAGACCA
TGTCTGGGACATCGCATCGGCACAGAGA
Found at i:42790928 original size:48 final size:48
Alignment explanation
Indices: 42790825--42790949 Score: 141
Period size: 48 Copynumber: 2.6 Consensus size: 48
42790815 GAGTTGTGCT
*
42790825 AGTGTAAGA-CATTCTGGGACAT-GCATCAACATGTATATACGAGAGCT
1 AGTGTAAGACCATTCTGGGACATGGCATCAACATGTATATA-GAGAGCC
* * * *
42790872 AGTATAAGACCATTCTAGGACATGGCATCAACCTCG-ATGAT-GATAGCC
1 AGTGTAAGACCATTCTGGGACATGGCATCAACAT-GTAT-ATAGAGAGCC
42790920 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGACCAT-TCTGGGACATGGCATC
42790950 GGCAACTTAT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
47 8 0.12
48 29 0.44
49 26 0.39
50 3 0.05
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATTCTGGGACATGGCATCAACATGTATATAGAGAGCC
Found at i:42798135 original size:35 final size:35
Alignment explanation
Indices: 42798095--42798166 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
42798085 TCCTACATAC
* *
42798095 CATGTGAGGATAAAGTCGACCCGCTCAACCCTACA
1 CATGTGAGGATAAAGTCGACCCACCCAACCCTACA
*
42798130 CATGTGGGGATAAAGTCGACCCACCCAACCCTACA
1 CATGTGAGGATAAAGTCGACCCACCCAACCCTACA
42798165 CA
1 CA
42798167 CCAAGTCCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.33, G:0.19, T:0.15
Consensus pattern (35 bp):
CATGTGAGGATAAAGTCGACCCACCCAACCCTACA
Found at i:42798785 original size:16 final size:16
Alignment explanation
Indices: 42798761--42798799 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
42798751 AGAACCCATA
*
42798761 TTTCGGCTTTTCACCT
1 TTTCAGCTTTTCACCT
**
42798777 TTTCAGCTTTTCGGCT
1 TTTCAGCTTTTCACCT
42798793 TTTCAGC
1 TTTCAGC
42798800 CTTTGTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.08, C:0.28, G:0.15, T:0.49
Consensus pattern (16 bp):
TTTCAGCTTTTCACCT
Found at i:42798811 original size:24 final size:23
Alignment explanation
Indices: 42798761--42798811 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 23
42798751 AGAACCCATA
42798761 TTTCGGCTTTTCACCTTTTCAGCT
1 TTTCGGCTTTTCACCTTTTCA-CT
42798785 TTTCGGCTTTTCAGCCTTTGTCA-T
1 TTTCGGCTTTTCA-CCTTT-TCACT
42798809 TTT
1 TTT
42798812 ACATCTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 17 0.68
25 5 0.20
26 3 0.12
ACGTcount: A:0.08, C:0.25, G:0.14, T:0.53
Consensus pattern (23 bp):
TTTCGGCTTTTCACCTTTTCACT
Found at i:42806582 original size:43 final size:43
Alignment explanation
Indices: 42806513--42806956 Score: 595
Period size: 43 Copynumber: 10.2 Consensus size: 43
42806503 CGGGGTAAAT
* * *
42806513 CTAGCAGGCTTCGTGCCGGTGTTGTGTATTCAGGCCTTCGTAC
1 CTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGC
*
42806556 CTAGCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGC
1 CTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGC
*
42806599 CTAGTAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGC
1 CTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGC
*
42806642 CTAGCAGGCTTTGTGCCGGTGATGTGTATTCGGGCCTTCGTGC
1 CTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGC
42806685 CTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGC
1 CTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGC
*
42806728 CTAACAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGC
1 CTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGC
* * *
42806771 CTTGCAGGCTTCGTGCCGGTAATGTGTATTCGGGCCTTCGTGT
1 CTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGC
* *
42806814 CTAGCAGGCTTCGTACTGGTGATGTGTATTCGGGCCTTCGTGC
1 CTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGC
* ** * * * *
42806857 CTAGCATGCTAT-GATGCCGGTGAAATACTCTTCGGGCCTTTGAGC
1 CTAGCAGGCT-TCG-TGCCGGTGATGT-GTATTCGGGCCTTCGTGC
** * * * *
42806902 CTAGCAGGCTATAATGCTGGTGA-GATACTATTCGGGCTTTCGAGC
1 CTAGCAGGCT-TCGTGCCGGTGATG-T-GTATTCGGGCCTTCGTGC
42806947 CTAGCAGGCT
1 CTAGCAGGCT
42806957 ATAGTACCGG
Statistics
Matches: 361, Mismatches: 35, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
43 292 0.81
44 9 0.02
45 60 0.17
ACGTcount: A:0.13, C:0.24, G:0.32, T:0.31
Consensus pattern (43 bp):
CTAGCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGC
Found at i:42810970 original size:16 final size:16
Alignment explanation
Indices: 42810945--42810983 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
42810935 ACAACCCACG
*
42810945 TTTT-GGCTTTTCACC
1 TTTTCGGCTTTTCAAC
42810960 TTTTCGGCTTTTCAAC
1 TTTTCGGCTTTTCAAC
42810976 TTTTCGGC
1 TTTTCGGC
42810984 CTTTGTCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.08, C:0.26, G:0.15, T:0.51
Consensus pattern (16 bp):
TTTTCGGCTTTTCAAC
Found at i:42815898 original size:40 final size:40
Alignment explanation
Indices: 42815853--42815991 Score: 165
Period size: 40 Copynumber: 3.5 Consensus size: 40
42815843 GGATATAGCT
*
42815853 ACTCGTTCAAATGCCTTCGGGACATAACCC-GATTATAGTA
1 ACTCGTACAAATGCCTTCGGGACATAACCCGGATT-TAGTA
*
42815893 ACTCGTACAAATGCCTTCGGGACTTAACCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGGACATAACCCGGATTTAGTA
* * * * * *
42815933 ACTCGCACCAATGCCTTCGGG-CTTAGCACGGAATTAGTA
1 ACTCGTACAAATGCCTTCGGGACATAACCCGGATTTAGTA
* *
42815972 TCTCGCACAAATGCCTTCGG
1 ACTCGTACAAATGCCTTCGG
42815992 ATCTTAGTTC
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 33 0.37
40 52 0.58
41 4 0.04
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
ACTCGTACAAATGCCTTCGGGACATAACCCGGATTTAGTA
Found at i:42823415 original size:79 final size:81
Alignment explanation
Indices: 42823306--42823488 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
42823296 TACTCGTTCA
* *
42823306 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
42823369 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
* **
42823386 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
42823449 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
42823465 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
42823489 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:42823488 original size:40 final size:40
Alignment explanation
Indices: 42823285--42823488 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
42823275 CGGAATTTAA
** *
42823285 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42823325 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42823365 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42823404 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
42823444 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42823484 CCGGA
1 CCGGA
42823489 CATCATTCGA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 93 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42892971 original size:21 final size:22
Alignment explanation
Indices: 42892945--42892988 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
42892935 TCTCTTCCTT
42892945 TATTTTT-TAGTAATGGTCGAA
1 TATTTTTGTAGTAATGGTCGAA
*
42892966 TATTTTTGTATTAATGGTCGAA
1 TATTTTTGTAGTAATGGTCGAA
42892988 T
1 T
42892989 TCTATCATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (22 bp):
TATTTTTGTAGTAATGGTCGAA
Found at i:42904503 original size:46 final size:45
Alignment explanation
Indices: 42904453--42904625 Score: 190
Period size: 46 Copynumber: 3.8 Consensus size: 45
42904443 TGGTTGAGCA
42904453 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
42904499 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
42904546 TCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
42904592 -CCTGAGCTCGTTGAGTTGAGTCTGAGTTCACTTA
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA
42904626 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 3 0.03
46 63 0.59
47 32 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:42904609 original size:93 final size:93
Alignment explanation
Indices: 42904450--42904620 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
42904440 GGATGGTTGA
*
42904450 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
42904515 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
42904543 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
*
42904607 TTGAGTCTGAGTTC
65 TTGAGTCCGAGTTC
42904621 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:42910225 original size:47 final size:49
Alignment explanation
Indices: 42910105--42910282 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 49
42910095 TGTAACCCGC
* * *
42910105 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGG--G-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
42910151 CCAT-AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-A-TTCACAT
* *
42910200 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
*
42910243 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
42910283 TCAACCATCC
Statistics
Matches: 111, Mismatches: 8, Indels: 23
0.78 0.06 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 31 0.28
46 33 0.30
47 31 0.28
48 3 0.03
49 3 0.03
50 2 0.02
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCATTCACAT
Found at i:42912689 original size:15 final size:15
Alignment explanation
Indices: 42912665--42912757 Score: 109
Period size: 15 Copynumber: 6.2 Consensus size: 15
42912655 CAAGAAACGA
42912665 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
42912680 ATAGAGAAATCC-AG
1 ATAAAGAAATCCAAG
42912694 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
*
42912709 AATAAAGAAATCCAAA
1 -ATAAAGAAATCCAAG
* *
42912725 ATAAAGAGATCCAGG
1 ATAAAGAAATCCAAG
*
42912740 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
42912755 ATA
1 ATA
42912758 CGATACTATG
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
14 2 0.03
15 64 0.96
16 1 0.01
ACGTcount: A:0.58, C:0.14, G:0.15, T:0.13
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:42912698 original size:30 final size:30
Alignment explanation
Indices: 42912663--42912748 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 30
42912653 AACAAGAAAC
*
42912663 GAATAAAGAAATCCAAGATAGAGAAATCCA
1 GAATAAAGAAATCCAAGATAAAGAAATCCA
42912693 GAATAAAGAAATCC-AGAATAAAGAAATCCA
1 GAATAAAGAAATCCAAG-ATAAAGAAATCCA
* * *
42912723 AAATAAAGAGATCCAGGATAAAGAAA
1 GAATAAAGAAATCCAAGATAAAGAAA
42912749 CCCAAGATAC
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.04
30 47 0.94
31 1 0.02
ACGTcount: A:0.59, C:0.12, G:0.16, T:0.13
Consensus pattern (30 bp):
GAATAAAGAAATCCAAGATAAAGAAATCCA
Found at i:42912717 original size:45 final size:45
Alignment explanation
Indices: 42912663--42912748 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
42912653 AACAAGAAAC
* *
42912663 GAATAAAGAAATCCAAGATAGAGAAATCCAGAATAAAGAAATCCA
1 GAATAAAGAAATCCAAAATAAAGAAATCCAGAATAAAGAAATCCA
* *
42912708 GAATAAAGAAATCCAAAATAAAGAGATCCAGGATAAAGAAA
1 GAATAAAGAAATCCAAAATAAAGAAATCCAGAATAAAGAAA
42912749 CCCAAGATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.59, C:0.12, G:0.16, T:0.13
Consensus pattern (45 bp):
GAATAAAGAAATCCAAAATAAAGAAATCCAGAATAAAGAAATCCA
Found at i:42915780 original size:47 final size:49
Alignment explanation
Indices: 42915662--42915838 Score: 189
Period size: 47 Copynumber: 3.8 Consensus size: 49
42915652 TGTAACCCGC
* *
42915662 CCATAAGCGAACTCGGACTCAACTCAACGAGCTC-G--G-C-GTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTT-ACAT
*
42915707 CCAT-AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCC-AGTTACAT
* * *
42915756 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA---CATTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACAT
*
42915799 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGC
42915839 TCACCATCCT
Statistics
Matches: 111, Mismatches: 8, Indels: 22
0.79 0.06 0.16
Matches are distributed among these distances:
43 6 0.05
44 29 0.26
45 7 0.06
46 29 0.26
47 31 0.28
48 3 0.03
49 3 0.03
50 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (49 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGATGCCAGTTACAT
Found at i:42915827 original size:93 final size:91
Alignment explanation
Indices: 42915669--42915838 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 91
42915659 CGCCCATAAG
*
42915669 CGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAGTGAACTCGGACTCAACTCAAC
1 CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAGTGAACTCGGACTCAACTCAAC
42915734 GAGTTCGGATGCCTAGTTACATCTCA
66 GAGTTCGGATGCCTAGTTACATCTCA
* *
42915760 CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCAT-AGTGAACTCGGACTCAACTCA
42915825 ACGAGTTCGGATGC
64 ACGAGTTCGGATGC
42915839 TCACCATCCT
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
91 28 0.38
92 11 0.15
93 35 0.47
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (91 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCA
Found at i:42927999 original size:23 final size:23
Alignment explanation
Indices: 42927972--42928024 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
42927962 TCTTTTTCTC
* *
42927972 TCACTTTCTCTTTAAATTTCTTT
1 TCACTCTCTCTTTAAAGTTCTTT
* *
42927995 TCACTCTCTTTTTCAAGTTCTTT
1 TCACTCTCTCTTTAAAGTTCTTT
*
42928018 TCTCTCT
1 TCACTCT
42928025 ATGATTTCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.13, C:0.26, G:0.02, T:0.58
Consensus pattern (23 bp):
TCACTCTCTCTTTAAAGTTCTTT
Found at i:42938411 original size:23 final size:25
Alignment explanation
Indices: 42938366--42938424 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 25
42938356 CTTATTTTCT
*
42938366 TCTCATTTTTTTTCCATTATCAATC
1 TCTCATTTTTTTTCCATTATCAAAC
42938391 TCTCATTTTCTTTT-C-TT-TCAAAC
1 TCTCATTTT-TTTTCCATTATCAAAC
*
42938414 TCTCATGTTTT
1 TCTCATTTTTT
42938425 CACACCCCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 2 0.06
23 13 0.42
24 2 0.06
25 10 0.32
26 4 0.13
ACGTcount: A:0.17, C:0.24, G:0.02, T:0.58
Consensus pattern (25 bp):
TCTCATTTTTTTTCCATTATCAAAC
Found at i:42943037 original size:20 final size:21
Alignment explanation
Indices: 42943000--42943042 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
42942990 GAACTTTTTT
42943000 AAAATAATATTGAAAATA-AAA
1 AAAATAATATTG-AAATAGAAA
42943021 AAAATAATACTTG-AATAGAAA
1 AAAATAATA-TTGAAATAGAAA
42943042 A
1 A
42943043 CTAACTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.20
21 13 0.65
22 3 0.15
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.23
Consensus pattern (21 bp):
AAAATAATATTGAAATAGAAA
Found at i:42943042 original size:22 final size:21
Alignment explanation
Indices: 42943000--42943042 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
42942990 GAACTTTTTT
*
42943000 AAAATAATATTGAAAATAAAA
1 AAAATAATATTGAAAAGAAAA
*
42943021 AAAATAATACTTGAATAGAAAA
1 AAAATAATA-TTGAAAAGAAAA
42943043 CTAACTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.23
Consensus pattern (21 bp):
AAAATAATATTGAAAAGAAAA
Found at i:42945693 original size:50 final size:52
Alignment explanation
Indices: 42945629--42945747 Score: 170
Period size: 50 Copynumber: 2.3 Consensus size: 52
42945619 TTAATAAAGT
* *
42945629 CATGCATTATGTAACTCTCATGTTAGTT-AAGTTTGCATCA-TAAATTATGA
1 CATGCATTATGTAACTCTCATGTTAGTTAAAGTTTACATCATTAAATTAAGA
* *
42945679 CATGCATTATGTAACTCTCATTTTAGTTAAAGTTTACATCATTAAATTAAGT
1 CATGCATTATGTAACTCTCATGTTAGTTAAAGTTTACATCATTAAATTAAGA
* *
42945731 CATGAATTAAGTAACTC
1 CATGCATTATGTAACTC
42945748 ATTTGTTCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 27 0.44
51 11 0.18
52 23 0.38
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (52 bp):
CATGCATTATGTAACTCTCATGTTAGTTAAAGTTTACATCATTAAATTAAGA
Found at i:42945750 original size:50 final size:50
Alignment explanation
Indices: 42945616--42945751 Score: 159
Period size: 50 Copynumber: 2.7 Consensus size: 50
42945606 ATGTGTTCTA
* * * *
42945616 CATTTAATAAAGTCATGCATTATGTAACTCTCATGTTAGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTATGTAAC-CTCATTTTAGTTAAGTTTACAT
* *
42945667 CA-TAAATTATGACATGCATTATGTAACTCTCATTTTAGTTAAAGTTTACAT
1 CATTAAATTAAGTCATGCATTATGTAAC-CTCATTTTAGTT-AAGTTTACAT
* *
42945718 CATTAAATTAAGTCATGAATTAAGTAA-CTCATTT
1 CATTAAATTAAGTCATGCATTATGTAACCTCATTT
42945752 GTTCATTTAG
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
50 40 0.55
51 13 0.18
52 20 0.27
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Consensus pattern (50 bp):
CATTAAATTAAGTCATGCATTATGTAACCTCATTTTAGTTAAGTTTACAT
Found at i:42946184 original size:13 final size:13
Alignment explanation
Indices: 42946166--42946193 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42946156 AAGGGGCATC
42946166 AATTAAACACATT
1 AATTAAACACATT
42946179 AATTAAACACATT
1 AATTAAACACATT
42946192 AA
1 AA
42946194 GGATACACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (13 bp):
AATTAAACACATT
Found at i:42948500 original size:14 final size:14
Alignment explanation
Indices: 42948481--42948528 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 14
42948471 TTATTTGATC
42948481 AATTAATTTAGATT
1 AATTAATTTAGATT
**
42948495 AATTAA-TT-GAAA
1 AATTAATTTAGATT
42948507 AATTAATTTAGATT
1 AATTAATTTAGATT
42948521 AATTAATT
1 AATTAATT
42948529 GAAAATATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 8 0.29
13 4 0.14
14 16 0.57
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (14 bp):
AATTAATTTAGATT
Found at i:42948504 original size:26 final size:26
Alignment explanation
Indices: 42948481--42948533 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
42948471 TTATTTGATC
42948481 AATTAATTTAGATTAATTAATTGAAA
1 AATTAATTTAGATTAATTAATTGAAA
42948507 AATTAATTTAGATTAATTAATTGAAA
1 AATTAATTTAGATTAATTAATTGAAA
42948533 A
1 A
42948534 TATTCTCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.42
Consensus pattern (26 bp):
AATTAATTTAGATTAATTAATTGAAA
Found at i:42951050 original size:21 final size:21
Alignment explanation
Indices: 42951021--42951076 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
42951011 TGTGGAGGCC
* **
42951021 CACATGCCCATGTGCAAGCTA
1 CACACGCCCATGTGCAAGAGA
* * *
42951042 CACACGCCCGTGTGGAGGAGA
1 CACACGCCCATGTGCAAGAGA
42951063 CACACGCCCATGTG
1 CACACGCCCATGTG
42951077 ACCAAGTTAC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.34, G:0.27, T:0.14
Consensus pattern (21 bp):
CACACGCCCATGTGCAAGAGA
Found at i:42954688 original size:22 final size:22
Alignment explanation
Indices: 42954663--42954706 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
42954653 ATGAGTCCAA
42954663 TATTGTATT-TATTAGTTATTTT
1 TATTGTATTAT-TTAGTTATTTT
* *
42954685 TATTTTATTATTTATTTATTTT
1 TATTGTATTATTTAGTTATTTT
42954707 GAATTTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (22 bp):
TATTGTATTATTTAGTTATTTT
Found at i:42961073 original size:54 final size:54
Alignment explanation
Indices: 42960883--42961143 Score: 330
Period size: 54 Copynumber: 4.8 Consensus size: 54
42960873 TTCCTTTTTT
* * * * * * *
42960883 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCGTTGCCTTAT-G
1 AACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATAG
* **
42960936 AA-TTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAG
1 AACTT-ATCAATGCCATGCCTTGGCATGGTCTTACATGATATCC-TTGCCTTATAG
* * * *
42960990 TAACTTATTAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAG
1 -AACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATAG
*
42961045 AACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATTTCCTTGCCTTATAG
1 AACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATAG
*
42961099 AACTTATCAGTGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 AACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTT
42961144 ATCTTACCAA
Statistics
Matches: 184, Mismatches: 18, Indels: 11
0.86 0.08 0.05
Matches are distributed among these distances:
52 3 0.02
53 41 0.22
54 95 0.52
55 41 0.22
56 4 0.02
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (54 bp):
AACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTATAG
Found at i:42961175 original size:47 final size:47
Alignment explanation
Indices: 42961122--42961243 Score: 208
Period size: 47 Copynumber: 2.6 Consensus size: 47
42961112 CATGCCTTGG
* * *
42961122 CATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCAATGTTCCAAA
*
42961169 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGTAATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCAATGTTCCAAA
42961216 CATGGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
42961244 GTGCCAAAAC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCAATGTTCCAAA
Found at i:42962057 original size:30 final size:31
Alignment explanation
Indices: 42962007--42962065 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
42961997 CTAACTCAAA
*
42962007 CTTTGACAAAATTACAATTTTGCCCCTAAAC
1 CTTTGACAAAATTACAATTTTGCACCTAAAC
* *
42962038 CTTT-ACAGAATTACGATTTTGCACCTAA
1 CTTTGACAAAATTACAATTTTGCACCTAA
42962066 GCTCGAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (31 bp):
CTTTGACAAAATTACAATTTTGCACCTAAAC
Found at i:42963576 original size:6 final size:6
Alignment explanation
Indices: 42963560--42963603 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
42963550 CCAAAAACAT
* *
42963560 AAAT-G AAATGA AAATGA AAATGG AAATGG AAATGG AAATGG AAA
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAA
42963604 CTTGCAATCC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.16
Consensus pattern (6 bp):
AAATGG
Found at i:42963785 original size:26 final size:27
Alignment explanation
Indices: 42963745--42963807 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
42963735 GATTTTTTTC
*
42963745 AAAATTTTACAAGGGGAAAAATCGT-T
1 AAAATTTTACAAGGGGAAAAATCGTCA
* *
42963771 AAAATTTTATC-AGGGGTAAAATTGTCA
1 AAAATTTTA-CAAGGGGAAAAATCGTCA
42963798 AAAATTTTAC
1 AAAATTTTAC
42963808 TGAGGTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 22 0.69
27 10 0.31
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (27 bp):
AAAATTTTACAAGGGGAAAAATCGTCA
Found at i:42967466 original size:23 final size:24
Alignment explanation
Indices: 42967430--42967475 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
42967420 AGCTATACGA
*
42967430 TATGGCTTGGTTTTGGT-TATGAT
1 TATGGCTTGATTTTGGTATATGAT
*
42967453 TATGGTTTGATTTTGGTATATGA
1 TATGGCTTGATTTTGGTATATGA
42967476 AATGTGATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.17, C:0.02, G:0.28, T:0.52
Consensus pattern (24 bp):
TATGGCTTGATTTTGGTATATGAT
Found at i:42974931 original size:23 final size:24
Alignment explanation
Indices: 42974905--42974950 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
42974895 AACCATGTGA
*
42974905 TATGGCTTGGTTTTGGT-TATGAT
1 TATGGCTTGATTTTGGTATATGAT
*
42974928 TATGGTTTGATTTTGGTATATGA
1 TATGGCTTGATTTTGGTATATGA
42974951 AATGTGATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.17, C:0.02, G:0.28, T:0.52
Consensus pattern (24 bp):
TATGGCTTGATTTTGGTATATGAT
Found at i:42977239 original size:40 final size:39
Alignment explanation
Indices: 42977175--42977260 Score: 127
Period size: 40 Copynumber: 2.2 Consensus size: 39
42977165 TATATATATA
*
42977175 TAGCCGAAGCTATCTCAAATTGCACACCAAGTGCCACTTT
1 TAGCCGAAGCTATCTCAAACTGCACACCAAGTGCCA-TTT
* * *
42977215 TAGCCGAAGCTATTTCGAACTGCACACTAAGTGCCATTT
1 TAGCCGAAGCTATCTCAAACTGCACACCAAGTGCCATTT
42977254 TAGCCGA
1 TAGCCGA
42977261 TAAGTCGTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 10 0.24
40 32 0.76
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (39 bp):
TAGCCGAAGCTATCTCAAACTGCACACCAAGTGCCATTT
Found at i:42981536 original size:6 final size:6
Alignment explanation
Indices: 42981522--42981559 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
42981512 CTTCTCCCTT
* *
42981522 TTCCTC TTCCCC TTCCCC TTCCCC TTCCCT TTCCCC TT
1 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TT
42981560 GGGTTGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (6 bp):
TTCCCC
Found at i:42984702 original size:21 final size:20
Alignment explanation
Indices: 42984651--42984702 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
42984641 GTCAAATACA
42984651 CTAAAAACATTAAAAATATTT
1 CTAAAAA-ATTAAAAATATTT
*
42984672 CTCAATAAATTAAAAATAAATTT
1 CT-AAAAAATTAAAAAT--ATTT
42984695 -TAAAAAAT
1 CTAAAAAAT
42984703 ATTTAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 17 0.65
22 5 0.19
23 4 0.15
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
CTAAAAAATTAAAAATATTT
Found at i:42984885 original size:22 final size:20
Alignment explanation
Indices: 42984854--42984893 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
42984844 GAAATGACAG
42984854 CAAAAGAATGGCAAAACAACGC
1 CAAAAGAATGG--AAACAACGC
*
42984876 CAAAATAATGGAAACAAC
1 CAAAAGAATGGAAACAAC
42984894 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.57, C:0.20, G:0.15, T:0.07
Consensus pattern (20 bp):
CAAAAGAATGGAAACAACGC
Found at i:42992058 original size:25 final size:25
Alignment explanation
Indices: 42992030--42992108 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 25
42992020 TGTTGAGAAA
42992030 ATATATAAAATGCTTTAATAAACCT
1 ATATATAAAATGCTTTAATAAACCT
* ** **
42992055 ATATATAAAAT-TTTGTTGTAAGAGCAA
1 ATATATAAAATGCTT-TAATAA-A-CCT
42992082 ATATATAAAATGCTTTAATAAACCT
1 ATATATAAAATGCTTTAATAAACCT
42992107 AT
1 AT
42992109 CCAGTGCAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
24 2 0.05
25 18 0.45
26 2 0.05
27 16 0.40
28 2 0.05
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.37
Consensus pattern (25 bp):
ATATATAAAATGCTTTAATAAACCT
Found at i:42992059 original size:48 final size:50
Alignment explanation
Indices: 42992007--42992108 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 50
42991997 TTAAAGGTAA
42992007 ATATAGAAAATTTTGTTG-AGA-AAATATATAAAATGCTTTAATAAACCT
1 ATATAGAAAATTTTGTTGAAGACAAATATATAAAATGCTTTAATAAACCT
*
42992055 ATATATAAAATTTTGTTGTAAGAGCAAATATATAAAATGCTTTAATAAACCT
1 ATATAGAAAATTTTGTTG-AAGA-CAAATATATAAAATGCTTTAATAAACCT
42992107 AT
1 AT
42992109 CCAGTGCAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
48 17 0.35
50 3 0.06
52 29 0.59
ACGTcount: A:0.47, C:0.07, G:0.10, T:0.36
Consensus pattern (50 bp):
ATATAGAAAATTTTGTTGAAGACAAATATATAAAATGCTTTAATAAACCT
Found at i:42996493 original size:46 final size:43
Alignment explanation
Indices: 42996324--42996494 Score: 155
Period size: 46 Copynumber: 3.7 Consensus size: 43
42996314 AACCCGCCCC
** *
42996324 TAAGTGAACTTAGACTCAACTCAACGAGCTTGGGCATTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAG-TT-CGCATTC-CATCCA
* * * *
42996370 TAAGTGAACTCGGATTCAACTCAACGAGTTCGGATGCCTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGCATTCC-A--TCCA
* *
42996416 GTTCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTC-G-CATTC-CATCCA
42996463 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCG
42996495 GATGCTCAAC
Statistics
Matches: 101, Mismatches: 15, Indels: 19
0.75 0.11 0.14
Matches are distributed among these distances:
43 1 0.01
44 5 0.05
45 5 0.05
46 54 0.53
47 28 0.28
48 3 0.03
49 4 0.04
50 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.23
Consensus pattern (43 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGCATTCCATCCA
Found at i:42996515 original size:46 final size:45
Alignment explanation
Indices: 42996326--42996515 Score: 124
Period size: 46 Copynumber: 4.1 Consensus size: 45
42996316 CCCGCCCCTA
** *
42996326 AGTGAACTTAGACTCAACTCAACGAGCTTGGGCAT--TC-ACATCCAT
1 AGTGAACTCGGACTCAACTCAACGAG-TTCGG-ATGCTCAACATCC-T
* *
42996371 AAGTGAACTCGGATTCAACTCAACGAGTTCGGATGC-CTAGTTACAGTTC-
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACA-TCCT
* * *** *
42996420 A-CGAACTCGGACTCAACTCAACGAGTTCAGACATTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACATCC-T
42996464 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAA-CATCCT
42996511 AGTGA
1 AGTGA
42996516 CATGTCACTT
Statistics
Matches: 110, Mismatches: 19, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 2 0.02
45 6 0.05
46 58 0.53
47 28 0.25
48 7 0.06
50 3 0.03
51 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACATCCT
Found at i:42996952 original size:30 final size:30
Alignment explanation
Indices: 42996918--42996977 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
42996908 ATTTAATACG
42996918 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
42996948 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
42996978 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:43004019 original size:92 final size:93
Alignment explanation
Indices: 43003861--43004030 Score: 279
Period size: 92 Copynumber: 1.8 Consensus size: 93
43003851 GCCCCTAAGT
* * *
43003861 GAACTTAGACTCAACTCAACGAACTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
43003926 CGAGTTCAGATGCCTAGTTACATTTCAC
66 CGAGTTCAGATGCCTAGTTACATTTCAC
**
43003954 GAACTCAGACTCAACTCAACGAGTTC-GACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
43004018 CGAGTTCGGATGC
66 CGAGTTCAGATGC
43004031 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 48 0.68
93 23 0.32
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAACTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATTTCAC
Found at i:43004482 original size:30 final size:30
Alignment explanation
Indices: 43004448--43004507 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
43004438 ATTTAATATG
43004448 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
43004478 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
43004508 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:43010045 original size:18 final size:18
Alignment explanation
Indices: 43010024--43010083 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
43010014 GACCTCACTC
43010024 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** *
43010042 TCTTTTTCAATCTCTTTT
1 TCTTTTTTGATTTCTTTT
43010060 TCTTTTCTTTTGATTTCTTTT
1 TC--TT-TTTTGATTTCTTTT
43010081 TCT
1 TCT
43010084 CGCTCGCACT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 17 0.52
19 1 0.03
20 2 0.06
21 13 0.39
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:43011060 original size:24 final size:24
Alignment explanation
Indices: 43011008--43011061 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
43010998 TTATACTTCA
*
43011008 AAATTTTTTTTTGAATTTTTTTTT
1 AAATTTTTTTTTGAATTTTTTTTC
*
43011032 GAATTTTTTTTTGAATTTTTTTTC
1 AAATTTTTTTTTGAATTTTTTTTC
43011056 AAATTT
1 AAATTT
43011062 CCTCTTCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (24 bp):
AAATTTTTTTTTGAATTTTTTTTC
Found at i:43011061 original size:12 final size:12
Alignment explanation
Indices: 43011009--43011054 Score: 92
Period size: 12 Copynumber: 3.8 Consensus size: 12
43010999 TATACTTCAA
43011009 AATTTTTTTTTG
1 AATTTTTTTTTG
43011021 AATTTTTTTTTG
1 AATTTTTTTTTG
43011033 AATTTTTTTTTG
1 AATTTTTTTTTG
43011045 AATTTTTTTT
1 AATTTTTTTT
43011055 CAAATTTCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:43012312 original size:72 final size:73
Alignment explanation
Indices: 43012229--43012375 Score: 190
Period size: 72 Copynumber: 2.0 Consensus size: 73
43012219 TTTAATGCTA
* * *
43012229 TCCCAAGTCCCATGCACACACTAAATTCGGCTG-GTTGGGAAAATACAACAG-CAACTTTCGCTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTT-GCTT
43012292 TAAATGCCG
65 TAAATGCCG
* * * * * *
43012301 TCCCAAGTCCCATGCACTCAATAAATTCGGCAGCTTTGGAAAAATGCAGCAGCCACCTTTTCTTT
1 TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
43012366 AAATGCCG
66 AAATGCCG
43012374 TC
1 TC
43012376 GATGTACCTG
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 30 0.47
73 28 0.44
74 6 0.09
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (73 bp):
TCCCAAGTCCCATGCACACAATAAATTCGGCAGCGTTGGAAAAATACAACAGCCAACTTTGCTTT
AAATGCCG
Found at i:43012584 original size:16 final size:16
Alignment explanation
Indices: 43012563--43012594 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43012553 CATTCTGCAT
43012563 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
43012579 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
43012595 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:43020225 original size:15 final size:17
Alignment explanation
Indices: 43020195--43020226 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
43020185 TTGATACTTG
43020195 TGAATGTGAGTTTGGTA
1 TGAATGTGAGTTTGGTA
43020212 TGAAT-TGA-TTTGGTA
1 TGAATGTGAGTTTGGTA
43020227 AATTATGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (17 bp):
TGAATGTGAGTTTGGTA
Found at i:43022327 original size:20 final size:20
Alignment explanation
Indices: 43022302--43022339 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43022292 TGTTATTTTA
*
43022302 TTAATAAAATAAATAAAAGG
1 TTAATAAAATAAAGAAAAGG
43022322 TTAATAAAATAAAGAAAA
1 TTAATAAAATAAAGAAAA
43022340 CATGATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
TTAATAAAATAAAGAAAAGG
Found at i:43023326 original size:38 final size:39
Alignment explanation
Indices: 43023255--43023339 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 39
43023245 GTGTTATACT
* * * * *
43023255 TTCTGTTTGGCATGATTCGAGTGGACTAGCTCTTTTGAGC
1 TTCTG-TTAGCATGATTCGAGAGGACCAACTCTTATGAGC
43023295 TTCTGTTAGCATG-TTCGAGAGGACCAACTCTTATGAGC
1 TTCTGTTAGCATGATTCGAGAGGACCAACTCTTATGAGC
*
43023333 TTTTGTT
1 TTCTGTT
43023340 GACGATGTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 27 0.69
39 7 0.18
40 5 0.13
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.40
Consensus pattern (39 bp):
TTCTGTTAGCATGATTCGAGAGGACCAACTCTTATGAGC
Found at i:43024487 original size:54 final size:54
Alignment explanation
Indices: 43024428--43024535 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
43024418 TTTGATGCCT
*
43024428 TATTGATGTATGTTATTTTTACAACATGTTAATGCATATTAAATAGCTAAAATG
1 TATTGATGTATGTTATTTTGACAACATGTTAATGCATATTAAATAGCTAAAATG
* ** * *
43024482 TATTGATGTGTGTTATTTTGACAATGTGTTAATGCATGTTAAATGGCTAAAATG
1 TATTGATGTATGTTATTTTGACAACATGTTAATGCATATTAAATAGCTAAAATG
43024536 GTAGGTGATG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (54 bp):
TATTGATGTATGTTATTTTGACAACATGTTAATGCATATTAAATAGCTAAAATG
Found at i:43026739 original size:15 final size:15
Alignment explanation
Indices: 43026693--43026739 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
43026683 TGCAATGAGA
43026693 ACAAGCAGATATCAT
1 ACAAGCAGATATCAT
* *
43026708 ACAA-CATA-ATAAT
1 ACAAGCAGATATCAT
43026721 ACAAGCAGATATCAT
1 ACAAGCAGATATCAT
43026736 ACAA
1 ACAA
43026740 CATAAGGATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 8 0.31
14 6 0.23
15 12 0.46
ACGTcount: A:0.53, C:0.19, G:0.09, T:0.19
Consensus pattern (15 bp):
ACAAGCAGATATCAT
Found at i:43027903 original size:21 final size:21
Alignment explanation
Indices: 43027879--43027927 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
43027869 ATTTTGGGTC
*
43027879 AATTTGAATAATGTGAGTCCT
1 AATTAGAATAATGTGAGTCCT
*
43027900 AATTAGGATAATGTGAGTCCT
1 AATTAGAATAATGTGAGTCCT
43027921 AATTAGA
1 AATTAGA
43027928 CTATATTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (21 bp):
AATTAGAATAATGTGAGTCCT
Found at i:43028223 original size:27 final size:27
Alignment explanation
Indices: 43028182--43028235 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
43028172 TGTCATGTGA
* *
43028182 AATTGAATGGCAAATTATTGTTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
43028209 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
43028236 GGTTGTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:43039723 original size:45 final size:46
Alignment explanation
Indices: 43039563--43039734 Score: 210
Period size: 45 Copynumber: 3.7 Consensus size: 46
43039553 TTGAGCATCT
*
43039563 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
* * *
43039609 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G--TCC
43039656 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
* *
43039701 GAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
43039735 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 37 0.34
46 26 0.24
47 29 0.27
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
Found at i:43047154 original size:11 final size:11
Alignment explanation
Indices: 43047138--43047164 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
43047128 ATTTGAACCA
43047138 TAGGAATAGAT
1 TAGGAATAGAT
43047149 TAGGAATAGAT
1 TAGGAATAGAT
43047160 TAGGA
1 TAGGA
43047165 TACAAGTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (11 bp):
TAGGAATAGAT
Found at i:43049251 original size:18 final size:18
Alignment explanation
Indices: 43049230--43049289 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
43049220 GACCTCACTC
43049230 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** *
43049248 TCTTTTTCAATCTCTTTT
1 TCTTTTTTGATTTCTTTT
43049266 TCTTTTCTTTTGATTTCTTTT
1 TC--TT-TTTTGATTTCTTTT
43049287 TCT
1 TCT
43049290 CGCTCGCACT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 17 0.52
19 1 0.03
20 2 0.06
21 13 0.39
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:43050262 original size:24 final size:24
Alignment explanation
Indices: 43050210--43050263 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
43050200 TTATACTTCA
*
43050210 AAATTTTTTTTTGAATTTTTTTTT
1 AAATTTTTTTTTGAATTTTTTTTC
*
43050234 GAATTTTTTTTTGAATTTTTTTTC
1 AAATTTTTTTTTGAATTTTTTTTC
43050258 AAATTT
1 AAATTT
43050264 CCTCTTCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (24 bp):
AAATTTTTTTTTGAATTTTTTTTC
Found at i:43050263 original size:12 final size:12
Alignment explanation
Indices: 43050211--43050256 Score: 92
Period size: 12 Copynumber: 3.8 Consensus size: 12
43050201 TATACTTCAA
43050211 AATTTTTTTTTG
1 AATTTTTTTTTG
43050223 AATTTTTTTTTG
1 AATTTTTTTTTG
43050235 AATTTTTTTTTG
1 AATTTTTTTTTG
43050247 AATTTTTTTT
1 AATTTTTTTT
43050257 CAAATTTCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (12 bp):
AATTTTTTTTTG
Done.